scholarly journals Diagnostic optical sequencing

2019 ◽  
Author(s):  
Lee E. Korshoj ◽  
Prashant Nagpal
Keyword(s):  
Single Molecule ◽  
Point Of Care ◽  
Cost Effective ◽  
Diagnostic Methods ◽  
Sequencing Platform ◽  
Molecular Variants ◽  
Cost Effective Method ◽  
Wide Range ◽  
Lactamase Gene ◽  
Modified Nucleobases

AbstractAdvances in precision medicine require high-throughput, inexpensive, point-of-care diagnostic methods with multi-omics capability for detecting a wide range of biomolecules and their molecular variants. Optical techniques have offered many promising advances towards such diagnostics. However, the inability to squeeze light with several hundred-nanometer wavelengths into angstrom-scale volume for single nucleotide measurements has hindered further progress. Recently, a block optical sequencing (BOS) method has been shown for determining relative nucleobase content in DNA k-mer blocks with Raman spectroscopy, and a block optical content scoring (BOCS) algorithm was developed for robust content-based genetic biomarker database searching. Here, we performed BOS measurements on positively-charged silver nanoparticles to achieve 93.3% accuracy for predicting nucleobase content in DNA k-mer blocks (where k=10), as well as measurements on RNA and chemically-modified nucleobases for extensions to transcriptomic and epigenetic studies. Our high-accuracy BOS measurements were then used with BOCS to correctly identify a β-lactamase gene from the MEGARes antibiotic resistance database and confirm the Pseudomonas aeruginosa pathogen of origin from <12 content measurements (<15% coverage) of the gene. These results prove the integration of BOS/BOCS as a diagnostic optical sequencing platform. With the versatile range of available plasmonic substrates offering simple data acquisition, varying resolution (single-molecule to ensemble), and multiplexing, this optical sequencing platform has potential as the rapid, cost-effective method needed for broad-spectrum biomarker detection.

scholarly journals Cost Effective Method for Toxicity Screening of Pharmaceutical Wastewater Containing Inorganic Salts and Harmful Organic Compounds

2019 ◽  
Vol 23 (1) ◽  
pp. 52-63 ◽  
Author(s):  
Elina Strade ◽  
Daina Kalnina
Keyword(s):  
Activated Sludge ◽  
Biological Treatment ◽  
Oxygen Demand ◽  
Cost Effective ◽  
Practical Implementation ◽  
Toxicity Screening ◽  
Pharmaceutical Wastewater ◽  
Cost Effective Method ◽  
Wide Range ◽  
Wastewater Biological Treatment

Abstract Pharmaceutical wastewater biological treatment plants are stressed with multi-component wastewater and unexpected variations in wastewater flow, composition and toxicity. To avoid operational problems and reduced wastewater treatment efficiency, accurate monitoring of influent toxicity on activated sludge microorganisms is essential. This paper outlines how to predict highly toxic streams, which should be avoided, using measurements of biochemical oxygen demand (BOD), if they are made in a wide range of initial concentration. The results indicated that wastewater containing multivalent Al3+ cations showed a strong toxic effect on activated sludge biocenosis irrespectively of dilutions, while toxicity of phenol and formaldehyde containing wastewater decreased considerably with increasing dilution. Activated sludge microorganisms were not sensitive to wastewater containing halogenated sodium salts (NaCl, NaF) and showed high treatment capacity of saline wastewater. Our findings confirm that combined indicators of contamination, such as chemical oxygen demand (COD), alone do not allow evaluating potential toxic influence of wastewater. Obtained results allow identifying key inhibitory substances in pharmaceutical wastewater and evaluating potential impact of new wastewater streams or increased loading on biological treatment system. Proposed method is sensitive and cost effective and has potential for practical implementation in multiproduct pharmaceutical wastewater biological treatment plants.

scholarly journals The Use of Motion Analysis as Particle Biomarkers in Lensless Optofluidic Projection Imaging for Point of Care Urine Analysis

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Jessica Kun ◽  
Marek Smieja ◽  
Bo Xiong ◽  
Leyla Soleymani ◽  
Qiyin Fang
Keyword(s):  
Trichomonas Vaginalis ◽  
Moving Objects ◽  
Urine Analysis ◽  
Point Of Care ◽  
White Blood Cells ◽  
Diagnostic Methods ◽  
Particle Analysis ◽  
Term Care ◽  
Wide Range ◽  
Urine Testing

AbstractUrine testing is an essential clinical diagnostic tool. The presence of urine sediments, typically analyzed through microscopic urinalysis or cell culture, can be indicative of many diseases, including bacterial, parasitic, and yeast infections, as well as more serious conditions like bladder cancer. Current urine analysis diagnostic methods are usually centralized and limited by high cost, inconvenience, and poor sensitivity. Here, we developed a lensless projection imaging optofluidic platform with motion-based particle analysis to rapidly detect urinary constituents without the need for concentration or amplification through culture. A removable microfluidics channel ensures that urine samples do not cross contaminate and the lens-free projection video is captured and processed by a low-cost integrated microcomputer. A motion tracking and analysis algorithm is developed to identify and track moving objects in the flow. Their motion characteristics are used as biomarkers to detect different urine species in near real-time. The results show that this technology is capable of detection of red and white blood cells, Trichomonas vaginalis, crystals, casts, yeast and bacteria. This cost-effective device has the potential to be implemented for timely, point-of-care detection of a wide range of disorders in hospitals, clinics, long-term care homes, and in resource-limited regions.

scholarly journals Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP)

2020 ◽  
Author(s):  
Lukas Bokelmann ◽  
Olaf Nickel ◽  
Tomislav Maricic ◽  
Svante Paabo ◽  
Matthias Meyer ◽  
...  
Keyword(s):  
Point Of Care ◽  
Rna Extraction ◽  
Lamp Assay ◽  
Cost Effective ◽  
Diagnostic Methods ◽  
Current Standard ◽  
Laboratory Equipment ◽  
Hybridization Capture ◽  
Level Of Automation ◽  
High Level

Efforts to contain the spread of SARS-CoV-2 have spurred the need for reliable, rapid, and cost-effective diagnostic methods which can easily be applied to large numbers of people. However, current standard protocols for the detection of viral nucleic acids while sensitive, require a high level of automation, sophisticated laboratory equipment and trained personnel to achieve throughputs that allow whole communities to be tested on a regular basis. Here we present Cap-iLAMP (capture and improved loop-mediated isothermal amplification). This method combines a hybridization capture-based RNA extraction of non-invasive gargle lavage samples to concentrate samples and remove inhibitors with an improved colorimetric RT-LAMP assay and smartphone-based color scoring. Cap-iLAMP is compatible with point-of-care testing and enables the detection of SARS-CoV-2 positive samples in less than one hour. In contrast to direct addition of the sample to improved LAMP (iLAMP), Cap-iLAMP does not result in false positives and single infected samples can be detected in a pool among 25 uninfected samples, thus reducing the technical cost per test to ~1 Euro per individual.

scholarly journals Cost-Effective Flexible CSRR-Based Sensor for Noninvasive Measurement of Permittivity of Biomaterials

2021 ◽  
Vol 10 (1) ◽  
pp. 26
Author(s):  
Faezeh Shanehsazzadeh ◽  
Nafise Azizi ◽  
Hosna Kazerooni Haghighat ◽  
Fatemeh Mashayekhi ◽  
Mehdi Fardmanesh
Keyword(s):  
Ring Resonator ◽  
Point Of Care ◽  
Cost Effective ◽  
Split Ring Resonator ◽  
Point Of Care Testing ◽  
Split Ring ◽  
Tissue Samples ◽  
Complementary Split Ring Resonator ◽  
Microwave Sensor ◽  
Wide Range

A novel, cost-effective, flexible microwave sensor is proposed to facilitate point-of-care testing (POCT) methods for medical diagnosis. The sensor is based on the complementary split-ring resonator (CSRR) to accurately measure the permittivity of biomaterials over a wide range of frequencies. This ability can be used to characterize various materials under test (MUT) such as blood, saliva, tissue samples, etc. The flexibility of the proposed sensor means that it can be used when the accessibility of the sample has technical difficulties, such as on curved surfaces. Firstly, the optimized structure and coupling to the readout transmission line are evaluated using finite element method (FEM) simulations. Then, the prototype of the optimized structure is fabricated on a thin polydimethylsiloxane (PDMS) substrate as a biocompatible economical polymer, and aluminium is carefully chosen for the fabrication of CSRR and readout parts. The proposed flexible sensor is tested and compared to conventional rigid CSRR sensors. The proposed structure withstood the different bending positions well, and also showed an improvement in the results for curved MUT.

DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing

2019 ◽  
Vol 36 (1) ◽  
pp. 26-32
Author(s):  
Davoud Torkamaneh ◽  
Jérôme Laroche ◽  
Brian Boyle ◽  
François Belzile
Keyword(s):  
Cost Effective ◽  
Read Depth ◽  
Supplementary Information ◽  
Nucleotide Polymorphisms ◽  
Reduced Representation ◽  
Sequencing Platform ◽  
Genome Complexity ◽  
Wide Range ◽  
Broad Array ◽  
Reduced Representation Sequencing

Abstract Motivation Identification of DNA sequence variations such as single nucleotide polymorphisms (SNPs) is a fundamental step toward genetic studies. Reduced-representation sequencing methods have been developed as alternatives to whole genome sequencing to reduce costs and enable the analysis of many more individual. Amongst these methods, restriction site associated sequencing (RSAS) methodologies have been widely used for rapid and cost-effective discovery of SNPs and for high-throughput genotyping in a wide range of species. Despite the extensive improvements of the RSAS methods in the last decade, the estimation of the number of reads (i.e. read depth) required per sample for an efficient and effective genotyping remains mostly based on trial and error. Results Herein we describe a bioinformatics tool, DepthFinder, designed to estimate the required read counts for RSAS methods. To illustrate its performance, we estimated required read counts in six different species (human, cattle, spruce budworm, salmon, barley and soybean) that cover a range of different biological (genome size, level of genome complexity, level of DNA methylation and ploidy) and technical (library preparation protocol and sequencing platform) factors. To assess the prediction accuracy of DepthFinder, we compared DepthFinder-derived results with independent datasets obtained from an RSAS experiment. This analysis yielded estimated accuracies of nearly 94%. Moreover, we present DepthFinder as a powerful tool to predict the most effective size selection interval in RSAS work. We conclude that DepthFinder constitutes an efficient, reliable and useful tool for a broad array of users in different research communities. Availability and implementation https://bitbucket.org/jerlar73/DepthFinder Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Towards Point-of-Care Heart Failure Diagnostic Platforms: BNP and NT-proBNP Biosensors

Sensors ◽  
2019 ◽  
Vol 19 (22) ◽  
pp. 5003 ◽  
Author(s):  
Hussein Alawieh ◽  
Trishia El Chemaly ◽  
Samir Alam ◽  
Massoud Khraiche
Keyword(s):  
Heart Failure ◽  
Performance Metrics ◽  
Point Of Care ◽  
Cost Effective ◽  
Diagnostic Techniques ◽  
Diagnostic Methods ◽  
Cardiac Biomarkers ◽  
Healthcare Sector ◽  
Effective Manner ◽  
Potential Integration

Heart failure is a class of cardiovascular diseases that remains the number one cause of death worldwide with a substantial economic burden of around $18 billion incurred by the healthcare sector in 2017 due to heart failure hospitalization and disease management. Although several laboratory tests have been used for early detection of heart failure, these traditional diagnostic methods still fail to effectively guide clinical decisions, prognosis, and therapy in a timely and cost-effective manner. Recent advances in the design and development of biosensors coupled with the discovery of new clinically relevant cardiac biomarkers are paving the way for breakthroughs in heart failure management. Natriuretic neurohormone peptides, B-type natriuretic peptide (BNP) and N-terminal prohormone of BNP (NT-proBNP), are among the most promising biomarkers for clinical use. Remarkably, they result in an increased diagnostic accuracy of around 80% owing to the strong correlation between their circulating concentrations and different heart failure events. The latter has encouraged research towards developing and optimizing BNP biosensors for rapid and highly sensitive detection in the scope of point-of-care testing. This review sheds light on the advances in BNP and NT-proBNP sensing technologies for point-of-care (POC) applications and highlights the challenges of potential integration of these technologies in the clinic. Optical and electrochemical immunosensors are currently used for BNP sensing. The performance metrics of these biosensors—expressed in terms of sensitivity, selectivity, reproducibility, and other criteria—are compared to those of traditional diagnostic techniques, and the clinical applicability of these biosensors is assessed for their potential integration in point-of-care diagnostic platforms.

A Practical Access to Functionalized Alkyl Sulfinates

Synlett ◽  
2018 ◽  
Vol 29 (12) ◽  
pp. 1622-1626
Author(s):  
M. Haddad ◽  
P. Phansavath ◽  
V. Ratovelomanana-Vidal ◽  
C. Tran ◽  
B. Flamme ◽  
...  
Keyword(s):  
Functional Groups ◽  
Cost Effective ◽  
Good Tolerance ◽  
Mild Conditions ◽  
Cost Effective Method ◽  
Wide Range

We describe herein a three-step synthesis of aliphatic sulfinates. This cost-effective method involves the use of 2-mercaptobenzothiazole under mild conditions and exhibits good yields (up to 78% over three steps). This approach provides an access to a wide range of functionalized sulfinates. A good tolerance with respect to diverse functional groups (alkene, alkyne, ether, acetal) was also noted.

scholarly journals A SIMPLE CO2 EXTRACTION METHOD FOR RADIOCARBON ANALYSES OF DISSOLVED INORGANIC CARBON IN WATER SAMPLES WITHOUT A CARRIER GAS

Radiocarbon ◽  
2021 ◽  
pp. 1-15
Author(s):  
Hiroshi A Takahashi ◽  
Hiroko Handa ◽  
Masayo Minami
Keyword(s):  
Water Samples ◽  
Extraction Method ◽  
Inorganic Carbon ◽  
Dissolved Inorganic Carbon ◽  
Cost Effective ◽  
Carrier Gas ◽  
Vacuum Line ◽  
Cost Effective Method ◽  
Wide Range ◽  
Cryogenic Trapping

ABSTRACT We developed a simple and cost-effective method for extracting carbon from dissolved inorganic carbon (DIC) in water samples without a carrier gas. This method only slightly modifies the existing vacuum line for CO2 purification in radiocarbon research laboratories by connecting several reservoirs and traps. The procedure consists of repeated cycles of CO2 extraction from water into the headspace of the reaction container, expansion of the extracted gas into the vacuum line, and cryogenic trapping of CO2. High CO2 yield (∼98%) was obtained from a variety of water samples with a wide range of DIC concentrations (0.4–100 mmol·L−1, in the case of 1.2 mgC). The δ13C fractionation depended on the CO2 yield, while the 14C concentration was constant within the error range, regardless of the CO2 yield. The average δ13C discrepancy between the results of this method and direct analyses made using the GC-IRMS was 0.02 ± 0.06‰. The standard deviations (1σ) in fraction of modern carbon (F14C) ranged from 0.0002 to 0.0004 for waters below 0.01 of F14C, and below 0.8% of F14C values for waters above 0.1. We conclude that this method is useful for effectively extracting CO2 from DIC in water and yields accurate 14C data.

scholarly journals A Simple Colorimetric Molecular Detection of Novel Coronavirus (COVID-19), an Essential Diagnostic Tool for Pandemic Screening

2020 ◽  
Author(s):  
Pazhanimuthu Annamalai ◽  
Madhu Kanta ◽  
Pazhanivel Ramu ◽  
Baskar Ravi ◽  
Kokilavani Veerapandian ◽  
...  
Keyword(s):  
Molecular Detection ◽  
Point Of Care ◽  
Lamp Assay ◽  
High Sensitivity ◽  
Cost Effective ◽  
Cost Effective Method ◽  
Recent Outbreak ◽  
Pcr Method ◽  
Novel Coronavirus ◽  
Virus Isolates

AbstractThe recent outbreak of the newly emerged novel coronavirus (SARS-CoV-2) presents a big challenge for public health laboratories as virus isolates are not available while there is an increasing evidence that the epidemic is more widespread than initially thought, as well as spreading internationally across borders through travellers does already happen warranting a methodology for the rapid detection of the infection to control SARS-CoV-2. Aim: We intended to develop and deploy a robust and rapid diagnostic methodology using LAMP assay for use in point of care settings to detect SARS-COV-2 infection. Methodology: In the present study, we have developed a validated rapid diagnostic procedure to detect SARS-CoV-2 using LAMP assay, its design relying on isothermal amplification of the nucleic acids of the SARS-CoV-2. Results: The LAMP assay developed detects SARS-CoV-2 infection rapidly with high sensitivity and reliability. The data generated by LAMP assay were comparable and at par with the data generated by real-time PCR method. Conclusion: The present study demonstrates that the LAMP assay developed was a rapid, reliable, sensitive and cost effective method to detect SARS-CoV-2 infection in a point of care as well as in laboratory settings.

scholarly journals Nanopore sequencing of RNA and cDNA molecules in Escherichia coli

RNA ◽  
2021 ◽  
pp. rna.078937.121
Author(s):  
Felix Grünberger ◽  
Sébastien Ferreira-Cerca ◽  
Dina Grohmann
Keyword(s):  
Escherichia Coli ◽  
Rna Sequencing ◽  
Single Molecule ◽  
High Throughput Sequencing ◽  
Model Organism ◽  
Cost Effective ◽  
Rna Seq ◽  
Sequencing Platform ◽  
Quantitative Measurements ◽  
Oxford Nanopore

High-throughput sequencing dramatically changed our view of transcriptome architectures and allowed for ground-breaking discoveries in RNA biology. Recently, sequencing of full-length transcripts based on the single-molecule sequencing platform from Oxford Nanopore Technologies (ONT) was introduced and is widely employed to sequence eukaryotic and viral RNAs. However, experimental approaches implementing this technique for prokaryotic transcriptomes remain scarce. Here, we present an experimental and bioinformatic workflow for ONT RNA-seq in the bacterial model organism Escherichia coli, which can be applied to any microorganism. Our study highlights critical steps of library preparation and computational analysis and compares the results to gold standards in the field. Furthermore, we comprehensively evaluate the applicability and advantages of different ONT-based RNA sequencing protocols, including direct RNA, direct cDNA, and PCR-cDNA. We find that (PCR)-cDNA-seq offers improved yield and accuracy compared to direct RNA sequencing. Notably, (PCR)-cDNA-seq is suitable for quantitative measurements and can be readily used for simultaneous and accurate detection of transcript 5'and 3' boundaries, analysis of transcriptional units and transcriptional heterogeneity. In summary, based on our comprehensive study, we show that Nanopore RNA-seq to be a ready-to-use tool allowing rapid, cost-effective, and accurate annotation of multiple transcriptomic features. Thereby Nanopore RNA-seq holds the potential to become a valuable alternative method for RNA analysis in prokaryotes.

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