scholarly journals FIGARO: An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters

2019 ◽  
Author(s):  
Michael M. Weinstein ◽  
Aishani Prem ◽  
Mingda Jin ◽  
Shuiquan Tang ◽  
Jeffrey M. Bhasin
Keyword(s):  
Rapid Assessment ◽  
Cost Effective ◽  
Bioinformatic Analysis ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Sequence Information ◽  
Bioinformatic Tools ◽  
Zymo Research ◽  
High Throughput Dna Sequencing ◽  
The Cost

ABSTRACTSummaryMicrobiome studies continue to provide tremendous insight into the importance of microorganism populations to the macroscopic world. High-throughput DNA sequencing technology (i.e., Next-generation Sequencing) has enabled the cost-effective, rapid assessment of microbial populations when combined with bioinformatic tools capable of identifying microbial taxa and calculating the diversity and composition of biological and environmental samples. Ribosomal RNA gene sequencing, where 16S and 18S rRNA gene sequences are used to identify prokaryotic and eukaryotic species, respectively, is one of the most widely-used techniques currently employed in microbiome analysis. Prior to bioinformatic analysis of these sequences, trimming parameters must be set so that post-trimming sequence information is maximized while expected errors in the sequences themselves are minimized. In this application note, we present FIGARO: a Python–based application designed to maximize read retention after trimming and filtering for quality. FIGARO was designed specifically to increase reproducibility and minimize trial-and-error in trimming parameter selection for a DADA2–based pipeline and will likely be useful for optimizing trimming parameters and minimizing sequence errors in other pipelines as well where paired-end overlap is required.Availability and implementationThe FIGARO application is freely available as source code at https://github.com/Zymo-Research/figaro.

First report on optimization of loop-mediated isothermal amplification (LAMP) for the diagnosis of Babesia felis

2017 ◽  
Author(s):  
Muhammad Awais Salim ◽  
Raheela Akhtar ◽  
Muhammad Lateef ◽  
Imran Rashid ◽  
Harron Akbar ◽  
...  
Keyword(s):  
Lamp Assay ◽  
Cost Effective ◽  
Conventional Polymerase Chain Reaction ◽  
18S Rrna Gene ◽  
Isothermal Amplification ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Loop Mediated Isothermal Amplification ◽  
Polymerase Chain ◽  
Effective Diagnosis

The objective of present study was to optimize loop mediated isothermal amplification (LAMP) assay for the diagnosis of Babesia felis in cats. LAMP primers were designed recognizing four sections of 18SribosomalRNA (18S rRNA) gene of B. felis. The blood samples of cats microscopically positive for Babesia felis were further used to extract deoxyribo neuclic acid (DNA) and the reaction mixture of 25 µL was standardized at 63°C temperature for 1 hour. LAMP assay provided more positive samples than conventional polymerase chain reaction (PCR). The prevalence of B. felis was also determined in cats using this optimized LAMP assay and it was found that the prevalence was more in younger cats as compare to adults. The application of LAMP can be helpful in rapid, reliable and cost effective diagnosis of B. felis in field.

scholarly journals Terminal Restriction Fragment Length Polymorphism for Identification of Cryptosporidium Species in Human Feces

2008 ◽  
Vol 75 (1) ◽  
pp. 108-112 ◽  
Author(s):  
L. S. Waldron ◽  
B. C. Ferrari ◽  
M. R. Gillings ◽  
M. L. Power
Keyword(s):  
Species Identification ◽  
Restriction Fragment ◽  
Rflp Analysis ◽  
Cost Effective ◽  
18S Rrna Gene ◽  
Individual Species ◽  
Rrna Gene ◽  
Species Identity ◽  
Cryptosporidium Hominis ◽  
Detection And Identification

ABSTRACT Effective management of human cryptosporidiosis requires efficient methods for detection and identification of the species of Cryptosporidium isolates. Identification of isolates to the species level is not routine for diagnostic assessment of cryptosporidiosis, which leads to uncertainty about the epidemiology of the Cryptosporidium species that cause human disease. We developed a rapid and reliable method for species identification of Cryptosporidium oocysts from human fecal samples using terminal restriction fragment polymorphism (T-RFLP) analysis of the 18S rRNA gene. This method generated diagnostic fragments unique to the species of interest. A panel of previously identified isolates of species was blind tested to validate the method, which determined the correct species identity in every case. The T-RFLP profiles obtained for samples spiked with known amounts of Cryptosporidium hominis and Cryptosporidium parvum oocysts generated the two expected diagnostic peaks. The detection limit for an individual species was 1% of the total DNA. This is the first application of T-RFLP to protozoa, and the method which we developed is a rapid, repeatable, and cost-effective method for species identification.

scholarly journals The importance in DNA barcoding of the regions which is covering rRNA genes and its sequences in the genus Quercus L.

2020 ◽  
Vol 27 (2) ◽  
pp. 261-271
Author(s):  
Yilmaz Aykut
Keyword(s):  
Species Recognition ◽  
Intergenic Spacer ◽  
Ecological Factors ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Species Number ◽  
Rrna Gene ◽  
Sequence Information ◽  
Climatic Effects ◽  
Quercus Species

Turkey with 18 oak (Quercus) species is one of the richest country according to species number and diversity. The most important reason of the species diversity in Turkey is its location and geomorphological structure which increase climatic effects and seperate Turkey into different phytogeographic regions. Furthermore, hybridization behaviours which frequently observed between oak species, genetic drift, gene flow and ecological factors cause morphological variations in the plants species. All of these factors make it difficult to define the species concept for plant groups like oaks. Therefore, the region covering 18S rRNA gene/ ITS1/ 5.8S rRNA gene/ ITS2/ 25S rRNA gene and secondly intergenic spacer (IGS)/ 5S rRNA gene for barcoding were obtained from genbank and used as a useful tool for the determination and solution of the phylogenetic relations of taxonomically problematic species, also these barcoding regions were compared with each other according to species recognition ability for oak species. As a result, it can be stated that both barcoding regions have high variable sites based on sequence information to identify the species and evaluate relationships of species studied. Bangladesh J. Plant Taxon. 27(2): 261-271, 2020 (December)

scholarly journals Detection and Discovery of Crustacean Parasites in Blue Crabs (Callinectes sapidus) by Using 18S rRNA Gene-Targeted Denaturing High-Performance Liquid Chromatography

2008 ◽  
Vol 74 (14) ◽  
pp. 4346-4353 ◽  
Author(s):  
Christofer Troedsson ◽  
Richard F. Lee ◽  
Tina Walters ◽  
Vivica Stokes ◽  
Karrie Brinkley ◽  
...  
Keyword(s):  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
18S Rrna ◽  
Callinectes Sapidus ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Sequence Information ◽  
Blue Crabs ◽  
Crustacean Parasites

ABSTRACT Recently, we described a novel denaturing high-performance liquid chromatography (DHPLC) approach useful for initial detection and identification of crustacean parasites. Because this approach utilizes general primers targeted to conserved regions of the 18S rRNA gene, a priori genetic sequence information on eukaryotic parasites is not required. This distinction provides a significant advantage over specifically targeted PCR assays that do not allow for the detection of unknown or unsuspected parasites. However, initial field evaluations of the DHPLC assay suggested that because of PCR-biased amplification of dominant host genes it was not possible to detect relatively rare parasite genes in infected crab tissue. Here, we describe the use of a peptide nucleic acid (PNA) PCR hybridization blocking probe in association with DHPLC (PNA-PCR DHPLC) to overcome inherent PCR bias associated with amplification of rare target genes by use of generic primers. This approach was utilized to detect infection of blue crabs (Callinectes sapidus) by the parasitic dinoflagellate Hematodinium sp. Evaluation of 76 crabs caught in Wassaw Sound, GA, indicated a 97% correspondence between detection of the parasite by use of a specific PCR diagnostic assay and that by use of PNA-PCR DHPLC. During these studies, we discovered one crab with an association with a previously undescribed protist symbiont. Phylogenetic analysis of the amplified symbiont 18S rRNA gene indicated that it is most closely related to the free-living kinetoplastid parasite Procryptobia sorokini. To our knowledge, this is the first report of this parasite group in a decapod crab and of this organism exhibiting a presumably parasitic life history.

scholarly journals The cost-effectiveness of comprehensive school reform and rapid assessment.

2008 ◽  
Vol 16 ◽  
pp. 13 ◽  
Author(s):  
Stuart S. Yeh
Keyword(s):  
Cost Effectiveness ◽  
School Reform ◽  
Math Achievement ◽  
Rapid Assessment ◽  
Cost Effective ◽  
Comprehensive School ◽  
Comprehensive School Reform ◽  
Reading And Math ◽  
Order Of Magnitude ◽  
The Cost

Analysis of the cost-effectiveness of 29 Comprehensive School Reform (CSR) models suggests that all 29 models are less cost-effective than an alternative approach for raising student achievement, involving rapid assessment systems that test students 2 to 5 times per week in math and reading and provide rapid feedback of the results to students and teachers. Results suggest that reading and math achievement could increase approximately one order of magnitude greater for every dollar invested in rapid assessment rather than CSR. The results also suggest that reading and math achievement could increase two orders of magnitude for every dollar invested in rapid assessment rather than class size reduction and three orders of magnitude for every dollar invested in rapid assessment rather than high quality preschool.

scholarly journals Genomic approaches and their contributions to understanding the European Neolithisation

2016 ◽  
Vol 43 ◽  
pp. 253-264
Author(s):  
Cristina Gamba
Keyword(s):  
High Throughput ◽  
Ancient Dna ◽  
Significant Contribution ◽  
Cost Effective ◽  
Petrous Bone ◽  
Molecular Technique ◽  
Complete Genomes ◽  
Technical Advances ◽  
High Throughput Dna Sequencing ◽  
The Cost

The contribution of ancient DNA to the understanding of past events has been increasing exponentially in recent years. This is mainly due to the synergy of technical advances, such as the molecular technique of high-throughput DNA sequencing, which has allowed for the reconstruction of complete genomes as old as 750 000 years. Another step toward the cost-effective characterisation of ancient genomes is the sampling of petrous bone, which has allowed sequencing of the first ancient African genome. Here I review the significant contribution of ancient genomics to our understanding of the European Neolithisation process.

scholarly journals Study of Novel Endophytic Bacteria for Biocontrol of Black Pepper Root-knot Nematodes in the Central Highlands of Vietnam

Agronomy ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 714 ◽  
Author(s):  
Thi Phuong Hanh Tran ◽  
San-Lang Wang ◽  
Van Bon Nguyen ◽  
Dinh Minh Tran ◽  
Dinh Sy Nguyen ◽  
...  
Keyword(s):  
Endophytic Bacteria ◽  
Cost Effective ◽  
Black Pepper ◽  
Good Effect ◽  
Rrna Gene ◽  
Pepper Plant ◽  
Bacterial Strains ◽  
Root Knot Nematodes ◽  
The Cost ◽  
Meloidogyne Sp

Black pepper is an industrial crop with high economic and export value. However, black pepper production in Vietnam has been seriously affected by the root-knot nematodes, Meloidogyne spp. The purpose of this study was to select active endophytic bacteria (EB) for the cost-effective and environmentally friendly management of Meloidogyne sp. Thirty-four EB strains were isolated. Of these, five isolates displayed the highest activity, demonstrating 100% mortality of J2 nematodes. These active EB were identified based on sequencing and phylogenetic analysis of the 16S rRNA gene; notably, all the potential endophytic bacterial strains belong to the genus of Bacillus. In greenhouse tests, Bacillus megaterium DS9 significantly reduced nematodes in the soil and pepper plant roots with great inhibition values of 81.86% and 73.11%, respectively, with the lowest rate of nematodes built up at 0.23. This active antinematodes strain also showed good effect on promoting pepper plant growth. Some enzymatic activities, including chitinase and protease activity related to the biocontrol of Meiloidogyne sp., were also detected. The results investigated in the current study suggested that these selected EB strains may be good candidates for biocontrol agents of Meloidogyne sp., and plant promoting effects. The results also enhanced the novel active antinematode endophytic bacterial communities.

The IBM-PC in electron microscopy

1996 ◽  
Vol 54 ◽  
pp. 612-613
Author(s):  
James F. Mancuso
Keyword(s):  
Head Start ◽  
Image Acquisition ◽  
Cost Effective ◽  
Financial Applications ◽  
Number Of Factors ◽  
Instrument Control ◽  
The Cost ◽  
Training And Support ◽  
Control Image ◽  
Ibm Pc

IBM PC compatible computers are widely used in microscopy for applications ranging from control to image acquisition and analysis. The choice of IBM-PC based systems over competing computer platforms can be based on technical merit alone or on a number of factors relating to economics, availability of peripherals, management dictum, or simple personal preference.IBM-PC got a strong “head start” by first dominating clerical, document processing and financial applications. The use of these computers spilled into the laboratory where the DOS based IBM-PC replaced mini-computers. Compared to minicomputer, the PC provided a more for cost-effective platform for applications in numerical analysis, engineering and design, instrument control, image acquisition and image processing. In addition, the sitewide use of a common PC platform could reduce the cost of training and support services relative to cases where many different computer platforms were used. This could be especially true for the microscopists who must use computers in both the laboratory and the office.

Sonographically guided, transcatheter foam sclerotherapy of the great saphenous vein

Phlebologie ◽  
2007 ◽  
Vol 36 (06) ◽  
pp. 309-312 ◽  
Author(s):  
T. Schulz ◽  
M. Jünger ◽  
M. Hahn
Keyword(s):  
Saphenous Vein ◽  
Great Saphenous Vein ◽  
Clinical Stage ◽  
Clinical Signs ◽  
Cost Effective ◽  
Duplex Sonography ◽  
Foam Sclerotherapy ◽  
Average Loss ◽  
One Year ◽  
The Cost

Summary Objective: The goal of the study was to assess the effectiveness and patient tolerability of single-session, sonographically guided, transcatheter foam sclerotherapy and to evaluate its economic impact. Patients, methods: We treated 20 patients with a total of 22 varicoses of the great saphenous vein (GSV) in Hach stage III-IV, clinical stage C2-C5 and a mean GSV diameter of 9 mm (range: 7 to 13 mm). We used 10 ml 3% Aethoxysklerol®. Additional varicoses of the auxiliary veins of the GSV were sclerosed immediately afterwards. Results: The occlusion rate in the treated GSVs was 100% one week after therapy as demonstrated with duplex sonography. The cost of the procedure was 207.91 E including follow-up visit, with an average loss of working time of 0.6 days. After one year one patient showed clinical signs of recurrent varicosis in the GSV; duplex sonography showed reflux in the region of the saphenofemoral junction in a total of seven patients (32% of the treated GSVs). Conclusion: Transcatheter foam sclerotherapy of the GSV is a cost-effective, safe method of treating varicoses of GSV and broadens the spectrum of therapeutic options. Relapses can be re-treated inexpensively with sclerotherapy.

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