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https://www.readbyqxmd.com/read/28634359/infections-of-horses-and-shrews-with-bornaviruses-in-upper-austria-a-novel-endemic-area-of-borna-disease
#1
Herbert Weissenböck, Zoltán Bagó, Jolanta Kolodziejek, Barbara Hager, Günter Palmetzhofer, Ralf Dürrwald, Norbert Nowotny
Borna disease, a lethal infection with Borna disease virus-1 (BoDV-1), was diagnosed in four horses from Upper Austria in 2015 and 2016. All cases occurred in winter (two cases in February 2015 and two cases in December 2016), and the maximal distance of the affected stables was 17 km. To demonstrate whether the causative agent was also harbored by its reservoir host, the bicolored white-toothed shrew (Crocidura leucodon), 28 shrews from this geographic area were collected in 2015 and investigated for the presence of BoDV-1...
June 21, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#2
Stephanie U Greer, Lincoln D Nadauld, Billy T Lau, Jiamin Chen, Christina Wood-Bouwens, James M Ford, Calvin J Kuo, Hanlee P Ji
BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing. METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater...
June 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28623498/minimal-barcode-distance-between-two-water-mite-species-from-madeira-island-a-cautionary-tale
#3
Ricardo García-Jiménez, Jose Luis Horreo, Antonio G Valdecasas
In this work, we compare morphological and molecular data in their ability to distinguish between species of water mites (Acari, Prostigmata, Hydrachnidia). We have focused on the two species of the genus Lebertia inhabiting the island of Madeira. While traditional morphological traits were initially sufficient to distinguish between these two species, the molecular data were more dependable on the kind of analysis carried out. Single arbitrary genetic distance (e.g. a K2P distance below 2%) may lead to the conclusion that the specimens under study belong to the same species...
June 16, 2017: Experimental & Applied Acarology
https://www.readbyqxmd.com/read/28622375/identification-of-benthic-diatoms-isolated-from-the-eastern-tidal-flats-of-the-yellow-sea-comparison-between-morphological-and-molecular-approaches
#4
Sung Min An, Dong Han Choi, Jung Ho Lee, Howon Lee, Jae Hoon Noh
Benthic diatoms isolated from tidal flats in the west coast of Korea were identified through both traditional morphological method and molecular phylogenetic method for methodological comparison. For the molecular phylogenetic analyses, we sequenced the 18S rRNA and the ribulose bisphosphate carboxylase large subunit coding gene, rbcL. Further, the comparative analysis allowed for the assessment of the suitability as a genetic marker for identification of closely related benthic diatom species and as potential barcode gene...
2017: PloS One
https://www.readbyqxmd.com/read/28611359/chloroplast-genomic-resource-of-paris-for-species-discrimination
#5
Yun Song, Shaojun Wang, Yuanming Ding, Jin Xu, Ming Fu Li, Shuifang Zhu, Naizhong Chen
Paris is famous in China for its medicinal value and has been included in the Chinese Pharmacopoeia. Inaccurate identification of these species could confound their effective exploration, conservation, and domestication. Due to the plasticity of the morphological characteristics, correct identification among Paris species remains problematic. In this regard, we report the complete chloroplast genome of P. thibetica and P. rugosa to develop highly variable molecular markers. Comparing three chloroplast genomes, we sought out the most variable regions to develop the best cpDNA barcodes for Paris...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28610203/new-species-of-i-ameletus-i-eaton-1885-from-the-russian-far-east-with-notes-on-i-ameletus-i-i-camtschaticus-i-ulmer-1927-ephemeroptera-ameletidae
#6
Tatiana M Tiunova, Aleksandr A Semenchenko, Oleg A Velyaev
The male imagoes, larvae, and eggs of Ameletus allengaensis sp. nov. and Ameletus sirotskii sp. nov. from the Russian Far East are described. Based on the structure of the male genitalia, the imago and larvae of A. allengaensis sp. nov. and A. sirotskii sp. nov. are similar to those of A. camtschaticus, but the discovery of these new species and separation from A. camtschaticus were confirmed by studies of the morphology of the larvae and male imago, as well as molecular analysis. Identity of various developmental stages of the new species were confirmed by analysis of the mitochondrial gene cytochrome oxidase 1 (COI) DNA barcode, which was also used to reconstruct the phylogenetic relationships within the genus Ameletus...
June 11, 2017: Zootaxa
https://www.readbyqxmd.com/read/28610073/new-or-little-known-species-of-i-chaetocladius-i-s-str-kieffer-1911-diptera-chironomidae-orthocladiinae-from-the-amur-river-basin-russian-far-east
#7
Eugenyi A Makarchenko, Marina A Makarchenko, Alexander A Semenchenko
Chironomids of the subgenus Chaetocladius s. str. from the Amur River basin are revised using both morphological characters and molecular data. Three new species, C. egorych sp. nov., C. lopatinskiy sp. nov. and C. yavorskayae sp. nov., are described and figured. The pupa of C. fedotkin is described for the first time. Adult males of C. ligni and C. piger, little-known in the Far East, are redescribed and annotated, and key to males of the Chaetocladius s. str. from the Amur River basin is provided. A reference 658 bp barcode sequence from a fragment of the mitochondrial gene cytochrome oxidase I (COI) was used as a tool for species delimitation...
March 27, 2017: Zootaxa
https://www.readbyqxmd.com/read/28610033/molecular-approaches-for-blood-meal-analysis-and-species-identification-of%C3%A2-mosquitoes-insecta-diptera-culicidae-in-rural-locations-in-southern-england-united-kingdom
#8
Luis Miguel Hernández-Triana, Victor Albert Brugman, Sean Williams John Prosser, Chris Weland, Nadya Nikolova, Leigh Thorne, Mar Fernández DE Marco, Anthony Richard Fooks, Nicholas Johnson
Thirty-four species of Culicidae are present in the UK, of which 15 have been implicated as potential vectors of arthropod-borne viruses such as West Nile virus. Identification of mosquito feeding preferences is paramount to the understanding of vector-host-pathogen interactions which, in turn, would assist in the control of disease outbreaks. Results are presented on the application of DNA barcoding for vertebrate species identification in blood-fed female mosquitoes in rural locations. Blood-fed females (n = 134) were collected in southern England from rural sites and identified based on morphological criteria...
April 3, 2017: Zootaxa
https://www.readbyqxmd.com/read/28609994/uncovering-the-hidden-biodiversity-of-natural-history-collections-insights-from-dna-barcoding-and-morphological-characters-of-the-neotropical-genus-i-orthocomotis-i-dognin-lepidoptera-tortricidae
#9
Józef Razowski, Volker Pelz, Sebastian Tarcz
We used a 227-bp fragment of the mitochondrial gene cytochrome oxidase I (DNA "barcode") in conjunction with morphological data to study specimens of the Neotropical genus Orthocomotis Dognin, 1906, acquired from natural history collections. We examined over 20 species of Orthocomotis from 17 localities in Colombia, Ecuador, and Peru. The analysis identified 32 haplotypes among the 62 specimens and found no haplotypes shared among species. The molecular study revealed not only the usefulness of short COI sequences in discriminating among Orthocomotis species but also showed distinctness of four clusters which correspond to those based on morphological (genitalia) characters...
April 10, 2017: Zootaxa
https://www.readbyqxmd.com/read/28609221/north-american-matsutake-names-clarified-and-a-new-species-described
#10
Steven A Trudell, Jianping Xu, Irja Saar, Alfredo Justo, Joaquin Cifuentes
Tricholoma matsutake, known widely as "matsutake," has great commercial and cultural significance in Japan. Because Japanese production is insufficient to meet the high domestic demand, morphologically similar mushrooms, thought by many to belong to T. magnivelare, are imported from western North America. However, molecular data produced since the early 2000s have indicated that more than one species of matsutake occur in North America and this raises the question of correct naming for the different species...
May 10, 2017: Mycologia
https://www.readbyqxmd.com/read/28596290/yeast-genetic-interaction-screen-of-human-genes-associated-with-amyotrophic-lateral-sclerosis-identification-of-map2k5-kinase-as-a-potential-drug-target
#11
Myungjin Jo, Ah Young Chung, Nozomu Yachie, Minchul Seo, Hyejin Jeon, Youngpyo Nam, Yeojin Seo, Eunmi Kim, Quan Zhong, Marc Vidal, Hae Chul Park, Frederick Roth, Kyoungho Suk
To understand disease mechanisms, a large-scale analysis of human-yeast genetic interactions was performed. Of 1,305 human disease genes assayed, 20 genes exhibited strong toxicity in yeast. Human-yeast genetic interactions were identified by en masse transformation of the human disease genes into a pool of 4,653 homozygous diploid yeast deletion mutants with unique barcode sequences, followed by multiplexed barcode sequencing of yeast toxicity modifiers. Subsequent network analyses focusing on amyotrophic lateral sclerosis (ALS)-associated genes, such as optineurin (OPTN) and angiogenin (ANG), showed that the human orthologs of the yeast toxicity modifiers of these ALS genes are enriched for several biological processes, such as cell death, lipid metabolism, and molecular transport...
June 8, 2017: Genome Research
https://www.readbyqxmd.com/read/28590228/phylogenetic-relationships-among-malaria-vectors-and-closely-related-species-in-thailand-using-multilocus-dna-sequences
#12
Prin Phunngam, Theeraphap Chareonviriyaphap, Michael J Bangs, Uraiwan Arunyawat
The evolutionary and taxonomic status is important for understanding speciation events and phylogenetic relationships between closely related vector and nonvector species. This information is useful for targeting important disease vector species groups for the development of novel genetic-based vector and pathogen control methods. In this study, different phylogenetic analyses were performed to reconstruct phylogenetic trees for the primary malaria vectors in Thailand based on sequence information of 4 DNA fragments from the nuclear and mitochondrial regions...
June 2017: Journal of the American Mosquito Control Association
https://www.readbyqxmd.com/read/28583065/application-of-nonsense-mediated-primer-exclusion-nope-for-preparation-of-unique-molecular-barcoded-libraries
#13
Dmitriy A Shagin, Maria A Turchaninova, Irina A Shagina, Mikhail Shugay, Andrew R Zaretsky, Olga I Zueva, Dmitriy A Bolotin, Sergey Lukyanov, Dmitriy M Chudakov
BACKGROUND: Recently we proposed efficient method to exclude undesirable primers at any stage of amplification reaction, here termed NOPE (NOnsense-mediated Primer Exclusion). According to this method, added oligonucleotide overlapping with the 3'-end of unwanted amplification primer (NOPE oligo) simultaneously provides a template for its elongation. This elongation disrupts specificity of unwanted primer, preventing its further participation in PCR. The suggested approach allows to rationally manage the course of PCR reactions in order to facilitate analysis of complex DNA mixtures as well as to perform multistage PCR bypassing intermediate purification steps...
June 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28579999/development-of-chloroplast-and-nuclear-dna-markers-for-chinese-oaks-quercus-subgenus-quercus-and-assessment-of-their-utility-as-dna-barcodes
#14
Jia Yang, Lucía Vázquez, Xiaodan Chen, Huimin Li, Hao Zhang, Zhanlin Liu, Guifang Zhao
Chloroplast DNA (cpDNA) is frequently used for species demography, evolution, and species discrimination of plants. However, the lack of efficient and universal markers often brings particular challenges for genetic studies across different plant groups. In this study, chloroplast genomes from two closely related species (Quercus rubra and Castanea mollissima) in Fagaceae were compared to explore universal cpDNA markers for the Chinese oak species in Quercus subgenus Quercus, a diverse species group without sufficient molecular differentiation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28579404/transcriptome-wide-measurement-of-translation-by-ribosome-profiling
#15
Nicholas J McGlincy, Nicholas T Ingolia
Translation is one of the fundamental processes of life. It comprises the assembly of polypeptides whose amino acid sequence corresponds to the codon sequence of an mRNA's ORF. Translation is performed by the ribosome; therefore, in order to understand translation and its regulation we must be able to determine the numbers and locations of ribosomes on mRNAs in vivo. Furthermore, we must be able to examine their redistribution in different physiological contexts and in response to experimental manipulations...
June 1, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28578677/description-of-culicoides-culicoides-bysta-n-sp-a-new-member-of-the-pulicaris-group-diptera-ceratopogonidae-from-slovakia
#16
Adela Sarvašová, Alica Kočišová, Ermanno Candolfi, Bruno Mathieu
BACKGROUND: Species of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) are mainly known as vectors of arboviruses such as bluetongue (BTV) and Schmallenberg (SBV). Among the known vectors, few species within the subgenus Culicoides Latreille, 1809 have been implicated in the transmission of BTV and SBV. Nevertheless, phylogenetic studies had revealed the presence of cryptic and undescribed species in Europe, raising questions about their vectorial role. A previous integrative study, associating morphology and barcode data, raised the hypothesis of the presence of undescribed species in Slovakia...
June 2, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28578667/molecular-characterization-of-anopheline-diptera-culicidae-mosquitoes-from-eight-geographical-locations-of-sri-lanka
#17
Thilini C Weeraratne, Sinnathambi N Surendran, Lisa J Reimer, Charles S Wondji, M Devika B Perera, Catherine Walton, S H P Parakrama Karunaratne
BACKGROUND: Genus Anopheles is a major mosquito group of interest in Sri Lanka as it includes vectors of malaria and its members exist as species complexes. Taxonomy of the group is mainly based on morphological features, which are not conclusive and can be easily erased while handling the specimens. A combined effort, using morphology and DNA barcoding (using the markers cytochrome c oxidase subunit I (COI) gene and internal transcribed spacer 2 (ITS2) region, was made during the present study to recognize anophelines collected from eight districts of Sri Lanka for the first time...
June 2, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28572161/ultrasensitive-detection-of-acute-myeloid-leukemia-minimal-residual-disease-using-single-molecule-molecular-inversion-probes
#18
Adam Waalkes, Kelsi Penewit, Brent L Wood, David Wu, Stephen J Salipante
The identification of minimal residual disease is the primary diagnostic finding which predicts relapse in patients treated for acute myeloid leukemia. Ultrasensitive detection of minimal residual disease would enable better patient risk stratification and could open opportunities for early therapeutic intervention. Here we apply single molecule molecular inversion probe capture, a technology combining multiplexed targeted sequencing with error correction schemes based on molecular barcoding, to detect mutations identifying minimal residual disease with ultrasensitive and quantitative precision...
June 1, 2017: Haematologica
https://www.readbyqxmd.com/read/28548029/digital-assays-part-ii-digital-protein-and-cell-assays
#19
Amar S Basu
A digital assay is one in which the sample is partitioned into many containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, . . .). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotype and phenotype. Where part I of this review focused on the fundamentals of partitioning and digital PCR, part II turns its attention to digital protein and cell assays...
May 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28545995/systematic-studies-on-ciliates-alveolata-ciliophora-in-china-progress-and-achievements-based-on-molecular-information
#20
REVIEW
Feng Gao, Jie Huang, Yan Zhao, Lifang Li, Weiwei Liu, Miao Miao, Qianqian Zhang, Jiamei Li, Zhenzhen Yi, Hamed A El-Serehy, Alan Warren, Weibo Song
Due to complex morphological and convergent morphogenetic characters, the systematics of ciliates has long been ambiguous. Since 1990, the Laboratory of Protozoology, Ocean University of China, in collaboration with other research groups worldwide, has carried out a series of integrative investigations on ciliate systematics. To date, genomic DNA has been extracted from about 1700 ciliate strains, and phylogenetic analyses have been performed for two-thirds of orders. Main findings are: (1) Classifications of about 50 hypotrichous species have been resolved, although the monophylies of three hypotrichous orders remain unconfirmed; (2) Euplotia and two orders and all seven families within them are monophyletic assemblages; (3) Lynnella represents an order-level taxon, and is separated from two sister monophyletic subclasses Oligotrichia and Choreotrichia; (4) the peritrich families Zoothamniidae and Vorticellidae are separated from each other, and Zoothamnium exhibits a high genetic diversity; (5) the scuticociliate order Philasterida is monophyletic and separated from loxocephalids, and the thigmotrichids is a suborder within Pleuronematida; (6) 14 classes were recovered including one new class Protocruziea, and Mesodiniea is basal to subphyla Intramacronucleata and Postciliodesmatophora; (7) mitochondrial cytochrome c oxidase subunit I heteroplasmy was reported in ciliates for the first time, and candidate barcoding genes for Frontonia species identification were identified...
May 6, 2017: European Journal of Protistology
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