Utility of a Luminex-based assay for multiplexed, rapid species identification of Candida isolates from an ongoing candidemia surveillance

2010 ◽  
Vol 56 (4) ◽  
pp. 348-351 ◽  
Author(s):  
Eszter Deak ◽  
Kizee A. Etienne ◽  
Shawn R. Lockhart ◽  
Lalitha Gade ◽  
Tom Chiller ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Species Identification ◽  
Population Based ◽  
Rapid Identification ◽  
Attractive Alternative ◽  
Candida Sp ◽  
Luminex Assay ◽  
Combination Of Methods ◽  
User Friendly ◽  
Correct Species Identification

A Candida -specific Luminex-based assay with 11 probes was employed for multiplexed, rapid identification of 1182 Candida sp. isolates that were received as part of an ongoing population-based surveillance. All the Candida isolates were previously identified by a combination of methods, including phenotype and sequence analysis. Results showed that the Luminex assay was an attractive alternative to reference methods, as it is rapid, yields correct species identification, and is user friendly.

scholarly journals Two User-Friendly Molecular Markers Developed for the Identification of Hybrid Lethality Genes in Brassica oleracea

Agronomy ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 982
Author(s):  
Zhiliang Xiao ◽  
Congcong Kong ◽  
Fengqing Han ◽  
Limei Yang ◽  
Mu Zhuang ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Brassica Oleracea ◽  
Rapid Identification ◽  
Inbred Lines ◽  
Hybrid Lethality ◽  
Specific Pcr ◽  
Allele Specific ◽  
User Friendly ◽  
Allele Specific Pcr ◽  
Kasp Marker

Cabbage (Brassica oleracea) is an important vegetable crop that is cultivated worldwide. Previously, we reported the identification of two dominant complementary hybrid lethality (HL) genes in cabbage that could result in the death of hybrids. To avoid such losses in the breeding process, we attempted to develop molecular markers to identify HL lines. Among 54 previous mapping markers closely linked to BoHL1 or BoHL2, only six markers for BoHL2 were available in eight cabbage lines (two BoHL1 lines; three BoHL2 lines; three lines without BoHL); however, they were neither universal nor user-friendly in more inbred lines. To develop more accurate markers, these cabbage lines were resequenced at an ~20× depth to obtain more nucleotide variations in the mapping regions. Then, an InDel in BoHL1 and a single-nucleotide polymorphism (SNP) in BoHL2 were identified, and the corresponding InDel marker MBoHL1 and the competitive allele-specific PCR (KASP) marker KBoHL2 were developed and showed 100% accuracy in eight inbred lines. Moreover, we identified 138 cabbage lines using the two markers, among which one inbred line carried BoHL1 and 11 inbred lines carried BoHL2. All of the lethal line genotypes obtained with the two markers matched the phenotype. Two markers were highly reliable for the rapid identification of HL genes in cabbage.

scholarly journals Care consumption of people with multiple sclerosis: A multichannel sequence analysis in a population-based setting in British Columbia, Canada

2021 ◽  
pp. 135245852110167
Author(s):  
Jonathan Roux ◽  
Elaine Kingwell ◽  
Feng Zhu ◽  
Helen Tremlett ◽  
Emmanuelle Leray ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
British Columbia ◽  
Sequence Analysis ◽  
Multidisciplinary Care ◽  
Median Number ◽  
Population Based ◽  
Service Planning ◽  
Physician Visits ◽  
Comorbidity Burden ◽  
Incident Cohort

Background: Persons with multiple sclerosis (PwMS) typically require complex multidisciplinary care, which is rarely formally assessed. Objectives: We applied multichannel sequence analysis (MCSA) to identify care consumption patterns by PwMS in British Columbia, Canada. Methods: We created two cohorts, comprising incident and prevalent MS cases, using linked clinical and administrative data. We applied MCSA to quantify and compare the care pathways of PwMS, based on all-cause hospitalizations and physician visits (divided into five specialities). Care consumption clusters were characterized using demographic and clinical features. Results: From 1048 incident and 3180 prevalent PwMS, the MCSA identified 12 and 6 distinct care consumption clusters over a median follow-up of 9.6 and 13.0 years, respectively. Large disparities between clusters were observed; the median number of annual consultations ranged from 5.6 to 21.3 for general practitioners, 1.2 to 4.6 for neurologists and 0 to 5.3 for psychiatrists in the incident cohort. Characteristics at MS symptom onset associated with the highest care consumption included high comorbidity burden and older age. There were similar disparities and associations for prevalent PwMS. Conclusion: The distinct patterns of care consumption, which were reminiscent of the heterogeneity of MS itself, may facilitate health service planning and evaluation, and provide a novel outcome measure in health research.

scholarly journals Gene Sequence Analysis of Mitochondrial COI in Genus Saperda (Coleoptera: Cerambycidae: Lamiinae)

2021 ◽  
Author(s):  
Wei XU ◽  
Qinhua Gan ◽  
Jian Pu ◽  
Yingwen Pan ◽  
Bo Cai ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Detection Rate ◽  
Gene Sequence ◽  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Nuclear Gene ◽  
Rapid Identification ◽  
Mitochondrial Coi ◽  
Gene Sequence Analysis ◽  
Total Dna

In this study, the total DNA of nine species of Saperda (Lopezcolonia) octopunctata (Scopoli, 1772), Saperda (Lopezcolonia) scalaris (Linnaeus, 1758), Saperda interrupta Gebler, Saperda Alberti (Plavilstshikov), Saperda (Saperda) similis Laicharting, 1784, Saperda (Compsidia) populnea (Linnaeus, 1758), Saperda (Saperda) carcharias (Linnaeus, 1758), Saperda (Lopezcolonia) perforata Pallas, 1773 and Saperda ohbayashi were extracted. Two partial sequences of mitochondrial gene and one partial sequence of nuclear gene were amplified. Comparing the COI sequence with the DNA barcode data in GenBank can effectively identify the related species of Saperda. It will be applied to the rapid identification of some species of Saperda in imported wood at ports, and improve the detection rate of plant quarantine.

scholarly journals REP-PCR analisis of single agent of cucumber bacterial diseases

2017 ◽  
Vol 15 (1) ◽  
pp. 25-31
Author(s):  
L. A. Dankevych
Keyword(s):  
Species Identification ◽  
Statistical Methods ◽  
Genetic Heterogeneity ◽  
Significant Relationship ◽  
Molecular Genetic ◽  
Single Agent ◽  
Genetic Homogeneity ◽  
Bacterial Diseases ◽  
Typical Strain ◽  
Correct Species Identification

Aim. For the purpose of correct species identification and estimation of population’s heterogeneity, the fingerprinting of the genome of isolated by us Pectobacterium sp., collection «Erwinia toxica» strains and typical representatives of certain species of Pectobacterium and Diskeya genera has been carried out. Methods. In the course of research, microbiological, molecular genetic (REP-PCR), mathematical-statistical methods of research were used. Results. On the basic of BOX, REP and ERIC profiles the significant affinity between isolated Pectobacterium sp. and collections «Erwinia toxica» strains with the typical P. carotovorum susp. carotovorum UCM B1075T has been established. Genetic heterogeneity of isolated Pectobacterium sp. and collections «Erwinia toxica» strains has been estimated. Conclusions. It has been found the significant relationship between isolates Pectobacterium sp. and the collection «Erwinia toxica» strains with the typical strain P. carotovorum susp carotovorum UCM B1075T on the basic of their BOX, REP and ERIC profiles. Most likely, this indicates that they belong to this species. The genetic homogeneity of isolated Pectobacterium sp. strains of and the genetic heterogeneity of the collection «Erwinia toxica» strains is probably due to the plant’s selection from similar or different region.Keywords: identification, genetic heterogeneity, REPPCR, «Erwinia toxica», Pectobacterium sp.

pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm

2019 ◽  
Vol 36 (8) ◽  
pp. 2584-2586 ◽  
Author(s):  
Dominika Labudová ◽  
Jiří Hon ◽  
Matej Lexa
Keyword(s):  
Sequence Analysis ◽  
Recursive Algorithm ◽  
Supplementary Information ◽  
Potassium Ions ◽  
Bioconductor Package ◽  
G Quadruplex ◽  
Weak Points ◽  
User Friendly

Abstract Motivation G-quadruplex is a DNA or RNA form in which four guanine-rich regions are held together by base pairing between guanine nucleotides in coordination with potassium ions. G-quadruplexes are increasingly seen as a biologically important component of genomes. Their detection in vivo is problematic; however, sequencing and spectrometric techniques exist for their in vitro detection. We previously devised the pqsfinder algorithm for PQS identification, implemented it in C++ and published as an R/Bioconductor package. We looked for ways to optimize pqsfinder for faster and user-friendly sequence analysis. Results We identified two weak points where pqsfinder could be optimized. We modified the internals of the recursive algorithm to avoid matching and scoring many sub-optimal PQS conformations that are later discarded. To accommodate the needs of a broader range of users, we created a website for submission of sequence analysis jobs that does not require knowledge of R to use pqsfinder. Availability and implementation https://pqsfinder.fi.muni.cz, https://bioconductor.org/packages/pqsfinder. Supplementary information Supplementary data are available at Bioinformatics online.

SUBSUMPTION DEGREES BETWEEN ENTITY TYPES AND NAMES FOR APPROXIMATE KNOWLEDGE RETRIEVAL

2007 ◽  
Vol 15 (supp01) ◽  
pp. 21-42 ◽  
Author(s):  
TRU H. CAO ◽  
DAT T. HUYNH
Keyword(s):  
Query Language ◽  
Research Work ◽  
Population Based ◽  
Conceptual Graphs ◽  
Query Graph ◽  
Front End ◽  
The One ◽  
User Friendly ◽  
Query Modification ◽  
Source Of Information

The Web has become a huge and indispensable source of information to be used and shared globally, where knowledge is commonly represented and stored in RDF, or alternatively, in conceptual graphs. Managing and searching for web information have gone beyond the relational database model, as the data are semi-structured and inexact answers are often the case. Usually, approximate searching results are due to mismatching between entity types and names in a query and an answer. Firstly, this research work focuses on partial subsumption of a query graph to an answer graph, which is an unsymmetric measure in contrast to similarity. Secondly, it proposes a population-based method for defining subsumption degrees between entity types, one to another, and a class-sensitive soft TF-IDF method for entity names. Lastly, on the one hand, for a user-friendly interface and easily readable query expressions, conceptual graphs are employed at the front-end. On the other hand, in order to take the advantage of the existing platform of SeRQL, an exact RDF query language, the query modification tactic is used to retrieve the knowledge graphs that are close to a query graph, before the subsumption degrees of the query graph to those answer graphs are calculated.

scholarly journals Breast Cancer Screening (BCS) by Mammography Tomosynthesis

2019 ◽  
Vol 29 (Supplement_4) ◽  
Author(s):  
M Correia ◽  
F Aleixo ◽  
A Lagoa ◽  
D Ferrinho ◽  
R Pereira ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Survival Rate ◽  
Cancer Diagnosis ◽  
Digital Mammography ◽  
Population Based ◽  
False Positives ◽  
Mobile Unit ◽  
Mobility Impairment ◽  
Adhesion Rate ◽  
User Friendly

Abstract Issue Breast cancer is the 2nd cause of death for women in Portugal and 6000 new cases are detected annually. The prognosis is better for women whose cancers are detected earlier. Description Algarve BCS begin in 2005 using a digital mammography with 2 incidences/breast with double reading and consensus by a 3rd radiologist. Each 2 years women age 50 to 69, are invited to a Mobile Unit to do the mammography, a partnership with Algarve Oncologic Association. In 2017, direct digital mammography with Tomosynthesis(DDMT)was implemented. This technique increase cancer detection, reduction of false positives, false negatives and radiation dose. Diagnostic accuracy is better and also improves accessibility to the most vulnerable population groups to this technology. Results BCS covers 100% of the region and the mobile unit is user friendly for women with mobility impairment. Adhesion rate is > 62%. Is the 1st screening using Tomosynthesis in Portugal.Preliminary results show that the confirmation rate increased (10 %), the detection rate per 1.000 women also increased and the positive predictive value >95%. Costs associated with the program decrease and less number of women called for false positives is observed. The number of positive mammograms increased, due to diagnostic acuity, with better visualization of the breast, namely in the patterns of greater mammary density; which leads to an improvement in further assessment rates. Lessons The technique increases the adhesion rate, with the same human resources. The decrease of the false positives improves the number of women send to further assessment and Senology Center. Earlier diagnoses, less aggressive treatments, and a higher survival rate are also expected. Messages- Using this technology is expected that cancer diagnosis will be earlier, more reliable and wiht higher survival rate for this disease. The possibility of a population based screening with DDMT is an opportunity to reduce inequalities in the region. Key messages Mammography Tomosynthesis is expected that cancer diagnosis will be earlier, more reliable and wiht higher survival rate for this disease. The possibility of a population based screening with Mammography Tomosynthesis is an opportunity to reduce inequalities in the region.

Improved subspecies identification in clinical Mycobacterium abscessus complex isolates using whole genome sequencing

2020 ◽  
Author(s):  
Dachuan Lin ◽  
Ruifeng Sun ◽  
Yaoju Tan ◽  
Jing Wang ◽  
Xinchun Chen ◽  
...  
Keyword(s):  
Soft Tissues ◽  
Single Gene ◽  
Rapid Identification ◽  
Mycobacterium Abscessus ◽  
Comprehensive Analysis ◽  
Clinical Isolates ◽  
Genome Database ◽  
Mycobacterium Abscessus Complex ◽  
Subspecies Level ◽  
User Friendly

Abstract BackgroundMycobacterium abscessus complex, which is frequently reported to cause a variety of skin and soft tissues diseases in humans, is composed of three subspecies, namely, M. abscessus subsp. abscessus, M. abscessus subsp. massiliense and M. abscessus subsp. bolletii. Currently, the differentiation of these three subspecies in clinical isolates still largely depends on single gene identification methods, including the genes hsp65 and 16s, with limited accuracy.ResultsThis study confirmed the limitations of the single gene-based method of subspecies identification. We performed a comprehensive analysis of MABC genomes in the NCBI database and tried to build an accurate and user-friendly identification method. Here, we describe an improved assay for Mycobacterium abscessus complex rapid identification using WGS data, based on the identities of rpoB, erm(41) and rpls. Comprehensive analysis has been performed to compare our software results with the traditional method. The results showed that the method built in this study could achieve 100% identification of subspecies for the Mycobacterium abscessus complex in a public genome database (893 genomes from the NCBI database and 6 clinical isolates from this study). This software can be easily integrated into a routine workflow to quickly and precisely provide subspecies-level identification and discrimination of different MABC subspecies in clinical isolates by WGS.ConclusionsThis assay will facilitate accurate molecular identification of species from the MABC complex in a variety of clinical specimens and diagnostic contexts.

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