scholarly journals A LAMP at the end of the tunnel: a rapid, field deployable assay for the kauri dieback pathogen,Phytophthora agathidicida

2019 ◽  
Author(s):  
Richard C. Winkworth ◽  
Briana C.W. Nelson ◽  
Stanley E. Bellgard ◽  
Chantal M. Probst ◽  
Patricia A. McLenachan ◽  
...  
Keyword(s):  
Hybrid Approach ◽  
Lamp Assay ◽  
High Specificity ◽  
Cost Effective ◽  
Direct Evaluation ◽  
Term Survival ◽  
Apocytochrome B ◽  
Specificity And Sensitivity ◽  
Laboratory Facility ◽  
Assay Performance

AbstractThe collar rot causing oomycete,Phytophthora agathidicida, threatens the long-term survival of the iconic New Zealand kauri. Currently, testing for this pathogen involves an extended soil bioassay that takes 14-20 days and requires specialised staff, consumables, and infrastructure. Here we describe a loop-mediated isothermal amplification (LAMP) assay for the detection ofP. agathidicidathat targets a portion of the mitochondrial apocytochrome b coding sequence. This assay has high specificity and sensitivity; it did not cross react with a range of otherPhytophthoraisolates and detected as little as 1 fg of totalP. agathidicidaDNA or 116 copies of the target locus. Assay performance was further investigated by testing plant tissue baits from flooded soil samples using both the extended bioassay and LAMP testing of DNA extracted from baits. In these comparisons,P. agathidicidawas detected more frequently using the LAMP assay. In addition to greater sensitivity, by removing the need for culturing, the hybrid baiting plus LAMP approach is more cost effective than the bioassay and, importantly, does not require a centralised laboratory facility with specialised staff, consumables, and equipment. Such testing will allow us to address outstanding questions aboutP. agathidicida. For example, the hybrid approach could enable monitoring of the pathogen beyond areas with visible disease symptoms, allow direct evaluation of rates and patterns of spread, and allow the effectiveness of disease control to be evaluated. The hybrid assay also has the potential to empower local communities. These communities could use this diagnostic tool to evaluate the pathogen status of local kauri stands, providing information around which to base their management and allowing informed engagement with wider initiatives.

scholarly journals Effects of exposure of honey bee colonies to neonicotinoid seed–treated maize crops

2013 ◽  
Vol 57 (2) ◽  
pp. 199-208 ◽  
Author(s):  
Krystyna Pohorecka ◽  
Piotr Skubida ◽  
Piotr Semkiw ◽  
Artur Miszczak ◽  
Dariusz Teper ◽  
...  
Keyword(s):  
Zea Mays ◽  
Honey Bee ◽  
High Specificity ◽  
Negative Effects ◽  
Term Survival ◽  
Pollen Loads ◽  
Modified Quechers ◽  
Specificity And Sensitivity ◽  
Bee Colonies

Abstract The effects to honeybee colonies (Apis mellifera L.) during and after exposure to flowering maize (Zea mays L.), grown from seeds coated with clothianidin and imidacloprid was assessed in field-realistic conditions. The experimental maize crops were adjacent to the other flowering agriculture plants. Honey bee colonies were placed in three differently protected maize fields throughout the blooming period, and thereafter they were transferred to a stationary apiary. Samples of pollen loads, bee bread, and adult bees were collected and analyzed for neonicotinoid residues. To ensure high specificity and sensitivity of detection of the analyzed pesticides, a modified QuEChERS extraction method and liquid chromatography coupled with tandem mass spectrometry were used. Clothianidin was detected only in the samples of pollen loads. Their residue levels ranged from 10.0 to 41.0 ng/g (average 27.0 ng/g). Imidacloprid was found in no investigated sample. No negative effects of neonicotinoid seed-treated maize on the development and long-term survival of honey bee colonies were observed. The low proportion of Zea mays pollen in total bee-collected pollen during the maize flowering period was noted. The findings suggest that maize plants are less attractive forage for honey bees than phacelia (Phacelia tanacetifolia Benth.), buckwheat (Fagopyrum Mill.), white clover (Trifolium repens L.), goldenrod (Solidago L.), and vegetation from Brassicaceae family. The results indicate a possibility of reducing the risk of bees being exposed to the toxic effect of insecticidal dusts dispersed during maize sowing by seeding, in the areas surrounding maize crops, plants that bloom later in the year.

scholarly journals Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

2016 ◽  
Vol 10 (1) ◽  
pp. 176-182 ◽  
Author(s):  
Reza Ranjbar ◽  
Payam Behzadi ◽  
Caterina Mammina
Keyword(s):  
Dna Microarray ◽  
Francisella Tularensis ◽  
High Specificity ◽  
Cost Effective ◽  
High Rate ◽  
Molecular Diagnostic ◽  
Microarray Technology ◽  
Microarray Probe ◽  
Specificity And Sensitivity ◽  
Oligo Microarray

Background:Francisella tularensis(F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification ofF. tularensis.Method:For performing this research, the complete genomes ofF. tularensissubsp.tularensisFSC198,F. tularensissubsp.holarcticaLVS,F. tularensissubsp.mediasiatica,F. tularensissubsp.novicida(F. novicidaU112), andF. philomiragiasubsp.philomiragiaATCC 25017 were studiedviaNCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processedviaAlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In thisin silicoinvestigation, a number of long oligo microarray probes were designed for detecting and identifyingF. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

scholarly journals The Use of Biomarkers in Early Diagnostics of Pancreatic Cancer

2018 ◽  
Vol 2018 ◽  
pp. 1-10 ◽  
Author(s):  
Lumir Kunovsky ◽  
Pavla Tesarikova ◽  
Zdenek Kala ◽  
Radek Kroupa ◽  
Petr Kysela ◽  
...  
Keyword(s):  
Radical Surgery ◽  
Early Stage ◽  
Locally Advanced ◽  
High Specificity ◽  
Cost Effective ◽  
Ductal Adenocarcinoma ◽  
Specificity And Sensitivity ◽  
Solid Malignancies ◽  
Late Detection ◽  
Resistance To Chemotherapy

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid malignancies with increasing incidence. The poor prognosis is due to the aggressive nature of the tumor, late detection, and the resistance to chemotherapy and radiotherapy. A radical surgery procedure is the only treatment that has been shown to improve the 5-year survival rate to 20-25%. However, the majority of patients (80-85%) are diagnosed with locally advanced or metastatic disease and just 15-20% patients are diagnosed in an early stage allowing them to undergo the potentially curative surgical resection. The early detection of PDAC without the use of invasive methods is challenging and discovery of a cost-effective biomarker with high specificity and sensitivity could significantly improve the treatment and survival in these patients. In this review, we summarize current and newly examined biomarkers in early PDAC detection.

scholarly journals Correlation of fine needle aspiration cytology and histopathology of neck swellings

2018 ◽  
Vol 4 (3) ◽  
pp. 648
Author(s):  
C. S. Asha ◽  
B. R. Suchit Roy
Keyword(s):  
Salivary Gland ◽  
Lymph Node ◽  
Predictive Value ◽  
Age Groups ◽  
Invasive Procedure ◽  
High Specificity ◽  
Cost Effective ◽  
Needle Aspiration ◽  
Predictive Values ◽  
Specificity And Sensitivity

<p class="abstract"><strong>Background:</strong> Neck swellings are a common clinical finding affecting all age groups. FNAC is a minimally invasive procedure helpful in the diagnosis of various neck swellings. The purpose of this study is to determine the accuracy of FNAC in the diagnosis of neck swellings by comparing it with the histopathology which is taken as the gold standard.</p><p class="abstract"><strong>Methods:</strong> A prospective study which included 90 patients who attended ENT and surgery departments of Government Medical College, Trivandrum with neck swellings from July 2006-2007. FNAC of the swelling was done and the FNAC results were compared with the histopathology results. The specificity, sensitivity, positive and negative predictive values and accuracy of FNAC were calculated.  </p><p class="abstract"><strong>Results:</strong> Of the 90 patients, thyroid swelling formed the major group followed by lymph node, salivary gland and miscellaneous swellings. Thyroid swellings had a female predominance while the other three groups namely lymph node, salivary gland and miscellaneous groups showed a male preponderance. When the neck swellings namely thyroid, salivary gland, lymph node and miscellaneous group were taken into consideration as a whole, the sensitivity of FNAC for detecting malignancy was 64.3%. The specificity, positive predictive value, negative predictive value and accuracy were 97.4%, 81.8%, 93.7% and 92% respectively.</p><p class="abstract"><strong>Conclusions:</strong> FNAC can be rated as a safe, simple, reliable, cost effective and rapid diagnostic tool with high specificity and sensitivity for the initial evaluation of neck swellings.</p>

scholarly journals Rapid Detection of Clostridium botulinum in Food Using Loop-Mediated Isothermal Amplification (LAMP)

2021 ◽  
Vol 18 (9) ◽  
pp. 4401
Author(s):  
Yufei Chen ◽  
Hao Li ◽  
Liu Yang ◽  
Lei Wang ◽  
Ruyi Sun ◽  
...  
Keyword(s):  
Rapid Detection ◽  
High Throughput Screening ◽  
Clostridium Botulinum ◽  
Lamp Assay ◽  
High Specificity ◽  
Isothermal Amplification ◽  
Clinical Samples ◽  
Loop Mediated Isothermal Amplification ◽  
Specificity And Sensitivity ◽  
Target Dna

Botulinum neurotoxins are considered as one of the most potent toxins and are produced by Clostridium botulinum. It is crucial to have a rapid and sensitive method to detect the bacterium Clostridium botulinum in food. In this study, a rapid detection assay of C. botulinum in food using loop-mediated isothermal amplification (LAMP) technology was developed. The optimal primers were identified among three sets of primers designed specifically based on the partial ntnh gene encoding nontoxic-nonhaemagglutinin (NTNH) for rapid detection of the target DNA in plasmids. The optimal temperature and reaction time of the LAMP assay were determined to be 64 °C and 60 min, respectively. The chemical kit could be assembled based on these optimized reaction conditions for quick, initial high-throughput screening of C. botulinum in food samples. The established LAMP assay showed high specificity and sensitivity in detecting the target DNA with a limit of 0.0001 pg/ul (i.e., ten times more sensitive than that of the PCR method) and an accuracy rate of 100%. This study demonstrated a potentially rapid, cost-effective, and easy-operating method to detect C. botulinum in food and clinical samples based on LAMP technology.

scholarly journals Glycoprotein- and Lectin-Based Approaches for Detection of Pathogens

Pathogens ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 694
Author(s):  
Sammer-ul Hassan ◽  
Ahmed Donia ◽  
Usman Sial ◽  
Xunli Zhang ◽  
Habib Bokhari
Keyword(s):  
Infectious Diseases ◽  
Point Of Care ◽  
Healthcare Providers ◽  
Basic Research ◽  
High Specificity ◽  
Cost Effective ◽  
Emerging Diseases ◽  
Public Healthcare ◽  
Point Of Use ◽  
Specificity And Sensitivity

Infectious diseases alone are estimated to result in approximately 40% of the 50 million total annual deaths globally. The importance of basic research in the control of emerging and re-emerging diseases cannot be overemphasized. However, new nanotechnology-based methodologies exploiting unique surface-located glycoproteins or their patterns can be exploited to detect pathogens at the point of use or on-site with high specificity and sensitivity. These technologies will, therefore, affect our ability in the future to more accurately assess risk. The critical challenge is making these new methodologies cost-effective, as well as simple to use, for the diagnostics industry and public healthcare providers. Miniaturization of biochemical assays in lab-on-a-chip devices has emerged as a promising tool. Miniaturization has the potential to shape modern biotechnology and how point-of-care testing of infectious diseases will be performed by developing smart microdevices that require minute amounts of sample and reagents and are cost-effective, robust, and sensitive and specific. The current review provides a short overview of some of the futuristic approaches using simple molecular interactions between glycoproteins and glycoprotein-binding molecules for the efficient and rapid detection of various pathogens at the point of use, advancing the emerging field of glyconanodiagnostics.

scholarly journals Rapid and selective detection of macrocyclic trichothecene producing Stachybotrys chartarum strains by loop-mediated isothermal amplification (LAMP)

2021 ◽  
Author(s):  
Johannes Köck ◽  
Christoph Gottschalk ◽  
Sebastian Ulrich ◽  
Karin Schwaiger ◽  
Manfred Gareis ◽  
...  
Keyword(s):  
Lamp Assay ◽  
High Specificity ◽  
Neutral Red ◽  
Fungal Species ◽  
Isothermal Amplification ◽  
Visual Signal ◽  
Stachybotrys Chartarum ◽  
Loop Mediated Isothermal Amplification ◽  
Specificity And Sensitivity ◽  
Macrocyclic Trichothecene

AbstractCytotoxic macrocyclic trichothecenes such as satratoxins are produced by chemotype S strains of Stachybotrys chartarum. Diseases such as stachybotryotoxicosis in animals and the sick building syndrome as a multifactorial disease complex in humans have been associated with this mold and its toxins. Less toxic non-chemotype S strains of S. chartarum are morphologically indistinguishable from chemotype S strains, which results in uncertainties in hazard characterization of isolates. To selectively identify macrocyclic trichothecene producing S. chartarum isolates, a set of sat14 gene-specific primers was designed and applied in a loop-mediated isothermal amplification (LAMP) assay using neutral red for visual signal detection. The assay was highly specific for S. chartarum strains of the macrocyclic trichothecene producing chemotype and showed no cross-reaction with non-macrocyclic trichothecene producing S. chartarum strains or 152 strains of 131 other fungal species. The assay’s detection limit was 0.635 pg/rxn (picogram per reaction) with a reaction time of 60 min. Its high specificity and sensitivity as well as the cost-saving properties make the new assay an interesting and powerful diagnostic tool for easy and rapid testing.

scholarly journals Concurrent and Convergent Validity of a Single, Brief Question for Physical Activity Assessment

2020 ◽  
Vol 17 (6) ◽  
pp. 1989 ◽  
Author(s):  
Antonio Moreno-Llamas ◽  
Jesús García-Mayor ◽  
Ernesto De la Cruz-Sánchez
Keyword(s):  
Physical Activity ◽  
Convergent Validity ◽  
High Specificity ◽  
Cost Effective ◽  
Classification Performance ◽  
Short Version ◽  
Operating Characteristics ◽  
Time Saving ◽  
Physically Active ◽  
Specificity And Sensitivity

An extensive number of self-reported methods for physical activity (PA) measurement are available, including short and long recall questionnaires ranging from a few to tens of questions. Due to the fact that simple, time-saving methods could be more practical and desirable for use in a busy clinical context, as well as in public health surveys, we evaluated how a single-item question might be a useful and cost-effective method for assessing compliance with PA guidelines. Using multiple receiver operating characteristics (ROC), we assessed the classification performance of a single brief question, employing the short version of the International Physical Activity Questionnaire as criterion instrument, in a total of 55,950 people (30,601 women and 25,349 men). Both those who practice PA almost daily and a few times a week presented an upper threshold (1042.5 metabolic equivalent minutes (MET) minutes/week) to the established compliance PA guidelines (600 MET minutes/week) with high specificity and sensitivity, using a sedentary group as reference. Otherwise, the occasionally physically active group did not reach the minimum (349.5 MET minutes/week) and obtained a poorer classification performance. A single brief question is a pragmatic and alternative method for assessment of compliance with PA guidelines.

scholarly journals Rapid Detection of Pine Pathogens Lecanosticta acicola, Dothistroma pini and D. septosporum on Needles by Probe-Based LAMP Assays

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 479
Author(s):  
Chiara Aglietti ◽  
Colton D. Meinecke ◽  
Luisa Ghelardini ◽  
Irene Barnes ◽  
Ariska van der Nest ◽  
...  
Keyword(s):  
Elongation Factor ◽  
Morphological Characteristics ◽  
Lamp Assay ◽  
High Specificity ◽  
Portable Devices ◽  
Forest Protection ◽  
Specific Pcr ◽  
Specificity And Sensitivity ◽  
Lecanosticta Acicola ◽  
Dothistroma Pini

Needle blights are serious needle fungal diseases affecting pines both in natural and productive forests. Among needle blight agents, the ascomycetes Lecanosticta acicola, Dothistroma pini and D. septosporum are of particular concern. These pathogens need specific, fast and accurate diagnostics since they are regulated species in many countries and may require differential management measures. Due to the similarities in fungal morphology and the symptoms they elicit, these species are hard to distinguish using morphological characteristics. The symptoms can also be confused with those caused by insects or abiotic agents. DNA-based detection is therefore recommended. However, the specific PCR assays that have been produced to date for the differential diagnosis of these pathogens can be applied only in a well-furnished laboratory and the procedure takes a relatively long execution time. Surveillance and forest protection would benefit from a faster diagnostic method, such as a loop-mediated isothermal amplification (LAMP) assay, which requires less sophisticated equipment and can also be deployed directly on-site using portable devices. LAMP assays for the rapid and early detection of L. acicola, D. pini and D. septosporum were developed in this work. Species-specific LAMP primers and fluorescent assimilating probes were designed for each assay, targeting the beta tubulin (β-tub2) gene for the two Dothistroma species and the elongation factor (EF-1α) region for L. acicola. Each reaction detected its respective pathogen rapidly and with high specificity and sensitivity in DNA extracts from both pure fungal cultures and directly from infected pine needles. These qualities and the compatibility with inexpensive portable instrumentation position these LAMP assays as an effective method for routine phytosanitary control of plant material in real time, and they could profitably assist the management of L. acicola, D. pini and D. septosporum.

scholarly journals Highly Sensitive and Cost-Effective Portable Sensor for Early Gastric Carcinoma Diagnosis

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2639
Author(s):  
Saw Lin Oo ◽  
Shishir Venkatesh ◽  
Vaithinathan Karthikeyan ◽  
Clement Manohar Arava ◽  
Spoorthy Pathikonda ◽  
...  
Keyword(s):  
Gastric Carcinoma ◽  
High Specificity ◽  
Cost Effective ◽  
Electrical Current ◽  
Early Gastric Carcinoma ◽  
Rna Modification ◽  
Dependent Manner ◽  
Cancer Antigen ◽  
Concentration Dependent Manner ◽  
Specificity And Sensitivity

Facile and efficient early detection of cancer is a major challenge in healthcare. Herein we developed a novel sensor made from a polycarbonate (PC) membrane with nanopores, followed by sequence-specific Oligo RNA modification for early gastric carcinoma diagnosis. In this design, the gastric cancer antigen CA72-4 is specifically conjugated to the Oligo RNA, thereby inhibiting the electrical current through the PC membrane in a concentration-dependent manner. The device can determine the concentration of cancer antigen CA72-4 in the range from 4 to 14 U/mL, possessing a sensitivity of 7.029 µAU−1mLcm−2 with a linear regression (R2) of 0.965 and a lower detection limit of 4 U/mL. This device has integrated advantages including high specificity and sensitivity and being simple, portable, and cost effective, which collectively enables a giant leap for cancer screening technologies towards clinical use. This is the first report to use RNA aptamers to detect CA72-4 for gastric carcinoma diagnosis.

Sign in / Sign up

Export Citation Format

Share Document