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https://www.readbyqxmd.com/read/28102341/lasing-in-live-mitotic-and-non-phagocytic-cells-by-efficient-delivery-of-microresonators
#1
Marcel Schubert, Klara Volckaert, Markus Karl, Andrew Morton, Philipp Liehm, Gareth B Miles, Simon J Powis, Malte C Gather
Reliable methods to individually track large numbers of cells in real time are urgently needed to advance our understanding of important biological processes like cancer metastasis, neuronal network development and wound healing. It has recently been suggested to introduce microscopic whispering gallery mode lasers into the cytoplasm of cells and to use their characteristic, size-dependent emission spectrum as optical barcode but so far there is no evidence that this approach is generally applicable. Here, we describe a method that drastically improves intracellular delivery of resonators for several cell types, including mitotic and non-phagocytic cells...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28100584/umi-tools-modelling-sequencing-errors-in-unique-molecular-identifiers-to-improve-quantification-accuracy
#2
Tom Sean Smith, Andreas Heger, Ian Sudbery
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR-amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network based methods to account for these errors when identifying PCR duplicates...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28099773/comparison-of-green-and-albino-individuals-of-the-partially-mycoheterotrophic-orchid-epipactis-helleborine-on-molecular-identities-of-mycorrhizal-fungi-nutritional-modes-and-gene-expression-in-mycorrhizal-roots
#3
Kenji Suetsugu, Masahide Yamato, Chihiro Miura, Katsushi Yamaguchi, Kazuya Takahashi, Yoshiko Ida, Shuji Shigenobu, Hironori Kaminaka
Some green orchids obtain carbon from their mycorrhizal fungi, as well as from photosynthesis. These partially mycoheterotrophic orchids sometimes produce fully achlorophyllous, leaf-bearing (albino) variants. Comparing green and albino individuals of these orchids will help to uncover the molecular mechanisms associated with mycoheterotrophy. We compared green and albino Epipactis helleborine by molecular barcoding of mycorrhizal fungi, nutrient sources based on (15) N and (13) C abundances, and gene expression in their mycorrhizae by RNA-seq and cDNA de novo assembly...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28099373/deconstructing-clinical-workflow-identifying-teaching-learning-principles-for-barcode-electronic-medication-administration-with-nursing-students
#4
Richard G Booth, Barbara Sinclair, Gillian Strudwick, Laura Brennan, Lisa Morgan, Stephanie Collings, Jessica Johnston, Brittany Loggie, James Tong, Chantal Singh
The purpose of this quality improvement project was to better understand how to teach medication administration underpinned by an electronic medication administration record (eMAR) system used in simulated, prelicensure nursing education. Methods included a workflow and integration analysis and a detailed process mapping of both an oral and a sublingual medication administration. Procedural and curriculum development considerations related to medication administration using eMAR technology are presented for nurse educators...
January 18, 2017: Nurse Educator
https://www.readbyqxmd.com/read/28098770/can-malaysian-young-adults-report-dietary-intake-using-a-food-diary-mobile-application-a-pilot-study-on-acceptability-and-compliance
#5
Yoke San Chen, Jyh Eiin Wong, Ainaa Fatehah Ayob, Nor Effendy Othman, Bee Koon Poh
Mobile applications may improve dietary reporting among young adults due to their high accessibility and embedded camera function. This pilot study aimed to (i) evaluate users' acceptability and compliance in reporting dietary intake using a newly developed food diary mobile application (food app); and (ii) identify issues and recommendations for improving dietary assessment using this food app via quantitative and qualitative protocols. Twenty-eight university students each used a food app for seven consecutive days and attended one of five focus group interviews...
January 13, 2017: Nutrients
https://www.readbyqxmd.com/read/28096019/tinker-tailor-deliberate-an-ethnographic-inquiry-into-the-institutionalized-practice-of-bar-coded-medication-administration-technology-by-nurses
#6
M J M H Boonen, Frans J H Vosman, Alistair R Niemeijer
AIM: Explore the practice of nurses working with bar-coded medication administration technology, to gain insight in the impact it has on their work. BACKGROUND: The widespread presumption of using Barcoded Medication Administration Technology (BCMA) is that it will effectively reduce the number of errors in the dispensing of medication to patients. However, it remains unclear whether this is the case in actual practice. METHOD: Two distinct but overlapping research methodologies of Institutional Ethnography and Praxeology were combined as a means to uncover the highly complex practice of BCMA by nurses...
February 2017: Applied Nursing Research: ANR
https://www.readbyqxmd.com/read/28095828/improved-genome-sequencing-using-an-engineered-transposase
#7
Amirali Kia, Christian Gloeckner, Trina Osothprarop, Niall Gormley, Erin Bomati, Michelle Stephenson, Igor Goryshin, Molly Min He
BACKGROUND: Next-generation sequencing (NGS) has transformed genomic research by reducing turnaround time and cost. However, no major breakthrough has been made in the upstream library preparation methods until the transposase-based Nextera method was invented. Nextera combines DNA fragmentation and barcoding in a single tube reaction and therefore enables a very fast workflow to sequencing-ready DNA libraries within a couple of hours. When compared to the traditional ligation-based methods, transposed-based Nextera has a slight insertion bias...
January 17, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28094568/barcode-based-species-delimitation-in-the-marine-realm-a-test-using-hexanauplia-multicrustacea-thecostraca-and-copepoda
#8
Robert G Young, Cathryn L Abbott, Thomas W Therriault, Sarah J Adamowicz
DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value...
October 21, 2016: Genome GĂ©nome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28092571/machine-learned-replacement-of-n-labels-for-basecalled-sequences-in-dna-barcoding
#9
Eddie Ma, Sujeevan Ratnasingham, Stefan Kremer
This study presents a machine learning method that increases the number of identified bases in Sanger Sequencing. The system post-processes a KB basecalled chromatogram. It selects a recoverable subset of N-labels in the KB-called chromatogram to replace with basecalls (A,C,G,T). An N-label correction is defined given an additional read of the same sequence, and a human finished sequence. Corrections are added to the dataset when an alignment determines the additional read and human agree on the identity of the N-label...
August 11, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28091577/identification-of-wood-boring-beetles-cerambycidae-and-buprestidae-intercepted-in-trade-associated-solid-wood-packaging-material-using-dna-barcoding-and-morphology
#10
Yunke Wu, Nevada F Trepanowski, John J Molongoski, Peter F Reagel, Steven W Lingafelter, Hannah Nadel, Scott W Myers, Ann M Ray
Global trade facilitates the inadvertent movement of insect pests and subsequent establishment of populations outside their native ranges. Despite phytosanitary measures, nonnative insects arrive at United States (U.S.) ports of entry as larvae in solid wood packaging material (SWPM). Identification of wood-boring larval insects is important for pest risk analysis and management, but is difficult beyond family level due to highly conserved morphology. Therefore, we integrated DNA barcoding and rearing of larvae to identify wood-boring insects in SWPM...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090265/identification-and-monitoring-of-korean-medicines-derived-from-cinnamomum-spp-by-using-its-and-dna-marker
#11
Eui Jeong Doh, Jung-Hoon Kim, Seung Eun Oh, Guemsan Lee
In this study, we identified and evaluated the genetic relationships among Cinnamomum plants, which are used in traditional medicine. We also attempted to monitor the distribution of traditional medicines derived from Cinnamomum cassia by using DNA barcoding and a species-specific DNA marker. Plants of the genus Cinnamomum, and in particular C. cassia, are commonly used as medicinal herbs in the form of Cinnamomi Ramulus, Cinnamomi Cortex, and Cassiae Cortex Interior. However, it is difficult to distinguish among different Cinnamomum species based on morphological features, and so to overcome this limitation, nucleotide sequences of the internal transcribed spacer (ITS) region of Cinnamomum DNA were determined and compared...
2017: Genes & Genomics
https://www.readbyqxmd.com/read/28089841/the-birth-of-aposematism-high-phenotypic-divergence-and-low-genetic-diversity-in-a-young-clade-of-poison-frogs
#12
Rebecca Dent Tarvin, Emily A Powell, Juan C Santos, Santiago R Ron, David C Cannatella
Rapid radiation coupled with low genetic divergence often hinders species delimitation and phylogeny estimation even if putative species are phenotypically distinct. Some aposematic species, such as poison frogs (Dendrobatidae), have high levels of intraspecific color polymorphism, which can lead to overestimation of species when phenotypic divergence primarily guides species delimitation. We explored this possibility in the youngest origin of aposematism (3-7 MYA) in poison frogs, Epipedobates, by comparing genetic divergence with color and acoustic divergence...
January 13, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28088131/number-crunching-towards-molecular-barcoding
#13
Soroush Sardari
No abstract text is available yet for this article.
2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28087539/quantitative-stability-of-hematopoietic-stem-and-progenitor-cell-clonal-output-in-transplanted-rhesus-macaques
#14
Samson J Koelle, Diego A Espinoza, Chuanfeng Wu, Jason Xu, Rong Lu, Brian Li, Robert E Donahue, Cynthia E Dunbar
Autologous transplantation of hematopoietic stem and progenitor cells lentivirally labeled with unique oligonucleotide barcodes flanked by sequencing primer targets enables quantitative assessment of the self-renewal and differentiation patterns of these cells in a myeloablative rhesus macaque model. Compared with other approaches to clonal tracking, this approach is highly quantitative and reproducible. We documented very stable multipotent long-term hematopoietic clonal output of monocytes, granulocytes, B cells and T cells from a polyclonal pool of hematopoietic stem and progenitor cells in four macaques followed for up to 49 months post-transplantation...
January 13, 2017: Blood
https://www.readbyqxmd.com/read/28080142/whole-genome-amplification-provides-suitable-control-dna-for-use-in-dna-barcoding-applications
#15
Danielle A Bourque, Amanda M Naaum, Dan L Distel, Robert H Hanner
No abstract text is available yet for this article.
January 12, 2017: Biopreservation and Biobanking
https://www.readbyqxmd.com/read/28077623/a-quality-improvement-project-to-decrease-human-milk-errors-in-the-nicu
#16
Reena Oza-Frank, Rashmi Kachoria, James Dail, Jasmine Green, Krista Walls, Richard E McClead
BACKGROUD AND OBJECTIVE: Ensuring safe human milk in the NICU is a complex process with many potential points for error, of which one of the most serious is administration of the wrong milk to the wrong infant. Our objective was to describe a quality improvement initiative that was associated with a reduction in human milk administration errors identified over a 6-year period in a typical, large NICU setting. METHODS: We employed a quasi-experimental time series quality improvement initiative by using tools from the model for improvement, Six Sigma methodology, and evidence-based interventions...
January 11, 2017: Pediatrics
https://www.readbyqxmd.com/read/28075039/using-dna-barcoding-to-track-seafood-mislabeling-in-los-angeles-restaurants
#17
Demian A Willette, Sara E Simmonds, Samantha H Cheng, Sofia Esteves, Tonya L Kane, Hayley Nuetzel, Nicholas Pilaud, Rita Rachmawati, Paul H Barber
Seafood mislabeling is common in both domestic and international markets. Previous studies on seafood fraud often report high rates of mislabeling (e.g. >70%), but these studies have been limited to a single sampling year, making it difficult to assess the impact of stricter governmental truth-in-labeling regulations. This study uses DNA barcoding to assess seafood mislabeling in Los Angeles over a four-year period. Sushi restaurants had a consistently high percentage of mislabeling (47%) from 2012 to 2015, yet mislabeling was not homogenous across species...
January 11, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28074500/level-of-environmental-threat-posed-by-horticultural-trade-in-cactaceae
#18
Ana Novoa, Johannes J Le Roux, David M Richardson, John R U Wilson
Ornamental horticulture has been identified as an important threat to plant biodiversity and the major pathway for plant invasions worldwide. In this context, the family Cactaceae is particularly interesting and challenging for three main reasons-it is considered the fifth most threatened major taxonomic group in the world; several cactus species are amongst the most widespread and damaging invasive species; and Cactaceae is one of the most popular horticultural plant groups. Based on CITES trade data and the eleven main auction sites selling cacti on the internet we document a substantial global trade from and to almost all continents...
January 11, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28072819/testing-the-efficacy-of-dna-barcodes-for-identifying-the-vascular-plants-of-canada
#19
Thomas W A Braukmann, Maria L Kuzmina, Jesse Sills, Evgeny V Zakharov, Paul D N Hebert
Their relatively slow rates of molecular evolution, as well as frequent exposure to hybridization and introgression, often make it difficult to discriminate species of vascular plants with the standard barcode markers (rbcL, matK, ITS2). Previous studies have examined these constraints in narrow geographic or taxonomic contexts, but the present investigation expands analysis to consider the performance of these gene regions in discriminating the species in local floras at sites across Canada. To test identification success, we employed a DNA barcode reference library with sequence records for 96% of the 5108 vascular plant species known from Canada, but coverage varied from 94% for rbcL to 60% for ITS2 and 39% for matK...
2017: PloS One
https://www.readbyqxmd.com/read/28070758/phylogeography-of-the-asian-rice-gall-midge-orseolia-oryzae-wood-mason-diptera-cecidomyiidae-in-thailand
#20
Solene Janique, Wantana Sriratanasak, Kulchana Ketsuwan, Jirapong Jairin, Ekgachai Jeratthitikul
The Asian rice gall midge (RGM) Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) is a major pest of rice, leading to yield losses in Thailand and many Asian countries. Despite an increasing number of reported midge outbreaks and the presence of many susceptible rice varieties, only a few studies have focused on the genetic variation of the midges. Therefore, we analyzed the phylogeography among Thai RGM populations covering north, northeast and central Thailand. Two mitochondrial DNA genes, cytochrome C oxidase I (COI) and 12S, and a non-coding repeat region (RR) situated just before COI were amplified...
January 9, 2017: Genetica
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