Read by QxMD icon Read

molecular barcoding

Emma L Betts, Eleni Gentekaki, Adele Thomasz, Vicki Breakell, Angus I Carpenter, Anastasios D Tsaousis
Blastocystis is an anaerobic protist, commonly inhabiting the intestinal tract of both humans and other animals. Blastocystis is extremely diverse comprising 17 genetically distinct subtypes in mammals and birds. Pathogenicity of this enteric microbe is currently disputed and knowledge regarding its distribution, diversity and zoonotic potential is fragmentary. Most research has focused on Blastocystis from primates, while sampling from other animals remains limited. Herein, we investigated the prevalence and distribution of Blastocystis in animals held within a conservation park in South East England...
January 17, 2018: Parasitology
Jun-Yuan Li, Dong-Hui Guo, Peng-Cheng Wu, Li-Sheng He
Ontogeny reversal, as seen in some cnidarians, is an unprecedented phenomenon in the animal kingdom involving reversal of the ordinary life cycle. Three species of Turritopsis have been shown to be capable of inverted metamorphosis, a process in which the pelagic medusa transforms back into a juvenile benthic polyp stage when faced with adverse conditions. Turritopsis sp.5 is a species of Turritopsis collected from Xiamen, China which presents a similar ability, being able to reverse its life cycle if injured by mechanical stress...
2018: PeerJ
Nerea Abrego, Veera Norros, Panu Halme, Panu Somervuo, Heini Ali-Kovero, Otso Ovaskainen
Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning, and are important for human health, food production, and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge. We present a method that allows anyone to generate a list of fungal species likely to occur in a region of interest, with minimal effort and without requiring taxonomical expertise...
January 13, 2018: Molecular Ecology Resources
Amy K Bei, Makhtar Niang, Awa B Deme, Rachel F Daniels, Fatoumata D Sarr, Cheikh Sokhna, Cheikh Talla, Joseph Faye, Nafissatou Diagne, Souleymane Doucoure, Souleymane Mboup, Dyann F Wirth, Adama Tall, Daouda Ndiaye, Daniel L Hartl, Sarah K Volkman, Aissatou Toure-Balde
Dramatic changes in transmission intensity can impact Plasmodium population diversity. Using samples from 2 distant time-points in the Dielmo/Ndiop longitudinal cohorts from Senegal, we applied a molecular barcode tool to detect changes in parasite genotypes and complexity of infection that corresponded to changes in transmission intensity. We observed a striking statistically significant difference in genetic diversity between the 2 parasite populations. Furthermore, we identified a genotype in Dielmo and Ndiop previously observed in Thiès, potentially implicating imported malaria...
January 9, 2018: Journal of Infectious Diseases
Ruichao Li, Miaomiao Xie, Ning Dong, Dachuan Lin, Xuemei Yang, Marcus Ho Yin Wong, Edward Wai-Chi Chan, Sheng Chen
Background: Multidrug resistance (MDR)-encoding plasmids are considered major molecular vehicles responsible for transmission of antibiotic resistance genes among bacteria of the same or different species. Delineating the complete sequences of such plasmids could provide valuable insight into the evolution and transmission mechanisms underlying bacterial antibiotic resistance development. However, due to the presence of multiple repeats of mobile elements, complete sequencing of MDR plasmids remains technically complicated, expensive and time-consuming...
January 9, 2018: GigaScience
Camila González, Cielo León, Andrea Paz, Marla López, Gisell Molina, Diana Toro, Mario Ortiz, Juan Manuel Cordovez, María Claudia Atencia, Germán Aguilera, Catalina Tovar
Leishmaniases are neglected tropical diseases exhibiting complex transmission cycles due to the number of parasite species circulating, sand fly species acting as vectors and infected mammals, including humans, which are defined in the New World as accidental hosts. However, current transmission scenarios are changing, and the disease is no longer exclusively related to forested areas but urban transmission foci occur, involving some species of domestic animals as suspected reservoirs. The aim of this study was to determine the transmission cycles in urban environments by evaluating sand fly diversity, detection of Leishmania DNA, and bloodmeal sources through intra and peridomestic collections...
2018: PloS One
Monica Nagendran, Daniel P Riordan, Pehr B Harbury, Tushar J Desai
A major challenge in biology is identifying distinct cell classes and mapping their interactions in vivo. Tissue-dissociative technologies enable deep single cell molecular profiling but do not provide spatial information. We developed a proximity ligation- in situ hybridization technology (PLISH) with exceptional signal strength, specificity, and sensitivity in tissue. Multiplexed data sets can be acquired using barcoded probes and rapid label-image-erase cycles, with automated calculation of single cell profiles, enabling clustering and anatomical re-mapping of cells...
January 10, 2018: ELife
Wendy Y Wang, Amrita Srivathsan, Maosheng Foo, Seiki Yamane, Rudolf Meier
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0...
January 5, 2018: Molecular Ecology Resources
Roberto Contreras, Ana M Figueiras, F Javier Gallego, Elena Benavente, Antonio J Manzaneda, César Benito
Aluminium (Al) toxicity is the main abiotic stress limiting plant productivity in acidic soils that are widely distributed among arable lands. Plant species differ in the level of Al resistance showing intraspecific and interspecific variation in many crop species. However, the origin of Al-tolerance is not well known. Three annual species, difficult to distinguish phenotypically and that were until recently misinterpreted as a single complex species under Brachypodium distachyon, have been recently separated into three distinct species: the diploids B...
November 2017: AoB Plants
Shi-Xiao Luo, Lian-Jie Zhang, Shuai Yuan, Zhong-Hui Ma, Dian-Xiang Zhang, Susanne S Renner
Insect pollination in basal angiosperms is assumed to mostly involve 'generalized' insects looking for food, but direct observations of ANITA grade (283 species) pollinators are sparse. We present new data for numerous Schisandraceae, the largest ANITA family, from fieldwork, nocturnal filming, electron microscopy, barcoding and molecular clocks to infer pollinator/plant interactions over multiple years at sites throughout China to test the extent of pollinator specificity. Schisandraceae are pollinated by nocturnal gall midges that lay eggs in the flowers and whose larvae then feed on floral exudates...
January 10, 2018: Proceedings. Biological Sciences
Erdene-Ochir Tseren-Ochir, Seong-Su Yuk, Bodisaikhan Khishgee, Jung-Hoon Kwon, Jin-Yong Noh, Woo-Tack Hong, Jei-Hyun Jeong, Gyeong-Bin Gwon, Sol Jeong, Yu-Jin Kim, Jun-Beom Kim, Ji-Ho Lee, Kyu-Jik Kim, Batchuluun Damdinjav, Chang-Seon Song
Avian paramyxoviruses (APMVs) constitute some of the most globally prevalent avian viruses and are frequently isolated from wild migratory bird species. Using 1,907 fresh fecal samples collected during the 2012 avian influenza surveillance program, we identified two serotypes of APMV: APMV-4 ( n=10) and APMV-8 ( n=1). Sequences for these isolates phylogenetically clustered with Asian APMV-4 and APMV-8 recently isolated from wild birds in Korea, Japan, China, and Kazakhstan. Analysis by DNA barcoding indicated that the Mongolian APMV-4 and APMV-8 strains were isolated from Anseriformes species including Mallards ( Anas platyrhynchos) and Whooper Swans ( Cygnus cygnus)...
December 29, 2017: Journal of Wildlife Diseases
Misbah Ullah, Yanling Dong, Pingping Qiao, Yalin Zhang, Zhaofu Yang
Integrative taxonomic study of three species of the genus Tylostega revealed that the genetic distances of the COI gene among the tested species was relatively large (3.27-7.60%). The Automatic Barcode Gap Discovery (ABGD) system performed better than the Barcode Index Number (BIN) in discriminating closely related species. This work provides a molecular baseline for future integrative taxonomic study of Crambidae.
December 27, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Chun-Xia Wang, Xin Xu, Shu-Qiang Li
Extreme environments, such as subterranean habitats, are suspected to be responsible for morphologically inseparable cryptic or sibling species and can bias biodiversity assessment. A DNA barcode is a short, standardized DNA sequence used for taxonomic purposes and has the potential to lessen the challenges presented by a biotic inventory. Here, we investigate the diversity of the genus Leptonetela Kratochvíl, 1978 that is endemic to karst systems in Eurasia using DNA barcoding. We analyzed 624 specimens using one mitochondrial gene fragment (COI)...
November 18, 2017: Zoological Research
Reyhan Akçaalan, Meric Albay, Latife Koker, Julia Baudart, Delphine Guillebault, Sabine Fischer, Wilfried Weigel, Linda K Medlin
Monitoring drinking water quality is an important public health issue. Two objectives from the 4 years, six nations, EU Project μAqua were to develop hierarchically specific probes to detect and quantify pathogens in drinking water using a PCR-free microarray platform and to design a standardised water sampling program from different sources in Europe to obtain sufficient material for downstream analysis. Our phylochip contains barcodes (probes) that specifically identify freshwater pathogens that are human health risks in a taxonomic hierarchical fashion such that if species is present, the entire taxonomic hierarchy (genus, family, order, phylum, kingdom) leading to it must also be present, which avoids false positives...
December 22, 2017: Environmental Monitoring and Assessment
Marcelo Vargas-Ortiz, Dante Bobadilla, Wilson Huanca-Mamani, Héctor A Vargas
Analysis of maternally inherited genes is especially helpful in population studies of host-specialized insects, as female dispersal is key to find an adequate host plant to ensure larval survival. Bucculatrix mirnae (Lepidoptera: Bucculatricidae) is a little-known Neotropical micromoth native to the arid environments of northern Chile whose hypermetamorphic larvae are miners and skeletonizers on leaves of two species of Baccharis (Asteraceae) shrubs. This micromoth has been detected in three isolated locations embracing a narrow geographic range: two from the coastal valleys of the Atacama Desert near sea level and one from the western slopes of the Andes at about 3000 m elevation...
December 22, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Mieke Titulaer, Alicia Melgoza-Castillo, Arvind O Panjabi, Alejandro Sanchez-Flores, José Hugo Martínez-Guerrero, Alberto Macías-Duarte, Jesús A Fernandez
We analyzed the diet of Baird's Sparrow (Ammodramus bairdii) and Grasshopper Sparrow (A. savannarum) in three different sites and sampling periods across the Chihuahuan Desert in northern Mexico. DNA from seeds in regurgitated stomach contents was sequenced using NGS technology and identified with a barcoding approach using the P6 loop of the trnL intron as genetic marker. During each sampling period, we collected random soil samples to estimate seed availability in the soil seed bank. Due to the variability and size of the genetic marker, the resolution was limited to a family level resolution for taxonomic classification of seeds, but in several cases a genus level was achieved...
2017: PloS One
Niels W L Van Steenkiste, Elizabeth R Herbert, Brian S Leander
Increasing evidence suggests that many widespread species of meiofauna are in fact regional complexes of (pseudo-)cryptic species. This knowledge has challenged the 'Everything is Everywhere' hypothesis and also partly explains the meiofauna paradox of widespread nominal species with limited dispersal abilities. Here, we investigated species diversity within the marine microturbellarian Astrotorhynchus bifidus sensu lato in the Northeast Pacific Ocean. We used a multiple-evidence approach combing multi-gene (18S, 28S, COI) phylogenetic analyses, several single-gene and multi-gene species delimitation methods, haplotype networks and conventional taxonomy to designate Primary Species Hypotheses (PSHs)...
December 14, 2017: Molecular Phylogenetics and Evolution
Riccardo Brunetti, Lucia Manni, Francesco Mastrototaro, Carmela Gissi, Fabio Gasparini
Botryllus schlosseri is a widespread colonial ascidian commonly considered cosmopolitan and amply used as model for researches ranging from developmental biology to immunobiology. Recently, molecular data lead to hypothesize that the species named B. schlosseri may consist of more than a single taxon. Indeed, five highly divergent clades, named A-E, have been genetically identified and are referred as cryptic species. In this context, and lacking both a type and a detailed morphological description, we believe that it is necessary, as a taxonomic reference point, to designate a neotype and re-describe the species...
November 22, 2017: Zootaxa
Mariusz Kanturski, Łukasz Kajtoch, Karina Wieczorek
The aphid genus Eulachnus in Europe is revised to include 12 species, using an integrative taxonomy approach, based on morphometric, molecular and biological traits. Fundatrix, apterous and alate viviparous female of a new species-Eulachnus stekolshchikovi Kanturski sp. nov. are described. Neotypes are designated for E. agilis, E. brevipilosus and E. nigricola. Lectotypes are designated for E. alticola, E. cembrae, E. rileyi and E. tuberculostemmatus. New synonyms are proposed: E. abameleki syn. nov. (= Cinara pini), E...
November 27, 2017: Zootaxa
Shaokun Guo, Jia He, Zihua Zhao, Lijun Liu, Liyuan Gao, Shuhua Wei, Xiaoyu Guo, Rong Zhang, Zhihong Li
Neoceratitis asiatica (Becker), which especially infests wolfberry (Lycium barbarum L.), could cause serious economic losses every year in China, especially to organic wolfberry production. In some important wolfberry plantings, it is difficult and time-consuming to rear the larvae or pupae to adults for morphological identification. Molecular identification based on DNA barcode is a solution to the problem. In this study, 15 samples were collected from Ningxia, China. Among them, five adults were identified according to their morphological characteristics...
December 12, 2017: Zootaxa
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"