Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.

PubMed

Schoch, Conrad L; Seifert, Keith A; Huhndorf, Sabine; Robert, Vincent; Spouge, John L; Levesque, C André; Chen, Wen

2012-04-17

Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

Morphometric and molecular characterization of fungus Pestalotiopsis using nuclear ribosomal DNA analysis.

PubMed

Gehlot, Praveen; Singh, S K; Pathak, Rakesh

2012-09-01

Taxonomy of the fungus Pestalotiopsis based on morphological characters has been equivocal. Molecular characterization often Pestalotiopsis species was done based on nuclear ribosomal DNA internal transcribed spacer (ITS) amplifications. Results of the analyses showed that species of genus Pestalotiopsis are monophyletic. We report ITS length variations, single nucleotide polymorphisms (SNPs) and insertions/ deletions (INDELS) among ten species of Pestalotiopsis that did not cause any phylogenetic error at either genus or species designation levels. New gene sequences have been assigned (Gen Accession numbers from HM 190146 to HM 190155) by the National Centre for Biotechnology Information, USA.

DNA barcoding of western North American taxa: Leymus (Poaceae) and Lepidium (Brassicaceae)

Treesearch

Catherine Mae Culumber

2007-01-01

My objective was to determine if polymorphic information from the 18S-5.8S-26S nuclear ribosomal DNA internal transcribed spacer regions and the trnK-psbA, trnK-rps16 chloroplast DNA spacer regions is sufficient 1) to identify a plant specimen to the species level, and 2) to establish the phylogenetic relationship between species. The first study examined the...

Genetic diversity and molecular evolution of Naga King Chili inferred from internal transcribed spacer sequence of nuclear ribosomal DNA.

PubMed

Kehie, Mechuselie; Kumaria, Suman; Devi, Khumuckcham Sangeeta; Tandon, Pramod

2016-02-01

Sequences of the Internal Transcribed Spacer (ITS1-5.8S-ITS2) of nuclear ribosomal DNAs were explored to study the genetic diversity and molecular evolution of Naga King Chili. Our study indicated the occurrence of nucleotide polymorphism and haplotypic diversity in the ITS regions. The present study demonstrated that the variability of ITS1 with respect to nucleotide diversity and sequence polymorphism exceeded that of ITS2. Sequence analysis of 5.8S gene revealed a much conserved region in all the accessions of Naga King Chili. However, strong phylogenetic information of this species is the distinct 13 bp deletion in the 5.8S gene which discriminated Naga King Chili from the rest of the Capsicum sp. Neutrality test results implied a neutral variation, and population seems to be evolving at drift-mutation equilibrium and free from directed selection pressure. Furthermore, mismatch analysis showed multimodal curve indicating a demographic equilibrium. Phylogenetic relationships revealed by Median Joining Network (MJN) analysis denoted a clear discrimination of Naga King Chili from its closest sister species (Capsicum chinense and Capsicum frutescens). The absence of star-like network of haplotypes suggested an ancient population expansion of this chili.

Systematics of marine brown alga Sargassum from Thailand: A preliminary study based on morphological data and nuclear ribosomal internal transcribed spacer 2 (ITS2) sequences

NASA Astrophysics Data System (ADS)

Kantachumpoo, Attachai; Uwai, Shinya; Noiraksar, Thidarat; Komatsu, Teruhisa

2015-06-01

The marine brown algal genus Sargassum has been investigated extensively based on genetic information. In this report, we performed the first comparative study of morphological and molecular data among common species of Sargassum found in Thailand and explored the phylogenetic diversity within the genus. Our results revealed an incongruent pattern for species classification in Thai Sargassum. Morphologically, our Sargassum specimens were distinguishable and represented 8 species, namely, S. aquifolium (Turner) C.Agardh, Sargassum baccularia (Mertens) C. Agardh, S. cinereum J. Agardh, S. ilicifolium (Turner) C.Agardh, S. oligocystum Montagne, S. plagiophyllum C. Agardh, S. polycystum C. Agardh and S. swartzii (Turuner) C. Agardh. In contrast, using three different methods, phylogenetic analysis of nuclear ribosomal internal transcribed spacer 2 (ITS2) revealed six distinct clades, including S. baccularia/ S. oligosyntum clade, S. aquifolium/ S. swartzii clade, S. cinereum clade, S. aquifolium/ S. ilicifolium clade, S. polycystum clade, and S. plagiophyllum clade, which was suggestive of a phenotypic plasticity species complex. Our molecular data also confirmed the paraphyletic relationship in the section Binderianae and suggested that this section requires reassessment. Overall, further studies are required to increase our understanding of the taxonomy, phylogenetic relationships and species boundaries among Sargassum species in Thailand.

Molecular Characterization and Antioxidant Potential of Three Wild Culinary-Medicinal Mushrooms from Tripura, Northeast India.

PubMed

Das, Aparajita Roy; Borthakur, Madhusmita; Saha, Ajay Krishna; Joshi, Santa Ram; Das, Panna

2017-01-01

The aim of this study was to characterize 3 wild culinary-medicinal mushrooms using molecular tools and to analyze their antioxidant activity. Antioxidant properties were studied by evaluating free radical scavenging, reducing power, and chelating effect. The mushrooms were identified as Lentinus squarrosulus, L. tuber-regium, and Macrocybe gigantean by amplifying internal transcribed spacer regions of ribosomal DNA. The results demonstrated that the methanolic extract of M. gigantean has the highest free radical scavenging effect and chelating effect, whereas the methanolic extract of L. squarrosulus has the highest reducing power. The highest total phenol content and the most ascorbic acid were found in the M. gigantean extracts. Among the 3 mushroom extracts, M. gigantean displayed the most potent antioxidant activity. Molecular characterization using the nuclear ribosomal internal transcribed spacer region as a universal DNA marker was an effective tool in the identification and phylogenetic analysis of the studied mushrooms. The study also indicated that these wild macrofungi are rich sources of natural antioxidants.

The Northeast Chinese species of Psathyrella (Agaricales, Psathyrellaceae).

PubMed

Yan, Jun-Qing; Bau, Tolgor

2018-01-01

Twenty seven species of Psathyrella have been found in Northeast China. Amongst them, P. conica , P. jilinensis , P. mycenoides and P. subsingeri are described as new species, based on studying morphological characteristics and phylogenetic analyses. Detailed morphological descriptions, line drawings and photographs of the new species are presented. Phylogenetic analysis of the nuclear ribosomal internal transcribed spacer (ITS) region and an identification key to the 27 Psathyrella species occuring in Northeast China are provided.

The Northeast Chinese species of Psathyrella (Agaricales, Psathyrellaceae)

PubMed Central

Yan, Jun-Qing; Bau, Tolgor

2018-01-01

Abstract Twenty seven species of Psathyrella have been found in Northeast China. Amongst them, P. conica, P. jilinensis, P. mycenoides and P. subsingeri are described as new species, based on studying morphological characteristics and phylogenetic analyses. Detailed morphological descriptions, line drawings and photographs of the new species are presented. Phylogenetic analysis of the nuclear ribosomal internal transcribed spacer (ITS) region and an identification key to the 27 Psathyrella species occuring in Northeast China are provided. PMID:29686502

Episomal HBV persistence within transcribed host nuclear chromatin compartments involves HBx.

PubMed

Hensel, Kai O; Cantner, Franziska; Bangert, Felix; Wirth, Stefan; Postberg, Jan

2018-06-22

In hepatocyte nuclei, hepatitis B virus (HBV) genomes occur episomally as covalently closed circular DNA (cccDNA). The HBV X protein (HBx) is required to initiate and maintain HBV replication. The functional nuclear localization of cccDNA and HBx remains unexplored. To identify virus-host genome interactions and the underlying nuclear landscape for the first time, we combined circular chromosome conformation capture (4C) with RNA-seq and ChIP-seq. Moreover, we studied HBx-binding to HBV episomes. In HBV-positive HepaRG hepatocytes, we observed preferential association of HBV episomes and HBx with actively transcribed nuclear domains on the host genome correlating in size with constrained topological units of chromatin. Interestingly, HBx alone occupied transcribed chromatin domains. Silencing of native HBx caused reduced episomal HBV stability. As part of the HBV episome, HBx might stabilize HBV episomal nuclear localization. Our observations may contribute to the understanding of long-term episomal stability and the facilitation of viral persistence. The exact mechanism by which HBx contributes to HBV nuclear persistence warrants further investigations.

Physical proximity of chromatin to nuclear pores prevents harmful R loop accumulation contributing to maintain genome stability.

PubMed

García-Benítez, Francisco; Gaillard, Hélène; Aguilera, Andrés

2017-10-10

During transcription, the mRNA may hybridize with DNA, forming an R loop, which can be physiological or pathological, constituting in this case a source of genomic instability. To understand the mechanism by which eukaryotic cells prevent harmful R loops, we used human activation-induced cytidine deaminase (AID) to identify genes preventing R loops. A screening of 400 Saccharomyces cerevisiae selected strains deleted in nuclear genes revealed that cells lacking the Mlp1/2 nuclear basket proteins show AID-dependent genomic instability and replication defects that were suppressed by RNase H1 overexpression. Importantly, DNA-RNA hybrids accumulated at transcribed genes in mlp1/2 mutants, indicating that Mlp1/2 prevents R loops. Consistent with the Mlp1/2 role in gene gating to nuclear pores, artificial tethering to the nuclear periphery of a transcribed locus suppressed R loops in mlp1 ∆ cells. The same occurred in THO-deficient hpr1 ∆ cells. We conclude that proximity of transcribed chromatin to the nuclear pore helps restrain pathological R loops.

Decoding the principles underlying the frequency of association with nucleoli for RNA polymerase III–transcribed genes in budding yeast

PubMed Central

Belagal, Praveen; Normand, Christophe; Shukla, Ashutosh; Wang, Renjie; Léger-Silvestre, Isabelle; Dez, Christophe; Bhargava, Purnima; Gadal, Olivier

2016-01-01

The association of RNA polymerase III (Pol III)–transcribed genes with nucleoli seems to be an evolutionarily conserved property of the spatial organization of eukaryotic genomes. However, recent studies of global chromosome architecture in budding yeast have challenged this view. We used live-cell imaging to determine the intranuclear positions of 13 Pol III–transcribed genes. The frequency of association with nucleolus and nuclear periphery depends on linear genomic distance from the tethering elements—centromeres or telomeres. Releasing the hold of the tethering elements by inactivating centromere attachment to the spindle pole body or changing the position of ribosomal DNA arrays resulted in the association of Pol III–transcribed genes with nucleoli. Conversely, ectopic insertion of a Pol III–transcribed gene in the vicinity of a centromere prevented its association with nucleolus. Pol III–dependent transcription was independent of the intranuclear position of the gene, but the nucleolar recruitment of Pol III–transcribed genes required active transcription. We conclude that the association of Pol III–transcribed genes with the nucleolus, when permitted by global chromosome architecture, provides nucleolar and/or nuclear peripheral anchoring points contributing locally to intranuclear chromosome organization. PMID:27559135

Comparison of laboratory colonies and field populations of Tamarixia radiata, an ecto-parasitoid of the Asian Citrus Psyllid, using internal transcribed spacer and cytochrome oxidase subunit l DNA sequences

USDA-ARS?s Scientific Manuscript database

The genetic diversity of Tamarixia radiata laboratory colonies derived from collections in China, northern Vietnam, Pakistan, and a mixed colony from Taiwan and southern Vietnam was evaluated using the internal transcribed spacer region 1 (ITS-1), internal transcribed spacer region 2 (ITS-2) and the...

Molecular systematics of Indian Alysicarpus (Fabaceae) based on analyses of nuclear ribosomal DNA sequences.

PubMed

Gholami, Akram; Subramaniam, Shweta; Geeta, R; Pandey, Arun K

2017-06-01

Alysicarpus Necker ex Desvaux (Fabaceae, Desmodieae) consists of ~30 species that are distributed in tropical and subtropical regions of theworld. In India, the genus is represented by ca. 18 species, ofwhich seven are endemic. Sequences of the nuclear Internal transcribed spacer from38 accessions representing 16 Indian specieswere subjected to phylogenetic analyses. The ITS sequence data strongly support the monophyly of the genus Alysicarpus. Analyses revealed four major well-supported clades within Alysicarpus. Ancestral state reconstructions were done for two morphological characters, namely calyx length in relation to pod (macrocalyx and microcalyx) and pod surface ornamentation (transversely rugose and nonrugose). The present study is the first report on molecular systematics of Indian Alysicarpus.

INTERNAL TRANSCRIBED SPACER (ITS), AN IDEAL DNA BARCODE FOR SPECIES DISCRIMINATION IN CRAWFURDIA WALL. (GENTIANACEAE).

PubMed

Zhang, Dequan; Jiang, Bei; Duan, Lizhen; Zhou, Nong

2016-01-01

DNA barcoding is a technique used to identify species based on species-specific differences in short regions of their DNA. It is widely used in species discrimination of medicinal plants and traditional medicines. In the present study, four potential DNA barcodes, namely rbcL , matK , trnH-psbA and ITS (nuclear ribosomal internal transcribed spacer) were adopted for species discrimination in Crawfurdia Wall (Genetiaceae). Identification ability of these DNA barcodes and combinations were evaluated using three classic methods (Distance, Blast and Tree-Building). As a result, ITS, trnH-psbA and rbcL regions showed great universality for a success rate of 100%; whereas matK was disappointing for which only 65% samples gained useful DNA sequences. ITS region, which could clearly and effectively identify the five species in Crawfurdia , performed very well in this study. On the contrary, trnH-psbA and rbcL performed poorly in discrimination among these species. ITS marker was an ideal DNA barcode in Crawfurdia and it should be incorporated into one of the core barcodes for seed plants.

First Molecular Identification and Phylogeny of Moroccan Anopheles sergentii (Diptera: Culicidae) Based on Second Internal Transcribed Spencer (ITS2) and Cytochrome c Oxidase I (COI) Sequences.

PubMed

Benabdelkrim Filali, Oumama; Kabine, Mostafa; El Hamouchi, Adil; Lemrani, Meryem; Debboun, Mustapha; Sarih, M'hammed

2018-06-05

Anopheles sergentii known as the "oasis vector" or the "desert malaria vector" is considered the main vector of malaria in the southern parts of Morocco. Its presence in Morocco is confirmed for the first time through sequencing of mitochondrial DNA (mDNA) cytochrome c oxidase subunit I (COI) barcodes and nuclear ribosomal DNA (rDNA) second internal transcribed spacer (ITS2) sequences and direct comparison with specimens of A. sergentii of other countries. The DNA barcodes (n = 39) obtained from A. sergentii collected in 2015 and 2016 showed more diversity with 10 haplotypes, compared with 3 haplotypes obtained from ITS2 sequences (n = 59). Moreover, the comparison using the ITS2 sequences showed closer evolutionary relationship between the Moroccan and Egyptian strains than the Iranian strain. Nevertheless, genetic differences due to geographical segregation were also observed. This study provides the first report on the sequence of rDNA-ITS2 and mtDNA COI, which could be used to better understand the biodiversity of A. sergentii.

Extensive 5.8S nrDNA polymorphism in Mammillaria (Cactaceae) with special reference to the identification of pseudogenic internal transcribed spacer regions.

PubMed

Harpke, Doerte; Peterson, Angela

2008-05-01

The internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, ITS2) represents the most widely applied nuclear marker in eukaryotic phylogenetics. Although this region has been assumed to evolve in concert, the number of investigations revealing high degrees of intra-individual polymorphism connected with the presence of pseudogenes has risen. The 5.8S rDNA is the most important diagnostic marker for functionality of the ITS region. In Mammillaria, intra-individual 5.8S rDNA polymorphisms of up to 36% and up to nine different types have been found. Twenty-eight of 30 cloned genomic Mammillaria sequences were identified as putative pseudogenes. For the identification of pseudogenic ITS regions, in addition to formal tests based on substitution rates, we attempted to focus on functional features of the 5.8S rDNA (5.8S motif, secondary structure). The importance of functional data for the identification of pseudogenes is outlined and discussed. The identification of pseudogenes is essential, because they may cause erroneous phylogenies and taxonomic problems.

Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences.

PubMed

Liston, A; Robinson, W A; Piñero, D; Alvarez-Buylla, E R

1999-02-01

A 650-bp portion of the nuclear ribosomal DNA internal transcribed spacer region was sequenced in 47 species of Pinus, representing all recognized subsections of the genus, and 2 species of Picea and Cathaya as outgroups. Parsimony analyses of these length variable sequences were conducted using a manual alignment, 13 different automated alignments, elision of the automated alignments, and exclusion of all alignment ambiguous sites. High and moderately supported clades were consistently resolved across the different analyses, while poorly supported clades were inconsistently recovered. Comparison of the topologies highlights taxa of particularly problematic placement including Pinus nelsonii and P. aristata. Within subgenus Pinus, there is moderate support for the monophyly of a narrowly circumscribed subsect. Pinus (=subsect. Sylvestres) and strong support for a clade of North and Central American hard pines. The Himalayan P. roxburghii may be sister species to these "New World hard pines," which have two well-supported subgroups, subsect. Ponderosae and a clade of the remaining five subsections. The position of subsect. Contortae conflicts with its placement in a chloroplast DNA restriction site study. Within subgenus Strobus there is consistent support for the monophyly of a broadly circumscribed subsect. Strobi (including P. krempfii and a polyphyletic subsect. Cembrae) derived from a paraphyletic grade of the remaining soft pines. Relationships among subsects. Gerardianae, Cembroides, and Balfourianae are poorly resolved. Support for the monophyly of subgenus Pinus and subgenus Strobus is not consistently obtained. Copyright 1999 Academic Press.

Molecular phylogeny of Oncaeidae (Copepoda) using nuclear ribosomal internal transcribed spacer (ITS rDNA)

PubMed Central

Di Capua, Iole; Maffucci, Fulvio; Pannone, Raimondo; Mazzocchi, Maria Grazia

2017-01-01

Copepods belonging to the Oncaeidae family are commonly and abundantly found in marine zooplankton. In the Mediterranean Sea, forty-seven oncaeid species occur, of which eleven in the Gulf of Naples. In this Gulf, several Oncaea species were morphologically analysed and described at the end of the XIX century by W. Giesbrecht. In the same area, oncaeids are being investigated over seasonal and inter-annual scales at the long-term coastal station LTER-MC. In the present work, we identified six oncaeid species using the nuclear ribosomal internal transcribed spacers (ITS rDNA) and the mitochondrial cytochrome c oxidase subunit I (mtCOI). Phylogenetic analyses based on these two genomic regions validated the sisterhood of the genera Triconia and the Oncaea sensu stricto. ITS1 and ITS2 phylogenies produced incongruent results about the position of Oncaea curta, calling for further investigations on this species. We also characterised the ITS2 region by secondary structure predictions and found that all the sequences analysed presented the distinct eukaryotic hallmarks. A Compensatory Base Change search corroborated the close relationship between O. venusta and O. curta and between O. media and O. venusta already identified by ITS phylogenies. The present results, which stem from the integration of molecular and morphological taxonomy, represent an encouraging step towards an improved knowledge of copepod biodiversity: The two complementary approaches, when applied to long-term copepod monitoring, will also help to better understanding their genetic variations and ecological niches of co-occurring species. PMID:28441395

Genetic analysis of Fasciola isolates from cattle in Korea based on second internal transcribed spacer (ITS-2) sequence of nuclear ribosomal DNA.

PubMed

Choe, Se-Eun; Nguyen, Thuy Thi-Dieu; Kang, Tae-Gyu; Kweon, Chang-Hee; Kang, Seung-Won

2011-09-01

Nuclear ribosomal DNA sequence of the second internal transcribed spacer (ITS-2) has been used efficiently to identify the liver fluke species collected from different hosts and various geographic regions. ITS-2 sequences of 19 Fasciola samples collected from Korean native cattle were determined and compared. Sequence comparison including ITS-2 sequences of isolates from this study and reference sequences from Fasciola hepatica and Fasciola gigantica and intermediate Fasciola in Genbank revealed seven identical variable sites of investigated isolates. Among 19 samples, 12 individuals had ITS-2 sequences completely identical to that of pure F. hepatica, five possessed the sequences identical to F. gigantica type, whereas two shared the sequence of both F. hepatica and F. gigantica. No variations in length and nucleotide composition of ITS-2 sequence were observed within isolates that belonged to F. hepatica or F. gigantica. At the position of 218, five Fasciola containing a single-base substitution (C>T) formed a distinct branch inside the F. gigantica-type group which was similar to those of Asian-origin isolates. The phylogenetic tree of the Fasciola spp. based on complete ITS-2 sequences from this study and other representative isolates in different locations clearly showed that pure F. hepatica, F. gigantica type and intermediate Fasciola were observed. The result also provided additional genetic evidence for the existence of three forms of Fasciola isolated from native cattle in Korea by genetic approach using ITS-2 sequence.

Taxonomic confirmation of mud crab species (genus Scylla) in Bangladesh by nuclear and mitochondrial DNA markers.

PubMed

Sarower, Mohammed Golam; Shahriar, Sheik Istiak Md; Nakamura, Hiromasa; Rouf, Muhammad Abdur; Okada, Shigeru

2017-11-01

Taxonomy of mud crabs genus Scylla has been misidentified for several years due to their high morphological plasticity. Several reports concerning mud crab have been published with misleading identification in Bangladesh. In this study, partial fragments of nuclear and mitochondrial DNA of Scylla species obtained from four locations along the Bangladesh coast were used to resolve taxonomical ambiguity of mud crab species. A single PCR product from the nuclear first internal transcribed spacer (ITS-1) marker and phylogenetic trees constructed based on 16S rDNA sequences indicated that all Scylla species obtained in this study were S. olivacea. Both molecular data and morphological characters revealed that S. olivacea is the only major species in Bangladesh coastal waters. Further, the 16S rDNA haplotypes significantly differed with known S. serrata by 33%. From this study it is clear that 'S. serrata' commonly reported from Bangladesh should be S. olivacea.

Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence

PubMed Central

Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

2016-01-01

Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided. PMID:27146605

Rapid authentication of the precious herb saffron by loop-mediated isothermal amplification (LAMP) based on internal transcribed spacer 2 (ITS2) sequence.

PubMed

Zhao, Mingming; Shi, Yuhua; Wu, Lan; Guo, Licheng; Liu, Wei; Xiong, Chao; Yan, Song; Sun, Wei; Chen, Shilin

2016-05-05

Saffron is one of the most expensive species of Chinese herbs and has been subjected to various types of adulteration because of its high price and limited production. The present study introduces a loop-mediated isothermal amplification (LAMP) technique for the differentiation of saffron from its adulterants. This novel technique is sensitive, efficient and simple. Six specific LAMP primers were designed on the basis of the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA of Crocus sativus. All LAMP amplifications were performed successfully, and visual detection occurred within 60 min at isothermal conditions of 65 °C. The results indicated that the LAMP primers are accurate and highly specific for the discrimination of saffron from its adulterants. In particular, 10 fg of genomic DNA was determined to be the limit for template accuracy of LAMP in saffron. Thus, the proposed novel, simple, and sensitive LAMP assay is well suited for immediate on-site discrimination of herbal materials. Based on the study, a practical standard operating procedure (SOP) for utilizing the LAMP protocol for herbal authentication is provided.

Decoding the principles underlying the frequency of association with nucleoli for RNA polymerase III-transcribed genes in budding yeast.

PubMed

Belagal, Praveen; Normand, Christophe; Shukla, Ashutosh; Wang, Renjie; Léger-Silvestre, Isabelle; Dez, Christophe; Bhargava, Purnima; Gadal, Olivier

2016-10-15

The association of RNA polymerase III (Pol III)-transcribed genes with nucleoli seems to be an evolutionarily conserved property of the spatial organization of eukaryotic genomes. However, recent studies of global chromosome architecture in budding yeast have challenged this view. We used live-cell imaging to determine the intranuclear positions of 13 Pol III-transcribed genes. The frequency of association with nucleolus and nuclear periphery depends on linear genomic distance from the tethering elements-centromeres or telomeres. Releasing the hold of the tethering elements by inactivating centromere attachment to the spindle pole body or changing the position of ribosomal DNA arrays resulted in the association of Pol III-transcribed genes with nucleoli. Conversely, ectopic insertion of a Pol III-transcribed gene in the vicinity of a centromere prevented its association with nucleolus. Pol III-dependent transcription was independent of the intranuclear position of the gene, but the nucleolar recruitment of Pol III-transcribed genes required active transcription. We conclude that the association of Pol III-transcribed genes with the nucleolus, when permitted by global chromosome architecture, provides nucleolar and/or nuclear peripheral anchoring points contributing locally to intranuclear chromosome organization. © 2016 Belagal et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Multiple horizontal transfers of nuclear ribosomal genes between phylogenetically distinct grass lineages.

PubMed

Mahelka, Václav; Krak, Karol; Kopecký, David; Fehrer, Judith; Šafář, Jan; Bartoš, Jan; Hobza, Roman; Blavet, Nicolas; Blattner, Frank R

2017-02-14

The movement of nuclear DNA from one vascular plant species to another in the absence of fertilization is thought to be rare. Here, nonnative rRNA gene [ribosomal DNA (rDNA)] copies were identified in a set of 16 diploid barley ( Hordeum ) species; their origin was traceable via their internal transcribed spacer (ITS) sequence to five distinct Panicoideae genera, a lineage that split from the Pooideae about 60 Mya. Phylogenetic, cytogenetic, and genomic analyses implied that the nonnative sequences were acquired between 1 and 5 Mya after a series of multiple events, with the result that some current Hordeum sp. individuals harbor up to five different panicoid rDNA units in addition to the native Hordeum rDNA copies. There was no evidence that any of the nonnative rDNA units were transcribed; some showed indications of having been silenced via pseudogenization. A single copy of a Panicum sp. rDNA unit present in H. bogdanii had been interrupted by a native transposable element and was surrounded by about 70 kbp of mostly noncoding sequence of panicoid origin. The data suggest that horizontal gene transfer between vascular plants is not a rare event, that it is not necessarily restricted to one or a few genes only, and that it can be selectively neutral.

Molecular authentication of Radix Puerariae Lobatae and Radix Puerariae Thomsonii by ITS and 5S rRNA spacer sequencing.

PubMed

Sun, Ye; Shaw, Pang-Chui; Fung, Kwok-Pui

2007-01-01

In the present study, we examined nuclear DNA sequences in an attempt to reveal the relationships between Pueraria lobata (Willd). Ohwi, P. thomsonii Benth., and P. montana (Lour.) Merr. We found that internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA are highly divergent in P. lobata and P. thomsonii, and four types of ITS with different length are found in the two species. On the other hand, DNA sequences of 5S rRNA gene spacer are highly conserved across multiple copies in P. lobata and P. thomsonii, they could be used to identify P. lobata, P. thomsonii, and P. montana of this complex, and may serve as a useful tool in medical authentication of Radix Puerariae Lobatae and Radix Puerariae Thomsonii.

A ruby-colored Pseudobaeospora species is described as new from material collected on the island of Hawaii.

PubMed

Desjardin, Dennis E; Hemmes, Don E; Perry, Brian A

2014-01-01

Pseudobaeospora wipapatiae is described as new based on material collected in alien wet habitats on the island of Hawaii. Unique features of this beautiful species include deep ruby-colored basidiomes with two-spored basidia, amyloid cheilocystidia and a hymeniderm pileipellis with abundant pileocystidia that is initially deep ruby in KOH then changes to lilac gray. Phylogenetic analysis of nuclear large ribosomal subunit sequence data suggest a close relationship between Pseudobaeospora and Tricholoma. BLAST comparisons of internal transcribed spacer and 5.8S nuclear ribosomal subunit regions sequence data reveal greatest similarity with existing sequences of Pseudobaeospora species. A comprehensive description, color photograph, illustrations of salient micromorphological features and comparisons with phenetically similar taxa are provided. © 2014 by The Mycological Society of America.

LATE PLEISTOCENE ENVIRONMENTAL CHANGES LEAD TO UNSTABLE DEMOGRAPHY AND POPULATION DIVERGENCE OF ANOPHELES ALBIMANUS IN THE NORTHERN NEOTROPICS

PubMed Central

Loaiza, Jose R.; Scott, Marilyn E.; Bermingham, Eldredge; Sanjur, Oris I.; Wilkerson, Richard; Rovira, Jose; Gutiérrez, Lina A.; Correa, Margarita M.; Grijalva, Mario; Birnberg, Lotty; Bickersmith, Sara; Conn, Jan E.

2011-01-01

We investigated the historical demography of Anopheles albimanus using mosquitoes from five countries and three different DNA regions, the mitochondrial cytochrome oxidase subunit I gene (COI), the single copy nuclear white gene and the ribosomal internal transcribed spacer two (ITS2). All the molecular markers supported the taxonomic status of a single species of An. albimanus. Furthermore, agreement between the COI and the white genes suggested a scenario of Pleistocene geographic fragmentation (i.e., population contraction) and subsequent range expansion across southern Central America. PMID:20888924

Molecular characterization of a Toxocara variant from cats in Kuala Lumpur, Malaysia.

PubMed

Zhu, X Q; Jacobs, D E; Chilton, N B; Sani, R A; Cheng, N A; Gasser, R B

1998-08-01

The ascaridoid nematode of cats from Kuala Lumpur, Malaysia, previously identified morphologically as Toxocara canis, was characterized using a molecular approach. The nuclear ribosomal DNA (rDNA) region spanning the first internal transcribed spacer (ITS-1), the 5.8S gene and the second internal transcribed spacer (ITS-2) was amplified and sequenced. The sequences for the parasite from Malaysian cats were compared with those for T. canis and T. cati. The sequence data showed that this taxon was genetically more similar to T. cati than to T. canis in the ITS-1, 5.8S and ITS-2. Differences in the ITS-1 and ITS-2 sequences between the taxa (9.4-26.1%) were markedly higher than variation between samples within T. canis and T. cati (0-2.9%). The sequence data demonstrate that the parasite from Malaysian cats is neither T. canis nor T. cati and indicate that it is a distinct species. Based on these data, PCR-linked restriction fragment length polymorphism (RFLP) and single-strand conformation polymorphism (SSCP) methods were employed for the unequivocal differentiation of the Toxocara variant from T. canis and T. cati. These methods should provide valuable tools for studying the life-cycle, transmission pattern(s) and zoonotic potential of this parasite.

Phylogeography of Trichuris populations isolated from different Cricetidae rodents.

PubMed

Callejón, Rocío; De Rojas, Manuel; Feliú, Carlos; Balao, Francisco; Marrugal, Angela; Henttonen, Heikki; Guevara, Diego; Cutillas, Cristina

2012-11-01

The phylogeography of Trichuris populations (Nematoda) collected from Cricetidae rodents (Muroidea) from different geographical regions was studied. Ribosomal DNA (Internal Transcribed Spacers 1 and 2, and mitochondrial DNA (cytochrome c- oxidase subunit 1 partial gene) have been used as molecular markers. The nuclear internal transcribed spacers (ITSs) 1 and 2 showed 2 clear-cut geographical and genetic lineages: one of the Nearctic region (Oregon), although the second was widespread throughout the Palaearctic region and appeared as a star-like structure in the minimum spanning network. The mitochondrial results revealed that T. arvicolae populations from the Palaearctic region were separated into 3 clear-cut geographical and genetic lineages: populations from Northern Europe, populations from Southern (Spain) and Eastern Europe (Croatia, Belarus, Kazahstan), and populations from Italy and France (Eastern Pyrénean Mountains). Phylogenetic analysis obtained on the basis of ITS1-5·8S-ITS2 rDNA sequences did not show a differential geographical structure; however, these markers suggest a new Trichuris species parasitizing Chionomys roberti and Cricetulus barabensis. The mitochondrial results revealed that Trichuris populations from arvicolinae rodents show signals of a post-glacial northward population expansion starting from the Pyrenees and Italy. Apparently, the Pyrenees and the Alps were not barriers to the dispersal of Trichuris populations.

Ribosomal Internal Transcribed Spacer of Prototheca wickerhamii Has Characteristic Structure Useful for Identification and Genotyping

PubMed Central

Hirose, Noriyuki; Nishimura, Kazuko; Inoue-Sakamoto, Maki; Masuda, Michiaki

2013-01-01

Prototheca species are achlorophyllous algae ubiquitous in nature and known to cause localized and systemic infection both in humans and animals. Although identification of the Prototheca species in clinical specimens is a challenge, there are an increasing number of cases in which molecular techniques have successfully been used for diagnosis of protothecosis. In this study, we characterized nuclear ribosomal DNA (rDNA) of a strain of Prototheca (FL11-0001) isolated from a dermatitis patient in Japan for its species identification. When nuclear rDNA of FL11-0001 and that of various other Prototheca strains were compared by polymerase chain reaction (PCR), the results indicated that the sizes of ribosomal internal transcribed spacer (ITS) were different in a species-dependent manner, suggesting that the variation might be useful for differentiation of Prototheca spp. Especially, ITS of P. wickerhamii, the most common cause of human protothecosis, was distinctively larger than that of other Prototheca spp. FL11-0001, whose ITS was comparably large, could easily be identified as P. wickerhamii. The usefulness of the PCR analysis of ITS was also demonstrated by the discovery that one of the clinical isolates that had previously been designated as P. wickerhamii was likely a novel species. Furthermore, our data demonstrated that nucleotide sequences of P. wickerhamii ITS are heterogenous between different rDNA copies in each strain and also polymorphic between strains. Phylogenetic analysis suggested that the ITS sequences could be classified to four clades, based on which P. wickerhamii strains might be grouped into at least two genotypes. Comprehensive characterization of Prototheca rDNA may provide valuable insights into diagnosis and epidemiology of protothecosis, as well as evolution and taxonomy of Prototheca and related organisms. PMID:24312279

Ribosomal internal transcribed spacer of Prototheca wickerhamii has characteristic structure useful for identification and genotyping.

PubMed

Hirose, Noriyuki; Nishimura, Kazuko; Inoue-Sakamoto, Maki; Masuda, Michiaki

2013-01-01

Prototheca species are achlorophyllous algae ubiquitous in nature and known to cause localized and systemic infection both in humans and animals. Although identification of the Prototheca species in clinical specimens is a challenge, there are an increasing number of cases in which molecular techniques have successfully been used for diagnosis of protothecosis. In this study, we characterized nuclear ribosomal DNA (rDNA) of a strain of Prototheca (FL11-0001) isolated from a dermatitis patient in Japan for its species identification. When nuclear rDNA of FL11-0001 and that of various other Prototheca strains were compared by polymerase chain reaction (PCR), the results indicated that the sizes of ribosomal internal transcribed spacer (ITS) were different in a species-dependent manner, suggesting that the variation might be useful for differentiation of Prototheca spp. Especially, ITS of P. wickerhamii, the most common cause of human protothecosis, was distinctively larger than that of other Prototheca spp. FL11-0001, whose ITS was comparably large, could easily be identified as P. wickerhamii. The usefulness of the PCR analysis of ITS was also demonstrated by the discovery that one of the clinical isolates that had previously been designated as P. wickerhamii was likely a novel species. Furthermore, our data demonstrated that nucleotide sequences of P. wickerhamii ITS are heterogenous between different rDNA copies in each strain and also polymorphic between strains. Phylogenetic analysis suggested that the ITS sequences could be classified to four clades, based on which P. wickerhamii strains might be grouped into at least two genotypes. Comprehensive characterization of Prototheca rDNA may provide valuable insights into diagnosis and epidemiology of protothecosis, as well as evolution and taxonomy of Prototheca and related organisms.

Nuclear internal transcribed spacer-1 as a sensitive genetic marker for environmental DNA studies in common carp Cyprinus carpio.

PubMed

Minamoto, Toshifumi; Uchii, Kimiko; Takahara, Teruhiko; Kitayoshi, Takumi; Tsuji, Satsuki; Yamanaka, Hiroki; Doi, Hideyuki

2017-03-01

The recently developed environmental DNA (eDNA) analysis has been used to estimate the distribution of aquatic vertebrates by using mitochondrial DNA (mtDNA) as a genetic marker. However, mtDNA markers have certain drawbacks such as variable copy number and maternal inheritance. In this study, we investigated the potential of using nuclear DNA (ncDNA) as a more reliable genetic marker for eDNA analysis by using common carp (Cyprinus carpio). We measured the copy numbers of cytochrome b (CytB) gene region of mtDNA and internal transcribed spacer 1 (ITS1) region of ribosomal DNA of ncDNA in various carp tissues and then compared the detectability of these markers in eDNA samples. In the DNA extracted from the brain and gill tissues and intestinal contents, CytB was detected at 95.1 ± 10.7 (mean ± 1 standard error), 29.7 ± 1.59 and 24.0 ± 4.33 copies per cell, respectively, and ITS1 was detected at 1760 ± 343, 2880 ± 503 and 1910 ± 352 copies per cell, respectively. In the eDNA samples from mesocosm, pond and lake water, the copy numbers of ITS1 were about 160, 300 and 150 times higher than those of CytB, respectively. The minimum volume of pond water required for quantification was 33 and 100 mL for ITS1 and CytB, respectively. These results suggested that ITS1 is a more sensitive genetic marker for eDNA studies of C. carpio. © 2016 John Wiley & Sons Ltd.

Secondary structural analyses of ITS1 in Paramecium.

PubMed

Hoshina, Ryo

2010-01-01

The nuclear ribosomal RNA gene operon is interrupted by internal transcribed spacer (ITS) 1 and ITS2. Although the secondary structure of ITS2 has been widely investigated, less is known about ITS1 and its structure. In this study, the secondary structure of ITS1 sequences for Paramecium and other ciliates was predicted. Each Paramecium ITS1 forms an open loop with three helices, A through C. Helix B was highly conserved among Paramecium, and similar helices were found in other ciliates. A phylogenetic analysis using the ITS1 sequences showed high-resolution, implying that ITS1 is a good tool for species-level analyses.

Development of novel low-copy nuclear markers for Hieraciinae (Asteraceae) and their perspective for other tribes.

PubMed

Krak, Karol; Alvarez, Inés; Caklová, Petra; Costa, Andrea; Chrtek, Jindrich; Fehrer, Judith

2012-02-01

The development of three low-copy nuclear markers for low taxonomic level phylogenies in Asteraceae with emphasis on the subtribe Hieraciinae is reported. Marker candidates were selected by comparing a Lactuca complementary DNA (cDNA) library with public DNA sequence databases. Interspecific variation and phylogenetic signal of the selected genes were investigated for diploid taxa from the subtribe Hieraciinae and compared to a reference phylogeny. Their ability to cross-amplify was assessed for other Asteraceae tribes. All three markers had higher variation (2.1-4.5 times) than the internal transcribed spacer (ITS) in Hieraciinae. Cross-amplification was successful in at least seven other tribes of the Asteraceae. Only three cases indicating the presence of paralogs or pseudogenes were detected. The results demonstrate the potential of these markers for phylogeny reconstruction in the Hieraciinae as well as in other Asteraceae tribes, especially for very closely related species.

Phylogeny and genetic diversity of Bridgeoporus nobilissimus inferred using mitochondrial and nuclear rDNA sequences

USGS Publications Warehouse

Redberg, G.L.; Hibbett, D.S.; Ammirati, J.F.; Rodriguez, R.J.

2003-01-01

The genetic diversity and phylogeny of Bridgeoporus nobilissimus have been analyzed. DNA was extracted from spores collected from individual fruiting bodies representing six geographically distinct populations in Oregon and Washington. Spore samples collected contained low levels of bacteria, yeast and a filamentous fungal species. Using taxon-specific PCR primers, it was possible to discriminate among rDNA from bacteria, yeast, a filamentous associate and B. nobilissimus. Nuclear rDNA internal transcribed spacer (ITS) region sequences of B. nobilissimus were compared among individuals representing six populations and were found to have less than 2% variation. These sequences also were used to design dual and nested PCR primers for B. nobilissimus-specific amplification. Mitochondrial small-subunit rDNA sequences were used in a phylogenetic analysis that placed B. nobilissimus in the hymenochaetoid clade, where it was associated with Oxyporus and Schizopora.

Phylogenetic Analysis of a ‘Jewel Orchid’ Genus Goodyera (Orchidaceae) Based on DNA Sequence Data from Nuclear and Plastid Regions

PubMed Central

Hu, Chao; Tian, Huaizhen; Li, Hongqing; Hu, Aiqun; Xing, Fuwu; Bhattacharjee, Avishek; Hsu, Tianchuan; Kumar, Pankaj; Chung, Shihwen

2016-01-01

A molecular phylogeny of Asiatic species of Goodyera (Orchidaceae, Cranichideae, Goodyerinae) based on the nuclear ribosomal internal transcribed spacer (ITS) region and two chloroplast loci (matK and trnL-F) was presented. Thirty-five species represented by 132 samples of Goodyera were analyzed, along with other 27 genera/48 species, using Pterostylis longifolia and Chloraea gaudichaudii as outgroups. Bayesian inference, maximum parsimony and maximum likelihood methods were used to reveal the intrageneric relationships of Goodyera and its intergeneric relationships to related genera. The results indicate that: 1) Goodyera is not monophyletic; 2) Goodyera could be divided into four sections, viz., Goodyera, Otosepalum, Reticulum and a new section; 3) sect. Reticulum can be further divided into two subsections, viz., Reticulum and Foliosum, whereas sect. Goodyera can in turn be divided into subsections Goodyera and a new subsection. PMID:26927946

Phylogenetic Analysis of a 'Jewel Orchid' Genus Goodyera (Orchidaceae) Based on DNA Sequence Data from Nuclear and Plastid Regions.

PubMed

Hu, Chao; Tian, Huaizhen; Li, Hongqing; Hu, Aiqun; Xing, Fuwu; Bhattacharjee, Avishek; Hsu, Tianchuan; Kumar, Pankaj; Chung, Shihwen

2016-01-01

A molecular phylogeny of Asiatic species of Goodyera (Orchidaceae, Cranichideae, Goodyerinae) based on the nuclear ribosomal internal transcribed spacer (ITS) region and two chloroplast loci (matK and trnL-F) was presented. Thirty-five species represented by 132 samples of Goodyera were analyzed, along with other 27 genera/48 species, using Pterostylis longifolia and Chloraea gaudichaudii as outgroups. Bayesian inference, maximum parsimony and maximum likelihood methods were used to reveal the intrageneric relationships of Goodyera and its intergeneric relationships to related genera. The results indicate that: 1) Goodyera is not monophyletic; 2) Goodyera could be divided into four sections, viz., Goodyera, Otosepalum, Reticulum and a new section; 3) sect. Reticulum can be further divided into two subsections, viz., Reticulum and Foliosum, whereas sect. Goodyera can in turn be divided into subsections Goodyera and a new subsection.

Redescription and molecular characterisation of Dujardinascaris madagascariensis and a note on D. dujardini (Nematoda: Heterocheilidae), parasites of Crocodylus niloticus, with a key to Dujardinascaris spp. in crocodilians.

PubMed

Mašová, Šárka; Baruš, Vlastimil; Seifertová, Mária; Malala, John; Jirků, Miloslav

2014-12-08

An examination of one specimen of Nile crocodile, Crocodylus niloticus (Laurenti, 1768), from Lake Turkana (Kenya), revealed the presence of two ascaridoid nematodes belonging to the genus Dujardinascaris Baylis, 1947. Dujardinascaris madagascariensis Chabaud & Caballero, 1966 was studied by scanning electron microscopy, redescribed, and differentiated from D. dujardini (Travassos, 1920). Dujardinascaris madagascariencsis is the second of the genus to be sequenced. An internal fragment of the small ribosomal subunit and nuclear ribosomal DNA internal transcribed spacer 2 region were amplified--the slowly evolving 18S gene region was used for phylogenetic analysis. Molecular data confirmed affinity of D. madagascariensis to the family Heterocheilidae and revealed its closest relationship with D. waltoni. A key to the species of Dujardinascaris parasitizing crocodiles is provided.

Unexpected high intragenomic variation in two of three major pest thrips species does not affect ribosomal internal transcribed spacer 2 (ITS2)utility for thrips identification

USDA-ARS?s Scientific Manuscript database

The mitochondrial gene mtCO1 and the internal transcribed spacer (ITS) region of the ribosomal DNA are among the most widely used molecular markers for insect taxonomic characterization. Three economically important species of thrips, Scirtothrips dorsalis, Thrips palmi, and Frankliniella occidental...

Use of DNA barcodes to identify flowering plants.

PubMed

Kress, W John; Wurdack, Kenneth J; Zimmer, Elizabeth A; Weigt, Lee A; Janzen, Daniel H

2005-06-07

Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

Genetic variability in Melipona quinquefasciata (Hymenoptera, Apidae, Meliponini) from northeastern Brazil determined using the first internal transcribed spacer (ITS1).

PubMed

Pereira, J O P; Freitas, B M; Jorge, D M M; Torres, D C; Soares, C E A; Grangeiro, T B

2009-01-01

Melipona quinquefasciata is a ground-nesting South American stingless bee whose geographic distribution was believed to comprise only the central and southern states of Brazil. We obtained partial sequences (about 500-570 bp) of first internal transcribed spacer (ITS1) nuclear ribosomal DNA from Melipona specimens putatively identified as M. quinquefasciata collected from different localities in northeastern Brazil. To confirm the taxonomic identity of the northeastern samples, specimens from the state of Goiás (Central region of Brazil) were included for comparison. All sequences were deposited in GenBank (accession numbers EU073751-EU073759). The mean nucleotide divergence (excluding sites with insertions/deletions) in the ITS1 sequences was only 1.4%, ranging from 0 to 4.1%. When the sites with insertions/deletions were also taken into account, sequence divergences varied from 0 to 5.3%. In all pairwise comparisons, the ITS1 sequence from the specimens collected in Goiás was most divergent compared to the ITS1 sequences of the bees from the other locations. However, neighbor-joining phylogenetic analysis showed that all ITS1 sequences from northeastern specimens along with the sample of Goiás were resolved in a single clade with a bootstrap support of 100%. The ITS1 sequencing data thus support the occurrence of M. quinquefasciata in northeast Brazil.

Rapid Molecular Identification of Pathogenic Yeasts by Pyrosequencing Analysis of 35 Nucleotides of Internal Transcribed Spacer 2 ▿

PubMed Central

Borman, Andrew M.; Linton, Christopher J.; Oliver, Debra; Palmer, Michael D.; Szekely, Adrien; Johnson, Elizabeth M.

2010-01-01

Rapid identification of yeast species isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. Here, we have evaluated the utility of pyrosequencing analysis of a portion of the internal transcribed spacer 2 region (ITS2) for identification of pathogenic yeasts. A total of 477 clinical isolates encompassing 43 different fungal species were subjected to pyrosequencing analysis in a strictly blinded study. The molecular identifications produced by pyrosequencing were compared with those obtained using conventional biochemical tests (AUXACOLOR2) and following PCR amplification and sequencing of the D1-D2 portion of the nuclear 28S large rRNA gene. More than 98% (469/477) of isolates encompassing 40 of the 43 fungal species tested were correctly identified by pyrosequencing of only 35 bp of ITS2. Moreover, BLAST searches of the public synchronized databases with the ITS2 pyrosequencing signature sequences revealed that there was only minimal sequence redundancy in the ITS2 under analysis. In all cases, the pyrosequencing signature sequences were unique to the yeast species (or species complex) under investigation. Finally, when pyrosequencing was combined with the Whatman FTA paper technology for the rapid extraction of fungal genomic DNA, molecular identification could be accomplished within 6 h from the time of starting from pure cultures. PMID:20702674

Zebrafish U6 small nuclear RNA gene promoters contain a SPH element in an unusual location.

PubMed

Halbig, Kari M; Lekven, Arne C; Kunkel, Gary R

2008-09-15

Promoters for vertebrate small nuclear RNA (snRNA) genes contain a relatively simple array of transcriptional control elements, divided into proximal and distal regions. Most of these genes are transcribed by RNA polymerase II (e.g., U1, U2), whereas the U6 gene is transcribed by RNA polymerase III. Previously identified vertebrate U6 snRNA gene promoters consist of a proximal sequence element (PSE) and TATA element in the proximal region, plus a distal region with octamer (OCT) and SphI postoctamer homology (SPH) elements. We have found that zebrafish U6 snRNA promoters contain the SPH element in a novel proximal position immediately upstream of the TATA element. The zebrafish SPH element is recognized by SPH-binding factor/selenocysteine tRNA gene transcription activating factor/zinc finger protein 143 (SBF/Staf/ZNF143) in vitro. Furthermore, a zebrafish U6 promoter with a defective SPH element is inefficiently transcribed when injected into embryos.

Saprolegniaceae identified on amphibian eggs throughout the Pacific Northwest, USA, by internal transcribed spacer sequences and phylogenetic analysis

Treesearch

Jill E. Petrisko; Christopher A. Pearl; David S. Pilliod; Peter P. Sheridan; Charles F. Williams; Charles R. Peterson; R. Bruce Bury

2008-01-01

We assessed the diversity and phylogeny of Saprolegniaceae on amphibian eggs from the Pacific Northwest, with particular focus on Saprolegnia ferax, a species implicated in high egg mortality. We identified isolates from eggs of six amphibians with the internal transcribed spacer (ITS) and 5.8S gene regions and BLAST of the GenBank database. We...

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

Treesearch

Daniel L. Lindner; Tor Carlsen; Henrik Nilsson; Marie Davey; Trond Schumacher; Havard. Kauserud

2013-01-01

The rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular...

Intersectional gene flow between insular endemics of Ilex (Aquifoliaceae) on the Bonin Islands and the Ryukyu Islands.

PubMed

Setoguchi, H; Watanabe, I

2000-06-01

Hybridization and introgression play important roles in plant evolution, and their occurrence on the oceanic islands provides good examples of plant speciation and diversification. Restriction fragment length polymorphisms (RFLPs) and trnL (UAA) 3'exon-trnF (GAA) intergenic spacer (IGS) sequences of chloroplast DNA (cpDNA), and the sequences of internal transcribed spacer (ITS) of nuclear ribosomal DNA were examined to investigate the occurrence of gene transfer in Ilex species on the Bonin Islands and the Ryukyu Islands in Japan. A gene phylogeny for the plastid genome is in agreement with the morphologically based taxonomy, whereas the nuclear genome phylogeny clusters putatively unrelated endemics both on the Bonin and the Ryukyu Islands. Intersectional hybridization and nuclear gene flow were independently observed in insular endemics of Ilex on both sets of islands without evidence of plastid introgression. Gene flow observed in these island systems can be explained by ecological features of insular endemics, i.e., limits of distribution range or sympatric distribution in a small land area.

Fungal endophyte diversity in Sarracenia.

PubMed

Glenn, Anthony; Bodri, Michael S

2012-01-01

Fungal endophytes were isolated from 4 species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, 8 within the Ascomycota and 4 within the Basidiomycota, were identified based on PCR amplification and sequencing of the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS rDNA) with taxonomic identity assigned using the NCBI nucleotide megablast search tool. Endophytes are known to produce a large number of metabolites, some of which may contribute to the protection and survival of the host. We speculate that endophyte-infected Sarracenia may benefit from their fungal associates by their influence on nutrient availability from within pitchers and, possibly, by directly influencing the biota within pitchers.

Unraveling systematic inventory of Echinops (Asteraceae) with special reference to nrDNA ITS sequence-based molecular typing of Echinops abuzinadianus.

PubMed

Ali, M A; Al-Hemaid, F M; Lee, J; Hatamleh, A A; Gyulai, G; Rahman, M O

2015-10-02

The present study explored the systematic inventory of Echinops L. (Asteraceae) of Saudi Arabia, with special reference to the molecular typing of Echinops abuzinadianus Chaudhary, an endemic species to Saudi Arabia, based on the internal transcribed spacer (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA. A sequence similarity search using BLAST and a phylogenetic analysis of the ITS sequence of E. abuzinadianus revealed a high level of sequence similarity with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. abuzinadianus could potentially be used for molecular genotyping.

Reverse Transcriptase Activity in Mature Spermatozoa of Mouse

PubMed Central

Giordano, Roberto; Magnano, Anna Rosa; Zaccagnini, Germana; Pittoggi, Carmine; Moscufo, Nicola; Lorenzini, Rodolfo; Spadafora, Corrado

2000-01-01

We show here that a reverse transcriptase (RT) activity is present in murine epididymal spermatozoa. Sperm cells incubated with human poliovirus RNA can take up exogenous RNA molecules and internalize them in nuclei. Direct PCR amplification of DNA extracted from RNA-incubated spermatozoa indicate that poliovirus RNA is reverse-transcribed in cDNA fragments. PCR analysis of two-cell embryos shows that poliovirus RNA-challenged spermatozoa transfer retrotranscribed cDNA molecules into eggs during in vitro fertilization. Finally, RT molecules can be visualized on sperm nuclear scaffolds by immunogold electron microscopy. These results, therefore, reveal a novel metabolic function in spermatozoa, which may play a role during early embryonic development. PMID:10725323

Four New Species of Amanita in Inje County, Korea

PubMed Central

Cho, Hae Jin; Park, Myung Soo; Lee, Hyun; Oh, Seung-Yoon; Jang, Yeongseon; Fong, Jonathan J.

2015-01-01

Amanita (Agaricales, Basidiomycota) is one of the most well-known genera composed of poisonous mushrooms. This genus of almost 500 species is distributed worldwide. Approximately 240 macrofungi were collected through an ongoing survey of indigenous fungi of Mt. Jeombong in Inje County, Korea in 2014. Among these specimens, 25 were identified as members of Amanita using macroscopic features. Specimens were identified to the species level by microscopic features and molecular sequence analyses of the internal transcribed spacer and large subunit of nuclear ribosomal RNA. We molecularly identified 13 Amanita species, with seven species matching previously recorded species, four species (A. caesareoides, A. griseoturcosa, A. imazekii, and A. sepiacea) new to Korea, and two unknown species. PMID:26839500

What triggers differential DNA methylation of genes and TEs: contribution of body methylation?

PubMed

Inagaki, S; Kakutani, T

2012-01-01

Transposable elements (TEs) are epigenetically silenced with extensive DNA methylation. The silent epigenetic marks should, however, be excluded from active genes. By genetic approaches, we study mechanisms to remove the heterochromatin marks from transcribed genes. Based on our observations on control of TE transcription, we propose a possible trigger for the TE-specific accumulation of DNA methylation. A critical difference between TEs and genes could be their responses to the DNA methylation in the internal part of transcribed regions. When their internal region is methylated, genes are still transcribed, but TEs could be silenced, which may reflect the obligatory position of every critical cis-acting element within the TE itself. This initial difference of TEs and genes will be amplified by positive feedback loops to stabilize active or silent states. Thus, the mechanisms to accumulate heterochromatin marks within transcribed regions could provide a trigger to induce differential DNA methylation between genes and TEs.

Site-specific labeling of RNA at internal ribose hydroxyl groups: terbium-assisted deoxyribozymes at work.

PubMed

Büttner, Lea; Javadi-Zarnaghi, Fatemeh; Höbartner, Claudia

2014-06-04

A general and efficient single-step method was established for site-specific post-transcriptional labeling of RNA. Using Tb(3+) as accelerating cofactor for deoxyribozymes, various labeled guanosines were site-specifically attached to 2'-OH groups of internal adenosines in in vitro transcribed RNA. The DNA-catalyzed 2',5'-phosphodiester bond formation proceeded efficiently with fluorescent, spin-labeled, biotinylated, or cross-linker-modified guanosine triphosphates. The sequence context of the labeling site was systematically analyzed by mutating the nucleotides flanking the targeted adenosine. Labeling of adenosines in a purine-rich environment showed the fastest reactions and highest yields. Overall, practically useful yields >70% were obtained for 13 out of 16 possible nucleotide (nt) combinations. Using this approach, we demonstrate preparative labeling under mild conditions for up to ~160-nt-long RNAs, including spliceosomal U6 small nuclear RNA and a cyclic-di-AMP binding riboswitch RNA.

A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects

PubMed Central

Kay, Kathleen M; Whittall, Justen B; Hodges, Scott A

2006-01-01

Background A full understanding of the patterns and processes of biological diversification requires the dating of evolutionary events, yet the fossil record is inadequate for most lineages under study. Alternatively, a molecular clock approach, in which DNA or amino acid substitution rates are calibrated with fossils or geological/climatic events, can provide indirect estimates of clade ages and diversification rates. The utility of this approach depends on the rate constancy of molecular evolution at a genetic locus across time and across lineages. Although the nuclear ribosomal internal transcribed spacer region (nrITS) is increasingly being used to infer clade ages in plants, little is known about the sources or magnitude of variation in its substitution rate. Here, we systematically review the literature to assess substitution rate variation in nrITS among angiosperms, and we evaluate possible correlates of the variation. Results We summarize 28 independently calibrated nrITS substitution rates ranging from 0.38 × 10-9 to 8.34 × 10-9 substitutions/site/yr. We find that herbaceous lineages have substitution rates almost twice as high as woody plants, on average. We do not find any among-lineage phylogenetic constraint to the rates, or any effect of the type of calibration used. Within life history categories, both the magnitude of the rates and the variance among rates tend to decrease with calibration age. Conclusion Angiosperm nrITS substitution rates vary by approximately an order of magnitude, and some of this variation can be attributed to life history categories. We make cautious recommendations for the use of nrITS as an approximate plant molecular clock, including an outline of more appropriate phylogenetic methodology and caveats against over interpretation of results. We also suggest that for lineages with independent calibrations, much of the variation in nrITS substitution rates may come from uncertainty in calibration date estimates, highlighting the importance of accurate and/or multiple calibration dates. PMID:16638138

Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China

PubMed Central

Li, Qin-Qin; Zhou, Song-Dong; He, Xing-Jin; Yu, Yan; Zhang, Yu-Cheng; Wei, Xian-Qin

2010-01-01

Background and Aims The genus Allium comprises more than 800 species, placing it among the largest monocotyledonous genera. It is a variable group that is spread widely across the Holarctic region. Previous studies of Allium have been useful in identifying and assessing its evolutionary lineages. However, there are still many gaps in our knowledge of infrageneric taxonomy and evolution of Allium. Further understanding of its phylogeny and biogeography will be achieved only through continued phylogenetic studies, especially of those species endemic to China that have often been excluded from previous analyses. Earlier molecular studies have shown that Chinese Allium is not monophyletic, so the goal of the present study was to infer the phylogeny and biogeography of Allium and to provide a classification of Chinese Allium by placement of Chinese species in the context of the entire phylogeny. Methods Phylogenetic studies were based on sequence data of the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast rps16 intron, analysed using parsimony and Bayesian approaches. Biogeographical patterns were conducted using statistical dispersal–vicariance analysis (S-DIVA). Key Results Phylogenetic analyses indicate that Allium is monophyletic and consists of three major clades. Optimal reconstructions have favoured the ancestors of Amerallium, Anguinum, Vvedenskya, Porphyroprason and Melanocrommyum as originating in eastern Asia. Conclusions Phylogenetic analyses reveal that Allium is monophyletic but that some subgenera are not. The large genetic distances imply that Allium is of ancient origin. Molecular data suggest that its evolution proceeded along three separate evolutionary lines. S-DIVA indicates that the ancestor of Amerallium, Anguinum, Vvedenskya, Porphyroprason and Melanocrommyum originated from eastern Asia and underwent different biogeographical pathways. A taxonomic synopsis of Chinese Allium at sectional level is given, which divides Chinese Allium into 13 subgenera and 34 sections. PMID:20966186

Use of DNA barcodes to identify flowering plants

PubMed Central

Kress, W. John; Wurdack, Kenneth J.; Zimmer, Elizabeth A.; Weigt, Lee A.; Janzen, Daniel H.

2005-01-01

Methods for identifying species by using short orthologous DNA sequences, known as “DNA barcodes,” have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short (≈450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes. PMID:15928076

Mitochondrial cytochrome c oxidase subunit 1 gene and nuclear rDNA regions of Enterobius vermicularis parasitic in captive chimpanzees with special reference to its relationship with pinworms in humans.

PubMed

Nakano, Tadao; Okamoto, Munehiro; Ikeda, Yatsukaho; Hasegawa, Hideo

2006-12-01

Sequences of mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, nuclear internal transcribed spacer 2 (ITS2) region of ribosomal DNA (rDNA), and 5S rDNA of Enterobius vermicularis from captive chimpanzees in five zoos/institutions in Japan were analyzed and compared with those of pinworm eggs from humans in Japan. Three major types of variants appearing in both CO1 and ITS2 sequences, but showing no apparent connection, were observed among materials collected from the chimpanzees. Each one of them was also observed in pinworms in humans. Sequences of 5S rDNA were identical in the materials from chimpanzees and humans. Phylogenetic analysis of CO1 gene revealed three clusters with high bootstrap value, suggesting considerable divergence, presumably correlated with human evolution, has occurred in the human pinworms. The synonymy of E. gregorii with E. vermicularis is supported by the molecular evidence.

Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences.

PubMed

Bunawan, Hamidun; Yen, Choong Chee; Yaakop, Salmah; Noor, Normah Mohd

2017-01-26

The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus. Phylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consisting of N. ampullaria, N. mirabilis, N. gracilis and N. rafflesiana, and another containing both intermediately distributed species (N. albomarginata and N. benstonei) and four highland species (N. sanguinea, N. macfarlanei, N. ramispina and N. alba). The trnL intron and ITS sequences proved to provide phylogenetic informative characters for deriving a phylogeny of Nepenthes species in Peninsular Malaysia. To our knowledge, this is the first molecular phylogenetic study of Nepenthes species occurring along an altitudinal gradient in Peninsular Malaysia.

A new species of Drepanocephalus Dietz, 1909 (Digenea: Echinostomatidae) from the double-crested cormorant Phalacrocorax auritus (Lesson) (Aves: Phalacrocoracidae) in North America.

PubMed

Kudlai, Olena; Kostadinova, Aneta; Pulis, Eric E; Tkach, Vasyl V

2015-03-01

Drepanocephalus auritus n. sp. is described based on specimens from the double-crested cormorant Phalacrocorax auritus (Lesson) in North America. The new species differs from its congeners in its very narrow, elongate body, long uterine field and widely separated testes. Sequences of the nuclear rRNA gene cluster, spanning the 3' end of the nuclear ribosomal 18S rRNA gene, internal transcribed spacer region (ITS1+5.8S gene+ITS2) and partial 28S gene (2,345 bp), were identical in specimens collected from North Dakota, Minnesota and Mississippi, USA. Sequences of the 651 bp long fragment of the mitochondrial cox1 gene exhibited very low intraspecific variability (< 1%). Comparisons of the newly-generated sequences with those available in the GenBank indicate that the sequences from North America published under the name D. spathans Dietz, 1909 in fact represent D. auritus n. sp.

Decrypting the Polyporus dictyopus complex: Recovery of Atroporus Ryvarden and segregation of Neodictyopus gen. nov. (Polyporales, Basidiomyocta).

PubMed

Palacio, Melissa; Robledo, Gerardo Lucio; Reck, Mateus Arduvino; Grassi, Emanuel; Góes-Neto, Aristóteles; Drechsler-Santos, Elisandro Ricardo

2017-01-01

Polyporus dictyopus, with a large number of heterotypic synonyms, has been traditionally considered a species complex, characterized by wide morphological variation and geographic distribution. Thus, neotropical specimens previously identified as P. dictyopus from Amazonia, Cerrado and Atlantic Forest biomes were studied based on detailed macro- and micromorphological examination and phylogenetic analyses, using distinct ribosomal and protein-coding genomic regions: the nuclear ribosomal internal transcribed spacer (nrITS), nuclear ribosomal large subunit (nrLSU), and RNA polymerase II second subunit (RPB2). Two unrelated generic lineages, each one represented by different species, are reported: Atroporus is recovered and re-circumscribed to include A. diabolicus and A. rufoatratus comb. nov.; Neodictyopus gen. nov. is proposed to accommodate N. dictyopus comb. nov. and two new species, N. atlanticae and N. gugliottae. Our study showed that at least five distinct species were hidden under the name P. dictyopus. Detailed descriptions, pictures, illustrations, and a key are provided for Atroporus and Neodictyopus species.

Decrypting the Polyporus dictyopus complex: Recovery of Atroporus Ryvarden and segregation of Neodictyopus gen. nov. (Polyporales, Basidiomyocta)

PubMed Central

Reck, Mateus Arduvino; Grassi, Emanuel; Góes-Neto, Aristóteles; Drechsler-Santos, Elisandro Ricardo

2017-01-01

Polyporus dictyopus, with a large number of heterotypic synonyms, has been traditionally considered a species complex, characterized by wide morphological variation and geographic distribution. Thus, neotropical specimens previously identified as P. dictyopus from Amazonia, Cerrado and Atlantic Forest biomes were studied based on detailed macro- and micromorphological examination and phylogenetic analyses, using distinct ribosomal and protein-coding genomic regions: the nuclear ribosomal internal transcribed spacer (nrITS), nuclear ribosomal large subunit (nrLSU), and RNA polymerase II second subunit (RPB2). Two unrelated generic lineages, each one represented by different species, are reported: Atroporus is recovered and re-circumscribed to include A. diabolicus and A. rufoatratus comb. nov.; Neodictyopus gen. nov. is proposed to accommodate N. dictyopus comb. nov. and two new species, N. atlanticae and N. gugliottae. Our study showed that at least five distinct species were hidden under the name P. dictyopus. Detailed descriptions, pictures, illustrations, and a key are provided for Atroporus and Neodictyopus species. PMID:29049417

Fungal Endophyte Diversity in Sarracenia

PubMed Central

Glenn, Anthony; Bodri, Michael S.

2012-01-01

Fungal endophytes were isolated from 4 species of the carnivorous pitcher plant genus Sarracenia: S. minor, S. oreophila, S. purpurea, and S. psittacina. Twelve taxa of fungi, 8 within the Ascomycota and 4 within the Basidiomycota, were identified based on PCR amplification and sequencing of the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS rDNA) with taxonomic identity assigned using the NCBI nucleotide megablast search tool. Endophytes are known to produce a large number of metabolites, some of which may contribute to the protection and survival of the host. We speculate that endophyte-infected Sarracenia may benefit from their fungal associates by their influence on nutrient availability from within pitchers and, possibly, by directly influencing the biota within pitchers. PMID:22427921

DNA Fingerprinting of Pearls to Determine Their Origins

PubMed Central

Meyer, Joana B.; Cartier, Laurent E.; Pinto-Figueroa, Eric A.; Krzemnicki, Michael S.; Hänni, Henry A.; McDonald, Bruce A.

2013-01-01

We report the first successful extraction of oyster DNA from a pearl and use it to identify the source oyster species for the three major pearl-producing oyster species Pinctada margaritifera, P. maxima and P. radiata. Both mitochondrial and nuclear gene fragments could be PCR-amplified and sequenced. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in the internal transcribed spacer (ITS) region was developed and used to identify 18 pearls of unknown origin. A micro-drilling technique was developed to obtain small amounts of DNA while maintaining the commercial value of the pearls. This DNA fingerprinting method could be used to document the source of historic pearls and will provide more transparency for traders and consumers within the pearl industry. PMID:24130725

DNA fingerprinting of pearls to determine their origins.

PubMed

Meyer, Joana B; Cartier, Laurent E; Pinto-Figueroa, Eric A; Krzemnicki, Michael S; Hänni, Henry A; McDonald, Bruce A

2013-01-01

We report the first successful extraction of oyster DNA from a pearl and use it to identify the source oyster species for the three major pearl-producing oyster species Pinctada margaritifera, P. maxima and P. radiata. Both mitochondrial and nuclear gene fragments could be PCR-amplified and sequenced. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay in the internal transcribed spacer (ITS) region was developed and used to identify 18 pearls of unknown origin. A micro-drilling technique was developed to obtain small amounts of DNA while maintaining the commercial value of the pearls. This DNA fingerprinting method could be used to document the source of historic pearls and will provide more transparency for traders and consumers within the pearl industry.

A new species of cellular slime mold from southern Portugal based on morphology, ITS and SSU sequences.

PubMed

Romeralo, M; Baldauf, S L; Cavender, J C

2009-01-01

Sampling soils to look for dictyostelids in southern Portugal we found an isolate that has a morphology that differed from any previously described species of the group. We sequenced the internally transcribed spacer (ITS) and small subunit (SSU) genes of the nuclear ribosomal RNA and found that both sequences are distinct from all previously described sequences. Phylogenetic analyses place the new species in dictyostelid Group 3 (Rhizostelids) together with D. potamoides, with which it shares 65.8% identity for ITS and 96.6% for SSU. In this paper we describe a new species of cellular slime mold, Dictyostelium ibericum, based on morphological and molecular characters. It is a small species with polar granules in its spores.

The ectomycorrhizas of Lactarius cuspidoaurantiacus and Lactarius herrerae associated with Alnus acuminata in Central Mexico.

PubMed

Montoya, Leticia; Bandala, Victor M; Garay-Serrano, Edith

2015-08-01

Two pure Alnus acuminata stands established in a montane forest in central Mexico (Puebla State) were monitored between 2010 and 2013 to confirm and recognize the ectomycorrhizal (EcM) systems of A. acuminata with Lactarius cuspidoaurantiacus and Lactarius herrerae, two recently described species. Through comparison of internal transcribed spacer (ITS) of nuclear ribosomal DNA sequences from basidiomes and ectomycorrhizas sampled in the forest stands, we confirmed their ectomycorrhizal association. The phytobiont was corroborated by comparing ITS sequences obtained from EcM root tips and leaves collected in the study site and from other sequences of A. acuminata available in Genbank. Detailed morphological and anatomical descriptions of the ectomycorrhizal systems are presented and complemented with photographs.

Efficiency of ITS Sequences for DNA Barcoding in Passiflora (Passifloraceae)

PubMed Central

Giudicelli, Giovanna Câmara; Mäder, Geraldo; de Freitas, Loreta Brandão

2015-01-01

DNA barcoding is a technique for discriminating and identifying species using short, variable, and standardized DNA regions. Here, we tested for the first time the performance of plastid and nuclear regions as DNA barcodes in Passiflora. This genus is a largely variable, with more than 900 species of high ecological, commercial, and ornamental importance. We analyzed 1034 accessions of 222 species representing the four subgenera of Passiflora and evaluated the effectiveness of five plastid regions and three nuclear datasets currently employed as DNA barcodes in plants using barcoding gap, applied similarity-, and tree-based methods. The plastid regions were able to identify less than 45% of species, whereas the nuclear datasets were efficient for more than 50% using “best match” and “best close match” methods of TaxonDNA software. All subgenera presented higher interspecific pairwise distances and did not fully overlap with the intraspecific distance, and similarity-based methods showed better results than tree-based methods. The nuclear ribosomal internal transcribed spacer 1 (ITS1) region presented a higher discrimination power than the other datasets and also showed other desirable characteristics as a DNA barcode for this genus. Therefore, we suggest that this region should be used as a starting point to identify Passiflora species. PMID:25837628

Rrp6 is recruited to transcribed genes and accompanies the spliced mRNA to the nuclear pore

PubMed Central

Hessle, Viktoria; von Euler, Anne; González de Valdivia, Ernesto; Visa, Neus

2012-01-01

Rrp6 is an exoribonuclease involved in the quality control of mRNA biogenesis. We have analyzed the association of Rrp6 with the Balbiani ring pre-mRNPs of Chironomus tentans to obtain insight into the role of Rrp6 in splicing surveillance. Rrp6 is recruited to transcribed genes and its distribution along the genes does not correlate with the positions of exons and introns. In the nucleoplasm, Rrp6 is bound to both unspliced and spliced transcripts. Rrp6 is released from the mRNPs in the vicinity of the nuclear pore before nucleo-cytoplasmic translocation. We show that Rrp6 is associated with newly synthesized transcripts during all the nuclear steps of gene expression and is associated with the transcripts independently of their splicing status. These observations suggest that the quality control of pre-mRNA splicing is not based on the selective recruitment of the exoribonuclease Rrp6 to unprocessed mRNAs. PMID:22745224

Phylogeny of Cirsium spp. in North America: host specificity does not follow phylogeny

USDA-ARS?s Scientific Manuscript database

Weedy invasive Cirsium spp. are widespread in temperate regions of North America and some of their biological control agents have attacked native Cirsium spp. A phylogenetic tree was developed from DNA sequences for the internal transcribed spacer and external transcribed spacer regions from native ...

Population genetic analysis of Enterocytozoon bieneusi in humans.

PubMed

Li, Wei; Cama, Vitaliano; Feng, Yaoyu; Gilman, Robert H; Bern, Caryn; Zhang, Xichen; Xiao, Lihua

2012-01-01

Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi. Published by Elsevier Ltd.

Decoding the function of nuclear long non-coding RNAs.

PubMed

Chen, Ling-Ling; Carmichael, Gordon G

2010-06-01

Long non-coding RNAs (lncRNAs) are mRNA-like, non-protein-coding RNAs that are pervasively transcribed throughout eukaryotic genomes. Rather than silently accumulating in the nucleus, many of these are now known or suspected to play important roles in nuclear architecture or in the regulation of gene expression. In this review, we highlight some recent progress in how lncRNAs regulate these important nuclear processes at the molecular level. Copyright 2010 Elsevier Ltd. All rights reserved.

Activity of Posaconazole and Other Antifungal Agents against Mucorales Strains Identified by Sequencing of Internal Transcribed Spacers▿

PubMed Central

Alastruey-Izquierdo, Ana; Castelli, Maria Victoria; Cuesta, Isabel; Monzon, Araceli; Cuenca-Estrella, Manuel; Rodriguez-Tudela, Juan Luis

2009-01-01

The antifungal susceptibility profiles of 77 clinical strains of Mucorales species, identified by internal transcribed spacer sequencing, were analyzed. MICs obtained at 24 and 48 h were compared. Amphotericin B was the most active agent against all isolates, except for Cunninghamella and Apophysomyces isolates. Posaconazole also showed good activity for all species but Cunninghamella bertholletiae. Voriconazole had no activity against any of the fungi tested. Terbinafine showed good activity, except for Rhizopus oryzae, Mucor circinelloides, and Rhizomucor variabilis isolates. PMID:19171801

Activity of posaconazole and other antifungal agents against Mucorales strains identified by sequencing of internal transcribed spacers.

PubMed

Alastruey-Izquierdo, Ana; Castelli, Maria Victoria; Cuesta, Isabel; Monzon, Araceli; Cuenca-Estrella, Manuel; Rodriguez-Tudela, Juan Luis

2009-04-01

The antifungal susceptibility profiles of 77 clinical strains of Mucorales species, identified by internal transcribed spacer sequencing, were analyzed. MICs obtained at 24 and 48 h were compared. Amphotericin B was the most active agent against all isolates, except for Cunninghamella and Apophysomyces isolates. Posaconazole also showed good activity for all species but Cunninghamella bertholletiae. Voriconazole had no activity against any of the fungi tested. Terbinafine showed good activity, except for Rhizopus oryzae, Mucor circinelloides, and Rhizomucor variabilis isolates.

Penicillium daejeonium sp. nov., a new species isolated from a grape and schisandra fruit in Korea.

PubMed

Sang, Hyunkyu; An, Tae-Jin; Kim, Chang Sun; Choi, Young Phil; Deng, Jian-Xin; Paul, Narayan Chandra; Sung, Gi-Ho; Yu, Seung Hun

2013-08-01

Two isolates of monoverticillate Penicillium species were collected from a grape and schisandra fruit in Korea. Multigene phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region and genes encoding β-tubulin (benA) and calmodulin (cmd), as well as morphological analyses revealed that the two isolates are members of the P. sclerotiorum complex in Penicillium subgenus Aspergilloides, but different from species of the P. sclerotiorum complex. The isolates are closely related to P. cainii, P. jacksonii, and P. viticola in terms of their multigene phylogeny, but their colony and conidiophore morphologies differ from those of closely related species. The name P. daejeonium is proposed for this unclassified new species belonging to the P. sclerotiorum complex in subgenus Aspergilloides.

RAPD and Internal Transcribed Spacer Sequence Analyses Reveal Zea nicaraguensis as a Section Luxuriantes Species Close to Zea luxurians

PubMed Central

Wang, Pei; Lu, Yanli; Zheng, Mingmin; Rong, Tingzhao; Tang, Qilin

2011-01-01

Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species. PMID:21525982

Role of Nuclear Matrix in Estrogen Regulated Gene Expression in Human Breast Cancer Cells

DTIC Science & Technology

1998-08-01

reticular pattern evenly distributed throughout the nucleus, excluding the nucleolus (Figure 4A). This is not so for T47D cells where a composite pattern...acetylation is required to maintain the unfolded nucleosome structure associated with transcribing DNA. Journal of Biological Chemistry 273:14516...nuclear matrix include ER, YY1, AML-1, Spl, Oct1, mutant p53, and Rb [25,28,31,34-40]. Appendix A, part 4 reviews alterations in nuclear matrix composition

Complete mitochondrial genomes of the ‘intermediate form’ of Fasciola and Fasciola gigantica, and their comparison with F. hepatica

PubMed Central

2014-01-01

Background Fascioliasis is an important and neglected disease of humans and other mammals, caused by trematodes of the genus Fasciola. Fasciola hepatica and F. gigantica are valid species that infect humans and animals, but the specific status of Fasciola sp. (‘intermediate form’) is unclear. Methods Single specimens inferred to represent Fasciola sp. (‘intermediate form’; Heilongjiang) and F. gigantica (Guangxi) from China were genetically identified and characterized using PCR-based sequencing of the first and second internal transcribed spacer regions of nuclear ribosomal DNA. The complete mitochondrial (mt) genomes of these representative specimens were then sequenced. The relationships of these specimens with selected members of the Trematoda were assessed by phylogenetic analysis of concatenated amino acid sequence datasets by Bayesian inference (BI). Results The complete mt genomes of representatives of Fasciola sp. and F. gigantica were 14,453 bp and 14,478 bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lack an atp8 gene. All protein-coding genes are transcribed in the same direction, and the gene order in both mt genomes is the same as that published for F. hepatica. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 protein-coding genes showed that the specimen of Fasciola sp. was more closely related to F. gigantica than to F. hepatica. Conclusions The mt genomes characterized here provide a rich source of markers, which can be used in combination with nuclear markers and imaging techniques, for future comparative studies of the biology of Fasciola sp. from China and other countries. PMID:24685294

Complete mitochondrial genomes of the 'intermediate form' of Fasciola and Fasciola gigantica, and their comparison with F. hepatica.

PubMed

Liu, Guo-Hua; Gasser, Robin B; Young, Neil D; Song, Hui-Qun; Ai, Lin; Zhu, Xing-Quan

2014-03-31

Fascioliasis is an important and neglected disease of humans and other mammals, caused by trematodes of the genus Fasciola. Fasciola hepatica and F. gigantica are valid species that infect humans and animals, but the specific status of Fasciola sp. ('intermediate form') is unclear. Single specimens inferred to represent Fasciola sp. ('intermediate form'; Heilongjiang) and F. gigantica (Guangxi) from China were genetically identified and characterized using PCR-based sequencing of the first and second internal transcribed spacer regions of nuclear ribosomal DNA. The complete mitochondrial (mt) genomes of these representative specimens were then sequenced. The relationships of these specimens with selected members of the Trematoda were assessed by phylogenetic analysis of concatenated amino acid sequence datasets by Bayesian inference (BI). The complete mt genomes of representatives of Fasciola sp. and F. gigantica were 14,453 bp and 14,478 bp in size, respectively. Both mt genomes contain 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes, but lack an atp8 gene. All protein-coding genes are transcribed in the same direction, and the gene order in both mt genomes is the same as that published for F. hepatica. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 protein-coding genes showed that the specimen of Fasciola sp. was more closely related to F. gigantica than to F. hepatica. The mt genomes characterized here provide a rich source of markers, which can be used in combination with nuclear markers and imaging techniques, for future comparative studies of the biology of Fasciola sp. from China and other countries.

Phylogeny, divergence time and historical biogeography of Laetiporus (Basidiomycota, Polyporales).

PubMed

Song, Jie; Cui, Bao-Kai

2017-04-20

The aim of this study was to characterize the molecular relationship, origin and historical biogeography of the species in important brown rot fungal genus Laetiporus from East Asia, Europe, Pan-America, Hawaii and South Africa. We used six genetic markers to estimate a genus-level phylogeny including (1) the internal transcribed spacer (ITS), (2) nuclear large subunit rDNA (nrLSU), (3) nuclear small subunit rDNA (nrSSU), (4) translation elongation factor 1-α (EF-1α), (5) DNA-directed RNA polymerase II subunit 2 (RPB2), and (6) mitochondrial small subunit rDNA (mtSSU). Results of multi-locus phylogenetic analyses show clade support for at least seventeen species-level lineages including two new Laetiporus in China. Molecular dating using BEAST estimated the present crown group diverged approximately 20.16 million years ago (Mya) in the early Miocene. Biogeographic analyses using RASP indicated that Laetiporus most likely originated in temperate zones with East Asia and North America having the highest probability (48%) of being the ancestral area. Four intercontinental dispersal routes and a possible concealed dispersal route were established for the first time.

Evaluation of the Systematic Status of Geographical Variations in Arcuphantes hibanus (Arachnida: Araneae: Linyphiidae), with Descriptions of Two New Species.

PubMed

Nakano, Takafumi; Ihara, Yoh; Kumasaki, Yusuke; Baba, Yuki G; Tomikawa, Ko

2017-08-01

The systematic status of geographical variants of Arcuphantes hibanus Saito, 1992 belonging to the A. longiscapus species group, indigenous to western Honshu and Shikoku, Japan, was evaluated using morphological and molecular data. Two species, A. enmusubi Ihara, Nakano and Tomikawa, sp. nov. and A. occidentalis Ihara, Nakano and Tomikawa, sp. nov., are described, and A. hibanus is redescribed with redefinition of its taxonomic status. These three species are diagnosed by the characteristics of paracymbium, pseudolamella, and epigynal basal part. Phylogenetic trees obtained with mitochondrial cytochrome c oxidase subunit I and 16S rRNA markers showed that the variants are mutually genetically highly diverged. However, the mtDNA phylogenies failed to recover the monophyly of A. hibanus redefined herein. Contrary to the mtDNA phylogenetic analyses, a neighbor-network analysis of nuclear internal transcribed spacer 1 sequences of A. hibanus, A. enmusubi and A. occidentalis spiders showed that each of them forms a cluster. The results of mitochondrial and nuclear DNA analyses in each of the three species are briefly discussed, along with their taxonomic identities.

Characterization of Trichuris trichiura from humans and T. suis from pigs in China using internal transcribed spacers of nuclear ribosomal DNA.

PubMed

Liu, G H; Zhou, W; Nisbet, A J; Xu, M J; Zhou, D H; Zhao, G H; Wang, S K; Song, H Q; Lin, R Q; Zhu, X Q

2014-03-01

Trichuris trichiura and Trichuris suis parasitize (at the adult stage) the caeca of humans and pigs, respectively, causing trichuriasis. Despite these parasites being of human and animal health significance, causing considerable socio-economic losses globally, little is known of the molecular characteristics of T. trichiura and T. suis from China. In the present study, the entire first and second internal transcribed spacer (ITS-1 and ITS-2) regions of nuclear ribosomal DNA (rDNA) of T. trichiura and T. suis from China were amplified by polymerase chain reaction (PCR), the representative amplicons were cloned and sequenced, and sequence variation in the ITS rDNA was examined. The ITS rDNA sequences for the T. trichiura and T. suis samples were 1222-1267 bp and 1339-1353 bp in length, respectively. Sequence analysis revealed that the ITS-1, 5.8S and ITS-2 rDNAs of both whipworms were 600-627 bp and 655-661 bp, 154 bp, and 468-486 bp and 530-538 bp in size, respectively. Sequence variation in ITS rDNA within and among T. trichiura and T. suis was examined. Excluding nucleotide variations in the simple sequence repeats, the intra-species sequence variation in the ITS-1 was 0.2-1.7% within T. trichiura, and 0-1.5% within T. suis. For ITS-2 rDNA, the intra-species sequence variation was 0-1.3% within T. trichiura and 0.2-1.7% within T. suis. The inter-species sequence differences between the two whipworms were 60.7-65.3% for ITS-1 and 59.3-61.5% for ITS-2. These results demonstrated that the ITS rDNA sequences provide additional genetic markers for the characterization and differentiation of the two whipworms. These data should be useful for studying the epidemiology and population genetics of T. trichiura and T. suis, as well as for the diagnosis of trichuriasis in humans and pigs.

Assessing mRNA nuclear export in mammalian cells by microinjection.

PubMed

Lee, Eliza S; Palazzo, Alexander F

2017-08-15

The nuclear export of mRNAs is an important yet little understood part of eukaryotic gene expression. One of the easiest methods for monitoring mRNA export in mammalian tissue culture cells is through the microinjection of DNA plasmids into the nucleus and monitoring the distribution of the transcribed product over time. Here we describe how to setup a microscope equipped with a micromanipulator used in cell microinjections, and we explain how to perform a nuclear mRNA export assay and obtain the nuclear export rate for any given mRNA. Copyright © 2017 Elsevier Inc. All rights reserved.

U6 small nuclear RNA is transcribed by RNA polymerase III.

PubMed Central

Kunkel, G R; Maser, R L; Calvet, J P; Pederson, T

1986-01-01

A DNA fragment homologous to U6 small nuclear RNA was isolated from a human genomic library and sequenced. The immediate 5'-flanking region of the U6 DNA clone had significant homology with a potential mouse U6 gene, including a "TATA box" at a position 26-29 nucleotides upstream from the transcription start site. Although this sequence element is characteristic of RNA polymerase II promoters, the U6 gene also contained a polymerase III "box A" intragenic control region and a typical run of five thymines at the 3' terminus (noncoding strand). The human U6 DNA clone was accurately transcribed in a HeLa cell S100 extract lacking polymerase II activity. U6 RNA transcription in the S100 extract was resistant to alpha-amanitin at 1 microgram/ml but was completely inhibited at 200 micrograms/ml. A comparison of fingerprints of the in vitro transcript and of U6 RNA synthesized in vivo revealed sequence congruence. U6 RNA synthesis in isolated HeLa cell nuclei also displayed low sensitivity to alpha-amanitin, in contrast to U1 and U2 RNA transcription, which was inhibited greater than 90% at 1 microgram/ml. In addition, U6 RNA synthesized in isolated nuclei was efficiently immunoprecipitated by an antibody against the La antigen, a protein known to bind most other RNA polymerase III transcripts. These results establish that, in contrast to the polymerase II-directed transcription of mammalian genes for U1-U5 small nuclear RNAs, human U6 RNA is transcribed by RNA polymerase III. Images PMID:3464970

Pleistocene climate change and the origin of two desert plant species, Pugionium cornutum and Pugionium dolabratum (Brassicaceae), in northwest China.

PubMed

Wang, Qian; Abbott, Richard J; Yu, Qiu-Shi; Lin, Kao; Liu, Jian-Quan

2013-07-01

Pleistocene climate change has had an important effect in shaping intraspecific genetic variation in many species; however, its role in driving speciation is less clear. We examined the possibility of a Pleistocene origin of the only two representatives of the genus Pugionium (Brassicaceae), Pugionium cornutum and Pugionium dolabratum, which occupy different desert habitats in northwest China. We surveyed sequence variation for internal transcribed spacer (ITS), three chloroplast (cp) DNA fragments, and eight low-copy nuclear genes among individuals sampled from 11 populations of each species across their geographic ranges. One ITS mutation distinguished the two species, whereas mutations in cpDNA and the eight low-copy nuclear gene sequences were not species-specific. Although interspecific divergence varied greatly among nuclear gene sequences, in each case divergence was estimated to have occurred within the Pleistocene when deserts expanded in northwest China. Our findings point to the importance of Pleistocene climate change, in this case an increase in aridity, as a cause of speciation in Pugionium as a result of divergence in different habitats that formed in association with the expansion of deserts in China. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

PubMed Central

Nilsson, R. Henrik; Kristiansson, Erik; Ryberg, Martin; Hallenberg, Nils; Larsson, Karl-Henrik

2008-01-01

The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra- and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3% threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names. PMID:19204817

Unveiling Members of Colletotrichum acutatum Species Complex Causing Colletotrichum Leaf Disease of Hevea brasiliensis in Sri Lanka.

PubMed

Hunupolagama, D M; Chandrasekharan, N V; Wijesundera, W S S; Kathriarachchi, H S; Fernando, T H P S; Wijesundera, R L C

2017-06-01

Colletotrichum is an important fungal genus with great diversity, which causes anthracnose of a variety of crop plants including rubber trees. Colletotrichum acutatum and Colletotrichum gloeosporioides have been identified as the major causative agents of Colletotrichum leaf disease of rubber trees in Sri Lanka based on morphology, pathogenicity, and the analysis of internally transcribed spacer sequences of the nuclear ribosomal DNA. This study has been conducted to investigate the members of the C. acutatum species complex causing rubber leaf disease using a morphological and multi gene approach. For the first time in Sri Lanka, Colletotrichum simmondsii, Colletotrichum laticiphilum, Colletotrichum nymphaeae, and Colletotrichum citri have been identified as causative agents of Colletotrichum leaf disease in addition to C. acutatum s. str. Among them, C. simmondsii has been recognized as the major causative agent.

Development of ITS sequence based molecular marker to distinguish, Tribulus terrestris L. (Zygophyllaceae) from its adulterants.

PubMed

Balasubramani, Subramani Paranthaman; Murugan, Ramar; Ravikumar, Kaliamoorthy; Venkatasubramanian, Padma

2010-09-01

Tribulus terrestris L. (Zygophyllaceae) is one of the highly traded raw drugs and also used as a stimulative food additive in Europe and USA. While, Ayurvedic Pharmacopoeia of India recognizes T. terrestris as Goksura, Tribulus lanuginosus and T. subramanyamii are also traded by the same name raising issues of quality control. The nuclear ribosomal RNA genes and ITS (internal transcribed spacer) sequence were used to develop species-specific DNA markers. The species-specific markers efficiently amplified 295bp for T. terrestris (TT1F and TT1R), 300bp for T. lanuginosus (TL1F and TL1R) and 214bp for T. subramanyamii (TS1F and TS1R). These DNA markers can be used to distinguish T. terrestris from its adulterants. Copyright (c) 2010 Elsevier B.V. All rights reserved.

A multi-gene phylogeny of Chlorophyllum (Agaricaceae, Basidiomycota): new species, new combination and infrageneric classification

PubMed Central

Ge, Zai-Wei; Jacobs, Adriaana; Vellinga, Else C.; Sysouphanthong, Phongeun; van der Walt, Retha; Lavorato, Carmine; An, Yi-Feng; Yang, Zhu L.

2018-01-01

Abstract Taxonomic and phylogenetic studies of Chlorophyllum were carried out on the basis of morphological differences and molecular phylogenetic analyses. Based on the phylogeny inferred from the internal transcribed spacer (ITS), the partial large subunit nuclear ribosomal DNA (nrLSU), the second largest subunit of RNA polymerase II (rpb2) and translation elongation factor 1-α (tef1) sequences, six well-supported clades and 17 phylogenetic species are recognised. Within this phylogenetic framework and considering the diagnostic morphological characters, two new species, C. africanum and C. palaeotropicum, are described. In addition, a new infrageneric classification of Chlorophyllum is proposed, in which the genus is divided into six sections. One new combination is also made. This study provides a robust basis for a more detailed investigation of diversity and biogeography of Chlorophyllum. PMID:29681738

Asexual-sexual morph connection in the type species of Berkleasmium.

PubMed

Tanney, Joey; Miller, Andrew N

2017-06-01

Berkleasmium is a polyphyletic genus comprising 37 dematiaceous hyphomycetous species. In this study, independent collections of the type species, B. concinnum , were made from Eastern North America. Nuclear internal transcribed spacer rDNA (ITS) and partial nuc 28S large subunit rDNA (LSU) sequences obtained from collections and subsequent cultures showed that Berkleasmium concinnum is the asexual morph of Neoacanthostigma septoconstrictum ( Tubeufiaceae , Tubeufiales ). Phylogenies inferred from Bayesian inference and maximum likelihood analyses of ITS-LSU sequence data confirmed this asexual-sexual morph connection and a re-examination of fungarium reference specimens also revealed the co-occurrence of N. septoconstrictum ascomata and B. concinnum sporodochia. Neoacanthostigma septoconstrictum is therefore synonymized under B. concinnum on the basis of priority. A specimen identified as N. septoconstrictum from Thailand is described as N. thailandicum sp. nov., based on morphological and genetic distinctiveness.

Hybrid origin of Asian aspermic Fasciola flukes is confirmed by analyzing two single-copy genes, pepck and pold

PubMed Central

HAYASHI, Kei; ICHIKAWA-SEKI, Madoka; MOHANTA, Uday Kumar; SHORIKI, Takuya; CHAICHANASAK, Pannigan; ITAGAKI, Tadashi

2017-01-01

Nuclear gene markers, phosphoenolpyruvate carboxykinase (pepck) and DNA polymerase delta (pold), have been developed for precise discrimination of Fasciola flukes instead of internal transcribed spacer 1. In this study, these two genes of 730 Fasciola flukes from eight Asian countries were analyzed. The results were compared with their mitochondrial NADH dehydrogenase subunit 1 (nad1) lineages for obtaining a definitive evidence of the hybrid origin of aspermic Fasciola flukes. All the flukes categorized into the aspermic nad1 lineages possessed both the fragment patterns of F. hepatica and F. gigantica (mixed types) in pepck and/or pold. These findings provide clear evidence for the hybrid origin of aspermic Fasciola lineages and suggest that “aspermic Fasciola flukes” should hereafter be called “hybrid Fasciola flukes”. PMID:29187710

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants.

PubMed

Li, De-Zhu; Gao, Lian-Ming; Li, Hong-Tao; Wang, Hong; Ge, Xue-Jun; Liu, Jian-Quan; Chen, Zhi-Duan; Zhou, Shi-Liang; Chen, Shi-Lin; Yang, Jun-Bo; Fu, Cheng-Xin; Zeng, Chun-Xia; Yan, Hai-Fei; Zhu, Ying-Jie; Sun, Yong-Shuai; Chen, Si-Yun; Zhao, Lei; Wang, Kun; Yang, Tuo; Duan, Guang-Wen

2011-12-06

A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.

A new cultivation independent approach to detect and monitor common Trichoderma species in soils.

PubMed

Hagn, Alexandra; Wallisch, Stefanie; Radl, Viviane; Charles Munch, Jean; Schloter, Michael

2007-04-01

A set of primers was developed for the detection, identification and quantification of common Trichoderma species in soil samples. Based on a broad range master alignment primers were derived to amplify an approximate 540 bp fragment comprising the internal transcribed spacer region 1 (ITS 1), 5.8S rDNA and internal transcribed spacer region 2 (ITS 2) from all taxonomic Clades of the genus Trichoderma. The primer set was applied to test strains as well as community DNA isolated from arable and forest soil. For all tested isolates the corresponding internal transcribed spacer regions of Trichoderma spp. strains were amplified, but none of non-Trichoderma origin. PCR with community DNA from soil yielded products of the expected size. Analysis of a clone library established for an arable site showed that all amplified sequences originated exclusively from Trichoderma species mainly being representatives of the Clades Hamatum, Harzianum and Pachybasioides and comprising most of the species known for biocontrol ability. In a realtime PCR approach the primer set uTf/uTr also proved to be a suitable system to quantify DNA of Trichoderma spp. in soils.

Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila

PubMed Central

Hur, Junho K.; Luo, Yicheng; Moon, Sungjin; Ninova, Maria; Marinov, Georgi K.; Chung, Yun D.; Aravin, Alexei A.

2016-01-01

The conserved THO/TREX (transcription/export) complex is critical for pre-mRNA processing and mRNA nuclear export. In metazoa, TREX is loaded on nascent RNA transcribed by RNA polymerase II in a splicing-dependent fashion; however, how TREX functions is poorly understood. Here we show that Thoc5 and other TREX components are essential for the biogenesis of piRNA, a distinct class of small noncoding RNAs that control expression of transposable elements (TEs) in the Drosophila germline. Mutations in TREX lead to defects in piRNA biogenesis, resulting in derepression of multiple TE families, gametogenesis defects, and sterility. TREX components are enriched on piRNA precursors transcribed from dual-strand piRNA clusters and colocalize in distinct nuclear foci that overlap with sites of piRNA transcription. The localization of TREX in nuclear foci and its loading on piRNA precursor transcripts depend on Cutoff, a protein associated with chromatin of piRNA clusters. Finally, we show that TREX is required for accumulation of nascent piRNA precursors. Our study reveals a novel splicing-independent mechanism for TREX loading on nascent RNA and its importance in piRNA biogenesis. PMID:27036967

Diversity in aconitine alkaloid profile of Aconitum plants in Hokkaido contrasts with their genetic similarity.

PubMed

Kakiuchi, Nobuko; Atsumi, Toshiyuki; Higuchi, Mari; Kamikawa, Shohei; Miyako, Haruka; Wakita, Yuriko; Ohtsuka, Isao; Hayashi, Shigeki; Hishida, Atsuyuki; Kawahara, Nobuo; Nishizawa, Makoto; Yamagishi, Takashi; Kadota, Yuichi

2015-01-01

Aconite tuber is a representative crude drug for warming the body internally in Japanese Kampo medicine and Chinese traditional medicine. The crude drug is used in major prescriptions for the aged. Varieties of Aconitum plants are distributed throughout the Japanese Islands, especially Hokkaido. With the aim of identifying the medicinal potential of Aconitum plants from Hokkaido, 107 specimens were collected from 36 sites in the summer of 2011 and 2012. Their nuclear DNA region, internal transcribed spacer (ITS), and aconitine alkaloid contents were analyzed. Phylogenic analysis of ITS by maximum parsimony analysis showed that the majority of the specimens were grouped into one cluster (cluster I), separated from the other cluster (cluster II) consisting of alpine specimens. The aconitine alkaloid content of the tuberous roots of 76 specimens showed 2 aspects-specimens from the same collection site showed similar aconitine alkaloid profiles, and cluster I specimens from different habitats showed various alkaloid profiles. Environmental pressure of each habitat is presumed to have caused the morphology and aconitine alkaloid profile of these genetically similar specimens to diversify.

Recent assembly of the global herbaceous flora: evidence from the paper daisies (Asteraceae: Gnaphalieae).

PubMed

Nie, Ze-Long; Funk, Vicki A; Meng, Ying; Deng, Tao; Sun, Hang; Wen, Jun

2016-03-01

The global flora is thought to contain a large proportion of herbs, and understanding the general spatiotemporal processes that shaped the global distribution of these communities is one of the most difficult issues in biogeography. We explored patterns of world-wide biogeography in a species-rich herbaceous group, the paper daisy tribe Gnaphalieae (Asteraceae), based on the hitherto largest taxon sampling, a total of 835 terminal accessions representing 80% of the genera, and encompassing the global geographic range of the tribe, with nuclear internal transcribed spacer (ITS) and external transcribed spacer (ETS) sequences. Biogeographic analyses indicate that Gnaphalieae originated in southern Africa during the Oligocene, followed by repeated migrations into the rest of Africa and the Mediterranean region, with subsequent entries into other continents during various periods starting in the Miocene. Expansions in the late Miocene to Pliocene appear to have been the driving force that shaped the global distribution of the tribe as forests were progressively broken up by the mid-continent aridification and savannas and grasslands expanded into the interior of the major continents. This pattern of recent colonizations may explain the world-wide distribution of many other organisms in open ecosystems and it is highlighted here as an emerging pattern in the evolution of the global flora. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Tissue-specific expression of silkmoth chorion genes in vivo using Bombyx mori nuclear polyhedrosis virus as a transducing vector.

PubMed Central

Iatrou, K; Meidinger, R G

1990-01-01

A pair of silkmoth chorion chromosomal genes, HcA.12-HcB.12, was inserted into a baculovirus transfer vector, pBmp2, derived from the nuclear polyhedrosis virus of Bombyx mori. This vector, which permits the insertion of foreign genetic material in the vicinity of a mutationally inactivated polyhedrin gene, was used to acquire the corresponding recombinant virus. Injection of mutant silkmoth pupae that lack all Hc chorion genes with the recombinant virus resulted in the infection of all internal organs including follicular tissue. Analysis of RNA from infected tissues has demonstrated that the two chorion genes present in the viral genome are correctly transcribed under the control of their own promoter in follicular cells, the tissue in which chorion genes are normally expressed. The chorion primary transcripts are also correctly processed in the infected follicular cells and yield mature mRNAs indistinguishable from authentic chorion mRNAs present in wild-type follicles. These results demonstrate that recombinant nuclear polyhedrosis viruses can be used as transducing vectors for introducing genetic material of host origin into the cells of the organism and that the transduced genes are transiently expressed in a tissue-specific manner under the control of their resident regulatory sequences. Thus we show the in vivo expression of cloned genes under cellular promoter control in an insect other than Drosophila melanogaster. The approach should be applicable to all insect systems that are subject to nuclear polyhedrosis virus infection. Images PMID:2187186

Reflections of Single Turkish International Graduate Students: Studies on Life at a Midwestern University

ERIC Educational Resources Information Center

Burkholder, Jessica Reno

2010-01-01

The research was guided by the research question: How do full-time single Turkish international graduate students conceptualize their experiences as international students? Participants in the study included three doctoral students and three master's students who participated in a series of semi-structured interviews. The data was transcribed and…

Phylogeny and taxonomy of the genus Gliocephalotrichum.

PubMed

Lombard, L; Serrato-Diaz, L M; Cheewangkoon, R; French-Monar, R D; Decock, C; Crous, P W

2014-06-01

Species in the genus Gliocephalotrichum (= Leuconectria) (Hypocreales, Nectriaceae) are soilborne fungi, associated with post-harvest fruit spoilage of several important tropical fruit crops. Contemporary taxonomic studies of these fungi have relied on morphology and DNA sequence comparisons of the internal transcribed spacer region of the nuclear rDNA (ITS) and the β-tubulin gene regions. Employing DNA sequence data from four loci (β-tubulin, histone H3, ITS, and translation elongation factor 1-alpha) and morphological comparisons, the taxonomic status of the genus Gliocephalotrichum was re-evaluated. As a result five species are newly described, namely G. humicola (Taiwan, soil), G. mexicanum (rambutan fruit from Mexico), G. nephelii (rambutan fruit from Guatemala), G. queenslandicum (Australia, endophytic isolations) and G. simmonsii (rambutan fruit from Guatemala). Although species of Gliocephalotrichum are generally not regarded as important plant pathogens, their ability to cause post-harvest fruit rot could have an impact on fruit export and storage.

Is ITS-2 rDNA suitable marker for genetic characterization of Sarcoptes mites from different wild animals in different geographic areas?

PubMed

Alasaad, S; Soglia, D; Spalenza, V; Maione, S; Soriguer, R C; Pérez, J M; Rasero, R; Degiorgis, M P Ryser; Nimmervoll, H; Zhu, X Q; Rossi, L

2009-02-05

The present study examined the relationship among individual Sarcoptes scabiei mites from 13 wild mammalian populations belonging to nine species in four European countries using the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) as genetic marker. The ITS-2 plus primer flanking 5.8S and 28S rDNA (ITS-2+) was amplified from individual mites by polymerase chain reaction (PCR) and the amplicons were sequenced directly. A total of 148 ITS-2+ sequences of 404bp in length were obtained and 67 variable sites were identified (16.59%). UPGMA analyses did not show any geographical or host-specific clustering, and a similar outcome was obtained using population pairwise Fst statistics. These results demonstrated that ITS-2 rDNA does not appear to be suitable for examining genetic diversity among mite populations.

Development of a PCR-based assay for rapid and reliable identification of pathogenic Fusaria.

PubMed

Mishra, Prashant K; Fox, Roland T V; Culham, Alastair

2003-01-28

Identification of Fusarium species has always been difficult due to confusing phenotypic classification systems. We have developed a fluorescent-based polymerase chain reaction assay that allows for rapid and reliable identification of five toxigenic and pathogenic Fusarium species. The species includes Fusarium avenaceum, F. culmorum, F. equiseti, F. oxysporum and F. sambucinum. The method is based on the PCR amplification of species-specific DNA fragments using fluorescent oligonucleotide primers, which were designed based on sequence divergence within the internal transcribed spacer region of nuclear ribosomal DNA. Besides providing an accurate, reliable, and quick diagnosis of these Fusaria, another advantage with this method is that it reduces the potential for exposure to carcinogenic chemicals as it substitutes the use of fluorescent dyes in place of ethidium bromide. Apart from its multidisciplinary importance and usefulness, it also obviates the need for gel electrophoresis.

Sequence analysis of chloroplast chlB gene of medicinal Ephedra species and its application to authentication of Ephedra Herb.

PubMed

Guo, Yahong; Tsuruga, Ayako; Yamaguchi, Shigeharu; Oba, Koji; Iwai, Kasumi; Sekita, Setsuko; Mizukami, Hajime

2006-06-01

Chloroplast chlB gene encoding subunit B of light-independent protochlorophyllide reductase was amplified from herbarium and crude drug specimens of Ephedra sinica, E. intermedia, E. equisetina, and E. przewalskii. Sequence comparison of the chlB gene indicated that all the E. sinica specimens have the same sequence type (Type S) distinctive from other species, while there are two sequence types (Type E1 and Type E2) in E. equisetina. E. intermedia and E. prezewalskii revealed an identical sequence type (Type IP). E. sinica was also identified by digesting the chlB fragment with Bcl I. A novel method for DNA authentication of Ephedra Herb based on the sequences of the chloroplast chlB gene and internal transcribed spacer of nuclear rRNA genes was developed and successfully applied for identification of the crude drugs obtained in the Chinese market.

A morphological and molecular study of Clinostomid metacercariae from African fish with a redescription of Clinostomum tilapiae.

PubMed

Caffara, Monica; Locke, Sean A; Echi, Paul C; Halajian, Ali; Benini, Deborah; Luus-Powell, Wilmien J; Tavakol, Sareh; Fioravanti, Maria L

2017-09-01

The genus Clinostomum Leidy, 1856 (Digenea: Clinostomidae) has been reported in all ecozones of the world and a clear separation between the species of the 'Old World' and 'New World' has been recognized based on molecular studies. Recent works on Afrotropical species include redescriptions of C. cutaneum and C. phalacrocoracis, while C. tilapiae has yet to be studied using modern taxonomic approaches. In the present research, morphological redescription of C. tilapiae metacercariae from a new host, Synodontis batensoda sampled at Anambra River Basin, Nigeria, together with molecular analysis of nuclear internal transcribed spacer rDNA and cytochrome c oxidase 1 mtDNA are reported. We also provide morphological and molecular data from four further putative species of Clinostomum (morphotypes 1-4) from different areas of Africa, as well as the first report of C. phalacrocoracis in South Africa.

Shape-shifting corals: Molecular markers show morphology is evolutionarily plastic in Porites

PubMed Central

Forsman, Zac H; Barshis, Daniel J; Hunter, Cynthia L; Toonen, Robert J

2009-01-01

Background Corals are notoriously difficult to identify at the species-level due to few diagnostic characters and variable skeletal morphology. This 'coral species problem' is an impediment to understanding the evolution and biodiversity of this important and threatened group of organisms. We examined the evolution of the nuclear ribosomal internal transcribed spacer (ITS) and mitochondrial markers (COI, putative control region) in Porites, one of the most taxonomically challenging and ecologically important genera of reef-building corals. Results Nuclear and mitochondrial markers were congruent, clearly resolving many traditionally recognized species; however, branching and mounding varieties were genetically indistinguishable within at least two clades, and specimens matching the description of 'Porites lutea' sorted into three genetically divergent groups. Corallite-level features were generally concordant with genetic groups, although hyper-variability in one group (Clade I) overlapped and obscured several others, and Synarea (previously thought to be a separate subgenus) was closely related to congeners despite its unique morphology. Scanning electron microscopy revealed subtle differences between genetic groups that may have been overlooked previously as taxonomic characters. Conclusion This study demonstrates that the coral skeleton can be remarkably evolutionarily plastic, which may explain some taxonomic difficulties, and obscure underlying patterns of endemism and diversity. PMID:19239678

Phylogeny and biogeography of Juglans (Juglandaceae) based on matK and ITS sequence data.

PubMed

Stanford, A M; Harden, R; Parks, C R

2000-06-01

We investigated phylogenetic and biogeographic relationships within Juglans (walnuts), a Tertiary disjunct genus, using 15 species of Juglans and related (Juglandaceae) outgroups. The relationships were analyzed using nucleotide sequences of the chloroplast gene matK and its flanking spacers and of the internal transcribed spacers (ITS) and 5.8S gene of the nuclear ribosomal DNA. The DNA sequences provided 246 informative characters for parsimony analysis. ITS data supported as monophyletic groups the four generic sections, Cardiocaryon, Dioscaryon, Rhysocaryon, and Trachycaryon. Within Rhysocaryon, the temperate black walnuts and the tropical black walnuts were supported as monophyletic groups. When the two data sets were combined, J. cinerea was nested within Cardiocaryon. Combined analysis with published nuclear DNA restriction site data placed J. cinerea in a monophyletic group with Cardiocaryon. These analyses consistently supported Juglans as a monophyletic group and as the sister group to the genus Pterocarya. The results of this work are consistent with the known geological history of Juglans. The fossil record suggests that the butternuts had evolved by the early Oligocene in North America. The presence of butternuts in Eurasia could be the result of migration from North America to Eurasia during the warming trend of the mid Oligocene.

Morphological and molecular differentiation of two new species of Pseudoacanthocephalus Petrochenko, 1958 (Acanthocephala: Echinorhynchidae) from amphibians and reptiles in the Philippines, with identification key for the genus.

PubMed

Tkach, Vasyl V; Lisitsyna, Olga I; Crossley, Janna L; Binh, Tran Thi; Bush, Sarah E

2013-05-01

The genus Pseudoacanthocephalus Petrochenko, 1958 currently includes 14 species of acanthocephalans parasitic in amphibians and reptiles worldwide. This work describes two new species of Pseudoacanthocephalus from amphibians and reptiles collected in several localities on Luzon Island, Philippines. Pseudoacanthocephalus nickoli n. sp. was found in two species of frogs, Rana luzonensis Boulenger and Rana similis (Günther), and Pseudoacanthocephalus smalesi n. sp. was found in a scincid lizard, Sphenomorphus abdictus Brown & Alcala. Differential diagnoses of the two new species of Pseudoacanthocephalus from their congeners are provided. Comparative analysis of nuclear ribosomal rRNA sequences encompassing the 3' end of 18S nuclear rDNA gene, internal transcribed spacer region (ITS1+5.8S+ITS2), and 5' end of the 28S gene strongly corroborated the morphological evidence and demonstrated significant differences between the two new species as well as between these species and closely related species from continental China and Vietnam. No intraspecific sequence variability was detected among different individuals representing each of the examined species. This is the first report of Pseudoacanthocephalus in the Philippines. A key to known species of Pseudoacanthocephalus is provided.

Lack of genetic structure in the jellyfish Pelagia noctiluca (Cnidaria: Scyphozoa: Semaeostomeae) across European seas.

PubMed

Stopar, Katja; Ramsak, Andreja; Trontelj, Peter; Malej, Alenka

2010-10-01

The genetic structure of the holopelagic scyphozoan Pelagia noctiluca was inferred based on the study of 144 adult medusae. The areas of study were five geographic regions in two European seas (Eastern Atlantic and Mediterranean Sea). A 655-bp sequence of mitochondrial cytochrome c oxidase subunit I (COI), and a 645-bp sequence of two nuclear internal transcribed spacers (ITS1 and ITS2) were analyzed. The protein coding COI gene showed a higher level of divergence than the combined nuclear ITS fragment (haplotype diversity 0.962 vs. 0.723, nucleotide diversity 1.16% vs. 0.31%). Phylogeographic analysis on COI gene revealed two clades, the larger consisting of specimens from all sampling sites, and the smaller mostly formed of specimens from the Mediterranean Sea. Haplotype diversity was very high throughout the sampled area, and within sample diversity was higher than diversity among geographical regions. No strongly supported genetically or geographically distinct groups of P. noctiluca were found. The results - long distance dispersal, insignificant F(ST) values, lack of isolation by distance - pointed toward an admixture among Mediterranean and East Atlantic populations. Copyright 2010 Elsevier Inc. All rights reserved.

A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease.

PubMed

Zuriaga, María Angeles; Mas-Coma, Santiago; Bargues, María Dolores

2015-05-01

A pseudogene, designated as "ps(5.8S+ITS-2)", paralogous to the 5.8S gene and internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA (rDNA), has been recently found in many triatomine species distributed throughout North America, Central America and northern South America. Among characteristics used as criteria for pseudogene verification, secondary structures and free energy are highlighted, showing a lower fit between minimum free energy, partition function and centroid structures, although in given cases the fit only appeared to be slightly lower. The unique characteristics of "ps(5.8S+ITS-2)" as a processed or retrotransposed pseudogenic unit of the ghost type are reviewed, with emphasis on its potential functionality compared to the functionality of genes and spacers of the normal rDNA operon. Besides the technical problem of the risk for erroneous sequence results, the usefulness of "ps(5.8S+ITS-2)" for specimen classification, phylogenetic analyses and systematic/taxonomic studies should be highlighted, based on consistence and retention index values, which in pseudogenic sequence trees were higher than in functional sequence trees. Additionally, intraindividual, interpopulational and interspecific differences in pseudogene amount and the fact that it is a pseudogene in the nuclear rDNA suggests a potential relationships with fitness, behaviour and adaptability of triatomine vectors and consequently its potential utility in Chagas disease epidemiology and control.

Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife

PubMed Central

Manen, Jean-François

2004-01-01

Background Intra-specific and intra-individual polymorphism is frequently observed in nuclear markers of Ilex (Aquifoliaceae) and discrepancy between plastid and nuclear phylogenies is the rule in this genus. These observations suggest that inter-specific plastid or/and nuclear introgression played an important role in the process of evolution of Ilex. With the aim of a precise understanding of the evolution of this genus, two distantly related sympatric species collected in Tenerife (Canary Islands), I. perado and I. canariensis, were studied in detail. Introgression between these two species was previously never reported. One plastid marker (the atpB-rbcL spacer) and two nuclear markers, the ribosomal internal transcribed spacer (ITS) and the nuclear encoded plastid glutamine synthetase (nepGS) were analyzed for 13 and 27 individuals of I. perado and I. canariensis, respectively. Results The plastid marker is intra-specifically constant and correlated with species identity. On the other hand, whereas the nuclear markers are conserved in I. perado, they are highly polymorphic in I. canariensis. The presence of pseudogenes and recombination in ITS sequences of I. canariensis explain this polymorphism. Ancestral sequence polymorphism with incomplete lineage sorting, or past or recent hybridization with an unknown species could explain this polymorphism, not resolved by concerted evolution. However, as already reported for many other plants, past or recent introgression of an alien genotype seem the most probable explanation for such a tremendous polymorphism. Conclusions Data do not allow the determination with certitude of the putative species introgressing I. canariensis, but I. perado is suspected. The introgression would be unilateral, with I. perado as the male donor, and the paternal sequences would be rapidly converted in highly divergent and consequently unidentifiable pseudogenes. At least, this study allows the establishment of precautionary measures when nuclear markers are used in phylogenetic studies of genera having experienced introgression such as the genus Ilex. PMID:15550175

Genetic differentiation of Ganaspis brasiliensis (Hymenoptera: Figitidae) from East and Southeast Asia

USDA-ARS?s Scientific Manuscript database

This study aims to clarify genetic differentiation of the Drosophila parasitoid Ganaspis brasiliensis (Hymenoptera; Figitidae; Eucoilinae) based on the nucleotide sequences of the cytochrome oxidase subunit 1 (CO1) and three nuclear DNA regions, the inter-transcribed spacers 1 and 2 (ITS1 and ITS2) ...

Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast.

PubMed

Chen, Miao; Gartenberg, Marc R

2014-05-01

tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC-tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs.

Coordination of tRNA transcription with export at nuclear pore complexes in budding yeast

PubMed Central

Chen, Miao; Gartenberg, Marc R.

2014-01-01

tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and temporal aspects of tRNA gene (tDNA) expression. We show that tDNA transcription fluctuates during cell cycle progression. In M phase, when tRNA synthesis peaks, tDNAs localize at nuclear pore complexes (NPCs). Docking of a tDNA requires the DNA sequence of the contacted gene, nucleoporins Nup60 and Nup2, and cohesin. Characterization of mutants that block NPC localization revealed that docking is a consequence of elevated tDNA transcription. NPC–tDNA contact falters in the absence of the principal exportin of nascent tRNA, Los1, and genetic assays indicate that gating of tDNAs at NPCs favors cytoplasmic accumulation of functional tRNA. Collectively, the data suggest that tDNAs associate with NPCs to coordinate RNA polymerase III transcription with the nuclear export of pre-tRNA. The M-phase specificity of NPC contact reflects a regulatory mechanism that may have evolved, in part, to avoid collisions between DNA replication forks and transcribing RNA polymerase III machinery at NPCs. PMID:24788517

Differences in the second internal transcribed spacer of four species of Nematodirus (Nematoda: Molineidae).

PubMed

Newton, L A; Chilton, N B; Beveridge, I; Gasser, R B

1998-02-01

Genetic differences among Nematodirus spathiger, Nematodirus filicollis, Nematodirus helvetianus and Nematodirus battus in the nucleotide sequence of the second internal transcribed spacer (ITS-2) of ribosomal DNA ranged from 3.9 to 24.7%. Pairwise comparisons of their ITS-2 sequences indicated that the most genetically similar species were N. spathiger and N. helvetianus. N. battus was the most genetically distinct species, with differences ranging from 22.8 to 24.7% with respect to the other three species. Some of the nucleotide differences among species provided different endonuclease restriction sites that could be used in restriction fragment length polymorphism studies. The ITS-2 sequence data may prove useful in studies of the systematics of molineid nematodes.

Technical note: use of internal transcribed spacer for ruminal yeast identification in dairy cows.

PubMed

Vargas-Bello-Pérez, E; Cancino-Padilla, N; Romero, J

2016-12-01

Molecular techniques are important tools for microbiological studies in different habitats, and the internal transcribed spacer (ITS) has been proved to be useful for analyzing fungal diversity. The aim of this study was to use the ITS region to generate ruminal yeast profile and to identify ruminal yeast. DNA from ruminal digesta was extracted to amplify the ribosomal ITS region. The profile from the PCR products was visualized and the excised bands from the profile were identified as the genera Millerozyma, Pichia, Rhizomucor and Hyphopichia. Overall, the ITS resulted to be a simple, fast and sensitive approach that allowed profiling and identification of ruminal yeast that have not been previously described (Millerozyma and Hyphopichia) in the rumen microbial community.

Evaluation of candidate barcoding markers in Orinus (Poaceae).

PubMed

Su, X; Liu, Y P; Chen, Z; Chen, K L

2016-04-26

Orinus is an alpine endemic genus of Poaceae. Because of the imperfect specimens, high level of intraspecific morphological variability, and homoplasies of morphological characters, it is relatively difficult to delimitate species of Orinus by using morphology alone. To this end, the DNA barcoding has shown great potential in identifying species. The present study is the first attempt to test the feasibility of four proposed DNA barcoding markers (matK, rbcL, trnH-psbA, and ITS) in identifying four currently revised species of Orinus from the Qinghai-Tibetan Plateau (QTP). Among all the single-barcode candidates, the differentiation power was the highest for the nuclear internal transcribed spacer (ITS), while the chloroplast barcodes matK (M), rbcL (R), and trnH-psbA (H) could not identify the species. Meanwhile, the differentiation efficiency of the nuclear ITS (I) was also higher than any two- or three-locus combination of chloroplast barcodes, or even a combination of ITS and any chloroplast barcode except H + I and R + I. All the combinations of chloroplast barcodes plus the nuclear ITS, H + I, and R + I differentiated the highest portion of species. The highest differentiation rate for the barcodes or barcode combinations examined here was 100% (H + I and R + I). In summary, this case study showed that the nuclear ITS region represents a more promising barcode than any maternally inherited chloroplast region or combination of chloroplast regions in differentiating Orinus species from the QTP. Moreover, combining the ITS region with chloroplast regions may improve the barcoding success rate.

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan

PubMed Central

CHU, Thi Thanh Huong; MURANO, Takako; UNO, Yukiko; USUI, Tatsufumi; YAMAGUCHI, Tsuyoshi

2015-01-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae. PMID:26074251

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan.

PubMed

Chu, Thi Thanh Huong; Murano, Takako; Uno, Yukiko; Usui, Tatsufumi; Yamaguchi, Tsuyoshi

2015-11-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae.

Morphological and molecular characterization of a new genus and new species of parazoanthid (Anthozoa: Hexacorallia: Zoantharia) associated with Japanese Red Coral

NASA Astrophysics Data System (ADS)

Reimer, J. D.; Nonaka, M.; Sinniger, F.; Iwase, F.

2008-12-01

The Order Zoantharia has long been taxonomically neglected primarily due to difficulty in examining the internal morphology of sand-encrusted zoanthids. However, recent work using molecular markers has shown an unexpectedly high diversity of previously “hidden” taxa (families and genera) within Zoantharia (=Zoanthidea, Zoanthiniaria). In this study, unidentified sediment-encrusting zoanthid specimens ( n = 8) were collected from living Japanese Red Coral Paracorallium japonicum (Family Coralliidae) during precious coral harvesting by Remotely Operated Vehicle (ROV) and manned submersible (February 2004-January 2006) at depths of 194-250 m at six locations between Ishigaki-jima Island and Kikai-jima Island, southern Japan. DNA sequences (mitochondrial 16S ribosomal DNA [mt 16S rDNA], cytochrome oxidase subunit I [COI], nuclear internal transcribed spacer of ribosomal DNA [ITS-rDNA]) unambiguously place these specimens in a previously undescribed, new monophyletic lineage within the family Parazoanthidae. Corallizoanthus tsukaharai, gen. n. et sp. n. is the first reported zoanthid species associated with the family Coralliidae and unlike other described gorgonian-associated zoanthids ( Savalia spp .) does not secrete its own hard axis. Morphologically, C. tsukaharai sp. n. is characterized by generally unitary polyps and bright yellow external coloration.

Genetic differentiation of Artyfechinostomum malayanum and A. sufrartyfex (Trematoda: Echinostomatidae) based on internal transcribed spacer sequences.

PubMed

Tantrawatpan, Chairat; Saijuntha, Weerachai; Sithithaworn, Paiboon; Andrews, Ross H; Petney, Trevor N

2013-01-01

Genetic differentiation between two synonymous echinostomes species, Artyfechinostomum malayanum and Artyfechinostomum sufrartyfex was determined by using the first and second internal transcribed spacers (ITS1 and ITS2), the non-coding region of rDNA as genetic makers. Of the 699 bp of combined ITS1 and ITS2 sequences examined, 18 variable nucleotide positions (2.58 %) were observed. Of these, 17 positions could be used as diagnostic position between these two sibling species, whereas the other one variation was intraspecific variation of A. malayanum. A clade of A. malayanum was closely aligned with A. sufrartyfex and clearly distance from the cluster of other echinostomes. Our results may sufficiently suggest that the current synonymy of these species is not valid.

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes of Apis mellifera (Insecta: Hymenoptera): structure, organization, and retrotransposable elements

PubMed Central

Gillespie, J J; Johnston, J S; Cannone, J J; Gutell, R R

2006-01-01

As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements. PMID:17069639

Analyses of mitochondrial genes reveal two sympatric but genetically divergent lineages of Rhipicephalus appendiculatus in Kenya.

PubMed

Kanduma, Esther G; Mwacharo, Joram M; Githaka, Naftaly W; Kinyanjui, Peter W; Njuguna, Joyce N; Kamau, Lucy M; Kariuki, Edward; Mwaura, Stephen; Skilton, Robert A; Bishop, Richard P

2016-06-22

The ixodid tick Rhipicephalus appendiculatus transmits the apicomplexan protozoan parasite Theileria parva, which causes East coast fever (ECF), the most economically important cattle disease in eastern and southern Africa. Recent analysis of micro- and minisatellite markers showed an absence of geographical and host-associated genetic sub-structuring amongst field populations of R. appendiculatus in Kenya. To assess further the phylogenetic relationships between field and laboratory R. appendiculatus tick isolates, this study examined sequence variations at two mitochondrial genes, cytochrome c oxidase subunit I (COI) and 12S ribosomal RNA (rRNA), and the nuclear encoded ribosomal internal transcribed spacer 2 (ITS2) of the rRNA gene, respectively. The analysis of 332 COI sequences revealed 30 polymorphic sites, which defined 28 haplotypes that were separated into two distinct haplogroups (A and B). Inclusion of previously published haplotypes in our analysis revealed a high degree of phylogenetic complexity never reported before in haplogroup A. Neither haplogroup however, showed any clustering pattern related to either the geographical sampling location, the type of tick sampled (laboratory stocks vs field populations) or the mammalian host species. This finding was supported by the results obtained from the analysis of 12S rDNA sequences. Analysis of molecular variance (AMOVA) indicated that 90.8 % of the total genetic variation was explained by the two haplogroups, providing further support for their genetic divergence. These results were, however, not replicated by the nuclear transcribed ITS2 sequences likely because of recombination between the nuclear genomes maintaining a high level of genetic sequence conservation. COI and 12S rDNA are better markers than ITS2 for studying intraspecific diversity. Based on these genes, two major genetic groups of R. appendiculatus that have gone through a demographic expansion exist in Kenya. The two groups show no phylogeographic structure or correlation with the type of host species from which the ticks were collected, nor to the evolutionary and breeding history of the species. The two lineages may have a wide geographic distribution range in eastern and southern Africa. The findings of this study may have implications for the spread and control of R. appendiculatus, and indirectly, on the transmission dynamics of ECF.

Oral Academic Discourse Socialisation: Challenges Faced by International Undergraduate Students in a Malaysian Public University

ERIC Educational Resources Information Center

Mahfoodh, Omer Hassan Ali

2014-01-01

This paper reports a qualitative study which examines the challenges faced by six international undergraduate students in their socialisation of oral academic discourse in a Malaysian public university. Data were collected employing interviews. Students' presentations were also collected. Semi-structured interviews were transcribed verbatim and…

Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens

PubMed Central

Chen, Jie; Moinard, Magalie; Xu, Jianping; Wang, Shouxian; Foulongne-Oriol, Marie; Zhao, Ruilin; Hyde, Kevin D.; Callac, Philippe

2016-01-01

The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated. PMID:27228131

Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

PubMed Central

Farah, Azman H.; Lee, Shiou Yih; Gao, Zhihui; Yao, Tze Leong; Madon, Maria; Mohamed, Rozi

2018-01-01

The tribe Aquilarieae of the family Thymelaeaceae consists of two genera, Aquilaria and Gyrinops, with a total of 30 species, distributed from northeast India, through southeast Asia and the south of China, to Papua New Guinea. They are an important botanical resource for fragrant agarwood, a prized product derived from injured or infected stems of these species. The aim of this study was to estimate the genome size of selected Aquilaria species and comprehend the evolutionary history of Aquilarieae speciation through molecular phylogeny. Five non-coding chloroplast DNA regions and a nuclear region were sequenced from 12 Aquilaria and three Gyrinops species. Phylogenetic trees constructed using combined chloroplast DNA sequences revealed relationships of the studied 15 members in Aquilarieae, while nuclear ribosomal DNA internal transcribed spacer (ITS) sequences showed a paraphyletic relationship between Aquilaria species from Indochina and Malesian. We exposed, for the first time, the estimated divergence time for Aquilarieae speciation, which was speculated to happen during the Miocene Epoch. The ancestral split and biogeographic pattern of studied species were discussed. Results showed no large variation in the 2C-values for the five Aquilaria species (1.35–2.23 pg). Further investigation into the genome size may provide additional information regarding ancestral traits and its evolution history. PMID:29896211

Complete nuclear ribosomal DNA sequence amplification and molecular analyses of Bangia (Bangiales, Rhodophyta) from China

NASA Astrophysics Data System (ADS)

Xu, Jiajie; Jiang, Bo; Chai, Sanming; He, Yuan; Zhu, Jianyi; Shen, Zonggen; Shen, Songdong

2016-09-01

Filamentous Bangia, which are distributed extensively throughout the world, have simple and similar morphological characteristics. Scientists can classify these organisms using molecular markers in combination with morphology. We successfully sequenced the complete nuclear ribosomal DNA, approximately 13 kb in length, from a marine Bangia population. We further analyzed the small subunit ribosomal DNA gene (nrSSU) and the internal transcribed spacer (ITS) sequence regions along with nine other marine, and two freshwater Bangia samples from China. Pairwise distances of the nrSSU and 5.8S ribosomal DNA gene sequences show the marine samples grouping together with low divergences (00.003; 0-0.006, respectively) from each other, but high divergences (0.123-0.126; 0.198, respectively) from freshwater samples. An exception is the marine sample collected from Weihai, which shows high divergence from both other marine samples (0.063-0.065; 0.129, respectively) and the freshwater samples (0.097; 0.120, respectively). A maximum likelihood phylogenetic tree based on a combined SSU-ITS dataset with maximum likelihood method shows the samples divided into three clades, with the two marine sample clades containing Bangia spp. from North America, Europe, Asia, and Australia; and one freshwater clade, containing Bangia atropurpurea from North America and China.

First survey of Cryptosporidium, Giardia and Enterocytozoon in diarrhoeic children from Wuhan, China.

PubMed

Wang, Tao; Fan, Yingying; Koehler, Anson V; Ma, Guangxu; Li, Tao; Hu, Min; Gasser, Robin B

2017-07-01

Intestinal protozoan pathogens cause significant diarrhoeal diseases in children. However, to date, there has been limited genetic study of the intestinal pathogens Cryptosporidium, Giardia and Enterocytozoon in humans in China, with the exception of research in a small number of cities/provinces. In the present study, PCR-based tools were used to detect and characterise these protistan parasites from 500 children with a history of diarrhoea in Wuhan and environs, Hubei province, China. Genomic DNAs from faecal samples were screened for the particular protists by PCR utilising regions in the small subunit (SSU) of the nuclear ribosomal RNA, the 60kDa glycoprotein (gp60), the internal transcribed spacer of nuclear ribosomal DNA (ITS) and/or the triose phosphate isomerase (tpi) genes as markers. Cryptosporidium meleagridis subtype IIIb (10/500, 2.0%), Giardia duodenalis assemblage A (7/500, 1.4%) and Enterocytozoon bieneusi genotype D (1/500, 0.2%) were identified in small percentages of the 500 samples. No significant gender- or age-associated differences in the prevalence of Cryptosporidium and Giardia infections were found. Future studies might focus on the occurrence of these protists in children as well as animals, with an emphasis on Cryptosporidium meleagridis in pets and agriculturally important birds, in different parts of Hubei province. Copyright © 2017 Elsevier B.V. All rights reserved.

Phylogenetic and chemical diversity of fungal endophytes isolated from Silybum marianum (L) Gaertn. (milk thistle)

PubMed Central

Raja, Huzefa A.; Kaur, Amninder; El-Elimat, Tamam; Figueroa, Mario; Kumar, Rahul; Deep, Gagan; Agarwal, Rajesh; Faeth, Stanley H.; Cech, Nadja B.; Oberlies, Nicholas H.

2015-01-01

Use of the herb milk thistle (Silybum marianum) is widespread, and its chemistry has been studied for over 50 years. However, milk thistle endophytes have not been studied previously for their fungal and chemical diversity. We examined the fungal endophytes inhabiting this medicinal herb to determine: (1) species composition and phylogenetic diversity of fungal endophytes; (2) chemical diversity of secondary metabolites produced by these organisms; and (3) cytotoxicity of the pure compounds against the human prostate carcinoma (PC-3) cell line. Forty-one fungal isolates were identified from milk thistle comprising 25 operational taxonomic units based on BLAST search via GenBank using published authentic sequences from nuclear ribosomal internal transcribed spacer sequence data. Maximum likelihood analyses of partial 28S rRNA gene showed that these endophytes had phylogenetic affinities to four major classes of Ascomycota, the Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Chemical studies of solid–substrate fermentation cultures led to the isolation of four new natural products. In addition, 58 known secondary metabolites, representing diverse biosynthetic classes, were isolated and characterized using a suite of nuclear magnetic resonance and mass spectrometry techniques. Selected pure compounds were tested against the PC-3 cell line, where six compounds displayed cytotoxicity. PMID:26000195

Characterization of Fasciola spp. in Myanmar on the basis of spermatogenesis status and nuclear and mitochondrial DNA markers.

PubMed

Ichikawa, Madoka; Bawn, Saw; Maw, Ni Ni; Htun, Lat Lat; Thein, Myint; Gyi, Aung; Sunn, Kyaw; Katakura, Ken; Itagaki, Tadashi

2011-12-01

Fasciola spp. in Myanmar were characterized on the basis of spermatogenesis status and DNA markers of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1). We collected 88 adult flukes from Yangon, Lashio, and Myitkyina. Spermatogenesis status was analyzed by the presence of sperm in the seminal vesicles, and 8 aspermic and 80 spermic flukes were detected. The flukes were identified on the basis of spermatogenesis status and ITS1 types which were analyzed by a PCR-RFLP method, and 80 spermic flukes were identified as F. gigantica. A very low detection rate of aspermic Fasciola sp. indicated that they are not established in Myanmar. In phylogenetic analyses, the 7 aspermic Fasciola sp. from Myitkyina displayed a haplotype in nad1 sequence, which was identical to that of aspermic Fasciola sp. from other Asian countries including China. Therefore, they were probably introduced from China through an infected domestic ruminant. On the other hand, 17 nad1 haplotypes detected in F. gigantica belonged to 2 clades unique to Myanmar, each with a distinct founder haplotype in a network analysis. This indicated a unique history of F. gigantica introduction into Myanmar involving ancient artificial movements of domestic ruminants. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Phylogenetic and chemical diversity of fungal endophytes isolated from Silybum marianum (L) Gaertn. (milk thistle).

PubMed

Raja, Huzefa A; Kaur, Amninder; El-Elimat, Tamam; Figueroa, Mario; Kumar, Rahul; Deep, Gagan; Agarwal, Rajesh; Faeth, Stanley H; Cech, Nadja B; Oberlies, Nicholas H

2015-01-02

Use of the herb milk thistle ( Silybum marianum ) is widespread, and its chemistry has been studied for over 50 years. However, milk thistle endophytes have not been studied previously for their fungal and chemical diversity. We examined the fungal endophytes inhabiting this medicinal herb to determine: (1) species composition and phylogenetic diversity of fungal endophytes; (2) chemical diversity of secondary metabolites produced by these organisms; and (3) cytotoxicity of the pure compounds against the human prostate carcinoma (PC-3) cell line. Forty-one fungal isolates were identified from milk thistle comprising 25 operational taxonomic units based on BLAST search via GenBank using published authentic sequences from nuclear ribosomal internal transcribed spacer sequence data. Maximum likelihood analyses of partial 28S rRNA gene showed that these endophytes had phylogenetic affinities to four major classes of Ascomycota, the Dothideomycetes, Sordariomycetes, Eurotiomycetes, and Leotiomycetes. Chemical studies of solid-substrate fermentation cultures led to the isolation of four new natural products. In addition, 58 known secondary metabolites, representing diverse biosynthetic classes, were isolated and characterized using a suite of nuclear magnetic resonance and mass spectrometry techniques. Selected pure compounds were tested against the PC-3 cell line, where six compounds displayed cytotoxicity.

A molecular phylogeny of Raddia and its allies within the tribe Olyreae (Poaceae, Bambusoideae) based on noncoding plastid and nuclear spacers.

PubMed

Oliveira, Reyjane P; Clark, Lynn G; Schnadelbach, Alessandra S; Monteiro, Silvana H N; Borba, Eduardo L; Longhi-Wagner, Hilda M; van den Berg, Cassio

2014-09-01

The plastid spacer trnD-trnT and the nuclear ribosomal internal transcribed spacer (ITS) were sequenced for 37 samples of herbaceous bamboos (Poaceae: Olyreae), including all Raddia species and allied genera, as well as two members of the woody bamboos (tribes Bambuseae and Arundinarieae), in order to examine their relationships. The sequences were analyzed using maximum parsimony and Bayesian inference. Both the individual and combined analyses of ITS and trnD-trnT supported Olyreae as a monophyletic group. All species of Raddia also formed a well-supported monophyletic group, and combined datasets allowed us to outline some relationships within this group. Individual analyses indicated incongruence regarding the sister group of Raddia, with ITS data weakly indicating Raddiella malmeana whereas trnD-trnT data supported Sucrea maculata in this position. However, the combined analysis supported Sucrea as sister to Raddia, although the monophyly of Sucrea is not well supported. Parodiolyra is paraphyletic to Raddiella in all analyses; Olyra is also paraphyletic, with species of Lithachne, Arberella and Cryptochloa nested within it. Eremitis and Pariana appeared as an isolated clade within Olyreae, and the position of the New Guinean Buergersiochloa remains uncertain within this tribe. Copyright © 2014 Elsevier Inc. All rights reserved.

Molecular evidence of hybrid zones of Cedrela (Meliaceae) in the Yungas of Northwestern Argentina.

PubMed

Zelener, Noga; Tosto, Daniela; de Oliveira, Luiz Orlando; Soldati, María Cristina; Inza, María Virginia; Fornes, Luis Fernando

2016-09-01

In the Yungas of Northwestern Argentina, three endangered species of Cedrela (C. angustifolia, C. saltensis, and C. balansae) follow altitudinal gradients of distribution with contact zones between them. We sampled 210 individuals from 20 populations that spanned most of Cedrela's geographical range in the Yungas, and used Amplified Fragment Length Polymorphism (AFLP) markers and DNA sequences of the nuclear Internal Transcribed Spacer (ITS) to investigate hybrid zones. Data analyses employed an array of complementary methods, including principal coordinate analyses, Bayesian clustering analyses, maximum likelihood tree-building, and network techniques. Both nuclear molecular systems - AFLP and ITS - provided insights into the evolutionary history of Cedrela in the Yungas in a congruent manner. We uncovered strong support for the occurrence of natural hybridization between C. balansae and C. saltensis. Additionally, we identified hybrid zones in areas of sympatry (at both the Calilegua National Park and the San Andrés farm) and in transition zones from 820 to 1100meters above sea level (localities of Pintascayo and Acambuco). There was no evidence for hybridization of either C. balansae or C. saltensis with C. angustifolia. The role of hybrid populations in conservation and use of genetic resources in the Yungas were discussed. Copyright © 2016 Elsevier Inc. All rights reserved.

Taxonomy of the Rhizopogon vinicolor species complex based on analysis of ITS sequences and microsatellite loci.

Treesearch

Annette M. Kretzer; Daniel L. Luoma; Randy Molina; Joseph W. Spatafora

2003-01-01

We are re-addressing species concepts in the Rhizopogon vinicolor species complex (Boletales, Basidiomycota) using sequence data from the interna transcribed spacer (ITS) region of the nuclear ribosomal repeat, as well as genoLypic data from five microsatellite loci. The R. vinicolor species complex by our definition includes,...

Investigation of Marine-Derived Fungal Diversity and Their Exploitable Biological Activities

PubMed Central

Hong, Joo-Hyun; Jang, Seokyoon; Heo, Young Mok; Min, Mihee; Lee, Hwanhwi; Lee, Young Min; Lee, Hanbyul; Kim, Jae-Jin

2015-01-01

Marine fungi are potential producers of bioactive compounds that may have pharmacological and medicinal applications. Fungi were cultured from marine brown algae and identified using multiple target genes to confirm phylogenetic placement. These target genes included the internal transcribed spacer (ITS), the nuclear large subunit (LSU), and the β-tubulin region. Various biological activities of marine-derived fungi were evaluated, including their antifungal, antioxidant and cellulolytic enzyme activities. As a result, a total of 50 fungi was isolated from the brown algae Sargassum sp. Among the 50 isolated fungi, Corollospora angusta was the dominant species in this study. The genus Arthrinium showed a relatively strong antifungal activity to all of the target plant pathogenic fungi. In particular, Arthrinium saccharicola KUC21221 showed high radical scavenging activity and the highest activities in terms of filter paper units (0.39 U/mL), endoglucanase activity (0.38 U/mL), and β-glucosidase activity (1.04 U/mL). PMID:26133554

Molecular Taxonomy Provides New Insights into Anopheles Species of the Neotropical Arribalzagia Series

PubMed Central

Gómez, Giovan F.; Bickersmith, Sara A.; González, Ranulfo; Conn, Jan E.; Correa, Margarita M.

2015-01-01

Phylogenetic analysis of partial mitochondrial cytochrome oxidase c subunit I (COI) and nuclear internal transcribed spacer 2 (ITS2) sequences were used to evaluate initial identification and to investigate phylogenetic relationships of seven Anopheles morphospecies of the Arribalzagia Series from Colombia. Phylogenetic trees recovered highly supported clades for An. punctimaculas.s., An. calderoni, An. malefactor s.l., An. neomaculipalpus, An. apicimacula s.l., An. mattogrossensis and An. peryassui. This study provides the first molecular confirmation of An. malefactorfrom Colombia and discovered conflicting patterns of divergence for the molecular markers among specimens from northeast and northern Colombia suggesting the presence of two previously unrecognized Molecular Operational Taxonomic Units (MOTUs). Furthermore, two highly differentiated An. apicimacula MOTUs previously found in Panama were detected. Overall, the combined molecular dataset facilitated the detection of known and new Colombian evolutionary lineages, and constitutes the baseline for future research on their bionomics, ecology and potential role as malaria vectors. PMID:25774795

Taxonomic revision of Aegista subchinensis (Möllendorff, 1884) (Stylommatophora, Bradybaenidae) and a description of a new species of Aegista from eastern Taiwan based on multilocus phylogeny and comparative morphology

PubMed Central

Huang, Chih-Wei; Lee, Yen-Chen; Lin, Si-Min; Wu, Wen-Lung

2014-01-01

Abstract Aegista subchinensis (Möllendorff, 1884) is a widely distributed land snail species with morphological variation and endemic to Taiwan. Three genetic markers (partial sequence of the mitochondrial cytochrome c oxidase subunit I [COI], the 16S rDNA and the nuclear internal transcribed spacer 2 [ITS2]) were analysed to infer phylogenetic relationships and genetic divergence of closely related species of the genus Aegista, Aegista vermis (Reeve, 1852) and Aegista oculus (Pfeiffer, 1850). A new species from Aegista subchinensis has been recognized on the basis of phylogenetic and morphological evidences. The nominal new species, Aegista diversifamilia sp. n. is distinguished from Aegista subchinensis (Möllendorff, 1884) by its larger shell size, aperture and apex angle; wider umbilicus and flatter shell shape. The northernmost distribution of Aegista diversifamilia sp. n. is limited by the Lanyang River, which is presumed to mark the geographic barrier between Aegista diversifamilia sp. n. and Aegista subchinensis. PMID:25349506

The occurrence of Toxocara malaysiensis in cats in China, confirmed by sequence-based analyses of ribosomal DNA.

PubMed

Li, Ming-Wei; Zhu, Xing-Quan; Gasser, Robin B; Lin, Rui-Qing; Sani, Rehana A; Lun, Zhao-Rong; Jacobs, Dennis E

2006-10-01

Non-isotopic polymerase chain reaction (PCR)-based single-strand conformation polymorphism and sequence analyses of the second internal transcribed spacer (ITS-2) of nuclear ribosomal DNA (rDNA) were utilized to genetically characterise ascaridoids from dogs and cats from China by comparison with those from other countries. The study showed that Toxocara canis, Toxocara cati, and Toxascaris leonina from China were genetically the same as those from other geographical origins. Specimens from cats from Guangzhou, China, which were morphologically consistent with Toxocara malaysiensis, were the same genetically as those from Malaysia, with the exception of a polymorphism in the ITS-2 but no unequivocal sequence difference. This is the first report of T. malaysiensis in cats outside of Malaysia (from where it was originally described), supporting the proposal that this species has a broader geographical distribution. The molecular approach employed provides a powerful tool for elucidating the biology, epidemiology, and zoonotic significance of T. malaysiensis.

PCR tools for the verification of the specific identity of ascaridoid nematodes from dogs and cats.

PubMed

Li, M W; Lin, R Q; Chen, H H; Sani, R A; Song, H Q; Zhu, X Q

2007-01-01

Based on the sequences of the internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA) of Toxocara canis, Toxocara cati, Toxocara malaysiensis and Toxascaris leonina, specific forward primers were designed in the ITS-1 or ITS-2 for each of the four ascaridoid species of dogs and cats. These primers were used individually together with a conserved primer in the large subunit of rDNA to amplify partial ITS-1 and/or ITS-2 of rDNA from 107 DNA samples from ascaridoids from dogs and cats in China, Australia, Malaysia, England and the Netherlands. This approach allowed their specific identification, with no amplicons being amplified from heterogeneous DNA samples, and sequencing confirmed the identity of the sequences amplified. The minimum amounts of DNA detectable using the PCR assays were 0.13-0.54ng. These PCR assays should provide useful tools for the diagnosis and molecular epidemiological investigations of toxocariasis in humans and animals.

Clonal reproduction with androgenesis and somatic recombination: the case of the ant Cardiocondyla kagutsuchi

NASA Astrophysics Data System (ADS)

Okita, Ichiro; Tsuchida, Koji

2016-04-01

In haplodiploid insects such as ants, male sexuals develop from unfertilised haploid eggs, while female sexuals and workers develop from fertilized diploid eggs. However, some ant species do not exchange their gene pool between sexes; both male and female sexuals are clonally produced, while workers are sexually produced. To date, three ant species, Wasmannia auropunctata, Vollenhovia emeryi, and Paratrechina longicornis, have been reported to reproduce using such reproductive systems. In this study, we reveal that in one lineage of the ant Cardiocondyla kagutsuchi, male and female sexuals are also clonally produced. In contrast to the abovementioned three species, the workers were not only sexually produced but had recombinant sequences in their nuclear internal transcribed spacer regions, although the recombinant sequences were not detected in male or female sexuals. These results suggest that the lineage likely possesses a mechanism to compensate for the reduction in genetic variation due to clonal reproduction with somatic recombination that occurs within the workers.

Sentinel trees as a tool to forecast invasions of alien plant pathogens.

PubMed

Vettraino, AnnaMaria; Roques, Alain; Yart, Annie; Fan, Jian-ting; Sun, Jiang-hua; Vannini, Andrea

2015-01-01

Recent disease outbreaks caused by alien invasive pathogens into European forests posed a serious threat to forest sustainability with relevant environmental and economic effects. Many of the alien tree pathogens recently introduced into Europe were not previously included on any quarantine lists, thus they were not subject to phytosanitary inspections. The identification and description of alien fungi potentially pathogenic to native European flora before their introduction in Europe, is a paramount need in order to limit the risk of invasion and the impact to forest ecosystems. To determine the potential invasive fungi, a sentinel trees plot was established in Fuyang, China, using healthy seedlings of European tree species including Quercus petreae, Q. suber, and Q. ilex. The fungal assemblage associated with symptomatic specimens was studied using the tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS 1). Taxa with probable Asiatic origin were identified and included plant pathogenic genera. These results indicate that sentinel plants may be a strategic tool to improve the prevention of bioinvasions.

Characterisation of seven Inocybe ectomycorrhizal morphotypes from a semiarid woody steppe.

PubMed

Seress, Diána; Dima, Bálint; Kovács, Gábor M

2016-04-01

Ectomycorrhizas (ECM) of Inocybe species (Inocybaceae, Basidiomycota) formed by three host plant species (Populus alba, Salix rosmarinifolia and Pinus nigra) in a semiarid woody steppe of Hungary were studied. To identify the fungal partners, we performed phylogenetic analyses of nucleotide sequences for the internal transcribed spacer region of nuclear DNA (nrDNA ITS) together with sequences gained from public databases. Seven Inocybe ectomycorrhiza morphotypes were morpho-anatomically characterised. Five morphotypes were identified (I. phaeoleuca, I. psammophila, I. semifulva, I. splendens and I. subporospora), whereas two morphotypes represented unidentified Inocybe species. Differences were discernible among the morphotypes, and they showed general anatomical characteristics of Inocybe ECM, such as the slightly organised plectenchymatic mantle (types A, B and E and the gelatinous C). The ECM of I. subporospora and I. phaeoleuca were detected from the introduced Pinus nigra. These two fungi are probably native to the area but capable of forming a novel ectomycorrhizal association with the invasive host.

Phylogeny of the Clinically Relevant Species of the Emerging Fungus Trichoderma and Their Antifungal Susceptibilities

PubMed Central

Sandoval-Denis, Marcelo; Sutton, Deanna A.; Cano-Lira, José F.; Fothergill, Annette W.; Wiederhold, Nathan P.; Guarro, Josep

2014-01-01

A set of 73 isolates of the emerging fungus Trichoderma isolated from human and animal clinical specimens were characterized morphologically and molecularly using a multilocus sequence analysis that included the internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA and fragments of the translation elongation factor 1 alpha (Tef1), endochitinase CHI18-5 (Chi18-5), and actin 1 (Act1) genes. The most frequent species was Trichoderma longibrachiatum (26%), followed by Trichoderma citrinoviride (18%), the Hypocrea lixii/Trichoderma harzianum species complex (15%), the newly described species Trichoderma bissettii (12%), and Trichoderma orientale (11%). The most common anatomical sites of isolation in human clinical specimens were the respiratory tract (40%), followed by deep tissue (30%) and superficial tissues (26%), while all the animal-associated isolates were obtained from superficial tissue samples. Susceptibilities of the isolates to eight antifungal drugs in vitro showed mostly high MICs, except for voriconazole and the echinocandins. PMID:24719448

Clonal reproduction with androgenesis and somatic recombination: the case of the ant Cardiocondyla kagutsuchi.

PubMed

Okita, Ichiro; Tsuchida, Koji

2016-04-01

In haplodiploid insects such as ants, male sexuals develop from unfertilised haploid eggs, while female sexuals and workers develop from fertilized diploid eggs. However, some ant species do not exchange their gene pool between sexes; both male and female sexuals are clonally produced, while workers are sexually produced. To date, three ant species, Wasmannia auropunctata, Vollenhovia emeryi, and Paratrechina longicornis, have been reported to reproduce using such reproductive systems. In this study, we reveal that in one lineage of the ant Cardiocondyla kagutsuchi, male and female sexuals are also clonally produced. In contrast to the abovementioned three species, the workers were not only sexually produced but had recombinant sequences in their nuclear internal transcribed spacer regions, although the recombinant sequences were not detected in male or female sexuals. These results suggest that the lineage likely possesses a mechanism to compensate for the reduction in genetic variation due to clonal reproduction with somatic recombination that occurs within the workers.

Authentication of medicinal herbs using PCR-amplified ITS2 with specific primers.

PubMed

Chiou, Shu-Jiau; Yen, Jui-Hung; Fang, Cheng-Li; Chen, Hui-Ling; Lin, Tsai-Yun

2007-10-01

Different parts of medicinal herbs have long been used as traditional Chinese drugs for treating many diseases, whereas materials of similar morphology and chemical fingerprints are often misidentified. Analyses of sequence variations in the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) have become a valid method for authentication of medicinal herbs at the intergenic and interspecific levels. DNA extracted from processed materials is usually severely degraded or contaminated by microorganisms, thus generates no or unexpected PCR products. The goal of this study is to apply the ITS fragments selectively amplified with two designed primer sets for efficient and precise authentication of medicinal herbs. The designed primers led to an accurate PCR product of the specific region in ITS2, which was confirmed with DNA extracted from 55 processed medicinal herbs belonging to 48 families. Moreover, the selectively amplified ITS2 authenticated five sets of easily confusable Chinese herbal materials. The designed primers were proven to be suitable for a broad application in the authentication of herbal materials.

Rapid and sensitive identification of the herbal tea ingredient Taraxacum formosanum using loop-mediated isothermal amplification.

PubMed

Lai, Guan-Hua; Chao, Jung; Lin, Ming-Kuem; Chang, Wen-Te; Peng, Wen-Huang; Sun, Fang-Chun; Lee, Meng-Shiunn; Lee, Meng-Shiou

2015-01-09

Taraxacum formosanum (TF) is a medicinal plant used as an important component of health drinks in Taiwan. In this study, a rapid, sensitive and specific loop-mediated isothermal amplification (LAMP) assay for authenticating TF was established. A set of four specific LAMP primers was designed based on the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA (nrDNA) of TF. LAMP amplicons were successfully amplified and detected when purified genomic DNA of TF was added in the LAMP reaction under isothermal condition (65 °C) within 45 min. These specific LAMP primers have high specificity and can accurately discriminate Taraxacum formosanum from other adulterant plants; 1 pg of genomic DNA was determined to be the detection limit of the LAMP assay. In conclusion, using this novel approach, TF and its misused plant samples obtained from herbal tea markets were easily identified and discriminated by LAMP assay for quality control.

Rapid and Sensitive Identification of the Herbal Tea Ingredient Taraxacum formosanum Using Loop-Mediated Isothermal Amplification

PubMed Central

Lai, Guan-Hua; Chao, Jung; Lin, Ming-Kuem; Chang, Wen-Te; Peng, Wen-Huang; Sun, Fang-Chun; Lee, Meng-Shiunn; Lee, Meng-Shiou

2015-01-01

Taraxacum formosanum (TF) is a medicinal plant used as an important component of health drinks in Taiwan. In this study, a rapid, sensitive and specific loop-mediated isothermal amplification (LAMP) assay for authenticating TF was established. A set of four specific LAMP primers was designed based on the nucleotide sequence of the internal transcribed spacer 2 (ITS2) nuclear ribosomal DNA (nrDNA) of TF. LAMP amplicons were successfully amplified and detected when purified genomic DNA of TF was added in the LAMP reaction under isothermal condition (65 °C) within 45 min. These specific LAMP primers have high specificity and can accurately discriminate Taraxacum formosanum from other adulterant plants; 1 pg of genomic DNA was determined to be the detection limit of the LAMP assay. In conclusion, using this novel approach, TF and its misused plant samples obtained from herbal tea markets were easily identified and discriminated by LAMP assay for quality control. PMID:25584616

Coccomyxa actinabiotis sp. nov. (Trebouxiophyceae, Chlorophyta), a new green microalga living in the spent fuel cooling pool of a nuclear reactor.

PubMed

Rivasseau, Corinne; Farhi, Emmanuel; Compagnon, Estelle; de Gouvion Saint Cyr, Diane; van Lis, Robert; Falconet, Denis; Kuntz, Marcel; Atteia, Ariane; Couté, Alain

2016-10-01

Life can thrive in extreme environments where inhospitable conditions prevail. Organisms which resist, for example, acidity, pressure, low or high temperature, have been found in harsh environments. Most of them are bacteria and archaea. The bacterium Deinococcus radiodurans is considered to be a champion among all living organisms, surviving extreme ionizing radiation levels. We have discovered a new extremophile eukaryotic organism that possesses a resistance to ionizing radiations similar to that of D. radiodurans. This microorganism, an autotrophic freshwater green microalga, lives in a peculiar environment, namely the cooling pool of a nuclear reactor containing spent nuclear fuels, where it is continuously submitted to nutritive, metallic, and radiative stress. We investigated its morphology and its ultrastructure by light, fluorescence and electron microscopy as well as its biochemical properties. Its resistance to UV and gamma radiation was assessed. When submitted to different dose rates of the order of some tens of mGy · h -1 to several thousands of Gy · h -1 , the microalga revealed to be able to survive intense gamma-rays irradiation, up to 2,000 times the dose lethal to human. The nuclear genome region spanning the genes for small subunit ribosomal RNA-Internal Transcribed Spacer (ITS) 1-5.8S rRNA-ITS2-28S rRNA (beginning) was sequenced (4,065 bp). The phylogenetic position of the microalga was inferred from the 18S rRNA gene. All the revealed characteristics make the alga a new species of the genus Coccomyxa in the class Trebouxiophyceae, which we name Coccomyxa actinabiotis sp. nov. © 2016 Phycological Society of America.

Cryptic Diversity within the Major Trypanosomiasis Vector Glossina fuscipes Revealed by Molecular Markers

PubMed Central

Choi, Kwang-Shik; Darby, Alistair C.; Causse, Sandrine; Kapitano, Berisha; Hall, Martin J. R.; Steen, Keith; Lutumba, Pascal; Madinga, Joules; Torr, Steve J.; Okedi, Loyce M.; Lehane, Michael J.; Donnelly, Martin J.

2011-01-01

Background The tsetse fly Glossina fuscipes s.l. is responsible for the transmission of approximately 90% of cases of human African trypanosomiasis (HAT) or sleeping sickness. Three G. fuscipes subspecies have been described, primarily based upon subtle differences in the morphology of their genitalia. Here we describe a study conducted across the range of this important vector to determine whether molecular evidence generated from nuclear DNA (microsatellites and gene sequence information), mitochondrial DNA and symbiont DNA support the existence of these taxa as discrete taxonomic units. Principal Findings The nuclear ribosomal Internal transcribed spacer 1 (ITS1) provided support for the three subspecies. However nuclear and mitochondrial sequence data did not support the monophyly of the morphological subspecies G. f. fuscipes or G. f. quanzensis. Instead, the most strongly supported monophyletic group was comprised of flies sampled from Ethiopia. Maternally inherited loci (mtDNA and symbiont) also suggested monophyly of a group from Lake Victoria basin and Tanzania, but this group was not supported by nuclear loci, suggesting different histories of these markers. Microsatellite data confirmed strong structuring across the range of G. fuscipes s.l., and was useful for deriving the interrelationship of closely related populations. Conclusion/Significance We propose that the morphological classification alone is not used to classify populations of G. fuscipes for control purposes. The Ethiopian population, which is scheduled to be the target of a sterile insect release (SIT) programme, was notably discrete. From a programmatic perspective this may be both positive, given that it may reflect limited migration into the area or negative if the high levels of differentiation are also reflected in reproductive isolation between this population and the flies to be used in the release programme. PMID:21858237

Phylogeny of Alternaria fungi known to produce host-specific toxins on the basis of variation in internal transcribed spacers of ribosomal DNA.

PubMed

Kusaba, M; Tsuge, T

1995-10-01

The internal transcribed spacer regions (ITS1 and ITS2) of ribosomal DNA from Alternaria species, including seven fungi known to produce host-specific toxins, were analyzed by polymerase chain reaction-amplification and direct sequencing. Phylogenetic analysis of the sequence data by the Neighbor-joining method showed that the seven toxin-producing fungi belong to a monophyletic group together with A. alternata. In contract, A. dianthi, A. panax, A. dauci, A. bataticola, A. porri, A. sesami and A. solani, species that can be morphologically distinguished from A. alternata, could be clearly separated from A. alternata by phylogenetic of the ITS variation. These results suggest that Alternaria pathogens which produce host-specific toxins are pathogenic variants within a single variable species, A. alternata.

Evolutionary history of the Afro-Madagascan Ixora species (Rubiaceae): species diversification and distribution of key morphological traits inferred from dated molecular phylogenetic trees

PubMed Central

Tosh, J.; Dessein, S.; Buerki, S.; Groeninckx, I.; Mouly, A.; Bremer, B.; Smets, E. F.; De Block, P.

2013-01-01

Background and Aims Previous work on the pantropical genus Ixora has revealed an Afro-Madagascan clade, but as yet no study has focused in detail on the evolutionary history and morphological trends in this group. Here the evolutionary history of Afro-Madagascan Ixora spp. (a clade of approx. 80 taxa) is investigated and the phylogenetic trees compared with several key morphological traits in taxa occurring in Madagascar. Methods Phylogenetic relationships of Afro-Madagascan Ixora are assessed using sequence data from four plastid regions (petD, rps16, rpoB-trnC and trnL-trnF) and nuclear ribosomal external transcribed spacer (ETS) and internal transcribed spacer (ITS) regions. The phylogenetic distribution of key morphological characters is assessed. Bayesian inference (implemented in BEAST) is used to estimate the temporal origin of Ixora based on fossil evidence. Key Results Two separate lineages of Madagascan taxa are recovered, one of which is nested in a group of East African taxa. Divergence in Ixora is estimated to have commenced during the mid Miocene, with extensive cladogenesis occurring in the Afro-Madagascan clade during the Pliocene onwards. Conclusions Both lineages of Madagascan Ixora exhibit morphological innovations that are rare throughout the rest of the genus, including a trend towards pauciflorous inflorescences and a trend towards extreme corolla tube length, suggesting that the same ecological and selective pressures are acting upon taxa from both Madagascan lineages. Novel ecological opportunities resulting from climate-induced habitat fragmentation and corolla tube length diversification are likely to have facilitated species radiation on Madagascar. PMID:24142919

Why Africa matters: evolution of Old World Salvia (Lamiaceae) in Africa

PubMed Central

Will, Maria; Claßen-Bockhoff, Regine

2014-01-01

Background and Aims Salvia is the largest genus in Lamiaceae and it has recently been found to be non-monophyletic. Molecular data on Old World Salvia are largely lacking. In this study, we present data concerning Salvia in Africa. The focus is on the colonization of the continent, character evolution and the switch of pollination systems in the genus. Methods Maximum likelihood and Bayesian inference were used for phylogenetic reconstruction. Analyses were based on two nuclear markers [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and one plastid marker (rpl32-trnL). Sequence data were generated for 41 of the 62 African taxa (66 %). Mesquite was used to reconstruct ancestral character states for distribution, life form, calyx shape, stamen type and pollination syndrome. Key Results Salvia in Africa is non-monophyletic. Each of the five major regions in Africa, except Madagascar, was colonized at least twice, and floristic links between North African, south-west Asian and European species are strongly supported. The large radiation in Sub-Saharan Africa (23 species) can be traced back to dispersal from North Africa via East Africa to the Cape Region. Adaptation to bird pollination in southern Africa and Madagascar reflects parallel evolution. Conclusions The phenotypic diversity in African Salvia is associated with repeated introductions to the continent. Many important evolutionary processes, such as colonization, adaptation, parallelism and character transformation, are reflected in this comparatively small group. The data presented in this study can help to understand the evolution of Salvia sensu lato and other large genera. PMID:24966353

Worldwide Report, Nuclear Development and Proliferation

DTIC Science & Technology

1984-03-05

transmissions and broadcasts. Materials from foreign- language sources are translated; those from English- language sources are transcribed or reprinted, with... Processing indicators such as [Text] or [Excerpt] in the first line of each item, or following the last line of a brief, indicate how the original...information was processed . Where no processing indicator is given, the infor- mation was summarized or extracted. Unfamiliar names rendered

Intra-isolate genome variation in arbuscular mycorrhizal fungi persists in the transcriptome.

PubMed

Boon, E; Zimmerman, E; Lang, B F; Hijri, M

2010-07-01

Arbuscular mycorrhizal fungi (AMF) are heterokaryotes with an unusual genetic makeup. Substantial genetic variation occurs among nuclei within a single mycelium or isolate. AMF reproduce through spores that contain varying fractions of this heterogeneous population of nuclei. It is not clear whether this genetic variation on the genome level actually contributes to the AMF phenotype. To investigate the extent to which polymorphisms in nuclear genes are transcribed, we analysed the intra-isolate genomic and cDNA sequence variation of two genes, the large subunit ribosomal RNA (LSU rDNA) of Glomus sp. DAOM-197198 (previously known as G. intraradices) and the POL1-like sequence (PLS) of Glomus etunicatum. For both genes, we find high sequence variation at the genome and transcriptome level. Reconstruction of LSU rDNA secondary structure shows that all variants are functional. Patterns of PLS sequence polymorphism indicate that there is one functional gene copy, PLS2, which is preferentially transcribed, and one gene copy, PLS1, which is a pseudogene. This is the first study that investigates AMF intra-isolate variation at the transcriptome level. In conclusion, it is possible that, in AMF, multiple nuclear genomes contribute to a single phenotype.

The RNA Exosome Adaptor ZFC3H1 Functionally Competes with Nuclear Export Activity to Retain Target Transcripts.

PubMed

Silla, Toomas; Karadoulama, Evdoxia; Mąkosa, Dawid; Lubas, Michal; Jensen, Torben Heick

2018-05-15

Mammalian genomes are promiscuously transcribed, yielding protein-coding and non-coding products. Many transcripts are short lived due to their nuclear degradation by the ribonucleolytic RNA exosome. Here, we show that abolished nuclear exosome function causes the formation of distinct nuclear foci, containing polyadenylated (pA + ) RNA secluded from nucleocytoplasmic export. We asked whether exosome co-factors could serve such nuclear retention. Co-localization studies revealed the enrichment of pA + RNA foci with "pA-tail exosome targeting (PAXT) connection" components MTR4, ZFC3H1, and PABPN1 but no overlap with known nuclear structures such as Cajal bodies, speckles, paraspeckles, or nucleoli. Interestingly, ZFC3H1 is required for foci formation, and in its absence, selected pA + RNAs, including coding and non-coding transcripts, are exported to the cytoplasm in a process dependent on the mRNA export factor AlyREF. Our results establish ZFC3H1 as a central nuclear pA + RNA retention factor, counteracting nuclear export activity. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Increased expression of hepatocyte nuclear factor 4 alpha transcribed by promoter 2 indicates a poor prognosis in hepatocellular carcinoma.

PubMed

Cai, Shao-Hang; Lu, Shi-Xun; Liu, Li-Li; Zhang, Chris Zhiyi; Yun, Jing-Ping

2017-10-01

Hepatocyte nuclear factor 4 alpha (HNF4α) plays an important role in tumourigenesis. There is growing evidence indicating that HNF4α transcribed by promoter 1 (P1-HNF4α) is expressed at relatively low levels in HCC and its presence predicts a favourable outcome for hepatocellular carcinoma (HCC) patients. However, the role of HNF4α transcribed by promoter 2 (P2-HNF4α) in HCC remains unclear. A total of 615 HCC specimens were obtained to construct tissue microarrays and perform immunohistochemistry. The relationship between P2-HNF4α and clinical features of HCC patients were analysed. Kaplan-Meier analysis was conducted to assess the prognostic value of P2-HNF4α. The results showed that the expression of P2-HNF4α in HCC was noticeably increased in HCC tissues compared with the nontumourous tissues. In addition, P1-HNF4α expression was negatively correlated with P2-HNF4α expression ( p  = 0.023). High P2-HNF4α expression was significantly associated with poor differentiation of HCC ( p = 0.002) and vascular invasion ( p = 0.017). Kaplan-Meier analysis showed that P2-HNF4α expression was closely correlated with overall survival in the training group ( p = 0.01), validation group ( p = 0.034), and overall group of patients with HCC ( p < 0.001). Our data show that the role of HNF4α in cancer development needs to be further refined. P2-HNF4α, different from P1-HNF4α, is markedly upregulated and serves as an oncogene-associated protein in HCC. Our study therefore provides a promising biomarker for prognostic prediction and a potential therapeutic target for HCC.

RNA polymerases IV and V influence the 3' boundaries of Polymerase II transcription units in Arabidopsis.

PubMed

McKinlay, Anastasia; Podicheti, Ram; Wendte, Jered M; Cocklin, Ross; Rusch, Douglas B

2018-02-01

Nuclear multisubunit RNA polymerases IV and V (Pol IV and Pol V) evolved in plants as specialized forms of Pol II. Their functions are best understood in the context of RNA-directed DNA methylation (RdDM), a process in which Pol IV-dependent 24 nt siRNAs direct the de novo cytosine methylation of regions transcribed by Pol V. Pol V has additional functions, independent of Pol IV and 24 nt siRNA biogenesis, in maintaining the repression of transposons and genomic repeats whose silencing depends on maintenance cytosine methylation. Here we report that Pol IV and Pol V play unexpected roles in defining the 3' boundaries of Pol II transcription units. Nuclear run-on assays reveal that in the absence of Pol IV or Pol V, Pol II occupancy downstream of poly A sites increases for approximately 12% of protein-coding genes. This effect is most pronounced for convergently transcribed gene pairs. Although Pols IV and V are detected near transcript ends of the affected Pol II - transcribed genes, their role in limiting Pol II read-through is independent of siRNA biogenesis or cytosine methylation for the majority of these genes. Interestingly, we observed that splicing was less efficient in pol IV or pol V mutant plants, compared to wild-type plants, suggesting that Pol IV or Pol V might affect pre-mRNA processing. We speculate that Pols IV and V (and/or their associated factors) play roles in Pol II transcription termination and pre-mRNA splicing by influencing polymerase elongation rates and/or release at collision sites for convergent genes.

The context of transcription start site regions is crucial for transcription of a plant tRNA(Lys)(UUU) gene group both in vitro and in vivo.

PubMed

Yukawa, Yasushi; Akama, Kazuhito; Noguchi, Kanta; Komiya, Masaaki; Sugiura, Masahiro

2013-01-10

Nuclear tRNA genes are transcribed by RNA polymerase III. The A- and B-boxes located within the transcribed regions are essential promoter elements for nuclear tRNA gene transcription. The Arabidopsis genome contains ten annotated genes encoding identical tRNA(Lys)(UUU) molecules, which are scattered on the five chromosomes. In this study, we prepared ten tDNA constructs including each of the tRNA(Lys)(UUU) coding sequences with their individual 5' and 3' flanking sequences, and assayed tRNA expression using an in vitro RNA polymerase III-dependent transcription system. Transcription levels differed significantly among the ten genes and two of the tRNA genes were transcribed at a very low level, despite possessing A- and B-boxes identical to those of the other tRNA genes. To examine whether the in vitro results were reproducible in vivo, the 5' flanking sequence of an amber suppressor tRNA gene was then replaced with those of the ten tRNA(Lys) genes. An in vivo experiment based on an amber suppressor tRNA that mediates suppression of a premature amber codon in a β-glucuronidase (GUS) reporter gene in plant tissues generated nearly identical results to those obtained in vitro. Analysis of mutated versions of the amber suppressor tRNA gene, which contained base substitutions around the transcription start site (TSS), showed that the context around the transcription start sites is a crucial determinant for transcription of plant tRNA(Lys)(UUU) both in vitro and in vivo. The above transcription regulation by context around TSS differed between tRNA genes and other Pol III-dependent genes. Copyright © 2012 Elsevier B.V. All rights reserved.

Rhabdovirus-like endogenous viral elements in the genome of Spodoptera frugiperda insect cells are actively transcribed: Implications for adventitious virus detection.

PubMed

Geisler, Christoph; Jarvis, Donald L

2016-07-01

Spodoptera frugiperda (Sf) cell lines are used to produce several biologicals for human and veterinary use. Recently, it was discovered that all tested Sf cell lines are persistently infected with Sf-rhabdovirus, a novel rhabdovirus. As part of an effort to search for other adventitious viruses, we searched the Sf cell genome and transcriptome for sequences related to Sf-rhabdovirus. To our surprise, we found intact Sf-rhabdovirus N- and P-like ORFs, and partial Sf-rhabdovirus G- and L-like ORFs. The transcribed and genomic sequences matched, indicating the transcripts were derived from the genomic sequences. These appear to be endogenous viral elements (EVEs), which result from the integration of partial viral genetic material into the host cell genome. It is theoretically impossible for the Sf-rhabdovirus-like EVEs to produce infectious virus particles as 1) they are disseminated across 4 genomic loci, 2) the G and L ORFs are incomplete, and 3) the M ORF is missing. Our finding of transcribed virus-like sequences in Sf cells underscores that MPS-based searches for adventitious viruses in cell substrates used to manufacture biologics should take into account both genomic and transcribed sequences to facilitate the identification of transcribed EVE's, and to avoid false positive detection of replication-competent adventitious viruses. Copyright © 2016 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

(385-388) Proposals to amend Art. 32.2, 23.5, and 24.2 to clarify the treatment of transcribed Greek terminations of epithets

USDA-ARS?s Scientific Manuscript database

The International Code of Nomenclature for algae, fungi and plants is revised every six years to incorporate decisions of the Nomenclature Section of successive International Botanical Congresses (IBC) on proposals to amend the Code. The proposals in this paper will be considered at the IBC in Shenz...

Molecular characterization of Fasciola spp. from the endemic area of northern Iran based on nuclear ribosomal DNA sequences.

PubMed

Amor, Nabil; Halajian, Ali; Farjallah, Sarra; Merella, Paolo; Said, Khaled; Ben Slimane, Badreddine

2011-07-01

Fasciolosis caused by Fasciola spp. (Platyhelminthes: Trematoda: Digenea) is considered as the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. In the endemic regions of the North of Iran, Fasciola hepatica and Fasciola gigantica have been previously characterized on the basis of morphometric differences, but the use of molecular markers is necessary to distinguish exactly between species and intermediate forms. Samples from buffaloes and goats from different localities of northern Iran were identified morphologically and then genetically characterized by sequences of the first (ITS-1) and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA). Comparison of the ITS of the northern Iranian samples with sequences of Fasciola spp. from GenBank showed that the examined specimens had sequences identical to those of the most frequent haplotypes of F. hepatica (n=25, 48.1%) and F. gigantica (n=20, 38.45%), which differed from each other in different variable nucleotide positions of ITS region sequences, and their intermediate forms (n=7, 13.45%), which had nucleotides overlapped between the two Fasciola species in all the positions. The ITS sequences from populations of Fasciola isolates in buffaloes and goats had experienced introgression/hybridization as previously reported in isolates from other ruminants and humans. Based on ITS-1 and ITS-2 sequences, flukes are scattered in pure F. hepatica, F. gigantica and intermediate Fasciola clades, revealing that multiple genotypes of Fasciola are able to infect goats and buffaloes in North of Iran. Furthermore, the phylogenetic trees based upon the ITS-1 and ITS-2 sequences showed a close relationship of the Iranian samples with isolates of F. hepatica and F. gigantica from different localities of Africa and Asia. In the present study, the intergenic transcribed spacers ITS-1 and ITS-2 showed to be reliable approaches for the genetic differentiation of Fasciola spp., providing bases for further studies on F. hepatica, F. gigantica and their intermediate forms in the endemic areas in Asia. Copyright © 2011 Elsevier Inc. All rights reserved.

Temporal programming of chloroplast and cytoplasmic ribosomal RNA transcription in the synchronous cell cycle of Chlamydomonas reinhardtii

PubMed Central

1977-01-01

Approximately 90% of the Chlamydomonas reinhardtii chloroplast and cytoplasmic rRNAs was transcribed in the nuclear G1 phase, which occurred during the light period under an alternating light-dark synchronization regime of 12 h each. The remaining 10% of chloroplast and cytoplasmic rRNAs was transcribed from its respective DNAs in the dark period, in the midst of an apparent turnover of a transcription appeared to be prokaryotic in sophistication. The transcription was not interrupted during chloroplast DNA synthesis which occurred during the light period. However, transcription of the nuclear DNA was repressed severely during the nuclear S phase in the dark period. The patterns of incorporation of 32P into chloroplast and cytoplasmic rRNA species in the cell cycle were similar to those of the actual rRNA synthesis as measured optically. However, the quantity of 32P incorporation per unit amount of rRNA synthesized varied considerably during the cell cycle, increasing in all rRNA's during the dark period. 32P incorporation data obtained from continuous and pulse 32P-labeling experiments also revealed a turnover of a small amount of both cytoplasmic and chloroplast rRNAs at the end of the S phase. The 32P incorporation into cytoplasmic and chloroplast rRNAs was well matched temporally with the 32P incorporation into their corresponding ribosomes, indicating that the newly synthesized rRNA molecules are utilized without delay throughout the cell cycle in the assembly of ribosomes. PMID:833204

Update on Pneumocystis carinii f. sp. hominis Typing Based on Nucleotide Sequence Variations in Internal Transcribed Spacer Regions of rRNA Genes

PubMed Central

Lee, Chao-Hung; Helweg-Larsen, Jannik; Tang, Xing; Jin, Shaoling; Li, Baozheng; Bartlett, Marilyn S.; Lu, Jang-Jih; Lundgren, Bettina; Lundgren, Jens D.; Olsson, Mats; Lucas, Sebastian B.; Roux, Patricia; Cargnel, Antonietta; Atzori, Chiara; Matos, Olga; Smith, James W.

1998-01-01

Pneumocystis carinii f. sp. hominis isolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 types are named types a through n. A total of 59 types of P. carinii f. sp. hominis were found in this study. PMID:9508304

A molecular phylogeny for Cercocarpus H.B.K. (Rosaceae) using the external transcribed spacer of the nuclear ribosomal repeat

Treesearch

Brian D. Vanden Heuvel; C. Randal Linder

2001-01-01

Cercocarpus H.B.K. (Rosaceae) taxa are important members of the plant communities of the western states and Mexico, yet the systematics of this genus are unknown primarily from lack of clear morphological delimitations between taxa. In recent years, molecular data have proven useful for resolving relationships among species and the diversity within species that have...

Comparison of internal transcribed spacers and intergenic spacer regions of five common Iranian sheep bursate nematodes.

PubMed

Nabavi, Reza; Conneely, Brendan; McCarthy, Elaine; Good, Barbara; Shayan, Parviz; DE Waal, Theo

2014-09-01

Accurate identification of sheep nematodes is a critical point in epidemiological studies and monitoring of drug resistance in flocks. However, due to a close morphological similarity between the eggs and larval stages of many of these nematodes, such identification is not a trivial task. There are a number of studies showing that molecular targets in ribosomal DNA (Internal transcribed spacer 1, 2 and Intergenic spacer) are suitable for accurate identification of sheep bursate nematodes. The objective of present study was to compare the ITS1, ITS2 and IGS regions of Iranian common bursate nematodes in order to choose best target for specific identification methods. The first and second internal transcribed spacers (ITS1and ITS2) and intergenic spacer (IGS) of the ribosomal DNA (rDNA) of 5 common Iranian bursate nematodes of sheep were sequenced. The sequences of some non-Iranian isolates were used for comparison in order to evaluate the variation in sequence homology between geographically different nematode populations. Comparison of the ITS1 and ITS2 sequences of Iranian nematodes showed greatest similarity among Teladorsagia circumcincta and Marshallagia marshalli of 94% and 88%, respectively. While Trichostrongylus colubriformis and M. marshalli showed the highest homology (99%) in the IGS sequences. Comparison of the spacer sequences of Iranian with non-Iranian isolates showed significantly higher variation in Haemonchus contortus compared to the other species. Both the ITS1 and ITS2 sequences are convenient targets to have species-specific identification of Iranian bursate nematodes. On the other hand the IGS region may be a less suitable molecular target.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preti, Milena; Guffanti, Elisa; Valitutto, Eleonora

The SNR52 gene, coding for a box C/D snoRNA, is the only snoRNA gene transcribed by RNA polymerase (Pol) III in Saccharomyces cerevisiae. Pol III transcription generates a precisely terminated primary transcript that undergoes extensive 5'-end processing. Here, we show that mutations of the box C/D core motif required for snoRNP assembly compromise 5'-end maturation of the SNR52 snoRNA. Upstream processing was also impaired by specific depletion of either Nop1p or Nop58p snoRNP proteins. We further show that the nuclear exosome is required for 3'-end maturation of SNR52 snoRNA, at variance with all the other known Pol III transcripts. Ourmore » data suggest a functional coupling between snoRNP assembly and 5'-end maturation of independently transcribed box C/D snoRNAs.« less

Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.

PubMed

Chen, Chun-Kan; Blanco, Mario; Jackson, Constanza; Aznauryan, Erik; Ollikainen, Noah; Surka, Christine; Chow, Amy; Cerase, Andrea; McDonel, Patrick; Guttman, Mitchell

2016-10-28

The Xist long noncoding RNA orchestrates X chromosome inactivation, a process that entails chromosome-wide silencing and remodeling of the three-dimensional (3D) structure of the X chromosome. Yet, it remains unclear whether these changes in nuclear structure are mediated by Xist and whether they are required for silencing. Here, we show that Xist directly interacts with the Lamin B receptor, an integral component of the nuclear lamina, and that this interaction is required for Xist-mediated silencing by recruiting the inactive X to the nuclear lamina and by doing so enables Xist to spread to actively transcribed genes across the X. Our results demonstrate that lamina recruitment changes the 3D structure of DNA, enabling Xist and its silencing proteins to spread across the X to silence transcription. Copyright © 2016, American Association for the Advancement of Science.

Phylogeographically concordant chloroplast DNA divergence in sympatric Nothofagus s.s. How deep can it be?

PubMed

Premoli, Andrea C; Mathiasen, Paula; Acosta, M Cristina; Ramos, Victor A

2012-01-01

• Here, we performed phylogenetic analyses and estimated the divergence times on mostly sympatric populations of five species within subgenus Nothofagus. We aimed to investigate whether phylogenetic relationships by nuclear internal transcribed spacer (ITS) and phylogeographic patterns by chloroplast DNA (cpDNA) mirror an ancient evolutionary history that was not erased by glacial eras. Extant species are restricted to Patagonia and share a pollen type that was formerly widespread in all southern land masses. Weak reproductive barriers exist among them. • Fifteen cpDNA haplotypes resulted from the analysis of three noncoding regions on 330 individuals with a total alignment of 1794 bp. Nuclear ITS data consisted of 822 bp. We found a deep cpDNA divergence dated 32 Ma at mid-latitudes of Patagonia that predates the phylogenetic divergence of extant taxa. Other more recent breaks by cpDNA occurred towards the north. • Complex paleogeographic features explain the genetic discontinuities. Long-lasting paleobasins and marine ingressions have impeded transoceanic dispersal during range expansion towards lower latitudes under cooler trends since the Oligocene. • Cycles of hybridization-introgression among extant and extinct taxa have resulted in widespread chloroplast capture events. Our data suggest that Nothofagus biogeography will be resolved only if thorough phylogeographic analyses and molecular dating methods are applied using distinct genetic markers. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Molecular phylogenetic, morphological, and mycotoxin data support reidentification of the Quorn mycoprotein fungus as Fusarium venenatum.

PubMed

O'Donnell, K; Cigelnik, E; Casper, H H

1998-02-01

Molecular phylogenetic, morphological, and mycotoxin data were obtained in order to investigate the relationships and identity of the Quorn mycoprotein fungus within Fusarium and to examine Quorn strains and commercial Quorn food products for trichothecene mycotoxins. Phylogenetic analyses of aligned DNA sequences obtained via the polymerase chain reaction from the nuclear 28S ribosomal DNA, nuclear ribosomal internal transcribed spacer region, and beta-tubulin gene exons and introns indicate that the Quorn fungus is Fusarium venenatum, rather than F. graminearum as previously reported. All of the Quorn strains examined were morphologically degenerate aconidial colonial mutants except for NRRL 25139, which produced chlamydospores in recurved terminal chains together with mostly 5-septate sporodochial conidia on doliform monophialides diagnostic of F. venenatum. Bootstrap and decay analyses provide strong support for a monophyletic lineage containing F. venenatum and several other type A trichothecene-producing species, while reference strains of F. graminearum were nested in a separate clade of species that produce type B trichothecenes and/or zearalenone. Analysis of mycotoxins from rice cultures inoculated with Quorn strain NRRL 25416 revealed that four type A trichothecenes are produced, but at low levels relative to strain NRRL 22198 of F. venenatum. No trichothecene mycotoxins, however, were detected from the analysis of three commercial Quorn products marketed for human consumption in England.

Novel methods for the molecular discrimination of Fasciola spp. on the basis of nuclear protein-coding genes.

PubMed

Shoriki, Takuya; Ichikawa-Seki, Madoka; Suganuma, Keisuke; Naito, Ikunori; Hayashi, Kei; Nakao, Minoru; Aita, Junya; Mohanta, Uday Kumar; Inoue, Noboru; Murakami, Kenji; Itagaki, Tadashi

2016-06-01

Fasciolosis is an economically important disease of livestock caused by Fasciola hepatica, Fasciola gigantica, and aspermic Fasciola flukes. The aspermic Fasciola flukes have been discriminated morphologically from the two other species by the absence of sperm in their seminal vesicles. To date, the molecular discrimination of F. hepatica and F. gigantica has relied on the nucleotide sequences of the internal transcribed spacer 1 (ITS1) region. However, ITS1 genotypes of aspermic Fasciola flukes cannot be clearly differentiated from those of F. hepatica and F. gigantica. Therefore, more precise and robust methods are required to discriminate Fasciola spp. In this study, we developed PCR restriction fragment length polymorphism and multiplex PCR methods to discriminate F. hepatica, F. gigantica, and aspermic Fasciola flukes on the basis of the nuclear protein-coding genes, phosphoenolpyruvate carboxykinase and DNA polymerase delta, which are single locus genes in most eukaryotes. All aspermic Fasciola flukes used in this study had mixed fragment pattern of F. hepatica and F. gigantica for both of these genes, suggesting that the flukes are descended through hybridization between the two species. These molecular methods will facilitate the identification of F. hepatica, F. gigantica, and aspermic Fasciola flukes, and will also prove useful in etiological studies of fasciolosis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Identification of Fasciola species based on mitochondrial and nuclear DNA reveals the co-existence of intermediate Fasciola and Fasciola gigantica in Thailand.

PubMed

Wannasan, Anchalee; Khositharattanakool, Pathamet; Chaiwong, Prasong; Piangjai, Somsak; Uparanukraw, Pichart; Morakote, Nimit

2014-11-01

Molecular techniques were used to identify Fasciola species collected from Chiang Mai Thailand. Morphometrically, 65 stained and 45 fresh worms collected from cattle suggested the possible occurrence of both F. gigantica and F. hepatica. Twenty-two worms comprising 15 from cattle and 7 from human patients, were identified subsequently based on three genetic markers: mitochondrial nicotinamide adenine dinucleotide dehydrogenase subunit 1 (nad1), mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS2). All of them presented the F. gigantica type in maternally inherited mitochondrial sequences (nad1 and cox1), with six types in each sequence (FgNDI-CM1 to FgNDI-CM6 and FgCOI-CM1 to FgCOI-CM6, respectively). Remarkably, the predominant nad1 type, FgNDI-CM6, was identical to that of aspermic Fasciola sp. formerly reported from Thailand, Japan, Korea, China, Vietnam, and Myanmar. ITS2 sequences were analyzed successfully in 20 worms. Fifteen worms showed the F. gigantica type and five (including one worm from a patient) had mixed ITS2 sequences of both F. gigantica and F. hepatica in the same worms, with additional heterogeneity within both ITS2 types. This study revealed the intermediate form of Fasciola coexisting with F. gigantica for the first time in Thailand.

Translations on Eastern Europe Political, Sociological, and Military Affairs, Number 1428

DTIC Science & Technology

1977-08-08

sources are translated; those from English-language sources are transcribed or reprinted, with the original phrasing and other characteristics retained...fraternity and firm affinity that is characteristic of the relations between good friends and communists. We are certain that your visit to our country...working class, the international unity, is more important than the national unity. These fundamental characteristics of proletarian international

Nuclear Envelope Protein SUN2 Promotes Cyclophilin-A-Dependent Steps of HIV Replication

PubMed Central

Lahaye, Xavier; Satoh, Takeshi; Gentili, Matteo; Cerboni, Silvia; Silvin, Aymeric; Conrad, Cécile; Ahmed-Belkacem, Abdelhakim; Rodriguez, Elisa C.; Guichou, Jean-François; Bosquet, Nathalie; Piel, Matthieu; Le Grand, Roger; King, Megan C.; Pawlotsky, Jean-Michel; Manel, Nicolas

2016-01-01

Summary During the early phase of replication, HIV reverse transcribes its RNA and crosses the nuclear envelope while escaping host antiviral defenses. The host factor Cyclophilin A (CypA) is essential for these steps and binds the HIV capsid; however, the mechanism underlying this effect remains elusive. Here, we identify related capsid mutants in HIV-1, HIV-2, and SIVmac that are restricted by CypA. This antiviral restriction of mutated viruses is conserved across species and prevents nuclear import of the viral cDNA. Importantly, the inner nuclear envelope protein SUN2 is required for the antiviral activity of CypA. We show that wild-type HIV exploits SUN2 in primary CD4+ T cells as an essential host factor that is required for the positive effects of CypA on reverse transcription and infection. Altogether, these results establish essential CypA-dependent functions of SUN2 in HIV infection at the nuclear envelope. PMID:27149839

Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes.

PubMed

Wu, Feinan; Yao, Jie

2017-03-07

Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (NL genes). Promoter regions of active NL genes are often excluded from NL-association, suggesting that NL-promoter interactions may repress transcription. Active NL genes with higher RNA polymerase II (Pol II) recruitment levels tend to display Pol II promoter-proximal pausing, while Pol II recruitment and Pol II pausing are not correlated among non-NL genes. At the genome-wide scale, NL-association and H3K27me3 distinguishes two large gene classes with low transcriptional activities. Notably, NL-association is anti-correlated with both transcription and active histone mark levels among genes not significantly enriched with H3K9me3 or H3K27me3, suggesting that NL-association may represent a novel gene repression pathway. Interestingly, an NL gene subgroup is not significantly enriched with H3K9me3 or H3K27me3 and is transcribed at higher levels than the rest of NL genes. Furthermore, we identified distal enhancers associated with active NL genes and reported their epigenetic features.

Why Africa matters: evolution of Old World Salvia (Lamiaceae) in Africa.

PubMed

Will, Maria; Claßen-Bockhoff, Regine

2014-07-01

Salvia is the largest genus in Lamiaceae and it has recently been found to be non-monophyletic. Molecular data on Old World Salvia are largely lacking. In this study, we present data concerning Salvia in Africa. The focus is on the colonization of the continent, character evolution and the switch of pollination systems in the genus. Maximum likelihood and Bayesian inference were used for phylogenetic reconstruction. Analyses were based on two nuclear markers [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and one plastid marker (rpl32-trnL). Sequence data were generated for 41 of the 62 African taxa (66 %). Mesquite was used to reconstruct ancestral character states for distribution, life form, calyx shape, stamen type and pollination syndrome. Salvia in Africa is non-monophyletic. Each of the five major regions in Africa, except Madagascar, was colonized at least twice, and floristic links between North African, south-west Asian and European species are strongly supported. The large radiation in Sub-Saharan Africa (23 species) can be traced back to dispersal from North Africa via East Africa to the Cape Region. Adaptation to bird pollination in southern Africa and Madagascar reflects parallel evolution. The phenotypic diversity in African Salvia is associated with repeated introductions to the continent. Many important evolutionary processes, such as colonization, adaptation, parallelism and character transformation, are reflected in this comparatively small group. The data presented in this study can help to understand the evolution of Salvia sensu lato and other large genera. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

PubMed Central

Boutte, Julien; Aliaga, Benoît; Lima, Oscar; Ferreira de Carvalho, Julie; Ainouche, Abdelkader; Macas, Jiri; Rousseau-Gueutin, Mathieu; Coriton, Olivier; Ainouche, Malika; Salmon, Armel

2015-01-01

Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. PMID:26530424

TFIIIC Bound DNA Elements in Nuclear Organization and Insulation

PubMed Central

Kirkland, Jacob G.; Raab, Jesse R.

2012-01-01

tRNA genes (tDNAs) have been known to have barrier insulator function in budding yeast, Saccharomyces cerevisiae, for over a decade. tDNAs also play a role in genome organization by clustering at sites in the nucleus and both of these functions are dependent on the transcription factor TFIIIC. More recently TFIIIC bound sites devoid of pol III, termed Extra-TFIIIC sites (ETC) have been identified in budding yeast and these sites also function as insulators and affect genome organization. Subsequent studies in Schizosaccharomyces pombe showed that TFIIIC bound sites were insulators and also functioned as Chromosome Organization Clamps (COC); tethering the sites to the nuclear periphery. Very recently studies have moved to mammalian systems where pol III genes and their associated factors have been investigated in both mouse and human cells. Short Interspersed Nuclear Elements (SINEs) that bind TFIIIC, function as insulator elements and tDNAs can also function as both enhancer -blocking and barrier insulators in these organisms. It was also recently shown that tDNAs cluster with other tDNAs and with ETCs but not with pol II transcribed genes. Intriguingly, TFIIIC is often found near pol II transcription start sites and it remains unclear what the consequences of TFIIIC based genomic organization are and what influence pol III factors have on pol II transcribed genes and vise versa. In this review we provide a comprehensive overview of the known data on pol III factors in insulation and genome organization and identify the many open questions that require further investigation. \\ PMID:23000638

A Novel Flucytosine-Resistant Yeast Species, Candida pseudoaaseri, Causes Disease in a Cancer Patient ▿

PubMed Central

Pfüller, Roland; Gräser, Yvonne; Erhard, Marcel; Groenewald, Marizeth

2011-01-01

Some members of the genus Candida are among the most common human fungal pathogens and cause serious diseases especially in immunocompromised people. A yeast was isolated from a blood culture from an immunocompromised cancer patient who suffered from acute pneumonia. The growth characteristics of the yeast on CHROMagar Candida were similar to those of Candida tropicalis, whereas the API ID 32C system identified the yeast as Candida silvicola. On the basis of the nucleotide divergence in the D1/D2 domain of the 26S nuclear rRNA (nrRNA) gene, as well as the internal transcribed spacer (ITS) domain of the nrRNA gene region, a new species, Candida pseudoaaseri sp. nov. with type strain VK065094 (CBS 11170T), which was found to be closely related to Candida aaseri, is proposed. While C. aaseri strains were susceptible to all tested antifungals, the new species is resistant to flucytosine and may also be distinguished from C. aaseri by its ability to assimilate l-rhamnose, whereas its colony morphology on CHROMagar Candida may be helpful for differentiation. PMID:21976765

Molecular systematics of European Hyalodaphnia: the role of contemporary hybridization in ancient species.

PubMed Central

Schwenk, K; Posada, D; Hebert, P D

2000-01-01

We examined phylogenetic relationships among Daphnia using mitochondrial DNA (mtDNA) sequences from the small subunit ribosomal RNA (12S), cytochrome c oxidase subunit I and nuclear DNA sequences from the first and second internal transcribed spacer representing 1612 base positions. Phylogenetic analyses using several species of the three main Daphnia subgenera, Ctenodaphnia, Hyalodaphnia and Daphnia, revealed that the Hyalodaphnia are a monophyletic sister group of the Daphnia. Most Hyalodaphnia species occur on one continent, whereas only three are found in North America and Europe. Endemicity of species is associated with variation in thermal tolerance and habitat differentiation. Although many species of the Hyalodaphnia are known to hybridize in nature, mtDNA divergence is relatively high ca. 9%) compared to other hybridizing arthropods (ca. 3%). Reproductive isolation in Daphnia seems to evolve significantly slower than genetic isolation. We related these findings to what is known about the ecology and genetics of Daphnia in order to better understand the evolutionary diversification of lineages. The relationship of these data to phylogenetic patterns is discussed in the context of speciation processes in Daphnia. PMID:11052533

First genetic characterization of Fasciola hepatica in Argentina by nuclear and mitochondrial gene markers.

PubMed

Carnevale, Silvana; Malandrini, Jorge Bruno; Pantano, María Laura; Soria, Claudia Cecilia; Rodrigues-Silva, Rosângela; Machado-Silva, José Roberto; Velásquez, Jorge Néstor; Kamenetzky, Laura

2017-10-15

Fasciola hepatica is a trematode showing genetic variation among isolates from different regions of the world. The objective of this work was to characterize for the first time F. hepatica isolates circulating in different regions of Argentina. Twenty-two adult flukes were collected from naturally infected bovine livers in different areas from Argentina and used for DNA extraction. We carried out PCR amplification and sequence analysis of the ribosomal internal transcribed spacer 1 (ITS1), mitochondrial nicotinamide adenine dinucleotide dehydrogenase subunits 4 and 5 (nad4 and nad5) and mitochondrial cytochrome c oxidase subunit I (cox1) genes as genetic markers. Phylogenies were reconstructed using maximum parsimony algorithm. A total of 6 haplotypes were found for cox1, 4 haplotypes for nad4 and 3 haplotypes for nad5. The sequenced ITS1 fragment was identical in all samples. The analyzed cox1 gene fragment is the most variable marker and is recommended for future analyses. No geographic association was found in the Argentinean samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Hybridization experiments indicate incomplete reproductive isolating mechanism between Fasciola hepatica and Fasciola gigantica.

PubMed

Itagaki, T; Ichinomiya, M; Fukuda, K; Fusyuku, S; Carmona, C

2011-09-01

Experiments on hybridization between Fasciola hepatica and Fasciola gigantica were carried out to clarify whether a reproductive isolating mechanism appears between the two Fasciola species. Molecular evidence for hybridization was based on the DNA sequence of the internal transcribed spacer 1 (ITS1) region in nuclear ribosomal DNA, which differs between the species. The results suggested that there were not pre-mating but post-mating isolating mechanisms between the two species. However, viable adults of the hybrids F1 and F2 were produced from both parental F. hepatica and F. gigantica. The hybrids inherited phenotypic characteristics such as ratio of body length and width and infectivity to rats from parental Fasciola hepatica and F. gigantica. These findings suggest that reproductive isolation is incomplete between Fasciola hepatica and F. gigantica. Adults of the hybrids F1 and F2 were completely different in mode of reproduction from aspermic Fasciola forms that occur in Asia and seem to be offspring originated from hybridization between F. hepatica and F. gigantica and to reproduce parthenogenetically.

A Study on the Phylogeny of the Dyer's Woad Rust Fungus and Other Species of Puccinia from Crucifers.

PubMed

Kropp, B R; Hansen, D R; Wolf, P G; Flint, K M; Thomson, S V

1997-05-01

ABSTRACT The identity of a Puccinia species occurring on the introduced weed dyer's woad (Isatis tinctoria) was studied using sequences from the internal transcribed spacer of the nuclear ribosomal DNA. The relationship of this fungus to other Puccinia species occurring on the family Brassicaceae in Europe and North America was examined, and we tested the hypothesis that P. thlaspeos and P. monoica are correlated species. The data suggest that the Puccinia species from dyer's woad is closely related to the North American species P. consimilis and may be derived from an indigenous strain of P. consimilis that switched hosts. Thus, the Puccinia species from dyer's woad is probably native to North America and is unlikely to cause disease epidemics on indigenous plants if used as a biological control agent against dyer's woad. P. thlaspeos appears to be polyphyletic and, therefore, P. thlaspeos and P. monoica do not appear to be correlated species. Additional DNA sequence data will be needed to clarify further the phylogeny of Puccinia species on the family Brassicaceae.

Common but different: The expanding realm of Cladosporium

PubMed Central

Bensch, K.; Groenewald, J.Z.; Braun, U.; Dijksterhuis, J.; de Jesús Yáñez-Morales, M.; Crous, P.W.

2015-01-01

The genus Cladosporium (Cladosporiaceae, Dothideomycetes), which represents one of the largest genera of dematiaceous hyphomycetes, has been intensively investigated during the past decade. In the process, three major species complexes (C. cladosporioides, C. herbarum and C. sphaerospermum) were resolved based on morphology and DNA phylogeny, and a monographic revision of the genus (s. lat.) published reflecting the current taxonomic status quo. In the present study a further 19 new species are described based on phylogenetic characters (nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, as well as partial actin and translation elongation factor 1-α gene sequences) and morphological differences. For a selection of the species with ornamented conidia, scanning electron microscopic photos were prepared to illustrate the different types of surface ornamentation. Surprisingly, during this study Cladosporium ramotenellum was found to be a quite common saprobic species, being widely distributed and occurring on various substrates. Therefore, an emended species description is provided. Furthermore, the host range and distribution data for several previously described species are also expanded. PMID:26955200

Genetic Diversity of Anopheles triannulatus s.l. (Diptera: Culicidae) from Northwestern and Southeastern Colombia

PubMed Central

Rosero, Doris A.; Jaramillo, Luz M.; Gutiérrez, Lina A.; Conn, Jan E.; Correa, Margarita M.

2012-01-01

Anopheles triannulatus s.l. is a species complex, however in Colombia its taxonomic status is unclear. This study was conducted to understand the level of genetic differentiation or population structure of specimens of An. triannulatus s.l. from northwestern and southeastern Colombia. Cytochrome oxidase subunit I (COI) and internal transcribed spacer (ITS2) sequence analyses suggested high genetic differentiation between the NW and SE populations. A TCS network and Bayesian inference analysis based on 814 bp of COI showed two main groups: group I included samples from the NW and group II samples from the SE. Two main ITS2-polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns were found. Pattern I is present in both the NW and SE, and pattern II is found in the SE specimens. To further elucidate the taxonomic status of An. triannulatus s.l. in Colombia and how these COI lineages are related to the Triannulatus Complex species, the evaluation of immature stages, male genitalia, and additional mitochondrial and nuclear markers will be needed. PMID:22949519

Genetic diversity of Anopheles triannulatus s.l. (Diptera: Culicidae) from northwestern and southeastern Colombia.

PubMed

Rosero, Doris A; Jaramillo, Luz M; Gutiérrez, Lina A; Conn, Jan E; Correa, Margarita M

2012-11-01

Anopheles triannulatus s.l. is a species complex, however in Colombia its taxonomic status is unclear. This study was conducted to understand the level of genetic differentiation or population structure of specimens of An. triannulatus s.l. from northwestern and southeastern Colombia. Cytochrome oxidase subunit I (COI) and internal transcribed spacer (ITS2) sequence analyses suggested high genetic differentiation between the NW and SE populations. A TCS network and Bayesian inference analysis based on 814 bp of COI showed two main groups: group I included samples from the NW and group II samples from the SE. Two main ITS2-polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) patterns were found. Pattern I is present in both the NW and SE, and pattern II is found in the SE specimens. To further elucidate the taxonomic status of An. triannulatus s.l. in Colombia and how these COI lineages are related to the Triannulatus Complex species, the evaluation of immature stages, male genitalia, and additional mitochondrial and nuclear markers will be needed.

The Evolution of Ribosomal DNA: Divergent Paralogues and Phylogenetic Implications

PubMed Central

Buckler-IV, E. S.; Ippolito, A.; Holtsford, T. P.

1997-01-01

Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies. PMID:9055091

Safety assessment of mushrooms in dietary supplements by combining analytical data with in silico toxicology evaluation.

PubMed

VanderMolen, Karen M; Little, Jason G; Sica, Vincent P; El-Elimat, Tamam; Raja, Huzefa A; Oberlies, Nicholas H; Baker, Timothy R; Mahony, Catherine

2017-05-01

Despite growing popularity in dietary supplements, many medicinal mushrooms have not been evaluated for their safe human consumption using modern techniques. The multifaceted approach described here relies on five key principles to evaluate the safety of non-culinary fungi for human use: (1) identification by sequencing the nuclear ribosomal internal transcribed spacer (ITS) region (commonly referred to as ITS barcoding), (2) screening an extract of each fungal raw material against a database of known fungal metabolites, (3) comparison of these extracts to those prepared from grocery store-bought culinary mushrooms using UHPLCPDA-ELS-HRMS, (4) review of the toxicological and chemical literature for each fungus, and (5) evaluation of data establishing presence in-market. This weight-of-evidence approach was used to evaluate seven fungal raw materials and determine safe human use for each. Such an approach may provide an effective alternative to conventional toxicological animal studies (or more efficiently identifies when studies are necessary) for the safety assessment of fungal dietary ingredients. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biogeography and floral evolution of baobabs (Adansonia, Bombacaceae) as inferred from multiple data sets.

PubMed

Baum, D A; Small, R L; Wendel, J F

1998-06-01

The phylogeny of baobab trees was analyzed using four data sets: chloroplast DNA restriction sites, sequences of the chloroplast rpl16 intron, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA, and morphology. We sampled each of the eight species of Adansonia plus three outgroup taxa from tribe Adansonieae. These data were analyzed singly and in combination using parsimony. ITS and morphology provided the greatest resolution and were largely concordant. The two chloroplast data sets showed concordance with one another but showed significant conflict with ITS and morphology. A possible explanation for the conflict is genealogical discordance within the Malagasy Longitubae, perhaps due to introgression events. A maximum-likelihood analysis of branching times shows that the dispersal between Africa and Australia occurred well after the fragmentation of Gondwana and therefore involved overwater dispersal. The phylogeny does not permit unambiguous reconstruction of floral evolution but suggests the plausible hypothesis that hawkmoth pollination was ancestral in Adansonia and that there were two parallel switches to pollination by mammals in the genus.

Sentinel Trees as a Tool to Forecast Invasions of Alien Plant Pathogens

PubMed Central

Vettraino, AnnaMaria; Roques, Alain; Yart, Annie; Fan, Jian-ting; Sun, Jiang-hua; Vannini, Andrea

2015-01-01

Recent disease outbreaks caused by alien invasive pathogens into European forests posed a serious threat to forest sustainability with relevant environmental and economic effects. Many of the alien tree pathogens recently introduced into Europe were not previously included on any quarantine lists, thus they were not subject to phytosanitary inspections. The identification and description of alien fungi potentially pathogenic to native European flora before their introduction in Europe, is a paramount need in order to limit the risk of invasion and the impact to forest ecosystems. To determine the potential invasive fungi, a sentinel trees plot was established in Fuyang, China, using healthy seedlings of European tree species including Quercus petreae, Q. suber, and Q. ilex. The fungal assemblage associated with symptomatic specimens was studied using the tag-encoded 454 pyrosequencing of the nuclear ribosomal internal transcribed spacer-1 (ITS 1). Taxa with probable Asiatic origin were identified and included plant pathogenic genera. These results indicate that sentinel plants may be a strategic tool to improve the prevention of bioinvasions. PMID:25826684

Molecular identification and antifungal susceptibility of Curvularia australiensis, C. hawaiiensis and C. spicifera isolated from human eye infections.

PubMed

Krizsán, Krisztina; Tóth, Eszter; Nagy, László G; Galgóczy, László; Manikandan, Palanisamy; Chandrasekaran, Muthusamy; Kadaikunnan, Shine; Alharbi, Naiyf S; Vágvölgyi, Csaba; Papp, Tamás

2015-10-01

A reliable identification method was developed for three closely related Curvularia species, which are frequently isolated from human keratomycoses. Since the traditionally used morphological method and the increasingly used internal transcribed spacer (ITS)-based molecular method proved to be insufficient to discern C. australiensis, C. hawaiiensis and C. spicifera, other molecular targets, such as β-tubulin, translation elongation factor 1-α and the nuclear ribosomal intergenic spacer (IGS), were tested. Among them, the use of the highly divergent IGS sequence is suggested and the species-specific discriminating characters were determined in appropriate reference strains. It was also concluded that C. hawaiiensis and C. spicifera can be predominantly isolated from eye infections among the three species. The in vitro antifungal susceptibility of 10 currently used antifungal agents against 32 Curvularia isolates was also investigated. MICs were determined in each case. Isolates of C. spicifera proved to be less susceptible to the tested antifungals than those of C. hawaiiensis, which underline the importance of the correct identification of these species. © 2015 Blackwell Verlag GmbH.

Recent oceanic long-distance dispersal and divergence in the amphi-Atlantic rain forest genus Renealmia L.f. (Zingiberaceae).

PubMed

Särkinen, Tiina E; Newman, Mark F; Maas, Paul J M; Maas, Hiltje; Poulsen, Axel D; Harris, David J; Richardson, James E; Clark, Alexandra; Hollingsworth, Michelle; Pennington, R Toby

2007-09-01

Renealmia L.f. (Zingiberaceae) is one of the few tropical plant genera with numerous species in both Africa and South America but not in Asia. Based on phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F DNA, Renealmia is shown to be monophyletic with high branch support. Low sequence divergence found in the two genome regions (ITS: 0-2.4%; trnL-F: 0-1.9%) suggests recent diversification within the genus. Molecular divergence age estimates give further support to the recent origin of the genus and show that Renealmia has attained its amphi-Atlantic distribution by an oceanic long-distance dispersal event from Africa to South America during the Miocene or Pliocene (15.8-2.7 My ago). Some support is found for the hypothesis that speciation in neotropical Renealmia was influenced by the Andean orogeny. Speciation has been approximately simultaneous on both sides of the Atlantic, but increased taxon sampling is required to compare the speciation rates between the New World and Old World tropics.

Defining the phylogenetic position of Amanita species from Andean Colombia.

PubMed

Vargas, Natalia; Pardo-de La Hoz, Carlos José; Danies, Giovanna; Franco-Molano, Ana Esperanza; Jiménez, Pedro; Restrepo, Silvia; Grajales, Alejandro

2017-01-01

Amanita is a worldwide-distributed fungal genus, with approximately 600 known species. Most species within the genus are ectomycorrhizal (ECM), with some saprotrophic representatives. In this study, we constructed the first comprehensive phylogeny including ECM species from Colombia collected in native Quercus humboldtii forests and in introduced Pinus patula plantations. We included 8 species (A. brunneolocularis, A. colombiana, A. flavoconia, A. fuligineodisca, A. muscaria, A. rubescens, A. sororcula, and A. xylinivolva) out of 16 species reported for the country, two new reports: A. citrina and A. virosa, and a new variety A. brunneolocularis var. pallida. Morphological taxonomic keys together with a phylogenetic approach using three nuclear gene regions: partial nuc rDNA 28S nuc rDNA internal transcribed spacers ITS1 and ITS2 and partial translation elongation factor 1-α gene (TEF1), were used to classify the specimens. Several highly supported clades were obtained from the phylogenetic hypotheses obtained by Bayesian inference and maximum likelihood approaches, allowing us to position the Colombian collections in a coherent infrageneric level and to contribute to the knowledge of local Amanita diversity.

Three new species and the molecular phylogeny of Antipathozoanthus from the Indo-Pacific Ocean (Anthozoa, Hexacorallia, Zoantharia).

PubMed

Kise, Hiroki; Fujii, Takuma; Masucci, Giovanni Diego; Biondi, Piera; Reimer, James Davis

2017-01-01

In this study, three new species of macrocnemic zoantharians (Hexacorallia, Zoantharia) are described from localities in the Indo-Pacific Ocean including the Red Sea, the Maldives, Palau, and southern Japan: Antipathozoanthus obscurus sp. n. , A. remengesaui sp. n. , and A. cavernus sp. n. Although the genus Antipathozoanthus is currently restricted to species living on antipatharians, A. obscurus sp. n. is not associated with any living substrate and instead is found on coral reef carbonate substrate within narrow caves or cracks. The two new species that have association with antipatharians, A. remengesaui sp. n. and A. cavernus sp. n. , can be distinguished by their relative coenenchyme development and the antipatharian species that each uses as substrate. Additionally, all new species described in this study have unique nuclear internal transcribed spacer region of ribosomal DNA (ITS-rDNA) sequences. Our results indicate that more phylogenetic studies focusing on increasing the numbers of species examined within each of the genera of Parazoanthidae are required in order to better understand the evolutionary history of substrate specificity within the family Parazoanthidae.

Molecular identification of Fasciola spp. (Digenea: Fasciolidae) in Egypt

PubMed Central

Dar, Y.; Amer, S.; Mercier, A.; Courtioux, B.; Dreyfuss, G.

2012-01-01

A total of 134 Egyptian liver flukes were collected from different definitive hosts (cattle, sheep, and buffaloes) to identify them via the use of PCR-RFLP and sequence analysis of the first nuclear ribosomal internal transcribed spacer (ITS1). Specimens of F. hepatica from France, as well as F. gigantica from Cameroon were included in the study for comparison. PCR products of ITS1 were subjected for digestion by RsaI restriction enzyme and visualized on agarose gel. According to RFLP pattern, Egyptian flukes were allocated into two categories. The first was identical to that of French hepatica flukes to have a pattern of 360, 100, and 60 (bp) band size, whereas the second resembled to that of Cameroonian gigantica worms to have a profile of 360, 170, and 60 bp in size. Results of RFLP analysis were confirmed by sequence analysis of representative ITS1 amplicons. No hybrid forms were detected in the present study. Taken together, this study concluded that both species of Fasciola are present in Egypt, whereas the hybrid form may be not very common. PMID:22550630

A fluorescence-based polymerase chain reaction-linked single-strand conformation polymorphism (F-PCR-SSCP) assay for the identification of Fasciola spp.

PubMed

Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

2011-06-01

The present study aimed to establish a fluorescence-based polymerase chain reaction-linked single-strand conformation polymorphism (F-PCR-SSCP) assay for the identification of Fasciola spp. Based on the sequences of the second internal transcribed spacer (ITS-2) of the nuclear ribosomal DNA, we designed a set of genus-specific primers for the amplification of Fasciola ITS-2, with an estimated size of 140 bp. These primers were labelled by fluorescence dyes, and the PCR products were analyzed by capillary electrophoresis under non-denaturing conditions (F-PCR-SSCP). Capillary electrophoresis analysis of the fluorescence-labelled DNA fragments displayed three different peak profiles that allowed the accurate identification of Fasciola species: one single peak specific for either Fasciola hepatica or Fasciola gigantica and a doublet peak corresponding to the "intermediate" Fasciola. Validation of our novel method was performed using Fasciola specimens from different host animals from China, Spain, Nigeria, and Egypt. This F-PCR-SSCP assay provides a rapid, simple, and robust tool for the identification and differentiation between Fasciola spp.

The importance of genetic verification for determination of Atlantic salmon in north Pacific waters

USGS Publications Warehouse

Nielsen, J.L.; Williams, I.; Sage, G.K.; Zimmerman, C.E.

2003-01-01

Genetic analyses of two unknown but putative Atlantic salmon Salmo salar captured in the Copper River drainage, Alaska, demonstrated the need for validation of morphologically unusual fishes. Mitochondrial DNA sequences (control region and cytochrome b) and data from two nuclear genes [first internal transcribed spacer (ITS-1) sequence and growth hormone (GH1) amplification product] indicated that the fish caught in fresh water on the Martin River was a coho salmon Oncorhynchus kisutch, while the other fish caught in the intertidal zone of the Copper River delta near Grass Island was an Atlantic salmon. Determination of unusual or cryptic fish based on limited physical characteristics and expected seasonal spawning run timing will add to the controversy over farmed Atlantic salmon and their potential effects on native Pacific species. It is clear that determination of all putative collections of Atlantic salmon found in Pacific waters requires validation. Due to uncertainty of fish identification in the field using plastic morphometric characters, it is recommended that genetic analyses be part of the validation process. ?? 2003 The Fisheries Society of the British Isles.

Distribution patterns of haplotypes for symbionts from Umbilicaria esculenta and U. muehlenbergii reflect the importance of reproductive strategy in shaping population genetic structure.

PubMed

Cao, Shunan; Zhang, Fang; Liu, Chuanpeng; Hao, Zhihua; Tian, Yuan; Zhu, Lingxiang; Zhou, Qiming

2015-10-15

The diversity of lichen fungal components and their photosynthetic partners reflects both ecological and evolutionary factors. In present study, molecular investigations of the internal transcribed spacer of the nuclear ribosomal DNA (ITS nrDNA) region were conducted to analyze the genetic diversity of Umbilicaria esculenta and U. muehlenbergii together with their associated green algae. It was here demonstrated that the reproductive strategy is a principal reason for fungal selectivity to algae. U. muehlenbergii, which disperses via sexual spores, exhibits lower selectivity to its photosynthetic partners than U. esculenta, which has a vegetative reproductive strategy. The difference of genotypic diversity (both fungal and algal) between these two Umbilicaria species is low, although their nucleotide diversity can vary greatly. The present study illustrates that lichen-forming fungi with sexual reproductive strategies are less selective with respect to their photobionts; and reveals that both sexual and vegetative reproduction allow lichens to generate similar amounts of diversity to adapt to the environments. The current study will be helpful for elucidating how lichens with different reproductive strategies adapt to changing environments.

Three new species and the molecular phylogeny of Antipathozoanthus from the Indo-Pacific Ocean (Anthozoa, Hexacorallia, Zoantharia)

PubMed Central

Kise, Hiroki; Fujii, Takuma; Masucci, Giovanni Diego; Biondi, Piera; Reimer, James Davis

2017-01-01

Abstract In this study, three new species of macrocnemic zoantharians (Hexacorallia, Zoantharia) are described from localities in the Indo-Pacific Ocean including the Red Sea, the Maldives, Palau, and southern Japan: Antipathozoanthus obscurus sp. n., A. remengesaui sp. n., and A. cavernus sp. n. Although the genus Antipathozoanthus is currently restricted to species living on antipatharians, A. obscurus sp. n. is not associated with any living substrate and instead is found on coral reef carbonate substrate within narrow caves or cracks. The two new species that have association with antipatharians, A. remengesaui sp. n. and A. cavernus sp. n., can be distinguished by their relative coenenchyme development and the antipatharian species that each uses as substrate. Additionally, all new species described in this study have unique nuclear internal transcribed spacer region of ribosomal DNA (ITS-rDNA) sequences. Our results indicate that more phylogenetic studies focusing on increasing the numbers of species examined within each of the genera of Parazoanthidae are required in order to better understand the evolutionary history of substrate specificity within the family Parazoanthidae. PMID:29362542

a Preliminary Characterisation of SYMBIODINIUM Diversity in Some Common Corals from Singapore

NASA Astrophysics Data System (ADS)

Isa Tanzil, Jani Thuaibah; Ng, Abigayle Pek Kaye; Tey, Yi Qing; Tan, Beverly Hsin Yi; Yun, Eric Yao; Huang, Danwei

The symbiosis between corals and Symbiodinium dinoflagellates is considered a major driver of the distribution and health of reefs worldwide. This study investigated the genetic identities and diversity of Symbiodinium in seven coral species (Porites lutea, Porites lobata, Acropora millepora, Merulina ampliata, Diploastrea heliopora, Pachyseris speciosa, Pocillopora acuta) from three shallow reefs around Singapore (Kusu Island, Pulau Tekukor, Pulau Satumu). Analyses of 31 colonies using denaturing gradient gel electrophoresis of the nuclear internal transcribed spacer region indicated the dominance of C and D Symbiodinium clades. The latter clade was the predominant symbiont in Pachyseris speciosa collected from Pulau Tekukor but those sampled from Pulau Satumu hosted C27, providing evidence for variable symbiosis in this species. The prevalence of the D clade - noted for their stress tolerance (e.g. to elevated temperatures and sedimentation) - in three of seven coral species examined could underlie the importance of this particular symbiotic relationship for the persistence of Singapore’s impacted reefs. Further characterisation of Symbiodinium communities may provide insights into corals’ response to stress and their bleaching patterns in the future.

Emerin and histone deacetylase 3 (HDAC3) cooperatively regulate expression and nuclear positions of MyoD, Myf5, and Pax7 genes during myogenesis

PubMed Central

Demmerle, Justin; Koch, Adam J.; Holaska, James M.

2016-01-01

The spatial organization of chromatin is critical in establishing cell-type dependent gene expression programs. The inner nuclear membrane protein emerin has been implicated in regulating global chromatin architecture. We show emerin associates with genomic loci of muscle differentiation promoting factors in murine myogenic progenitors, including Myf5 and MyoD. Prior to their transcriptional activation Myf5 and MyoD loci localized to the nuclear lamina in proliferating progenitors and moved to the nucleoplasm upon transcriptional activation during differentiation. The Pax7 locus, which is transcribed in proliferating progenitors, localized to the nucleoplasm and Pax7 moved to the nuclear lamina upon repression during differentiation. Localization of Myf5, MyoD, and Pax7 to the nuclear lamina and proper temporal expression of these genes required emerin and HDAC3. Interestingly, activation of HDAC3 catalytic activity rescued both Myf5 localization to the nuclear lamina and its expression. Collectively, these data support a model whereby emerin facilitates repressive chromatin formation at the nuclear lamina by activating the catalytic activity of HDAC3 to regulate the coordinated spatiotemporal expression of myogenic differentiation genes. PMID:24062260

Differences in molecular characteristics between Cronartium quercuum from Japan and fusiform rust from USA

Treesearch

Hitoshi Nakamura; Shigeru Kaneko; Pauline Spaine

1998-01-01

The molecular characteristics were compared among Cronartium quercuum f. sp. densiflorae and C. quercuum f. sp. thunbergii from Japan and C. quercuum f. sp. fusiforme, fusiform rust from the USA. The authors examined the PCR-amplified internal transcribed...

Expanding the species and chemical diversity of Penicillium section Cinnamopurpurea

USDA-ARS?s Scientific Manuscript database

A set of isolates genetically similar to or potentially conspecific with an unidentified Penicillium isolate NRRL 735, was assembled using a Basic Local Alignment Search Tool (BLAST) search of internal transcribed spacer (ITS) similarity among described (GenBank) and undescribed Penicillium isolates...

FUNGAL-SPECIFIC PCR PRIMERS DEVELOPED FOR ANALYSIS OF THE ITS REGION OF ENVIRONMENTAL DNA EXTRACTS

EPA Science Inventory

Background The Internal Transcribed Spacer (ITS) regions of fungal ribosomal DNA (rDNA) are highly variable sequences of great importance in distinguishing fungal species by PCR analysis. Previously published PCR primers available for amplifying these sequences from environmenta...

Identification of Nematodirus species (Nematoda: Molineidae) from wild ruminants in Italy using ribosomal DNA markers.

PubMed

Gasser, R B; Rossi, L; Zhu, X

1999-11-01

The sequence of the second internal transcribed spacer of ribosomal DNA was determined for four species of Nematodirus (Nematodirus rupicaprae, Nematodirus oiratianus, Nematodirus davtiani alpinus and Nematodirus europaeus) from roe deer or alpine chamois. The second internal transcribed spacer of the four species varied in length from 228 to 236 bp, and the G + C contents ranged from 41 to 44%. While no intraspecific sequence variation was detected among multiple samples representing three of the taxa, sequence differences of 5.9-9.7% were detected among the four species, Nematodirus davtiani alpinus and N. rupicaprae were genetically most similar (94.1%), followed by N. oiratianus, N. europaeus and N. rupicaprae (91.1-91.5%), whereas N. oiratianus was genetically most different from N. davtiani alpinus. The interspecific sequence differences were exploited for the delineation of the four species by PCR-based restriction fragment length polymorphism (using two enzymes) and single-strand conformation polymorphism. The results have implications for diagnosis, epidemiology and for studying the systematics of the Nematodirinae.

Characterization of Dermanyssus gallinae (Acarina: Dermanissydae) by sequence analysis of the ribosomal internal transcribed spacer regions.

PubMed

Potenza, L; Cafiero, M A; Camarda, A; La Salandra, G; Cucchiarini, L; Dachà, M

2009-10-01

In the present work mites previously identified as Dermanyssus gallinae De Geer (Acari, Mesostigmata) using morphological keys were investigated by molecular tools. The complete internal transcribed spacer 1 (ITS1), 5.8S ribosomal DNA, and ITS2 region of the ribosomal DNA from mites were amplified and sequenced to examine the level of sequence variations and to explore the feasibility of using this region in the identification of this mite. Conserved primers located at the 3'end of 18S and at the 5'start of 28S rRNA genes were used first, and amplified fragments were sequenced. Sequence analyses showed no variation in 5.8S and ITS2 region while slight intraspecific variations involving substitutions as well as deletions concentrated in the ITS1 region. Based on the sequence analyses a nested PCR of the ITS2 region followed by RFLP analyses has been set up in the attempt to provide a rapid molecular diagnostic tool of D. gallinae.

Systematic internal transcribed spacer sequence analysis for identification of clinical mold isolates in diagnostic mycology: a 5-year study.

PubMed

Ciardo, Diana E; Lucke, Katja; Imhof, Alex; Bloemberg, Guido V; Böttger, Erik C

2010-08-01

The implementation of internal transcribed spacer (ITS) sequencing for routine identification of molds in the diagnostic mycology laboratory was analyzed in a 5-year study. All mold isolates (n = 6,900) recovered in our laboratory from 2005 to 2009 were included in this study. According to a defined work flow, which in addition to troublesome phenotypic identification takes clinical relevance into account, 233 isolates were subjected to ITS sequence analysis. Sequencing resulted in successful identification for 78.6% of the analyzed isolates (57.1% at species level, 21.5% at genus level). In comparison, extended in-depth phenotypic characterization of the isolates subjected to sequencing achieved taxonomic assignment for 47.6% of these, with a mere 13.3% at species level. Optimization of DNA extraction further improved the efficacy of molecular identification. This study is the first of its kind to testify to the systematic implementation of sequence-based identification procedures in the routine workup of mold isolates in the diagnostic mycology laboratory.

Microscopic boson approach to nuclear collective motion

NASA Astrophysics Data System (ADS)

Kuchta, R.

1989-10-01

A quantum mechanical approach to the maximally decoupled nuclear collective motion is proposed. The essential idea is to transcribe the original shell-model hamiltonian in terms of boson operators, then to isolate the collective one-boson eigenstates of the mapped hamiltonian and to perform a canonical transformation which eliminates (up to the two-body terms) the coupling between the collective and noncollective bosons. Unphysical states arising due to the violation of the Pauli principle in the boson space are identified and removed within a suitable approximation. The method is applied to study the low-lying collective states of nuclei which are successfully described by the exactly solvable multi-level pairing hamiltonian (Sn, Ni, Pb).

Transcription Mapping of the Kaposi’s Sarcoma-Associated Herpesvirus (Human Herpesvirus 8) Genome in a Body Cavity-Based Lymphoma Cell Line (BC-1)

PubMed Central

Sarid, Ronit; Flore, Ornella; Bohenzky, Roy A.; Chang, Yuan; Moore, Patrick S.

1998-01-01

Kaposi’s sarcoma-associated herpesvirus (KSHV) gene transcription in the BC-1 cell line (KSHV and Epstein-Barr virus coinfected) was examined by using Northern analysis with DNA probes extending across the viral genome except for a 3-kb unclonable rightmost region. Three broad classes of viral gene transcription have been identified. Class I genes, such as those encoding the v-cyclin, latency-associated nuclear antigen, and v-FLIP, are constitutively transcribed under standard growth conditions, are unaffected by tetradecanoylphorbol acetate (TPA) induction, and presumably represent latent viral transcripts. Class II genes are primarily clustered in nonconserved regions of the genome and include small polyadenylated RNAs (T0.7 and T1.1) as well as most of the virus-encoded cytokines and signal transduction genes. Class II genes are transcribed without TPA treatment but are induced to higher transcription levels by TPA treatment. Class III genes are primarily structural and replication genes that are transcribed only following TPA treatment and are presumably responsible for lytic virion production. These results indicate that BC-1 cells have detectable transcription of a number of KSHV genes, particularly nonconserved genes involved in cellular signal transduction and regulation, during noninduced (latent) virus culture. PMID:9444993

Plastid, nuclear and reverse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between organelles via RNA?

PubMed Central

Schuster, W; Brennicke, A

1987-01-01

We describe an open reading frame (ORF) with high homology to reverse transcriptase in the mitochondrial genome of Oenothera. This ORF displays all the characteristics of an active plant mitochondrial gene with a possible ribosome binding site and 39% T in the third codon position. It is located between a sequence fragment from the plastid genome and one of nuclear origin downstream from the gene encoding subunit 5 of the NADH dehydrogenase. The nuclear derived sequence consists of 528 nucleotides from the small ribosomal RNA and contains an expansion segment unique to nuclear rRNAs. The plastid sequence contains part of the ribosomal protein S4 and the complete tRNA(Ser). The observation that only transcribed sequences have been found i more than one subcellular compartment in higher plants suggests that interorganellar transfer of genetic information may occur via RNA and subsequent local reverse transcription and genomic integration. PMID:14650433

Increased expression of hepatocyte nuclear factor 4 alpha transcribed by promoter 2 indicates a poor prognosis in hepatocellular carcinoma

PubMed Central

Cai, Shao-hang; Lu, Shi-xun; Liu, Li-li; Zhang, Chris Zhiyi; Yun, Jing-ping

2017-01-01

Background: Hepatocyte nuclear factor 4 alpha (HNF4α) plays an important role in tumourigenesis. There is growing evidence indicating that HNF4α transcribed by promoter 1 (P1-HNF4α) is expressed at relatively low levels in HCC and its presence predicts a favourable outcome for hepatocellular carcinoma (HCC) patients. However, the role of HNF4α transcribed by promoter 2 (P2-HNF4α) in HCC remains unclear. Methods: A total of 615 HCC specimens were obtained to construct tissue microarrays and perform immunohistochemistry. The relationship between P2-HNF4α and clinical features of HCC patients were analysed. Kaplan–Meier analysis was conducted to assess the prognostic value of P2-HNF4α. Results: The results showed that the expression of P2-HNF4α in HCC was noticeably increased in HCC tissues compared with the nontumourous tissues. In addition, P1-HNF4α expression was negatively correlated with P2-HNF4α expression (p = 0.023). High P2-HNF4α expression was significantly associated with poor differentiation of HCC (p = 0.002) and vascular invasion (p = 0.017). Kaplan–Meier analysis showed that P2-HNF4α expression was closely correlated with overall survival in the training group (p = 0.01), validation group (p = 0.034), and overall group of patients with HCC (p < 0.001). Conclusions: Our data show that the role of HNF4α in cancer development needs to be further refined. P2-HNF4α, different from P1-HNF4α, is markedly upregulated and serves as an oncogene-associated protein in HCC. Our study therefore provides a promising biomarker for prognostic prediction and a potential therapeutic target for HCC. PMID:29051787

Phylogenetic Analysis and Molecular Characterization of Xanthium sibiricum Using DNA Barcoding, PCR-RFLP, and Specific Primers.

PubMed

Tomasello, Salvatore; Heubl, Günther

2017-07-01

The fruits of Xanthium sibiricum have been widely used in traditional Chinese medicine for the treatment of nasal sinusitis and headaches. The genus Xanthium (cocklebur) is a taxonomically complex genus. Different taxonomic concepts have been proposed, some including several species, others lumping the different taxa in a few extremely polymorphic species. Due to the morphological similarities between species, the correct authentication of X. sibiricum is very difficult. Therefore, we established a polymerase chain reaction-restriction fragment length polymorphism method and diagnostic PCR based on nuclear internal transcribed spacer and chloroplast trnQ-rps16 barcodes to differentiate X. sibirium from related species.Results from the phylogenetic analyses based on sequence information from four marker regions (plastidal psbA-trnH and trnQ-rps16 and nuclear ITS and D35 ) support those taxonomic concepts accepting a reduced number of species, as four to five major clades are revealed in the phylogenetic reconstructions. X. sibiricum , together with some accessions from closely related taxa, is always supported as monophyletic, constituting a well-defined genetic entity. Allele-specific primer pairs for ITS and trnQ-rps16 were designed to amplify diagnostic products from the genomic DNA of X. sibiricum . Specific PCR in combination with digestion using the restriction enzyme Mse I allowed for the identification of X. sibiricum by producing specific restriction patterns. The results demonstrate that the applied techniques provide effective and accurate authentication of X. sibiricum . Georg Thieme Verlag KG Stuttgart · New York.

Identification of Fasciola flukes in Thailand based on their spermatogenesis and nuclear ribosomal DNA, and their intraspecific relationships based on mitochondrial DNA.

PubMed

Chaichanasak, Pannigan; Ichikawa, Madoka; Sobhon, Prasert; Itagaki, Tadashi

2012-12-01

We analyzed 147 Fasciola flukes obtained from cattle in Thailand based on their spermatogenetic ability, and nuclear ribosomal internal transcribed spacer 1 (ITS1) and mitochondrial nicotiamide adenine dinucleotide dehydrogenase subunit 1 (ND1) genes as molecular markers. One hundred twenty-eight flukes, which had abundant sperm in their seminal vesicles (spermic) and showed the PCR-RFLP pattern of F. gigantica in the ITS1, were accurately identified as F. gigantica. The other 19 flukes that had no sperm in their seminal vesicles were aspermic Fasciola sp. with the RFLP patterns identical to that of F. gigantica. Twenty-nine ND1 haplotypes (Fg-ND1-Thai 2-30) were distinguished in the 128 F. gigantica flukes and were divided into haplotypes unique to Thailand and those common to other countries, suggesting the possibility that ancestral haplotypes were introduced into Thailand. Three haplotypes (Fg-ND1-Thai 7, 9 and 27) appeared to be the major haplotypes found in F. gigantica from Thailand. Only one haplotype (Fg-ND1-Thai 1) was found in the 19 aspermic Fasciola sp. flukes obtained from geographical regions, and the nucleotide sequence of Fg-ND1-Thai 1 was identical to that of the aspermic Fasciola sp. from Japan, Korea, China, Vietnam and Myanmar, suggesting that they were descendants with a common provenance and expanded to these countries in the relatively recent past. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Rapid radiation and dispersal out of the Qinghai-Tibetan Plateau of an alpine plant lineage Rhodiola (Crassulaceae).

PubMed

Zhang, Jian-Qiang; Meng, Shi-Yong; Allen, Geraldine A; Wen, Jun; Rao, Guang-Yuan

2014-08-01

Rhodiola L. (Crassulaceae) is a mid-sized plant genus consisting of about 70 species, with most species distributed on the Qinghai-Tibetan Plateau (QTP) and the adjacent areas, and several species in north-east Asia, Europe, and North America. This study explored the origin and diversification history of Rhodiola and tested the biogeographic relationships between the QTP and other regions of the Northern Hemisphere. We sequenced the nuclear ribosomal internal transcribed spacers and eight plastid DNA fragments representing 55 species of Rhodiola, and reconstructed phylogenetic relationships with maximum parsimony, maximum likelihood and Bayesian inference. Several instances of incongruence between the nuclear and the plastid data sets were revealed, which can best be explained by reticulate evolution. Species of Rhodiola and Pseudosedum form a well-supported clade sister to Phedimus. Dating analysis suggested that the origin and diversification times of this group are largely correlated with the extensive uplifts of the Qinghai-Tibetan Plateau. Ancestral state reconstruction supports the hypothesis that Rhodiola originated on the QTP, and then dispersed to other regions of the Northern Hemisphere. Our findings highlight the importance of the uplifts of the Qinghai-Tibetan Plateau in promoting species diversification and the possible role of reticulate evolution in the diversification process. Our results also suggest the biogeographic significance of QTP as the source area in alpine plant evolution in the Northern Hemisphere. Copyright © 2014 Elsevier Inc. All rights reserved.

Nuclear Matrix Association: Switching to the Invasive Cytotrophoblast

PubMed Central

Drennan, Kathryn J.; Linnemann, Amelia K.; Platts, Adrian E.; Heng, Henry H.; Armant, D. Randall; Krawetz, Stephen A.

2010-01-01

Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy. The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood. The aim of this study was to characterize the transcriptome of the HTR-8/SVneo human cytotrophoblast cell line which displays well characterized invasive and non-invasive behavior, and to correlate the activity of the transcriptome with nuclear matrix attachment and cell phenotype. Comparison of the invasive to non-invasive HTR transcriptomes was unremarkable. In contrast, comparison of the MARs on chromosomes 14–18 revealed an increased number of MARs associated with the invasive phenotype. These attachment areas were more likely to be associated with silent rather than actively transcribed genes. This study supports that view that that nuclear matrix attachment may play an important role in cytotrophoblast invasion by ensuring specific silencing that facilitates invasion. PMID:20346505

Phytophthora-ID.org: A sequence-based Phytophthora identification tool

Treesearch

N.J. Grünwald; F.N. Martin; M.M. Larsen; C.M. Sullivan; C.M. Press; M.D. Coffey; E.M. Hansen; J.L. Parke

2010-01-01

Contemporary species identification relies strongly on sequence-based identification, yet resources for identification of many fungal and oomycete pathogens are rare. We developed two web-based, searchable databases for rapid identification of Phytophthora spp. based on sequencing of the internal transcribed spacer (ITS) or the cytochrome oxidase...

Aspergillus section Versicolores: nine new species and multilocus DNA sequence based phylogeny

USDA-ARS?s Scientific Manuscript database

ß-tubulin, calmodulin, internal transcribed spacer and partial lsu-rDNA, RNA polymerase, DNA replication licensing factor Mcm7, and pre-rRNA processing protein Tsr1 were amplified and sequenced from 62 A. versicolor clade isolates and analyzed phylogenetically using the concordance model to establis...

Aspergillus section Versicolores, nine new species and multilocus DNA sequence based phylogeny

USDA-ARS?s Scientific Manuscript database

ß-tubulin, calmodulin, internal transcribed spacer and partial lsu-rDNA, RNA polymerase, DNA replication licensing factor Mcm7, and pre-rRNA processing protein Tsr1 were amplified and sequenced from 62 A. versicolor clade isolates and analyzed phylogenetically using the concordance model to establis...

Cyberlindnera xylolytica sp. nov., a xylitol-producing yeast species isolated from lignocellulosic materials

USDA-ARS?s Scientific Manuscript database

Independent surveys of yeasts associated with lignocellulosic-related materials led to the discovery of a novel yeast species belonging to the Cyberlindnera clade (Saccharomycotina, Ascomycota). Analysis of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the la...

TFIIIC bound DNA elements in nuclear organization and insulation.

PubMed

Kirkland, Jacob G; Raab, Jesse R; Kamakaka, Rohinton T

2013-01-01

tRNA genes (tDNAs) have been known to have barrier insulator function in budding yeast, Saccharomyces cerevisiae, for over a decade. tDNAs also play a role in genome organization by clustering at sites in the nucleus and both of these functions are dependent on the transcription factor TFIIIC. More recently TFIIIC bound sites devoid of pol III, termed Extra-TFIIIC sites (ETC) have been identified in budding yeast and these sites also function as insulators and affect genome organization. Subsequent studies in Schizosaccharomyces pombe showed that TFIIIC bound sites were insulators and also functioned as Chromosome Organization Clamps (COC); tethering the sites to the nuclear periphery. Very recently studies have moved to mammalian systems where pol III genes and their associated factors have been investigated in both mouse and human cells. Short interspersed nuclear elements (SINEs) that bind TFIIIC, function as insulator elements and tDNAs can also function as both enhancer - blocking and barrier insulators in these organisms. It was also recently shown that tDNAs cluster with other tDNAs and with ETCs but not with pol II transcribed genes. Intriguingly, TFIIIC is often found near pol II transcription start sites and it remains unclear what the consequences of TFIIIC based genomic organization are and what influence pol III factors have on pol II transcribed genes and vice versa. In this review we provide a comprehensive overview of the known data on pol III factors in insulation and genome organization and identify the many open questions that require further investigation. This article is part of a Special Issue entitled: Transcription by Odd Pols. Copyright © 2012 Elsevier B.V. All rights reserved.

Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.

PubMed

Carnevali, Davide; Conti, Anastasia; Pellegrini, Matteo; Dieci, Giorgio

2017-02-01

With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority of Pol III-transcribed MIR elements are cell-specific, we discovered a small set of ubiquitously transcribed MIRs mapping within Pol II-transcribed genes in antisense orientation that could influence the expression of the overlapping gene. We also identified novel Pol III-transcribed ncRNAs, deriving from transcription of annotated MIR fragments flanked by unique MIR-unrelated sequences, and confirmed the role of Pol III-specific internal promoter elements in MIR transcription. Besides demonstrating widespread transcription at these retrotranspositionally inactive elements in human cells, the ability to profile MIR expression at single-locus resolution will facilitate their study in different cell types and states including pathological alterations. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Necessity of Internal Monitoring for Nuclear Medicine Staff in a Large Specialized Chinese Hospital

PubMed Central

Wang, Hong-Bo; Zhang, Qing-Zhao; Zhang, Zhen; Hou, Chang-Song; Li, Wen-Liang; Yang, Hui; Sun, Quan-Fu

2016-01-01

This work intends to quantify the risk of internal contaminations in the nuclear medicine staff of one hospital in Henan province, China. For this purpose, the criteria proposed by the International Atomic Energy Agency (IAEA) to determine whether it is necessary to conduct internal individual monitoring was applied to all of the 18 nuclear medicine staff members who handled radionuclides. The activity of different radionuclides used during a whole calendar year and the protection measures adopted were collected for each staff member, and the decision as to whether nuclear medicine staff in the hospital should be subjected to internal monitoring was made on the basis of the criteria proposed by IAEA. It is concluded that for all 18 members of the nuclear medicine staff in the hospital, internal monitoring is required. Internal exposure received by nuclear medicine staff should not be ignored, and it is necessary to implement internal monitoring for nuclear medicine staff routinely. PMID:27077874

Necessity of Internal Monitoring for Nuclear Medicine Staff in a Large Specialized Chinese Hospital.

PubMed

Wang, Hong-Bo; Zhang, Qing-Zhao; Zhang, Zhen; Hou, Chang-Song; Li, Wen-Liang; Yang, Hui; Sun, Quan-Fu

2016-04-12

This work intends to quantify the risk of internal contaminations in the nuclear medicine staff of one hospital in Henan province, China. For this purpose, the criteria proposed by the International Atomic Energy Agency (IAEA) to determine whether it is necessary to conduct internal individual monitoring was applied to all of the 18 nuclear medicine staff members who handled radionuclides. The activity of different radionuclides used during a whole calendar year and the protection measures adopted were collected for each staff member, and the decision as to whether nuclear medicine staff in the hospital should be subjected to internal monitoring was made on the basis of the criteria proposed by IAEA. It is concluded that for all 18 members of the nuclear medicine staff in the hospital, internal monitoring is required. Internal exposure received by nuclear medicine staff should not be ignored, and it is necessary to implement internal monitoring for nuclear medicine staff routinely.

Myc Dynamically and Preferentially Relocates to a Transcription Factory Occupied by Igh

PubMed Central

Osborne, Cameron S; Chakalova, Lyubomira; Mitchell, Jennifer A; Horton, Alice; Wood, Andrew L; Bolland, Daniel J; Corcoran, Anne E; Fraser, Peter

2007-01-01

Transcription in mammalian nuclei is highly compartmentalized in RNA polymerase II-enriched nuclear foci known as transcription factories. Genes in cis and trans can share the same factory, suggesting that genes migrate to preassembled transcription sites. We used fluorescent in situ hybridization to investigate the dynamics of gene association with transcription factories during immediate early (IE) gene induction in mouse B lymphocytes. Here, we show that induction involves rapid gene relocation to transcription factories. Importantly, we find that the Myc proto-oncogene on Chromosome 15 is preferentially recruited to the same transcription factory as the highly transcribed Igh gene located on Chromosome 12. Myc and Igh are the most frequent translocation partners in plasmacytoma and Burkitt lymphoma. Our results show that transcriptional activation of IE genes involves rapid relocation to preassembled transcription factories. Furthermore, the data imply a direct link between the nonrandom interchromosomal organization of transcribed genes at transcription factories and the incidence of specific chromosomal translocations. PMID:17622196

MOLECULAR CHARACTERIZATION OF MICROSPORIDIA INDICATES THAT FUR-BEARING WILD MAMMALS CAN BE A SOURCE OF HUMAN PATHOGENIC ENTEROCYTOZOON BIENEUSI

EPA Science Inventory

Over 13 months, 465 beavers, foxes, muskrats, otters, and raccoons were trapped in four counties in eastern Maryland and examined by molecular methods for microsporidia. A two-step nested PCR protocol was developed to amplify a 392 bp fragment of the internal transcribed spacer (...

Confirmation of hybrid origin of Cyrtanthus based on the sequence analysis of internal transcribed spacer

USDA-ARS?s Scientific Manuscript database

The objectives of this study were to create interspecific hybrids between Cyrtanthus elatus and C. sanguineus and to confirm the hybrid origin of the progeny based on morphological characters and using molecular markers. The tip of the leaves, the shape and size of cells, and stomata distribution i...

First Report of Botrytis cinerea as a Postharvest Pathogen of Blueberry in Korea

PubMed Central

Cheon, Mi-Geon; Choi, Okhee; Kim, Jinwoo

2011-01-01

Gray mold of blueberry caused by Botrytis sp. is reported for the first time in Korea. A detailed description of the fungus is given, along with its rDNA internal transcribed spacer sequence. The fungus was identified as Botrytis cinerea based on mycological characteristics and molecular data. PMID:22783073

Isolation of Candidatus Bartonella melophagi from Human Blood1

PubMed Central

Maggi, Ricardo G.; Kosoy, Michael; Mintzer, Melanie

2009-01-01

Candidatus Bartonella melophagi was isolated by blood culture from 2 women, 1 of whom was co-infected with B. henselae. Partial 16S rRNA, RNA polymerase B, and citrate synthase genes and 16S–23S internal transcribed spacer sequences indicated that human isolates were similar to Candidatus B. melophagi. PMID:19116054

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

Treesearch

Alena K. Oliver; Shawn P. Brown; Mac A. Callaham; Ari Jumpponen

2015-01-01

Rare taxa overwhelm metabarcoding data generated using next-generation sequencing (NGS). Low frequency Operational Taxonomic Units (OTUs) may be artifacts generated by PCR-amplification errors resulting from polymerase mispairing. We analyzed two Internal Transcribed Spacer 2 (ITS2) MiSeq libraries generated with proofreading (ThermoScientific Phusion

Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples

NASA Astrophysics Data System (ADS)

Su, Lei; Zhang, Qianqian; Gong, Jun

2017-07-01

Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specific PCR primers were newly designed to amplify a fragment including the internal transcribed spacer (ITS) region of ribosomal rDNA from environmental samples. The primers showed high specificity in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18S rDNA in peritrichs. The newly designed specific primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in different systems.

rRNA Gene Internal Transcribed Spacer 1 and 2 Sequences of Asexual, Anthropophilic Dermatophytes Related to Trichophyton rubrum

PubMed Central

Summerbell, R. C.; Haugland, R. A.; Li, A.; Gupta, A. K.

1999-01-01

The ribosomal region spanning the two internal transcribed spacer (ITS) regions and the 5.8S ribosomal DNA region was sequenced for asexual, anthropophilic dermatophyte species with morphological similarity to Trichophyton rubrum, as well as for members of the three previously delineated, related major clades in the T. mentagrophytes complex. Representative isolates of T. raubitschekii, T. fischeri, and T. kanei were found to have ITS sequences identical to that of T. rubrum. The ITS sequences of T. soudanense and T. megninii differed from that of T. rubrum by only a small number of base pairs. Their continued status as species, however, appears to meet criteria outlined in the population genetics-based cohesion species concept of A. R. Templeton. The ITS sequence of T. tonsurans differed from that of the biologically distinct T. equinum by only 1 bp, while the ITS sequence of the recently described species T. krajdenii had a sequence identical to that of T. mentagrophytes isolates related to the teleomorph Arthroderma vanbreuseghemii. PMID:10565922

Molecular variation of Sporisorium scitamineum in Mainland China revealed by internal transcribed spacers.

PubMed

Zhang, Y Y; Huang, N; Xiao, X H; Huang, L; Liu, F; Su, W H; Que, Y X

2015-07-14

Sugarcane smut caused by the fungus Sporisorium scitamineum is a worldwide disease and also one of the most prevalent diseases in sugarcane production in mainland China. To study molecular variation in S. scitamineum, 23 S. scitamineum isolates from the 6 primary sugar-cane production areas in mainland, China (Guangxi, Yunnan, Guangdong, Hainan, Fujian, and Jiangxi Provinces), were assessed using internal transcribed spacer (ITS) methods. The results of ITS sequence analysis showed that the organisms can be defined at the genus level, including Ustilago and Sporisorium, and can also differentiate between closely related species. This method was not suitable for phylogenetic relationship analysis of different S. scitamineum isolates and could not provide support regarding their race ascription at the molecular level. The results of the present study will be useful for studies examining the molecular diversity of S. scitamineum and for establishing a genetic foundation for their pathogenicity differentiation and new race detection. In addition, our results can provide useful information for the pathogen selection principle in sugarcane smut resistance breeding and variety distribution.

Genetic differences in internal transcribed spacer 1 between Dermanyssus gallinae from wild birds and domestic chickens.

PubMed

Brännström, S; Morrison, D A; Mattsson, J G; Chirico, J

2008-06-01

We investigated the presence of the poultry red mite or the chicken mite, Dermanyssus gallinae De Geer, Acari: Dermanyssidae, in wild bird populations in four different geographical regions of Sweden. The mites identified as D. gallinae were compared genetically with D. gallinae from egg-producing poultry farms in the same regions. The small subunit (SSU) gene, the 5.8S ribosomal RNA (rRNA) gene and the two internal transcribed spacers (ITS) of the rRNA genes were used in the genetic analysis. All D. gallinae mites had identical SSU rRNA, 5.8S rRNA and ITS2 sequences independent of their origin. By contrast, we identified significant differences in the ITS1 sequences. Based on the differences in the ITS1 sequences, the mites could be divided into two genotypes, of wild and domesticated origin, with no variation within the groups. These results imply that wild bird populations are of low importance, if any, as natural reservoirs of D. gallinae in these four geographical regions of Sweden.

Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

PubMed

Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

2014-04-08

The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

Systematic Internal Transcribed Spacer Sequence Analysis for Identification of Clinical Mold Isolates in Diagnostic Mycology: a 5-Year Study▿ †

PubMed Central

Ciardo, Diana E.; Lucke, Katja; Imhof, Alex; Bloemberg, Guido V.; Böttger, Erik C.

2010-01-01

The implementation of internal transcribed spacer (ITS) sequencing for routine identification of molds in the diagnostic mycology laboratory was analyzed in a 5-year study. All mold isolates (n = 6,900) recovered in our laboratory from 2005 to 2009 were included in this study. According to a defined work flow, which in addition to troublesome phenotypic identification takes clinical relevance into account, 233 isolates were subjected to ITS sequence analysis. Sequencing resulted in successful identification for 78.6% of the analyzed isolates (57.1% at species level, 21.5% at genus level). In comparison, extended in-depth phenotypic characterization of the isolates subjected to sequencing achieved taxonomic assignment for 47.6% of these, with a mere 13.3% at species level. Optimization of DNA extraction further improved the efficacy of molecular identification. This study is the first of its kind to testify to the systematic implementation of sequence-based identification procedures in the routine workup of mold isolates in the diagnostic mycology laboratory. PMID:20573873

Ribosomal RNA maturation in Schizosaccharomyces pombe is dependent on a large ribonucleoprotein complex of the internal transcribed spacer 1.

PubMed

Lalev, A I; Abeyrathne, P D; Nazar, R N

2000-09-08

The interdependency of steps in the processing of pre-rRNA in Schizosaccharomyces pombe suggests that RNA processing, at least in part, acts as a quality control mechanism which helps assure that only functional RNA is incorporated into mature ribosomes. To determine further the role of the transcribed spacer regions in rRNA processing and to detect interactions which underlie the interdependencies, the ITS1 sequence was examined for its ability to form ribonucleoprotein complexes with cellular proteins. When incubated with protein extract, the spacer formed a specific large RNP. This complex was stable to fractionation by agarose or polyacrylamide gel electrophoresis. Modification exclusion analyses indicated that the proteins interact with a helical domain which is conserved in the internal transcribed spacers. Mutagenic analyses confirmed an interaction with this sequence and indicated that this domain is critical to the efficient maturation of the precursor RNA. The protein constituents, purified by affinity chromatography using the ITS1 sequence, retained an ability to form stable RNP. Protein analyses of gel purified complex, prepared with affinity-purified proteins, indicated at least 20 protein components ranging in size from 20-200 kDa. Peptide mapping by Maldi-Toff mass spectroscopy identified eight hypothetical RNA binding proteins which included four different RNA-binding motifs. Another protein was putatively identified as a pseudouridylate synthase. Additional RNA constituents were not detected. The significance of this complex with respect to rRNA maturation and interdependence in rRNA processing is discussed. Copyright 2000 Academic Press.

Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts.

PubMed

Cendejas-Bueno, E; Kolecka, A; Alastruey-Izquierdo, A; Theelen, B; Groenewald, M; Kostrzewa, M; Cuenca-Estrella, M; Gómez-López, A; Boekhout, T

2012-11-01

The Candida haemulonii species complex is currently known as C. haemulonii groups I and II. Here we describe C. haemulonii group II as a new species, Candida duobushaemulonii sp. nov., and C. haemulonii var. vulnera as new a variety of C. haemulonii group I using phenotypic and molecular methods. These taxa and other relatives of C. haemulonii (i.e., Candida auris and Candida pseudohaemulonii) cannot be differentiated by the commercial methods now used for yeast identification. Four isolates (C. haemulonii var. vulnera) differed from the other isolates of C. haemulonii in the sequence of the internal transcribed spacer (ITS) regions of the nuclear rRNA gene operon. The new species and the new variety have a multiresistant antifungal profile, which includes high MICs of amphotericin B (geometric mean MIC, 1.18 mg/liter for C. haemulonii var. vulnera and 2 mg/liter for C. duobushaemulonii sp. nov) and cross-resistance to azole compounds. Identification of these species should be based on molecular methods, such as sequence analysis of ITS regions and matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina).

PubMed

Dentinger, Bryn T M; Didukh, Maryna Y; Moncalvo, Jean-Marc

2011-01-01

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (~450 bp) representing ~100 morphospecies from ~650 collections of Agaricomycotina using several sets of new primers. Large introns (~1500 bp) at variable locations were detected in ~5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (~30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.

PubMed

Nilsson, R Henrik; Tedersoo, Leho; Ryberg, Martin; Kristiansson, Erik; Hartmann, Martin; Unterseher, Martin; Porter, Teresita M; Bengtsson-Palme, Johan; Walker, Donald M; de Sousa, Filipe; Gamper, Hannes Andres; Larsson, Ellen; Larsson, Karl-Henrik; Kõljalg, Urmas; Edgar, Robert C; Abarenkov, Kessy

2015-01-01

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

A Simple Method to Decode the Complete 18-5.8-28S rRNA Repeated Units of Green Algae by Genome Skimming.

PubMed

Lin, Geng-Ming; Lai, Yu-Heng; Audira, Gilbert; Hsiao, Chung-Der

2017-11-06

Green algae, Chlorella ellipsoidea , Haematococcus pluvialis and Aegagropila linnaei (Phylum Chlorophyta) were simultaneously decoded by a genomic skimming approach within 18-5.8-28S rRNA region. Whole genomic DNAs were isolated from green algae and directly subjected to low coverage genome skimming sequencing. After de novo assembly and mapping, the size of complete 18-5.8-28S rRNA repeated units for three green algae were ranged from 5785 to 6028 bp, which showed high nucleotide diversity (π is around 0.5-0.6) within ITS1 and ITS2 (Internal Transcribed Spacer) regions. Previously, the evolutional diversity of algae has been difficult to decode due to the inability design universal primers that amplify specific marker genes across diverse algal species. In this study, our method provided a rapid and universal approach to decode the 18-5.8-28S rRNA repeat unit in three green algal species. In addition, the completely sequenced 18-5.8-28S rRNA repeated units provided a solid nuclear marker for phylogenetic and evolutionary analysis for green algae for the first time.

A morel improved growth and suppressed Fusarium infection in sweet corn.

PubMed

Yu, Dan; Bu, Fangfang; Hou, Jiaojiao; Kang, Yongxiang; Yu, Zhongdong

2016-12-01

A post-fire morel collected from Populus simonii stands in Mt. Qingling was identified as Morchella crassipes Mes-20 by using nuclear ribosomal DNA internal transcribed spacer phylogeny. It was inoculated into sweet corn to observe colonized roots in purified culture and in greenhouse experiments. The elongation and maturation zones of sweet corn were remarkably colonized at the cortex intercellular and intracellular cells, vessel cells, and around the Casparian strip, forming ectendomycorrhiza-like structures. Colonization was also observed in the zone of cell division proximal to the root cap. Greenhouse assays with sweet corn showed that this morel stimulated the development of the root system and significantly increased the dry root biomass. M. crassipes also significantly reduced the incidence of Fusarium verticillioides in the kernels of mature ears when inoculated into young ears before Fusarium inoculation and prevented Fusarium infection in corn ears compared with that of the control in the greenhouse. When grown under axenic conditions, M. crassipes produced the phytohormones abscisic acid, indole-3-acetic acid, and salicylic acid. The benefits to plants elicited by M. crassipes may result from these phytohormones which may improve the drought resistance, biomass growth and resistance to Fusarium.

Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

PubMed Central

Dentinger, Bryn T. M.; Didukh, Maryna Y.; Moncalvo, Jean-Marc

2011-01-01

DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (∼450 bp) representing ∼100 morphospecies from ∼650 collections of Agaricomycotina using several sets of new primers. Large introns (∼1500 bp) at variable locations were detected in ∼5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (∼30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms. PMID:21966418

DNA-based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi.

PubMed

Krüger, Manuela; Stockinger, Herbert; Krüger, Claudia; Schüssler, Arthur

2009-01-01

* At present, molecular ecological studies of arbuscular mycorrhizal fungi (AMF) are only possible above species level when targeting entire communities. To improve molecular species characterization and to allow species level community analyses in the field, a set of newly designed AMF specific PCR primers was successfully tested. * Nuclear rDNA fragments from diverse phylogenetic AMF lineages were sequenced and analysed to design four primer mixtures, each targeting one binding site in the small subunit (SSU) or large subunit (LSU) rDNA. To allow species resolution, they span a fragment covering the partial SSU, whole internal transcribed spacer (ITS) rDNA region and partial LSU. * The new primers are suitable for specifically amplifying AMF rDNA from material that may be contaminated by other organisms (e.g., samples from pot cultures or the field), characterizing the diversity of AMF species from field samples, and amplifying a SSU-ITS-LSU fragment that allows phylogenetic analyses with species level resolution. * The PCR primers can be used to monitor entire AMF field communities, based on a single rDNA marker region. Their application will improve the base for deep sequencing approaches; moreover, they can be efficiently used as DNA barcoding primers.

Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

NASA Astrophysics Data System (ADS)

Hasan, Nor'Aishah; Rafii, Mohd Y.; Rahim, Harun A.; Ali, Nusaibah Syd; Mazlan, Norida; Abdullah, Shamsiah

2016-02-01

Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberang Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.

Genetic variation and geographic differentiation in the marine triclad Bdelloura candida (Platyhelminthes, Tricladida, Maricola), ectocommensal on the American horseshoe crab Limulus polyphemus.

PubMed

Riesgo, Ana; Burke, Emily A; Laumer, Christopher; Giribet, Gonzalo

2017-01-01

Bdelloura candida (Platyhelminthes, Tricladida, Maricola) is an ectocommensal symbiont on the American horseshoe crab Limulus polyphemus , living on the book gills and appendages, where it spends its entire life. Given its limited dispersal capabilities and its inability to live outside of the host, we hypothesized a genetic structure that parallels that of its host. We obtained 84 planarian individuals from 19 horseshoe crabs collected from 10 sites from Massachusetts to Florida. We amplified the mitochondrial 16S rRNA and the nuclear internal transcribed spacer 2 and conducted phylogeographic and population genetic analyses, which show a clear and strong genetic break between the populations in the Atlantic and the Gulf coasts. Among the Atlantic populations, two additional, weaker barriers located along Cape Hatteras and Cape Cod restrict gene flow. Even though previous studies have suggested that the populations of the host may be in decline, those of B. candida remain stable, and some even shows signatures of expansion. Our results indicate that the phylogeography of these marine ectocommensal triclads closely mirrors that of its Limulus host, and highlight the challenges to both host and symbiont to genetically connect populations across their distribution.

Morphological and molecular characterization of fungal pathogen, Magnaphorthe oryzae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, Nor’Aishah, E-mail: aishahnh@ns.uitm.edu.my; Rafii, Mohd Y., E-mail: mrafii@upm.edu.my; Department of Crop Science, Universiti Putra Malaysia

2016-02-01

Rice is arguably the most crucial food crops supplying quarter of calories intake. Fungal pathogen, Magnaphorthe oryzae promotes blast disease unconditionally to gramineous host including rice species. This disease spurred an outbreaks and constant threat to cereal production. Global rice yield declining almost 10-30% including Malaysia. As Magnaphorthe oryzae and its host is model in disease plant study, the rice blast pathosystem has been the subject of intense interest to overcome the importance of the disease to world agriculture. Therefore, in this study, our prime objective was to isolate samples of Magnaphorthe oryzae from diseased leaf obtained from MARDI Seberangmore » Perai, Penang, Malaysia. Molecular identification was performed by sequences analysis from internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes. Phylogenetic affiliation of the isolated samples were analyzed by comparing the ITS sequences with those deposited in the GenBank database. The sequence of the isolate demonstrated at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaphorthe oryzae. Morphological observed under microscope demonstrated that the structure of conidia followed similar characteristic as M. oryzae. Finding in this study provide useful information for breeding programs, epidemiology studies and improved disease management.« less

Acrophialophora, a Poorly Known Fungus with Clinical Significance

PubMed Central

Sandoval-Denis, Marcelo; Sutton, Deanna A.; Wiederhold, Nathan P.; Guarro, Josep

2015-01-01

Acrophialophora fusispora is an emerging opportunistic fungus capable of causing human infections. The taxonomy of the genus is not yet resolved and, in order to facilitate identification of clinical specimens, we have studied a set of clinical and environmental Acrophialophora isolates by morphological and molecular analyses. This set included the available type strains of Acrophialophora species and similar fungi, some of which were considered by various authors to be synonyms of A. fusispora. Sequence analysis of the large subunit (LSU) and internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA and a fragment of the β-tubulin (Tub) gene revealed that Acrophialophora belongs in the family Chaetomiaceae and comprises three different species, i.e., A. fusispora, Acrophialophora levis, and Acrophialophora seudatica; the latter was previously included in the genus Ampullifera. The most prevalent species among clinical isolates was A. levis (72.7%), followed by A. fusispora (27.3%), both of which were isolated mostly from respiratory specimens (72.7%), as well as subcutaneous and corneal tissue samples. In general, of the eight antifungal drugs tested, voriconazole had the greatest in vitro activity, while all other agents showed poor in vitro activity against these fungi. PMID:25716450

Combining morphometrics with molecular taxonomy: how different are similar foliose keratose sponges from the Australian tropics?

PubMed

Abdul Wahab, M A; Fromont, J; Whalan, S; Webster, N; Andreakis, N

2014-04-01

Sponge taxonomy can be challenging as many groups exhibit extreme morphological plasticity induced by local environmental conditions. Foliose keratose sponges of the sub-family Phyllospongiinae (Dictyoceratida, Thorectidae: Strepsichordaia, Phyllospongia and Carteriospongia) are commonly found in intertidal and subtidal habitats of the Indo-Pacific. Lacking spicules, these sponges can be difficult to differentiate due to the lack of reliable morphological characters for species delineation. We use molecular phylogenies inferred from the nuclear Internal Transcribed Spacer 2 region (ITS2) and morphometrics (19 characters; 52 character states) to identify evolutionarily significant units (ESUs; sensu Moritz) within foliose Phyllosponginiids collected from seven geographic locations across tropical eastern and Western Australia. The ITS2 topology was congruent with the tree derived from Bayesian inference of discrete morphological characters supporting expected taxonomic relationships at the genus level and the identification of five ESUs. However, phylogenies inferred from the ITS2 marker revealed multiple sequence clusters, some of which were characterised by distinct morphological features and specific geographic ranges. Our results are discussed in light of taxonomic incongruences within this study, hidden sponge diversity and the role of vicariant events in influencing present day distribution patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

A Streamlined DNA Tool for Global Identification of Heavily Exploited Coastal Shark Species (Genus Rhizoprionodon)

PubMed Central

Pinhal, Danillo; Shivji, Mahmood S.; Nachtigall, Pedro G.; Chapman, Demian D.; Martins, Cesar

2012-01-01

Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus Rhizoprionodon) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here we present a highly streamlined molecular genetics approach based on seven species-specific PCR primers in a multiplex format that can simultaneously discriminate body parts from the seven described sharpnose shark species commonly occurring in coastal fisheries worldwide. The species-specific primers are based on nucleotide sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus (ITS2). This approach also distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the world. PMID:22496864

The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops.

PubMed

Udayanga, Dhanushka; Castlebury, Lisa A; Rossman, Amy Y; Chukeatirote, Ekachai; Hyde, Kevin D

2015-05-01

Phytopathogenic species of Diaporthe are associated with a number of soybean diseases including seed decay, pod and stem blight and stem canker and lead to considerable crop production losses worldwide. Accurate morphological identification of the species that cause these diseases has been difficult. In this study, we determined the phylogenetic relationships and species boundaries of Diaporthe longicolla, Diaporthe phaseolorum, Diaporthe sojae and closely related taxa. Species boundaries for this complex were determined based on combined phylogenetic analysis of five gene regions: partial sequences of calmodulin (CAL), beta-tubulin (TUB), histone-3 (HIS), translation elongation factor 1-α (EF1-α), and the nuclear ribosomal internal transcribed spacers (ITS). Phylogenetic analyses revealed that this large complex of taxa is comprised of soybean pathogens as well as species associated with herbaceous field crops and weeds. Diaporthe arctii, Diaporthe batatas, D. phaseolorum and D. sojae are epitypified. The seed decay pathogen D. longicolla was determined to be distinct from D. sojae. D. phaseolorum, originally associated with stem and leaf blight of Lima bean, was not found to be associated with soybean. A new species, Diaporthe ueckerae on Cucumis melo, is introduced with description and illustrations. Published by Elsevier Ltd.

First report of fatal disseminated microsporidiosis in two inland bearded dragons Pogona vitticeps in Japan.

PubMed

Shibasaki, Kojiro; Tokiwa, Toshihiro; Sukegawa, Akihiro; Kondo, Hirotaka; Tamukai, Kenichi; Haga, Yumiko; Ike, Kazunori

2017-04-01

Introduction. Encephalitozoon pogonae is a newly described pathogen belonging to the phylum Microsporidia. In Austria and the USA, this species has been isolated from fatal and disseminated cases of captive-bred inland bearded dragons. Here, we report the case of fatal disseminated microsporidiosis caused by E. pogonae in two bearded dragons in Japan. Case Presentation. The two lizards from different private households in Tokyo, Japan, had been brought to an animal hospital for examination. In both cases, the animal presented with a history of weight loss for several weeks. There were no improvements in clinical symptoms and the lizards deteriorated and finally died. Histopathological examination demonstrated necrotizing granulomatous inflammation attributed to disseminated microsporidian infection. Nucleotide sequencing of the nuclear ribosomal internal transcribed spacer region identified the microsporidian as E. pogonae with sequence identity of 100 %. Conclusion. We report the first case, to our knowledge, of disseminated microsporidiosis caused by E. pogonae in inland bearded dragons in Japan. Although it is difficult to diagnose prenatally since the signs are nonspecific, the disease should be considered in the differential diagnosis of chronic infections that do not respond to antibiotics.

First report of fatal disseminated microsporidiosis in two inland bearded dragons Pogona vitticeps in Japan

PubMed Central

Sukegawa, Akihiro; Kondo, Hirotaka; Tamukai, Kenichi; Haga, Yumiko; Ike, Kazunori

2017-01-01

Introduction. Encephalitozoon pogonae is a newly described pathogen belonging to the phylum Microsporidia. In Austria and the USA, this species has been isolated from fatal and disseminated cases of captive-bred inland bearded dragons. Here, we report the case of fatal disseminated microsporidiosis caused by E. pogonae in two bearded dragons in Japan. Case Presentation. The two lizards from different private households in Tokyo, Japan, had been brought to an animal hospital for examination. In both cases, the animal presented with a history of weight loss for several weeks. There were no improvements in clinical symptoms and the lizards deteriorated and finally died. Histopathological examination demonstrated necrotizing granulomatous inflammation attributed to disseminated microsporidian infection. Nucleotide sequencing of the nuclear ribosomal internal transcribed spacer region identified the microsporidian as E. pogonae with sequence identity of 100 %. Conclusion. We report the first case, to our knowledge, of disseminated microsporidiosis caused by E. pogonae in inland bearded dragons in Japan. Although it is difficult to diagnose prenatally since the signs are nonspecific, the disease should be considered in the differential diagnosis of chronic infections that do not respond to antibiotics. PMID:29026616

Mitochondrial and Nuclear Ribosomal DNA Evidence Supports the Existence of a New Trichuris Species in the Endangered François’ Leaf-Monkey

PubMed Central

Liu, Guo-Hua; Gasser, Robin B.; Nejsum, Peter; Wang, Yan; Chen, Qiang; Song, Hui-Qun; Zhu, Xing-Quan

2013-01-01

The whipworm of humans, Trichuris trichiura, is responsible for a neglected tropical disease (NTD) of major importance in tropical and subtropical countries of the world. Whipworms also infect animal hosts, including pigs, dogs and non-human primates, cause clinical disease (trichuriasis) similar to that of humans. Although Trichuris species are usually considered to be host specific, it is not clear whether non-human primates are infected with T. trichiura or other species. In the present study, we sequenced the complete mitochondrial (mt) genome as well as the first and second internal transcribed spacers (ITS-1 and ITS-2) of Trichuris from the François’ leaf-monkey (langur), and compared them with homologous sequences from human- and pig-derived Trichuris. In addition, sequence comparison of a conserved mt ribosomal gene among multiple individual whipworms revealed substantial nucleotide differences among these three host species but limited sequence variation within each of them. The molecular data indicate that the monkey-derived whipworm is a separate species from that of humans. Future work should focus on detailed population genetic and morphological studies (by electron microscopy) of whipworms from various non-humans primates and humans. PMID:23840431

Mitochondrial and nuclear ribosomal DNA evidence supports the existence of a new Trichuris species in the endangered françois' leaf-monkey.

PubMed

Liu, Guo-Hua; Gasser, Robin B; Nejsum, Peter; Wang, Yan; Chen, Qiang; Song, Hui-Qun; Zhu, Xing-Quan

2013-01-01

The whipworm of humans, Trichuris trichiura, is responsible for a neglected tropical disease (NTD) of major importance in tropical and subtropical countries of the world. Whipworms also infect animal hosts, including pigs, dogs and non-human primates, cause clinical disease (trichuriasis) similar to that of humans. Although Trichuris species are usually considered to be host specific, it is not clear whether non-human primates are infected with T. trichiura or other species. In the present study, we sequenced the complete mitochondrial (mt) genome as well as the first and second internal transcribed spacers (ITS-1 and ITS-2) of Trichuris from the François' leaf-monkey (langur), and compared them with homologous sequences from human- and pig-derived Trichuris. In addition, sequence comparison of a conserved mt ribosomal gene among multiple individual whipworms revealed substantial nucleotide differences among these three host species but limited sequence variation within each of them. The molecular data indicate that the monkey-derived whipworm is a separate species from that of humans. Future work should focus on detailed population genetic and morphological studies (by electron microscopy) of whipworms from various non-humans primates and humans.

An integrative study of Necremnus Thomson (Hymenoptera: Eulophidae) associated with invasive pests in Europe and North America: taxonomic and ecological implications

PubMed Central

Gebiola, Marco; Bernardo, Umberto; Ribes, Antoni; Gibson, Gary A P

2015-01-01

The species of Necremnus attacking two invasive pests of tomato and canola in Europe and North America, respectively, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) and Ceutorhynchus obstrictus (Marsham) (Coleoptera: Curculionidae), have been revised using an integrative taxonomy approach. Molecular data from the mitochondrial cytochrome oxidase c subunit I and the nuclear D2 expansion region of the 28S ribosomal subunit and internal transcribed spacer 2, the discovery of new morphological features, and study of type material resulted in the delineation of three species groups, the Necremnus artynes, Necremnus cosconius, and Necremnus tidius groups, the discovery of four new species, and the resurrection of three taxa from synonymy. Lectotypes have been designated for 13 species originally described in Eulophus by Walker. Although Necremnus has not been revised, an illustrated key is given to differentiate 23 recognized European species. The key, type images, and treatments of the three species groups will enable more accurate identification of the valid species of Necremnus in the future. They will also benefit biological control practitioners of pest species. The ecological consequences of the new taxonomic concepts are discussed. PMID:25745268

Tracking the algal origin of the Ulva bloom in the Yellow Sea by a combination of molecular, morphological and physiological analyses.

PubMed

Pang, Shao Jun; Liu, Feng; Shan, Ti Feng; Xu, Na; Zhang, Zhi Huai; Gao, Su Qin; Chopin, Thierry; Sun, Song

2010-05-01

In 2008, Qingdao (36 degrees 06'N, 120 degrees 25'E, PR China) experienced the world largest drifting macroalgal bloom composed of the filamentous macroalga Ulva prolifera. No convincing biologic evidence regarding the algal source is available so far. A series of field collections of both Ulva sp. and waters in various sites along Jiangsu coasts were conducted in March to May of 2009. Density of microscopic Ulva germlings in the waters sampled from different sites ranged from 7 to 3140 individuals L(-1), indicating the wide-spreading and long-term existence of the algae in the investigated region. Morphological and the nuclear ribosomal internal transcribed spacer ITS nrDNA and the chloroplast-encoded rbcL gene comparisons of 26 algal samples revealed that the algae collected from land-based animal aquaculture ponds mostly resembled the dominating blooming alga in 2008. Mismatch of Porphyra farming period with the occurrence of the green tide bloom, as well as the negative identification results of the sampled green algae from the Porphyra rafts eliminated Porphyra rafts as the principal and original source of the dominating blooming alga. Copyright 2009 Elsevier Ltd. All rights reserved.

Morphological and molecular characterization of lymnaeid snails and their potential role in transmission of Fasciola spp. in Vietnam.

PubMed

Dung, Bui Thi; Doanh, Pham Ngoc; The, Dang Tat; Loan, Ho Thi; Losson, Bertrand; Caron, Yannick

2013-12-01

Freshwater snails of the family Lymnaeidae play an important role in the transmission of fascioliasis worldwide. In Vietnam, 2 common lymnaeid species, Lymnaea swinhoei and Lymnaea viridis, can be recognized on the basis of morphology, and a third species, Lymnaea sp., is known to exist. Recent studies have raised controversy about their role in transmission of Fasciola spp. because of confusion in identification of the snail hosts. The aim of this study is, therefore, to clarify the identities of lymnaeid snails in Vietnam by a combination of morphological and molecular approaches. The molecular analyses using the second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA clearly showed that lymnaeids in Vietnam include 3 species, Austropeplea viridis (morphologically identified as L. viridis), Radix auricularia (morphologically identified as L. swinhoei) and Radix rubiginosa (morphologically identified as Lymnaea sp.). R. rubiginosa is a new record for Vietnam. Among them, only A. viridis was found to be infected with Fasciola spp. These results provide a new insight into lymnaeid snails in Vietnam. Identification of lymnaeid snails in Vietnam and their role in the liver fluke transmission should be further investigated.

Molecular microbial and chemical investigation of the bioremediation of two-phase olive mill waste using laboratory-scale bioreactors.

PubMed

Morillo, J A; Aguilera, M; Antízar-Ladislao, B; Fuentes, S; Ramos-Cormenzana, A; Russell, N J; Monteoliva-Sánchez, M

2008-05-01

Two-phase olive mill waste (TPOMW) is a semisolid effluent that is rich in contaminating polyphenols and is produced in large amounts by the industry of olive oil production. Laboratory-scale bioreactors were used to investigate the biodegradation of TPOMW by its indigenous microbiota. The effect of nutrient addition (inorganic N and P) and aeration of the bioreactors was studied. Microbial changes were investigated by PCR-temperature time gradient electrophoresis (TTGE) and following the dynamics of polar lipid fatty acids (PLFA). The greatest decrease in the polyphenolic and organic matter contents of bioreactors was concomitant with an increase in the PLFA fungal/bacterial ratio. Amplicon sequences of nuclear ribosomal internal transcribed spacer region (ITS) and 16S rDNA allowed identification of fungal and bacterial types, respectively, by comparative DNA sequence analyses. Predominant fungi identified included members of the genera Penicillium, Candida, Geotrichum, Pichia, Cladosporium, and Aschochyta. A total of 14 bacterial genera were detected, with a dominance of organisms that have previously been associated with plant material. Overall, this work highlights that indigenous microbiota within the bioreactors through stimulation of the fungal fraction, is able to degrade the polyphenolic content without the inoculation of specific microorganisms.

Molecular characterization and phylogenetic analysis of Fasciola hepatica from Peru.

PubMed

Ichikawa-Seki, Madoka; Ortiz, Pedro; Cabrera, Maria; Hobán, Cristian; Itagaki, Tadashi

2016-06-01

The causative agent of fasciolosis in South America is thought to be Fasciola hepatica. In this study, Fasciola flukes from Peru were analyzed to investigate their genetic structure and phylogenetic relationships with those from other countries. Fasciola flukes were collected from the three definitive host species: cattle, sheep, and pigs. They were identified as F. hepatica because mature sperms were observed in their seminal vesicles, and also they displayed Fh type, which has an identical fragment pattern to F. hepatica in the nuclear internal transcribed spacer 1. Eight haplotypes were obtained from the mitochondrial NADH dehydrogenase subunit 1 (nad1) sequences of Peruvian F. hepatica; however, no special difference in genetic structure was observed between the three host species. Its extremely low genetic diversity suggests that the Peruvian population was introduced from other regions. Nad1 haplotypes identical to those of Peruvian F. hepatica were detected in China, Uruguay, Italy, Iran, and Australia. Our results indicate that F. hepatica rapidly expanded its range due to human migration. Future studies are required to elucidate dispersal route of F. hepatica from Europe, its probable origin, to other areas, including Peru. Copyright © 2015. Published by Elsevier Ireland Ltd.

Authentication and chemical study of isodonis herba and isodonis extracts.

PubMed

Maruyama, Takuro; Sugimoto, Naoki; Kuroyanagi, Masanori; Kim, Ik Hwi; Kamakura, Hiroyuki; Kawasaki, Takeshi; Fujita, Masao; Shimada, Hiroshi; Yamamoto, Yutaka; Tada, Atsuko; Yamazaki, Takeshi; Goda, Yukihiro

2007-11-01

Isodonis Herba is used as a Japanese dietary supplement and folk medicine. The extract of the herb (Isodonis extract) is also used as a food additive whose major compound is enmein (1). Here we compared internal transcribed spacer sequences of nuclear ribosomal DNA from Isodonis Herba available on the Japanese and Chinese crude drug markets, and found that the former derived from Isodon japonicus and Isodon trichocarpus, while the latter derived from distinct species such as Isodon eriocalyx. The liquid chromatography/mass spectrometry profiles of Isodonis Herba were classified into four chemotypes (A to D) according to the ratio of the major constituents. Types B and C contained 1 and oridonin (2) as major components, respectively. An intermediate (or mixed) form of types B and C in various ratios was designed type A. Type D contained eriocalyxin B (3) as its major component. Japanese herba were types A-C, while Chinese herba were types C and D. The commercial Isodonis extract products tested were classified as type D, suggesting that they originated from Chinese Herba. Understanding the relationship between extract constituents and DNA profiles is important for the official specification of dietary supplements and food additives of plant origin.

Morphological and Molecular Characterization of Lymnaeid Snails and Their Potential Role in Transmission of Fasciola spp. in Vietnam

PubMed Central

Doanh, Pham Ngoc; The, Dang Tat; Loan, Ho Thi; Losson, Bertrand; Caron, Yannick

2013-01-01

Freshwater snails of the family Lymnaeidae play an important role in the transmission of fascioliasis worldwide. In Vietnam, 2 common lymnaeid species, Lymnaea swinhoei and Lymnaea viridis, can be recognized on the basis of morphology, and a third species, Lymnaea sp., is known to exist. Recent studies have raised controversy about their role in transmission of Fasciola spp. because of confusion in identification of the snail hosts. The aim of this study is, therefore, to clarify the identities of lymnaeid snails in Vietnam by a combination of morphological and molecular approaches. The molecular analyses using the second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA clearly showed that lymnaeids in Vietnam include 3 species, Austropeplea viridis (morphologically identified as L. viridis), Radix auricularia (morphologically identified as L. swinhoei) and Radix rubiginosa (morphologically identified as Lymnaea sp.). R. rubiginosa is a new record for Vietnam. Among them, only A. viridis was found to be infected with Fasciola spp. These results provide a new insight into lymnaeid snails in Vietnam. Identification of lymnaeid snails in Vietnam and their role in the liver fluke transmission should be further investigated. PMID:24516270

Homogeneous Population of the Brown Alga Sargassum polycystum in Southeast Asia: Possible Role of Recent Expansion and Asexual Propagation

PubMed Central

Chan, Sze Wai; Cheang, Chi Chiu; Chirapart, Anong; Gerung, Grevo; Tharith, Chea; Ang, Put

2013-01-01

Southeast Asia has been known as one of the biodiversity hotspots in the world. Repeated glacial cycles during Pleistocene were believed to cause isolation of marine taxa in refugia, resulting in diversification among lineages. Recently, ocean current was also found to be another factor affecting gene flow by restricting larval dispersal in animals. Macroalgae are unique in having mode of reproduction that differs from that of animals. Our study on the phylogeographical pattern of the brown macroalga Sargassum polycystum using nuclear Internal Transcribed Spacer 2 (ITS2), plastidal RuBisCO spacer (Rub spacer) and mitochondrial cytochrome oxidase subunit-III (Cox3) as molecular markers revealed genetic homogeneity across 27 sites in Southeast Asia and western Pacific, in sharp contrast to that revealed from most animal studies. Our data suggested that S. polycystum persisted in single refugium during Pleistocene in a panmixia pattern. Expansion occurred more recently after the Last Glacial Maximum and recolonization of the newly flooded Sunda Shelf could have involved asexual propagation of the species. High dispersal ability through floating fronds carrying developing germlings may also contribute to the low genetic diversity of the species. PMID:24147050

Characterization of Fasciola samples by ITS of rDNA sequences revealed the existence of Fasciola hepatica and Fasciola gigantica in Yunnan Province, China.

PubMed

Shu, Fan-Fan; Lv, Rui-Qing; Zhang, Yi-Fang; Duan, Gang; Wu, Ding-Yu; Li, Bi-Feng; Yang, Jian-Fa; Zou, Feng-Cai

2012-08-01

On mainland China, liver flukes of Fasciola spp. (Digenea: Fasciolidae) can cause serious acute and chronic morbidity in numerous species of mammals such as sheep, goats, cattle, and humans. The objective of the present study was to examine the taxonomic identity of Fasciola species in Yunnan province by sequences of the first and second internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA). The ITS rDNA was amplified from 10 samples representing Fasciola species in cattle from 2 geographical locations in Yunnan Province, by polymerase chain reaction (PCR), and the products were sequenced directly. The lengths of the ITS-1 and ITS-2 sequences were 422 and 361-362 base pairs, respectively, for all samples sequenced. Using ITS sequences, 2 Fasciola species were revealed, namely Fasciola hepatica and Fasciola gigantica. This is the first demonstration of F. gigantica in cattle in Yunnan Province, China using a molecular approach; our findings have implications for studying the population genetic characterization of the Chinese Fasciola species and for the prevention and control of Fasciola spp. in this province.

Homogeneous population of the brown alga Sargassum polycystum in Southeast Asia: possible role of recent expansion and asexual propagation.

PubMed

Chan, Sze Wai; Cheang, Chi Chiu; Chirapart, Anong; Gerung, Grevo; Tharith, Chea; Ang, Put

2013-01-01

Southeast Asia has been known as one of the biodiversity hotspots in the world. Repeated glacial cycles during Pleistocene were believed to cause isolation of marine taxa in refugia, resulting in diversification among lineages. Recently, ocean current was also found to be another factor affecting gene flow by restricting larval dispersal in animals. Macroalgae are unique in having mode of reproduction that differs from that of animals. Our study on the phylogeographical pattern of the brown macroalga Sargassum polycystum using nuclear Internal Transcribed Spacer 2 (ITS2), plastidal RuBisCO spacer (Rub spacer) and mitochondrial cytochrome oxidase subunit-III (Cox3) as molecular markers revealed genetic homogeneity across 27 sites in Southeast Asia and western Pacific, in sharp contrast to that revealed from most animal studies. Our data suggested that S. polycystum persisted in single refugium during Pleistocene in a panmixia pattern. Expansion occurred more recently after the Last Glacial Maximum and recolonization of the newly flooded Sunda Shelf could have involved asexual propagation of the species. High dispersal ability through floating fronds carrying developing germlings may also contribute to the low genetic diversity of the species.

A common origin for woody Sonchus and five related genera in the Macaronesian islands: molecular evidence for extensive radiation.

PubMed Central

Kim, S C; Crawford, D J; Francisco-Ortega, J; Santos-Guerra, A

1996-01-01

Woody Sonchus and five related genera (Babcockia, Taeckholmia, Sventenia, Lactucosonchus, and Prenanthes) of the Macaronesian islands have been regarded as an outstanding example of adaptive radiation in angiosperms. Internal transcribed spacer region of the nuclear rDNA (ITS) sequences were used to demonstrate that, despite the extensive morphological and ecological diversity of the plants, the entire alliance in insular Macaronesia has a common origin. The sequence data place Lactucosonchus as sister group to the remainder of the alliance and also indicate that four related genera are in turn sister groups to subg. Dendrosonchus and Taeckholmia. This implies that the woody members of Sonchus were derived from an ancestor similar to allied genera now present on the Canary Islands. It is also evident that the alliance probably occurred in the Canary Islands during the late Miocene or early Pliocene. A rapid radiation of major lineages in the alliance is consistent with an unresolved polytomy near the base and low ITS sequence divergence. Increase of woodiness is concordant with other insular endemics and refutes the relictural nature of woody Sonchus in the Macaronesian islands. PMID:8755546

A streamlined DNA tool for global identification of heavily exploited coastal shark species (genus Rhizoprionodon).

PubMed

Pinhal, Danillo; Shivji, Mahmood S; Nachtigall, Pedro G; Chapman, Demian D; Martins, Cesar

2012-01-01

Obtaining accurate species-specific landings data is an essential step toward achieving sustainable shark fisheries. Globally distributed sharpnose sharks (genus Rhizoprionodon) exhibit life-history characteristics (rapid growth, early maturity, annual reproduction) that suggests that they could be fished in a sustainable manner assuming an investment in monitoring, assessment and careful management. However, obtaining species-specific landings data for sharpnose sharks is problematic because they are morphologically very similar to one another. Moreover, sharpnose sharks may also be confused with other small sharks (either small species or juveniles of large species) once they are processed (i.e., the head and fins are removed). Here we present a highly streamlined molecular genetics approach based on seven species-specific PCR primers in a multiplex format that can simultaneously discriminate body parts from the seven described sharpnose shark species commonly occurring in coastal fisheries worldwide. The species-specific primers are based on nucleotide sequence differences among species in the nuclear ribosomal internal transcribed spacer 2 locus (ITS2). This approach also distinguishes sharpnose sharks from a wide range of other sharks (52 species) and can therefore assist in the regulation of coastal shark fisheries around the world.

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts

PubMed Central

Nilsson, R. Henrik; Tedersoo, Leho; Ryberg, Martin; Kristiansson, Erik; Hartmann, Martin; Unterseher, Martin; Porter, Teresita M.; Bengtsson-Palme, Johan; Walker, Donald M.; de Sousa, Filipe; Gamper, Hannes Andres; Larsson, Ellen; Larsson, Karl-Henrik; Kõljalg, Urmas; Edgar, Robert C.; Abarenkov, Kessy

2015-01-01

The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric—artificially joined—DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation. PMID:25786896

Endogenous TRIM5α Function Is Regulated by SUMOylation and Nuclear Sequestration for Efficient Innate Sensing in Dendritic Cells

PubMed Central

Portilho, Débora M.; Fernandez, Juliette; Ringeard, Mathieu; Machado, Anthony K.; Boulay, Aude; Mayer, Martha; Müller-Trutwin, Michaela; Beignon, Anne-Sophie; Kirchhoff, Frank; Nisole, Sébastien; Arhel, Nathalie J.

2015-01-01

Summary During retroviral infection, viral capsids are subject to restriction by the cellular factor TRIM5α. Here, we show that dendritic cells (DCs) derived from human and non-human primate species lack efficient TRIM5α-mediated retroviral restriction. In DCs, endogenous TRIM5α accumulates in nuclear bodies (NB) that partly co-localize with Cajal bodies in a SUMOylation-dependent manner. Nuclear sequestration of TRIM5α allowed potent induction of type I interferon (IFN) responses during infection, mediated by sensing of reverse transcribed DNA by cGAS. Overexpression of TRIM5α or treatment with the SUMOylation inhibitor ginkgolic acid (GA) resulted in enforced cytoplasmic TRIM5α expression and restored efficient viral restriction but abrogated type I IFN production following infection. Our results suggest that there is an evolutionary trade-off specific to DCs in which restriction is minimized to maximize sensing. TRIM5α regulation via SUMOylation-dependent nuclear sequestration adds to our understanding of how restriction factors are regulated. PMID:26748714

α-Amanitin-Resistant Viral RNA Synthesis in Nuclei Isolated from Nuclear Polyhedrosis Virus-Infected Heliothis zea Larvae and Spodoptera frugiperda Cells

PubMed Central

Grula, Marjori A.; Buller, Patricia L.; Weaver, Robert F.

1981-01-01

[3H]RNA was synthesized in nuclei isolated at various times postinfection from the fat bodies of Heliothis zea larvae infected with H. zea nuclear polyhedrosis virus and from cultured Spodoptera frugiperda cells infected with Autographa californica nuclear polyhedrosis virus. To detect virus-specific RNA synthesis, the [3H]RNA was hybridized to denatured viral DNA immobilized on nitrocellulose filters. Nuclear polyhedrosis virus-specific RNA synthesis in the infected nuclei isolated from H. zea larval fat bodies and S. frugiperda cells was only inhibited 20 to 25% by concentrations of α-amanitin sufficient to inhibit the host RNA polymerase II. In addition, a productive nuclear polyhedrosis virus infection was obtained in S. frugiperda cells grown in the presence of an α-amanitin concentration that inhibited 90% of the cellular RNA polymerase II activity. The cellular RNA polymerase II enzyme remained sensitive to α-amanitin during infection, and there was no evidence that a virus-coded, α-amanitin-resistant enzyme was synthesized after the onset of infection. The data suggest that the bulk of nuclear polyhedrosis virus-specific RNA synthesis in isolated nuclei is transcribed by an enzyme other than the host RNA polymerase II. PMID:16789208

Diagnostic characters within ITS2 DNA support molecular identification of Anastrepha suspensa

USDA-ARS?s Scientific Manuscript database

An approximately 220 bp fragment of the internal transcribed spacer 2 (ITS2) is screened as a diagnostic of Anastrepha suspensa and other pest fruit flies in the genus Anastrepha. The majority (96%) of the sites in this fragment are invariant among the test species but A. suspensa can be separated f...

Phylogeny and taxonomy of Echinodontium and related genera

Treesearch

Shi-Liang Liu; Yan Zhao; Yu-Cheng Dai; Karen K. Nakasone; Shuang-Hui He

2017-01-01

The phylogenetic relationship of eight species of Echinodontium, Laurilia, and Perplexostereum of Russulales were analyzed based on sequences of the nuc rDNA ITS1-5.8S-ITS2 (ITS [internal transcribed spacer]) and D1–D2 domains of nuc 28S rDNA (28S). Our results show that Echinodontium tinctorium, E. ryvardenii...

Facilitation of American chestnut (Castanea dentata) seedling establishment by Pinus virginiana in mine restoration

Treesearch

Jenise M. Bauman; Carolyn H. Keiffer; Shiv Hiremath

2012-01-01

This study evaluated the influence of planting sites on the establishment and ectomycorrhizal (ECM) colonization of American chestnut (Castanea denetata (Marsh.) Borkh.) on an abandoned coal mine in an Appalachian region of the United States. Root morphotyping and sequencing of the fungal internal transcribed spacer (ITS) region were used to identify...

Suillus quiescens, a new species commonly found in the spore bank in California and Oregon

Treesearch

Thomas D. Bruns; Lisa C. Grubisha; James M. Trappe; Jennifer F. Kerekes; Else C. Vellinga

2010-01-01

Suillus quiescens sp. nov. is common under Pinus muricata on Santa Cruz and Santa Rosa Islands in the northern Channel Islands of California, and we subsequently found it fruiting at Point Reyes National Seashore on the central coast of California. Sequences from the internal transcribed spacer region show that it is distinct...

Evolutionary consequences of putative intra- and interspecific hybridiation in agaric fungi

Treesearch

Karen W. Hughes; Ronald H. Petersen; D. Jean Lodge; Sarah E. Bergemann; Kendra Baumgartner; Rodham E. Tulloss; Edgar Lickey; Joaquin. Cifuentes

2013-01-01

Agaric fungi of the southern Appalachian Mountains including Great Smoky Mountains National Park are often heterozygous for the rDNA internal transcribed spacer region (ITS) with .42% of collections showing some heterozygosity for indels and/or base-pair substitutions. For these collections, intra-individual haplotype divergence is typically less than 2%, but for 3% of...

USSR Report, International Affairs

DTIC Science & Technology

1986-11-21

Materials from foreign- language sources are translated; those from English- language sources are transcribed or reprinted, with the original phrasing...Message at the mediation of Spanish Foreign Minister F. Ordonez, while the new president of Guatemala, Vinicio Cerezo, came out with a proposal to...internacional. Caracteristicas generales y particulares de los procesos revolucionarios. Memorias. La Habana, 1982, p 49.) The Izquierda

USSR Report, International Affairs.

DTIC Science & Technology

1986-07-29

English-language sources are transcribed or reprinted, with the original phrasing and other characteristics retained. Headlines, editorial reports...following the last line of a brief, indicate how the original information was processed. Where no processing indicator is given, the information was...mark and enclosed in parentheses were not clear in the original but have been supplied as appropriate in context. Other unattributed parenthetical

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

Treesearch

Jonathan M. Palmer; Michelle A. Jusino; Mark T. Banik; Daniel L. Lindner

2018-01-01

High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer...

Molecular analysis of aspermic Fasciola flukes from Korea on the basis of the nuclear ITS1 region and mitochondrial DNA markers and comparison with Japanese aspermic Fasciola flukes.

PubMed

Ichikawa, Madoka; Itagaki, Tadashi

2012-07-01

It has been speculated that populations of aspermic Fasciola flukes in Korea and Japan have a close phylogenetic relationship. To evaluate this, we analyzed 33 Korean aspermic Fasciola flukes on the basis of nuclear ribosomal internal transcribed spacer 1 (ITS1) and mitochondrial NADH dehydrogenase subunit 1 (nad1) and cytochrome c oxidase 1 (cox1) sequences. Fh, Fg, and Fh/Fg types were detected in the ITS1 region and displayed the fragment patterns of F. hepatica, F. gigantica, and both species, respectively by a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Additionally, three concatenated haplotypes of nad1 and cox1(nad1/cox1) were detected, and 2 of these, Kor1/Kor1 (Fsp1/Fsp1) haplotype and Kor2a/Kor2 (Fsp2/Fsp2) haplotype, were shared by Korean and Japanese aspermic flukes. The Fst value (0.019), calculated using the concatenated sequences, indicated that Korean and Japanese aspermic Fasciola populations were genetically undifferentiated. Interestingly, a combination of the Fh/Fg type and Kor1/Kor1 haplotype was found at the highest frequency in Korean aspermic flukes, whereas the Fg type and Fsp2/Fsp2 haplotype combination was found at a conspicuously high frequency in Japanese aspermic flukes. This indicates that a founder effect caused by the introduction of infected hosts may have played a key role in the introduction of aspermic Fasciola flukes from Korea into Japan.

A Validated Methodology for Genetic Identification of Tuna Species (Genus Thunnus)

PubMed Central

Viñas, Jordi; Tudela, Sergi

2009-01-01

Background Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue. Methodology After testing several genetic markers, a complete discrimination of the eight tuna species was achieved using Forensically Informative Nucleotide Sequencing based primarily on the sequence variability of the hypervariable genetic marker mitochondrial DNA control region (mtDNA CR), followed, in some specific cases, by a second validation by a nuclear marker rDNA first internal transcribed spacer (ITS1). This methodology was able to distinguish all tuna species, including those belonging to the subgenus Neothunnus that are very closely related, and in consequence can not be differentiated with other genetic markers of lower variability. This methodology also took into consideration the presence of introgression that has been reported in past studies between T. thynnus, T. orientalis and T. alalunga. Finally, we applied the methodology to cross-check the species identity of 26 processed tuna samples. Conclusions Using the combination of two genetic markers, one mitochondrial and another nuclear, allows a full discrimination between all eight tuna species. Unexpectedly, the genetic marker traditionally used for DNA barcoding, cytochrome oxidase 1, could not differentiate all species, thus its use as a genetic marker for tuna species identification is questioned. PMID:19898615

A validated methodology for genetic identification of tuna species (genus Thunnus).

PubMed

Viñas, Jordi; Tudela, Sergi

2009-10-27

Tuna species of the genus Thunnus, such as the bluefin tunas, are some of the most important and yet most endangered trade fish in the world. Identification of these species in traded forms, however, may be difficult depending on the presentation of the products, which may hamper conservation efforts on trade control. In this paper, we validated a genetic methodology that can fully distinguish between the eight Thunnus species from any kind of processed tissue. After testing several genetic markers, a complete discrimination of the eight tuna species was achieved using Forensically Informative Nucleotide Sequencing based primarily on the sequence variability of the hypervariable genetic marker mitochondrial DNA control region (mtDNA CR), followed, in some specific cases, by a second validation by a nuclear marker rDNA first internal transcribed spacer (ITS1). This methodology was able to distinguish all tuna species, including those belonging to the subgenus Neothunnus that are very closely related, and in consequence can not be differentiated with other genetic markers of lower variability. This methodology also took into consideration the presence of introgression that has been reported in past studies between T. thynnus, T. orientalis and T. alalunga. Finally, we applied the methodology to cross-check the species identity of 26 processed tuna samples. Using the combination of two genetic markers, one mitochondrial and another nuclear, allows a full discrimination between all eight tuna species. Unexpectedly, the genetic marker traditionally used for DNA barcoding, cytochrome oxidase 1, could not differentiate all species, thus its use as a genetic marker for tuna species identification is questioned.

HYBRIDIZATION PROPERTIES OF DNA SEQUENCES DIRECTING THE SYNTHESIS OF MESSENGER RNA AND HETEROGENEOUS NUCLEAR RNA

PubMed Central

Greenberg, Jay R.; Perry, Robert P.

1971-01-01

The relationship of the DNA sequences from which polyribosomal messenger RNA (mRNA) and heterogeneous nuclear RNA (NRNA) of mouse L cells are transcribed was investigated by means of hybridization kinetics and thermal denaturation of the hybrids. Hybridization was performed in formamide solutions at DNA excess. Under these conditions most of the hybridizing mRNA and NRNA react at values of Dot (DNA concentration multiplied by time) expected for RNA transcribed from the nonrepeated or rarely repeated fraction of the genome. However, a fraction of both mRNA and NRNA hybridize at values of Dot about 10,000 times lower, and therefore must be transcribed from highly redundant DNA sequences. The fraction of NRNA hybridizing to highly repeated sequences is about 1.7 times greater than the corresponding fraction of mRNA. The hybrids formed by the rapidly reacting fractions of both NRNA and mRNA melt over a narrow temperature range with a midpoint about 11°C below that of native L cell DNA. This indicates that these hybrids consist of partially complementary sequences with approximately 11% mismatching of bases. Hybrids formed by the slowly reacting fraction of NRNA melt within 4°–6°C of native DNA, indicating very little, if any, mismatching of bases. Hybrids of the slowly reacting components of mRNA, formed under conditions of sufficiently low RNA input, have a high thermal stability, similar to that observed for hybrids of the slowly reacting NRNA component. However, when higher inputs of mRNA are used, hybrids are formed which have a strikingly lower thermal stability. This observation can be explained by assuming that there is sufficient similarity among the relatively rare DNA sequences coding for mRNA so that under hybridization conditions, in which these DNA sequences are not truly in excess, reversible hybrids exhibiting a considerable amount of mispairing are formed. The fact that a comparable phenomenon has not been observed for NRNA may mean that there is less similarity among the relatively rare DNA sequences coding for NRNA than there is among the rare sequences coding for mRNA. PMID:4999767

Evolutionary history of tall fescue morphotypes inferred from molecular phylogenetics of the Lolium-Festuca species complex

PubMed Central

2010-01-01

Background The agriculturally important pasture grass tall fescue (Festuca arundinacea Schreb. syn. Lolium arundinaceum (Schreb.) Darbysh.) is an outbreeding allohexaploid, that may be more accurately described as a species complex consisting of three major (Continental, Mediterranean and rhizomatous) morphotypes. Observation of hybrid infertility in some crossing combinations between morphotypes suggests the possibility of independent origins from different diploid progenitors. This study aims to clarify the evolutionary relationships between each tall fescue morphotype through phylogenetic analysis using two low-copy nuclear genes (encoding plastid acetyl-CoA carboxylase [Acc1] and centroradialis [CEN]), the nuclear ribosomal DNA internal transcribed spacer (rDNA ITS) and the chloroplast DNA (cpDNA) genome-located matK gene. Other taxa within the closely related Lolium-Festuca species complex were also included in the study, to increase understanding of evolutionary processes in a taxonomic group characterised by multiple inter-specific hybridisation events. Results Putative homoeologous sequences from both nuclear genes were obtained from each polyploid species and compared to counterparts from 15 diploid taxa. Phylogenetic reconstruction confirmed F. pratensis and F. arundinacea var. glaucescens as probable progenitors to Continental tall fescue, and these species are also likely to be ancestral to the rhizomatous morphotype. However, these two morphotypes are sufficiently distinct to be located in separate clades based on the ITS-derived data set. All four of the generated data sets suggest independent evolution of the Mediterranean and Continental morphotypes, with minimal affinity between cognate sequence haplotypes. No obvious candidate progenitor species for Mediterranean tall fescues were identified, and only two putative sub-genome-specific haplotypes were identified for this morphotype. Conclusions This study describes the first phylogenetic analysis of the Festuca genus to include representatives of each tall fescue morphotype, and to use low copy nuclear gene-derived sequences to identify putative progenitors of the polyploid species. The demonstration of distinct tall fescue lineages has implications for both taxonomy and molecular breeding strategies, and may facilitate the generation of morphotype and/or sub-genome-specific molecular markers. PMID:20937141

Mycobacterium tuberculosis Infection of Domesticated Asian Elephants, Thailand

PubMed Central

Angkawanish, Taweepoke; Sirimalaisuwan, Anucha; Kaewsakhorn, Thattawan; Boonsri, Kittikorn; Rutten, Victor P.M.G.

2010-01-01

Four Asian elephants were confirmed to be infected with Mycobacterium tuberculosis by bacterial culture, other diagnostic procedures, and sequencing of 16S–23S rDNA internal transcribed spacer region, 16S rRNA, and gyrase B gene sequences. Genotyping showed that the infectious agents originated from 4 sources in Thailand. To identify infections, a combination of diagnostic assays is essential. PMID:21122228

The first ITS phylogeny of the genus Cantharocybe (Agaricales, Hygrophoraceae) with a new record of C. virosa from Bangladesh

Treesearch

Md. Iqbal Hosen; Tai-Hui Li; D. Jean Lodge; Alan Rockefeller

2016-01-01

This is the first internal transcribed spacer (ITS) phylogeny of the enigmatic genus Cantharocybe and includes ITS sequences from two out of the three holotype collections. Two species are reported from the Americas and only a single species from Asia. Additionally, a collection of Cantharocybe virosa collected from tropical...

Hierarchical recruitment of ribosomal proteins and assembly factors remodels nucleolar pre-60S ribosomes.

PubMed

Biedka, Stephanie; Micic, Jelena; Wilson, Daniel; Brown, Hailey; Diorio-Toth, Luke; Woolford, John L

2018-04-24

Ribosome biogenesis involves numerous preribosomal RNA (pre-rRNA) processing events to remove internal and external transcribed spacer sequences, ultimately yielding three mature rRNAs. Removal of the internal transcribed spacer 2 spacer RNA is the final step in large subunit pre-rRNA processing and begins with endonucleolytic cleavage at the C 2 site of 27SB pre-rRNA. C 2 cleavage requires the hierarchical recruitment of 11 ribosomal proteins and 14 ribosome assembly factors. However, the function of these proteins in C 2 cleavage remained unclear. In this study, we have performed a detailed analysis of the effects of depleting proteins required for C 2 cleavage and interpreted these results using cryo-electron microscopy structures of assembling 60S subunits. This work revealed that these proteins are required for remodeling of several neighborhoods, including two major functional centers of the 60S subunit, suggesting that these remodeling events form a checkpoint leading to C 2 cleavage. Interestingly, when C 2 cleavage is directly blocked by depleting or inactivating the C 2 endonuclease, assembly progresses through all other subsequent steps. © 2018 Biedka et al.

Symbiodinium diversity in the soft coral Heteroxenia sp. and its nudibranch predator Phyllodesmium lizardensis

NASA Astrophysics Data System (ADS)

FitzPatrick, S. K.; Liberatore, K. L.; Garcia, J. R.; Burghardt, I.; Colman, D. R.; Moquin, S. A.; Takacs-Vesbach, C. D.; Shepherd, U. L.

2012-09-01

We examined the diversity of the photosynthetic dinoflagellate, Symbiodinium, over a 2-year period in two invertebrates from Australia's Northern Great Barrier Reef: the nudibranch Phyllodesmium lizardensis and an octocoral of the genus Heteroxenia. In years one and two, we used denaturing gradient gel electrophoresis with internal transcribed spacer 2 (ITS2) region amplicons and identified two nearly identical genotypes of clade C (C64 and a variant) in all samples of each species. We examined the secondary structure of both sequences and found that each had predicted ∆G values within the range of stable free energy values for Symbiodinium ITS2 sequences. In year two, we also used real-time quantitative polymerase chain reaction assays (qPCR) with clade-specific internal transcribed spacer 1 primers to determine whether there were cryptic clades (A, B, and/or D) associated with either host in addition to clade C. qPCR revealed that clades B, C, and D were present in all animals of both species and that all but two nudibranch samples also harbored clade A. These findings suggest that there may be more flexibility in this host/symbiont interaction than has previously been assumed.

Phylogenetic Relationships Based on DNA Barcoding Among 16 Species of the Ant Genus Formica (Hymenoptera: Formicidae) from China

PubMed Central

Chen, Yuan

2017-01-01

Abstract In this study, we sequenced fragments of cytochrome oxidase subunit 1 (CO1), internal transcribed spacer 1 (ITS1), and internal transcribed spacer 2 (ITS2) genes from 150 specimens belonging to 16 species of the ant genus Formica from China. Odontoponera transversa from Ponerinae and Polyergus samurai from Formicinae were added as distant relative and close relative outgroups, respectively. Neighbor-joining, maximum parsimony, and Bayesian interference methods were used to analyze their phylogenetic relationships based on CO1 gene sequence as well as combined sequence data of CO1 + ITS1, CO1 + ITS2, and CO1 + ITS1 + ITS2. The results showed that nine Formica species (i.e., Formica sinensis, Formica manchu, Formica uralensis, Formica sanguinea, Formica gagatoides, Formica candida, Formica fusca, Formica glauca, and Formica sp.) formed monophyletic clades, which in agreement with the results based on morphological taxonomy. By comparing the results of DNA barcoding and morphological taxonomy, we propose that Formica aquilonia maybe a junior synonym of F. polyctena and that cryptic species could likely existed in Formica sinae. Further studies on morphology, biology, and geography are needed to confirm this notion.

Influence of Molecular Resolution on Sequence-Based Discovery of Ecological Diversity among Synechococcus Populations in an Alkaline Siliceous Hot Spring Microbial Mat ▿ †

PubMed Central

Melendrez, Melanie C.; Lange, Rachel K.; Cohan, Frederick M.; Ward, David M.

2011-01-01

Previous research has shown that sequences of 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions may not have enough genetic resolution to define all ecologically distinct Synechococcus populations (ecotypes) inhabiting alkaline, siliceous hot spring microbial mats. To achieve higher molecular resolution, we studied sequence variation in three protein-encoding loci sampled by PCR from 60°C and 65°C sites in the Mushroom Spring mat (Yellowstone National Park, WY). Sequences were analyzed using the ecotype simulation (ES) and AdaptML algorithms to identify putative ecotypes. Between 4 and 14 times more putative ecotypes were predicted from variation in protein-encoding locus sequences than from variation in 16S rRNA and 16S-23S rRNA internal transcribed spacer sequences. The number of putative ecotypes predicted depended on the number of sequences sampled and the molecular resolution of the locus. Chao estimates of diversity indicated that few rare ecotypes were missed. Many ecotypes hypothesized by sequence analyses were different in their habitat specificities, suggesting different adaptations to temperature or other parameters that vary along the flow channel. PMID:21169433

16S-23S rRNA gene internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Porphyromonas.

PubMed

Conrads, Georg; Citron, Diane M; Tyrrell, Kerin L; Horz, Hans-Peter; Goldstein, Ellie J C

2005-03-01

The 16S-23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260(T) divided the sequences into two clusters, of which one was alpha-fucosidase-positive (like the type strain) while the other was alpha-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of 'Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called 'Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of alpha-fucosidase-negative P. asaccharolytica strains as a new species should also be considered.

Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293

PubMed Central

Kanhayuwa, Lakkhana; Coutts, Robert H. A.

2016-01-01

Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4–14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140–493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3’-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50–65% and 60–75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259–343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity. PMID:27736869

Short Interspersed Nuclear Element (SINE) Sequences in the Genome of the Human Pathogenic Fungus Aspergillus fumigatus Af293.

PubMed

Kanhayuwa, Lakkhana; Coutts, Robert H A

2016-01-01

Novel families of short interspersed nuclear element (SINE) sequences in the human pathogenic fungus Aspergillus fumigatus, clinical isolate Af293, were identified and categorised into tRNA-related and 5S rRNA-related SINEs. Eight predicted tRNA-related SINE families originating from different tRNAs, and nominated as AfuSINE2 sequences, contained target site duplications of short direct repeat sequences (4-14 bp) flanking the elements, an extended tRNA-unrelated region and typical features of RNA polymerase III promoter sequences. The elements ranged in size from 140-493 bp and were present in low copy number in the genome and five out of eight were actively transcribed. One putative tRNAArg-derived sequence, AfuSINE2-1a possessed a unique feature of repeated trinucleotide ACT residues at its 3'-terminus. This element was similar in sequence to the I-4_AO element found in A. oryzae and an I-1_AF long nuclear interspersed element-like sequence identified in A. fumigatus Af293. Families of 5S rRNA-related SINE sequences, nominated as AfuSINE3, were also identified and their 5'-5S rRNA-related regions show 50-65% and 60-75% similarity to respectively A. fumigatus 5S rRNAs and SINE3-1_AO found in A. oryzae. A. fumigatus Af293 contains five copies of AfuSINE3 sequences ranging in size from 259-343 bp and two out of five AfuSINE3 sequences were actively transcribed. Investigations on AfuSINE distribution in the fungal genome revealed that the elements are enriched in pericentromeric and subtelomeric regions and inserted within gene-rich regions. We also demonstrated that some, but not all, AfuSINE sequences are targeted by host RNA silencing mechanisms. Finally, we demonstrated that infection of the fungus with mycoviruses had no apparent effects on SINE activity.

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

PubMed Central

O’Sullivan, Justin M.; Pai, Dave A.; Cridge, Andrew G.; Engelke, David R.; Ganley, Austen R. D.

2016-01-01

The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfil the cellular demand for rRNA, the ribosomal RNA genes (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spatial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization. PMID:25436580

The nucleolus: a raft adrift in the nuclear sea or the keystone in nuclear structure?

PubMed

O'Sullivan, Justin M; Pai, Dave A; Cridge, Andrew G; Engelke, David R; Ganley, Austen R D

2013-06-01

The nucleolus is a prominent nuclear structure that is the site of ribosomal RNA (rRNA) transcription, and hence ribosome biogenesis. Cellular demand for ribosomes, and hence rRNA, is tightly linked to cell growth and the rRNA makes up the majority of all the RNA within a cell. To fulfill the cellular demand for rRNA, the ribosomal RNA (rDNA) genes are amplified to high copy number and transcribed at very high rates. As such, understanding the rDNA has profound consequences for our comprehension of genome and transcriptional organization in cells. In this review, we address the question of whether the nucleolus is a raft adrift the sea of nuclear DNA, or actively contributes to genome organization. We present evidence supporting the idea that the nucleolus, and the rDNA contained therein, play more roles in the biology of the cell than simply ribosome biogenesis. We propose that the nucleolus and the rDNA are central factors in the spatial organization of the genome, and that rapid alterations in nucleolar structure in response to changing conditions manifest themselves in altered genomic structures that have functional consequences. Finally, we discuss some predictions that result from the nucleolus having a central role in nuclear organization.

Loss of a Trans-Splicing nad1 Intron from Geraniaceae and Transfer of the Maturase Gene matR to the Nucleus in Pelargonium

PubMed Central

Grewe, Felix; Zhu, Andan; Mower, Jeffrey P.

2016-01-01

The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron. In the common ancestor of Pelargonium, matR was transferred to the nuclear genome, where it was split into two unlinked genes that encode either its reverse transcriptase or maturase domain. Both nuclear genes are transcribed and contain predicted mitochondrial targeting signals, suggesting that they express functional proteins that are imported into mitochondria. The nuclear localization and split domain structure of matR in the Pelargonium nuclear genome offers a unique opportunity to assess the function of these two domains using transgenic approaches. PMID:27664178

Study of nuclear medicine practices in Portugal from an internal dosimetry perspective.

PubMed

Bento, J; Teles, P; Neves, M; Santos, A I; Cardoso, G; Barreto, A; Alves, F; Guerreiro, C; Rodrigues, A; Santos, J A M; Capelo, C; Parafita, R; Martins, B

2012-05-01

Nuclear medicine practices involve the handling of a wide range of pharmaceuticals labelled with different radionuclides, for diagnostic and therapeutic purposes. This work intends to evaluate the potential risks of internal contamination of nuclear medicine staff in several Portuguese nuclear medicine services and to conclude about the requirement of a routine internal monitoring. A methodology proposed by the International Atomic Energy Agency (IAEA), providing a set of criteria to determine the need, or not, for an internal monitoring programme, was applied. The evaluation of the risk of internal contaminations in a given set of working conditions is based on the type and amount of radionuclides being handled, as well as the safety conditions with which they are manipulated. The application of the IAEA criteria showed that 73.1% of all the workers included in this study should be integrated in a routine monitoring programme for internal contaminations; more specifically, 100% of workers performing radioimmunoassay techniques should be monitored. This study suggests that a routine monitoring programme for internal exposures should be implemented in Portugal for most nuclear medicine workers.

Locus of Control and Likelihood of Nuclear War: Two Studies.

ERIC Educational Resources Information Center

Erdahl, Paul; Rounds, James B.

The Nuclear Locus of Control (NLOC) scales were constructed to assess beliefs as to whether nuclear war and nuclear policy decisions are, or can be, influenced by oneself, powerful others, or chance. Three scales measuring internal, powerful others, and chance nuclear LOC show internal consistency estimates (Cronbach's Alpha) of .87, .76, and .85,…

10 CFR 74.43 - Internal controls, inventory, and records.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false Internal controls, inventory, and records. 74.43 Section 74.43 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) MATERIAL CONTROL AND ACCOUNTING OF SPECIAL NUCLEAR MATERIAL Special Nuclear Material of Moderate Strategic Significance § 74.43 Internal controls, inventory, and records. (a) General. Licensees...

10 CFR 74.43 - Internal controls, inventory, and records.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 2 2012-01-01 2012-01-01 false Internal controls, inventory, and records. 74.43 Section 74.43 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) MATERIAL CONTROL AND ACCOUNTING OF SPECIAL NUCLEAR MATERIAL Special Nuclear Material of Moderate Strategic Significance § 74.43 Internal controls, inventory, and records. (a) General. Licensees...

10 CFR 74.43 - Internal controls, inventory, and records.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 2 2011-01-01 2011-01-01 false Internal controls, inventory, and records. 74.43 Section 74.43 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) MATERIAL CONTROL AND ACCOUNTING OF SPECIAL NUCLEAR MATERIAL Special Nuclear Material of Moderate Strategic Significance § 74.43 Internal controls, inventory, and records. (a) General. Licensees...

10 CFR 74.43 - Internal controls, inventory, and records.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false Internal controls, inventory, and records. 74.43 Section 74.43 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) MATERIAL CONTROL AND ACCOUNTING OF SPECIAL NUCLEAR MATERIAL Special Nuclear Material of Moderate Strategic Significance § 74.43 Internal controls, inventory, and records. (a) General. Licensees...

International nuclear fuel cycle fact book. Revision 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harmon, K.M.; Lakey, L.T.; Leigh, I.W.

This Fact Book has been compiled in an effort to provide (1) an overview of worldwide nuclear power and fuel cycle programs and (2) current data concerning fuel cycle and waste management facilities, R and D programs, and key personnel in countries other than the United States. Additional information on each country's program is available in the International Source Book: Nuclear Fuel Cycle Research and Development, PNL-2478, Rev. 2. The Fact Book is organized as follows: (1) Overview section - summary tables which indicate national involvement in nuclear reactor, fuel cycle, and waste management development activities; (2) national summaries -more » a section for each country which summarizes nuclear policy, describes organizational relationships and provides addresses, names of key personnel, and facilities information; (3) international agencies - a section for each of the international agencies which has significant fuel cycle involvement; (4) energy supply and demand - summary tables, including nuclear power projections; (5) fuel cycle - summary tables; and (6) travel aids - international dialing instructions, international standard time chart, passport and visa requirements, and currency exchange rate.« less

International Nuclear Fuel Cycle Fact Book. Revision 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harmon, K.M.; Lakey, L.T.; Leigh, I.W.

This Fact Book has been compiled in an effort to provide: (1) an overview of worldwide nuclear power and fuel cycle programs; and (2) current data concerning fuel cycle and waste management facilities, R and D programs, and key personnel in countries other than the United States. Additional information on each country's program is available in the International Source Book: Nuclear Fuel Cycle Research and Development, PNL-2478, Rev. 2. The Fact Book is organized as follows: (1) Overview section - summary tables which indicate national involvement in nuclear reactor, fuel cycle, and waste management development activities; (2) national summaries -more » a section for each country which summarizes nuclear policy, describes organizational relationships and provides addresses, names of key personnel, and facilities information; (3) international agencies - a section for each of the international agencies which has significant fuel cycle involvement; (4) energy supply and demand - summary tables, including nuclear power projections; (5) fuel cycle - summary tables; and (6) travel aids international dialing instructions, international standard time chart, passport and visa requirements, and currency exchange rate.« less

Understanding the Value of a Computer Emergency Response Capability for Nuclear Security

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gasper, Peter Donald; Rodriguez, Julio Gallardo

The international nuclear community has a great understanding of the physical security needs relating to the prevention, detection, and response of malicious acts associated with nuclear facilities and radioactive material. International Atomic Energy Agency (IAEA) Nuclear Security Recommendations (INFCIRC_225_Rev 5) outlines specific guidelines and recommendations for implementing and maintaining an organization’s nuclear security posture. An important element for inclusion into supporting revision 5 is the establishment of a “Cyber Emergency Response Team (CERT)” focused on the international communities cybersecurity needs to maintain a comprehensive nuclear security posture. Cybersecurity and the importance of nuclear cybersecurity require that there be a specificmore » focus on developing an International Nuclear CERT (NS-CERT). States establishing contingency plans should have an understanding of the cyber threat landscape and the potential impacts to systems in place to protect and mitigate malicious activities. This paper will outline the necessary components, discuss the relationships needed within the international community, and outline a process by which the NS-CERT identifies, collects, processes, and reports critical information in order to establish situational awareness (SA) and support decision-making« less

[The compulsory isolation of Hansen's disease patients: memories of the elderly].

PubMed

de Castro, Selma Munhoz Sanches; Watanabe, Helena Akemi Wada

2009-01-01

From 1924 to 1962, Brazil used compulsory internment of Hansen's disease patients as one of the ways of controlling the disease in the community. After this policy ended, many patients continued to live in these units. The former Asilo Pirapitingui, now the Hospital Dr. Francisco Ribeiro Arantes, is the only old-style asylum for the socially determined internment of those suffering from Hansen's disease. Through recorded and transcribed interviews of eight of those remaining, we sought to learn their history and the meaning of this isolation in their lives. The thematic analysis of the discourse enabled identification of the following analysis categories: Hansen's disease; internment day-to-day life; the institution; current health conditions; and staying in the institution after the end of compulsory internment.

Co-ordination of the International Network of Nuclear Structure and Decay Data Evaluators; Summary Report of an IAEA Technical Meeting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abriola, D.; Tuli, J.

The IAEA Nuclear Data Section convened the 18th meeting of the International Network of Nuclear Structure and Decay Data Evaluators at the IAEA Headquarters, Vienna, 23 to 27 March 2009. This meeting was attended by 22 scientists from 14 Member States, plus IAEA staff, concerned with the compilation, evaluation and dissemination of nuclear structure and decay data. A summary of the meeting, recommendations/conclusions, data centre reports, and various proposals considered, modified and agreed by the participants are contained within this document. The International Network of Nuclear Structure and Decay Data (NSDD) Evaluators holds biennial meetings under the auspices of themore » IAEA, and consists of evaluation groups and data service centres in several countries. This network has the objective of providing up-to-date nuclear structure and decay data for all known nuclides by evaluating all existing experimental data. Data resulting from this international evaluation collaboration is included in the Evaluated Nuclear Structure Data File (ENSDF) and published in the journals Nuclear Physics A and Nuclear Data Sheets (NDS).« less

Hypogeous ectomycorrhizal fungal species on roots and in small mammal diet in a mixed-conifer forest

Treesearch

Antonio D. Izzo; Marc Meyer; James M. Trappe; Malcolm North; Thomas D. Bruns

2005-01-01

The purpose of this study was to estimate the portion of an ectomycorrhizal (ECM) fungi root community with a hypogeous fruiting habit. We used molecular methods (DNA sequence analysis of the internally transcribed spacer [ITS] region of rDNA) to compare three viewpoints: ECM fungi on the roots in a southern Sierra Nevada Abies-dominated old-growth...

USSR Report, International Affairs, The Working Class and the Contemporary World

DTIC Science & Technology

1987-05-26

foreign newspapers, periodicals and books, but also from news agency transmissions and broad- casts o Materials from foreign- language sources are...translated; those from English- language sources are transcribed or reprinted, with the original phrasing and other characteristics retained...Except where indicated otherwise in the table of contents the following is a complete translation of the Russian- language journal RABOCHIY KLASS I

5. international workshop on the identification of transcribed sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1995-12-31

This workshop was held November 5--8, 1995 in Les Embiez, France. The purpose of this conference was to provide a multidisciplinary forum for exchange of state-of-the-art information on mapping the human genome. Attention is focused on the following topics: transcriptional maps; functional analysis; techniques; model organisms; and tissue specific libraries and genes. Abstracts are included of the papers that were presented.

Going nuclear: The spread of nuclear weapons 1986-1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spector, L.S.

1987-01-01

In the third annual report of the Carnegie Endowment for International Peace on the spread of nuclear weapons, Spector provides a critical survey of the status of nuclear proliferation throughout the world and examines the nuclear potential of nations in the Middle East, Asia, Africa, and Latin America. Drawing on both historical documents and up-to-date reports, the author addresses such specific topics as Israel's nuclear arsenal, nuclear terrorism and its global security implications, arms control and nuclear safeguards, international treaties, weapons buildup, and political radicalism and unrest in nuclear-threshold nations.

Identification of Three Kinds of Citri Reticulatae Pericarpium Based on Deoxyribonucleic Acid Barcoding and High-performance Liquid Chromatography-diode Array Detection-electrospray Ionization/Mass Spectrometry/Mass Spectrometry Combined with Chemometric Analysis

PubMed Central

Yu, Xiaoxue; Zhang, Yafeng; Wang, Dongmei; Jiang, Lin; Xu, Xinjun

2018-01-01

Background: Citri Reticulatae Pericarpium is the dried mature pericarp of Citrus reticulata Blanco which can be divided into “Chenpi” and “Guangchenpi.” “Guangchenpi” is the genuine Chinese medicinal material in Xinhui, Guangdong province; based on the greatest quality and least amount, it is most expensive among others. Hesperidin is used as the marker to identify Citri Reticulatae Pericarpium described in the Chinese Pharmacopoeia 2010. However, both “Chenpi” and “Guangchenpi” contain hesperidin so that it is impossible to differentiate them by measuring hesperidin. Objective: Our study aims to develop an efficient and accurate method to separate and identify “Guangchenpi” from other Citri Reticulatae Pericarpium. Materials and Methods: The genomic deoxyribonucleic acid (DNA) of all the materials was extracted and then the internal transcribed spacer 2 was amplified, sequenced, aligned, and analyzed. The secondary structures were created in terms of the database and website established by Jörg Schultz et al. High-performance liquid chromatography-diode array detection-electrospray Ionization/mass spectrometry (HPLC-DAD-ESI-MS)/MS coupled with chemometric analysis was applied to compare the differences in chemical profiles of the three kinds of Citri Reticulatae Pericarpium. Results: A total of 22 samples were classified into three groups. The results of DNA barcoding were in accordance with principal component analysis and hierarchical cluster analysis. Eight compounds were deduced from HPLC-DAD-ESI-MS/MS. Conclusions: This method is a reliable and effective tool to differentiate the three Citri Reticulatae Pericarpium. SUMMARY The internal transcribed spacer 2 regions and the secondary structure among three kinds of Citri Reticulatae Pericarpium varied considerablyAll the 22 samples were analyzed by high-performance liquid chromatography (HPLC) to obtain the chemical profilesPrincipal component analysis and hierarchical cluster analysis were used in the chemometric analysisdeoxyribonucleic acid barcoding and HPLC-diode array detection-electrospray ionization/mass spectrometry/MS coupled with chemometric analysis provided an accurate and strong proof to identify these three herbs. Abbreviations used: CTAB: Hexadecyltrimethylammonium bromide, DNA: Deoxyribonucleic acid, ITS2: Internal transcribed spacer 2, PCR: Polymerase chain reaction. PMID:29576703

The Importance of International Technical Nuclear Forensics to Deter Illicit Trafficking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, D K

2007-01-30

Illicit trafficking of nuclear materials is a transboundary problem that requires a cooperative approach involving international nuclear forensics to ensure all states understand the threat posed by nuclear smuggling as well as a means to best deter the movement of nuclear contraband. To achieve the objectives, all cases involving illicit trafficking of nuclear and radiological materials must be vigorously pursued and prosecuted when appropriate. The importance of outreach and formal government-to-government relationships with partner nations affected by nuclear trafficking cannot be under-estimated. States that are situated on smuggling routes may be well motivated to counter nuclear crimes to bolster theirmore » own border and transportation security as well as strengthen their economic and political viability. National law enforcement and atomic energy agencies in these states are aggressively pursuing a comprehensive strategy to counter nuclear smuggling through increasing reliance on technical nuclear forensics. As part of these activities, it is essential that these organizations be given adequate orientation to the best practices in this emerging discipline including the categorization of interdicted nuclear material, collection of traditional and nuclear forensic evidence, data analysis using optimized analytical protocols, and how to best fuse forensics information with reliable case input to best develop a law enforcement or national security response. The purpose of formalized USG relationship is to establish an institutional framework for collaboration in international forensics, improve standards of forensics practice, conduct joint exercises, and pursue case-work that benefits international security objectives. Just as outreach and formalized relationships are important to cultivate international nuclear forensics, linking nuclear forensics to ongoing national assistance in border and transpiration security, including port of entry of entry monitoring, nuclear safeguards, and emerging civilian nuclear power initiatives including the Global Nuclear Energy Partnership are crucial components of a successful nuclear detection and security architecture. Once illicit shipments of nuclear material are discovered at a border, the immediate next question will be the nature and the source of the material, as well as the identity of the individual(s) involved in the transfer as well as their motivations. The Nuclear Smuggling International Technical Working Group (ITWG) is a forum for the first responder, law enforcement, policy, and diplomatic community to partner with nuclear forensics experts worldwide to identify requirements and develop technical solutions in common. The ITWG was charted in 1996 and since that time approximately 30 member states and organizations have participated in 11 annual international meetings. The ITWG also works closely with the IAEA to provide countries with support for forensic analyses. Priorities include the development of common protocols for the collection of nuclear forensic evidence and laboratory investigations, organization of forensic round-robin analytical exercises and technical forensic assistance to requesting nations. To promote the science of nuclear forensics within the ITWG the Nuclear Forensics Laboratory Group was organized in 2004. A Model Action Plan for nuclear forensics was developed by the ITWG and published as an IAEA Nuclear security Series document to guide member states in their own forensics investigations. Through outreach, formalized partnerships, common approaches and security architectures, and international working groups, nuclear forensics provides an important contribution to promoting nuclear security and accountability.« less

Afraid of being "witchy with a 'b'": a qualitative study of how gender influences residents' experiences leading cardiopulmonary resuscitation.

PubMed

Kolehmainen, Christine; Brennan, Meghan; Filut, Amarette; Isaac, Carol; Carnes, Molly

2014-09-01

Ineffective leadership during cardiopulmonary resuscitation ("code") can negatively affect a patient's likelihood of survival. In most teaching hospitals, internal medicine residents lead codes. In this study, the authors explored internal medicine residents' experiences leading codes, with a particular focus on how gender influences the code leadership experience. The authors conducted individual, semistructured telephone or in-person interviews with 25 residents (May 2012 to February 2013) from 9 U.S. internal medicine residency programs. They audio recorded and transcribed the interviews and then thematically analyzed the transcribed text. Participants viewed a successful code as one with effective leadership. They agreed that the ideal code leader was an authoritative presence; spoke with a deep, loud voice; used clear, direct communication; and appeared calm. Although equally able to lead codes as their male colleagues, female participants described feeling stress from having to violate gender behavioral norms in the role of code leader. In response, some female participants adopted rituals to signal the suspension of gender norms while leading a code. Others apologized afterwards for their counternormative behavior. Ideal code leadership embodies highly agentic, stereotypical male behaviors. Female residents employed strategies to better integrate the competing identities of code leader and female gender. In the future, residency training should acknowledge how female gender stereotypes may conflict with the behaviors required to enact code leadership and offer some strategies, such as those used by the female residents in this study, to help women integrate these dual identities.

Molecular and phenotypic characterization of Colletotrichum species associated with anthracnose disease in peppers from Sichuan Province, China

PubMed Central

Liu, Fangling; Tang, Guiting; Zheng, Xiaojuan; Li, Ying; Sun, Xiaofang; Qi, Xiaobo; Zhou, You; Xu, Jing; Chen, Huabao; Chang, Xiaoli; Zhang, Sirong; Gong, Guoshu

2016-01-01

The anthracnose caused by Colletotrichum species is an important disease that primarily causes fruit rot in pepper. Eighty-eight strains representing seven species of Colletotrichum were obtained from rotten pepper fruits in Sichuan Province, China, and characterized according to morphology and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) sequence. Fifty-two strains were chosen for identification by phylogenetic analyses of multi-locus sequences, including the nuclear ribosomal internal transcribed spacer (ITS) region and the β-tubulin (TUB2), actin (ACT), calmodulin (CAL) and GAPDH genes. Based on the combined datasets, the 88 strains were identified as Colletotrichum gloeosporioides, C. siamense, C. fructicola, C. truncatum, C. scovillei, and C. brevisporum, and one new species was detected, described as Colletotrichum sichuanensis. Notably, C. siamense and C. scovillei were recorded for the first time as the causes of anthracnose in peppers in China. In addition, with the exception of C. truncatum, this is the first report of all of the other Colletotrichum species studied in pepper from Sichuan. The fungal species were all non-host-specific, as the isolates were able to infect not only Capsicum spp. but also Pyrus pyrifolia in pathogenicity tests. These findings suggest that the fungal species associated with anthracnose in pepper may inoculate other hosts as initial inoculum. PMID:27609555

Molecular and phenotypic characterization of Colletotrichum species associated with anthracnose disease in peppers from Sichuan Province, China.

PubMed

Liu, Fangling; Tang, Guiting; Zheng, Xiaojuan; Li, Ying; Sun, Xiaofang; Qi, Xiaobo; Zhou, You; Xu, Jing; Chen, Huabao; Chang, Xiaoli; Zhang, Sirong; Gong, Guoshu

2016-09-09

The anthracnose caused by Colletotrichum species is an important disease that primarily causes fruit rot in pepper. Eighty-eight strains representing seven species of Colletotrichum were obtained from rotten pepper fruits in Sichuan Province, China, and characterized according to morphology and the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) sequence. Fifty-two strains were chosen for identification by phylogenetic analyses of multi-locus sequences, including the nuclear ribosomal internal transcribed spacer (ITS) region and the β-tubulin (TUB2), actin (ACT), calmodulin (CAL) and GAPDH genes. Based on the combined datasets, the 88 strains were identified as Colletotrichum gloeosporioides, C. siamense, C. fructicola, C. truncatum, C. scovillei, and C. brevisporum, and one new species was detected, described as Colletotrichum sichuanensis. Notably, C. siamense and C. scovillei were recorded for the first time as the causes of anthracnose in peppers in China. In addition, with the exception of C. truncatum, this is the first report of all of the other Colletotrichum species studied in pepper from Sichuan. The fungal species were all non-host-specific, as the isolates were able to infect not only Capsicum spp. but also Pyrus pyrifolia in pathogenicity tests. These findings suggest that the fungal species associated with anthracnose in pepper may inoculate other hosts as initial inoculum.

New light on the systematics of fungi associated with attine ant gardens and the description of Escovopsis kreiselii sp. nov.

PubMed

Meirelles, Lucas A; Montoya, Quimi V; Solomon, Scott E; Rodrigues, Andre

2015-01-01

Since the formal description of fungi in the genus Escovopsis in 1990, only a few studies have focused on the systematics of this group. For more than two decades, only two Escovopsis species were described; however, in 2013, three additional Escovopsis species were formally described along with the genus Escovopsioides, both found exclusively in attine ant gardens. During a survey for Escovopsis species in gardens of the lower attine ant Mycetophylax morschi in Brazil, we found four strains belonging to the pink-colored Escovopsis clade. Careful examination of these strains revealed significant morphological differences when compared to previously described species of Escovopsis and Escovopsioides. Based on the type of conidiogenesis (sympodial), as well as morphology of conidiogenous cells (percurrent), non-vesiculated conidiophores, and DNA sequences, we describe the four new strains as a new species, Escovopsis kreiselii sp. nov. Phylogenetic analyses using three nuclear markers (Large subunit RNA; translation elongation factor 1-alpha; and internal transcribed spacer) from the new strains as well as available sequences in public databases confirmed that all known fungi infecting attine ant gardens comprise a monophyletic group within the Hypocreaceae family, with very diverse morphological characteristics. Specifically, Escovopsis kreiselii is likely associated with gardens of lower-attine ants and its pathogenicity remains uncertain.

Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera).

PubMed

Gómez, Africa; Serra, Manuel; Carvalho, Gary R; Lunt, David H

2002-07-01

Continental lake-dwelling zooplanktonic organisms have long been considered cosmopolitan species with little geographic variation in spite of the isolation of their habitats. Evidence of morphological cohesiveness and high dispersal capabilities support this interpretation. However, this view has been challenged recently as many such species have been shown either to comprise cryptic species complexes or to exhibit marked population genetic differentiation and strong phylogeographic structuring at a regional scale. Here we investigate the molecular phylogeny of the cosmopolitan passively dispersing rotifer Brachionus plicatilis (Rotifera: Monogononta) species complex using nucleotide sequence variation from both nuclear (ribosomal internal transcribed spacer 1, ITS1) and mitochondrial (cytochrome c oxidase subunit I, COI) genes. Analysis of rotifer resting eggs from 27 salt lakes in the Iberian Peninsula plus lakes from four continents revealed nine genetically divergent lineages. The high level of sequence divergence, absence of hybridization, and extensive sympatry observed support the specific status of these lineages. Sequence divergence estimates indicate that the B. plicatilis complex began diversifying many millions of years ago, yet has showed relatively high levels of morphological stasis. We discuss these results in relation to the ecology and genetics of aquatic invertebrates possessing dispersive resting propagules and address the apparent contradiction between zooplanktonic population structure and their morphological stasis.

Mitochondrial and nuclear markers reveal a lack of genetic structure in the entocommensal nemertean Malacobdella arrokeana in the Patagonian gulfs

NASA Astrophysics Data System (ADS)

Alfaya, José E. F.; Bigatti, Gregorio; Machordom, Annie

2013-06-01

Malacobdella arrokeana is an entocommensal nemertean exclusively found in the bivalve geoduck Panopea abbreviata, and it is the only representative of the genus in the southern hemisphere. To characterize its genetic diversity, population structure and recent demographic history, we conducted the first genetic survey on this species, using sequence data for the cytochrome oxidase I gene (COI), 16S rRNA (16S) and the internal transcribed spacer (ITS2). Only four different ITS2 genotypes were found in the whole sample, and the two main haplotypes identified in the mitochondrial dataset were present among all localities with a diversity ranging from 0.583 to 0.939. Nucleotide diversity was low (π = 0.001-0.002). No significant genetic structure was detected between populations, and mismatch distribution patterns and neutrality tests results are consistent with a population in expansion or under selection. Analysis of molecular variance (AMOVA) revealed that the largest level of variance observed was due to intrapopulation variation (100, 100 and 94.39 % for 16S, COI and ITS2, respectively). F st values were also non-significant. The observed lack of population structure is likely due to high levels of genetic connectivity in combination with the lack or permeability of biogeographic barriers and episodes of habitat modification.

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity

PubMed Central

Yuan, Zhilin; Druzhinina, Irina S.; Labbé, Jessy; Redman, Regina; Qin, Yuan; Rodriguez, Russell; Zhang, Chulong; Tuskan, Gerald A.; Lin, Fucheng

2016-01-01

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found the genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. This work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity. PMID:27572178

Natural hybridization and introgression between Ligularia cymbulifera and L. tongolensis (Asteraceae, Senecioneae) in four different locations.

PubMed

Yu, Jiaojun; Kuroda, Chiaki; Gong, Xun

2014-01-01

Natural hybridization has been considered to represent an important factor influencing the high diversity of the genus Ligularia Cass. in the Hengduan Mountains, China. Natural hybridization has been confirmed to occur frequently in Ligularia. To date, however, it has been demonstrated only within a single population. In this paper, we present evidence of natural hybridization in Ligularia from four different locations. The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA and three chloroplast intergenic spacers (trnK-rps16, trnL-rpl32 and trnQ-5'rps16) of 149 accessions of putative hybrids and their putative parents (L. cymbulifera and L. tongolensis) were analyzed for evidence of hybridization. The ITS data clearly distinguished two putative parental species and sympatric L. vellerea and supported the hypothesis that those morphological intermediates were products of natural hybridization between L. cymbulifera and L. tongolensis. Moreover, several identified morphological parents were actual introgressed products. Because of hybridization and introgression, chloroplast DNA sequences generated a poorly resolved network. The present results indicate that varying degrees of hybridization and introgression occur differently depending on the habitat context. We conclude that gene flow caused by natural hybridization in Ligularia indeed plays an important role in the species diversity.

Molecular phylogeny of Subtribe Artemisiinae (Asteraceae), including Artemisia and its allied and segregate genera

PubMed Central

Watson, Linda E; Bates, Paul L; Evans, Timothy M; Unwin, Matthew M; Estes, James R

2002-01-01

Background Subtribe Artemisiinae of Tribe Anthemideae (Asteraceae) is composed of 18 largely Asian genera that include the sagebrushes and mugworts. The subtribe includes the large cosmopolitan, wind-pollinated genus Artemisia, as well as several smaller genera and Seriphidium, that altogether comprise the Artemisia-group. Circumscription and taxonomic boundaries of Artemisia and the placements of these small segregate genera is currently unresolved. Results We constructed a molecular phylogeny for the subtribe using the internal transcribed spacers (ITS) of nuclear ribosomal DNA analyzed with parsimony, likelihood, and Bayesian criteria. The resulting tree is comprised of three major clades that correspond to the radiate genera (e.g., Arctanthemum and Dendranthema), and two clades of Artemisia species. All three clades have allied and segregate genera embedded within each. Conclusions The data support a broad concept of Artemisia s.l. that includes Neopallasia, Crossostephium, Filifolium, Seriphidium, and Sphaeromeria. However, the phylogeny excludes Elachanthemum, Kaschgaria, and Stilnolepis from the Artemisia-group. Additionally, the monophyly of the four subgenera of Artemisia is also not supported, with the exception of subg. Dracunculus. Homogamous, discoid capitula appear to have arisen in parallel four to seven times, with the loss of ray florets. Thus capitular morphology is not a reliable taxonomic character, which traditionally has been one of the defining characters. PMID:12350234

Historical climate change and speciation: neotropical seasonally dry forest plants show patterns of both tertiary and quaternary diversification.

PubMed Central

Pennington, R Toby; Lavin, Matt; Prado, Darién E; Pendry, Colin A; Pell, Susan K; Butterworth, Charles A

2004-01-01

Historical climate changes have had a major effect on the distribution and evolution of plant species in the neotropics. What is more controversial is whether relatively recent Pleistocene climatic changes have driven speciation, or whether neotropical species diversity is more ancient. This question is addressed using evolutionary rate analysis of sequence data of nuclear ribosomal internal transcribed spacers in diverse taxa occupying neotropical seasonally dry forests, including Ruprechtia (Polygonaceae), robinioid legumes (Fabaceae), Chaetocalyx and Nissolia (Fabaceae), and Loxopterygium (Anacardiaceae). Species diversifications in these taxa occurred both during and before the Pleistocene in Central America, but were primarily pre-Pleistocene in South America. This indicates plausibility both for models that predict tropical species diversity to be recent and that invoke a role for Pleistocene climatic change, and those that consider it ancient and implicate geological factors such as the Andean orogeny and the closure of the Panama Isthmus. Cladistic vicariance analysis was attempted to identify common factors underlying evolution in these groups. In spite of the similar Mid-Miocene to Pliocene ages of the study taxa, and their high degree of endemism in the different fragments of South American dry forests, the analysis yielded equivocal, non-robust patterns of area relationships. PMID:15212100

Sexual reproduction as the cause of heat resistance in the food spoilage fungus Byssochlamys spectabilis (anamorph Paecilomyces variotii).

PubMed

Houbraken, Jos; Varga, János; Rico-Munoz, Emilia; Johnson, Shawn; Samson, Robert A

2008-03-01

Paecilomyces variotii is a common cosmopolitan species that is able to spoil various food- and feedstuffs and is frequently encountered in heat-treated products. However, isolates from heat-treated products rarely form ascospores. In this study we examined by using molecular techniques and mating tests whether this species can undergo a sexual cycle and form ascospores. The population structure of this species was examined by analyzing the nuclear ribosomal internal transcribed spacer 1 (ITS1) and ITS2 and the 5.8S rRNA gene, as well as partial beta-tubulin, actin, and calmodulin gene sequences. Phylogenetic analyses revealed that P. variotii is a highly variable species. Partition homogeneity tests revealed that P. variotii has a recombining population structure. In addition to sequence analyses, mating experiments indicated that P. variotii is able to form ascomata and ascospores in culture in a heterothallic manner. The distribution of MAT1-1 and MAT1-2 genes showed a 1:1 ratio in the progeny of the mating experiments. From the sequence analyses and mating data we conclude that P. variotii is the anamorph of Talaromyces spectabilis and that it has a biallelic heterothallic mating system. Since Paecilomyces sensu stricto anamorphs group within Byssochlamys, a new combination Byssochlamys spectabilis is proposed.

Diversification and biogeography of Juniperus (Cupressaceae): variable diversification rates and multiple intercontinental dispersals.

PubMed

Mao, Kangshan; Hao, Gang; Liu, Jianquan; Adams, Robert P; Milne, Richard I

2010-10-01

• A central aim of biogeography is to understand when and how modern patterns of species diversity and distribution developed. Many plant groups have disjunct distributions within the Northern Hemisphere, but among these very few have been studied that prefer warm semi-arid habitats. • Here we examine the biogeography and diversification history of Juniperus, which occurs in semi-arid habitats through much of the Northern Hemisphere. A phylogeny was generated based on > 10,000 bp of cpDNA for 51 Juniperus species plus many outgroups. Phylogenies based on fewer species were also constructed based on nuclear internal transcribed spacer (nrITS) and combined nrITS/cpDNA data sets to check for congruence. Divergence time-scales and ancestral distributions were further inferred. • Both long dispersal and migration across land bridges probably contributed to the modern range of Juniperus, while long-term climatic changes and the uplift of the Qinghai-Tibetan plateau probably drove its diversification. Diversification apparently slowed down during climate-stable period of the Oligocene, and then speeded up from the Miocene onwards. • Juniperus probably originated in Eurasia, and was a part of the south Eurasian Tethyan vegetation of the Eocene to Oligocene. It reached America once at this time, once in the Miocene and once more recently.

Antarctomyces pellizariae sp. nov., a new, endemic, blue, snow resident psychrophilic ascomycete fungus from Antarctica.

PubMed

de Menezes, Graciéle C A; Godinho, Valéria M; Porto, Bárbara A; Gonçalves, Vívian N; Rosa, Luiz H

2017-03-01

In the present study, we have identified and characterised a new snow resident ascomycete blue stain fungus from Antarctica named Antarctomyces pellizariae sp. nov. Menezes, Godinho, Porto, Gonçalves and Rosa, using polyphasic taxonomy techniques. This fungal species was recovered from the seasonal snow of the Antarctic Peninsula. Antarctomyces pellizariae displayed different macro- and micromorphology when compared with A. psychrotrophicus Stchigel and Guarro, the only other Antarctomyces species reported until date. Antarctomyces pellizariae showed psychrophilic behavior and very low growth rate at 22-25 °C, quite different from A. psychrotrophicus that has a higher growth rate at mesophilic temperatures. In addition, micromorphological characteristics and the analysis of the nuclear rDNA internal transcribed spacer, β-tubulin, and RNA polymerase II regions revealed that A. pellizariae is a new species that is related to A. psychrotrophicus and Thelebolus species. Since the Antarctic Peninsula is reported to be one of the main regions of the earth experiencing the effects of global change in climate, species, such as A. pellizariae, might provide information about these effects on the endemic Antarctic biota. In addition, A. pellizariae displayed psychrophilic behavior and might be a source of interesting anti-freeze compounds that might prove useful in biotechnological processes.

Novel species of Botryosphaeriaceae associated with shoot blight of pistachio.

PubMed

Chen, ShuaiFei; Li, GuoQing; Liu, FeiFei; Michailides, Themis J

2015-01-01

Various species of phytopathogenic Botryosphaeriaceae were identified previously from pistachio trees worldwide. Disease symptoms caused by pathogens in Botryosphaeriaceae on pistachio include panicle and shoot blight, leaf defoliation, fruit discoloration and decay. In this study species of Botryosphaeriaceae were collected from blighted pistachio shoots in Arizona, USA, and Greece. The aims of this study were to identify these Botryosphaeriaceae isolates and to test their pathogenicity to pistachio. The fungi were identified based on comparisons of DNA sequence data of the nuclear rDNA internal transcribed spacer region (ITS), a partial translation elongation factor 1-alpha gene (TEF1), a partial β-tubulin gene (TUB2) and morphological characteristics. Results indicated that some isolates collected from pistachio represent two previously undescribed species, which we described here as Lasiodiplodia americana sp. nov. from the United States and Neofusicoccum hellenicum sp. nov. from Greece. Field inoculations of L. americana and N. hellenicum on branches of four pistachio cultivars showed that both L. americana and N. hellenicum are pathogenic on pistachio. The four pistachio cultivars differed in their susceptibility to the Botryosphaeriaceae species. Results of this study suggested that the two new species of Botryosphaeriaceae need to be monitored carefully to determine the distribution of these pathogens and the possible spread to other areas. © 2015 by The Mycological Society of America.

Curvularia malina sp. nov. incites a new disease of warm-season turfgrasses in the southeastern United States.

PubMed

Tomaso-Peterson, Maria; Jo, Young-Ki; Vines, Phillip L; Hoffmann, Federico G

2016-09-01

A novel species of Curvularia was identified as a foliar pathogen of Cynodon dactylon (bermudagrass) and Zoysia matrella (zoysiagrass), two important warm-season turfgrasses in the southeastern United States. Field symptoms were conspicuous chocolate brown to black spots in turf of both species on golf course putting greens and fairways. Leaves of plants within these spots exhibited prominent, black eyespot lesions from which a darkly pigmented fungus was consistently isolated. The fungus produced gray- to black-olivaceous mycelium within 10 d on potato dextrose agar at 25 C but never produced conidia despite numerous attempts to induce them. Field symptoms were reproduced in inoculated plants of both grasses, and re-isolation of the pathogen from symptomatic tissues confirmed its pathogenicity in fulfillment of Koch's postulates. A phylogenetic analysis was performed using sequence markers of internal nuclear ribosomal transcribed spacer region (ITS), glyceralde-hyde-3-phosphate dehydrogenase (GPD1) and translation elongation factor 1-α (TEF 1). The concatenated phylogenetic tree showed strong support for a new species within Curvularia that is distinctly divergent from other Curvularia spp. Therefore, the darkly pigmented pathogen of warm-season turfgrasses is described and illustrated as a new species, Curvularia malina. © 2016 by The Mycological Society of America.

Specific detection of Angiostrongylus cantonensis in the snail Achatina fulica using a loop-mediated isothermal amplification (LAMP) assay.

PubMed

Liu, Chun-Yan; Song, Hui-Qun; Zhang, Ren-Li; Chen, Mu-Xin; Xu, Min-Jun; Ai, Lin; Chen, Xiao-Guang; Zhan, Xi-Mei; Liang, Shao-Hui; Yuan, Zi-Guo; Lin, Rui-Qing; Zhu, Xing-Quan

2011-08-01

Angiostrongylus cantonensis, a rat lungworm, can cause eosinophilic meningitis and angiostrongyliasis in humans following ingestion of contaminated foods or intermediate/paratenic hosts with infective larvae. The snail Achatina fulica is one of the important intermediate hosts of A. cantonensis and is commonly eaten by humans in some countries. In the present study, we developed a loop-mediated isothermal amplification (LAMP) method for the specific detection of A. cantonensis in Ac. fulica. Primers for LAMP were designed based on the first internal transcribed spacer (ITS-1) of nuclear ribosomal DNA (rDNA) of A. cantonensis. Specificity tests showed that only the products of A. cantonensis were detected when DNA samples of A. cantonensis and the heterologous control samples Anisakis simplex s.s, Trichuris trichiura, Toxocara canis, Trichinella spiralis and Ascaris lumbricoides were amplified by LAMP. Sensitivity evaluation indicated that the LAMP assay is 10 times more sensitive than the conventional polymerase chain reaction (PCR) assay. The established LAMP assay is rapid, inexpensive and easy to be performed. It can be used in clinical applications for rapid and sensitive detection of A. cantonensis in snails, which has implications for the effective control of angiostrongyliasis. Copyright © 2011 Elsevier Ltd. All rights reserved.

A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda)

PubMed Central

Oono, Ryoko; Lefèvre, Emilie; Simha, Anita; Lutzoni, François

2015-01-01

Fungal endophytes represent one of the most ubiquitous plant symbionts on Earth and are phylogenetically diverse. The structure and diversity of endophyte communities have been shown to depend on host taxa and climate, but there have been relatively few studies exploring endophyte communities throughout host maturity. We compared foliar fungal endophyte communities between seedlings and adult trees of loblolly pines (Pinus taeda) at the same seasons and locations by culturing and culture-independent methods. We sequenced the internal transcribed spacer region and adjacent partial large subunit nuclear ribosomal RNA gene (ITS–LSU amplicon) to delimit operational taxonomic units and phylogenetically characterize the communities. Despite the lower infection frequency in seedlings compared to adult trees, seedling needles were receptive to a more diverse community of fungal endophytes. Culture-free method confirmed the presence of commonly cultured OTUs from adult needles but revealed several new OTUs from seedling needles that were not found with culturing methods. The two most commonly cultured OTUs in adults were rarely cultured from seedlings, suggesting that host age is correlated with a selective enrichment for specific endophytes. This shift in endophyte species dominance may be indicative of a functional change between these fungi and their loblolly pine hosts. PMID:26399186

Competitive Dominance among Strains of Luminous Bacteria Provides an Unusual Form of Evidence for Parallel Evolution in Sepiolid Squid-Vibrio Symbioses

PubMed Central

Nishiguchi, Michele K.; Ruby, Edward G.; McFall-Ngai, Margaret J.

1998-01-01

One of the principal assumptions in symbiosis research is that associated partners have evolved in parallel. We report here experimental evidence for parallel speciation patterns among several partners of the sepiolid squid-luminous bacterial symbioses. Molecular phylogenies for 14 species of host squids were derived from sequences of both the nuclear internal transcribed spacer region and the mitochondrial cytochrome oxidase subunit I; the glyceraldehyde phosphate dehydrogenase locus was sequenced for phylogenetic determinations of 7 strains of bacterial symbionts. Comparisons of trees constructed for each of the three loci revealed a parallel phylogeny between the sepiolids and their respective symbionts. Because both the squids and their bacterial partners can be easily cultured independently in the laboratory, we were able to couple these phylogenetic analyses with experiments to examine the ability of the different symbiont strains to compete with each other during the colonization of one of the host species. Our results not only indicate a pronounced dominance of native symbiont strains over nonnative strains, but also reveal a hierarchy of symbiont competency that reflects the phylogenetic relationships of the partners. For the first time, molecular systematics has been coupled with experimental colonization assays to provide evidence for the existence of parallel speciation among a set of animal-bacterial associations. PMID:9726861

Phylogeny and classification of Naucleeae s.l. (Rubiaceae) inferred from molecular (ITS, rBCL, and tRNT-F) and morphological data.

PubMed

Razafimandimbison, Sylvain G; Bremer, Birgitta

2002-07-01

Parsimony analyses of the tribe Naucleeae sensu lato (s.l.) using the noncoding internal transcribed spacer (ITS) regions of nuclear rDNA, the protein-coding rbcL and noncoding trnT-F regions of chloroplast DNA, and morphological data were performed to construct new intratribal classification, test the monophyly of previous subtribal circumscriptions, and evaluate the generic status of Naucleeae s.l. Fifty-two ITS, 45 rbcL, and 55 trnT-F new sequences are published here. Our study supports the monophyly of the subtribes Anthocephalidae, Mitragynae, Uncariae all sensu Haviland and Naucleinae sensu Ridsdale. There was no support for Cephalanthidae sensu Haviland and Adininae sensu Ridsdale. Naucleeae can be subdivided into six highly supported and morphologically distinct subtribes, Breoniinae, Cephalanthinae, Corynantheinae, Naucleinae, and Mitragyninae, Uncarinae, plus one, Adininae, which is poorly supported. The relationships among these subtribes were largely unresolved. We maintain the following 22 genera: Adina, Adinauclea, Breonadia, Breonia, Burttdavya, Cephalanthus, Gyrostipula, Haldina, Janotia, Ludekia, Metadina, Mitragyna, Myrmeconauclea, Nauclea, Neolamarckia, Neonauclea, Ochreinauclea, Pausinystalia, Pertusadina, Sarcocephalus, Sinoadina, and Uncaria. Pseudocinchona is reestablished. Corynanthe is restricted to C. paniculata and Hallea is reincluded in Mitragyna. Our results were inconclusive for assessing the relationships among Adina, Adinauclea, Metadina, and Pertusadina due to lack of resolution.

Diversity and taxonomy of endophytic xylariaceous fungi from medicinal plants of Dendrobium (Orchidaceae).

PubMed

Chen, Juan; Zhang, Li-Chun; Xing, Yong-Mei; Wang, Yun-Qiang; Xing, Xiao-Ke; Zhang, Da-Wei; Liang, Han-Qiao; Guo, Shun-Xing

2013-01-01

Dendrobium spp. are traditional Chinese medicinal plants, and the main effective ingredients (polysaccharides and alkaloids) have pharmacologic effects on gastritis infection, cancer, and anti-aging. Previously, we confirmed endophytic xylariaceous fungi as the dominant fungi in several Dendrobium species of tropical regions from China. In the present study, the diversity, taxonomy, and distribution of culturable endophytic xylariaceous fungi associated with seven medicinal species of Dendrobium (Orchidaceae) were investigated. Among the 961 endophytes newly isolated, 217 xylariaceous fungi (morphotaxa) were identified using morphological and molecular methods. The phylogenetic tree constructed using nuclear ribosomal internal transcribed spacer (ITS), large subunit of ribosomal DNA (LSU), and beta-tubulin sequences divided these anamorphic xylariaceous isolates into at least 18 operational taxonomic units (OTUs). The diversity of the endophytic xylariaceous fungi in these seven Dendrobium species was estimated using Shannon and evenness indices, with the results indicating that the dominant Xylariaceae taxa in each Dendrobium species were greatly different, though common xylariaceous fungi were found in several Dendrobium species. These findings implied that different host plants in the same habitats exhibit a preference and selectivity for their fungal partners. Using culture-dependent approaches, these xylariaceous isolates may be important sources for the future screening of new natural products and drug discovery.

High-throughput sequencing-based analysis of endogenetic fungal communities inhabiting the Chinese Cordyceps reveals unexpectedly high fungal diversity

PubMed Central

Xia, Fei; Chen, Xin; Guo, Meng-Yuan; Bai, Xiao-Hui; Liu, Yan; Shen, Guang-Rong; Li, Yu-Ling; Lin, Juan; Zhou, Xuan-Wei

2016-01-01

Chinese Cordyceps, known in Chinese as “DongChong XiaCao”, is a parasitic complex of a fungus (Ophiocordyceps sinensis) and a caterpillar. The current study explored the endogenetic fungal communities inhabiting Chinese Cordyceps. Samples were collected from five different geographical regions of Qinghai and Tibet, and the nuclear ribosomal internal transcribed spacer-1 sequences from each sample were obtained using Illumina high-throughput sequencing. The results showed that Ascomycota was the dominant fungal phylum in Chinese Cordyceps and its soil microhabitat from different sampling regions. Among the Ascomycota, 65 genera were identified, and the abundant operational taxonomic units showed the strongest sequence similarity to Ophiocordyceps, Verticillium, Pseudallescheria, Candida and Ilyonectria Not surprisingly, the genus Ophiocordyceps was the largest among the fungal communities identified in the fruiting bodies and external mycelial cortices of Chinese Cordyceps. In addition, fungal communities in the soil microhabitats were clustered separately from the external mycelial cortices and fruiting bodies of Chinese Cordyceps from different sampling regions. There was no significant structural difference in the fungal communities between the fruiting bodies and external mycelial cortices of Chinese Cordyceps. This study revealed an unexpectedly high diversity of fungal communities inhabiting the Chinese Cordyceps and its microhabitats. PMID:27625176

Diversity and Taxonomy of Endophytic Xylariaceous Fungi from Medicinal Plants of Dendrobium (Orchidaceae)

PubMed Central

Chen, Juan; Zhang, Li-Chun; Xing, Yong-Mei; Wang, Yun-Qiang; Xing, Xiao-Ke; Zhang, Da-Wei; Liang, Han-Qiao; Guo, Shun-Xing

2013-01-01

Dendrobium spp. are traditional Chinese medicinal plants, and the main effective ingredients (polysaccharides and alkaloids) have pharmacologic effects on gastritis infection, cancer, and anti-aging. Previously, we confirmed endophytic xylariaceous fungi as the dominant fungi in several Dendrobium species of tropical regions from China. In the present study, the diversity, taxonomy, and distribution of culturable endophytic xylariaceous fungi associated with seven medicinal species of Dendrobium (Orchidaceae) were investigated. Among the 961 endophytes newly isolated, 217 xylariaceous fungi (morphotaxa) were identified using morphological and molecular methods. The phylogenetic tree constructed using nuclear ribosomal internal transcribed spacer (ITS), large subunit of ribosomal DNA (LSU), and beta-tubulin sequences divided these anamorphic xylariaceous isolates into at least 18 operational taxonomic units (OTUs). The diversity of the endophytic xylariaceous fungi in these seven Dendrobium species was estimated using Shannon and evenness indices, with the results indicating that the dominant Xylariaceae taxa in each Dendrobium species were greatly different, though common xylariaceous fungi were found in several Dendrobium species. These findings implied that different host plants in the same habitats exhibit a preference and selectivity for their fungal partners. Using culture-dependent approaches, these xylariaceous isolates may be important sources for the future screening of new natural products and drug discovery. PMID:23472167

Long-distance dispersal or postglacial contraction? Insights into disjunction between Himalaya-Hengduan Mountains and Taiwan in a cold-adapted herbaceous genus, Triplostegia.

PubMed

Niu, Yan-Ting; Ye, Jian-Fei; Zhang, Jin-Long; Wan, Ji-Zhong; Yang, Tuo; Wei, Xiao-Xin; Lu, Li-Min; Li, Jian-Hua; Chen, Zhi-Duan

2018-01-01

Current disjunct patterns can result from long-distance dispersal or postglacial contraction. We herein investigate the evolutionary history of Triplostegia to elucidate the disjunction between the Himalaya-Hengduan Mountain region (HHM) and Taiwan (TW). Genetic structure of Triplostegia was investigated for 48 populations using sequences from five chloroplast loci and the ribosomal nuclear internal transcribed spacer. Divergence time estimation, ancestral area reconstruction, and species distribution modeling (SDM) were employed to examine the biogeographic history of Triplostegia . Substantial genetic differentiation among populations from southwestern China (SW), Central China (CC), and TW was detected. Triplostegia was inferred to have originated in SW, and diversification began during the late Miocene; CC was colonized in the mid-Pliocene, and TW was finally colonized in the early Pleistocene. SDM suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last interglacial in Triplostegia . Disjunction between HHM and TW in Triplostegia is most likely the consequence of topographic isolation and postglacial contraction. The potential climatic suitability areas for Triplostegia by 2070s (2061-2080) are predicted to slightly shrink and move northward. With continued global warming and human-induced deforestation, extinction risk may increase for the cold-adapted species, and appropriate strategies should be employed for ecosystem conservation.

DNA barcoding in Atlantic Forest plants: What is the best marker for Sapotaceae species identification?

PubMed Central

Vivas, Caio Vinicius; Moraes, Ramiris César Souza; Alves-Araújo, Anderson; Alves, Marccus; Mariano-Neto, Eduardo; van den Berg, Cássio; Gaiotto, Fernanda Amato

2014-01-01

The Atlantic Forest is a phytogeographic domain with a high rate of endemism and large species diversity. The Sapotaceae is a botanical family for which species identification in the Atlantic Forest is difficult. An approach that facilitates species identification in the Sapotaceae is urgently needed because this family includes threatened species and valuable timber species. In this context, DNA barcoding could provide an important tool for identifying species in the Atlantic Forest. In this work, we evaluated four plant barcode markers (matK, rbcL, trnH-psbA and the nuclear ribosomal internal transcribed spacer region - ITS) in 80 samples from 26 species of Sapotaceae that occur in the Atlantic Forest. ITS yielded the highest average interspecific distance (0.122), followed by trnH-psbA (0.019), matK (0.008) and rbcL (0.002). For species discrimination, ITS provided the best results, followed by matK, trnH-psbA and rbcL. Furthermore, the combined analysis of two, three or four markers did not result in higher rates of discrimination than obtained with ITS alone. These results indicate that the ITS region is the best option for molecular identification of Sapotaceae species from the Atlantic Forest. PMID:25505841

Genetic characterization and phylogenetic analysis of Eimeria arloingi in Iranian native kids.

PubMed

Khodakaram-Tafti, A; Hashemnia, M; Razavi, S M; Sharifiyazdi, H; Nazifi, S

2013-09-01

Among the 16 species of Eimeria from goats, Eimeria arloingi and Eimeria ninakohlyakimovae are regarded as the most pathogenic species in the world and cause clinical caprine coccidiosis. E. arloingi is known to be an important cause of coccidiosis in Iranian kids. Molecular analyses of two portions of nuclear ribosomal DNA (internal transcribed spacer1 (ITS1) and 18S rDNA) were used for the genetic characterization of the E. arloingi. Comparison of the sequencing data of E. arloingi obtained in the present study (ITS1: KC507793 and 18S rDNA: KC507792) with other Eimeria species in the GenBank database revealed a particularly close relationship between E. arloingi and Eimeria spp. from the cattle and sheep. The phylogram based on the ITS1 sequences shows that the E. arloingi, Eimeria bovis, and Eimeria zuernii formed a distinct group separate from the other remaining Eimeria spp. in cattle and poultry. In pairwise alignment, 18S rDNA sequence derived from E. arloingi showed 99% similarity to Eimeria ahsata with differences observed at only three nucleotides. This study showed that the ITS1 and 18S rDNA gene are useful genetic markers for the specific identification and differentiation of Eimeria spp. in ruminants.

New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones.

PubMed

Moorhouse-Gann, Rosemary J; Dunn, Jenny C; de Vere, Natasha; Goder, Martine; Cole, Nik; Hipperson, Helen; Symondson, William O C

2018-06-04

DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187-387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.

New Light on the Systematics of Fungi Associated with Attine Ant Gardens and the Description of Escovopsis kreiselii sp. nov.

PubMed Central

Meirelles, Lucas A.; Montoya, Quimi V.; Solomon, Scott E.; Rodrigues, Andre

2015-01-01

Since the formal description of fungi in the genus Escovopsis in 1990, only a few studies have focused on the systematics of this group. For more than two decades, only two Escovopsis species were described; however, in 2013, three additional Escovopsis species were formally described along with the genus Escovopsioides, both found exclusively in attine ant gardens. During a survey for Escovopsis species in gardens of the lower attine ant Mycetophylax morschi in Brazil, we found four strains belonging to the pink-colored Escovopsis clade. Careful examination of these strains revealed significant morphological differences when compared to previously described species of Escovopsis and Escovopsioides. Based on the type of conidiogenesis (sympodial), as well as morphology of conidiogenous cells (percurrent), non-vesiculated conidiophores, and DNA sequences, we describe the four new strains as a new species, Escovopsis kreiselii sp. nov. Phylogenetic analyses using three nuclear markers (Large subunit RNA; translation elongation factor 1-alpha; and internal transcribed spacer) from the new strains as well as available sequences in public databases confirmed that all known fungi infecting attine ant gardens comprise a monophyletic group within the Hypocreaceae family, with very diverse morphological characteristics. Specifically, Escovopsis kreiselii is likely associated with gardens of lower-attine ants and its pathogenicity remains uncertain. PMID:25617836

Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes.

PubMed

Gernandt, D S; Liston, A; Piñero, D

2001-12-01

The pinyon pines (Pinus subsection Cembroides), distributed in semiarid regions of the western United States and Mexico, include a mixture of relictual and more recently evolved taxa. To investigate relationships among the pinyons, we screened and partially sequenced 3000-bp clones of the nuclear ribosomal DNA internal transcribed spacer (ITS) region for 16 taxa from subsect. Cembroides and nine representatives from four other subsections of subgenus Strobus. Restriction digests of clones reveal within-individual heterogeneity, suggesting that concerted evolution is operating slowly on the ITS in pine species. Two ITS clones were identified as pseudogenes. Tandem subrepeats in the ITS1 form stem loops comparable to those in other genera of Pinaceae and may be promoting recombination between rDNA repeats, resulting in ITS1 chimeras. Within the pinyon clade, phylogenetic structure is present, but different clones from the same (or different) individuals of a species are polyphyletic, indicating that coalescence of ITS copies within individual genomes predates evolutionary divergence in the group. At the level of subsection and above, the ITS region corresponds well with morphological and cpDNA evidence. Except for P. nelsonii, the pinyons are monophyletic, with both subsect. Cembroides and P. nelsonii forming a clade with the foxtail and bristlecone pines (subsect. Balfourianae) of western North America.

Sharing the load: Mex67–Mtr2 cofunctions with Los1 in primary tRNA nuclear export

PubMed Central

Chatterjee, Kunal; Majumder, Shubhra; Wan, Yao; Shah, Vijay; Wu, Jingyan; Huang, Hsiao-Yun

2017-01-01

Eukaryotic transfer RNAs (tRNAs) are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function for protein synthesis. The evolutionarily conserved β-importin family member Los1 (Exportin-t) has been the only exporter known to execute nuclear export of newly transcribed intron-containing pre-tRNAs. Interestingly, LOS1 is unessential in all tested organisms. As tRNA nuclear export is essential, we previously interrogated the budding yeast proteome to identify candidates that function in tRNA nuclear export. Here, we provide molecular, genetic, cytological, and biochemical evidence that the Mex67–Mtr2 (TAP–p15) heterodimer, best characterized for its essential role in mRNA nuclear export, cofunctions with Los1 in tRNA nuclear export. Inactivation of Mex67 or Mtr2 leads to rapid accumulation of end-matured unspliced tRNAs in the nucleus. Remarkably, merely fivefold overexpression of Mex67–Mtr2 can substitute for Los1 in los1Δ cells. Moreover, in vivo coimmunoprecipitation assays with tagged Mex67 document that the Mex67 binds tRNAs. Our data also show that tRNA exporters surprisingly exhibit differential tRNA substrate preferences. The existence of multiple tRNA exporters, each with different tRNA preferences, may indicate that the proteome can be regulated by tRNA nuclear export. Thus, our data show that Mex67–Mtr2 functions in primary nuclear export for a subset of yeast tRNAs. PMID:29212662

Sharing the load: Mex67-Mtr2 cofunctions with Los1 in primary tRNA nuclear export.

PubMed

Chatterjee, Kunal; Majumder, Shubhra; Wan, Yao; Shah, Vijay; Wu, Jingyan; Huang, Hsiao-Yun; Hopper, Anita K

2017-11-01

Eukaryotic transfer RNAs (tRNAs) are exported from the nucleus, their site of synthesis, to the cytoplasm, their site of function for protein synthesis. The evolutionarily conserved β-importin family member Los1 (Exportin-t) has been the only exporter known to execute nuclear export of newly transcribed intron-containing pre-tRNAs. Interestingly, LOS1 is unessential in all tested organisms. As tRNA nuclear export is essential, we previously interrogated the budding yeast proteome to identify candidates that function in tRNA nuclear export. Here, we provide molecular, genetic, cytological, and biochemical evidence that the Mex67-Mtr2 (TAP-p15) heterodimer, best characterized for its essential role in mRNA nuclear export, cofunctions with Los1 in tRNA nuclear export. Inactivation of Mex67 or Mtr2 leads to rapid accumulation of end-matured unspliced tRNAs in the nucleus. Remarkably, merely fivefold overexpression of Mex67-Mtr2 can substitute for Los1 in los1 Δ cells. Moreover, in vivo coimmunoprecipitation assays with tagged Mex67 document that the Mex67 binds tRNAs. Our data also show that tRNA exporters surprisingly exhibit differential tRNA substrate preferences. The existence of multiple tRNA exporters, each with different tRNA preferences, may indicate that the proteome can be regulated by tRNA nuclear export. Thus, our data show that Mex67-Mtr2 functions in primary nuclear export for a subset of yeast tRNAs. © 2017 Chatterjee et al.; Published by Cold Spring Harbor Laboratory Press.

Phylogeography of Eomecon chionantha in subtropical China: the dual roles of the Nanling Mountains as a glacial refugium and a dispersal corridor.

PubMed

Tian, Shuang; Kou, Yixuan; Zhang, Zhirong; Yuan, Lin; Li, Derong; López-Pujol, Jordi; Fan, Dengmei; Zhang, Zhiyong

2018-02-09

Mountains have not only provided refuge for species, but also offered dispersal corridors during the Neogene and Quaternary global climate changes. Compared with a plethora of studies on the refuge role of China's mountain ranges, their dispersal corridor role has received little attention in plant phylogeographic studies. Using phylogeographic data of Eomecon chionantha Hance (Papaveraceae), this study explicitly tested whether the Nanling Mountains, which spans from west to east for more than 1000 km in subtropical China, could have functioned as a dispersal corridor during the late Quaternary in addition to a glacial refugium. Our analyses revealed a range-wide lack of phylogeographic structure in E. chionantha across three kinds of molecular markers [two chloroplast intergenic spacers, nuclear ribosomal internal transcribed spacer (nrITS), and six nuclear microsatellite loci]. Demographic inferences based on chloroplast and nrITS sequences indicated that E. chionantha could have experienced a strong postglacial range expansion between 6000 and 1000 years ago. Species distribution modelling showed that the Nanling Mountains and the eastern Yungui Plateau were the glacial refugia of E. chionantha. Reconstruction of dispersal corridors indicated that the Nanling Mountains also have acted as a corridor of population connectivity for E. chionantha during the late Quaternary. Our results suggest that the Nanling Mountains may acted dual roles as a dispersal corridor in east-west direction and as a glacial refugium in subtropical China during the late Quaternary. The population connectivity mediated by the mountain range and a strong postglacial range expansion are the most likely reasons for the lack of phylogeographic structure in E. chionantha. The hypothesis of dual roles of the mountain range presented here sheds new insights into the phylogeographic patterns of organisms in subtropical China.

Molecular phylogenetic and scanning electron microscopical analyses places the Choanephoraceae and the Gilbertellaceae in a monophyletic group within the Mucorales (Zygomycetes, Fungi).

PubMed

Voigt, Kerstin; Olsson, L

2008-09-01

A multi-gene genealogy based on maximum parsimony and distance analyses of the exonic genes for actin (act) and translation elongation factor 1 alpha (tef), the nuclear genes for the small (18S) and large (28S) subunit ribosomal RNA (comprising 807, 1092, 1863, 389 characters, respectively) of all 50 genera of the Mucorales (Zygomycetes) suggests that the Choanephoraceae is a monophyletic group. The monotypic Gilbertellaceae appears in close phylogenetic relatedness to the Choanephoraceae. The monophyly of the Choanephoraceae has moderate to strong support (bootstrap proportions 67% and 96% in distance and maximum parsimony analyses, respectively), whereas the monophyly of the Choanephoraceae-Gilbertellaceae clade is supported by high bootstrap values (100% and 98%). This suggests that the two families can be joined into one family, which leads to the elimination of the Gilbertellaceae as a separate family. In order to test this hypothesis single-locus neighbor-joining analyses were performed on nuclear genes of the 18S, 5.8S, 28S and internal transcribed spacer (ITS) 1 ribosomal RNA and the translation elongation factor 1 alpha (tef) and beta tubulin (betatub) nucleotide sequences. The common monophyletic origin of the Choanephoraceae-Gilbertellaceae clade could be confirmed in all gene trees and by investigation of their ultrastructure. Sporangia with persistent, sutured walls splitting in half at maturity and ellipsoidal sporangiospores with striated ornamentations and polar ciliate appendages arising from spores in persistent sporangia and dehiscent sporangiola represent synapomorphic characters of this group. We discuss our data in the context of the historical development of their taxonomy and physiology and propose a reduction of the two families to one family, the Choanephoraceae sensu lato comprising species which are facultative plant pathogens and parasites, especially in subtropical to tropical regions.

Isolation of the Entomopathogenic Fungal Strain Cod-MK1201 from a Cicada Nymph and Assessment of Its Antibacterial Activities.

PubMed

Sangdee, Kusavadee; Nakbanpote, Woranan; Sangdee, Aphidech

2015-01-01

The entomopathogenic fungus Cod-MK1201 was isolated from a dead cicada nymph. Three regions of ribosomal nuclear DNA, the internal transcribed spacers of nuclear ribosomal DNA repeats (ITS), the partial small subunit of rDNA (nrSSU) , and the partial large subunit of rDNA (nrLSU), and two protein-coding regions, the elongation factor 1α (EF-1α), and the largest subunit of the RNA polymerase II (rpb1) gene, were sequenced and used for fungal identification. The phylogenetic analysis of the ITS and the combined data set of the five genes indicated that the fungal isolate Cod-MK1201 is a new strain of Cordyceps sp. that is closely related to Cordyceps nipponica and C. kanzashiana. Crude extracts of mycelium-cultured Cod-MK1201 were obtained using distilled water and 50% (v/v) ethanol, and the antibacterial activity of each was determined. Both extracts had activity against Gram-positive and Gram-negative bacteria, but the ethanol extract was the more potent of the two. The antibacterial activity of the protein fractions of these extracts was also determined. The protein fraction from the ethanol extract was more antibacterial than the protein fraction from the aqueous extract. Three antibacterial constituents including adenosine, the total phenolic content (TPC), and the total flavonoid content (TFC) was also determined. The results showed that the adenosine content, the TPC, and the TFC of the ethanol extract were more active than those of the aqueous extract. Moreover, synergism was detected between these antibacterial constituents. In conclusion, the entomopathogenic fungal isolate Cod-MK1201 represents a natural source of antibacterial agents.

Hypothesis testing clarifies the systematics of the main Central American Chagas disease vector, Triatoma dimidiata (Latreille, 1811), across its geographic range.

PubMed

Dorn, Patricia L; de la Rúa, Nicholas M; Axen, Heather; Smith, Nicholas; Richards, Bethany R; Charabati, Jirias; Suarez, Julianne; Woods, Adrienne; Pessoa, Rafaela; Monroy, Carlota; Kilpatrick, C William; Stevens, Lori

2016-10-01

The widespread and diverse Triatoma dimidiata is the kissing bug species most important for Chagas disease transmission in Central America and a secondary vector in Mexico and northern South America. Its diversity may contribute to different Chagas disease prevalence in different localities and has led to conflicting systematic hypotheses describing various populations as subspecies or cryptic species. To resolve these conflicting hypotheses, we sequenced a nuclear (internal transcribed spacer 2, ITS-2) and mitochondrial gene (cytochrome b) from an extensive sampling of T. dimidiata across its geographic range. We evaluated the congruence of ITS-2 and cyt b phylogenies and tested the support for the previously proposed subspecies (inferred from ITS-2) by: (1) overlaying the ITS-2 subspecies assignments on a cyt b tree and, (2) assessing the statistical support for a cyt b topology constrained by the subspecies hypothesis. Unconstrained phylogenies inferred from ITS-2 and cyt b are congruent and reveal three clades including two putative cryptic species in addition to T. dimidiata sensu stricto. Neither the cyt b phylogeny nor hypothesis testing support the proposed subspecies inferred from ITS-2. Additionally, the two cryptic species are supported by phylogenies inferred from mitochondrially-encoded genes cytochrome c oxidase I and NADH dehydrogenase 4. In summary, our results reveal two cryptic species. Phylogenetic relationships indicate T. dimidiata sensu stricto is not subdivided into monophyletic clades consistent with subspecies. Based on increased support by hypothesis testing, we propose an updated systematic hypothesis for T. dimidiata based on extensive taxon sampling and analysis of both mitochondrial and nuclear genes. Copyright © 2016 Elsevier B.V. All rights reserved.

Influence of Pleistocene glacial/interglacial cycles on the genetic structure of the mistletoe cactus Rhipsalis baccifera (Cactaceae) in Mesoamerica.

PubMed

Ornelas, Juan Francisco; Rodríguez-Gómez, Flor

2015-01-01

Phylogeographical work on cloud forest-adapted species provides inconsistent evidence on cloud forest dynamics during glacial cycles. A study of Rhipsalis baccifera (Cactaceae), a bird-dispersed epiphytic mistletoe cactus, was conducted to investigate genetic variation at sequence data from nuclear [internal transcribed spacer (ITS), 677 bp] and chloroplast (rpl32-trnL, 1092bp) DNA for 154 individuals across the species range in Mesoamerica to determine if such patterns are consistent with the expansion/contraction model of cloud forest during glacial cycles. We conducted population and spatial genetic analyses as well as gene flow and divergence time estimates between 24 populations comprising the distribution of R. baccifera in Mexico and Guatemala to gain insight of the evolutionary history of these populations, and a complementary species distribution modeling approach to frame information derived from the genetic analyses into an explicit paleoecological context. The results revealed a phylogeographical break at the Isthmus of Tehuantepec, and high levels of genetic diversity among populations and cloud forest areas. Despite the genetic differentiation of some R. baccifera populations, the widespread ITS ribotypes suggest effective nuclear gene flow via pollen and population differentiation shown by the rpl32-trnL suggests more restricted seed flow. Predictions of species distribution models under past last glacial maximum (LGM) climatic conditions and a significant signal of demographic expansion suggest that R. baccifera populations experienced a range expansion tracking the conditions of the cloud forest distribution and shifted to the lowlands with population connectivity during the LGM. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Characteristics and molecular phylogeny of Fasciola flukes from Bangladesh, determined based on spermatogenesis and nuclear and mitochondrial DNA analyses.

PubMed

Mohanta, Uday Kumar; Ichikawa-Seki, Madoka; Shoriki, Takuya; Katakura, Ken; Itagaki, Tadashi

2014-07-01

This study aimed to precisely discriminate Fasciola spp. based on DNA sequences of nuclear internal transcribed spacer 1 (ITS1) and mitochondrial nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 1 (nad1) gene. We collected 150 adult flukes from the bile ducts of cattle, buffaloes, sheep, and goats from six different regions of Bangladesh. Spermatogenic status was determined by analyzing stained seminal vesicles. The ITS1 types were analyzed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The nad1 haplotypes were identified based on PCR and direct sequencing and analyzed phylogenetically by comparing with nad1 haplotypes of Fasciola spp. from other Asian countries. Of the 127 aspermic flukes, 98 were identified as Fg type in ITS1, whereas 29 were identified as Fh/Fg type, indicating a combination of ITS1 sequences of Fasciola hepatica and Fasciola gigantica. All the 127 aspermic flukes showed Fsp-NDI-Bd11 in nad1 haplotype with nucleotide sequences identical to aspermic Fasciola sp. from Asian countries. Further, 20 spermic flukes were identified as F. gigantica based on their spermatogenic status and Fg type in ITS1. F. gigantica population was thought to be introduced into Bangladesh considerably earlier than the aspermic Fasciola sp. because 11 haplotypes with high haplotype diversity were detected from the F. gigantica population. However, three flukes from Bangladesh could not be precisely identified, because their spermatogenic status, ITS1 types, and nad1 haplotypes were ambiguous. Therefore, developing a robust method to distinguish aspermic Fasciola sp. from other Fasciola species is necessary in the future.

Phylogeography of ostreopsis along west Pacific coast, with special reference to a novel clade from Japan.

PubMed

Sato, Shinya; Nishimura, Tomohiro; Uehara, Keita; Sakanari, Hiroshi; Tawong, Wittaya; Hariganeya, Naohito; Smith, Kirsty; Rhodes, Lesley; Yasumoto, Takeshi; Taira, Yosuke; Suda, Shoichiro; Yamaguchi, Haruo; Adachi, Masao

2011-01-01

A dinoflagellate genus Ostreopsis is known as a potential producer of Palytoxin derivatives. Palytoxin is the most potent non-proteinaceous compound reported so far. There has been a growing number of reports on palytoxin-like poisonings in southern areas of Japan; however, the distribution of Ostreopsis has not been investigated so far. Morphological plasticity of Ostreopsis makes reliable microscopic identification difficult so the employment of molecular tools was desirable. In total 223 clones were examined from samples mainly collected from southern areas of Japan. The D8-D10 region of the nuclear large subunit rDNA (D8-D10) was selected as a genetic marker and phylogenetic analyses were conducted. Although most of the clones were unable to be identified, there potentially 8 putative species established during this study. Among them, Ostreopsis sp. 1-5 did not belong to any known clade, and each of them formed its own clade. The dominant species was Ostreopsis sp. 1, which accounted for more than half of the clones and which was highly toxic and only distributed along the Japanese coast. Comparisons between the D8-D10 and the Internal Transcribed Spacer (ITS) region of the nuclear rDNA, which has widely been used for phylogenetic/phylogeographic studies in Ostreopsis, revealed that the D8-D10 was less variable than the ITS, making consistent and reliable phylogenetic reconstruction possible. This study unveiled a surprisingly diverse and widespread distribution of Japanese Ostreopsis. Further study will be required to better understand the phylogeography of the genus. Our results posed the urgent need for the development of the early detection/warning systems for Ostreopsis, particularly for the widely distributed and strongly toxic Ostreopsis sp. 1. The D8-D10 marker will be suitable for these purposes.

Non-coding RNA derived from the region adjacent to the human HO-1 E2 enhancer selectively regulates HO-1 gene induction by modulating Pol II binding

PubMed Central

Maruyama, Atsushi; Mimura, Junsei; Itoh, Ken

2014-01-01

Recent studies have disclosed the function of enhancer RNAs (eRNAs), which are long non-coding RNAs transcribed from gene enhancer regions, in transcriptional regulation. However, it remains unclear whether eRNAs are involved in the regulation of human heme oxygenase-1 gene (HO-1) induction. Here, we report that multiple nuclear-enriched eRNAs are transcribed from the regions adjacent to two human HO-1 enhancers (i.e. the distal E2 and proximal E1 enhancers), and some of these eRNAs are induced by the oxidative stress-causing reagent diethyl maleate (DEM). We demonstrated that the expression of one forward direction (5′ to 3′) eRNA transcribed from the human HO-1 E2 enhancer region (named human HO-1enhancer RNA E2-3; hereafter called eRNA E2-3) was induced by DEM in an NRF2-dependent manner in HeLa cells. Conversely, knockdown of BACH1, a repressor of HO-1 transcription, further increased DEM-inducible eRNA E2-3 transcription as well as HO-1 expression. In addition, we showed that knockdown of eRNA E2-3 selectively down-regulated DEM-induced HO-1 expression. Furthermore, eRNA E2-3 knockdown attenuated DEM-induced Pol II binding to the promoter and E2 enhancer regions of HO-1 without affecting NRF2 recruitment to the E2 enhancer. These findings indicate that eRNAE2-3 is functional and is required for HO-1 induction. PMID:25404134

The Power of Integrators, Financiers, and Insurers to Reduce Proliferation Risks: Nuclear Dual-Use Goods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weise, Rachel A.; Hund, Gretchen

2015-05-01

Globalization of manufacturing supply chains has changed the nature of nuclear proliferation. Before 1991, nonproliferation efforts focused almost exclusively on limiting the spread of materials and equipment specifically designed for nuclear use -- reactors, centrifuges, and fissile material. Dual-use items, those items with both nuclear and non-nuclear applications, were not closely scrutinized or controlled. However, in 1991 the international community discovered that Iraq had developed a fairly sophisticated nuclear weapons program by importing dual-use items; this discovery spurred the international community to increase controls on dual-use technologies. Despite these international efforts, dual-use items are still a challenge for those seekingmore » to limit proliferation.« less

Recent studies implicate the nucleolus as the major site of nuclear translation.

PubMed

McLeod, Tina; Abdullahi, Akilu; Li, Min; Brogna, Saverio

2014-08-01

The nucleolus is the most prominent morphological feature within the nucleus of eukaryotic cells and is best known for its role in ribosome biogenesis. It forms around highly transcribed ribosomal RNA gene repeats which yield precursor rRNAs that are co-transcriptionally processed, folded and, while still within the nucleolus, associate with most of the ribosomal proteins. The nucleolus is therefore often thought of as a factory for making ribosomal subunits, which are exported as inactive precursors to the cytoplasm where late maturation makes them capable of mRNA binding and translation initiation. However, recent studies have shown substantial evidence for the presence of functional, translation competent ribosomal subunits within the nucleus, particularly in the nucleolus. These observations raise the intriguing possibility that the nucleolus, as well as being a ribosome factory, is also an important nuclear protein-synthesis plant.

Identification and characterization of a HeLa nuclear protein that specifically binds to the trans-activation-response (TAR) element of human immunodeficiency virus.

PubMed Central

Marciniak, R A; Garcia-Blanco, M A; Sharp, P A

1990-01-01

Human immunodeficiency virus type 1 RNAs contain a sequence, trans-activation-response (TAR) element, which is required for tat protein-mediated trans-activation of viral gene expression. We have identified a nuclear protein from extracts of HeLa cells that binds to the TAR element RNA in a sequence-specific manner. The binding of this 68-kDa polypeptide was detected by UV cross-linking proteins to TAR element RNA transcribed in vitro. Competition experiments were performed by using a partially purified preparation of the protein to quantify the relative binding affinities of TAR element RNA mutants. The binding affinity of the TAR mutants paralleled the reported ability of those mutants to support tat trans-activation in vivo. We propose that this cellular protein moderates TAR activity in vivo. Images PMID:2333305

Deploying Nuclear Detection Systems: A Proposed Strategy for Combating Nuclear Terrorism

DTIC Science & Technology

2007-07-01

lower cost than other gamma radiation detectors (if increased count rate is all one is looking for). Low cost makes plastic scintillation detectors...material, particularly enriched uranium and plutonium, the basic fuel for nuclear bombs. • Measures to strengthen international institutions to... uranium to specifications required for a nuclear weapon.1 This illicit shipment of centrifuges was part of an international nuclear materials

Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export.

PubMed

Karijolich, John; Zhao, Yang; Alla, Ravi; Glaunsinger, Britt

2017-06-02

Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28 270 SINE loci, with ∼50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA-RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Searching for non-transposable targets of planarian nuclear PIWI in pluripotent stem cells and differentiated cells.

PubMed

Kashima, Makoto; Agata, Kiyokazu; Shibata, Norito

2018-06-01

Nuclear PIWIs together with their guide RNAs (piRNAs) epigenetically silence various genes including transposons in many organisms. In planarians, the nuclear piwi family gene, DjpiwiB is specifically transcribed in adult pluripotent stem cells (adult PSC, neoblast), but not in differentiated cells. However, the protein accumulates in the nuclei of both neoblasts and their descendant differentiated cells. Interestingly, PIWI(DjPiwiB)-piRNA complexes are indispensable for the repression of transposable genes at the onset of differentiation from neoblasts. Here, we conducted a comparative transcriptome analysis between control and DjpiwiB(RNAi) animals to identify non-transposable target genes of the DjPiwiB-piRNA complexes. Using bioinformatic analyses and RNAi we demonstrate that DjPiwiB-piRNA complexes are required for the proper expression of Djmcm2 and Djhistone h4 in neoblasts and that DjPiwiB-piRNA complexes regulate the transient expression of Djcalu during neoblast differentiation. Thus, DjPiwiB-piRNA complexes regulate the correct expression patterns during neoblast self-renewal and differentiation. © 2018 Japanese Society of Developmental Biologists.

Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export

PubMed Central

Zhao, Yang; Alla, Ravi

2017-01-01

Abstract Short interspersed nuclear elements (SINEs) are retrotransposons evolutionarily derived from endogenous RNA Polymerase III RNAs. Though SINE elements have undergone exaptation into gene regulatory elements, how transcribed SINE RNA impacts transcriptional and post-transcriptional regulation is largely unknown. This is partly due to a lack of information regarding which of the loci have transcriptional potential. Here, we present an approach (short interspersed nuclear element sequencing, SINE-seq), which selectively profiles RNA Polymerase III-derived SINE RNA, thereby identifying transcriptionally active SINE loci. Applying SINE-seq to monitor murine B2 SINE expression during a gammaherpesvirus infection revealed transcription from 28 270 SINE loci, with ∼50% of active SINE elements residing within annotated RNA Polymerase II loci. Furthermore, B2 RNA can form intermolecular RNA–RNA interactions with complementary mRNAs, leading to nuclear retention of the targeted mRNA via a mechanism involving p54nrb. These findings illuminate a pathway for the selective regulation of mRNA export during stress via retrotransposon activation. PMID:28334904

Assuaging Nuclear Energy Risks: The Angarsk International Uranium Enrichment Center

NASA Astrophysics Data System (ADS)

Myers, Astasia

2011-06-01

The recent nuclear renaissance has motivated many countries, especially developing nations, to plan and build nuclear power reactors. However, domestic low enriched uranium demands may trigger nations to construct indigenous enrichment facilities, which could be redirected to fabricate high enriched uranium for nuclear weapons. The potential advantages of establishing multinational uranium enrichment sites are numerous including increased low enrichment uranium access with decreased nuclear proliferation risks. While multinational nuclear initiatives have been discussed, Russia is the first nation to actualize this concept with their Angarsk International Uranium Enrichment Center (IUEC). This paper provides an overview of the historical and modern context of the multinational nuclear fuel cycle as well as the evolution of Russia's IUEC, which exemplifies how international fuel cycle cooperation is an alternative to domestic facilities.

Pathways in Learning to Teach Elementary Science: Navigating Contexts, Roles, Affordances and Constraints

NASA Astrophysics Data System (ADS)

Smith, Deborah C.; Jang, Shinho

2011-12-01

This case study of a fifth-year elementary intern's pathway in learning to teach science focused on her science methods course, placement science teaching, and reflections as a first-year teacher. We studied the sociocultural contexts within which the intern learned, their affordances and constraints, and participants' perspectives on their roles and responsibilities, and her learning. Semi-structured interviews were conducted with all participants. Audiotapes of the science methods class, videotapes of her science teaching, and field notes were collected. Data were transcribed and searched for affordances or constraints within contexts, perspectives on roles and responsibilities, and how views of her progress changed. Findings show the intern's substantial progress, the ways in which affordances sometimes became constraints, and participants' sometimes contradictory perspectives.

International perceptions of US nuclear policy.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stanley, Elizabeth A.

The report presents a summary of international perceptions and beliefs about US nuclear policy, focusing on four countries--China, Iran, Pakistan and Germany--chosen because they span the spectrum of states with which the United States has relationships. A paradox is pointed out: that although the goal of US nuclear policy is to make the United States and its allies safer through a policy of deterrence, international perceptions of US nuclear policy may actually be making the US less safe by eroding its soft power and global leadership position. Broadly held perceptions include a pattern of US hypocrisy and double standards--one setmore » for the US and its allies, and another set for all others. Importantly, the US nuclear posture is not seen in a vacuum, but as one piece of the United States behavior on the world stage. Because of this, the potential direct side effects of any negative international perceptions of US nuclear policy can be somewhat mitigated, dependent on other US policies and actions. The more indirect and long term relation of US nuclear policy to US international reputation and soft power, however, matters immensely to successful multilateral and proactive engagement on other pressing global issues.« less

Divergent population genetic structure of the endangered Helianthemum (Cistaceae) and its implication to conservation in northwestern China

Treesearch

Zhihao Su; Bryce A. Richardson; Li Zhuo; Xiaolong Jiang

2017-01-01

Population genetic studies provide a foundation for conservation planning, especially for endangered species. Three chloroplast SSRs (mtrnSf-trnGr, mtrnL2-trnF, and mtrnL5-trnL3) and the internal transcribed spacer were used to examine the population structure of Helianthemum in northwestern China. A total of 15 populations of the genus were collected. Nine chloroplast...

PCR-based identification of Erysiphe pulchra and Phyllactinia guttata from Cornus florida using ITS-specific primers

Treesearch

M. T. Mmbaga; N. B. Klopfenstein; M. -S. Kim; N. C. Mmbaga

2004-01-01

The internal transcribed spacer (ITS) regions of rDNA and the intervening 5.8S rRNA gene for the powdery mildew fungi Erysiphe (sect. Microsphaera) pulchra and Phyllactinia guttata were amplified using standard polymerase chain reaction (PCR) protocols and the universal primer pairs, ITS1 and ITS4. PCR products for ITS were analysed by electrophoresis in a 1.5% agarose...

Isolation and molecular typing of Naegleria fowleri from the brain of a cow that died of primary amebic meningoencephalitis.

PubMed

Visvesvara, Govinda S; De Jonckheere, Johan F; Sriram, Rama; Daft, Barbara

2005-08-01

Naegleria fowleri causes an acute and rapidly fatal central nervous system infection called primary amebic meningoencephalitis (PAM) in healthy children and young adults. We describe here the identification of N. fowleri isolated from the brain of one of several cows that died of PAM based on sequencing of the internal transcribed spacers, including the 5.8S rRNA genes.

Phylogenetic and ecological analyses of soil and sporocarp DNA sequences reveal high diversity and strong habitat partitioning in the boreal ectomycorrhizal genus Russula (Russulales; Basidiomycota)

Treesearch

József Geml; Gary A. Laursen; Ian C. Herriott; Jack M. McFarland; Michael G. Booth; Niall Lennon; H. Chad Nusbaum; D. Lee Taylor

2010-01-01

Although critical for the functioning of ecosystems, fungi are poorly known in high-latitude regions. Here, we provide the first genetic diversity assessment of one of the most diverse and abundant ectomycorrhizal genera in Alaska: Russula. We analyzed internal transcribed spacer rDNA sequences from sporocarps and soil samples using phylogenetic...

Data mining for discovery of endophytic and epiphytic fungal diversity in short-read genomic data from deciduous trees

Treesearch

Nicholas R. ​LaBonte; James Jacobs; Aziz Ebrahimi; Shaneka Lawson; Keith Woeste

2018-01-01

High-throughput sequencing of DNA barcodes, such as the internal transcribed spacer (ITS) of the 16s rRNA sequence, has expanded the ability of researchers to investigate the endophytic fungal communities of living plants. With a large and growing database of complete fungal genomes, it may be possible to utilize portions of fungal symbiont genomes outside conventional...

PCR-Internal Transcribed Spacer (ITS) genes sequencing and phylogenetic analysis of clinical and environmental Aspergillus species associated with HIV-TB co infected patients in a hospital in Abeokuta, southwestern Nigeria.

PubMed

Shittu, Olufunke Bolatito; Adelaja, Oluwabunmi Molade; Obuotor, Tolulope Mobolaji; Sam-Wobo, Sam Olufemi; Adenaike, Adeyemi Sunday

2016-03-01

Aspergillosis has been identified as one of the hospital acquired infections but the contribution of water and inhouse air as possible sources of Aspergillus infection in immunocompromised individuals like HIV-TB patients have not been studied in any hospital setting in Nigeria. To identify and investigate genetic relationship between clinical and environmental Aspergillus sp. associated with HIV-TB co infected patients. DNA extraction, purification, amplification and sequencing of Internal Transcribed Spacer (ITS) genes were performed using standard protocols. Similarity search using BLAST on NCBI was used for species identification and MEGA 5.0 was used for phylogenetic analysis. Analyses of sequenced ITS genes of selected fourteen (14) Aspergillus isolates identified in the GenBank database revealed Aspergillus niger (28.57%), A. tubingensis (7.14%), A. flavus (7.14%) and A. fumigatus (57.14%). Aspergillus in sputum of HIV patients were Aspergillus niger, A. fumigatus, A. tubingensis and A. flavus. Also, A. niger and A. fumigatus were identified from water and open-air. Phylogenetic analysis of sequences yielded genetic relatedness between clinical and environmental isolates. Water and air in health care settings in Nigeria are important sources of Aspergillus sp. for HIV-TB patients.

Characterization of four species of Trichuris (Nematoda: Enoplida) by their second internal transcribed spacer ribosomal DNA sequence.

PubMed

Oliveros, R; Cutillas, C; De Rojas, M; Arias, P

2000-12-01

Adult worms of Trichuris ovis and T. globulosa were collected from Ovis aries (sheep) and Capra hircus (goats). T. suis was isolated from Sus scrofa domestica (swine) and T. leporis was isolated from Lepus europaeus (rabbits) in Spain. Genomic DNA was isolated and a ribosomal internal transcribed spacer (ITS2) was amplified and sequenced using polymerase-chain-reaction (PCR) techniques. The ITS2 of T. ovis and T. globulosa was 407 nucleotides in length and had a GC content of about 62%. Furthermore, the ITS2 of T. suis and T. leporis was 534 and 418 nucleotides in length and had a GC content of about 64.8% and 62.4%, respectively. There was evidence of slight variation in the sequence within individuals of all species analyzed, indicating intraindividual variation in the sequence of different copies of the ribosomal DNA. Furthermore, low-level intraspecific variation was detected. Sequence analyses of ITS2 products of T. ovis and T. globulosa demonstrated no sequence difference between them. Nevertheless, differences were detected between the ITS2 sequences of T. suis, T. leporis, and T. ovis, indicating that Trichuris species can reliably be differentiated by their ITS2 sequences and PCR-linked restriction-fragment-length polymorphism (RFLP).

Specific detection and identification of [Actinobacillus] muris by PCR using primers targeting the 16S-23S rRNA internal transcribed spacer regions.

PubMed

Benga, Laurentiu; Benten, W Peter M; Engelhardt, Eva; Gougoula, Christina; Sager, Martin

2013-08-01

[Actinobacillus] muris represents along with [Pasteurella] pneumotropica the most prevalent Pasteurellaceae species isolated from the laboratory mouse. Despite the biological and economic importance of Pasteurellaceae in relation to experimental animals, no molecular based methods for the identification of [A.] muris are available. The aim of the present investigation was to develop a PCR method allowing detection and identification of [A.] muris. In this assay, a Pasteurellaceae common forward primer based on a conserved region of the 16S rRNA gene was used in conjunction with two different reverse primers specific for [A.] muris, targeting the 16S-23S internal transcribed spacer sequences. The specificity of the assay was tested against 78 reference and clinical isolates of Pasteurellaceae, including 37 strains of [A.] muris. In addition, eight other mice associated bacterial species which could pose a diagnostic problem were included. The assay showed 100% sensitivity and 97.95% specificity. Identification of the clinical isolates was validated by ITS profiling and when necessary by 16S rRNA sequencing. This multiplex PCR represents the first molecular tool able to detect [A.] muris and may become a reliable alternative to the present diagnostic methods. Copyright © 2013 Elsevier B.V. All rights reserved.

Improved Selection of Internal Transcribed Spacer-Specific Primers Enables Quantitative, Ultra-High-Throughput Profiling of Fungal Communities

PubMed Central

Bokulich, Nicholas A.

2013-01-01

Ultra-high-throughput sequencing (HTS) of fungal communities has been restricted by short read lengths and primer amplification bias, slowing the adoption of newer sequencing technologies to fungal community profiling. To address these issues, we evaluated the performance of several common internal transcribed spacer (ITS) primers and designed a novel primer set and work flow for simultaneous quantification and species-level interrogation of fungal consortia. Primer comparison and validation were predicted in silico and by sequencing a “mock community” of mixed yeast species to explore the challenges of amplicon length and amplification bias for reconstructing defined yeast community structures. The amplicon size and distribution of this primer set are smaller than for all preexisting ITS primer sets, maximizing sequencing coverage of hypervariable ITS domains by very-short-amplicon, high-throughput sequencing platforms. This feature also enables the optional integration of quantitative PCR (qPCR) directly into the HTS preparatory work flow by substituting qPCR with these primers for standard PCR, yielding quantification of individual community members. The complete work flow described here, utilizing any of the qualified primer sets evaluated, can rapidly profile mixed fungal communities and capably reconstructed well-characterized beer and wine fermentation fungal communities. PMID:23377949

Nucleotide sequencing and identification of some wild mushrooms.

PubMed

Das, Sudip Kumar; Mandal, Aninda; Datta, Animesh K; Gupta, Sudha; Paul, Rita; Saha, Aditi; Sengupta, Sonali; Dubey, Priyanka Kumari

2013-01-01

The rDNA-ITS (Ribosomal DNA Internal Transcribed Spacers) fragment of the genomic DNA of 8 wild edible mushrooms (collected from Eastern Chota Nagpur Plateau of West Bengal, India) was amplified using ITS1 (Internal Transcribed Spacers 1) and ITS2 primers and subjected to nucleotide sequence determination for identification of mushrooms as mentioned. The sequences were aligned using ClustalW software program. The aligned sequences revealed identity (homology percentage from GenBank data base) of Amanita hemibapha [CN (Chota Nagpur) 1, % identity 99 (JX844716.1)], Amanita sp. [CN 2, % identity 98 (JX844763.1)], Astraeus hygrometricus [CN 3, % identity 87 (FJ536664.1)], Termitomyces sp. [CN 4, % identity 90 (JF746992.1)], Termitomyces sp. [CN 5, % identity 99 (GU001667.1)], T. microcarpus [CN 6, % identity 82 (EF421077.1)], Termitomyces sp. [CN 7, % identity 76 (JF746993.1)], and Volvariella volvacea [CN 8, % identity 100 (JN086680.1)]. Although out of 8 mushrooms 4 could be identified up to species level, the nucleotide sequences of the rest may be relevant to further characterization. A phylogenetic tree is constructed using Neighbor-Joining method showing interrelationship between/among the mushrooms. The determined nucleotide sequences of the mushrooms may provide additional information enriching GenBank database aiding to molecular taxonomy and facilitating its domestication and characterization for human benefits.

Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology.

PubMed

Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K P; Woo, Patrick C Y

2015-10-22

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10-49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n=2), Pichia (Candida) norvegensis (n=2), Candida tropicalis (n=1) and Saccharomyces cerevisiae (n=1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study.

Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology

PubMed Central

Zhao, Ying; Tsang, Chi-Ching; Xiao, Meng; Cheng, Jingwei; Xu, Yingchun; Lau, Susanna K. P.; Woo, Patrick C. Y.

2015-01-01

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study. PMID:26506340

Application of Partial Internal Transcribed Spacer Sequences for the Discrimination of Artemisia capillaris from Other Artemisia Species

PubMed Central

Doh, Eui Jeong; Paek, Seung-Ho; Lee, Guemsan; Lee, Mi-Young; Oh, Seung-Eun

2016-01-01

Several Artemisia species are used as herbal medicines including the dried aerial parts of Artemisia capillaris, which are used as Artemisiae Capillaris Herba (known as “Injinho” in Korean medicinal terminology and “Yin Chen Hao” in Chinese). In this study, we developed tools for distinguishing between A. capillaris and 11 other Artemisia species that grow and/or are cultured in China, Japan, and Korea. Based on partial nucleotide sequences in the internal transcribed spacer (ITS) that differ between the species, we designed primers to amplify a DNA marker for A. capillaris. In addition, to detect other Artemisia species that are contaminants of A. capillaris, we designed primers to amplify DNA markers of A. japonica, A. annua, A. apiacea, and A. anomala. Moreover, based on random amplified polymorphic DNA analysis, we confirmed that primers developed in a previous study could be used to identify Artemisia species that are sources of Artemisiae Argyi Folium and Artemisiae Iwayomogii Herba. By using these primers, we found that multiplex polymerase chain reaction (PCR) was a reliable tool to distinguish between A. capillaris and other Artemisia species and to identify other Artemisia species as contaminants of A. capillaris in a single PCR. PMID:27313651

Phylogenetic Relationships of Yessotoxin-Producing Dinoflagellates, Based on the Large Subunit and Internal Transcribed Spacer Ribosomal DNA Domains▿

PubMed Central

Howard, Meredith D. A.; Smith, G. Jason; Kudela, Raphael M.

2009-01-01

Yessotoxin (YTX) is a globally distributed marine toxin produced by some isolates of the dinoflagellate species Protoceratium reticulatum, Lingulodinium polyedrum, and Gonyaulax spinifera within the order Gonyaulacales. The process of isolating cells and testing each isolate individually for YTX production during toxic blooms are labor intensive, and this impedes our ability to respond quickly to toxic blooms. In this study, we used molecular sequences from the large subunit and internal transcribed spacer genomic regions in the ribosomal operon of known YTX-producing dinoflagellates to determine if genetic differences exist among geographically distinct populations or between toxic and nontoxic isolates within species. In all analyses, all three YTX-producing species fell within the Gonyaulacales order in agreement with morphological taxonomy. Phylogenetic analyses of available rRNA gene sequences indicate that the capacity for YTX production appears to be confined to the order Gonyaulacales. These findings indicate that Gonyaulacoloid dinoflagellate species are the most likely to produce YTX and thus should be prioritized for YTX screening during events. Dinoflagellate species that fall outside of the Gonyaulacales order are unlikely to produce YTX. Although the rRNA operon offers multiple sequence domains to resolve species level diversification within this dinoflagellate order, these domains are not sufficiently variable to provide robust markers for YTX toxicity. PMID:19011074

Cloning and restriction enzyme mapping of ribosomal DNA of Giardia duodenalis, Giardia ardeae and Giardia muris.

PubMed

van Keulen, H; Campbell, S R; Erlandsen, S L; Jarroll, E L

1991-06-01

In an attempt to study Giardia at the DNA sequence level, the rRNA genes of three species, Giardia duodenalis, Giardia ardeae and Giardia muris were cloned and restriction enzyme maps were constructed. The rDNA repeats of these Giardia show completely different restriction enzyme recognition patterns. The size of the rDNA repeat ranges from approximately 5.6 kb in G. duodenalis to 7.6 kb in both G. muris and G. ardeae. These size differences are mainly attributable to the variation in length of the spacer. Minor differences exist among these Giardia in the sizes of their small subunit rRNA and the internal transcribed spacer between small and large subunit rRNA. The genetic maps were constructed by sequence analysis of the DNA around the 5' and 3' ends of the mature rRNA genes and between the rRNA covering the 5.8S rRNA gene and internal transcribed spacer. Comparison of the 5.8S rDNA and 3' end of large subunit rDNA from these three Giardia species showed considerable sequence variation, but the rDNA sequences of G. duodenalis and G. ardeae appear more closely related to each other than to G. muris.

Identification of Giardia species and Giardia duodenalis assemblages by sequence analysis of the 5.8S rDNA gene and internal transcribed spacers.

PubMed

Cacciò, Simone M; Beck, Relja; Almeida, Andre; Bajer, Anna; Pozio, Edoardo

2010-05-01

PCR assays have been developed mainly to assist investigations into the epidemiology of Giardia duodenalis, the only species in the Giardia genus having zoonotic potential. However, a reliable identification of all species is of practical importance, particularly when water samples and samples from wild animals are investigated. The aim of the present work was to genotype Giardia species and G. duodenalis assemblages using as a target the region spanning the 5.8S gene and the 2 flanking internal transcribed spacers (ITS1 and ITS2) of the ribosomal gene. Primers were designed to match strongly conserved regions in the 3' end of the small subunit and in the 5' end of the large subunit ribosomal genes. The corresponding region (about 310 bp) was amplified from 49 isolates of both human and animal origin, representing all G. duodenalis assemblages as well as G. muris and G. microti. Sequence comparison and phylogenetic analysis showed that G. ardeae, G. muris, G. microti as well as the 7 G. duodenalis assemblages can be easily distinguished. Since the major subgroups within the zoonotic assemblages A and B can be identified by sequence analysis, this assay is also informative for molecular epidemiological studies.

Sequence analysis of the internal transcribed spacer (ITS) region reveals a novel clade of Ichthyophonus sp. from rainbow trout

USGS Publications Warehouse

Rasmussen, C.; Purcell, M.K.; Gregg, J.L.; LaPatra, S.E.; Winton, J.R.; Hershberger, P.K.

2010-01-01

The mesomycetozoean parasite Ichthyophonus hoferi is most commonly associated with marine fish hosts but also occurs in some components of the freshwater rainbow trout Oncorhynchus mykiss aquaculture industry in Idaho, USA. It is not certain how the parasite was introduced into rainbow trout culture, but it might have been associated with the historical practice of feeding raw, ground common carp Cyprinus carpio that were caught by commercial fisherman. Here, we report a major genetic division between west coast freshwater and marine isolates of Ichthyophonus hoferi. Sequence differences were not detected in 2 regions of the highly conserved small subunit (18S) rDNA gene; however, nucleotide variation was seen in internal transcribed spacer loci (ITS1 and ITS2), both within and among the isolates. Intra-isolate variation ranged from 2.4 to 7.6 nucleotides over a region consisting of ~740 bp. Majority consensus sequences from marine/anadromous hosts differed in only 0 to 3 nucleotides (99.6 to 100% nucleotide identity), while those derived from freshwater rainbow trout had no nucleotide substitutions relative to each other. However, the consensus sequences between isolates from freshwater rainbow trout and those from marine/anadromous hosts differed in 13 to 16 nucleotides (97.8 to 98.2% nucleotide identity).

Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2

PubMed Central

Wang, Xiaoyue; Yang, Pei; Wang, Lili

2017-01-01

Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification. PMID:29181391

Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2.

PubMed

Wang, Xiaoyue; Chen, Xiaochen; Yang, Pei; Wang, Lili; Han, Jianping

2017-01-01

Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.

Molecular characterization of the Indian poultry nodular tapeworm, Raillietina echinobothrida (Cestoda: Cyclophyllidea: Davaineidae) based on rDNA internal transcribed spacer 2 region.

PubMed

Ramnath; Jyrwa, D B; Dutta, A K; Das, B; Tandon, V

2014-03-01

The nodular tapeworm, Raillietina echinobothrida is a well studied avian gastrointestinal parasite of family Davaineidae (Cestoda: Cyclophyllidea). It is reported to be the largest in size and second most prevalent species infecting chicken in north-east India. In the present study, morphometrical methods coupled with the molecular analysis of the second internal transcribed spacer (ITS2) region of ribosomal DNA were employed for precise identification of the parasite. The annotated ITS2 region was found to be 446 bp long and further utilized to elucidate the phylogenetic relationships and its species-interrelationships at the molecular level. In phylogenetic analysis similar topology was observed among the trees obtained by distance-based neighbor-joining as well as character-based maximum parsimony tree building methods. The query sequence R. echinobothrida is well aligned and placed within the Davaineidae group, with all Raillietina species well separated from the other cyclophyllidean (taeniid and hymenolepid) cestodes, while Diphyllobothrium latum (Pseudophyllidea: Diphyllobothriidae) was rooted as an out-group. Sequence similarities indeed confirmed our hypothesis that Raillietina spp. are neighboring the position with other studied species of order Cyclophyllidea against the out-group order Pseudophyllidea. The present study strengthens the potential of ITS2 as a reliable marker for phylogenetic reconstructions.

International nuclear waste management fact book

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abrahms, C W; Patridge, M D; Widrig, J E

1995-11-01

The International Nuclear Waste Management Fact Book has been compiled to provide current data on fuel cycle and waste management facilities, R and D programs, and key personnel in 24 countries, including the US; four multinational agencies; and 20 nuclear societies. This document, which is in its second year of publication supersedes the previously issued International Nuclear Fuel Cycle Fact Book (PNL-3594), which appeared annually for 12 years. The content has been updated to reflect current information. The Fact Book is organized as follows: National summaries--a section for each country that summarizes nuclear policy, describes organizational relationships, and provides addressesmore » and names of key personnel and information on facilities. International agencies--a section for each of the international agencies that has significant fuel cycle involvement and a list of nuclear societies. Glossary--a list of abbreviations/acronyms of organizations, facilities, and technical and other terms. The national summaries, in addition to the data described above, feature a small map for each country and some general information that is presented from the perspective of the Fact Book user in the US.« less

International nuclear fuel cycle fact book. Revision 6

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harmon, K.M.; Lakey, L.T.; Leigh, I.W.

1986-01-01

The International Fuel Cycle Fact Book has been compiled in an effort to provide (1) an overview of worldwide nuclear power and fuel cycle programs and (2) current data concerning fuel cycle and waste management facilities, R and D programs and key personnel. Additional information on each country's program is available in the International Source Book: Nuclear Fuel Cycle Research and Development, PNL-2478, Rev. 2.

Determining the pregnancy status of patients before diagnostic nuclear medicine procedures: the Australian experience.

PubMed

James, Daphne J; Cardew, Paul; Warren-Forward, Helen M

2011-09-01

Ionizing radiation used in diagnostic nuclear medicine procedures has the potential to have biologic effects on a fetus. Nuclear medicine technologists (NMTs) therefore have a responsibility to ensure that they question all patients of childbearing age about their pregnancy status before starting any procedure, to avoid unnecessary fetal irradiation. In Australia, there are no clearly defined practice guidelines to assist NMTs in determining whom to question or how to question their patients. Semistructured interviews were conducted with chief NMTs and staff NMTs in 8 nuclear medicine departments in Australia. Questions were based around 5 areas: regulations and policy, fetal radiation exposure, questioning of the patient, difficulties in determining pregnancy status, and the impact of the use of hybrid imaging. Audio files of the interviews were transcribed and coded. Topics were coded into 5 themes: policy and awareness of guidelines, questioning the patient, radiation knowledge, decisions and assumptions made by NMTs, and the use of pregnancy testing. There was a wide variation in practice between and within departments. NMTs demonstrated a lack of knowledge and awareness of the possible biologic effects of radiation. This study identified a need in Australia for nuclear medicine to arrive at a consensus approach to verifying a patient's pregnancy status so that NMTs can successfully question patients about their pregnancy status. Continuing education programs are also required to keep NMTs up to date in their knowledge.

16th International Conference on Nuclear Structure: NS2016

DOE PAGES

Galindo-Uribarri, Alfredo

2016-10-28

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

16th International Conference on Nuclear Structure: NS2016

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galindo-Uribarri, Alfredo

Every two years the Nuclear Structure (NS) conference series brings together researchers from an international community of experimental and theoretical nuclear physicists to present and discuss their latest results in nuclear structure. This biennial conference covered the latest results on experimental and theoretical research into the structure of nuclei at the extremes of isospin, excitation energy, mass, and angular momentum. Topics included many of the most exciting areas of modern nuclear structure research such as transitional behavior, nuclear structure and its evolution across the nuclear landscape, shell structure, collectivity, nuclear structure with radioactive beams, and macroscopic and microscopic approaches tomore » nuclear structure.« less

Kaposi's Sarcoma-Associated Herpesvirus Hijacks RNA Polymerase II To Create a Viral Transcriptional Factory

PubMed Central

Chen, Christopher Phillip; Lyu, Yuanzhi; Chuang, Frank; Nakano, Kazushi; Izumiya, Chie; Jin, Di; Campbell, Mel

2017-01-01

ABSTRACT Locally concentrated nuclear factors ensure efficient binding to DNA templates, facilitating RNA polymerase II recruitment and frequent reutilization of stable preinitiation complexes. We have uncovered a mechanism for effective viral transcription by focal assembly of RNA polymerase II around Kaposi's sarcoma-associated herpesvirus (KSHV) genomes in the host cell nucleus. Using immunofluorescence labeling of latent nuclear antigen (LANA) protein, together with fluorescence in situ RNA hybridization (RNA-FISH) of the intron region of immediate early transcripts, we visualized active transcription of viral genomes in naturally infected cells. At the single-cell level, we found that not all episomes were uniformly transcribed following reactivation stimuli. However, those episomes that were being transcribed would spontaneously aggregate to form transcriptional “factories,” which recruited a significant fraction of cellular RNA polymerase II. Focal assembly of “viral transcriptional factories” decreased the pool of cellular RNA polymerase II available for cellular gene transcription, which consequently impaired cellular gene expression globally, with the exception of selected ones. The viral transcriptional factories localized with replicating viral genomic DNAs. The observed colocalization of viral transcriptional factories with replicating viral genomic DNA suggests that KSHV assembles an “all-in-one” factory for both gene transcription and DNA replication. We propose that the assembly of RNA polymerase II around viral episomes in the nucleus may be a previously unexplored aspect of KSHV gene regulation by confiscation of a limited supply of RNA polymerase II in infected cells. IMPORTANCE B cells infected with Kaposi's sarcoma-associated herpesvirus (KSHV) harbor multiple copies of the KSHV genome in the form of episomes. Three-dimensional imaging of viral gene expression in the nucleus allows us to study interactions and changes in the physical distribution of these episomes following stimulation. The results showed heterogeneity in the responses of individual KSHV episomes to stimuli within a single reactivating cell; those episomes that did respond to stimulation, aggregated within large domains that appear to function as viral transcription factories. A significant portion of cellular RNA polymerase II was trapped in these factories and served to transcribe viral genomes, which coincided with an overall decrease in cellular gene expression. Our findings uncover a strategy of KSHV gene regulation through focal assembly of KSHV episomes and a molecular mechanism of late gene expression. PMID:28331082

Safeguards Guidance Document for Designers of Commercial Nuclear Facilities: International Nuclear Safeguards Requirements and Practices For Uranium Enrichment Plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robert Bean; Casey Durst

2009-10-01

This report is the second in a series of guidelines on international safeguards requirements and practices, prepared expressly for the designers of nuclear facilities. The first document in this series is the description of generic international nuclear safeguards requirements pertaining to all types of facilities. These requirements should be understood and considered at the earliest stages of facility design as part of a new process called “Safeguards-by-Design.” This will help eliminate the costly retrofit of facilities that has occurred in the past to accommodate nuclear safeguards verification activities. The following summarizes the requirements for international nuclear safeguards implementation at enrichmentmore » plants, prepared under the Safeguards by Design project, and funded by the U.S. Department of Energy (DOE) National Nuclear Security Administration (NNSA), Office of NA-243. The purpose of this is to provide designers of nuclear facilities around the world with a simplified set of design requirements and the most common practices for meeting them. The foundation for these requirements is the international safeguards agreement between the country and the International Atomic Energy Agency (IAEA), pursuant to the Treaty on the Non-proliferation of Nuclear Weapons (NPT). Relevant safeguards requirements are also cited from the Safeguards Criteria for inspecting enrichment plants, found in the IAEA Safeguards Manual, Part SMC-8. IAEA definitions and terms are based on the IAEA Safeguards Glossary, published in 2002. The most current specification for safeguards measurement accuracy is found in the IAEA document STR-327, “International Target Values 2000 for Measurement Uncertainties in Safeguarding Nuclear Materials,” published in 2001. For this guide to be easier for the designer to use, the requirements have been restated in plainer language per expert interpretation using the source documents noted. The safeguards agreement is fundamentally a legal document. As such, it is written in a legalese that is understood by specialists in international law and treaties, but not by most outside of this field, including designers of nuclear facilities. For this reason, many of the requirements have been simplified and restated. However, in all cases, the relevant source document and passage is noted so that readers may trace the requirement to the source. This is a helpful living guide, since some of these requirements are subject to revision over time. More importantly, the practices by which the requirements are met are continuously modernized by the IAEA and nuclear facility operators to improve not only the effectiveness of international nuclear safeguards, but also the efficiency. As these improvements are made, the following guidelines should be updated and revised accordingly.« less

Developing a Nuclear Global Health Workforce Amid the Increasing Threat of a Nuclear Crisis.

PubMed

Burkle, Frederick M; Dallas, Cham E

2016-02-01

This study argues that any nuclear weapon exchange or major nuclear plant meltdown, in the categories of human systems failure and conflict-based crises, will immediately provoke an unprecedented public health emergency of international concern. Notwithstanding nuclear triage and management plans and technical monitoring standards within the International Atomic Energy Agency and the World Health Organization (WHO), the capacity to rapidly deploy a robust professional workforce with the internal coordination and collaboration capabilities required for large-scale nuclear crises is profoundly lacking. A similar dilemma, evident in the early stages of the Ebola epidemic, was eventually managed by using worldwide infectious disease experts from the Global Outbreak Alert and Response Network and multiple multidisciplinary WHO-supported foreign medical teams. This success has led the WHO to propose the development of a Global Health Workforce. A strategic format is proposed for nuclear preparedness and response that builds and expands on the current model for infectious disease outbreak currently under consideration. This study proposes the inclusion of a nuclear global health workforce under the technical expertise of the International Atomic Energy Agency and WHO's Radiation Emergency Medical Preparedness and Assistance Network leadership and supported by the International Health Regulations Treaty. Rationales are set forth for the development, structure, and function of a nuclear workforce based on health outcomes research that define the unique health, health systems, and public health challenges of a nuclear crisis. Recent research supports that life-saving opportunities are possible, but only if a rapidly deployed and robust multidisciplinary response component exists.

Genomic structure, promoter identification, and chromosomal mapping of a mouse nuclear orphan receptor expressed in embryos and adult testes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, C.H.; Wei, Li-Na; Copeland, N.G.

We have isolated and characterized overlapping genomic clones containing the complete transcribed region of a newly isolated mouse cDNA encoding an orphan receptor expressed specifically in midgestation embryos and adult testis. This gene spans a distance of more than 50 kb and is organized into 13 exons. The transcription initiation site is located at the 158th nucleotide upstream from the translation initiation codon. All the exon/intron junction sequences follow the GT/AG rule. Based upon Northern blot analysis and the size of the transcribed region of the gene, its transcript was determined to be approximately 2.5 kb. Within approximately 500 hpmore » upstream from the transcription initiation site, several immune response regulatory elements were identified but no TATA box was located. This gene was mapped to the distal region of mouse chromosome 10 and its locus has been designated Tr2-11. Immunohistochemical studies show that the Tr2-11 protein is present mainly in advanced germ cell populations of mature testes and that Tr2-11 gene expression is dramatically decreased in vitamin A-depleted animals. 23 refs., 7 figs.« less

History and Perspectives of Nuclear Medicine in Myanmar

PubMed Central

Mar, Win

2018-01-01

Nuclear Medicine was established in Myanmar in 1963 by Dr Soe Myint and International Atomic Energy expert Dr R. Hochel at Yangon General Hospital. Nuclear medicine diagnostic and therapeutic services started with Probe Scintillation Detector Systems and rectilinear scanner. In the early stage, many Nuclear Medicine specialists from the International Atomic Energy Agency (IAEA) spent some time in Myanmar and made significant contributions to the development of Nuclear Medicine in our country. The department participated in various IAEA technical cooperation projects and regional cooperation projects. By the late 1990s, new centers were established in Mandalay, Naypyidaw, and North Okkalapa Teaching Hospital of University of Medicine 11, Yangon. The training program related to Nuclear Medicine includes a postgraduate master’s degree (three years) at the University of Medicine. Currently, all centers are equipped with SPECT, SPECT-CT, PET-CT, and cyclotron in Yangon General Hospital. Up until now, the International Atomic Energy Agency has been playing a crucial role in the growth and development of Nuclear Medicine in Myanmar. Our vision is to provide a wide spectrum of nuclear medicine services at a level compatible with the international standards to become a Center of Excellence. PMID:29333470

77 FR 53236 - Proposed International Isotopes Fluorine Extraction Process and Depleted Uranium Deconversion...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-31

... NUCLEAR REGULATORY COMMISSION [NRC-2010-0143] Proposed International Isotopes Fluorine Extraction Process and Depleted Uranium Deconversion Plant in Lea County, New Mexico AGENCY: Nuclear Regulatory... U.S. Nuclear Regulatory Commission (NRC or the Commission) has published the Final Environmental...

Information exchange of the Atomic Energy Society of Japan with nuclear societies worldwide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hori, Masao; Tomita, Yasushi

2000-07-01

The Atomic Energy Society of Japan (AESJ) exchanges information with nuclear societies worldwide by intersocietal communication through international councils of nuclear societies and through bilateral agreements between foreign societies and by such media as international meetings, publications, and Internet applications.

76 FR 51357 - Notice of Availability: American Assured Fuel Supply

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-18

... nonproliferation objectives by supporting civil nuclear energy development while minimizing proliferation risks... to the Atomic Energy of 1954, as amended (Pub. L. 83-703), and the Nuclear Non-Proliferation Act of... the International Atomic Energy Agency's (IAEA) International Nuclear Fuel Bank (INFB) initiative...

Fourth Collaborative Materials Exercise of the Nuclear Forensics International Technical Working Group

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwantes, J. M.; Marsden, O.; Reilly, D.

Abstract The Nuclear Forensics International Technical Working Group is a community of nuclear forensic practitioners who respond to incidents involving nuclear and other radioactive material out of regulatory control. The Group is dedicated to advancing nuclear forensic science in part through periodic participation in materials exercises. The Group completed its fourth Collaborative Materials Exercise in 2015 in which laboratories from 15 countries and one multinational organization analyzed three samples of special nuclear material in support of a mock nuclear forensic investigation. This special section of the Journal for Radioanalytical and Nuclear Chemistry is devoted to summarizing highlights from this exercise.

Nuclear weapons are illegal threats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyrowitz, E.L.

Challenging Harry Almond's position that nuclear deterrence is workable, the author contends that there is no historical basis for believing that anticipation of the horrors of war will be an effective deterrent. He questions the belief that the nuclear balance of terror has maintained the peace for the past 40 years because an arms race is inherently unstable. The argument that the pursuit of national interests takes precedence over any limitation imposed by international law reflects a perception of international law that is comparable to the Third Reich. The bases for a legal evaluation of the status of nuclear weaponsmore » under international law come from express and implicit treaty provisions, international custom, general principles of international law, judicial decisions, resolutions at the United Nations, and the opinions of qualified jurists as well as military necessity.« less

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types.

PubMed

Kawaji, Hideya; Kasukawa, Takeya; Forrest, Alistair; Carninci, Piero; Hayashizaki, Yoshihide

2017-08-29

The latest project from the FANTOM consortium, an international collaborative effort initiated by RIKEN, generated atlases of transcriptomes, in particular promoters, transcribed enhancers, and long-noncoding RNAs, across a diverse set of mammalian cell types. Here, we introduce the FANTOM5 collection, bringing together data descriptors, articles and analyses of FANTOM5 data published across the Nature Research journals. Associated data are openly available for reuse by all.

Isolation and Molecular Typing of Naegleria fowleri from the Brain of a Cow That Died of Primary Amebic Meningoencephalitis

PubMed Central

Visvesvara, Govinda S.; De Jonckheere, Johan F.; Sriram, Rama; Daft, Barbara

2005-01-01

Naegleria fowleri causes an acute and rapidly fatal central nervous system infection called primary amebic meningoencephalitis (PAM) in healthy children and young adults. We describe here the identification of N. fowleri isolated from the brain of one of several cows that died of PAM based on sequencing of the internal transcribed spacers, including the 5.8S rRNA genes. PMID:16081978

Identification Sponges-Associated Fungi From Karimunjawa National Park

NASA Astrophysics Data System (ADS)

Trianto, Agus; Sabdono, Agus; Rochaddi, Baskoro; Wulan Triningsih, Desy; Seswita Zilda, Dewi

2018-02-01

Marine sponges are rich sources of bioactive substances with various pharmacological activities. Previous studies have shown that most bioactive compounds were originally produced by associated-microorganisms. Fungi associated with the marine sponges collected off Karimunjawa National Park were isolated and identified by morphological characteristics and molecular level analyses based on internal transcribed spacer (ITS) regions. A total of 2 isolates which were characterized, the fungi Penicillium spinulosum and Trichoderma virens have been revealed.

Exploration of the Genomic Diversity and Core Genome of the Bifidobacterium adolescentis Phylogenetic Group by Means of a Polyphasic Approach

PubMed Central

Duranti, Sabrina; Turroni, Francesca; Milani, Christian; Foroni, Elena; Bottacini, Francesca; Dal Bello, Fabio; Ferrarini, Alberto; Delledonne, Massimo; van Sinderen, Douwe

2013-01-01

In the current work, we describe genome diversity and core genome sequences among representatives of three bifidobacterial species, i.e., Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Bifidobacterium pseudocatenulatum, by employing a polyphasic approach involving analysis of 16S rRNA gene and 16S-23S internal transcribed spacer (ITS) sequences, pulsed-field gel electrophoresis (PFGE), and comparative genomic hybridization (CGH) assays. PMID:23064340

Lessons from Plectocephalus (Compositae, Cardueae-Centaureinae): ITS disorientation in annuals and Beringian dispersal as revealed by molecular analyses

PubMed Central

Susanna, Alfonso; Galbany-Casals, Mercè; Romaschenko, Konstantyn; Barres, Laia; Martín, Joan; Garcia-Jacas, Núria

2011-01-01

Background and Aims The geographic distribution of the genus Plectocephalus comprises a single species in Ethiopia, two in North America and possibly four more in South America, in a striking disjunction that is exceptional for genera of the tribe Cardueae. The enormity of this disjunction cast doubts on the precise taxonomic delineation of the genus, which is not unanimously recognized as a natural entity. The aims of this study were to define the generic boundaries of Plectocephalus and to formulate a hypothesis that would explain its natural range. Methods A combined molecular approach, using nuclear internal transcribed spacers (ITS) and external transcribed spacers (ETS), and plastid trnL-trnL-F, rpl32-trnLUAG and ndhF markers, was chosen for phylogenetic reconstruction by maximum parsimony and Bayesian inference. Key Results Phylogenetic analysis shows that Plectocephalus is a natural genus that includes the African species P. varians, together with all the native South American species, currently classified as Centaurea, C. cachinalensis, C. floccosa and C. tweediei. The recognition of Centaurodendron as an independent genus, which we consider appropriate, would make Plectocephalus paraphyletic. Affinities of Plectocephalus should lie with eastern representatives of Centaureinae. Geographic disjunction is explained as a consequence of dispersal via the Bering Land Bridge during the Miocene–Pliocene. The phylogeny of the basal grade of Centaureinae differs from previous phylogenies, and artefacts resulting from differences in mutation rates of annual and perennial taxa are confirmed. Sensitivity of ITS to these differences was the highest observed for all DNA regions used in this study. Conclusions The natural status of the genus Plectocephalus is confirmed and several nomenclatural combinations are proposed. New evidence contributes to the debate concerning problems posed by the use of ITS in the phylogenetic reconstruction of groups that differ in terms of their life cycles. Dispersal from Caucasus and Anatolia along the Siberian route and then across the Bering Land Bridge follows a route previously proposed for other taxonomic groups. PMID:21712295

“Afraid of Being Witchy with a ‘B’”: A Qualitative Study of How Gender Influences Residents’ Experiences Leading Cardiopulmonary Resuscitation

PubMed Central

Kolehmainen, Christine; Brennan, Meghan; Filut, Amarette; Isaac, Carol; Carnes, Molly

2014-01-01

Purpose Ineffective leadership during cardiopulmonary resuscitation (“code”) can negatively affect a patient’s likelihood of survival. In most teaching hospitals, internal medicine residents lead codes. In this study, the authors explored internal medicine residents’ experiences leading codes, with a particular focus on how gender influences the code leadership experience. Method The authors conducted individual, semi-structured telephone or in-person interviews with 25 residents (May 2012 to February 2013) from 9 U.S. internal medicine residency programs. They audio recorded and transcribed the interviews then thematically analyzed the transcribed text. Results Participants viewed a successful code as one with effective leadership. They agreed that the ideal code leader was an authoritative presence; spoke with a deep, loud voice; used clear, direct communication; and appeared calm. Although equally able to lead codes as their male colleagues, female participants described feeling stress from having to violate gender behavioral norms in the role of code leader. In response, some female participants adopted rituals to signal the suspension of gender norms while leading a code. Others apologized afterwards for their counter normative behavior. Conclusions Ideal code leadership embodies highly agentic, stereotypical male behaviors. Female residents employed strategies to better integrate the competing identities of code leader and female gender. In the future, residency training should acknowledge how female gender stereotypes may conflict with the behaviors required to enact code leadership and offer some strategies, such as those used by the female residents in this study, to help women integrate these dual identities. PMID:24979289

Elementary! A Nuclear Forensics Workshop Teaches Vital Skills to International Practitioners

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brim, Cornelia P.; Minnema, Lindsay T.

The article describes the Nuclear Forensics Workshop sponsored by the International Atomic Energy Agency (IAEA), the Office of Nonproliferation and International Security (NIS) and hosted by Pacific Northwest National Laboratory October 28-November 8, 2013 in Richland,Washington. Twenty-six participants from 10 countries attended the workshop. Experts from from Los Alamos, Lawrence Livermore, and Pacific Northwest national laboratories collaborated with an internationally recognized cadre of experts from the U.S. Department of Homeland Security and other U.S. agencies, IAEA, the Australian Nuclear Science and Technology Organisation, the United Kingdom Atomic Weapons Establishment (AWE), and the European Union Joint Research Center Institute for Transuraniummore » Elements, to train practitioners in basic methodologies of nuclear forensic examinations.« less

Promoting Intercultural Competency in the Nuclear Workplace

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bachner K. M.

Intercultural preparedness training is a staple of many workplaces that require international competence, including government, business, and non-profits. Even highly experienced diplomats are often advised to attend training sessions on this topic. Intercultural preparedness training promises to be especially relevant and useful for professionals working in the field of nuclear nonproliferation, including in the application of international nuclear safeguards. This paper outlines the fundamental philosophies underlying a training program that will benefit professionals in the nuclear arena, whether practitioners of nonproliferation or other sub-fields relying on international cooperation and collaboration, and how such a training program might be implemented efficiently.

10 CFR 1.29 - Office of International Programs.

Code of Federal Regulations, 2013 CFR

2013-01-01

... maintains working relationships with individual countries and international nuclear organizations, as well... 10 Energy 1 2013-01-01 2013-01-01 false Office of International Programs. 1.29 Section 1.29 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION Headquarters Commission...

10 CFR 1.29 - Office of International Programs.

Code of Federal Regulations, 2010 CFR

2010-01-01

... maintains working relationships with individual countries and international nuclear organizations, as well... 10 Energy 1 2010-01-01 2010-01-01 false Office of International Programs. 1.29 Section 1.29 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION Headquarters Commission...

10 CFR 1.29 - Office of International Programs.

Code of Federal Regulations, 2011 CFR

2011-01-01

... maintains working relationships with individual countries and international nuclear organizations, as well... 10 Energy 1 2011-01-01 2011-01-01 false Office of International Programs. 1.29 Section 1.29 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION Headquarters Commission...

10 CFR 1.29 - Office of International Programs.

Code of Federal Regulations, 2012 CFR

2012-01-01

... maintains working relationships with individual countries and international nuclear organizations, as well... 10 Energy 1 2012-01-01 2012-01-01 false Office of International Programs. 1.29 Section 1.29 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION Headquarters Commission...

10 CFR 1.29 - Office of International Programs.

Code of Federal Regulations, 2014 CFR

2014-01-01

... maintains working relationships with individual countries and international nuclear organizations, as well... 10 Energy 1 2014-01-01 2014-01-01 false Office of International Programs. 1.29 Section 1.29 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION Headquarters Commission...

Assessment of the risk of medium-term internal contamination in Minamisoma City, Fukushima, Japan, after the Fukushima Dai-ichi nuclear accident.

PubMed

Sugimoto, Amina; Gilmour, Stuart; Tsubokura, Masaharu; Nomura, Shuhei; Kami, Masahiro; Oikawa, Tomoyoshi; Kanazawa, Yukio; Shibuya, Kenji

2014-06-01

The Fukushima Dai-ichi nuclear disaster, the first level-7 major nuclear disaster since Chernobyl, raised concerns about the future health consequences of exposure to and intake of radionuclides. Factors determining the risk and level of internal radiation contamination after a nuclear accident, which are a key to understanding and improving current nuclear disaster management, are not well studied. We investigated both the prevalence and level of internal contamination in residents of Minamisoma, and identified factors determining the risk and levels of contamination. We implemented a program assessing internal radiation contamination using a whole body counter (WBC) measurement and a questionnaire survey in Minamisoma, between October 2011 and March 2012. Approximately 20% of the city's population (8,829 individuals) participated in the WBC measurement for internal contamination, of which 94% responded to the questionnaire. The proportion of participants with detectable internal contamination was 40% in adults and 9% in children. The level of internal contamination ranged from 2.3 to 196.5 Bq/kg (median, 11.3 Bq/kg). Tobit regression analysis identified two main risk factors: more time spent outdoors, and intake of potentially contaminated foods and water. Our findings suggest that, with sensible and reasonable precautions, people may be able to live continuously in radiation-affected areas with limited contamination risk. To enable this, nuclear disaster response should strictly enforce food and water controls and disseminate evidence-based and up-to-date information about avoidable contamination risks.

Technical Training Workshop on International Safeguards: An Introduction to Safeguards for Emerging Nuclear States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Frazar, Sarah L.; Gastelum, Zoe N.; Olson, Jarrod

2009-10-06

The U.S. Department of Energy/National Nuclear Security Administration (DOE/NNSA) hosted a workshop from May 4-22, 2009, on the fundamental elements of international safeguards. Entitled "A Technical Training Workshop on International Safeguards," the workshop introduced post-graduate students from Malaysia, Vietnam, Indonesia, Thailand, Morocco, Egypt, Algeria and Tunisia to the fundamental issues and best practices associated with international safeguards and encouraged them to explore potential career paths in safeguards. Workshops like these strengthen the international safeguards regime by promoting the development of a "safeguards culture" among young nuclear professionals within nascent nuclear countries. While this concept of safeguards culture is sometimes hardmore » to define and even harder to measure, this paper will demonstrate that the promotion of safeguards cultures through workshops like these justifies the investment of U.S. taxpayer dollars.« less

International nuclear safety concerns. Hearing before the Subcommittee on Energy, Nuclear Proliferation, and Government Processes of the Committee on Governmental Affairs, United States Senate, Ninety-Ninth Congress, Second Session, May 8, 1986

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1986-01-01

Allan I. Mendelowitz of the General Accounting Office (GAO) and James R. Shea of the Nuclear Regulatory Commission were the principal witnesses at a hearing on international concerns about reactor safety. The hearing focused on the Soviet accident at Chernobyl as a demonstration that safety matters are a legitimate area of international concern. Among the issues under discussion were safety standards and inspection procedures of the International Atomic Energy Agency (IAEA). Estimates developed by the GAO show that developing countries, which lack a strong technical base or nuclear background to handle emergencies, will have half the reactors in the worldmore » by the year 2000. Mendelowitz and Shea, together with supporting testimony from others in their agencies described international efforts to improve safeguards.« less

International Nuclear Security

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doyle, James E.

2012-08-14

This presentation discusses: (1) Definitions of international nuclear security; (2) What degree of security do we have now; (3) Limitations of a nuclear security strategy focused on national lock-downs of fissile materials and weapons; (4) What do current trends say about the future; and (5) How can nuclear security be strengthened? Nuclear security can be strengthened by: (1) More accurate baseline inventories; (2) Better physical protection, control and accounting; (3) Effective personnel reliability programs; (4) Minimize weapons-usable materials and consolidate to fewer locations; (5) Consider local threat environment when siting facilities; (6) Implement pledges made in the NSS process; andmore » (7) More robust interdiction, emergency response and special operations capabilities. International cooperation is desirable, but not always possible.« less

Nuclear reference materials to meet the changing needs of the global nuclear community

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martin, H.R.; Gradle, C.G.; Narayanan, U.I.

New Brunswick Laboratory (NBL) serves as the US Government`s Certifying Authority for nuclear reference materials and measurement calibration standards. In this role, NBL provides nuclear reference materials certified for chemical and/or isotopic compositions traceable to a nationally accepted, internationally compatible reference base. Emphasis is now changing as to the types of traceable nuclear reference materials needed as operations change within the Department of Energy (DOE) complex and at nuclear facilities around the world. Environmental and waste minimization issues, facilities and materials transitioning from processing to storage modes with corresponding changes in the types of measurements being performed, emphasis on requirementsmore » for characterization of waste materials, difficulties in transporting nuclear materials, and International factors, including International Atomic Energy Agency (IAEA) inspection of excess US nuclear materials, are all contributing influences. During these changing times, ft is critical that traceable reference materials be provided for calibration or validation of the performance of measurement systems. This paper will describe actions taken and planned to meet the changing reference material needs of the global nuclear community.« less

77 FR 16270 - Updated Aging Management Criteria for Reactor Vessel Internal Components of Pressurized Water...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-20

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0070] Updated Aging Management Criteria for Reactor Vessel Internal Components of Pressurized Water Reactors AGENCY: Nuclear Regulatory Commission. ACTION: Draft..., ``Updated Aging Management Criteria for PWR Reactor Vessel Internal Components.'' This draft LR-ISG revises...

77 FR 23513 - Updated Aging Management Criteria for Reactor Vessel Internal Components of Pressurized Water...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-19

... NUCLEAR REGULATORY COMMISSION [NRC-2012-0070] Updated Aging Management Criteria for Reactor Vessel Internal Components of Pressurized Water Reactors AGENCY: Nuclear Regulatory Commission. ACTION: Draft...-ISG), LR-ISG-2011-04, ``Updated Aging Management Criteria for PWR Reactor Vessel Internal Components...

Nuclear Forensics International Technical Working Group (ITWG): a collaboration of scientists, law enforcement officials, and regulators working to combat nuclear terrorism and proliferation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwantes, Jon M.

Founded in 1996 upon the initiative of the “Group of 8” governments (G8), the Nuclear Forensics International Technical Working Group (ITWG) is an ad hoc organization of official Nuclear Forensics practitioners (scientists, law enforcement, and regulators) that can be called upon to provide technical assistance to the global community in the event of a seizure of nuclear or radiological materials. The ITWG is supported by and is affiliated with nearly 40 countries and international partner organizations including the International Atomic Energy Agency (IAEA), EURATOM, INTERPOL, EUROPOL, and the United Nations Interregional Crime and Justice Research Institute (UNICRI) (Figure 1). Besidesmore » providing a network of nuclear forensics laboratories that are able to assist the global community during a nuclear smuggling event, the ITWG is also committed to the advancement of the science of nuclear forensic analysis, largely through participation in periodic table top and Collaborative Materials Exercises (CMXs). Exercise scenarios use “real world” samples with realistic forensics investigation time constraints and reporting requirements. These exercises are designed to promote best practices in the field and test, evaluate, and improve new technical capabilities, methods and techniques in order to advance the science of nuclear forensics. Past efforts to advance nuclear forensic science have also included scenarios that asked laboratories to adapt conventional forensics methods (e.g. DNA, fingerprints, tool marks, and document comparisons) for collecting and preserving evidence comingled with radioactive materials.« less

Leveraging existing information for use in a National Nuclear Forensics Library (NNFL)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davydov, Jerry; Dion, Heather; LaMont, Stephen

A National Nuclear Forensics Library (NNFL) assists a State to assess whether nuclear material encountered out of regulatory control is of domestic or international origin. And by leveraging nuclear material registries, nuclear enterprise records, and safeguards accountancy information, as well as existing domestic technical capability and subject-matter domain expertise, states can better assess the effort required for setting up an NNFL. For states who are largely recipients of nuclear and radiological materials and have no internal production capabilities may create an NNFL that relies on existing information rather than carry out advanced analyses on domestic materials.

Leveraging existing information for use in a National Nuclear Forensics Library (NNFL)

DOE PAGES

Davydov, Jerry; Dion, Heather; LaMont, Stephen; ...

2015-12-16

A National Nuclear Forensics Library (NNFL) assists a State to assess whether nuclear material encountered out of regulatory control is of domestic or international origin. And by leveraging nuclear material registries, nuclear enterprise records, and safeguards accountancy information, as well as existing domestic technical capability and subject-matter domain expertise, states can better assess the effort required for setting up an NNFL. For states who are largely recipients of nuclear and radiological materials and have no internal production capabilities may create an NNFL that relies on existing information rather than carry out advanced analyses on domestic materials.

Molecular systematics of Gagea and Lloydia (Liliaceae; Liliales): implications of analyses of nuclear ribosomal and plastid DNA sequences for infrageneric classification

PubMed Central

Zarrei, M.; Wilkin, P.; Fay, M. F.; Ingrouille, M. J.; Zarre, S.; Chase, M. W.

2009-01-01

Background and Aims Gagea is a Eurasian genus of petaloid monocots, with a few species in North Africa, comprising between 70 and approximately 275 species depending on the author. Lloydia (thought to be the closest relative of Gagea) consists of 12–20 species that have a mostly eastern Asian distribution. Delimitation of these genera and their subdivisions are unresolved questions in Liliaceae taxonomy. The objective of this study is to evaluate generic and infrageneric circumscription of Gagea and Lloydia using DNA sequence data. Methods A phylogenetic study of Gagea and Lloydia (Liliaceae) was conducted using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid (rpl16 intron, trnL intron, trnL-F spacer, matK and the psbA-trnH spacer) DNA regions. This included 149 accessions (seven as outgroups), with multiple accessions of some taxa; 552 sequences were included, of which 393 were generated as part of this research. Key Results A close relationship of Gagea and Lloydia was confirmed in analyses using different datasets, but neither Gagea nor Lloydia forms a monophyletic group as currently circumscribed; however, the ITS and plastid analyses did not produce congruent results for the placement of Lloydia relative to the major groups within Gagea. Gagea accessions formed five moderately to strongly supported clades in all trees, with most Lloydia taxa positioned at the basal nodes; in the strict consensus trees from the combined data a basal polytomy occurs. There is limited congruence between the classical, morphology-derived infrageneric taxonomy in Gagea (including Lloydia) and clades in the present phylogenetic analyses. Conclusions The analyses support monophyly of Gagea/Lloydia collectively, and they clearly comprise a single lineage, as some previous authors have hypothesized. The results provide the basis for a new classification of Gagea that has support from some morphological features. Incongruence between plastid and nuclear ITS results is interpreted as potentially due to ancient hybridization and/or paralogy of ITS rDNA. PMID:19451146

History and Organizations for Radiological Protection.

PubMed

Kang, Keon Wook

2016-02-01

International Commission on Radiological Protection (ICRP), an independent international organization established in 1925, develops, maintains, and elaborates radiological protection standards, legislation, and guidelines. United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) provides scientific evidence. World Health Organization (WHO) and International Atomic Energy Agency (IAEA) utilise the ICRP recommendations to implement radiation protection in practice. Finally, radiation protection agencies in each country adopt the policies, and adapt them to each situation. In Korea, Nuclear Safety and Security Commission is the governmental body for nuclear safety regulation and Korea Institute of Nuclear Safety is a public organization for technical support and R&D in nuclear safety and radiation protection.

The anti-tumor drug bleomycin preferentially cleaves at the transcription start sites of actively transcribed genes in human cells.

PubMed

Murray, Vincent; Chen, Jon K; Galea, Anne M

2014-04-01

The genome-wide pattern of DNA cleavage at transcription start sites (TSSs) for the anti-tumor drug bleomycin was examined in human HeLa cells using next-generation DNA sequencing. It was found that actively transcribed genes were preferentially cleaved compared with non-transcribed genes. The 143,600 identified human TSSs were split into non-transcribed genes (82,596) and transcribed genes (61,004) for HeLa cells. These transcribed genes were further split into quintiles of 12,201 genes comprising the top 20, 20-40, 40-60, 60-80, and 80-100 % of expressed genes. The bleomycin cleavage pattern at highly transcribed gene TSSs was greatly enhanced compared with purified DNA and non-transcribed gene TSSs. The top 20 and 20-40 % quintiles had a very similar enhanced cleavage pattern, the 40-60 % quintile was intermediate, while the 60-80 and 80-100 % quintiles were close to the non-transcribed and purified DNA profiles. The pattern of bleomycin enhanced cleavage had peaks that were approximately 200 bp apart, and this indicated that bleomycin was identifying the presence of phased nucleosomes at TSSs. Hence bleomycin can be utilized to detect chromatin structures that are present at actively transcribed genes. In this study, for the first time, the pattern of DNA damage by a clinically utilized cancer chemotherapeutic agent was performed on a human genome-wide scale at the nucleotide level.

The phylogenetic position of an Armillaria species from Amami-Oshima, a subtropical island of Japan, based on elongation factor and ITS sequences

Treesearch

Yuko Ota; Mee-Sook Kim; Hitoshi Neda; Ned B. Klopfenstein; Eri Hasegawa

2011-01-01

An undetermined Armillaria species was collected on Amami-Oshima, a subtropical island of Japan. The phylogenetic position of the Armillaria sp. was determined using sequences of the elongation factor-1a (EF-1a) gene and the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) of ribosomal DNA (rDNA). The phylogenetic analyses based on EF-1a and ITS sequences...

Discovering Potential Pathogens among Fungi Identified as Nonsporulating Molds▿

PubMed Central

Pounder, June I.; Simmon, Keith E.; Barton, Claudia A.; Hohmann, Sheri L.; Brandt, Mary E.; Petti, Cathy A.

2007-01-01

Fungal infections are increasing, particularly among immunocompromised hosts, and a rapid diagnosis is essential to initiate antifungal therapy. Often fungi cannot be identified by conventional methods and are classified as nonsporulating molds (NSM).We sequenced internal transcribed spacer regions from 50 cultures of NSM and found 16 potential pathogens that can be associated with clinical disease. In selected clinical settings, identification of NSM could prove valuable and have an immediate impact on patient management. PMID:17135442

Two Endophytic Diaporthe Species Isolated from the Leaves of Astragalus membranaceus in Korea

PubMed Central

Kim, Jin-Hee; Kim, Dong-Yeo; Park, Hyeok

2017-01-01

We characterized two endophyte fungi from the leaves of Astragalus membranaceus in Korea. The isolated strains were identified on the basis of the morphological characters and sequences analysis of the internal transcribed spacer and large subunit regions of the rDNA and β-tubulin gene. To the best of our knowledge, this is the first report of Diaporthe oncostoma and Diaporthe infecunda in Korea, and we have provided descriptions and figures. PMID:29371813

Preliminary analysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals.

PubMed

Chow, S; Ueno, Y; Toyokawa, M; Oohara, I; Takeyama, H

2009-01-01

Length and guanine-cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 sequences (118 to 422 bp) with lower GC content (35.8% to 61.7%) than the other animal taxa. Mollusca and Crustacea were diverse groups with respect to ITS1 length, ranging from 108 to 1,118 and 182 to 1,613 bp, respectively. No universal relationship between length and GC content was observed. Our data indicated that ITS1 has a limited utility for phylogenetic analysis as obtaining confident sequence alignment was often impossible between different genera of the same family and even between congeneric species.

Identification of Aspergillus fumigatus and Related Species by Nested PCR Targeting Ribosomal DNA Internal Transcribed Spacer Regions

PubMed Central

Zhao, Jun; Kong, Fanrong; Li, Ruoyu; Wang, Xiaohong; Wan, Zhe; Wang, Duanli

2001-01-01

Aspergillus fumigatus is the most common species that causes invasive aspergillosis. In order to identify A. fumigatus, partial ribosomal DNA (rDNA) from two to six strains of five different Aspergillus species was sequenced. By comparing sequence data from GenBank, we designed specific primer pairs targeting rDNA internal transcribed spacer (ITS) regions of A. fumigatus. A nested PCR method for identification of other A. fumigatus-related species was established by using the primers. To evaluate the specificities and sensitivities of those primers, 24 isolates of A. fumigatus and variants, 8 isolates of Aspergillus nidulans, 7 isolates of Aspergillus flavus and variants, 8 isolates of Aspergillus terreus, 9 isolates of Aspergillus niger, 1 isolate each of Aspergillus parasiticus, Aspergillus penicilloides, Aspergillus versicolor, Aspergillus wangduanlii, Aspergillus qizutongii, Aspergillus beijingensis, and Exophiala dermatitidis, 4 isolates of Candida, 4 isolates of bacteria, and human DNA were used. The nested PCR method specifically identified the A. fumigatus isolates and closely related species and showed a high degree of sensitivity. Additionally, four A. fumigatus strains that were recently isolated from our clinic were correctly identified by this method. Our results demonstrate that these primers are useful for the identification of A. fumigatus and closely related species in culture and suggest further studies for the identification of Aspergillus fumigatus species in clinical specimens. PMID:11376067

ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences

PubMed Central

Santamaria, Monica; Fosso, Bruno; Licciulli, Flavio; Balech, Bachir; Larini, Ilaria; Grillo, Giorgio; De Caro, Giorgio; Liuni, Sabino

2018-01-01

Abstract A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels. As metabarcoding data analysis rely on the availability of a well-curated barcode reference resource, a comprehensive collection of ITS1 sequences supplied with robust taxonomies, is highly needed. To address this issue, we created ITSoneDB (available at http://itsonedb.cloud.ba.infn.it/) which in its current version hosts 985 240 ITS1 sequences spanning over 134 000 eukaryotic species. Each ITS1 is mapped on the NCBI reference taxonomy with its start and end positions precisely annotated. ITSoneDB has been developed in agreement to the FAIR guidelines by enabling the users to query and download its content through a simple web-interface and access relevant metadata by cross-linking to European Nucleotide Archive. PMID:29036529

Rapid Identification and Differentiation of Trichophyton Species, Based on Sequence Polymorphisms of the Ribosomal Internal Transcribed Spacer Regions, by Rolling-Circle Amplification▿

PubMed Central

Kong, Fanrong; Tong, Zhongsheng; Chen, Xiaoyou; Sorrell, Tania; Wang, Bin; Wu, Qixuan; Ellis, David; Chen, Sharon

2008-01-01

DNA sequencing analyses have demonstrated relatively limited polymorphisms within the fungal internal transcribed spacer (ITS) regions among Trichophyton spp. We sequenced the ITS region (ITS1, 5.8S, and ITS2) for 42 dermatophytes belonging to seven species (Trichophyton rubrum, T. mentagrophytes, T. soudanense, T. tonsurans, Epidermophyton floccosum, Microsporum canis, and M. gypseum) and developed a novel padlock probe and rolling-circle amplification (RCA)-based method for identification of single nucleotide polymorphisms (SNPs) that could be exploited to differentiate between Trichophyton spp. Sequencing results demonstrated intraspecies genetic variation for T. tonsurans, T. mentagrophytes, and T. soudanense but not T. rubrum. Signature sets of SNPs between T. rubrum and T. soudanense (4-bp difference) and T. violaceum and T. soudanense (3-bp difference) were identified. The RCA assay correctly identified five Trichophyton species. Although the use of two “group-specific” probes targeting both the ITS1 and the ITS2 regions were required to identify T. soudanense, the other species were identified by single ITS1- or ITS2-targeted species-specific probes. There was good agreement between ITS sequencing and the RCA assay. Despite limited genetic variation between Trichophyton spp., the sensitive, specific RCA-based SNP detection assay showed potential as a simple, reproducible method for the rapid (2-h) identification of Trichophyton spp. PMID:18234865

Internal transcribed spacer sequence-based rapid molecular identification of Prototheca zopfii and Prototheca blaschkeae directly from milk of infected cows.

PubMed

Marques, S; Huss, V A R; Pfisterer, K; Grosse, C; Thompson, G

2015-05-01

The increasing incidence of rare mastitis-causing pathogens has urged the implementation of fast and efficient diagnostic and control measures. Prototheca algae are known to be associated with diseases in humans and animals. In the latter, the most prevalent form of protothecosis is bovine mastitis with Prototheca zopfii and Prototheca blaschkeae representing the most common pathogenic species. These nonphotosynthetic and colorless green algae are ubiquitous in different environments and are widely resistant against harmful conditions and antimicrobials. Hence, the association of Prototheca with bovine mastitis represents a herd problem, requiring fast and easy identification of the infectious agent. The purpose of this study was to develop a reliable and rapid method, based on the internal transcribed spacer (ITS) sequences of ribosomal DNA, for molecular identification and discrimination between P. zopfii and P. blaschkeae in bovine mastitic milk. The complete ITS sequences of 32 Prototheca isolates showed substantial interspecies but moderate intraspecies variability facilitating the design of species-specific PCR amplification primers. The species-specific PCR was successfully applied to the identification of P. zopfii and P. blaschkeae directly from milk samples. The intraspecific ITS phylogeny was compared for each species with the geographical distribution of the respective Prototheca isolates, but no significant correlation was found. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Detection and Identification of Decay Fungi in Spruce Wood by Restriction Fragment Length Polymorphism Analysis of Amplified Genes Encoding rRNA†

PubMed Central

Jasalavich, Claudia A.; Ostrofsky, Andrea; Jellison, Jody

2000-01-01

We have developed a DNA-based assay to reliably detect brown rot and white rot fungi in wood at different stages of decay. DNA, isolated by a series of CTAB (cetyltrimethylammonium bromide) and organic extractions, was amplified by the PCR using published universal primers and basidiomycete-specific primers derived from ribosomal DNA sequences. We surveyed 14 species of wood-decaying basidiomycetes (brown-rot and white-rot fungi), as well as 25 species of wood-inhabiting ascomycetes (pathogens, endophytes, and saprophytes). DNA was isolated from pure cultures of these fungi and also from spruce wood blocks colonized by individual isolates of wood decay basidiomycetes or wood-inhabiting ascomycetes. The primer pair ITS1-F (specific for higher fungi) and ITS4 (universal primer) amplified the internal transcribed spacer region from both ascomycetes and basidiomycetes from both pure culture and wood, as expected. The primer pair ITS1-F (specific for higher fungi) and ITS4-B (specific for basidiomycetes) was shown to reliably detect the presence of wood decay basidiomycetes in both pure culture and wood; ascomycetes were not detected by this primer pair. We detected the presence of decay fungi in wood by PCR before measurable weight loss had occurred to the wood. Basidiomycetes were identified to the species level by restriction fragment length polymorphisms of the internal transcribed spacer region. PMID:11055916

The internal transcribed spacer of ribosomal RNA genes in plant trypanosomes (Phytomonas spp.) resolves 10 groups.

PubMed

Dollet, Michel; Sturm, Nancy R; Campbell, David A

2012-03-01

The distinction between plant trypanosomatids and opportunistic monoxenous insect trypanosomatids has not been demarcated clearly due to the mass placement of all trypanosomatids isolated from plants into the arbitrary genus Phytomonas spp. The advent of molecular markers has been useful in distinguishing plant trypanosomatids from the rest of the Trypanosomatidae family. Here we have examined the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) locus for classification purposes. This region contains two distinct ITSs flanked by the small subunit and large subunit of ribosomal RNA genes and separated by the 5.8S ribosomal RNA gene. Sequences within the 5.8S ribosomal RNA gene and in the ITS sequences can serve as specific markers for several of the Phytomonas groups. Microsatellite sequences were identified in Phytomonas spp. in both ITS regions. Several classes of microsatellites were seen, with inter-isolate variation that has potential for future use. Maximum Likelihood analysis of the ITS sequences of 20 Phytomonas isolates representing the eight defined groups and a few unclassified isolates revealed a total of 10 distinct subgroups within our collection, of which two are new. The ITS region, which includes the 5.8S sequence, is a robust marker for the subdivisions within the genus Phytomonas spp. Copyright © 2011 Elsevier B.V. All rights reserved.

An outlook on the fungal internal transcribed spacer sequences in GenBank and the introduction of a web-based tool for the exploration of fungal diversity.

PubMed

Ryberg, Martin; Kristiansson, Erik; Sjökvist, Elisabet; Nilsson, R Henrik

2009-01-01

The environmental and distributional data associated with fungal internal transcribed spacer (ITS) sequences in GenBank are investigated and a new web-based tool with which these sequences can be explored is introduced. All fungal ITS sequences in GenBank were classified as either identified to species level or insufficiently identified and compared using BLAST. The results are made available as a biweekly updated web service that can be queried to retrieve all insufficiently identified sequences (IIS) associated with any fungal genus. The most commonly available annotation items in GenBank are isolation source (55%); country of origin (50%); and specific host (38%). The molecular sampling of fungi shows a bias towards North America, Europe, China, and Japan whereas vast geographical areas remain effectively unexplored. Mycorrhizal and parasitic genera are on average associated with more IIS than are saprophytic taxa. Glomus, Alternaria, and Tomentella are the genera represented by the highest number of insufficiently identified ITS sequences in GenBank. The web service presented (http://andromeda.botany.gu.se/emerencia.html#genus_search) offers new means, particularly for mycorrhizal and plant pathogenic fungi, to examine the IIS in GenBank in a taxon-oriented framework and to explore their metadata in an easily accessible and time-efficient manner.

Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure.

PubMed

Ghosh, Jayadri Sekhar; Bhattacharya, Samik; Pal, Amita

2017-06-01

The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.

Novel species including Mycobacterium fukienense sp. is found from tuberculosis patients in Fujian Province, China, using phylogenetic analysis of Mycobacterium chelonae/abscessus complex.

PubMed

Zhang, Yuan Yuan; Li, Yan Bing; Huang, Ming Xiang; Zhao, Xiu Qin; Zhang, Li Shui; Liu, Wen En; Wan, Kang Lin

2013-11-01

To identify the novel species 'Mycobacterium fukienense' sp. nov of Mycobacterium chelonae/abscessus complex from tuberculosis patients in Fujian Province, China. Five of 27 clinical Mycobacterium isolates (Cls) were previously identified as M. chelonae/abscessus complex by sequencing the hsp65, rpoB, 16S-23S rRNA internal transcribed spacer region (its), recA and sodA house-keeping genes commonly used to describe the molecular characteristics of Mycobacterium. Clinical Mycobacterium isolates were classified according to the gene sequence using a clustering analysis program. Sequence similarity within clusters and diversity between clusters were analyzed. The 5 isolates were identified with distinct sequences exhibiting 99.8% homology in the hsp65 gene. However, a complete lack of homology was observed among the sequences of the rpoB, 16S-23S rRNA internal transcribed spacer region (its), sodA, and recA genes as compared with the M. abscessus. Furthermore, no match for rpoB, sodA, and recA genes was identified among the published sequences. The novel species, Mycobacterium fukienense, is identified from tuberculosis patients in Fujian Province, China, which does not belong to any existing subspecies of M. chelonea/abscessus complex. Copyright © 2013 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Definition of Eight Mulberry Species in the Genus Morus by Internal Transcribed Spacer-Based Phylogeny

PubMed Central

Zeng, Qiwei; Chen, Hongyu; Zhang, Chao; Han, Minjing; Li, Tian; Qi, Xiwu; Xiang, Zhonghuai; He, Ningjia

2015-01-01

Mulberry, belonging to the order Rosales, family Moraceae, and genus Morus, has received attention because of both its economic and medicinal value, as well as for its important ecological function. The genus Morus has a worldwide distribution, however, its taxonomy remains complex and disputed. Many studies have attempted to classify Morus species, resulting in varied numbers of designated Morus spp. To address this issue, we used information from internal transcribed spacer (ITS) genetic sequences to study the taxonomy of all the members of generally accepted genus Morus. We found that intraspecific 5.8S rRNA sequences were identical but that interspecific 5.8S sequences were diverse. M. alba and M. notabilis showed the shortest (215 bp) and the longest (233 bp) ITS1 sequence length, respectively. With the completion of the mulberry genome, we could identify single nucleotide polymorphisms within the ITS locus in the M. notabilis genome. From reconstruction of a phylogenetic tree based on the complete ITS data, we propose that the Morus genus should be classified into eight species, including M. alba, M. nigra, M. notabilis, M. serrata, M. celtidifolia, M. insignis, M. rubra, and M. mesozygia. Furthermore, the classification of the ITS sequences of known interspecific hybrid clones into both paternal and maternal clades indicated that ITS variation was sufficient to distinguish interspecific hybrids in the genus Morus. PMID:26266951

Retrograde movement of tRNAs from the cytoplasm to the nucleus in Saccharomyces cerevisiae

PubMed Central

Shaheen, Hussam H.; Hopper, Anita K.

2005-01-01

In eukaryotes, tRNAs transcribed in the nucleus function in cytoplasmic protein synthesis. The Ran-GTP-binding exportin, Los1p/Xpo-t, and additional pathway(s) mediate tRNA transport to the cytoplasm. Although tRNA movement was thought to be unidirectional, recent reports that yeast precursor tRNA splicing occurs in the cytoplasm, whereas fully spliced tRNAs can reside in the nucleus, require that either the precursor tRNA splicing machinery or mature tRNAs move from the cytoplasm to the nucleus. Our data argue against the first possibility and strongly support the second. Combining heterokaryon analysis with fluorescence in situ hybridization, we show that a foreign tRNA encoded by one nucleus can move from the cytoplasm to a second nucleus that does not encode the tRNA. We also discovered nuclear accumulation of endogenous cytoplasmic tRNAs in haploid yeast cells in response to nutritional deprivation. Nuclear accumulation of cytoplasmic tRNA requires Ran and the Mtr10/Kap111 member of the importin-β family. Retrograde tRNA nuclear import may provide a novel mechanism to regulate gene expression in eukaryotes. PMID:16040803

Retrograde movement of tRNAs from the cytoplasm to the nucleus in Saccharomyces cerevisiae.

PubMed

Shaheen, Hussam H; Hopper, Anita K

2005-08-09

In eukaryotes, tRNAs transcribed in the nucleus function in cytoplasmic protein synthesis. The Ran-GTP-binding exportin, Los1p/Xpo-t, and additional pathway(s) mediate tRNA transport to the cytoplasm. Although tRNA movement was thought to be unidirectional, recent reports that yeast precursor tRNA splicing occurs in the cytoplasm, whereas fully spliced tRNAs can reside in the nucleus, require that either the precursor tRNA splicing machinery or mature tRNAs move from the cytoplasm to the nucleus. Our data argue against the first possibility and strongly support the second. Combining heterokaryon analysis with fluorescence in situ hybridization, we show that a foreign tRNA encoded by one nucleus can move from the cytoplasm to a second nucleus that does not encode the tRNA. We also discovered nuclear accumulation of endogenous cytoplasmic tRNAs in haploid yeast cells in response to nutritional deprivation. Nuclear accumulation of cytoplasmic tRNA requires Ran and the Mtr10/Kap111 member of the importin-beta family. Retrograde tRNA nuclear import may provide a novel mechanism to regulate gene expression in eukaryotes.

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

PubMed Central

Yap, Karen; Lim, Zhao Qin; Khandelia, Piyush; Friedman, Brad; Makeyev, Eugene V.

2012-01-01

Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the underlying regulation is not well understood. Here we show that genes encoding critical presynaptic proteins are transcribed at a detectable level in both neurons and nonneuronal cells. However, in nonneuronal cells, the splicing of 3′-terminal introns within these genes is repressed by the polypyrimidine tract-binding protein (Ptbp1). This inhibits the export of incompletely spliced mRNAs to the cytoplasm and triggers their nuclear degradation. Clearance of these intron-containing transcripts occurs independently of the nonsense-mediated decay (NMD) pathway but requires components of the nuclear RNA surveillance machinery, including the nuclear pore-associated protein Tpr and the exosome complex. When Ptbp1 expression decreases during neuronal differentiation, the regulated introns are spliced out, thus allowing the accumulation of translation-competent mRNAs in the cytoplasm. We propose that this mechanism counters ectopic and precocious expression of functionally linked neuron-specific genes and ensures their coherent activation in the appropriate developmental context. PMID:22661231

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention.

PubMed

Yap, Karen; Lim, Zhao Qin; Khandelia, Piyush; Friedman, Brad; Makeyev, Eugene V

2012-06-01

Differentiated cells acquire unique structural and functional traits through coordinated expression of lineage-specific genes. An extensive battery of genes encoding components of the synaptic transmission machinery and specialized cytoskeletal proteins is activated during neurogenesis, but the underlying regulation is not well understood. Here we show that genes encoding critical presynaptic proteins are transcribed at a detectable level in both neurons and nonneuronal cells. However, in nonneuronal cells, the splicing of 3'-terminal introns within these genes is repressed by the polypyrimidine tract-binding protein (Ptbp1). This inhibits the export of incompletely spliced mRNAs to the cytoplasm and triggers their nuclear degradation. Clearance of these intron-containing transcripts occurs independently of the nonsense-mediated decay (NMD) pathway but requires components of the nuclear RNA surveillance machinery, including the nuclear pore-associated protein Tpr and the exosome complex. When Ptbp1 expression decreases during neuronal differentiation, the regulated introns are spliced out, thus allowing the accumulation of translation-competent mRNAs in the cytoplasm. We propose that this mechanism counters ectopic and precocious expression of functionally linked neuron-specific genes and ensures their coherent activation in the appropriate developmental context.

Assessment of the Risk of Medium-Term Internal Contamination in Minamisoma City, Fukushima, Japan, after the Fukushima Dai-ichi Nuclear Accident

PubMed Central

Gilmour, Stuart; Tsubokura, Masaharu; Nomura, Shuhei; Kami, Masahiro; Oikawa, Tomoyoshi; Kanazawa, Yukio; Shibuya, Kenji

2014-01-01

Background: The Fukushima Dai-ichi nuclear disaster, the first level-7 major nuclear disaster since Chernobyl, raised concerns about the future health consequences of exposure to and intake of radionuclides. Factors determining the risk and level of internal radiation contamination after a nuclear accident, which are a key to understanding and improving current nuclear disaster management, are not well studied. Objective: We investigated both the prevalence and level of internal contamination in residents of Minamisoma, and identified factors determining the risk and levels of contamination. Methods: We implemented a program assessing internal radiation contamination using a whole body counter (WBC) measurement and a questionnaire survey in Minamisoma, between October 2011 and March 2012. Results: Approximately 20% of the city’s population (8,829 individuals) participated in the WBC measurement for internal contamination, of which 94% responded to the questionnaire. The proportion of participants with detectable internal contamination was 40% in adults and 9% in children. The level of internal contamination ranged from 2.3 to 196.5 Bq/kg (median, 11.3 Bq/kg). Tobit regression analysis identified two main risk factors: more time spent outdoors, and intake of potentially contaminated foods and water. Conclusions: Our findings suggest that, with sensible and reasonable precautions, people may be able to live continuously in radiation-affected areas with limited contamination risk. To enable this, nuclear disaster response should strictly enforce food and water controls and disseminate evidence-based and up-to-date information about avoidable contamination risks. Citation: Sugimoto A, Gilmour S, Tsubokura M, Nomura S, Kami M, Oikawa T, Kanazawa Y, Shibuya K. 2014. Assessment of the risk of medium-term internal contamination in Minamisoma City, Fukushima, Japan, after the Fukushima Dai-ichi Nuclear accident. Environ Health Perspect 122:587–593; http://dx.doi.org/10.1289/ehp.1306848 PMID:24633072

State of practice and emerging application of analytical techniques of nuclear forensic analysis: highlights from the 4th Collaborative Materials Exercise of the Nuclear Forensics International Technical Working Group (ITWG)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwantes, Jon M.; Marsden, Oliva; Pellegrini, Kristi L.

Founded in 1996 upon the initiative of the “Group of 8” governments (G8), the Nuclear Forensics International Technical Working Group (ITWG) is an ad hoc organization of official nuclear forensics practitioners (scientists, law enforcement, and regulators) that can be called upon to provide technical assistance to the global community in the event of a seizure of nuclear or radiological materials. The ITWG is supported by and is affiliated with roughly 40 countries and international partner organizations including the International Atomic Energy Agency (IAEA), EURATOM, INTERPOL, EUROPOL, and the United Nations Interregional Crime and Justice Research Institute (UNICRI). Besides providing amore » network of nuclear forensics laboratories that are able to assist law enforcement during a nuclear smuggling event, the ITWG is also committed to the advancement of the science of nuclear forensic analysis, largely through participation in periodic table top and Collaborative Materials Exercises (CMXs). Exercise scenarios use “real world” samples with realistic forensics investigation time constraints and reporting requirements. These exercises are designed to promote best practices in the field and test, evaluate, and improve new technical capabilities, methods and techniques in order to advance the science of nuclear forensics. The ITWG recently completed its fourth CMX in the 20 year history of the organization. This was also the largest materials exercise to date, with participating laboratories from 16 countries or organizations. Three samples of low enriched uranium were shipped to these laboratories as part of an illicit trafficking scenario, for which each laboratory was asked to conduct nuclear forensic analyses in support of a fictitious criminal investigation. An objective review of the State Of Practice and Art of international nuclear forensic analysis based upon the outcome of this most recent exercise is provided.« less

Nuclear accumulation and activation of p53 in embryonic stem cells after DNA damage.

PubMed

Solozobova, Valeriya; Rolletschek, Alexandra; Blattner, Christine

2009-06-17

P53 is a key tumor suppressor protein. In response to DNA damage, p53 accumulates to high levels in differentiated cells and activates target genes that initiate cell cycle arrest and apoptosis. Since stem cells provide the proliferative cell pool within organisms, an efficient DNA damage response is crucial. In proliferating embryonic stem cells, p53 is localized predominantly in the cytoplasm. DNA damage-induced nuclear accumulation of p53 in embryonic stem cells activates transcription of the target genes mdm2, p21, puma and noxa. We observed bi-phasic kinetics for nuclear accumulation of p53 after ionizing radiation. During the first wave of nuclear accumulation, p53 levels were increased and the p53 target genes mdm2, p21 and puma were transcribed. Transcription of noxa correlated with the second wave of nuclear accumulation. Transcriptional activation of p53 target genes resulted in an increased amount of proteins with the exception of p21. While p21 transcripts were efficiently translated in 3T3 cells, we failed to see an increase in p21 protein levels after IR in embryonal stem cells. In embryonic stem cells where (anti-proliferative) p53 activity is not necessary, or even unfavorable, p53 is retained in the cytoplasm and prevented from activating its target genes. However, if its activity is beneficial or required, p53 is allowed to accumulate in the nucleus and activates its target genes, even in embryonic stem cells.

Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae.

PubMed

Kramer, Emily B; Hopper, Anita K

2013-12-24

In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional--from the nucleus to the cytoplasm. It is now known that mature tRNAs also move in a retrograde direction from the cytoplasm to the nucleus via retrograde tRNA nuclear import, a process that is conserved from yeast to vertebrates. The biological significance of this tRNA nuclear import is not entirely clear. We hypothesized that retrograde tRNA nuclear import might function in proofreading tRNAs to ensure that only proper tRNAs reside in the cytoplasm and interact with the translational machinery. Here we identify two major types of aberrant tRNAs in yeast: a 5', 3' end-extended, spliced tRNA and hypomodified tRNAs. We show that both types of aberrant tRNAs accumulate in mutant cells that are defective in tRNA nuclear traffic, suggesting that they are normally imported into the nucleus and are repaired or degraded. The retrograde pathway functions in parallel with the cytoplasmic rapid tRNA decay pathway previously demonstrated to monitor tRNA quality, and cells are not viable if they lack both pathways. Our data support the hypothesis that the retrograde process provides a newly discovered level of tRNA quality control as a pathway that monitors both end processing of pre-tRNAs and the modification state of mature tRNAs.

Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae

PubMed Central

Kramer, Emily B.; Hopper, Anita K.

2013-01-01

In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional—from the nucleus to the cytoplasm. It is now known that mature tRNAs also move in a retrograde direction from the cytoplasm to the nucleus via retrograde tRNA nuclear import, a process that is conserved from yeast to vertebrates. The biological significance of this tRNA nuclear import is not entirely clear. We hypothesized that retrograde tRNA nuclear import might function in proofreading tRNAs to ensure that only proper tRNAs reside in the cytoplasm and interact with the translational machinery. Here we identify two major types of aberrant tRNAs in yeast: a 5′, 3′ end-extended, spliced tRNA and hypomodified tRNAs. We show that both types of aberrant tRNAs accumulate in mutant cells that are defective in tRNA nuclear traffic, suggesting that they are normally imported into the nucleus and are repaired or degraded. The retrograde pathway functions in parallel with the cytoplasmic rapid tRNA decay pathway previously demonstrated to monitor tRNA quality, and cells are not viable if they lack both pathways. Our data support the hypothesis that the retrograde process provides a newly discovered level of tRNA quality control as a pathway that monitors both end processing of pre-tRNAs and the modification state of mature tRNAs. PMID:24297920

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

PubMed

Szczecińska, Monika; Sawicki, Jakub

2015-09-15

The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

PubMed Central

Szczecińska, Monika; Sawicki, Jakub

2015-01-01

Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae. PMID:26389887

Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.

PubMed

Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

2010-01-07

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

Pollen-mediated gene flow from transgenic perennial creeping bentgrass and hybridization at the landscape level

PubMed Central

Mallory-Smith, Carol Ann

2017-01-01

The planting of 162 ha of transgenic glyphosate-resistant creeping bentgrass (Agrostis stolonifera) near Madras, OR, USA, allowed a unique opportunity to study gene flow over time from a perennial outcrossing species at the landscape level. While conducting a four year in situ survey, we collected panicles and leaf tissue samples from creeping bentgrass and its sexually compatible species. Seeds from the panicles were planted, and seedlings were tested in the greenhouse for expression of the transgene. Gene flow via pollen was found in all four years, at frequencies of 0.004 to 2.805%. Chloroplast markers, in combination with internal transcribed spacer nuclear sequence analysis, were used to aid in identification of transgenic interspecific and intergeneric hybrid seedlings found during the testing and of established plants that could not be positively identified in the field. Interspecific transgenic hybrids produced on redtop (Agrostis gigantea) plants in situ were identified three of the four years and one intergeneric transgenic creeping bentgrass x rabbitfoot grass (Polypogon monspeliensis) hybrid was identified in 2005. In addition, we confirmed a non-transgenic creeping bentgrass x redtop hybrid in situ, demonstrating that interspecific hybrids have established in the environment outside production fields. Results of this study should be considered for deregulation of transgenic events, studies of population dynamics, and prediction of gene flow in the environment. PMID:28257488

Origins and Widespread Distribution of Co-existing Polyploids in Arnica cordifolia (Asteraceae)

PubMed Central

Kao, Rebecca Hufft

2008-01-01

Background and Aims Polyploidy is a central force structuring genetic diversity in angiosperms, but its ecological significance and modes of origin are not fully understood. This work investigated the patterns of coexistence and molecular relatedness of polyploids in the perennial herb, Arnica cordifolia. Methods The local- and broad-scale distributions of cytotypes were analysed using flow cytometry. Samples were collected from both roadside and understorey habitats to test the hypothesis of niche separation between triploids and tetraploids. The nuclear rDNA internal transcribed spacer (ITS) and plastid rpl16 spacer, trnL intron plus trnL-trnF spacer and trnK 3' intron regions were sequenced. Key Results Broad-scale sampling established that both triploids and tetraploids were common throughout the range of the species, pentaploids were rare, and diploids were not found. Local-scale sampling revealed coexistence of both triploids and tetraploids within the majority of sites. Triploids and tetraploids were equally represented in the understorey and roadside habitat. Triploids were more variable than tetraploids, but both cytotypes shared polymorphisms in ITS. Conclusions Coexistence of cytotypes appears to be the norm in A. cordifolia, but habitat differentiation (roadside vs. understorey) is not supported as a coexistence mechanism. Molecular analyses supported multiple events creating triploids but revealed a lack of variation in the tetraploids. Additionally, sequence polymorphisms in ITS suggested a hybridization event prior to polyploidization. PMID:17993653

Origins and widespread distribution of co-existing Polyploids in Arnica cordifolia (Asteraceae).

PubMed

Kao, Rebecca Hufft

2008-01-01

Polyploidy is a central force structuring genetic diversity in angiosperms, but its ecological significance and modes of origin are not fully understood. This work investigated the patterns of coexistence and molecular relatedness of polyploids in the perennial herb, Arnica cordifolia. The local- and broad-scale distributions of cytotypes were analysed using flow cytometry. Samples were collected from both roadside and understorey habitats to test the hypothesis of niche separation between triploids and tetraploids. The nuclear rDNA internal transcribed spacer (ITS) and plastid rpl16 spacer, trnL intron plus trnL-trnF spacer and trnK 3' intron regions were sequenced. Broad-scale sampling established that both triploids and tetraploids were common throughout the range of the species, pentaploids were rare, and diploids were not found. Local-scale sampling revealed coexistence of both triploids and tetraploids within the majority of sites. Triploids and tetraploids were equally represented in the understorey and roadside habitat. Triploids were more variable than tetraploids, but both cytotypes shared polymorphisms in ITS. Coexistence of cytotypes appears to be the norm in A. cordifolia, but habitat differentiation (roadside vs. understorey) is not supported as a coexistence mechanism. Molecular analyses supported multiple events creating triploids but revealed a lack of variation in the tetraploids. Additionally, sequence polymorphisms in ITS suggested a hybridization event prior to polyploidization.

Development of Species-Specific Primers for Agronomical Thrips and Multiplex Assay for Quarantine Identification of Western Flower Thrips.

PubMed

Yeh, W B; Tseng, M J; Chang, N T; Wu, S Y; Tsai, Y S

2014-10-01

While morphological identification of thrips species has been difficult because of their minute size and a lack of easily recognizable characteristics, molecular identification based on the development of specific molecular markers can be easily and reliably carried out. Among the known molecular markers, the nuclear internal transcribed spacer (ITS) exhibits distinguishable variations among thrips species. In this study, sequences of ITS2 region of 10 agriculturally important thrips were established to design species-specific primers for polymerase chain reaction (PCR). ITS2 sequence variations within these species were far less than those among species, indicating the suitability of this marker for species-specific primers design. These primers, though with one or two sporadically variable positions, showed a good efficacy within species. The specificity of these primers, examined on thrips species belonging to 15 genera, proved satisfactory. Furthermore, a multiplex PCR was used successfully for identifying Frankliniella occidentalis (Pergande), an insect pest monitored for quarantine purpose, and three additional thrips also commonly found in imported agricultural products and field samples, i.e., Thrips tabaci Lindeman, Thrips hawaiiensis (Morgan), and Frankliniella intonsa (Trybom). This study has demonstrated that specific primers and multiplex PCR based on ITS2 are reliable, convenient, and diagnostic tool to discriminate thrips species of quarantine and agricultural importance. © 2014 Entomological Society of America.

Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, Zhilin; Druzhinina, Irina S.; Labbé, Jessy

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found themore » genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. As a result, this work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.« less

Metabolic Profiling of Alpine and Ecuadorian Lichens.

PubMed

Mittermeier, Verena K; Schmitt, Nicola; Volk, Lukas P M; Suárez, Juan Pablo; Beck, Andreas; Eisenreich, Wolfgang

2015-10-01

Non-targeted ¹H-NMR methods were used to determine metabolite profiles from crude extracts of Alpine and Ecuadorian lichens collected from their natural habitats. In control experiments, the robustness of metabolite detection and quantification was estimated using replicate measurements of Stereocaulon alpinum extracts. The deviations in the overall metabolite fingerprints were low when analyzing S. alpinum collections from different locations or during different annual and seasonal periods. In contrast, metabolite profiles observed from extracts of different Alpine and Ecuadorian lichens clearly revealed genus- and species-specific profiles. The discriminating functions determining cluster formation in principle component analysis (PCA) were due to differences in the amounts of genus-specific compounds such as sticticin from the Sticta species, but also in the amounts of ubiquitous metabolites, such as sugar alcohols or trehalose. However, varying concentrations of these metabolites from the same lichen species e.g., due to different environmental conditions appeared of minor relevance for the overall cluster formation in PCA. The metabolic clusters matched phylogenetic analyses using nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences of lichen mycobionts, as exemplified for the genus Sticta. It can be concluded that NMR-based non-targeted metabolic profiling is a useful tool in the chemo-taxonomy of lichens. The same approach could also facilitate the discovery of novel lichen metabolites on a rapid and systematical basis.

Penicillium simile sp. nov. revealed by morphological and phylogenetic analysis.

PubMed

Davolos, Domenico; Pietrangeli, Biancamaria; Persiani, Anna Maria; Maggi, Oriana

2012-02-01

The morphology of three phenetically identical Penicillium isolates, collected from the bioaerosol in a restoration laboratory in Italy, displayed macro- and microscopic characteristics that were similar though not completely ascribable to Penicillium raistrickii. For this reason, a phylogenetic approach based on DNA sequencing analysis was performed to establish both the taxonomic status and the evolutionary relationships of these three peculiar isolates in relation to previously described species of the genus Penicillium. We used four nuclear loci (both rRNA and protein coding genes) that have previously proved useful for the molecular investigation of taxa belonging to the genus Penicillium at various evolutionary levels. The internal transcribed spacer region (ITS1-5.8S-ITS2), domains D1 and D2 of the 28S rDNA, a region of the tubulin beta chain gene (benA) and part of the calmodulin gene (cmd) were amplified by PCR and sequenced. Analysis of the rRNA genes and of the benA and cmd sequence data indicates the presence of three isogenic isolates belonging to a genetically distinct species of the genus Penicillium, here described and named Penicillium simile sp. nov. (ATCC MYA-4591(T)  = CBS 129191(T)). This novel species is phylogenetically different from P. raistrickii and other related species of the genus Penicillium (e.g. Penicillium scabrosum), from which it can be distinguished on the basis of morphological trait analysis.

Towards the onset of fruit tree growing north of the Alps: ancient DNA from waterlogged apple (Malus sp.) seed fragments.

PubMed

Schlumbaum, Angela; van Glabeke, Sabine; Roldan-Ruiz, Isabel

2012-01-20

Wild apples (Malus sp.) have been a major food source in the northern Alpine region since prehistory and their use is well understood. The onset of deliberate fruit tree growing in the area is, however, less clear. It is generally assumed that horticulture was practised in Roman times, but it might be even earlier. In the archaeological record seed testa and pericarp remains are particularly frequent at sites with waterlogged preservation such as lakeshore settlements or wells, pits and ditches, but the distinction between wild and domestic plants is not morphologically possible. With waterlogged remains being one main source of information about past fruit cultivation, we have tested the feasibility of analysing ancient DNA from waterlogged preserved bulk samples of testa fragments. We studied apple seeds from three Neolithic and three Roman sites with waterlogged preservation in the Alpine foreland. Chloroplast markers failed in all samples, but nuclear ITS1 (internal transcribed spacer region 1) of the ribosomal DNA was successfully typed in two Roman samples from the site Oedenburg/Biesheim-Kunheim (Haut-Rhin, F). The retrieved ITS1 sequences are identical to each other and are shared with wild Malus sylvestris and Malus sieversii, and with domestic apple cultivars, supporting the potential of using waterlogged remains for identifying the genetic status of apple diachronically. Copyright © 2011 Elsevier GmbH. All rights reserved.

Low Genetic Diversity in Wide-Spread Eurasian Liver Fluke Opisthorchis felineus Suggests Special Demographic History of This Trematode Species

PubMed Central

Brusentsov, Ilja I.; Katokhin, Alexey V.; Brusentsova, Irina V.; Shekhovtsov, Sergei V.; Borovikov, Sergei N.; Goncharenko, Grigoriy G.; Lider, Lyudmila A.; Romashov, Boris V.; Rusinek, Olga T.; Shibitov, Samat K.; Suleymanov, Marat M.; Yevtushenko, Andrey V.; Mordvinov, Viatcheslav A.

2013-01-01

Opisthorchis felineus or Siberian liver fluke is a trematode parasite (Opisthorchiidae) that infects the hepato-biliary system of humans and other mammals. Despite its public health significance, this wide-spread Eurasian species is one of the most poorly studied human liver flukes and nothing is known about its population genetic structure and demographic history. In this paper, we attempt to fill this gap for the first time and to explore the genetic diversity in O. felineus populations from Eastern Europe (Ukraine, European part of Russia), Northern Asia (Siberia) and Central Asia (Northern Kazakhstan). Analysis of marker DNA fragments from O. felineus mitochondrial cytochrome c oxidase subunit 1 and 3 (cox1, cox3) and nuclear rDNA internal transcribed spacer 1 (ITS1) sequences revealed that genetic diversity is very low across the large geographic range of this species. Microevolutionary processes in populations of trematodes may well be influenced by their peculiar biology. Nevertheless, we suggest that lack of population genetics structure observed in O. felineus can be primarily explained by the Pleistocene glacial events and subsequent sudden population growth from a very limited group of founders. Rapid range expansion of O. felineus through Asian and European territories after severe bottleneck points to a high dispersal potential of this trematode species. PMID:23634228

Root Character Evolution and Systematics in Cranichidinae, Prescottiinae and Spiranthinae (Orchidaceae, Cranichideae)

PubMed Central

Figueroa, Coyolxauhqui; Salazar, Gerardo A.; Zavaleta, H. Araceli; Engleman, E. Mark

2008-01-01

Background and Aims Previous studies have suggested that velamen characteristics are useful as taxonomic markers in Orchidaceae. Members of tribe Cranichideae have been assigned to two velamen types constructed based on combinations of characters such as the presence of secondary cell-wall thickenings and pores. However, such characters have not been analysed on an individual basis in explicit cladistic analyses. Methods The micromorphology of roots of 26 species of Cranichideae was examined through scanning electron microscopy and light microscopy, scoring the variation and distribution of four characters: number of velamen cell layers, velamen cell-wall thickenings, presence and type of tilosomes, and supraendodermal spaces. The last three characters were analysed cladistically in combination with DNA sequence data of plastid trnK/matK and nuclear ribosomal internal transcribed spacer (ITS) regions and optimized on the resulting phylogenetic tree. Key Results Thickenings of velamen cell walls group Prescottiinae with Spiranthinae, whereas tilosomes, documented here for the first time in Cranichideae, provide an unambiguous synapomorphy for subtribe Spiranthinae. Supraendodermal spaces occur mostly in species dwelling in seasonally dry habitats and appear to have evolved three times. Conclusions Three of the four structural characters assessed are phylogenetically informative, marking monophyletic groups recovered in the combined molecular–morphological analysis. This study highlights the need for conducting character-based structural studies to overcome analytical shortcomings of the typological approach. PMID:18263628

RAPHIDOPHYCEAE [CHADEFAUD EX SILVA] SYSTEMATICS AND RAPID IDENTIFICATION: SEQUENCE ANALYSES AND REAL-TIME PCR ASSAYS

PubMed Central

Bowers, Holly A.; Tomas, Carmelo; Tengs, Torstein; Kempton, Jason W.; Lewitus, Alan J.; Oldach, David W.

2010-01-01

Species within the class Raphidophyceae were associated with fish kill events in Japanese, European, Canadian, and U.S. coastal waters. Fish mortality was attributable to gill damage with exposure to reactive oxygen species (peroxide, superoxide, and hydroxide radicals), neurotoxins, physical clogging, and hemolytic substances. Morphological identification of these organisms in environmental water samples is difficult, particularly when fixatives are used. Because of this difficulty and the continued global emergence of these species in coastal estuarine waters, we initiated the development and validation of a suite of real-time polymerase chain reaction (PCR) assays. Sequencing was used to generate complete data sets for nuclear encoded small-subunit ribosomal RNA (SSU rRNA; 18S); internal transcribed spacers 1 and 2, 5.8S; and plastid encoded SSU rRNA (16S) for confirmed raphidophyte cultures from various geographic locations. Sequences for several Chattonella species (C. antiqua, C. marina, C. ovata, C. subsalsa, and C. verruculosa), Heterosigma akashiwo, and Fibrocapsa japonica were generated and used to design rapid and specific PCR assays for several species including C. verruculosa Hara et Chihara, C. subsalsa Biecheler, the complex comprised of C. marina Hara et Chihara, C. antiqua Ono and C. ovata, H. akashiwo Ono, and F. japonica Toriumi et Takano using appropriate loci. With this comprehensive data set, we were also able to perform phylogenetic analyses to determine the relationship between these species. PMID:20411032

Disseminated toxoplasmosis Toxoplasma gondii in a wild Florida manatee Trichechus manatus latirostris and seroprevalence in two wild populations.

PubMed

Smith, Lauren N; Waltzek, Thomas B; Rotstein, David S; Francis-Floyd, Ruth; Walsh, Michael T; Wellehan, James F X; Gerhold, Rick; Chapman, Alycia E; de Wit, Martine

2016-11-22

Marine mammals are important indicators for ecosystem health and serve as sentinel species for infectious agents including zoonoses. Histological examination of tissues from a stranded Florida manatee Trichechus manatus latirostris revealed protozoal cysts in the cerebrum and intrahistiocytic tachyzoites in the liver and caudal mesenteric lymph node. Disseminated Toxoplasma gondii infection was confirmed by immunohistochemistry and sequencing of the nuclear ribosomal internal transcribed spacer region of formalin-fixed tissues. The lack of baseline information on Florida manatees' exposure to this pathogen prompted a study into the seroprevalence of T. gondii in 2 separate geographic habitats in Florida, USA, during the winters from 2011-2014. Serum was collected during routine health assessments of 44 apparently healthy manatees from Crystal River (n = 26) on the west central coast of Florida and Brevard County (n = 18) on the east coast of Florida. Serum was screened for detection of T. gondii immunoglobulin G (IgG) antibodies via the modified agglutination test. Two animals from Crystal River from 2011 and 2012 (7.7%) and one animal from Brevard County from 2011 (5.6%) tested positive for T. gondii antibodies. Overall seroprevalence for T. gondii was low in the 2 sampled populations and may reflect a low seroprevalence or animal susceptibility. However, continued monitoring of this pathogen in aquatic ecosystems is warranted due to both possible anthropogenic sources and zoonotic potential.

A molecular phylogeny and classification of Leptochloa (Poaceae: Chloridoideae: Chlorideae) sensu lato and related genera

PubMed Central

Peterson, Paul M.; Romaschenko, Konstantin; Snow, Neil; Johnson, Gabriel

2012-01-01

Background and Aims Leptochloa (including Diplachne) sensu lato (s.l.) comprises a diverse assemblage of C4 (NAD-ME and PCK) grasses with approx. 32 annual or perennial species. Evolutionary relationships and a modern classification of Leptochloa spp. based on the study of molecular characters have only been superficially investigated in four species. The goals of this study were to reconstruct the evolutionary history of Leptochloa s.l. with molecular data and broad taxon sampling. Methods A phylogenetic analysis was conducted of 130 species (mostly Chloridoideae), of which 22 are placed in Leptochloa, using five plastid (rpL32-trn-L, ndhA intron, rps16 intron, rps16-trnK and ccsA) and the nuclear ITS 1 and 2 (ribosomal internal transcribed spacer regions) to infer evolutionary relationships and revise the classification. Key results Leptochloa s.l. is polyphyletic and strong support was found for five lineages. Embedded within the Leptochloa sensu stricto (s.s.) clade are two Trichloris spp. and embedded in Dinebra are Drake-brockmania and 19 Leptochloa spp. Conclusions The molecular results support the dissolution of Leptochloa s.l. into the following five genera: Dinebra with 23 species, Diplachne with two species, Disakisperma with three species, Leptochloa s.s. with five species and a new genus, Trigonochloa, with two species. PMID:22628365

Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain.

PubMed

Esteves, F; Montes-Cano, M A; de la Horra, C; Costa, M C; Calderón, E J; Antunes, F; Matos, O

2008-04-01

Pneumonia caused by the opportunistic organism Pneumocystis jirovecii is a clinically important infection affecting AIDS and other immunocompromised patients. The present study aimed to compare and characterise the frequency pattern of DNA sequences from the P. jirovecii mitochondrial large-subunit rRNA (mtLSU rRNA) gene, the dihydropteroate synthase (DHPS) gene and the internal transcribed spacer (ITS) regions of the nuclear rRNA operon in specimens from Lisbon (Portugal) and Seville (Spain). Total DNA was extracted and used for specific molecular sequence analysis of the three loci. In both populations, mtLSU rRNA gene analysis revealed an overall prevalence of genotype 1. In the Portuguese population, genotype 2 was the second most common, followed by genotype 3. Inversely, in the Spanish population, genotype 3 was the second most common, followed by genotype 2. The DHPS wild-type sequence was the genotype observed most frequently in both populations, and the DHPS genotype frequency pattern was identical to distribution patterns revealed in other European studies. ITS types showed a significant diversity in both populations because of the high sequence variability in these genomic regions. The most prevalent ITS type in the Portuguese population was Eg, followed by Cg. In contrast to other European studies, Bi was the most common ITS type in the Spanish samples, followed by Eg. A statistically significant association between mtLSU rRNA genotype 1 and ITS type Eg was revealed.

Pneumocystis jiroveci in Portuguese immunocompromised patients: association of specific ITS genotypes with treatment failure, bad clinical outcome and childhood.

PubMed

Matos, Olga; Lee, Chao-Hung; Jin, Shaoling; Li, Baozheng; Costa, Marina C; Gonçalves, Luzia; Antunes, Francisco

2003-11-01

We analyzed the genetic variation among isolates of Pneumocystis jiroveci from Portuguese immunocompromised patients with PCP at the internal transcribed spacer (ITS) regions of the nuclear rRNA operon and at the dihydropteroate synthase (DHPS) gene. Pulmonary secretions from 42 patients with PCP corresponding to 43 episodes were studied. Demographic, immunological, and clinical data were obtained from all patients. By combining the two regions ITS1 and ITS2, we found 17 different ITS types of P. jiroveci, two of them were new types (Pb and Pe). The four most prevalent ITS types were Eg (23.3%), Eb and Ne (11.6% each), and Bi (9.3%). A single type was detected in 95.3% of the samples and 4.7% had mixed infections with three different ITS types. DHPS mutants were present in 17 (46%), and the wildtype was present in 20 (54%) of 37 isolates. No association was found between ITS and DHPS types and between DHPS types and therapy or response to anti-PCP treatment. Type Ne presented an association with negative response to anti-PCP treatment (P<0.001) and with death before 120 days after PCP diagnosis (P=0.025). Type Eb was significantly more common in children than in adults (P=0.001). Our data suggest an association of specific ITS genotypes with treatment failure, bad clinical outcome and childhood.

Inter-individual and intragenomic variations in the ITS region of Clonorchis sinensis (Trematoda: Opisthorchiidae) from Russia and Vietnam.

PubMed

Tatonova, Yulia V; Chelomina, Galina N; Nguyen, Hung Manh

2017-11-01

Here we examined the intraspecific genetic variability of Clonorchis sinensis from Russia and Vietnam using nuclear DNA sequences (the 5.8S gene and two internal transcribed spacers of the ribosomal cluster). Despite the low level of variability in the ITS1 region, this marker has revealed some features of C. sinensis across multiple geographic regions. The genetic diversity levels for the Russian and Vietnamese populations were similar (0.1 and 0.09%, respectively) but were significantly lower than the C. sinensis from China (0.31%). About half of the sequences of the Chinese (53%) and Korean (47%) populations and about a tenth of the Vietnamese (12%) and Russian (8%) sequences included a 5bp insertion. No sequences with nucleotide substitutions both upstream and downstream of the 5bp insertion were found within the whole data set. The population of northern China had both sequence variants (with substitutions either upstream or downstream of the insertion), while only one of these variants was presented at the other localities. The Vietnamese population had a higher frequency of intragenomic polymorphism than the Russian population (69% vs. 46% and 23% vs. 3% at the 114bp and 339bp positions, respectively). These data are discussed in connection with parasite origin and adaptation, and also its invasive capacity and drug-resistance. Copyright © 2017 Elsevier B.V. All rights reserved.

Specialized microbiome of a halophyte and its role in helping non-host plants to withstand salinity

DOE PAGES

Yuan, Zhilin; Druzhinina, Irina S.; Labbé, Jessy; ...

2016-08-30

Root microbiota is a crucial determinant of plant productivity and stress tolerance. Here, we hypothesize that the superior halo-tolerance of seepweed Suaeda salsa is tightly linked to a specialized belowground microbiome. To test this hypothesis, we performed a phylogenetic trait-based framework analysis based on bacterial 16S rRNA gene and fungal nuclear rRNA internal transcribed spacer profiling. Data showed that the dominant α-proteobacteria and γ-proteobacteria communities in bulk soil and root endosphere tend to be phylogenetically clustered and at the same time exhibit phylogenetic over-dispersion in rhizosphere. Likewise, the dominant fungal genera occurred at high phylogenetic redundancy. Interestingly, we found themore » genomes of rhizospheric and endophytic bacteria associated with S. salsa to be enriched in genes contributing to salt stress acclimatization, nutrient solubilization and competitive root colonization. A wide diversity of rhizobacteria with similarity to known halotolerant taxa further supported this interpretation. These findings suggest that an ecological patterned root-microbial interaction strategy has been adopted in S. salsa system to confront soil salinity. We also demonstrated that the potential core microbiome members improve non-host plants growth and salt tolerance. As a result, this work provides a platform to improve plant fitness with halophytes-microbial associates and novel insights into the functions of plant microbiome under salinity.« less

Pollen-mediated gene flow from transgenic perennial creeping bentgrass and hybridization at the landscape level.

PubMed

Zapiola, María Luz; Mallory-Smith, Carol Ann

2017-01-01

The planting of 162 ha of transgenic glyphosate-resistant creeping bentgrass (Agrostis stolonifera) near Madras, OR, USA, allowed a unique opportunity to study gene flow over time from a perennial outcrossing species at the landscape level. While conducting a four year in situ survey, we collected panicles and leaf tissue samples from creeping bentgrass and its sexually compatible species. Seeds from the panicles were planted, and seedlings were tested in the greenhouse for expression of the transgene. Gene flow via pollen was found in all four years, at frequencies of 0.004 to 2.805%. Chloroplast markers, in combination with internal transcribed spacer nuclear sequence analysis, were used to aid in identification of transgenic interspecific and intergeneric hybrid seedlings found during the testing and of established plants that could not be positively identified in the field. Interspecific transgenic hybrids produced on redtop (Agrostis gigantea) plants in situ were identified three of the four years and one intergeneric transgenic creeping bentgrass x rabbitfoot grass (Polypogon monspeliensis) hybrid was identified in 2005. In addition, we confirmed a non-transgenic creeping bentgrass x redtop hybrid in situ, demonstrating that interspecific hybrids have established in the environment outside production fields. Results of this study should be considered for deregulation of transgenic events, studies of population dynamics, and prediction of gene flow in the environment.

Allopolyploidization and evolution of species with reduced floral structures in Lepidium L. (Brassicaceae)

PubMed Central

Lee, Ji-Young; Mummenhoff, Klaus; Bowman, John L.

2002-01-01

Understanding the pattern of speciation in a group of plants is critical for understanding its morphological evolution. Lepidium is the genus with the largest variation in floral structure in Brassicaceae, a family in which the floral ground plan is remarkably stable. However, flowers in more than half of Lepidium species have reduced stamen numbers, and most of these also have reduced petals. The species with reduced flowers are geographically biased, distributed mostly in the Americas and Australia/ New Zealand. Previous phylogenetic studies using noncoding regions of chloroplast DNA and rDNA internal transcribed spacer were incongruent in most New World species relationships. These data, combined with the presence of many polyploid Lepidium species, implied a reticulate history of the genus but did not provide enough information to infer the evolutionary pattern of flower structures. To address this question more thoroughly, sequences of the first intron of a single copy nuclear gene, PISTILLATA, were determined from 43 species. Phylogenetic analysis of the PI intron suggests that many species in the New World have originated from allopolyploidization, and that this is correlated with floral reduction. Interspecific hybrids were generated to understand why allopolyploidization is associated with reduced flowers. The phenotypes of F1 flowers indicate allelic dominance of the absence of lateral stamens, suggesting that propagation of dominant alleles through interspecific hybridization could account for the abundance of the allopolyploid species without lateral stamens. PMID:12481035

Novel Curvularia species from clinical specimens.

PubMed

Madrid, H; da Cunha, K C; Gené, J; Dijksterhuis, J; Cano, J; Sutton, D A; Guarro, J; Crous, P W

2014-12-01

The fungal genus Curvularia includes numerous plant pathogens and some emerging opportunistic pathogens of humans. In a previous study we used morphology and sequences of the nuclear ribosomal internal transcribed spacer region (ITS) and the glyceraldehyde-3-phosphate dehydrogenase (gpd) gene to identify species within a set of 99 clinical Curvularia isolates from the USA. Seventy-two isolates could be identified while the remaining 27 isolates belonged in three unclassified clades that were tentatively labelled Curvularia sp. I, II and III. In the present study, we further assess the taxonomic placement of these isolates using sequences of ITS, gpd, the large subunit rDNA, and the second largest subunit of RNA polymerase II. DNA sequence comparisons with a set of 87 isolates representing 33 Curvularia spp. and members of the closely-related genera Bipolaris and Exserohilum revealed that Curvularia sp. I, II and III represent novel lineages in Curvularia. These lineages are morphologically different from the currently accepted species. In the phylogenetic tree, Curvularia sp. I and sp. III were each split into two distinct lineages. Morphology and phylogeny supported the proposal of five new species, to be named C. americana, C. chlamydospora, C. hominis, C. muehlenbeckiae and C. pseudolunata. The concatenated 4-locus phylogeny revealed the existence of six clades in Curvularia, which are associated with particular morphological features. They were named after representative species, namely americana, eragrostidis, hominis, lunata, spicifera and trifolii.

Diverse tulasnelloid fungi form mycorrhizas with epiphytic orchids in an Andean cloud forest.

PubMed

Suárez, Juan Pablo; Weiss, Michael; Abele, Andrea; Garnica, Sigisfredo; Oberwinkler, Franz; Kottke, Ingrid

2006-11-01

The mycorrhizal state of epiphytic orchids has been controversially discussed, and the state and mycobionts of the pleurothallid orchids, occurring abundantly and with a high number of species on stems of trees in the Andean cloud forest, were unknown. Root samples of 77 adult individuals of the epiphytic orchids Stelis hallii, S. superbiens, S. concinna and Pleurothallis lilijae were collected in a tropical mountain rainforest of southern Ecuador. Ultrastructural evidence of symbiotic interaction was combined with molecular sequencing of fungi directly from the mycorrhizas and isolation of mycobionts. Ultrastructural analyses displayed vital orchid mycorrhizas formed by fungi with an imperforate parenthesome and cell wall slime bodies typical for the genus Tulasnella. Three different Tulasnella isolates were obtained in pure culture. Phylogenetic analysis of nuclear rDNA sequences from coding regions of the ribosomal large subunit (nucLSU) and the 5.8S subunit, including parts of the internal transcribed spacers, obtained directly from the roots and from the fungal isolates, yielded seven distinct Tulasnella clades. Tulasnella mycobionts in Stelis concinna were restricted to two Tulasnella sequence types while the other orchids were associated with up to six Tulasnella sequence types. All Tulasnella sequences are new to science and distinct from known sequences of mycobionts of terrestrial orchids. The results indicate that tulasnelloid fungi, adapted to the conditions on tree stems, might be important for orchid growth and maintenance in the Andean cloud forest.

Rapid nested PCR-based detection of Ramularia collo-cygni direct from barley.

PubMed

Havis, Neil D; Oxley, Simonj P; Piper, Stephen R; Langrell, Stephen R H

2006-03-01

Ramularia collo-cygni is a barley pathogen of increasing importance in Northern and Central Europe, New Zealand and South America. Accurate visual and microscopic identification of the pathogen from diseased tissue is difficult. A nested PCR-based diagnostic test has been developed as part of an initiative to map the distribution of the pathogen in Scotland. The entire nuclear ribosomal internal transcribed spacer and 5.8S rRNA gene regions from 14 isolates of diverse global origin exhibited complete homology following sequence characterization. Two pairs of species-specific primers, based on inter-specific sequence divergence with closely related species, were designed and empirically evaluated for diagnostic nested PCR. Nested primers Rcc3 and Rcc4 consistently amplified a single product of 256 bp from DNA of 24 R. collo-cygni isolates of diverse global provenance, but not from other Ramularia species, or other fungi commonly encountered in cereal pathosystems, as well as Hordeum or Secale DNA preparations. Using this approach, R. collo-cygni was successfully identified from naturally infected barley leaf, awn and grain samples of diverse geographical provenance, in particular from symptoms that lacked the presence of characteristic conidiophores. It is envisaged that this assay will become established as an important tool in continuing studies into the ecology, aetiology and epidemiology of this poorly understood yet economically damaging plant pathogen.

Soft Coral Sarcophyton (Cnidaria: Anthozoa: Octocorallia) Species Diversity and Chemotypes

PubMed Central

Aratake, Satoe; Tomura, Tomohiko; Saitoh, Seikoh; Yokokura, Ryouma; Kawanishi, Yuichi; Shinjo, Ryuichi; Reimer, James Davis; Tanaka, Junichi; Maekawa, Hideaki

2012-01-01

Research on the soft coral genus Sarcophyton extends over a wide range of fields, including marine natural products and the isolation of a number of cembranoid diterpenes. However, it is still unknown how soft corals produce this diverse array of metabolites, and the relationship between soft coral diversity and cembranoid diterpene production is not clear. In order to understand this relationship, we examined Sarcophyton specimens from Okinawa, Japan, by utilizing three methods: morphological examination of sclerites, chemotype identification, and phylogenetic examination of both Sarcophyton (utilizing mitochondrial protein-coding genes MutS homolog: msh1) and their endosymbiotic Symbiodinium spp. (utilizing nuclear internal transcribed spacer of ribosomal DNA: ITS- rDNA). Chemotypes, molecular phylogenetic clades, and sclerites of Sarcophyton trocheliophorum specimens formed a clear and distinct group, but the relationships between chemotypes, molecular phylogenetic clade types and sclerites of the most common species, Sarcophyton glaucum, was not clear. S. glaucum was divided into four clades. A characteristic chemotype was observed within one phylogenetic clade of S. glaucum. Identities of symbiotic algae Symbiodinium spp. had no apparent relation to chemotypes of Sarcophyton spp. This study demonstrates that the complex results observed for S. glaucum are due to the incomplete and complex taxonomy of this species group. Our novel method of identification should help contribute to classification and taxonomic reassessment of this diverse soft coral genus. PMID:22272344

Soft coral Sarcophyton (Cnidaria: Anthozoa: Octocorallia) species diversity and chemotypes.

PubMed

Aratake, Satoe; Tomura, Tomohiko; Saitoh, Seikoh; Yokokura, Ryouma; Kawanishi, Yuichi; Shinjo, Ryuichi; Reimer, James Davis; Tanaka, Junichi; Maekawa, Hideaki

2012-01-01

Research on the soft coral genus Sarcophyton extends over a wide range of fields, including marine natural products and the isolation of a number of cembranoid diterpenes. However, it is still unknown how soft corals produce this diverse array of metabolites, and the relationship between soft coral diversity and cembranoid diterpene production is not clear. In order to understand this relationship, we examined Sarcophyton specimens from Okinawa, Japan, by utilizing three methods: morphological examination of sclerites, chemotype identification, and phylogenetic examination of both Sarcophyton (utilizing mitochondrial protein-coding genes MutS homolog: msh1) and their endosymbiotic Symbiodinium spp. (utilizing nuclear internal transcribed spacer of ribosomal DNA: ITS- rDNA). Chemotypes, molecular phylogenetic clades, and sclerites of Sarcophyton trocheliophorum specimens formed a clear and distinct group, but the relationships between chemotypes, molecular phylogenetic clade types and sclerites of the most common species, Sarcophyton glaucum, was not clear. S. glaucum was divided into four clades. A characteristic chemotype was observed within one phylogenetic clade of S. glaucum. Identities of symbiotic algae Symbiodinium spp. had no apparent relation to chemotypes of Sarcophyton spp. This study demonstrates that the complex results observed for S. glaucum are due to the incomplete and complex taxonomy of this species group. Our novel method of identification should help contribute to classification and taxonomic reassessment of this diverse soft coral genus.

Taxonomic study on Japanese Salvia (Lamiaceae): Phylogenetic position of S. akiensis, and polyphyletic nature of S. lutescens var. intermedia.

PubMed

Takano, Atsuko

2017-01-01

Both Salvia akiensis and S. lutescens (Lamiaceae) are endemic to Japan. Salvia akiensis was recently described in 2014 in the Chugoku (= SW Honshu) region, and each four varieties of S. lutescens distributed allopatrically. Among varieties in S. lutescens , var. intermedia show a disjunctive distribution in the Kanto (=E Honshu) and Kinki (= W Honshu) regions. Recent field studies of S. lutescens var. intermedia revealed several morphological differences between the Kanto and Kinki populations. Here, I evaluated these differences among Salvia lutescens var. intermedia and its allies with morphological analysis and molecular phylogenetic analyses of nuclear ribosomal DNA (internal and external transcribed spacer regions) and plastid DNA ( ycf1-rps15 spacer, rbcL , and trnL-F ) sequences. Both morphological analysis and molecular phylogenetic analyses showed that S. lutescens var. intermedia from the Kinki region and var. lutescens were closely related to each other. However, var. intermedia from the Kanto region exhibited an association with S. lutescens var. crenata and var. stolonifera, which also grew in eastern Japan, rather than var. intermedia in the Kinki region. These results indicated that S. lutescens var. intermedia is not a taxon with a disjunctive distribution, but a combination of two or more allopatric taxa. Present study also suggested that S. akiensis was most closely related to S. omerocalyx .

Evidence that the Ceratobasidium-like white-thread blight and black rot fungal pathogens from persimmon and tea crops in the Brazilian Atlantic Forest agroecosystem are two distinct phylospecies.

PubMed

Ceresini, Paulo C; Costa-Souza, Elaine; Zala, Marcello; Furtado, Edson L; Souza, Nilton L

2012-04-01

The white-thread blight and black rot (WTBR) caused by basidiomycetous fungi of the genus Ceratobasidium is emerging as an important plant disease in Brazil, particularly for crop species in the Ericales such as persimmon (Diospyros kaki) and tea (Camellia sinensis). However, the species identity of the fungal pathogen associated with either of these hosts is still unclear. In this work, we used sequence variation in the internal transcribed spacer regions, including the 5.8S coding region of rDNA (ITS-5.8S rDNA), to determine the phylogenetic placement of the local white-thread-blight-associated populations of Ceratobasidium sp. from persimmon and tea, in relation to Ceratobasidium species already described world-wide. The two sister populations of Ceratobasidium sp. from persimmon and tea in the Brazilian Atlantic Forest agroecosystem most likely represent distinct species within Ceratobasidium and are also distinct from C. noxium, the etiological agent of the first description of white-thread blight disease that was reported on coffee in India. The intraspecific variation for the two Ceratobasidium sp. populations was also analyzed using three mitochondrial genes (ATP6, nad1 and nad2). As reported for other fungi, variation in nuclear and mitochondrial DNA was incongruent. Despite distinct variability in the ITS-rDNA region these two populations shared similar mitochondrial DNA haplotypes.

Applications of three DNA barcodes in assorting intertidal red macroalgal flora in Qingdao, China

NASA Astrophysics Data System (ADS)

Zhao, Xiaobo; Pang, Shaojun; Shan, Tifeng; Liu, Feng

2013-03-01

This study is part of the endeavor to construct a comprehensive DNA barcoding database for common seaweeds in China. Identifications of red seaweeds, which have simple morphology and anatomy, are sometimes difficult solely depending on morphological characteristics. In recent years, DNA barcode technique has become a more and more effective tool to help solve some of the taxonomic difficulties. Some DNA markers such as COI (cytochrome oxidase subunit I) are proposed as standardized DNA barcodes for all seaweed species. In this study, COI, UPA (universal plastid amplicon, domain V of 23S rRNA), and ITS (nuclear internal transcribed spacer) were employed to analyze common species of intertidal red seaweeds in Qingdao (119.3°-121°E, 35.35°-37.09°N). The applicability of using one or a few combined barcodes to identify red seaweed species was tested. The results indicated that COI is a sensitive marker at species level. However, not all the tested species gave PCR amplification products due to lack of the universal primers. The second barcode UPA had effective universal primers but needed to be tested for the effectiveness of resolving closely related species. More than one ITS sequence types were found in some species in this investigation, which might lead to confusion in further analysis. Therefore ITS sequence is not recommended as a universal barcode for seaweeds identification.

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

PubMed

Schoch, Conrad L; Robbertse, Barbara; Robert, Vincent; Vu, Duong; Cardinali, Gianluigi; Irinyi, Laszlo; Meyer, Wieland; Nilsson, R Henrik; Hughes, Karen; Miller, Andrew N; Kirk, Paul M; Abarenkov, Kessy; Aime, M Catherine; Ariyawansa, Hiran A; Bidartondo, Martin; Boekhout, Teun; Buyck, Bart; Cai, Qing; Chen, Jie; Crespo, Ana; Crous, Pedro W; Damm, Ulrike; De Beer, Z Wilhelm; Dentinger, Bryn T M; Divakar, Pradeep K; Dueñas, Margarita; Feau, Nicolas; Fliegerova, Katerina; García, Miguel A; Ge, Zai-Wei; Griffith, Gareth W; Groenewald, Johannes Z; Groenewald, Marizeth; Grube, Martin; Gryzenhout, Marieka; Gueidan, Cécile; Guo, Liangdong; Hambleton, Sarah; Hamelin, Richard; Hansen, Karen; Hofstetter, Valérie; Hong, Seung-Beom; Houbraken, Jos; Hyde, Kevin D; Inderbitzin, Patrik; Johnston, Peter R; Karunarathna, Samantha C; Kõljalg, Urmas; Kovács, Gábor M; Kraichak, Ekaphan; Krizsan, Krisztina; Kurtzman, Cletus P; Larsson, Karl-Henrik; Leavitt, Steven; Letcher, Peter M; Liimatainen, Kare; Liu, Jian-Kui; Lodge, D Jean; Luangsa-ard, Janet Jennifer; Lumbsch, H Thorsten; Maharachchikumbura, Sajeewa S N; Manamgoda, Dimuthu; Martín, María P; Minnis, Andrew M; Moncalvo, Jean-Marc; Mulè, Giuseppina; Nakasone, Karen K; Niskanen, Tuula; Olariaga, Ibai; Papp, Tamás; Petkovits, Tamás; Pino-Bodas, Raquel; Powell, Martha J; Raja, Huzefa A; Redecker, Dirk; Sarmiento-Ramirez, J M; Seifert, Keith A; Shrestha, Bhushan; Stenroos, Soili; Stielow, Benjamin; Suh, Sung-Oui; Tanaka, Kazuaki; Tedersoo, Leho; Telleria, M Teresa; Udayanga, Dhanushka; Untereiner, Wendy A; Diéguez Uribeondo, Javier; Subbarao, Krishna V; Vágvölgyi, Csaba; Visagie, Cobus; Voigt, Kerstin; Walker, Donald M; Weir, Bevan S; Weiß, Michael; Wijayawardene, Nalin N; Wingfield, Michael J; Xu, J P; Yang, Zhu L; Zhang, Ning; Zhuang, Wen-Ying; Federhen, Scott

2014-01-01

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353. Published by Oxford University Press 2013. This work is written by US Government employees and is in the public domain in the US.

The Voice Transcription Technique: Use of Voice Recognition Software to Transcribe Digital Interview Data in Qualitative Research

ERIC Educational Resources Information Center

Matheson, Jennifer L.

2007-01-01

Transcribing interview data is a time-consuming task that most qualitative researchers dislike. Transcribing is even more difficult for people with physical limitations because traditional transcribing requires manual dexterity and the ability to sit at a computer for long stretches of time. Researchers have begun to explore using an automated…

Technical Guidance from the International Safety Framework for Nuclear Power Source Applications in Outer Space for Design and Development Phases

NASA Astrophysics Data System (ADS)

Summerer, Leopold

2014-08-01

In 2009, the International Safety Framework for Nuclear Power Source Applications in Outer Space [1] has been adopted, following a multi-year process that involved all major space faring nations in the frame of the International Atomic Energy Agency and the UN Committee on the Peaceful Uses of Outer Space. The safety framework reflects an international consensus on best practices. After the older 1992 Principles Relevant to the Use of Nuclear Power Sources in Outer Space, it is the second document at UN level dedicated entirely to space nuclear power sources.This paper analyses aspects of the safety framework relevant for the design and development phases of space nuclear power sources. While early publications have started analysing the legal aspects of the safety framework, its technical guidance has not yet been subject to scholarly articles. The present paper therefore focuses on the technical guidance provided in the safety framework, in an attempt to assist engineers and practitioners to benefit from these.

International nuclear fuel cycle fact book. [Contains glossary of organizations, facilities, technical and other terms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1992-09-01

The International Nuclear Fuel Cycle Fact Book has been compiled in an effort to provide current data concerning fuel cycle and waste management facilities, R D programs and key personnel on 23 countries, including the US, four multi-national agencies, and 21 nuclear societies. The Fact Book is organized as follows: National summaries-a section for each country which summarizes nuclear policy, describes organizational relationships, and provides addresses and names of key personnel and information on facilities. International agencies-a section for each of the international agencies which has significant fuel cycle involvement and a listing of nuclear societies. Glossary-a list of abbreviations/acronymsmore » of organizations, facilities, technical and other terms. The national summaries, in addition to the data described above, feature a small map for each country as well as some general information. The latter presented from the perspective of the Fact Book user in the United States.« less

International Maritime Organizational Code For Safe Carriage Of Irradiated Nuclear Fuel, Plutonium and High-Level Radioactive Wastes in Flasks On Board Ships -- IMO Resolution A.748(18)

DOT National Transportation Integrated Search

1994-05-26

This Circular calls the attention of Coast Guard field units, marine surveyors, shippers and carriers of nuclear materials to the International Maritime Organization (IMO) Code for the Safe Carriage of Irradiated Nuclear Fuel, Plutonium and High-Leve...

Serine/Threonine kinase dependent transcription from the polyhedrin promoter of SpltNPV-I

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Gourav; Gautam, Hemant K.; Das, Rakha H.

2007-07-06

Polyhedrin (polh) and p10 are the two hyper-expressed very late genes of nucleopolyhedroviruses. Alpha amanitin resistant transcription from Spodoptera litura nucleopolyhedrovirus (SpltNPV-I) polyhedrin promoter was observed with virus infected nuclear extract of NIV-HA-197 cells but not with that from uninfected nuclear extract. Anti-protein kinase-1 (pk1) antibody inhibited the transcription and the inhibition reversed on addition of pk1, however, pk1 mutant protein, K50M having no phosphorylation activity did not overcome the transcription inhibition. Chromatin immuno-precipitation assays with viral anti-pk1 antibody showed the interaction of pk1 with the polh while electrophoretic mobility shift assays indicated the strong binding affinity (K {sub d}more » {approx} 5.5 x 10{sup -11}) of purified pk1 with the polh promoter. These results suggested that the viral coded pk1 acts as a transcription factor in transcribing baculovirus very late genes.« less

International Considerations Associated with Economic Planning for Recovery from a Generalized Disaster

DTIC Science & Technology

1988-06-01

typical approach in addressing the recovery problem has been to impose a hypothetical nuclear disaster scenario on the U.S. economy and to speculate on...system and international trade in the aftermath of a nuclear disaster in Chapter 7 is provided in the context of a number of dimensions of a...hypothetical nuclear conflict. The dimensions of a hypothetical nuclear disaster must be defined because planning must necessarily be flexible enough to

THE AIMS AND ACTIVITIES OF THE INTERNATIONAL NETWORK OF NUCLEAR STRUCTURE AND DECAY DATA EVALUATORS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

NICHOLS,A.L.; TULI, J.K.

International Network of Nuclear Structure and Decay Data (NSDD) Evaluators consists of a number of evaluation groups and data service centers in several countries that appreciate the merits of working together to maintain and ensure the quality and comprehensive content of the ENSDF database (Evaluated Nuclear Structure Data File). Biennial meetings of the network are held under the auspices of the International Atomic Energy Agency (IAEA) to assign evaluation responsibilities, monitor progress, discuss improvements and emerging difficulties, and agree on actions to be undertaken by individual members. The evaluated data and bibliographic details are made available to users via variousmore » media, such as the journals ''Nuclear Physics A'' and ''Nuclear Data Sheets'', the World Wide Web, on CD-ROM, wall charts of the nuclides and ''Nuclear Wallet Cards''. While the ENSDF master database is maintained by the US National Nuclear Data Center at the Brookhaven National Laboratory, these data are also available from other nuclear data centers including the IAEA Nuclear Data Section. The Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy, in cooperation with the IAEA, organizes workshops on NSDD at regular intervals. The primary aims of these particular workshops are to provide hands-on training in the data evaluation processes, and to encourage new evaluators to participate in NSDD activities. The technical contents of these NSDD workshops are described, along with the rationale for the inclusion of various topics.« less

Nuclear Terrorism - Dimensions, Options, and Perspectives in Moldova

NASA Astrophysics Data System (ADS)

Vaseashta, Ashok; Susmann, P.; Braman, Eric W.; Enaki, Nicolae A.

Securing nuclear materials, controlling contraband and preventing proliferation is an international priority to resolve using technology, diplomacy, strategic alliances, and if necessary, targeted military exercises. Nuclear security consists of complementary programs involving international legal and regulatory structure, intelligence and law enforcement agencies, border and customs forces, point and stand-off radiation detectors, personal protection equipment, preparedness for emergency and disaster, and consequence management teams. The strategic goal of UNSCR 1540 and the GICNT is to prevent nuclear materials from finding their way into the hands of our adversaries. This multi-jurisdictional and multi-agency effort demands tremendous coordination, technology assessment, policy development and guidance from several sectors. The overall goal envisions creating a secured environment that controls and protects nuclear materials while maintaining the free flow of commerce and individual liberty on international basis. Integral to such efforts are technologies to sense/detect nuclear material, provide advance information of nuclear smuggling routes, and other advanced means to control nuclear contraband and prevent proliferation. We provide an overview of GICNT and several initiatives supporting such efforts. An overview is provided of technological advances in support of point and stand-off detection and receiving advance information of nuclear material movement from perspectives of the Republic of Moldova.

Suppression of prolactin gene expression in GH cells correlates with site-specific DNA methylation.

PubMed

Zhang, Z X; Kumar, V; Rivera, R T; Pasion, S G; Chisholm, J; Biswas, D K

1989-10-01

Prolactin- (PRL) producing and nonproducing subclones of the GH line of (rat) pituitary tumor cells have been compared to elucidate the regulatory mechanisms of PRL gene expression. Particular emphasis was placed on delineating the molecular basis of the suppressed state of the PRL gene in the prolactin-nonproducing (PRL-) GH subclone (GH(1)2C1). We examined six methylatable cytosine residues (5, -CCGG- and 1, -GCGC-) within the 30-kb region of the PRL gene in these subclones. This analysis revealed that -CCGG-sequences of the transcribed region, and specifically, one in the fourth exon of the PRL gene, were heavily methylated in the PRL-, GH(1)2C1 cells. Furthermore, the inhibition of PRL gene expression in GH(1)2C1 was reversed by short-term treatment of the cells with a sublethal concentration of azacytidine (AzaC), an inhibitor of DNA methylation. The reversion of PRL gene expression by AzaC was correlated with the concurrent demethylation of the same -CCGG- sequences in the transcribed region of PRL gene. An inverse correlation between PRL gene expression and the level of methylation of the internal -C- residues in the specific -CCGG-sequence of the transcribed region of the PRL gene was demonstrated. The DNase I sensitivity of these regions of the PRL gene in PRL+, PRL-, and AzaC-treated cells was also consistent with an inverse relationship between methylation state, a higher order of structural modification, and gene expression.(ABSTRACT TRUNCATED AT 250 WORDS)

75 FR 7337 - Certifications Pursuant to Section 104 of the United States-India Nuclear Cooperation Approval...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-19

... Agreement Between India and the International Atomic Energy Agency Memorandum for the Secretary of State... Government of India and the International Atomic Energy Agency for the Application of Safeguards to Civilian Nuclear Facilities, as approved by the Board of Governors of the International Atomic Energy Agency on...

Nuclear Forensics: Report of the AAAS/APS Working Group

NASA Astrophysics Data System (ADS)

Tannenbaum, Benn

2008-04-01

This report was produced by a Working Group of the American Physical Society's Program on Public Affairs in conjunction with the American Association for the Advancement of Science Center for Science, Technology and Security Policy. The primary purpose of this report is to provide the Congress, U.S. government agencies and other institutions involved in nuclear forensics with a clear unclassified statement of the state of the art of nuclear forensics; an assessment of its potential for preventing and identifying unattributed nuclear attacks; and identification of the policies, resources and human talent to fulfill that potential. In the course of its work, the Working Group observed that nuclear forensics was an essential part of the overall nuclear attribution process, which aims at identifying the origin of unidentified nuclear weapon material and, in the event, an unidentified nuclear explosion. A credible nuclear attribution capability and in particular nuclear forensics capability could deter essential participants in the chain of actors needed to smuggle nuclear weapon material or carry out a nuclear terrorist act and could also encourage states to better secure such materials and weapons. The Working Group also noted that nuclear forensics result would take some time to obtain and that neither internal coordination, nor international arrangements, nor the state of qualified personnel and needed equipment were currently enough to minimize the time needed to reach reliable results in an emergency such as would be caused by a nuclear detonation or the intercept of a weapon-size quantity of material. The Working Group assesses international cooperation to be crucial for forensics to work, since the material would likely come from inadequately documented foreign sources. In addition, international participation, if properly managed, could enhance the credibility of the deterrent effect of attribution. Finally the Working Group notes that the U.S. forensics capability involved a number of agencies and other groups that would have to cooperate rapidly in an emergency and that suitable exercises to ensure such cooperation were needed.