scholarly journals ADVANCES IN THE IDENTIFICATION TECHNIQUES FOR PATHOGENIC MICROORGANISMS

2021 ◽  
pp. 10
Author(s):  
Keyword(s):  
Latin American ◽  
Dna Sequences ◽  
New Technologies ◽  
Low Cost ◽  
High Sensitivity ◽  
Rrna Gene ◽  
Pathogenic Microorganisms ◽  
Microbial Identification ◽  
Flight Mass Spectrometry ◽  
Sensitivity Specificity

Objectives: The research objective was to present the main techniques for identifying pathogenic microorganisms and the application of new technologies for the clinical diagnosis of infectious diseases. Methods: It was made a search for free and recent journals available online in the databases of Pubmed (National Library of Medicine and the National Institutes), Lilacs (Latin American and Caribbean Literature in Health Sciences), and Scielo (Scientific Electronic Library Online), based on keywords related to the proposed theme. Results: From the researched literature, it was possible to verify that conventional techniques, despite their limitations, are still widely used for the identification and microbial characterization. However, in the last decades, molecular methods have been widely inserted in the laboratory routine seeking to increase the capacity to detect infectious agents with high sensitivity, specificity, speed, and low cost. Among the various techniques, amplification of DNA sequences is highlighted by the polymerase chain reaction (PCR), the sequencing of the 16S rRNA gene, and other variations of PCR. In addition to these, new technologies have been developed, such as new generation sequencing (NGS) and Matrix-assisted Laser Desorption/ionization-time-of-flight Mass Spectrometry (MALDI-TOF MS). Conclusion: The development of new technologies that allow rapid, sensitive, reproducible, and low-cost microbial identification, it is of great relevance for clinical microbiology, and consequently, for public health.

scholarly journals Validation of an NGS Panel Designed for Detection of Actionable Mutations in Tumors Common in Latin America

2021 ◽  
Vol 11 (9) ◽  
pp. 899
Author(s):  
Mauricio Salvo ◽  
Evelin González-Feliú ◽  
Jessica Toro ◽  
Iván Gallegos ◽  
Ignacio Maureira ◽  
...  
Keyword(s):  
Latin America ◽  
Latin American ◽  
Hedgehog Signaling ◽  
Predictive Biomarkers ◽  
High Sensitivity ◽  
Clinical Samples ◽  
Dna Integrity ◽  
Precision Oncology ◽  
Single Nucleotide Variants ◽  
Sensitivity Specificity

Next-generation sequencing (NGS) is progressively being used in clinical practice. However, several barriers preclude using this technology for precision oncology in most Latin American countries. To overcome some of these barriers, we have designed a 25-gene panel that contains predictive biomarkers for most current and near-future available therapies in Chile and Latin America. Library preparation was optimized to account for low DNA integrity observed in formalin-fixed paraffin-embedded tissue. The workflow includes an automated bioinformatic pipeline that accounts for the underrepresentation of Latin Americans in genome databases. The panel detected small insertions, deletions, and single nucleotide variants down to allelic frequencies of 0.05 with high sensitivity, specificity, and reproducibility. The workflow was validated in 272 clinical samples from several solid tumor types, including gallbladder (GBC). More than 50 biomarkers were detected in these samples, mainly in BRCA1/2, KRAS, and PIK3CA genes. In GBC, biomarkers for PARP, EGFR, PIK3CA, mTOR, and Hedgehog signaling inhibitors were found. Thus, this small NGS panel is an accurate and sensitive method that may constitute a more cost-efficient alternative to multiple non-NGS assays and costly, large NGS panels. This kind of streamlined assay with automated bioinformatics analysis may facilitate the implementation of precision medicine in Latin America.

scholarly journals MALDI-TOF mass spectrometry in clinical diagnostic microbiology

JMS SKIMS ◽  
2017 ◽  
Vol 20 (1) ◽  
pp. 54
Author(s):  
Editor SKIMS
Keyword(s):  
Mass Spectrometry ◽  
Low Cost ◽  
Microbial Identification ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Clinical Diagnostic ◽  
Routine Identification ◽  
Identification Technique ◽  
Diagnostic Microbiology ◽  
Identification Techniques

Microbial identification in clinical diagnostic laboratories mainly relies on conventional phenotypic and gene sequencing identification techniques. Recently development of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) devices has revolutionized the routine identification of microorganisms in clinical microbiology laboratories. This is an easy, rapid, high throughput, low-cost, and efficient identification technique and has been adapted to the constraint of clinical diagnostic laboratories. This technology has the potential to replace and/or complement conventional identification techniques for both bacterial and fungal strains. JMS 2017; 20(1):54

scholarly journals Nanozyme Applications: A Glimpse of Insight in Food Safety

2021 ◽  
Vol 9 ◽  
Author(s):  
Long Wu ◽  
Shuhong Zhou ◽  
Gonglei Wang ◽  
Yonghuan Yun ◽  
Guozhen Liu ◽  
...  
Keyword(s):  
Low Cost ◽  
Analytical Techniques ◽  
High Sensitivity ◽  
Food Contaminants ◽  
Electrochemical Assay ◽  
Enzyme Mimicking ◽  
Surface Enhanced Raman ◽  
Food Applications ◽  
Enhanced Raman Scattering ◽  
Sensitivity Specificity

Nanozymes own striking merits, including high enzyme-mimicking activity, good stability, and low cost. Due to the powerful and distinguished functions, nanozymes exhibit widespread applications in the field of biosensing and immunoassay, attracting researchers in various fields to design and engineer nanozymes. Recently, nanozymes have been innovatively used to bridge nanotechnology with analytical techniques to achieve the high sensitivity, specificity, and reproducibility. However, the applications of nanozymes in food applications are seldom reviewed. In this review, we summarize several typical nanozymes and provide a comprehensive description of the history, principles, designs, and applications of nanozyme-based analytical techniques in food contaminants detection. Based on engineering and modification of nanozymes, the food contaminants are classified and then discussed in detail via discriminating the roles of nanozymes in various analytical methods, including fluorescence, colorimetric and electrochemical assay, surface-enhanced Raman scattering, magnetic relaxing sensing, and electrochemiluminescence. Further, representative examples of nanozymes-based methods are highlighted for contaminants analysis and inhibition. Finally, the current challenges and prospects of nanozymes are discussed.

scholarly journals SMILE Platform: An Innovative Microfluidic Approach for On-Chip Sample Manipulation and Analysis in Oral Cancer Diagnosis

Micromachines ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 885
Author(s):  
Sofia Zoupanou ◽  
Annalisa Volpe ◽  
Elisabetta Primiceri ◽  
Caterina Gaudiuso ◽  
Antonio Ancona ◽  
...  
Keyword(s):  
Oral Cancer ◽  
Low Cost ◽  
High Sensitivity ◽  
Ease Of Use ◽  
Early Screening ◽  
Chip Sample ◽  
Large Audience ◽  
On Chip ◽  
Sensitivity Specificity ◽  
Large Diffusion

Oral cancer belongs to the group of head and neck cancers, and, despite its large diffusion, it suffers from low consideration in terms of prevention and early diagnosis. The main objective of the SMILE platform is the development of a low-cost device for oral cancer early screening with features of high sensitivity, specificity, and ease of use, with the aim of reaching a large audience of possible users and realizing real prevention of the disease. To achieve this goal, we realized two microfluidic devices exploiting low-cost materials and processes. They can be used in combination or alone to obtain on-chip sample preparation and/or detection of circulating tumor cells, selected as biomarkers of oral cancer. The realized devices are completely transparent with plug-and-play features, obtained thanks to a highly customized architecture which enables users to easily use them, with potential for a common use among physicians or dentists with minimal training.

Development of oligonucleotides and multiplex probes for quick and accurate identification of wheat and Thinopyrum bessarabicum chromosomes

Genome ◽  
2017 ◽  
Vol 60 (2) ◽  
pp. 93-103 ◽  
Author(s):  
Pei Du ◽  
Lifang Zhuang ◽  
Yanzhi Wang ◽  
Li Yuan ◽  
Qing Wang ◽  
...  
Keyword(s):  
Dna Sequences ◽  
High Efficiency ◽  
Low Cost ◽  
High Sensitivity ◽  
Fish Analysis ◽  
Chromosome Identification ◽  
Accurate Identification ◽  
Design Synthesis ◽  
Repeat Units ◽  
Thinopyrum Bessarabicum

In comparison with general FISH for preparing probes in terms of time and cost, synthesized oligonucleotide (oligo hereafter) probes for FISH have many advantages such as ease of design, synthesis, and labeling. Low cost and high sensitivity and resolution of oligo probes greatly simplify the FISH procedure as a simple, fast, and efficient method of chromosome identification. In this study, we developed new oligo and oligo multiplex probes to accurately and efficiently distinguish wheat (Triticum aestivum, 2n = 6x, AABBDD) and Thinopyrum bessarabicum (2n = 2x = 14, JJ) chromosomes. The oligo probes contained more nucleotides or more repeat units that produced stronger signals for more efficient chromosome painting. Four Th. bessarabicum-specific oligo probes were developed based on genomic DNA sequences of Th. bessarabicum chromosome arm 4JL, and one of them (oligo DP4J27982) was pooled with the oligo multiplex #1 to simultaneously detect wheat and Th. bessarabicum chromosomes for quick and accurate identification of Chinese Spring (CS) – Th. bessarabicum alien chromosome introgression lines. Oligo multiplex #4 revealed chromosome variations among CS and eight wheat cultivars by a single round of FISH analysis. This research demonstrated the high efficiency of using oligos and oligo multiplexes in chromosome identification and manipulation.

scholarly journals Designing Efficient Low-Cost Paper-Based Sensing Plasmonic Nanoplatforms

Sensors ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 3035 ◽  
Author(s):  
Laurentiu Susu ◽  
Andreea Campu ◽  
Ana Craciun ◽  
Adriana Vulpoi ◽  
Simion Astilean ◽  
...  
Keyword(s):  
Limit Of Detection ◽  
Low Cost ◽  
High Sensitivity ◽  
Dark Field ◽  
Ease Of Use ◽  
Localized Surface Plasmon ◽  
Surface Enhanced Raman ◽  
Resonance Surface ◽  
Sensitivity Specificity ◽  
Plasmonic Paper

Paper-based platforms can be a promising choice as portable sensors due to their low-cost and facile fabrication, ease of use, high sensitivity, specificity and flexibility. By combining the qualities of these 3D platforms with the optical properties of gold nanoparticles, it is possible to create efficient nanodevices with desired biosensing functionalities. In this work, we propose a new plasmonic paper-based dual localized surface plasmon resonance–surface-enhanced Raman scattering (LSPR-SERS) nanoplatform with improved detection abilities in terms of high sensitivity, uniformity and reproducibility. Specifically, colloidal gold nanorods (GNRs) with a well-controlled plasmonic response were firstly synthesized and validated as efficient dual LSPR-SERS nanosensors in solution using the p-aminothiophenol (p-ATP) analyte. GNRs were then efficiently immobilized onto the paper via the immersion approach, thus obtaining plasmonic nanoplatforms with a modulated LSPR response. The successful deposition of the nanoparticles onto the cellulose fibers was confirmed by LSPR measurements, which demonstrate the preserved plasmonic response after immobilization, as well as by dark-field microscopy and scanning electron microscopy investigations, which confirm their uniform distribution. Finally, a limit of detection for p-ATP as low as 10−12 M has been achieved by our developed SERS-based paper nanoplatform, proving that our optimized plasmonic paper-based biosensing design could be further considered as an excellent candidate for miniaturized biomedical applications.

scholarly journals Cytological Study of Palpable Breast Lumps with their Histological Correlation

2013 ◽  
Vol 2 (2) ◽  
pp. 128
Author(s):  
R. Bhagat ◽  
M. S. Bal ◽  
V. K. Bodal ◽  
A. K. Suri ◽  
K. Jindal
Keyword(s):  
Diagnostic Accuracy ◽  
Ductal Carcinoma ◽  
Histopathological Examination ◽  
Low Cost ◽  
Benign Lesion ◽  
Malignant Lesion ◽  
High Sensitivity ◽  
Breast Lesions ◽  
Breast Cancers ◽  
Sensitivity Specificity

<strong>Background:</strong>FNAC is an inexpensive and highly accurate means of diagnosing both benign and malignant breast lesions. The procedure provides a rapid and non-morbid diagnosis before the operation which enables the patient and the surgeon to discuss and plan therapeutic alternatives in a rational atmosphere.<p><strong>Objectives:</strong> To evaluate role of fine needle aspiration cytology in the diagnosis of breast lesions and to compare the cytological findings with the histopathology wherever possible. In addition the sensitivity, specificity and accuracy of FNAC in breast lesions are carried out.</p><p><strong>Material and Methods:</strong> The present study was carried out on 200 patients who presented with palpable lump in the breast in the Department of Pathology, Government Medical College, Patiala over a period of 2 years. Cytological Diagnosis was correlated with histological findings wherever possible.</p><p><strong>Results:</strong> Cytologically, the lesions were categorized into 4 major categories, benign 143 (71.5%), malignant 37 (18.5%), suspicious or atypical 10 (5%) and unsatisfactory 10 (5%). Out of these 200 cases, 85 cases (42.5%) were available for histopathological examination. The most common benign lesion in this study was fibroadenoma 23/52 (44.2%) and the most common malignant lesion was infiltrating ductal carcinoma (28/33) Diagnostic accuracy of FNAC for benign lesion was 94.2% while for malignant lesion, it was 96.7%. The sensitivity, specificity and overall diagnostic accuracy of FNAC came out to be 93.7%, 98.1% and 96.4% respectively.</p><p><strong>Conclusion</strong>: FNAC is a simple and reliable method for diagnosis of both benign and malignant lesions quite accurately thus reducing unnecessary surgeries. The present study proved that the procedure has high sensitivity, specificity and diagnostic accuracy. Though it cannot categorize the lesion in some cases but it can rule out malignancy in most of the cases. Considering its low cost and quick results, it can be a potential tool for screening of breast cancers.</p>

TO SEPARATELY ASSESS THE DIAGNOSTIC POTENTIAL OF TVS & MRI IN THE TERMS OF SENSITIVITY AND SPECIFICITY BY CORRELATING THE IMAGING FINDINGS WITH HISTOPATHOLOGY

2020 ◽  
Vol 4 (6) ◽  
Author(s):  
Suraj Mathur
Keyword(s):  
Transvaginal Ultrasound ◽  
High Sensitivity ◽  
Imaging Evaluation ◽  
Medical College ◽  
Conventional Mri ◽  
Diagnostic Potential ◽  
Adc Mapping ◽  
Malignant Lesions ◽  
Sensitivity Specificity

This prospective study was done in the Department of Radio diagnosis Govt. Medical College, Kozhikode. A total of 65 patients who were referred to our department with clinical suspicion of endometrial lesions and incidentally detected endometrial lesions on ultrasonography underwent transvaginal ultrasound and subsequent Imaging evaluation of pelvis MRI has very high sensitivity (95%) and specificity (98%) and is almost as accurate (97%) as histopathology in differentiating benign from malignant lesions. Addition of DWI with ADC mapping to conventional MRI increases its accuracy even more. However there is inherent limitation to MRI in detecting carcinoma in situ and micrometastasis. Keywords: TVS, MRI, Sensitivity, Specificity, Histopathology.

Understanding the Role of Chlorine and Ozone to Control Postharvest Diseases in Fruit and Vegetables: A Review

2020 ◽  
Vol 16 (4) ◽  
pp. 455-461
Author(s):  
Gabriela M. Baia ◽  
Otniel Freitas-Silva ◽  
Murillo F. Junior
Keyword(s):  
Chlorine Dioxide ◽  
Broad Spectrum ◽  
Fruits And Vegetables ◽  
Low Cost ◽  
Residual Effects ◽  
Pathogenic Microorganisms ◽  
Postharvest Diseases ◽  
Post Harvest ◽  
By Products

Fruits and vegetables are foods that come into contact with various types of microorganisms from planting to their consumption. A lack or poor sanitation of these products after harvest can cause high losses due to deterioration and/ or pathogenic microorganisms. There are practically no post-harvest fungicides or bactericides with a broad spectrum of action that have no toxic residual effects and are safe. However, to minimize such problems, the use of sanitizers is an efficient device against these microorganisms. Chlorine is the most prevalent sanitizing agent because of its broad spectrum, low cost and well-established practices. However, the inevitable formation of disinfection by-products, such as trihalomethanes (THMs) and haloacetic acids (HAAs), is considered one of the main threats to food safety. Alternative sanitizers, such as chlorine dioxide (ClO2) and ozone, are becoming popular as a substitute for traditional post-harvest treatments. Thus, this review addresses the use of chlorine, chlorine dioxide and ozone emphasizing aspects, such as usage, safe application, spectrum of action and legislation. In order to ensure the quality and safety of final products, the adoption of well-prepared sanitation and sanitation programs for post-harvest fruits and vegetables is essential.

scholarly journals Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Amrita Srivathsan ◽  
Emily Hartop ◽  
Jayanthi Puniamoorthy ◽  
Wan Ting Lee ◽  
Sujatha Narayanan Kutty ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Large Scale ◽  
Low Cost ◽  
Small Body ◽  
Small Subset ◽  
Similar Species ◽  
Large Species ◽  
Morphological Examination ◽  
Species Discovery ◽  
Short Period

Abstract Background More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundance and large species richness. For such clades, using morphology for species discovery is slow because large numbers of specimens must be sorted based on detailed microscopic investigations. Fortunately, species discovery could be greatly accelerated if DNA sequences could be used for sorting specimens to species. Morphological verification of such “molecular operational taxonomic units” (mOTUs) could then be based on dissection of a small subset of specimens. However, this approach requires cost-effective and low-tech DNA barcoding techniques because well-equipped, well-funded molecular laboratories are not readily available in many biodiverse countries. Results We here document how MinION sequencing can be used for large-scale species discovery in a specimen- and species-rich taxon like the hyperdiverse fly family Phoridae (Diptera). We sequenced 7059 specimens collected in a single Malaise trap in Kibale National Park, Uganda, over the short period of 8 weeks. We discovered > 650 species which exceeds the number of phorid species currently described for the entire Afrotropical region. The barcodes were obtained using an improved low-cost MinION pipeline that increased the barcoding capacity sevenfold from 500 to 3500 barcodes per flowcell. This was achieved by adopting 1D sequencing, resequencing weak amplicons on a used flowcell, and improving demultiplexing. Comparison with Illumina data revealed that the MinION barcodes were very accurate (99.99% accuracy, 0.46% Ns) and thus yielded very similar species units (match ratio 0.991). Morphological examination of 100 mOTUs also confirmed good congruence with morphology (93% of mOTUs; > 99% of specimens) and revealed that 90% of the putative species belong to the neglected, megadiverse genus Megaselia. We demonstrate for one Megaselia species how the molecular data can guide the description of a new species (Megaselia sepsioides sp. nov.). Conclusions We document that one field site in Africa can be home to an estimated 1000 species of phorids and speculate that the Afrotropical diversity could exceed 200,000 species. We furthermore conclude that low-cost MinION sequencers are very suitable for reliable, rapid, and large-scale species discovery in hyperdiverse taxa. MinION sequencing could quickly reveal the extent of the unknown diversity and is especially suitable for biodiverse countries with limited access to capital-intensive sequencing facilities.

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