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molecular barcoding

Elisa Banchi, Claudio Gennaro Ametrano, David Stanković, Pierluigi Verardo, Olga Moretti, Francesca Gabrielli, Stefania Lazzarin, Maria Francesca Borney, Francesca Tassan, Mauro Tretiach, Alberto Pallavicini, Lucia Muggia
Fungal spores and mycelium fragments are particles which become and remain airborne and have been subjects of aerobiological studies. The presence and the abundance of taxa in aerobiological samples can be very variable and impaired by changeable climatic conditions. Because many fungi produce mycotoxins and both their mycelium fragments and spores are potential allergens, monitoring the presence of these taxa is of key importance. So far data on exposure and sensitization to fungal allergens are mainly based on the assessment of few, easily identifiable taxa and focused only on certain environments...
2018: PloS One
Seynabou Séne, Marc-André Selosse, Mathieu Forget, Josie Lambourdière, Khoudia Cissé, Abdala Gamby Diédhiou, Elsie Rivera-Ocasio, Hippolyte Kodja, Norikazu Kameyama, Kazuhide Nara, Lucie Vincenot, Jean-Louis Mansot, Jean Weber, Mélanie Roy, Samba Ndao Sylla, Amadou Bâ
Global trade increases plant introductions, but joint introduction of associated microbes is overlooked. We analyzed the ectomycorrhizal fungi of a Caribbean beach tree, seagrape (Coccoloba uvifera, Polygonacaeae), introduced pantropically to stabilize coastal soils and produce edible fruits. Seagrape displays a limited symbiont diversity in the Caribbean. In five regions of introduction (Brazil, Japan, Malaysia, Réunion and Senegal), molecular barcoding showed that seagrape mostly or exclusively associates with Scleroderma species (Basidiomycota) that were hitherto only known from Caribbean seagrape stands...
March 13, 2018: ISME Journal
Jinho Lee, Gary K Geiss, Gokhan Demirkan, Christopher P Vellano, Brian Filanoski, Yiling Lu, Zhenlin Ju, Shuangxing Yu, Huifang Guo, Lisa Y Bogatzki, Warren E Carter, Rhonda K Meredith, Savitri Krishnamurthy, Zhiyong Ding, Joseph M Beechem, Gordon Mills
Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy.  Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application.  Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples...
March 12, 2018: Molecular & Cellular Proteomics: MCP
Satisha Hegde, Archana Saini, Harsha Vasudev Hegde, Sanjiva D Kholkute, Subarna Roy
Saraca asoca (Roxb.) De Wilde is an important medicinal plant from the Western Ghats of India, traditionally used in treatment of various gynecological disorders. Increasing commercial demand and decreasing numbers has resulted in this plant becoming endangered with crude drug materials being extensively substituted/adulterated with other plant species. The present study was undertaken with the objective of development and evaluation of multivariate cluster analysis of ISSR fingerprints against rbcL -based DNA barcodes as tool to understand the relationships and to differentiate common adulterants and substituents from S...
March 2018: 3 Biotech
Pavel Bashtrykov, Albert Jeltsch
Methylation of cytosine bases in DNA is one of the main epigenetic signals regulating gene expression and chromatin structure. The distribution of DNA methylation in the genome has a cell-type-specific pattern and can be modulated by internal or external stimuli. One of the most powerful approaches to investigate DNA methylation patterns is bisulfite conversion of the DNA followed by DNA sequencing, which allows to determine methylation patterns at a single-cytosine resolution. Here, we present a protocol for bisulfite DNA methylation analysis of targeted genomic regions using amplicon-based next-generation sequencing (NGS) on an Illumina sequencing system...
2018: Methods in Molecular Biology
Rômulo V Paixão, Josiane Ribolli, Evoy Zaniboni-Filho
Steindachneridion scriptum is an important species as a resource for fisheries and aquaculture; it is currently threatened and has a reduced occurrence in South America. The damming of rivers, overfishing, and contamination of freshwater environments are the main impacts on the maintenance of this species. We accessed the genetic diversity and structure of S. scriptum using the DNA barcode and control region (D-loop) sequences of 43 individuals from the Upper Uruguay River Basin (UUR) and 10 sequences from the Upper Paraná River Basin (UPR), which were obtained from GenBank...
2018: Frontiers in Genetics
Paul Simion, Khalid Belkhir, Clémentine François, Julien Veyssier, Jochen C Rink, Michaël Manuel, Hervé Philippe, Maximilian J Telford
BACKGROUND: Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same sequencing run. While different samples can be separated post sequencing using sample barcodes, the possibility of cross contamination between biological samples from different species that have been processed or sequenced in parallel has the potential to be extremely deleterious for downstream analyses. RESULTS: We present CroCo, a software package for identifying and removing such cross contaminants from assembled transcriptomes...
March 5, 2018: BMC Biology
José Ferreira Saraiva, Raimundo Nonato Picanço Souto, Vera Margarete Scarpassa
Recent studies have shown that Anopheles oswaldoi sensu lato comprises a cryptic species complex in South America. Anopheles konderi, which was previously raised to synonymy with An. oswaldoi, has also been suggested to form a species complex. An. oswaldoi has been incriminated as a malaria vector in some areas of the Brazilian Amazon, Colombia, Peru and Venezuela, but was not recognized as a vector in the remaining regions in its geographic distribution. The role of An. konderi as a malaria vector is unknown or has been misattributed to An...
2018: PloS One
I Skrede, T Carlsen, T Schumacher
Helvella is a widespread, speciose genus of large apothecial ascomycetes ( Pezizomycete : Pezizales ) that are found in terrestrial biomes of the Northern and Southern Hemispheres. This study represents a beginning on assessing species limits and applying correct names for Helvella species based on type material and specimens in the university herbaria (fungaria) of Copenhagen (C), Harvard (FH) and Oslo (O). We use morphology and phylogenetic evidence from four loci - heat shock protein 90 ( hsp ), translation elongation factor alpha ( tef ), RNA polymerase II ( rpb2 ) and the nuclear large subunit ribosomal DNA (LSU) - to assess species boundaries in an expanded sample of Helvella specimens from Europe...
December 2017: Persoonia
B Violi, M R Gaither, F Burns, A Rus Hoelzel, F Neat
This study investigated taxonomic validity of the pale ghost shark Hydrolagus pallidus Hardy & Stehmann, 1990, which was described as a species distinct from the smalleyed rabbitfish H. affinis (de Brito Capello 1868). While few morphological characters distinguish the two taxa, a striking difference in sex ratio and fixed differences (1·1-1·6% divergence) in the cytochrome oxidase subunit I barcoding gene support the recognition of both species.
March 1, 2018: Journal of Fish Biology
Ekaterina A Komech, Mikhail V Pogorelyy, Evgeniy S Egorov, Olga V Britanova, Denis V Rebrikov, Anna G Bochkova, Evgeniya I Shmidt, Nadejda A Shostak, Mikhail Shugay, Sergey Lukyanov, Ilgar Z Mamedov, Yuriy B Lebedev, Dmitriy M Chudakov, Ivan V Zvyagin
Objective: The risk of AS is associated with genomic variants related to antigen presentation and specific cytokine signalling pathways, suggesting the involvement of cellular immunity in disease initiation/progression. The aim of the present study was to explore the repertoire of TCR sequences in healthy donors and AS patients to uncover AS-linked TCR variants. Methods: Using quantitative molecular-barcoded 5'-RACE, we performed deep TCR β repertoire profiling of peripheral blood (PB) and SF samples for 25 AS patients and 108 healthy donors...
February 22, 2018: Rheumatology
Deborah Wall-Palmer, Alice K Burridge, Erica Goetze, Frank R Stokvis, Arie W Janssen, Lisette Mekkes, María Moreno-Alcántara, Nina Bednaršek, Tom Schiøtte, Martin Vinther Sørensen, Christopher W Smart, Katja T C A Peijnenburg
The atlantid heteropods are regularly encountered, but rarely studied marine planktonic gastropods. Relying on a small (<14 mm), delicate aragonite shell and living in the upper ocean means that, in common with pteropods, atlantids are likely to be affected by imminent ocean changes. Variable shell morphology and widespread distributions indicate that the family is more diverse than the 23 currently known species. Uncovering this diversity is fundamental to determining the distribution of atlantids and to understanding their environmental tolerances...
January 2018: Progress in Oceanography
Anne-Nina Lörz, Anne Helene S Tandberg, Endre Willassen, Amy Driskell
The genus Rhachotropis has the widest geographic and bathymetric distribution of all amphipod genera worldwide. Molecular and morphological investigations of specimens sampled around Iceland and off the Norwegian coast allow the first insights into the relationships of North East Atlantic Rhachotropis . The 31 cytochrome oxidase subunit I (COI) sequences generated for this study were assigned 13 Barcode Index Numbers (BINs) in the Barcode of Life database (BOLD), of which 12 are new to the database. Molecular analyses of COI and 16S sequences could not confirm a theory that depth has a greater influence on the phylogeny of Rhachotropis than geographic distance...
2018: ZooKeys
Anna M Jażdżewska, Laure Corbari, Amy Driskell, Inmaculada Frutos, Charlotte Havermans, Ed Hendrycks, Lauren Hughes, Anne-Nina Lörz, Bente Stransky, Anne Helene S Tandberg, Wim Vader, Saskia Brix
Amphipods constitute an abundant part of Icelandic deep-sea zoobenthos yet knowledge of the diversity of this fauna, particularly at the molecular level, is scarce. The present work aims to use molecular methods to investigate genetic variation of the Amphipoda sampled during two IceAGE collecting expeditions. The mitochondrial cytochrome oxidase subunit 1 (COI) of 167 individuals originally assigned to 75 morphospecies was analysed. These targeted morhospecies were readily identifiable by experts using light microscopy and representative of families where there is current ongoing taxonomic research...
2018: ZooKeys
Xiaobing Li, Xuejuan Shen, Xiao Chen, Dan Xiang, Robert W Murphy, Yongyi Shen
Fishes are, by far, the most diverse group of vertebrates. Their classification relies heavily on morphology. In practice, the correct morphological identification of species often depends on personal experience because many species vary in their body shape, color and other external characters. Thus, the identification of a species may be prone to errors. Due to the rapid development of molecular biology, the number of sequences of fishes deposited in GenBank has grown explosively. These published data likely contain errors owing to invalid or incorrectly identified species...
2018: Frontiers in Genetics
Jianguo Zhou, Yingxian Cui, Xinlian Chen, Ying Li, Zhichao Xu, Baozhong Duan, Yonghua Li, Jingyuan Song, Hui Yao
Papaver rhoeas L. and P. orientale L., which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively...
February 16, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Andrew J Hill, José L McFaline-Figueroa, Lea M Starita, Molly J Gasperini, Kenneth A Matreyek, Jonathan Packer, Dana Jackson, Jay Shendure, Cole Trapnell
Several groups recently coupled CRISPR perturbations and single-cell RNA-seq for pooled genetic screens. We demonstrate that vector designs of these studies are susceptible to ∼50% swapping of guide RNA-barcode associations because of lentiviral template switching. We optimized a published alternative, CROP-seq, in which the guide RNA also serves as the barcode, and here confirm that this strategy performs robustly and doubled the rate at which guides are assigned to cells to 94%.
February 19, 2018: Nature Methods
Emmanouil Dokianakis, Nikolaos Tsirigotakis, Vasiliki Christodoulou, Nikos Poulakakis, Maria Antoniou
BACKGROUND: Phlebotomine sand flies (Diptera: Psychodidae) are vectors of Leishmania spp., protozoan parasites responsible for a group of neglected diseases called leishmaniases. Two sand fly genera, Phlebotomus and Sergentomyia, contain species that are present in the Mediterranean islands of Crete and Cyprus where the visceral (VL), cutaneous (CL) and canine (CanLei) leishmaniases are a public health concern. The risk of transmission of different Leishmania species can be studied in an area by monitoring their vectors...
February 17, 2018: Parasites & Vectors
Yoji Kukita, Kazuyoshi Ohkawa, Ryoji Takada, Hiroyuki Uehara, Kazuhiro Katayama, Kikuya Kato
The accuracy of next-generation sequencing (NGS) for detecting tumor-specific mutations in plasma DNA is hindered by errors introduced during PCR/sequencing, base substitutions caused by DNA damage, and pre-existing mutations in normal cells that are present at a low frequency. Here, we performed NGS of genes related to pancreatic cancer (comprising 2.8 kb of genomic DNA) in plasma DNA (average 4.5 ng) using molecular barcodes. The average number of sequenced molecules was 900, and the sequencing depth per molecule was 100 or more...
2018: PloS One
Rosario Briosio-Aguilar, Hudson Alves Pinto, Maria Amparo Rodríguez-Santiago, Karina López-García, Martin Garcia-Varela, Gerardo Perez-Ponce de Leon
The phylogenetic position of Clinostomum heluans Braun, 1899 within the genus Clinostomum Leidy, 1856 is reported in this study based on sequences of the barcoding region of the mitochondrial cytochrome c oxidase subunit 1 gene (COX1). Additionally, molecular data are used to link the adult and the metacercariae of the species. The metacercariae of C. heluans were found encysted infecting the cichlid fish Australoheros sp. in Minas Gerais, Brazil, whereas the adults were obtained from the mouth cavity of the Great White egret Ardea alba, in Campeche, Mexico...
February 16, 2018: Journal of Parasitology
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