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Nigel W Beebe
Mosquitoes' importance as vectors of pathogens that drive disease underscores the importance of precise and comparable methods of taxa identification among their species. While several molecular targets have been used to study mosquitoes since the initiation of PCR in the 1980s, its application to mosquito identification took off in the early 1990s. This review follows the research's recent journey into the use of mitochondrial DNA (mtDNA) cytochrome oxidase 1 (COI or COX1) as a DNA barcode target for mosquito species identification - a target whose utility for discriminating mosquitoes is now escalating...
March 22, 2018: Parasitology
Sajan C Raju, Sonja Lagström, Pekka Ellonen, Willem M de Vos, Johan G Eriksson, Elisabete Weiderpass, Trine B Rounge
Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index...
March 18, 2018: Journal of Microbiological Methods
Bruno Leite Rodrigues, Luís Fernando Carvalho-Costa, Israel de Souza Pinto, José Manuel Macário Rebêlo
Sand fly (Diptera: Psychodidae) taxonomy is complex and time-consuming, which hampers epidemiological efforts directed toward controlling leishmaniasis in endemic regions such as northeastern Brazil. Here, we used a fragment of the mitochondrial cytochrome c oxidase I (COI) gene to identify sand fly species in Maranhão State (northeastern Brazil) and to assess cryptic diversity occurring at different spatial scales. For this, we obtained 148 COI sequences of 15 sand fly species (10 genera) from Maranhão (fine spatial scale), and joined them to COI sequences from other Brazilian localities (distant about 2,000 km from Maranhão, broad spatial scale) available in GenBank...
March 17, 2018: Journal of Medical Entomology
Sicheng Tang, Yang Zhang, Pravat Dhakal, Laura Ravelo, Cheyenne L Anderson, Kevin M Collins, Françisco M Raymo
A photochemical strategy to encode fluorescence signals in vivo with spatial control was designed around the unique properties of a photoactivatable borondipyrromethene (BODIPY). The photoinduced disconnection of two oxazines, flanking a single BODIPY, in two consecutive steps produces a mixture of three emissive molecules with resolved fluorescence inside polymer beads. The relative amounts and emission intensities of the three fluorophores can be regulated precisely in each bead by adjusting the dose of activating photons to mark individual particles with distinct codes of fluorescence signals...
March 21, 2018: Journal of the American Chemical Society
R Henrik Nilsson, Andy F S Taylor, Rachel I Adams, Christiane Baschien, Johan Bengtsson-Palme, Patrik Cangren, Claudia Coleine, Heide-Marie Daniel, Sydney I Glassman, Yuuri Hirooka, Laszlo Irinyi, Reda Iršėnaitė, Pedro M Martin-Sanchez, Wieland Meyer, Seung-Yoon Oh, Jose Paulo Sampaio, Keith A Seifert, Frantisek Sklenář, Dirk Stubbe, Sung-Oui Suh, Richard Summerbell, Sten Svantesson, Martin Unterseher, Cobus M Visagie, Michael Weiss, Joyce Hc Woudenberg, Christian Wurzbacher, Silke Van den Wyngaert, Neriman Yilmaz, Andrey Yurkov, Urmas Kõljalg, Kessy Abarenkov
Recent DNA-based studies have shown that the built environment is surprisingly rich in fungi. These indoor fungi - whether transient visitors or more persistent residents - may hold clues to the rising levels of human allergies and other medical and building-related health problems observed globally. The taxonomic identity of these fungi is crucial in such pursuits. Molecular identification of the built mycobiome is no trivial undertaking, however, given the large number of unidentified, misidentified, and technically compromised fungal sequences in public sequence databases...
2018: MycoKeys
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
Jamie R Wood
Ancient samples present a number of technical challenges for DNA barcoding, including damaged DNA with low endogenous copy number and short fragment lengths. Nevertheless, techniques are available to overcome these issues, and DNA barcoding has now been used to successfully recover parasite DNA from a wide variety of ancient substrates, including coprolites, cesspit sediment, mummified tissues, burial sediments and permafrost soils. The study of parasite DNA from ancient samples can provide a number of unique scientific insights, for example: (1) into the parasite communities and health of prehistoric human populations; (2) the ability to reconstruct the natural parasite faunas of rare or extinct host species, which has implications for conservation management and de-extinction; and (3) the ability to view in 'real-time' processes that may operate over century- or millenial-timescales, such as how parasites responded to past climate change events or how they co-evolved alongside their hosts...
March 20, 2018: Parasitology
Taeman Han, Seung-Hyun Kim, Hyung Joo Yoon, In Gyun Park, Haechul Park
We reassessed species diversity and genetic structure in Korean bumble bees using DNA barcode analyses of 484 cytochrome c oxidase subunit I (COI) sequences from 24 morphospecies. Based on COI, all of the Korean species formed distinct clades in the phylogenetic trees, except for Bombus (Megabombus) koreanus in the maximum likelihood tree. Five species exhibited low interspecific genetic distances (range: 1.2-2.7%), indicating that they are recently diverged species. COI data could not be used to identify bumble bees at the subspecies level...
March 20, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Erika Viljoen, Damaris A Odeny, Martin P A Coetzee, Dave K Berger, David J G Rees
Amaranthus species are an emerging and promising nutritious traditional vegetable food source. Morphological plasticity and poorly resolved dendrograms have led to the need for well resolved species phylogenies. We hypothesized that whole chloroplast phylogenomics would result in more reliable differentiation between closely related amaranth species. The aims of the study were therefore: to construct a fully assembled, annotated chloroplast genome sequence of Amaranthus tricolor; to characterize Amaranthus accessions phylogenetically by comparing barcoding genes (matK, rbcL, ITS) with whole chloroplast sequencing; and to use whole chloroplast phylogenomics to resolve deeper phylogenetic relationships...
March 19, 2018: Journal of Molecular Evolution
Guiping Wang, Jeffrey R Moffitt, Xiaowei Zhuang
As an image-based single-cell transcriptomics approach, multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows hundreds to thousands of RNA species to be identified, counted and localized in individual cells while preserving the native spatial context of RNAs. In MERFISH, RNAs are identified via a combinatorial labeling approach that encodes RNA species with error-robust barcodes followed by sequential rounds of single-molecule FISH (smFISH) to read out these barcodes. The accuracy of RNA identification relies on spatially separated signals from individual RNA molecules, which limits the density of RNAs that can be measured and makes the multiplexed imaging of a large number of high-abundance RNAs challenging...
March 19, 2018: Scientific Reports
Camila S Souza, Guilherme J Costa-Silva, Fábio F Roxo, Fausto Foresti, Claudio Oliveira
Schizolecis is a monotypic genus of Siluriformes widely distributed throughout isolated coastal drainages of southeastern Brazil. Previous studies have shown that fish groups found in isolated river basins tend to differentiate over time in the absence of gene flow, resulting in allopatric speciation. In this study, we used partial sequences of the mitochondrial gene COI with the analysis of the General Mixed Yule Coalescent model (GMYC) and the Automatic Barcode Gap Discovery (ABGD) for single locus species delimitation, and a Principal Component Analysis (PCA) of external morphology to test the hypothesis that Schizolecis guntheri is a complex of species...
2018: Frontiers in Genetics
Mei-Yi Lu, Syuan-Shao Lu, Shiann-Luen Chang, Fang Liao
CCR6 is a G protein-coupled receptor (GPCR) that recognizes a single chemokine ligand, CCL20 and is primarily expressed by leukocytes. Upon ligand binding, CCR6 activates Gαi heterotrimeric G proteins to induce various potential cellular outcomes through context-specific cell signaling. It is well known that differential phosphorylation of Ser and Thr residues in the C-terminal domains or intracellular loops of GPCRs can generate barcodes that regulate GPCR function by regulating the recruitment of β-arrestins...
2018: Frontiers in Immunology
Cheng-Hong Yang, Kuo-Chuan Wu, Li-Yeh Chuang, Hsueh-Wei Chang
DNA barcode sequences are accumulating in large data sets. A barcode is generally a sequence larger than 1000 base pairs and generates a computational burden. Although the DNA barcode was originally envisioned as straightforward species tags, the identification usage of barcode sequences is rarely emphasized currently. Single-nucleotide polymorphism (SNP) association studies provide us an idea that the SNPs may be the ideal target of feature selection to discriminate between different species. We hypothesize that SNP-based barcodes may be more effective than the full length of DNA barcode sequences for species discrimination...
2018: Evolutionary Bioinformatics Online
Hector Urbina, Martin F Breed, Weizhou Zhao, Kanaka Lakshmi Gurrala, Siv G E Andersson, Jon Ågren, Sandra Baldauf, Anna Rosling
Biotic and abiotic conditions in soil pose major constraints on growth and reproductive success of plants. Fungi are important agents in plant soil interactions but the belowground mycobiota associated with plants remains poorly understood. We grew one genotype each from Sweden and Italy of the widely-studied plant model Arabidopsis thaliana. Plants were grown under controlled conditions in organic topsoil local to the Swedish genotype, and harvested after ten weeks. Total DNA was extracted from three belowground compartments: endosphere (sonicated roots), rhizosphere and bulk soil, and fungal communities were characterized from each by amplification and sequencing of the fungal barcode region ITS2...
April 2018: Fungal Biology
Alexander B Rosenberg, Charles M Roco, Richard A Muscat, Anna Kuchina, Paul Sample, Zizhen Yao, Lucas Gray, David J Peeler, Sumit Mukherjee, Wei Chen, Suzie H Pun, Drew L Sellers, Bosiljka Tasic, Georg Seelig
To facilitate scalable profiling of single cells, we developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed cells or nuclei, allows efficient sample multiplexing and requires no customized equipment. We used SPLiT-seq to analyze 156,049 single-nucleus transcriptomes from postnatal day 2 and 11 mouse brains and spinal cords. Over 100 cell types were identified, with gene expression patterns corresponding to cellular function, regional specificity, and stage of differentiation...
March 15, 2018: Science
He Chen, Jiacheng Yao, Yusi Fu, Yuhong Pang, Jianbin Wang, Yanyi Huang
The next generation sequencing (NGS) technologies have been rapidly evolved and applied to various research fields, but often suffer from losing long-range information due to short library size and read length. Here, we develop a simple, cost-efficient and versatile NGS library preparation method, called tagmentation on microbeads (TOM). This method is capable of recovering long-range information through tagmentation mediated by microbead-immobilized transposomes. Using transposomes with DNA barcodes to identically labeling adjacent sequences during tagmentation, we can restore inter-read connection of each fragment from original DNA molecule by fragment-barcode linkage after sequencing...
March 15, 2018: ACS Applied Materials & Interfaces
Linkun Wu, Jun Chen, Zhigang Xiao, Xiaocheng Zhu, Juanying Wang, Hongmiao Wu, Yanhong Wu, Zhongyi Zhang, Wenxiong Lin
The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture...
March 14, 2018: International Journal of Molecular Sciences
Beiyuan Fan, Junbo Wang, Ying Xu, Jian Chen
Quantification of single-cell proteomics provides key insights in the field of cellular heterogeneity. This chapter discusses the emerging techniques that are being used to measure the protein copy numbers at the single-cell level, which includes flow cytometry, mass cytometry, droplet cytometry, microengraving, and single-cell barcoding microchip. The advantages and limitations of each technique are compared, and future research opportunities are highlighted.
2018: Methods in Molecular Biology
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
M Summa, H Henttonen, L Maunula
Human noroviruses (HuNoVs) are one of the leading global causes of diarrhoeal diseases and are transmitted mainly from person to person but also through contaminated food, water and fomites. The possible zoonotic nature of NoVs has occasionally been discussed, although the viruses are generally considered to be host-species-specific. We investigated whether wild birds and rodents could serve as carriers of HuNoVs, thereby transmitting the virus to humans directly or indirectly by contaminating foods. All samples, 115 avian and 100 rat faeces collected in springs 2009-2013 from dump sites, and 85 faeces from yellow-necked mice trapped in late autumn 2008 and 2009 after the rodents entered human settlements due to the first night frosts, were screened for HuNoV using real-time reverse transcription PCR...
March 12, 2018: Zoonoses and Public Health
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