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Zaharias P, Kantor YI, Fedosov AE, Puillandre N. Coupling DNA barcodes and exon-capture to resolve the phylogeny of Turridae (Gastropoda, Conoidea). Mol Phylogenet Evol 2024; 191:107969. [PMID: 38007006 DOI: 10.1016/j.ympev.2023.107969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Taxon sampling in most phylogenomic studies is often based on known taxa and/or morphospecies, thus ignoring undescribed diversity and/or cryptic lineages. The family Turridae is a group of venomous snails within the hyperdiverse superfamily Conoidea that includes many undescribed and cryptic species. Therefore 'traditional' taxon sampling could constitute a strong risk of undersampling or oversampling Turridae lineages. To minimize potential biases, we establish a robust sampling strategy, from species delimitation to phylogenomics. More than 3,000 cox-1 "barcode" sequences were used to propose 201 primary species hypotheses, nearly half of them corresponding to species potentially new to science, including several cryptic species. A 110-taxa exon-capture tree, including species representatives of the diversity uncovered with the cox-1 dataset, was build using up to 4,178 loci. Our results show the polyphyly of the genus Gemmula, that is split into up to 10 separate lineages, of which half would not have been detected if the sampling strategy was based only on described species. Our results strongly suggest that the use of blind, exploratory and intensive barcode sampling is necessary to avoid sampling biases in phylogenomic studies.
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Affiliation(s)
- Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France.
| | - Yuri I Kantor
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Alexander E Fedosov
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France
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Pagliusi S, Madrid Y, Bramanti Y, Wilmansyah T, Yu H, Acebal A, Krishnamurthy KR, Raju Pinnamaraju V, Jadhav P, Park R, Yang L. Vaccine traceability: Key learnings from the supply chain initiative by manufacturers from emerging countries. Vaccine X 2023; 15:100366. [PMID: 37663047 PMCID: PMC10470265 DOI: 10.1016/j.jvacx.2023.100366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
The use of global standards, and the placement of barcodes and data matrix codes on vaccine labels and other levels of packaging are crucial elements for the traceability of finished vaccine products. Vaccine manufacturers are committed to improving health through their products, as vaccine production offers opportunities that can be leveraged to benefit immunization systems. In 2019 the Developing Countries Vaccine Manufacturers Network (DCVMN) created the Supply Chain Initiative aimed at prioritize and explore traceability opportunities; concomitantly procurement agencies announced traceability requirements for vaccine global supply. Vaccine traceability brings benefits including supply chain reliability and safety through enhanced product movement visibility, and a reduction of falsified and expired vaccines circulating in the supply chain. DCVMN has coordinated the development and implementation of global traceability standards, at both primary and secondary vaccine packaging levels, to encourage and enable sharing these experiences. Six pilot studies in four different countries showed successful implementation, and constituted part of larger vaccine traceability work within the respective organizations. The main findings from these pilot studies indicated that stepwise approaches to the adoption of traceability standards allowed vaccine manufacturers to learn by doing, initially with lower risk, and to spread their investments over time. Because the value of traceability is in its scale of adoption and the use of the data, it remains important for all stakeholders to engage in and prioritize the journey of vaccine traceability, but also to suitably manage the financial risks. The DCVMN Supply Chain Initiative has demonstrated that its members are committed to driving supply system changes that benefit immunization, while recognizing that supply chain traceability is part of a larger healthcare ecosystem and should be adopted by countries and immunization programmes as well.
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Affiliation(s)
- Sonia Pagliusi
- DCVMN International, Route de Crassier 7, 1262 Eysins-Nyon, Switzerland
| | | | - Yudha Bramanti
- PT BioFarma, Jl. Pasteur No. 28, Kota Bandung, Jawa Barat 40161, Indonesia
| | - Taufik Wilmansyah
- PT BioFarma, Jl. Pasteur No. 28, Bandung, Jawa Barat 40161, Indonesia
| | - Huilin Yu
- Xiamen Innovax Biotech CO., LTD., #50 Shanbianhong East Road, Haicang District, Xiamen, Fujian, China
| | - Analia Acebal
- Sinergium Biotech, Ruta Panamericana KM 38,7, Garin, CP1619 Buenos Aires, Argentina
| | | | | | - Padmakar Jadhav
- Vaccine Division, Biological E Limited, Shameerpet, Hyderabad, India
| | - Rachel Park
- EuBiologics, 8F, Seongdo Building, 207, Dosan-daero, Sinsa-dong, Gangnam-gu, Seoul, South Korea
| | - Lingjiang Yang
- ChengDu Institute of Biological Products Co. Ltd, 379#, 3rd Section, Jinhua Road, Jinjiang District, Chengdu 610023, China
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Khemira H, Mahdhi M, Afzal M, Oteef MD, Tounekti T, AL-Faifi Z, Alsolami W. Assessment of genetic diversity and phylogenetic relationship of local coffee populations in southwestern Saudi Arabia using DNA barcoding. PeerJ 2023; 11:e16486. [PMID: 38025745 PMCID: PMC10680449 DOI: 10.7717/peerj.16486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
The genetic diversity of local coffee populations is crucial to breed new varieties better adapted to the increasingly stressful environment due to climate change and evolving consumer preferences. Unfortunately, local coffee germplasm conservation and genetic assessment have not received much attention. Molecular tools offer substantial benefits in identifying and selecting new cultivars or clones suitable for sustainable commercial utilization. New annotation methods, such as chloroplast barcoding, are necessary to produce accurate and high-quality phylogenetic analyses. This study used DNA barcoding techniques to examine the genetic relationships among fifty-six accessions collected from the southwestern part of Saudi Arabia. PCR amplification and sequence characterization were used to investigate the effectiveness of four barcoding loci: atpB-rbcl, trnL-trnF, trnT-trnL, and trnL. The maximum nucleotide sites, nucleotide diversity, and an average number of nucleotide differences were recorded for atpB-rbcl, while trnT-trnL had the highest variable polymorphic sites, segregating sites, and haploid diversity. Among the four barcode loci, trnT-trnL recorded the highest singleton variable sites, while trnL recorded the highest parsimony information sites. Furthermore, the phylogenetic analysis clustered the Coffea arabica genotypes into four different groups, with three genotypes (KSA31, KSA38, and KSA46) found to be the most divergent genotypes standing alone in the cluster and remained apart during the analysis. The study demonstrates the presence of considerable diversity among coffee populations in Saudi Arabia. Furthermore, it also shows that DNA barcoding is an effective technique for identifying local coffee genotypes, with potential applications in coffee conservation and breeding efforts.
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Affiliation(s)
- Habib Khemira
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
| | - Mosbah Mahdhi
- Centre for Environmental Research and Studies, Jazan University, Jazan, Saudi Arabia
- Laboratory of Biodiversity and Valorization of Bioresources in Arid Zones, Faculty of Sciences of Gabes, University of Gabes, Gabes, Tunisia
| | - Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed D.Y. Oteef
- Department of Chemistry, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Taieb Tounekti
- Laboratory of Process Engineering & Industrial Systems (LR11ES54), National Engineering School of Gabes, University of Gabes, Gabes, Tunisia
| | - Zarraq AL-Faifi
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
| | - Wail Alsolami
- Department of Biology, College of Science, Jazan University, Jazan, Saudi Arabia
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Guimarães Riva H, Montoya LMH, Gutiérrez MF, Flórez MD, Olaciregui C, Andrade E, Acevedo-Garcés YA, Soto-Calderón ID. Urban biodiversity: Cuterebriasis in free-ranging Robinson's mouse opossum ( Marmosa robinsoni) in the suburbs of Barranquilla, Colombia. Int J Parasitol Parasites Wildl 2023; 21:83-88. [PMID: 37159725 PMCID: PMC10163466 DOI: 10.1016/j.ijppaw.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 05/11/2023]
Abstract
The tropical dry forest is one of the world's most threatened ecosystems and is the habitat of the Robinson's Mouse Opossum (Marmosa robinsoni), a small marsupial within the Didelphidae family. This study aimed to describe cases of cuterebriases in free-ranging M. robinsoni by examining individuals caught in live animal traps. Sherman traps were deployed in four different sites over three different periods in five days. All animals passed through biometry, weighing, sampling parasites, and sampling feces. Only animals captured in the study site located close to the city were anesthetized and examined. The evaluation included blood samples and a clinical examination. Animals received anesthesia under physical restraint by intramuscular injections of ketamine and xylazine. For anesthetic reversion, the protocol was Yohimbine administered before release. In total, 8% (5/60) of all captured animals had fly larvae extracted from wounds. The molecular Barcode of the mitochondrial Cytochrome Oxidase I gene showed no match with any recognized species of Cuterebra. The animals weighed from 35 to 80 g and had lesions in the scapular region with parasites under their skin in sizes ranging from 1.3 to 2.2 cm. The animals with parasites were in good physical condition without evidence of disturbances in health conditions. This is compatible with literature, reporting little effect on population dynamics of other host species infected with Cuterebra larvae. The study included 24 animals captured in three areas far from any city, which showed no evidence of cuterebrid infection, suggesting that proximity to the city could increase exposure to cuterebriasis. There are reports of cuterebrids in M. robinsoni in Brazil; however, this is the first report of cuterebriasis in M. robinsoni in Colombia.
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Affiliation(s)
- Henrique Guimarães Riva
- Coordenadoria de Fauna Silvestre, Governo do Estado de São Paulo (CFS-SEMIL- SP), Brazil
- Corresponding author.
| | | | | | | | | | | | - Yuliet Andrea Acevedo-Garcés
- Agrociencias, Biodiversidad y Territorio (GAMMA), Laboratorio de Genética Animal, Universidad de Antioquia, Calle 67 No. 53 - 108, Medellín, Antioquia, 50010, Colombia
| | - Iván Darío Soto-Calderón
- Agrociencias, Biodiversidad y Territorio (GAMMA), Laboratorio de Genética Animal, Universidad de Antioquia, Calle 67 No. 53 - 108, Medellín, Antioquia, 50010, Colombia
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Guichard A, Legeai F, Tagu D, Lemaitre C. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinformatics 2023; 24:284. [PMID: 37452278 PMCID: PMC10347852 DOI: 10.1186/s12859-023-05395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. RESULTS We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. CONCLUSIONS MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.
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Affiliation(s)
- Anne Guichard
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France.
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Denis Tagu
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Li F, Tarkington J, Sherlock G. Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays. J Mol Evol 2023; 91:334-344. [PMID: 36877292 PMCID: PMC10276102 DOI: 10.1007/s00239-023-10098-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 02/02/2023] [Indexed: 03/07/2023]
Abstract
The fitness of a genotype is defined as its lifetime reproductive success, with fitness itself being a composite trait likely dependent on many underlying phenotypes. Measuring fitness is important for understanding how alteration of different cellular components affects a cell's ability to reproduce. Here, we describe an improved approach, implemented in Python, for estimating fitness in high throughput via pooled competition assays.
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Affiliation(s)
- Fangfei Li
- Department of Genetics, Stanford University, Stanford, USA
| | | | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, USA.
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Liu T, Tian Y, Cao Y, Wang Z, Zha G, Liu W, Wei L, Xiao H, Zhang Q, Cao C. Isoelectric point barcode and similarity analysis with the earth mover's distance for identification of species origin of raw meat. Food Res Int 2023; 166:112600. [PMID: 36914325 DOI: 10.1016/j.foodres.2023.112600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 02/07/2023] [Accepted: 02/14/2023] [Indexed: 02/20/2023]
Abstract
In this work, by combining the microcolumn isoelectric focusing (mIEF) and similarity analysis with the earth mover's distance (EMD) metric, we proposed the concept of isoelectric point (pI) barcode for the identification of species origin of raw meat. At first, we used the mIEF to analyze 14 meat species, including 8 species of livestock and 6 species of poultry, to generate 140 electropherograms of myoglobin/hemoglobin (Mb/Hb) markers. Secondly, we binarized the electropherograms and converted them into the pI barcodes that only showed the major Mb/Hb bands for the EMD analysis. Thirdly, we efficiently developed the barcode database of 14 meat species and successfully used the EMD method to identify 9 meat products thanks to the high throughput of mIEF and the simplified format of the barcode for similarity analysis. The developed method had the merits of facility, rapidity and low cost. The developed concept and method had evident potential to the facile identification of meat species.
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Affiliation(s)
- Tian Liu
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Youli Tian
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiren Cao
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zihao Wang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Genhan Zha
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weiwen Liu
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li Wei
- Shanghai 6(th) People's Hospital, Shanghai Jiao Tong University, Shanghai 200233, China
| | - Hua Xiao
- School of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Qiang Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China; School of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Chengxi Cao
- School of Life Sciences and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai 6(th) People's Hospital, Shanghai Jiao Tong University, Shanghai 200233, China.
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Jessurun JG, Hunfeld NGM, van Dijk M, van den Bemt PMLA, Polinder S. Cost-effectiveness of central automated unit dose dispensing with barcode-assisted medication administration in a hospital setting. Res Social Adm Pharm 2022; 18:3980-3987. [PMID: 35853809 DOI: 10.1016/j.sapharm.2022.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/14/2022] [Accepted: 07/10/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Central automated unit dose dispensing (cADD) with barcode-assisted medication administration (BCMA) has been shown to reduce medication administration errors (MAEs). Little is known about the cost-effectiveness of this intervention. OBJECTIVE To estimate the cost-effectiveness of cADD with BCMA compared to usual care. METHODS An economic evaluation was conducted alongside a prospective before-and-after effectiveness study in a Dutch university hospital. The primary effect measure was the difference between the rate of MAEs before and after implementation of cADD with BCMA, obtained by disguised observation in six clinical wards and subsequent extrapolation to the entire hospital. The cost-analysis was conducted from a hospital perspective with a 12-month incremental costing approach. The total costs covered the pharmaceutical service, nurse medication handling, wastage, and materials related to cADD. The primary outcome was the cost-effectiveness ratio expressed as costs per avoided MAE, obtained by dividing the annual incremental costs by the number of avoided MAEs. The secondary outcome was the cost-effectiveness ratio expressed as costs per avoided potentially harmful MAE (i.e. MAEs with the potential to cause harm). RESULTS The intervention was associated with an absolute MAE reduction of 4.5% and a reduction of 2.7% for potentially harmful MAEs. Based on 2,260,870 administered medications in the entire hospital annually, a total of 102,210 MAEs and 59,830 potentially harmful MAEs were estimated to be avoided. The intervention was associated with an increased incremental cost of €1,808,600 annually. The cost-effectiveness ratio was €17.69 per avoided MAE and €30.23 per avoided potentially harmful MAE. CONCLUSIONS The implementation of cADD with BCMA was associated with a reduced rate of medication errors, including harmful ones, at higher overall costs. The costs per avoided error are relatively low, and therefore, this intervention could be an important strategy to improve patient safety in hospitals.
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Affiliation(s)
- Janique Gabriëlle Jessurun
- Department of Hospital Pharmacy, Erasmus MC, University Medical Center Rotterdam, Rotterdam, P.O. Box 2040, 3000 CA, the Netherlands.
| | - Nicole Geertruida Maria Hunfeld
- Department of Hospital Pharmacy, Erasmus MC, University Medical Center Rotterdam, Rotterdam, P.O. Box 2040, 3000 CA, the Netherlands; Department of Intensive Care, Erasmus MC, University Medical Center Rotterdam, Rotterdam, P.O. Box 2040, 3000 CA, the Netherlands.
| | - Monique van Dijk
- Department of Internal Medicine, Section of Nursing Science, Erasmus MC, University Medical Center Rotterdam, Rotterdam, P.O. Box 2040, 3000 CA, the Netherlands.
| | - Patricia Maria Lucia Adriana van den Bemt
- Department of Hospital Pharmacy, Erasmus MC, University Medical Center Rotterdam, Rotterdam, P.O. Box 2040, 3000 CA, the Netherlands; Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, Groningen, P.O. Box 30.001, 9700 RB, the Netherlands.
| | - Suzanne Polinder
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, P.O. Box 2040, 3000 CA, the Netherlands.
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Snyman LP, Penning KE, Williams KA. The first reported case of accidental intestinal myiasis in a domestic dog by the flesh fly, Sarcophaga africa (Wiedeman, 1824). Res Vet Sci 2022; 149:71-73. [PMID: 35777281 DOI: 10.1016/j.rvsc.2022.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
Abstract
Myiasis occurs when fly larvae, or maggots, feed on the tissue, secretions or digestive content of a live vertebrate. Here, a rare case of accidental intestinal or enteric myiasis is reported in a domestic dog. The species of fly is molecularly identified as Sarcophaga africa (Wiedeman, 1824) using the barcoding region of cytochrome oxidase I (COI). A brief critique on the usage of the term "pseudomyiasis" is provided and the complex taxonomy of S. africa is briefly summarised in order to shed light on the erroneous use of S. cruenata and S. haemorrhoidalis with obvious downstream effects. Finally, a comparative assessment to the limited cases in the literature is provided. These few cases are however highly fragmented and our understanding of accidental intestinal myiasis and the clinical manifestations thereof remain incomplete.
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Affiliation(s)
- Louwrens P Snyman
- Department of Veterinary Microbiology, University of Saskatchewan, Canada; Department of Veterinary Tropical Diseases, University of Pretoria, South Africa.
| | | | - Kirstin A Williams
- Natural Science Department, KwaZulu-Natal Museum, Pietermaritzburg, South Africa; Department of Zoology and Entomology, Rhodes University, South Africa
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Shashank PR, Naveena NL, Rajgopal NN, Elliott TA, Sreedevi K, Sunil S, Meshram NM. DNA barcoding of insects from India: Current status and future perspectives. Mol Biol Rep 2022; 49:10617-26. [PMID: 35716293 DOI: 10.1007/s11033-022-07628-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 11/01/2022]
Abstract
Insect fauna occupy the largest proportion of animal biodiversity on earth, but the assessment or quantification in terms of species diversity is far from complete. Several recent studies have demonstrated the rapid pace at which insect population decline is occurring. There is an urgent need to document and quantify the diversity of insect fauna for a proper understanding of terrestrial ecosystems. This can be achieved by using modern technology to identify species much faster than relying on traditional methods alone. In line with this, the molecular approach through DNA barcoding coupled with morphological identification needs to be focused and accelerated. The present paper describes the current status of barcoding of insect species in India along with the gaps that need to be remedied. This analysis shows that barcoded specimens cover a very meagre proportion of less than 3.73% of the known taxa/described species and the most represented orders are Lepidoptera and Hemiptera followed by Diptera and Coleoptera. There is a need to expedite insect species discovery and documentation in a collaborative mode between traditional taxonomists and molecular biologists, to accomplish the DNA barcoding of all known insect taxa from India.
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Reimsbach M, Aycock J. Decoding the Cauzin Softstrip: a case study in extracting information from old media. Arch Sci (Dordr) 2021; 21:281-294. [PMID: 34803479 PMCID: PMC8591774 DOI: 10.1007/s10502-021-09358-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2021] [Indexed: 12/03/2022]
Abstract
Having content in an archive is of limited value if it cannot be read and used. As a case study of extricating information from obsolete media, making it readable once again through deep learning techniques, we examine the Cauzin Softstrip: one of the first two-dimensional bar codes, released in 1985 by Cauzin Systems, which could be used for encoding all manner of digital data. Softstrips occupy a curious middle ground, as they were both physical and digital. The bar codes were printed on paper, and in that sense are no different in an archival way than any printed material. Softstrips can be found in old computer magazines, computer books, and booklets of software Cauzin produced. However, managing the digital nature of these physical artifacts falls within the scope of digital curation. To make the information on them readable and useful, the digital information needs to be extracted, which originally would have occurred using a physical Cauzin Softstrip reader. Obtaining a working Softstrip reader is already extremely difficult and will most likely be impossible in the coming years. In order to extract the encoded data, we created a digital Softstrip reader, making Softstrip data accessible without needing a physical reader. Our decoding strategy is able to decode over 91% of the 1229 Softstrips in our Softstrip corpus; this rises to 99% if we only consider Softstrip images produced under controlled conditions. Furthermore, we later acquired another set of 117 Softstrips and we were able to decode nearly 95% of them with no adjustments to the decoder. These excellent results underscore the fact that technology like deep learning is readily accessible to non-experts; we obtained these results using a convolutional neural network, even though neither of the authors are expert in the area.
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Affiliation(s)
| | - John Aycock
- Department of Computer Science, University of Calgary, 2500 University Drive N.W., Calgary, AB T2N 1N4 Canada
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Barbosa-Silva RG, Coutinho TS, Vasconcelos S, da Silva DF, Oliveira G, Zappi DC. Preliminary placement and new records of an overlooked Amazonian tree, Christiana mennegae (Malvaceae). PeerJ 2021; 9:e12244. [PMID: 34820158 PMCID: PMC8601058 DOI: 10.7717/peerj.12244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/13/2021] [Indexed: 11/20/2022] Open
Abstract
Christiana mennegae is a phylogenetically enigmatic taxon and represents a case in point of a species whose presence escaped the radar of the Amazon lists and the Brazilian Flora project. Here we expand its distribution by adding new records from Peru and overlooked ones from Brazil. To investigate its phylogenetic placement in the Brownlowioideae, part of the rbcL gene of the plastid and the intergenic ITS2 region were sequenced. Macro- and micro-morphological investigation of features of C. mennegae using SEM of foliar, flower, fruit and seed structures are presented. A lectotype for the name is designated here. The morphology of trichomes revealed five types of trichomes ranging from glandular to branched and unbranched and we also report stomata on the seed surface for the first time in Brownlowioideae. Christiana mennegae and C. africana were recovered as sister species in the phylogenetic analysis, albeit with low to moderate support, and more species of this and closely related genera must be sampled and analyzed in order to obtain a clearer picture of the group's affinities and relationships. We provide an update of its conservation status from Vulnerable to Least Concern. We also highlight the need for investment in the digitization of biological collections, botanical capacity building at the local level and the importance of the availability of online literature to speed the study of Amazonian plant diversity.
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Affiliation(s)
- Rafael G. Barbosa-Silva
- Instituto Tecnológico Vale de Desenvolvimento Sustentável, Belém, Pará, Brazil
- Coord. Botânica, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
| | - Thales Silva Coutinho
- Programa de Pós-graduação em Biologia Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | - Delmo Fonseca da Silva
- Parque Zoobotânico, Departamento de Ferrosos Norte, Gerência de Meio Ambiente–Minas de Carajás, Parauapebas, Pará, Brazil
| | - Guilherme Oliveira
- Instituto Tecnológico Vale de Desenvolvimento Sustentável, Belém, Pará, Brazil
| | - Daniela C. Zappi
- Instituto Tecnológico Vale de Desenvolvimento Sustentável, Belém, Pará, Brazil
- Coord. Botânica, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
- Programa de Pós-graduação em Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
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13
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Hoek A, Maibach K, Özmen E, Vazquez-Armendariz AI, Mengel JP, Hain T, Herold S, Goesmann A. WASP: a versatile, web-accessible single cell RNA-Seq processing platform. BMC Genomics 2021; 22:195. [PMID: 33736596 PMCID: PMC7977290 DOI: 10.1186/s12864-021-07469-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Background The technology of single cell RNA sequencing (scRNA-seq) has gained massively in popularity as it allows unprecedented insights into cellular heterogeneity as well as identification and characterization of (sub-)cellular populations. Furthermore, scRNA-seq is almost ubiquitously applicable in medical and biological research. However, these new opportunities are accompanied by additional challenges for researchers regarding data analysis, as advanced technical expertise is required in using bioinformatic software. Results Here we present WASP, a software for the processing of Drop-Seq-based scRNA-Seq data. Our software facilitates the initial processing of raw reads generated with the ddSEQ or 10x protocol and generates demultiplexed gene expression matrices including quality metrics. The processing pipeline is realized as a Snakemake workflow, while an R Shiny application is provided for interactive result visualization. WASP supports comprehensive analysis of gene expression matrices, including detection of differentially expressed genes, clustering of cellular populations and interactive graphical visualization of the results. The R Shiny application can be used with gene expression matrices generated by the WASP pipeline, as well as with externally provided data from other sources. Conclusions With WASP we provide an intuitive and easy-to-use tool to process and explore scRNA-seq data. To the best of our knowledge, it is currently the only freely available software package that combines pre- and post-processing of ddSEQ- and 10x-based data. Due to its modular design, it is possible to use any gene expression matrix with WASP’s post-processing R Shiny application. To simplify usage, WASP is provided as a Docker container. Alternatively, pre-processing can be accomplished via Conda, and a standalone version for Windows is available for post-processing, requiring only a web browser. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07469-6.
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Affiliation(s)
- Andreas Hoek
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany.
| | - Katharina Maibach
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany.,Algorithmic Bioinformatics, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Ebru Özmen
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Ana Ivonne Vazquez-Armendariz
- Department of Internal Medicine II, and Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL) and The Institute of Lung Health (ILH), 35392, Giessen, Germany
| | - Jan Philipp Mengel
- Institute of Medical Microbiology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University Giessen, 35392, Giessen, Germany.,Center for Infection Research (DZIF), Justus-Liebig-University Giessen, Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine II, and Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL) and The Institute of Lung Health (ILH), 35392, Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, 35392, Giessen, Germany.,Center for Infection Research (DZIF), Justus-Liebig-University Giessen, Partner Site Giessen-Marburg-Langen, 35392, Giessen, Germany
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14
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Wang W, Wang W, Wei S, Huang W, Qi B, Wang Q, Li Y. Design of potentially universal SSU primers in myxomycetes using next-generation sequencing. J Microbiol Methods 2021; 184:106203. [PMID: 33722637 DOI: 10.1016/j.mimet.2021.106203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 11/18/2022]
Abstract
Unlike fungi, which have a universally accepted barcode marker, universal primers still lack in myxomycetes. Typically, DNA barcode primers were designed based on comparing existing myxomycetes sequences and targeting the conserved regions. However, the extreme genetic diversity within major myxomycetes groups and the frequent occurrence of group I introns have made the development of universal DNA barcode a severe challenge. The emergence of next-generation sequencing provides an opportunity to address this problem. We sequenced the mixed genomic DNA of 81 myxomycetes and extracted the SSU gene's reads using next-generation sequencing. After alignment and assembly, we designed a set of SSU primers that matched all potential SNPs, avoided all known group I intron insertion sites, and were highly conserved between major myxomycetes orders. This set of SSU primers has the potential to become one of the universal primer combinations. Due to the high genetic divergence caused by long and complicated evolutionary histories, the lack of universal barcode primers is common in protists. Our research provides a new method to solve this problem.
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Affiliation(s)
- Wan Wang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Wei Wang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Shuwei Wei
- Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Wei Huang
- Key Laboratory of Applied Statistics of Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Bao Qi
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
| | - Qi Wang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China
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15
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Choudhary P, Singh BN, Chakdar H, Saxena AK. DNA barcoding of phytopathogens for disease diagnostics and bio-surveillance. World J Microbiol Biotechnol 2021; 37:54. [PMID: 33604719 DOI: 10.1007/s11274-021-03019-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
DNA barcoding has proven to be a versatile tool for plant disease diagnostics in the genomics era. As the mass parallel and next generation sequencing techniques gained importance, the role of specific barcodes came under immense scrutiny. Identification and accurate classification of phytopathogens need a universal approach which has been the main application area of the concept of barcode. The present review entails a detailed description of the present status of barcode application in plant disease diagnostics. A case study on the application of Internal Transcribed Spacer (ITS) as barcode for Aspergillus and Fusarium spp. sheds light on the requirement of other potential candidates as barcodes for accurate identification. The challenges faced while barcoding novel pathogens have also been discussed with a comprehensive outline of integrating more recent technologies like meta-barcoding and genome skimming for detecting plant pathogens.
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Affiliation(s)
- Prassan Choudhary
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Bansh Narayan Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India.
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Maunath Bhanjan, Uttar Pradesh, 275103, India
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16
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Cui N, Liao BS, Liang CL, Li SF, Zhang H, Xu J, Li XW, Chen SL. Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis. Chin J Nat Med 2021; 18:563-572. [PMID: 32768163 DOI: 10.1016/s1875-5364(20)30068-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 02/07/2023]
Abstract
Salvia plebeia has been in use as traditional Chinese medicine (TCM) for more than 500 years. In this study, the complete chloroplast (cp) genome of S. plebeia was sequenced, assembled and compared to those of other five published Salvia cp genomes. It was found that the cp genome structure of S. plebeia was well conserved and had a total size of 151 062 bp. Four parameters were used to display the usage conditions of the codons of the amino acids in Salvia genus. Although the number of protein-coding genes in each species was the same, the total number of codons was different. Except for amino acids Trp and Met whose Relative Synonymous Codon Usage (RSCU) value of one condon was equal to 1, the remaining 19 amino acids had 1-3 preferred codons. The preferred codon names of each amino acid were coincident. The period size for the tandem repeats of six species ranged from 9 to 410 bp. Salvia cp genomes mainly possessed tandem repeats with a copy number less than or equal to 3. The sequence length of tandem repeats of the six species ranged from 25 to 824 bp. Highly viarable regions including four intergenic spacers and six partial genes were discovered as potential specific barcodes for Salvia species through cp genome-wide comparison. Finally, we performed phylogenetic analyses based on the complete cp genome and coding sequences respectively. These results provide information to help construct the cp genome library for Salvia, which may support studies of phylogenetics, DNA barcoding, population and transplastomics.
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Affiliation(s)
- Ning Cui
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Ji'nan 250300, China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Central Laboratory, Shandong Academy of Chinese Medicine, Ji'nan 250014, China
| | - Bao-Sheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Cong-Lian Liang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Ji'nan 250300, China
| | - Shi-Feng Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hao Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Xi-Wen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
| | - Shi-Lin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
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17
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Abstract
Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny (i) to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties, and (ii) to avoid phylogenetic redundancy. We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites (as a proxy for phylogenetic-based criteria). This procedure demonstrates that, for short barcodes (e.g., 11 sites), there are thousands of informative site combinations that improve previous proposals. We also show that barcodes based on worldwide databases inevitably prioritize variants located at the basal nodes of the phylogeny, such that most representative genomes in these ancestral nodes are no longer in circulation. Consequently, coronavirus phylodynamics cannot be properly captured by universal genomic barcodes because most SARS-CoV-2 variation is generated in geographically restricted areas by the continuous introduction of domestic variants.
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Affiliation(s)
- Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain.,Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain.,Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain.,Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain.,Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia 15706, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain.,Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain. E-mail:
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18
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Abstract
Analysis of SARS-CoV-2 genome variation using a minimal number of selected informative sites conforming a genetic barcode presents several drawbacks. We show that purely mathematical procedures for site selection should be supervised by known phylogeny (i) to ensure that solid tree branches are represented instead of mutational hotspots with poor phylogeographic proprieties, and (ii) to avoid phylogenetic redundancy. We propose a procedure that prevents information redundancy in site selection by considering the cumulative informativeness of previously selected sites (as a proxy for phylogenetic-based criteria). This procedure demonstrates that, for short barcodes (e.g., 11 sites), there are thousands of informative site combinations that improve previous proposals. We also show that barcodes based on worldwide databases inevitably prioritize variants located at the basal nodes of the phylogeny, such that most representative genomes in these ancestral nodes are no longer in circulation. Consequently, coronavirus phylodynamics cannot be properly captured by universal genomic barcodes because most SARS-CoV-2 variation is generated in geographically restricted areas by the continuous introduction of domestic variants.
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Affiliation(s)
- Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela (SERGAS), Galicia 15706, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia 15706, Spain
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago (IDIS) and Universidad de Santiago de Compostela (USC), Galicia 15706, Spain. E-mail:
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19
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Alfonso-Toledo JA, Paredes-León R. Molecular and Morphological Identification of Dermanyssoid Mites (Parasitiformes: Mesostigmata: Dermanyssoidea) Causatives of a Parasitic Outbreak on Captive Snakes. J Med Entomol 2021; 58:246-251. [PMID: 33432352 DOI: 10.1093/jme/tjaa164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Indexed: 06/12/2023]
Abstract
A parasitic outbreak caused by dermanyssoid mites in a herpetarium of the Metropolitan area of the Valley of Mexico is revealed. This outbreak was caused by Hemilaelaps triangulus (Ewing), but a second mite species, Ophionyssus natricis (Gervais), was found in low abundance. The parasitic load is analyzed, and the morphological and molecular diagnostic characters to identify each of the two species involved are given. A barcode analysis is presented, and two more molecular markers are presented and analyzed. Hemilaelaps triangulus is recorded for the first time in Mexico, and this is the first record of massive infestation on captive snakes caused by ixodorhynchid mites, and DNA sequences of ixodorhynchid mites are publicly available for the first time.
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Affiliation(s)
- Jorge Alberto Alfonso-Toledo
- Unidad de Posgrado, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, Ciudad de México C.P., México
| | - Ricardo Paredes-León
- Colección Nacional de Ácaros, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito zona deportiva s/n, Ciudad Universitaria, Coyoacán, Ciudad de México C.P., México
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20
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Jarrett S, Wilmansyah T, Bramanti Y, Alitamsar H, Alamsyah D, Krishnamurthy KR, Yang L, Pagliusi S. The role of manufacturers in the implementation of global traceability standards in the supply chain to combat vaccine counterfeiting and enhance safety monitoring. Vaccine 2020; 38:8318-25. [PMID: 33199075 DOI: 10.1016/j.vaccine.2020.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/31/2020] [Accepted: 11/04/2020] [Indexed: 11/21/2022]
Abstract
The counterfeiting of vaccines is an increasing problem globally with the safety of persons vaccinated, the trust in vaccines generally and the associated reputation of vaccine manufacturers and regulatory agencies at risk. This risk is especially critical with the on-going development of COVID-19 vaccines. The ability to track and trace vaccines through the vaccine supply chain down to persons vaccinated has to be enhanced. In this context of traceability, the global immunization community has recently set the barcoding of the primary packaging of vaccines, specifically vaccine vials and pre-filled syringes, as a top priority. Emerging vaccine manufacturers are already engaged in investigating ways to incorporate barcoding in their labelling and packaging using GS1 international standards. A specific pilot taking place in Indonesia by the national vaccine manufacturer, Bio Farma, shows the innovation of barcoding on primary packaging already underway with a relatively modest level of investment and success at this stage. This article highlights the efforts of industry and governments on the value of traceability and introduction to 2D barcodes. Access to financial resources and support from the international immunization community would accelerate such innovations leading to enhanced security of the vaccine supply chain.
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21
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Russini V, Di Filippo MM, Fanelli R, Polidori M, Berrilli F, Di Cave D, Novelletto A, Calderini P. Characterization of prevalence and genetic subtypes of Blastocystis sp. in wild and domestic Suidae of central Italy aided by amplicon NGS. Vet Parasitol Reg Stud Reports 2020; 22:100472. [PMID: 33308752 DOI: 10.1016/j.vprsr.2020.100472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/06/2023]
Abstract
Blastocystis spp. is a common single-celled intestinal symbiont, comprising several genetic subtypes (ST) and transmissible by animal-to-animal, human-to-human, animal-to-human and, possibly, human-to-animal routes. This work was designed to explore the presence of Blastocystis in sympatric domestic and wild suids and their ability to carry zoonotic STs, in a condition of widespread opportunity to come in contact with the microorganism through their shared water and food resources, and other carriers. We sampled 42 and 37 stool samples from wild boars and domestic pigs, respectively. STs were first identified by PCR followed by Sanger sequencing. Sequences represented in double-band PCR products or in Sanger chromatograms displaying multiple peaks, were resolved by next generation sequencing (NGS). Twenty-six (61.9%) wild boar and 26 (70.2%) pig samples were PCR-positive, respectively. ST3, ST5 and ST15 were found in 3.8%, 38.4% and 80.8% of the positive wild boars and 11.5%, 88.5%, 11.5% of the positive pigs, respectively. ST1 was found only in pigs (3.8%). STs 5 and 15 were common in both groups of animals, but in reversed proportions, suggesting preferential colonization. We found significantly different ST distributions among wild boars and domestic pigs. This might indicate that lifestyle differences between the two populations influence their risk for contracting certain subtypes, or that ST5 and ST15 can colonize preferentially wild or domestic animals. Based on the STs described here, wild boars and domestic pigs can act as reservoirs with zoonotic potential. The ability of suids to carry zoonotic STs appears to be higher when using NGS than Sanger sequencing, and resolution of complex sequencing profiles is imperative before excluding the presence of STs of human concern.
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Affiliation(s)
- Valeria Russini
- Istituto Zooprofilattico Sperimentale di Lazio e Toscana, sezione di Rieti, Italy
| | | | - Rita Fanelli
- Istituto Zooprofilattico Sperimentale di Lazio e Toscana, sezione di Rieti, Italy
| | - Miriam Polidori
- Istituto Zooprofilattico Sperimentale di Lazio e Toscana, sezione di Rieti, Italy
| | - Federica Berrilli
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - David Di Cave
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Pietro Calderini
- Istituto Zooprofilattico Sperimentale di Lazio e Toscana, sezione di Rieti, Italy
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22
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An J, Zheng W, Liang J, Xi Q, Chen R, Jia J, Lu X, Jakovlić I. Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness. BMC Genomics 2020; 21:607. [PMID: 32883208 PMCID: PMC7469299 DOI: 10.1186/s12864-020-07021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of specimens from North-American populations. We sequenced and characterised the complete mitogenome of a specimen collected in the Yellow Sea. RESULTS It exhibited a barcode (cox1) similarity level of only 87-89% with North-American populations, which is unusually low for conspecifics. Its mitogenome is among the largest in isopods (≈16.5 Kbp), mostly due to a large duplicated palindromic genomic segment (2 Kbp) comprising three genes. However, it lost a segment comprising three genes, nad4L-trnP-nad6, and many genes exhibited highly divergent sequences in comparison to isopod orthologues, including numerous mutations, deletions and insertions. Phylogenetic and selection analyses corroborated that this is one of the handful of most rapidly evolving available isopod mitogenomes, and that it evolves under highly relaxed selection constraints (as opposed to positive selection). However, its nuclear 18S gene is highly conserved, which suggests that rapid evolution is limited to its mitochondrial genome. The cox1 sequence analysis indicates that elevated mitogenomic evolutionary rates are not shared by North-American conspecifics, which suggests a breakdown of cox1 barcoding in this species. CONCLUSIONS A highly architecturally disrupted mitogenome and decoupling of mitochondrial and nuclear rates would normally be expected to have strong negative impacts on the fitness of the organism, so the existence of this lineage is a puzzling evolutionary question. Additional studies are needed to assess the phylogenetic breadth of this disrupted mitochondrial architecture and its impact on fitness.
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Affiliation(s)
- Jianmei An
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China.
| | - Wanrui Zheng
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Jielong Liang
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Qianqian Xi
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ruru Chen
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Junli Jia
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Xia Lu
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, 430075, Hubei, PR China
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23
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Abstract
BACKGROUND Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease that primarily affects premature infants. Despite medical advances, mortality and morbidity from NEC are still unacceptably high. This is partly because of the lack of specific biomarkers and therapies for this disease. Availability of high-quality biological samples and the associated data from premature infants are key to advance our understanding of NEC, and for biomarker discovery and drug development. To that end, the NEC Society Biorepository was established with the goal of promoting studies in human infants through sharing specialized biospecimen and data procurement for NEC research. OBJECTIVE In this review, we will discuss the required infrastructure for biobanks, discuss the importance of informatics management, and emphasize the logistical requirements for sharing specimens. Finally, we will discuss the mechanism for how tissues and material will be shared between the institutions. CONCLUSION We have developed a state-of-the-art biobank for human infants to advance the field of NEC research. With the NEC Society Biorepository, we seek to facilitate and accelerate the basic and translational studies on NEC to provide hope to the infants afflicted with NEC and their families. STUDY TYPE Review article, level V.
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MESH Headings
- Biomarkers/metabolism
- Biomedical Research
- Enterocolitis, Necrotizing/diagnosis
- Enterocolitis, Necrotizing/metabolism
- Enterocolitis, Necrotizing/pathology
- Enterocolitis, Necrotizing/therapy
- Humans
- Infant
- Infant, Newborn
- Infant, Premature
- Infant, Premature, Diseases/diagnosis
- Infant, Premature, Diseases/metabolism
- Infant, Premature, Diseases/pathology
- Infant, Premature, Diseases/therapy
- Informatics
- Reference Standards
- Specimen Handling/ethics
- Specimen Handling/methods
- Specimen Handling/standards
- Tissue Banks/ethics
- Tissue Banks/organization & administration
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Affiliation(s)
- Hala Chaaban
- Department of Pediatrics, Section of Neonatal-Perinatal Medicine, University of Oklahoma, Oklahoma City, OK, USA
| | - Troy A Markel
- Department of Surgery, Section of Pediatric Surgery, The Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Misty Good
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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24
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Dong F, Lin J, You J, Ji J, Xu X, Zhang L, Jin Y, Du S. A chemometric modeling-free near infrared barcode strategy for smart authentication and geographical origin discrimination of Chinese ginseng. Spectrochim Acta A Mol Biomol Spectrosc 2020; 226:117555. [PMID: 31634710 DOI: 10.1016/j.saa.2019.117555] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/29/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
With the growing interest in alternative medicine, handy identification and differentiation of herbal medicines are becoming increasingly important. Here we report a chemometric modeling-free near infrared (NIR) barcode strategy for the smart identification and geographical origin discrimination of Chinese ginseng. The novel strategy demands the transformation of Chinese ginseng (standard and sample) NIR spectra into a barcode representation through assigning zero intensity to every NIR peak except the peaks having intensities greater than average peak intensity. Meanwhile, for Chinese ginseng standard NIR barcode, barcoding condition such as padding size was carefully optimized. It has been demonstrated that the padding size for each bar in the barcode is 8 cm-1. By comparing the percentage of nonzero overlap between Chinese ginseng standard barcode and sample barcodes, eight batches of samples (including Chinese ginseng, American ginseng and counterfeit) were successfully identified with 100% accuracy, respectively. Interestingly, the discrimination of the origin of ginsengs from three provinces (Jilin, Liaoning and Heilongjiang) of Northeastern China was achieved utilizing NIR barcode method. Two characteristic bars at 7750 and 8250 cm-1 were inspected in the ginseng sample from Jilin province, two specific bars at 6780 and 7015 cm-1 were displayed in the ginseng sample from Liaoning province and three distinct bars at 6560, 6910 and 7995 cm-1 were monitored in the ginseng sample from Heilongjiang province. The results indicate that the proposed method will be greatly expanded and applied as an inspecting platform for the on-site analysis and valid identification of Chinese ginseng in herbal markets by a handheld spectrometer or barcode scanner.
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Affiliation(s)
- Fang Dong
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Jiating Lin
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Junhui You
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Jiangrong Ji
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Xin Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Liying Zhang
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Yang Jin
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Shuhu Du
- School of Pharmacy, Nanjing Medical University, Nanjing, Jiangsu, 211166, China.
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25
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Belderbos ME, Jacobs S, Koster TK, Ausema A, Weersing E, Zwart E, de Haan G, Bystrykh LV. Donor-to-Donor Heterogeneity in the Clonal Dynamics of Transplanted Human Cord Blood Stem Cells in Murine Xenografts. Biol Blood Marrow Transplant 2019; 26:16-25. [PMID: 31494231 DOI: 10.1016/j.bbmt.2019.08.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/31/2019] [Accepted: 08/26/2019] [Indexed: 01/12/2023]
Abstract
Umbilical cord blood (UCB) provides an alternative source of hematopoietic stem cells (HSCs) for allogeneic transplantation. Administration of sufficient donor HSCs is critical to restore recipient hematopoiesis and to maintain long-term polyclonal blood formation. However, due to lack of unique markers, the frequency of HSCs among UCB CD34+ cells is the subject of ongoing debate, urging for reproducible strategies for their counting. Here, we used cellular barcoding to determine the frequency and clonal dynamics of human UCB HSCs and to determine how data analysis methods affect these parameters. We transplanted lentivirally barcoded CD34+ cells from 20 UCB donors into Nod/Scid/IL2Ry-/- (NSG) mice (n = 30). Twelve recipients (of 8 UCB donors) engrafted with >1% GFP+ cells, allowing for clonal analysis by multiplexed barcode deep sequencing. Using multiple definitions of clonal diversity and strategies for data filtering, we demonstrate that differences in data analysis can change clonal counts by several orders of magnitude and propose methods to improve their consistency. Using these methods, we show that the frequency of NSG-repopulating cells was low (median ∼1 HSC/104 CD34+ UCB cells) and could vary up to 10-fold between donors. Clonal patterns in blood became increasingly consistent over time, likely reflecting initial output of transient progenitors, followed by long-term HSCs with stable hierarchies. The majority of long-term clones displayed multilineage output, yet clones with lymphoid- or myeloid-biased output were also observed. Altogether, this study uncovers substantial interdonor and analysis-induced variability in the frequency of UCB CD34+ clones that contribute to post-transplant hematopoiesis. As clone tracing is increasingly relevant, we urge for universal and transparent methods to count HSC clones during normal aging and upon transplantation.
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Affiliation(s)
- Mirjam E Belderbos
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands; Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands.
| | - Sabrina Jacobs
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Taco K Koster
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Albertina Ausema
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Ellen Weersing
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Erik Zwart
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Gerald de Haan
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
| | - Leonid V Bystrykh
- Department of Stem Cell Biology and Ageing, European Research Institute for the Biology of Ageing, University of Groningen, Groningen, Netherlands
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26
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Zhang D, Bian F, Cai L, Wang T, Kong T, Zhao Y. Bioinspired photonic barcodes for multiplexed target cycling and hybridization chain reaction. Biosens Bioelectron 2019; 143:111629. [PMID: 31470170 DOI: 10.1016/j.bios.2019.111629] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023]
Abstract
Multiplexed detection of microRNA (miRNA) is of great value in clinical diagnosis. Here, a new type of polydopamine (PDA) encapsulated photonic crystal (PhC) barcodes are employed for target-triggering cycle amplification and hybridization chain reaction (HCR) to achieve multiplex miRNA quantification. The PDA-decorated PhC barcodes not only exhibit distinctive structural color for different encoding miRNAs, they also can immobilize biomolecules, allowing subsequent reaction with amino-modified hairpin probes (H1). When the PDA-decorated PhC barcodes are used in assays, target miRNAs can be circularly used to initiate HCR for cycle amplification. Therefore, by tuning the structural colors of the PDA-integrated PhC, the multiplexed miRNA quantification could be realized. We demonstrate that our strategy for multiplexed detection of miRNA is reasonably accurate, reliable and repeatable, with a detection limit as low as 8.0 fM. Our results show that PDA encapsulated PhC barcodes as a novel platform offer a pathway toward the multiplex analysis of low-abundance biomarkers for biomedical assays.
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Affiliation(s)
- Dagan Zhang
- Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Feika Bian
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Lijun Cai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Tianfu Wang
- Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Tiantian Kong
- Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Yuanjin Zhao
- Guangdong Key Laboratory of Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.
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27
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Omelina ES, Ivankin AV, Letiagina AE, Pindyurin AV. Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries. BMC Genomics 2019; 20:536. [PMID: 31291895 PMCID: PMC6620194 DOI: 10.1186/s12864-019-5847-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Background Massively parallel reporter assays (MPRAs) enable high-throughput functional evaluation of various DNA regulatory elements and their mutant variants. The assays are based on construction of highly diverse plasmid libraries containing two variable fragments, a region of interest (a sequence under study; ROI) and a barcode (BC) used to uniquely tag each ROI, which are separated by a constant spacer sequence. The sequences of BC–ROI combinations present in the libraries may be either known a priori or not. In the latter case, it is necessary to identify these combinations before performing functional experiments. Typically, this is done by PCR amplification of the BC–ROI regions with flanking primers, followed by next-generation sequencing (NGS) of the products. However, chimeric DNA molecules formed on templates with identical spacer fragment during the amplification process may substantially hamper the identification of genuine BC–ROI combinations, and as a result lower the performance of the assays. Results To identify settings that minimize formation of chimeric products we tested a number of PCR amplification parameters, such as conventional and emulsion types of PCR, one- or two-round amplification strategies, amount of DNA template, number of PCR cycles, and the duration of the extension step. Using specific MPRA libraries as templates, we found that the two-round amplification of the BC–ROI regions with a very low initial template amount, an elongated extension step, and a specific number of PCR cycles result in as low as 0.30 and 0.32% of chimeric products for emulsion and conventional PCR approaches, respectively. Conclusions We have identified PCR parameters that ensure synthesis of specific (non-chimeric) products from highly diverse MPRA plasmid libraries. In addition, we found that there is a negligible difference in performance of emulsion and conventional PCR approaches performed with the identified settings. Electronic supplementary material The online version of this article (10.1186/s12864-019-5847-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Anton V Ivankin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Anna E Letiagina
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
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28
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Serebrennikova KV, Samsonova JV, Osipov AP. A semi-quantitative rapid multi-range gradient lateral flow immunoassay for procalcitonin. Mikrochim Acta 2019; 186:423. [PMID: 31187212 DOI: 10.1007/s00604-019-3550-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/24/2019] [Indexed: 12/27/2022]
Abstract
A rapid semi-quantitative gradient lateral flow immunoassay (LFIA) of procalcitonin (PCT), a peptide precursor of the hormone calcitonin, was developed. The method is based on particular analyte cut-offs by immobilizing specific antibodies on the test strip with a consistent (gradient) increase in concentration from line to line. Semi-quantitative multi-range analysis is evaluated visually by counting the number of colored test lines corresponding to a certain concentration range of sepsis marker: [PCT]˂0.25; 0.25 ≤ [PCT] < 0.5; 0.5 ≤ [PCT] < 2; 2 ≤ [PCT] < 10; [PCT] ≥ 10 ng·mL-1. This multi-range gradient LFIA was implemented by using two types of label: spherical gold nanoparticles (35 nm) and hierarchical popcorn-like gold nanoparticles (100 nm). The comparison of this LFIA with an ELISA (for n = 82) yielded 87.5% and 76.6% sensitivities, and 92.3% and 92.3% specificities, respectively. Thus, multi-range gradient LFIA performs well at PCT thresholds, which is important for early diagnosis of sepsis and severe bacterial infection. In our perception, this method has a wide scope in that it may be implemented in numerous other LFIA based test systems. Graphical abstract Schematic of the gradient lateral flow immunoassay for determination of clinically relevant procalcitonin ranges. It allows to reach the correlation between the number of developed test lines and procalcitonin concentration range in serum by pre-immobilization of capture antibodies in a consistently (gradient) increasing concentration.
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29
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Bian F, Sun L, Cai L, Wang Y, Zhao Y, Wang S, Zhou M. Molybdenum disulfide-integrated photonic barcodes for tumor markers screening. Biosens Bioelectron 2019; 133:199-204. [PMID: 30933711 DOI: 10.1016/j.bios.2019.02.066] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 01/11/2023]
Abstract
As a new class of two-dimensional (2D) materials, molybdenum disulfide (MoS2) has huge potential in biomedical area; while its applications in multiplex bioassays are still a challenge. Here, we present novel MoS2-integrated silica colloidal crystal barcode (SCCB) for multiplex microRNA (miRNA) screening. MoS2 was adsorbed on SCCBs by electrostatic interaction, and quantum dots (QDs) decorated hairpin probes were coupled on MoS2 by covalent linkage. As the MoS2 could quench the QDs of the hairpin probes, they together formed a molecular beacon (MB) structure before the detection. When used in assays, target miRNA could form a double strand with the probe and made QDs keep away from MoS2 sheets to recovery their fluorescence. Because the released QDs were positively correlated with the concentration of the hybridized nucleic acid, the target miRNAs could be quantified by measuring the fluorescence signal of the QDs on the SCCBs. In addition, by utilizing different MoS2-integrated structural color encoded SCCBs, multiplexed miRNA quantification could also be realized. Based on this strategy, we have demonstrated that several pancreatic cancer-related miRNAs could be selectivity and sensitivity detected with a detection limit of 4.2 ± 0.3 nM. These features make the MoS2-integrated SCCB ideal for many potential applications.
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Affiliation(s)
- Feika Bian
- Pancreatitis Center, Precision Medicine Center, and Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Lingyu Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Lijun Cai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yu Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Yuanjin Zhao
- Pancreatitis Center, Precision Medicine Center, and Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Shuqi Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Mengtao Zhou
- Pancreatitis Center, Precision Medicine Center, and Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China.
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30
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Zahra A, Hussain B, Jamil A, Ahmed Z, Mahboob S. Forensic STR profiling based smart barcode, a highly efficient and cost effective human identification system. Saudi J Biol Sci 2018; 25:1720-1723. [PMID: 30591790 PMCID: PMC6303164 DOI: 10.1016/j.sjbs.2018.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/30/2018] [Accepted: 10/01/2018] [Indexed: 11/21/2022] Open
Abstract
In forensic science, the human identification is the major goal in criminal cases and in paternity dispute, based on DNA profiling of individual. Analysis of short tandem repeat (STRs) markers used as a reliable technique for this purpose. In this study the main objective was to develop a human identification based on DNA fingerprinting using Human Identification Barcode System (HIBS). HIBS may be used to provide a unique molecular signature of human in the form of a barcode. DNA was isolated from blood by using PCR technique to detect bands to design human barcode using self-designed system. HIBS is a web based application that can be accessed via www.hibs.com.pk. HIBS can be accessed with internet access and may be introduced on security checkpoints to identify an individual based on his own DNA instead of conventional procedures of identification. The barcode generated through DNA fingerprinting will be stored in a HIBS, and may also be a part of CNIC. It may be successfully used against suicide bombers, target killers, etc., as even a single blood spot, a few skin cells, root of the hair etc., to identify such culprits. It may also be effectively used to relieve the individuals with false accusations.
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Affiliation(s)
- Andleeb Zahra
- Department of Bioinformatics, Government College, University Faisalabad, Pakistan
| | - Bilal Hussain
- Department of Zoology, Government College University, Faisalabad, Pakistan
| | - Amer Jamil
- Department of Biochemistry, University of Agriculture, Jail Road, Faisalabad Pakistan
| | - Z Ahmed
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.,Department of Zoology, Government College University, Faisalabad, Pakistan
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31
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Bankole BE, Kayode AT, Nosamiefan IO, Eromon P, Baniecki ML, Daniels RF, Hamilton EJ, Durfee K, MacInnis B, Okafor H, Sowunmi A, Volkman SK, Sabeti P, Wirth D, Happi CT, Folarin OA. Characterization of Plasmodium falciparum structure in Nigeria with malaria SNPs barcode. Malar J 2018; 17:472. [PMID: 30558627 PMCID: PMC6296064 DOI: 10.1186/s12936-018-2623-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium falciparum malaria remains a major health challenge in Nigeria despite the global decline of its incidence and mortality rates. Although significant progress has been made in preventing the transmission of P. falciparum and controlling the spread of the infection, there is much to be done in the area of proper monitoring, surveillance of the parasite, investigating the population dynamics and drug resistance profiling of the parasite as these are important to its eventual eradication. Polymorphic loci of msp1, msp2 and/or glurp genes or microsatellites have been traditionally used to characterize P. falciparum population structure in various parts of Nigeria. The lack of standardization in the interpretation of results, as well as the inability of these methods to distinguish closely related parasites, remains a limitation of these techniques. Conversely, the recently developed 24 single nucleotide polymorphism (SNP)-based molecular barcode assay has the possibility of differentiating between closely related parasites and offer additional information in determining the population diversity of P. falciparum within and between parasite populations. This study is therefore aimed at defining the population diversity of P. falciparum in and between two localities in Nigeria using the SNPs barcode technique. METHODS The 24-SNP high-resolution melt (HRM) barcode assay and msp2 genotyping was used to investigate both intra and inter population diversity of the parasite population in two urban cities of Nigeria. RESULTS Based on SNP barcode analysis, polygenomic malaria infections were observed in 17.9% and 13.5% of population from Enugu and Ibadan, respectively, while msp2 analyses showed 21% and 19.4% polygenomic infections in Enugu and Ibadan, respectively. Low levels of genetic diversity (π) of 0.328 and 0.318 were observed in Enugu and Ibadan parasite populations, respectively, while the FST value of 0.02 (p = 0.055) was obtained when the genetic divergence of both populations was considered. CONCLUSIONS The 24-SNP barcode assay was effective in analysing P. falciparum population diversity. This study also showed that P. falciparum populations in Enugu and Ibadan had a degree of intra-population diversity, but very low divergence between the population. A low degree of polygenomic infections were also observed in the two parasite populations unlike previous years. This maybe as a result of the effect of artemisinin-based combination therapy (ACT), long-lasting insecticide-treated nets (LLITNs) and intermittent preventive treatments in the study populations.
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Affiliation(s)
- Bolajoko E Bankole
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Adeyemi T Kayode
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Iguosadolo O Nosamiefan
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Philomena Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | | | | | | | - Katelyn Durfee
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Henrietta Okafor
- Department of Paediatrics, Institute of Child Health, University of Nigeria Teaching Hospital, Enugu, Enugu State, Nigeria
| | - Akintunde Sowunmi
- Department of Pharmacology and Therapeutics, College of Basic Medical Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Sarah K Volkman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pardis Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Simmons College, Boston, MA, USA
| | - Dyann Wirth
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria.,Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe A Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria. .,Department of Biological Sciences, Redeemer's University, Ede, Osun State, Nigeria.
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Joyce AL, Torres MM, Torres R, Moreno M. Genetic variability of the Aedes aegypti (Diptera: Culicidae) mosquito in El Salvador, vector of dengue, yellow fever, chikungunya and Zika. Parasit Vectors 2018; 11:637. [PMID: 30547835 PMCID: PMC6295114 DOI: 10.1186/s13071-018-3226-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 11/21/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aedes aegypti is associated with dengue, yellow fever, chikungunya and Zika viruses. This vector is widespread in tropical and subtropical areas, and can also occur in temperate areas at higher latitudes. The geographical distribution of Ae. aegypti continues to spread due to human activities. This is the first study to examine the population genetic structure of this insect in El Salvador, Central America. METHODS Aedes aegypti larvae were collected from six geographical regions of El Salvador: Sonsonate, San Salvador, Chalatenango, Usulután, San Miguel and Morazán. Larvae were raised into adults, identified and preserved. Two molecular markers, amplified fragment length polymorphism (AFLP) genotyping and mitochondrial DNA (mtDNA) cytochrome c oxidase subunit 1 (cox1) sequencing, were used to investigate population genetic structure. RESULTS Structure analysis found two genetically distinct populations; one occurs predominantly in the north and west, and a mix of two populations occurs in the southeast of the country. Genetic distances ranged from 0.028 (2.8%) to 0.091 (9%), and an AMOVA analysis found 11% variation between populations. Mitochondrial DNA cox1 sequences produced a haplotype network which consisted of 3 haplogroups and 10 haplotypes. Haplogroup 1 had low haplotype and nucleotide diversity and was found in all six regions. Haplogroups 2 and 3 had higher haplotype and nucleotide diversity, and were less abundant; haplogroup 3 was found in only 3 of the six regions studied. Bottleneck tests were significant, suggesting that populations had undergone a recent bottleneck. A maximum likelihood tree, which combined samples from this study with available sequences in GenBank, suggested that two genetically divergent lineages had been introduced. CONCLUSIONS Relatively high genetic diversity was found in Ae. aegypti in El Salvador. The mtDNA sequences clustered into two lineages, as found in previous studies. Samples in El Salvador may be introduced from regions in North and South America where past eradication was not complete. Future study of genotypes in surrounding countries would provide a more complete picture of the movement and potential source of introductions of this vector. The distribution of the lineages and haplogroups may further our understanding of the epidemiology of Ae. aegypti associated vector borne diseases.
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Affiliation(s)
- Andrea L Joyce
- Public Health, University of California, 5200 North Lake Road, Merced, CA, 95343, USA.
| | - Melany Murillo Torres
- Departmento de Biología, Universidad de El Salvador, Final de Av. Mártires y Héroes del 30 Julio, San Salvador, El Salvador
| | - Ryan Torres
- Public Health, University of California, 5200 North Lake Road, Merced, CA, 95343, USA
| | - Miguel Moreno
- Departmento de Biología, Universidad de El Salvador, Final de Av. Mártires y Héroes del 30 Julio, San Salvador, El Salvador
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Wong TKF, Ranjard L, Lin Y, Rodrigo AG. HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations. BMC Bioinformatics 2018; 19:389. [PMID: 30348075 PMCID: PMC6198429 DOI: 10.1186/s12859-018-2424-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes. Three sub-samples were mixed in different known proportions (i.e. 62.5%, 25% and 12.5%), and a method was developed to use these proportions to reconstruct the three haplotypes effectively. Results HaploJuice provides an alternative haplotype reconstruction algorithm for Ranjard et al.’s pooling strategy. HaploJuice significantly increases the accuracy by first identifying the empirical proportions of the three mixed sub-samples and then assembling the haplotypes using a dynamic programming approach. HaploJuice was evaluated against five different assembly algorithms, Hmmfreq (Ranjard et al., PLoS ONE 13:0195090, 2018), ShoRAH (Zagordi et al., BMC Bioinformatics 12:119, 2011), SAVAGE (Baaijens et al., Genome Res 27:835-848, 2017), PredictHaplo (Prabhakaran et al., IEEE/ACM Trans Comput Biol Bioinform 11:182-91, 2014) and QuRe (Prosperi and Salemi, Bioinformatics 28:132-3, 2012). Using simulated and real data sets, HaploJuice reconstructed the true sequences with the highest coverage and the lowest error rate. Conclusion HaploJuice provides high accuracy in haplotype reconstruction, making Ranjard et al.’s pooling strategy more efficient, feasible, and applicable, with the benefit of reducing the sequencing cost.
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Affiliation(s)
- Thomas K F Wong
- The Research School of Biology, The Australian National University, Acton ACT, 2601, Australia.
| | - Louis Ranjard
- The Research School of Biology, The Australian National University, Acton ACT, 2601, Australia
| | - Yu Lin
- College of Engineering and Computer Science, The Australian National University, Acton ACT, 2601, Australia
| | - Allen G Rodrigo
- The Research School of Biology, The Australian National University, Acton ACT, 2601, Australia
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Fujinaka CM, Waas M, Gundry RL. Mass Spectrometry-Based Identification of Extracellular Domains of Cell Surface N-Glycoproteins: Defining the Accessible Surfaceome for Immunophenotyping Stem Cells and Their Derivatives. Methods Mol Biol 2018; 1722:57-78. [PMID: 29264798 DOI: 10.1007/978-1-4939-7553-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Human stem cells and their progeny are valuable for a variety of research applications and have the potential to revolutionize approaches to regenerative medicine. However, we currently have limited tools to permit live isolation of homogeneous populations of cells apt for mechanistic studies or cellular therapies. While these challenges can be overcome through the use of immunophenotyping based on accessible cell surface markers, the success of this process depends on the availability of reliable antibodies and well-characterized markers, which are lacking for most stem cell lineages. This chapter outlines an iterative process for the development of new cell surface marker barcodes for identifying and selecting stem cell derived progeny of specific cell types, subtypes, and maturation stages, where antibody-independent identification of cell surface proteins is achieved using a modern chemoproteomic approach to specifically identify N-glycoproteins localized to the cell surface. By taking advantage of a large repository of available cell surfaceome data, proteins that are unlikely to confer cell type specificity can be rapidly eliminated from consideration. Subsequently, targeted quantitation by mass spectrometry can be used to refine candidates of interest, and a bioinformatic visualization tool is key to mapping experimental data to candidate protein sequences for the purpose of epitope selection during the antibody development phase. Overall, the process of developing cell surface barcodes for immunophenotyping is iterative and can include multiple rounds of discovery, refinement, and validation depending on the phenotypic resolution required.
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Affiliation(s)
- Chelsea M Fujinaka
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Matthew Waas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
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Somervuo P, Koskinen P, Mei P, Holm L, Auvinen P, Paulin L. BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing. BMC Bioinformatics 2018; 19:257. [PMID: 29976145 PMCID: PMC6034344 DOI: 10.1186/s12859-018-2262-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/25/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, the samples are binned by identifying the barcode sequence within each sequence read. In order to tolerate sequencing errors, barcodes should be sufficiently apart from each other in sequence space. An additional constraint due to both nucleotide usage and basecalling accuracy is that the proportion of different nucleotides should be in balance in each barcode position. The number of samples to be mixed in each sequencing run may vary and this introduces a problem how to select the best subset of available barcodes at sequencing core facility for each sequencing run. There are plenty of tools available for de novo barcode design, but they are not suitable for subset selection. RESULTS We have developed a tool which can be used for three different tasks: 1) selecting an optimal barcode set from a larger set of candidates, 2) checking the compatibility of user-defined set of barcodes, e.g. whether two or more libraries with existing barcodes can be combined in a single sequencing pool, and 3) augmenting an existing set of barcodes. In our approach the selection process is formulated as a minimization problem. We define the cost function and a set of constraints and use integer programming to solve the resulting combinatorial problem. Based on the desired number of barcodes to be selected and the set of candidate sequences given by user, the necessary constraints are automatically generated and the optimal solution can be found. The method is implemented in C programming language and web interface is available at http://ekhidna2.biocenter.helsinki.fi/barcosel . CONCLUSIONS Increasing capacity of sequencing platforms raises the challenge of mixing barcodes. Our method allows the user to select a given number of barcodes among the larger existing barcode set so that both sequencing errors are tolerated and the nucleotide balance is optimized. The tool is easy to access via web browser.
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Affiliation(s)
- Panu Somervuo
- Mathematical Biology Group, Department of Biosciences, FIN-00014 University of Helsinki, P.O.Box 65 Finland
- Holm Group, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Patrik Koskinen
- Holm Group, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Peng Mei
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Liisa Holm
- Holm Group, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Petri Auvinen
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
| | - Lars Paulin
- DNA Sequencing and Genomics Laboratory, Institute of Biotechnology, FIN-00014 University of Helsinki, P.O.Box 56 Finland
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Seena S, Marvanová L, Letourneau A, Bärlocher F. Articulospora - Phylogeny vs morphology. Fungal Biol 2018; 122:965-976. [PMID: 30227932 DOI: 10.1016/j.funbio.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 05/31/2018] [Accepted: 06/08/2018] [Indexed: 01/29/2023]
Abstract
The taxonomy of the aquatic hyphomycete genus Articulospora (Ascomycota, Pezizomycotima, Leotiales, Helotiaceae) is based on the morphology of the generative phase of its lifecycle. The type species is Articulospora tetracladia, which is distributed worldwide. Its most frequent populations in nature have dimorphic conidia, differing by the extent of conidial branching (i.e., one or two levels of branching). Some strains, stable in culture, produce exclusively conidia of one type. With the molecular analyses employed here and the relatively low number of available isolates (20), separation based on branching of conidia has not been fully supported. Therefore we propose to retain the broad concept of A. tetracladia with dimorphic conidia. Among the three gene sequences tested as potential barcodes, the internal transcribed spacer (ITS) gene was the most promising region. All strains yielded amplifiable DNA which provided adequate resolution, according to accepted ranges in inter/intraspecific differences, to differentiate among the three Articulospora and two Fontanospora species that were tested (Articulospora atra, Articulospora proliferata, A. tetracladia, Fontanospora eccentrica, Fontanospora fusiramosa). D1/D2 primers also permitted amplification in all strains, however without much resolution. Amplification of the COX1 gene sequence was least consistent.
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Affiliation(s)
- Sahadevan Seena
- MARE-Marine and Environmental Sciences Centre, University of Coimbra, PT-3004-517, Coimbra, Portugal
| | - Ludmila Marvanová
- Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic
| | - Allan Letourneau
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X9, Canada
| | - Felix Bärlocher
- Department of Biology, Mount Allison University, Sackville, NB, E4L 1G7, Canada.
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Sun X, Bedos A, Deharveng L. Unusually low genetic divergence at COI barcode locus between two species of intertidal Thalassaphorura (Collembola: Onychiuridae). PeerJ 2018; 6:e5021. [PMID: 29938135 PMCID: PMC6011825 DOI: 10.7717/peerj.5021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 05/29/2018] [Indexed: 01/30/2023] Open
Abstract
Species classification is challenging when taxa display limited morphological differences. In this paper, we combined morphology and DNA barcode data to investigate the complicated taxonomy of two Onychiurid Collembolan species. Thalassaphorura thalassophila and Thalassaphorura debilis are among the most common arthropod species in intertidal ecosystems and are often considered to be synonymous. Based on morphological and barcode analyses of fresh material collected in their type localities, we redescribed and compared the two species. However, their morphological distinctiveness was supported by a molecular divergence much smaller than previously reported at the interspecific level among Collembola. This divergence was even smaller than inter-population divergences recognized in the related edaphic species T. zschokkei, as well as those known between MOTUs within many Collembolan species. Our results may indicate a link between low genetic interspecific divergence and intertidal habitat, as the only biological peculiarity of the two species of interest compared to other Collembolan species analyzed to date is their strict intertidal life.
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Affiliation(s)
- Xin Sun
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China.,J.F. Blumenbach Institute of Zoology and Anthropology, University of Göttingen, Göttingen, Germany
| | - Anne Bedos
- Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Museum national d'Histoire naturelle, Paris, France
| | - Louis Deharveng
- Institut de Systématique, Evolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Sorbonne Universités, Museum national d'Histoire naturelle, Paris, France
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Viljoen E, Odeny DA, Coetzee MPA, Berger DK, Rees DJG. Application of Chloroplast Phylogenomics to Resolve Species Relationships Within the Plant Genus Amaranthus. J Mol Evol 2018; 86:216-239. [PMID: 29556741 DOI: 10.1007/s00239-018-9837-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/16/2018] [Indexed: 02/06/2023]
Abstract
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. We generated a complete A. tricolor chloroplast sequence of 150,027 bp. The three barcoding genes revealed poor inter- and intra-species resolution with low bootstrap support. Whole chloroplast phylogenomics of 59 Amaranthus accessions increased the number of parsimoniously informative sites from 92 to 481 compared to the barcoding genes, allowing improved separation of amaranth species. Our results support previous findings that two geographically independent domestication events of Amaranthus hybridus likely gave rise to several species within the Hybridus complex, namely Amaranthus dubius, Amaranthus quitensis, Amaranthus caudatus, Amaranthus cruentus and Amaranthus hypochondriacus. Poor resolution of species within the Hybridus complex supports the recent and ongoing domestication within the complex, and highlights the limitation of chloroplast data for resolving recent evolution. The weedy Amaranthus retroflexus and Amaranthus powellii was found to share a common ancestor with the Hybridus complex. Leafy amaranth, Amaranthus tricolor, Amaranthus blitum, Amaranthus viridis and Amaranthus graecizans formed a stable sister lineage to the aforementioned species across the phylogenetic trees. This study demonstrates the power of next-generation sequencing data and reference-based assemblies to resolve phylogenies, and also facilitated the identification of unknown Amaranthus accessions from a local genebank. The informative phylogeny of the Amaranthus genus will aid in selecting accessions for breeding advanced genotypes to satisfy global food demand.
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Affiliation(s)
- Erika Viljoen
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa.,Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Nairobi, Kenya
| | - Martin P A Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Hatfield, 0083, South Africa.
| | - David J G Rees
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, Pretoria, 0110, South Africa.,Department of Life and Consumer Sciences, College of Agricultural and Environmental Sciences, University of South Africa, Florida, 1710, South Africa
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Abstract
Protein glycosylation is one of the key processes that play essential roles in biological functions and dysfunctions. However, progress in glycomics has considerably lagged behind genomics and proteomics, due in part to the enormous challenges associated with the analysis of glycans. Here we present a new integrated and automated microfluidic lectin barcode platform to substantially improve the performance of lectin array for focused glycomic profiling. The chip design and flow control were optimized to promote the lectin-glycan binding kinetics and the speed of lectin microarrays. Moreover, we established an on-chip lectin assay which employs a very simple blocking method to effectively suppress the undesired background due to lectin binding of antibodies. Using this technology, we demonstrated focused differential profiling of tissue-specific glycosylation changes of a biomarker, the CA125 protein purified from ovarian cancer cell lines, and different tissues from ovarian cancer patients in a fast, reproducible, and high-throughput fashion. Highly sensitive CA125 detection was also demonstrated with a detection limit much lower than the clinical cutoff value for cancer diagnosis. This microfluidic platform holds the potential to integrate with sample preparation functions to construct a fully integrated "sample-to-answer" microsystem for focused differential glycomic analysis. Thus, our technology should present a powerful tool in support of rapid advance in glycobiology and glycobiomarker development.
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Affiliation(s)
- Yuqin Shang
- University of Kansas, Lawrence, KS, United States
| | - Yong Zeng
- University of Kansas, Lawrence, KS, United States; The University of Kansas Cancer Center, Kansas City, KS, United States.
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40
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Staffen CF, Staffen MD, Becker ML, Löfgren SE, Muniz YCN, de Freitas RHA, Marrero AR. DNA barcoding reveals the mislabeling of fish in a popular tourist destination in Brazil. PeerJ 2017; 5:e4006. [PMID: 29201560 PMCID: PMC5712207 DOI: 10.7717/peerj.4006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/18/2017] [Indexed: 11/20/2022] Open
Abstract
The consumption of raw fish has increased considerably in the West, since it is said to be potentially healthier than processed fish (for containing omega 3 and 6, essential amino acids and vitamins). However this potential benefit, as well as the taste, value and even the risk of extinction are not the same for all species of fish, constituting grounds for fraud. Using the principles of the DNA barcode we revealed mislabelling of fish in Japanese restaurants and fishmarkets in Florianópolis, a popular tourist capital in Brazil. We sequenced the COI gene of 65 samples from fisheries and 80 from restaurants and diagnosed 30% of mislabeled samples in fisheries and 26% in restaurants. We discussed that frauds may have occurred for different reasons: to circumvent surveillance on threatened species; to sell fish with sizes smaller than allowed or abundant species as being a much rarer species (law of supply); to induce product consumption using species with better taste. It should be noted that some substitutions are derived from incorrect identification and are not a fraud per se; they are due to confusion of popular names or misunderstanding by the sellers. Therefore, we suggest the implementation of a systematic regulatory program conducted by governmental agencies to reduce mislabelling in order to avoid further damage to the community (in health and financial issues) and fish stocks.
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Affiliation(s)
- Clisten Fátima Staffen
- Biologia Celular, Embriologia e Genética (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mari Dalva Staffen
- Biologia Celular, Embriologia e Genética (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mariana Londero Becker
- Biologia Celular, Embriologia e Genética (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Sara Emelie Löfgren
- Biologia Celular, Embriologia e Genética (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Yara Costa Netto Muniz
- Biologia Celular, Embriologia e Genética (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | | | - Andrea Rita Marrero
- Biologia Celular, Embriologia e Genética (LAPOGE), Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
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Xu Y, Wang H, Luan C, Liu Y, Chen B, Zhao Y. Aptamer-based hydrogel barcodes for the capture and detection of multiple types of pathogenic bacteria. Biosens Bioelectron 2017; 100:404-410. [PMID: 28957705 DOI: 10.1016/j.bios.2017.09.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/12/2017] [Accepted: 09/18/2017] [Indexed: 11/16/2022]
Abstract
Rapid and sensitive diagnosing hematological infections based on the separation and detection of pathogenic bacteria in the patient's blood is a significant challenge. To address this, we herein present a new barcodes technology that can simultaneously capture and detect multiple types of pathogenic bacteria from a complex sample. The barcodes are poly (ethylene glycol) (PEG) hydrogel inverse opal particles with characteristic reflection peak codes that remain stable during bacteria capture on their surfaces. As the spherical surface of the particles has ordered porous nanostructure, the barcodes can provide not only more surface area for probe immobilization and reaction, but also a nanopatterned platform for highly efficient bioreactions. In addition, the PEG hydrogel scaffold could decrease the non-specificity adsorption by its anti-adhesive effect, and the decorated aptamer probes in the scaffolds could increase the sensitivity, reliability, and specificity of the bacteria capture and detection. Moreover, the tagged magnetic nanoparticles in the PEG scaffold could impart the barcodes with controllable movement under magnetic fields, which can be used to significantly increase the reaction speed and simplify the processing of the bioassays. Based on the describe barcodes, it was demonstrated that the bacteria could be captured and identified even at low bacterial concentrations (100 CFU mL-1) within 2.5h, which is effectively shortened in comparison with the "gold standard" in clinic. These features make the barcodes ideal for capturing and detecting multiple bacteria from clinical samples for hematological infection diagnostics.
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Affiliation(s)
- Yueshuang Xu
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Huan Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Chengxin Luan
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China
| | - Yuxiao Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Baoan Chen
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China.
| | - Yuanjin Zhao
- Department of Hematology and Oncology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, China; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Mantelatto FL, Terossi M, Negri M, Buranelli RC, Robles R, Magalhães T, Tamburus AF, Rossi N, Miyazaki MJ. DNA sequence database as a tool to identify decapod crustaceans on the São Paulo coastline. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:805-815. [PMID: 28872375 DOI: 10.1080/24701394.2017.1365848] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
DNA barcoding has emerged as an efficient tool for taxonomy and other biodiversity fields. The vast and speciose group of decapod crustaceans is not an exception in the current scenario and comparing short DNA fragments has enabled researchers to overcome some taxonomic impediments to help broadening knowledge on the diversity of this group of crustaceans. Brazil is considered as an important area in terms of global marine biodiversity and some regions stand out in terms of decapod fauna, such as the São Paulo coastline. Thus, the aim of this study is to obtain sequences of the mitochondrial markers (COI and 16S) for decapod crustaceans distributed at the São Paulo coastline and to test the accuracy of these markers for species identification from this region by comparing our sequences to those already present in the GenBank database. We sampled along almost the 300 km of the São Paulo coastline from estuaries to offshore islands during the development of a multidisciplinary research project that took place for 5 years. All the species were processed to obtain the DNA sequences. The diversity of the decapod fauna on the São Paulo coastline comprises at least 404 species. We were able to collect 256 of those species and sequence of at least one of the target genes from 221. By testing the accuracy of these two DNA markers as a tool for identification, we were able to check our own identifications, including new records in GenBank, spot potential mistakes in GenBank, and detect potential new species.
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Affiliation(s)
- Fernando L Mantelatto
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Mariana Terossi
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Mariana Negri
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Raquel C Buranelli
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Rafael Robles
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Tatiana Magalhães
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Ana Francisca Tamburus
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Natália Rossi
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
| | - Mayara J Miyazaki
- a Laboratory of Bioecology and Crustacean Systematics, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto , University of São Paulo , Ribeirão Preto , SP , Brazil
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Lu M, Chan BM, Schow PW, Chang WS, King CT. High-throughput screening of hybridoma supernatants using multiplexed fluorescent cell barcoding on live cells. J Immunol Methods 2017; 451:20-27. [PMID: 28803843 DOI: 10.1016/j.jim.2017.08.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/08/2017] [Accepted: 08/08/2017] [Indexed: 10/19/2022]
Abstract
With current available assay formats using either immobilized protein (ELISA, enzyme-linked immunosorbent assay) or immunostaining of fixed cells for primary monoclonal antibody (mAb) screening, researchers often fail to identify and characterize antibodies that recognize the native conformation of cell-surface antigens. Therefore, screening using live cells has become an integral and important step contributing to the successful identification of therapeutic antibody candidates. Thus the need for developing high-throughput screening (HTS) technologies using live cells has become a major priority for therapeutic mAb discovery and development. We have developed a novel technique called Multiplexed Fluorescent Cell Barcoding (MFCB), a flow cytometry-based method based upon the Fluorescent Cell Barcoding (FCB) technique and the Luminex fluorescent bead array system, but is applicable to high-through mAb screens on live cells. Using this technique in our system, we can simultaneously identify or characterize the antibody-antigen binding of up to nine unique fluorescent labeled cell populations in the time that it would normally take to process a single population. This has significantly reduced the amount of time needed for the identification of potential lead candidates. This new technology enables investigators to conduct large-scale primary hybridoma screens using flow cytometry. This in turn has allowed us to screen antibodies more efficiently than before and streamline identification and characterization of lead molecules.
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Affiliation(s)
- Mei Lu
- Therapeutic Discovery, Amgen Inc., South San Francisco, CA 94080, United States.
| | - Brian M Chan
- Therapeutic Discovery, Amgen Inc., Burnaby, British Columbia V5A 1V7, Canada
| | - Peter W Schow
- Medical Sciences, Amgen Inc., South San Francisco, CA 94080, United States
| | - Wesley S Chang
- Medical Sciences, Amgen Inc., South San Francisco, CA 94080, United States
| | - Chadwick T King
- Therapeutic Discovery, Amgen Inc., Burnaby, British Columbia V5A 1V7, Canada.
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Maloukh L, Kumarappan A, Jarrar M, Salehi J, El-Wakil H, Rajya Lakshmi TV. Discriminatory power of rbcL barcode locus for authentication of some of United Arab Emirates (UAE) native plants. 3 Biotech 2017; 7:144. [PMID: 28597155 DOI: 10.1007/s13205-017-0746-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
DNA barcoding of United Arab Emirates (UAE) native plants is of high practical and scientific value as the plants adapt to very harsh environmental conditions that challenge their identification. Fifty-one plant species belonged to 22 families, 2 monocots, and 20 eudicots; a maximum number of species being legumes and grasses were collected. To authenticate the morphological identification of the wild plant taxa, rbcL and matK regions were used in the study. The primer universality and discriminatory power of rbcL is 100%, while it is 35% for matK locus for these plant species. The sequences were submitted to GenBank; accession numbers were obtained for all the rbcL sequences and for 6 of matK sequences. We suggest rbcL as a promising barcode locus for the tested group of 51 plants. In the present study, an inexpensive, simple method of identification of rare desert plant taxa through rbcL barcode is being reported.
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Charbonneau ARL, Forman OP, Cain AK, Newland G, Robinson C, Boursnell M, Parkhill J, Leigh JA, Maskell DJ, Waller AS. Defining the ABC of gene essentiality in streptococci. BMC Genomics 2017; 18:426. [PMID: 28569133 PMCID: PMC5452409 DOI: 10.1186/s12864-017-3794-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Utilising next generation sequencing to interrogate saturated bacterial mutant libraries provides unprecedented information for the assignment of genome-wide gene essentiality. Exposure of saturated mutant libraries to specific conditions and subsequent sequencing can be exploited to uncover gene essentiality relevant to the condition. Here we present a barcoded transposon directed insertion-site sequencing (TraDIS) system to define an essential gene list for Streptococcus equi subsp. equi, the causative agent of strangles in horses, for the first time. The gene essentiality data for this group C Streptococcus was compared to that of group A and B streptococci. RESULTS Six barcoded variants of pGh9:ISS1 were designed and used to generate mutant libraries containing between 33,000-66,000 unique mutants. TraDIS was performed on DNA extracted from each library and data were analysed separately and as a combined master pool. Gene essentiality determined that 19.5% of the S. equi genome was essential. Gene essentialities were compared to those of group A and group B streptococci, identifying concordances of 90.2% and 89.4%, respectively and an overall concordance of 83.7% between the three species. CONCLUSIONS The use of barcoded pGh9:ISS1 to generate mutant libraries provides a highly useful tool for the assignment of gene function in S. equi and other streptococci. The shared essential gene set of group A, B and C streptococci provides further evidence of the close genetic relationships between these important pathogenic bacteria. Therefore, the ABC of gene essentiality reported here provides a solid foundation towards reporting the functional genome of streptococci.
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Affiliation(s)
- Amelia R L Charbonneau
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
| | | | - Amy K Cain
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia
| | - Graham Newland
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Carl Robinson
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Mike Boursnell
- Animal Health Trust, Lanwades Park, Newmarket, Suffolk, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - James A Leigh
- The School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, Leicestershire, Nottingham, UK
| | - Duncan J Maskell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Lehmitz R, Decker P. The nuclear 28S gene fragment D3 as species marker in oribatid mites (Acari, Oribatida) from German peatlands. Exp Appl Acarol 2017; 71:259-276. [PMID: 28405837 DOI: 10.1007/s10493-017-0126-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
To make oribatid mites an applicable tool in monitoring programs it is necessary to find a molecular species marker that allows distinct, rapid and easy species identification. In previous studies, the common barcoding sequence COI showed to be too variable to serve as species marker in oribatid mites. The aim of the present study is to evaluate the potential use of the D3 region of the nuclear 28S rDNA gene for species identification. Therefore, we generated a reference DNA library of 28S D3 to identify specimens of the Oribatida from Germany, with focus on species occurring in peatlands being one of the most endangered habitats in Europe. New DNA sequences were obtained from 325 individuals and 64 species (58 genera, 34 families). By adding 28S D3-sequences from GenBank we altogether analysed 385 sequences from 89 German species, 32 of them restricted to peatlands and further 42 occurring in peatlands occasionally, representing 46 and 33% of the oribatids in German peatlands, respectively. P-distances were measured between species within families as well as for intraspecific divergence. 28S D3 showed low intraspecific genetic p-distances between 0 and 0.5%, interspecific distances within families varied between 0 and 9.7%. Most species pairs within families were further separated by one to four indels in addition to substitutions. Altogether, 93% of all analysed species are clearly delineated by 28S D3. Our study emphasises that 28S D3 rDNA is a useful barcode for the identification of oribatid mite specimens and represents an important step in building-up a comprehensive barcode library to allow metabarcoding analyses of environmental peatland samples for Oribatida in Germany as well as in Central Europe.
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Affiliation(s)
- Ricarda Lehmitz
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826, Görlitz, Germany.
| | - Peter Decker
- Senckenberg Museum of Natural History Görlitz, Am Museum 1, 02826, Görlitz, Germany
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Ehteshami A. Barcode Technology Acceptance and Utilization in Health Information Management Department at Academic Hospitals According to Technology Acceptance Model. Acta Inform Med 2017; 25:4-8. [PMID: 28484289 PMCID: PMC5402383 DOI: 10.5455/aim.2017.25.4-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/04/2017] [Indexed: 11/04/2022] Open
Abstract
Nowdays, due to the increasing importance of quality care, organizations focuse on the improving provision, management and distribution of health. On one hand, incremental costs of the new technologies and on the other hand, increased knowledge of health care recipients and their expectations for high quality services have doubled the need to make changes in order to respond to resource constraints (financial, human, material). For this purpose, several technologies, such as barcode, have been used in hospitals to improve services and staff productivity; but various factors effect on the adoption of new technologies and despite good implementation of a technology and its benefits, sometimes personnel don't accept and don't use it. METHODS This is an applied descriptive cross-sectional study in which all the barcode users in health information management department of the three academic hospitals (Feiz, Al-Zahra, Ayatollah Kashani) affiliated to Isfahan University of Medical Sciences were surveyed by the barcode technology acceptance questionnaire, in six areas as following: barcode ease of learning, capabilities, perception of its usefulness and its ease of use, users attitudes towards its using, and users intention. RESULTS The finding showed that barcode technology total acceptance was relatively desirable (%76.9); the most compliance with TAM model was related to the user perceptions about the ease of use of barcode technology and the least compliance was related to the ease of learning barcode technology (respectively %83.7 and %71.5). CONCLUSION Ease of learning and barcode capability effect of usefulness and perceived ease of barcode technology. Users perceptions effect their attitudes toward greater use of technology and their attitudes have an effect on their intention to use the technology and finally, their intention makes actual use of the technology (acceptance). Therefore, considering the six elements related to technology implementation can be important in the barcode acceptance; because their chained relationship is clearly visible.
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Affiliation(s)
- Asghar Ehteshami
- Health Information Technology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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Abstract
OBJECTIVES To evaluate the impact that an electronic ordering system has on the rate of rejection of blood type and screen testing samples and the impact on the number of ABO blood-type discrepancies over a 4-year period. METHODS An electronic ordering system was implemented in May 2011. Rejection rates along with reasons for rejection were tracked between January 2010 and December 2013. RESULTS A total of 40,104 blood samples were received during this period, of which 706 (1.8%) were rejected for the following reasons: 382 (54.0%) unsigned samples, 235 (33.0%) mislabeled samples, 57 (8.0%) unsigned requisitions, 18 (2.5%) incorrect tubes, and 14 (1.9%) ABO discrepancies. Of the samples, 2.5% were rejected in the year prior to implementing the electronic ordering system compared with 1.2% in the year following implementation ( P < .0001). CONCLUSIONS Our data demonstrate that implementation of an electronic ordering system significantly decreased the rate of blood sample rejection.
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Affiliation(s)
- Stefanie K Forest
- From the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
- NewYork-Presbyterian Hospital, New York, NY
| | - Maryam Shirazi
- From the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
- NewYork-Presbyterian Hospital, New York, NY
| | | | - Brie A Stotler
- From the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY
- NewYork-Presbyterian Hospital, New York, NY
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Torres-Gutierrez C, Bergo ES, Emerson KJ, de Oliveira TM, Greni S, Sallum MAM. Mitochondrial COI gene as a tool in the taxonomy of mosquitoes Culex subgenus Melanoconion. Acta Trop 2016; 164:137-149. [PMID: 27609637 DOI: 10.1016/j.actatropica.2016.09.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 09/01/2016] [Accepted: 09/05/2016] [Indexed: 01/03/2023]
Abstract
The subgenus Melanoconion is the second largest subgenus within the genus Culex, with 160 described species. Several of the species are proven vectors of arboviruses, including West Nile virus, Venezuelan equine encephalitis virus complex and Eastern equine encephalomyelitis virus. Species of Melanoconion are well distributed from southern North America to most countries of South America and display the highest species diversity in tropical regions. Taxonomical identification within this group has been primarily based on morphological characters, with the male genitalia as the source of the most solid diagnostic features. The difficulty in reaching accurate species determinations when studying specimens of Culex (Melanoconion) has been extensively documented as a real limitation to expand knowledge of these insects. We tested the utility of the mitochondrial gene COI as a complementary tool in the taxonomy of Melanoconion. Using a data set of 120 COI sequences from Culex specimen captured in several localities in Brazil, the utility of COI barcodes for species delimitation is discussed through the evaluation of genetic divergences among specimens and the clustering patterns of species in three topologies obtained with Neighbor Joining, Maximum Likelihood and Bayesian phylogenetic inference. For all specimens included in this study a previous morphological examination was performed, and most of the taxonomical determinations were corroborated using the COI barcode. We generated COI sequences that belong to 48 species of Melanoconion, with a mean intraspecific K2P genetic divergence of 3%; and all interspecific divergence values higher than the intraspecific divergence values. This is the first comprehensive study of subgenus Melanoconion, with evidence of COI as a useful and accessible DNA barcode.
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Cihalova K, Hegerova D, Jimenez AM, Milosavljevic V, Kudr J, Skalickova S, Hynek D, Kopel P, Vaculovicova M, Adam V. Antibody-free detection of infectious bacteria using quantum dots-based barcode assay. J Pharm Biomed Anal 2017; 134:325-32. [PMID: 27894780 DOI: 10.1016/j.jpba.2016.10.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/26/2016] [Accepted: 10/30/2016] [Indexed: 01/18/2023]
Abstract
Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae are the most representative bacteria causing infectious diseases. Due to the increased application of antibiotics, the bacterial resistance is growing causing severe complications. Therefore, a sensitive determination of these pathogens is crucial for effective treatment. The aim of this study was to design an effective method for multiplex detection of Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae taking advantage from properties of magnetic particles as well as fluorescent nanoparticles (quantum dots). The method was able to detect as low concentrations of bacteria as 102 CFU/mL using the bacteria-specific genes (fnbA, mecA and wcaG).
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