scholarly journals Automated DNA Extraction Monitoring System Based on MTConnect Technology

2021 ◽  
Vol 11 (2) ◽  
pp. 684
Author(s):  
Sang-Ho Han ◽  
Ae-Ja Park ◽  
Ah-Reum Park ◽  
Mun-Ho Ryu
Keyword(s):  
Dna Extraction ◽  
Point Of Care ◽  
Molecular Genetic ◽  
Disease Diagnosis ◽  
Extraction Process ◽  
Raspberry Pi ◽  
Client Application ◽  
Extensible Markup ◽  
Amplification Process ◽  
Automated Dna Extraction

MTConnect standard technology provides simplicity, flexibility, and scalability in integrating various equipment and operating systems and enabling accurate and consistent data collection from any MTConnect-compatible system. Using MTConnect technology, it is possible to immediately identify the cause of a problem and respond quickly when a problem occurs. Molecular genetic diagnostic point-of-care testing (POCT) devices have received attention in recent years because they enable rapid disease diagnosis. A molecular genetic diagnostic POCT device is under development by the authors. The system consists of a gene extraction process and a real-time PCR-based gene amplification process. In this study, we propose and demonstrate a system based on MTConnect technology to monitor an automated DNA extraction process. The proposed system consists of an automated DNA extraction system, an MTConnect adapter, an MTConnect agent, and a client application. The adapter and agent were developed on a Raspberry Pi single-board computer. The agent publishes the collected data in Extensible Markup Language (XML) format over a network. The performance and reliability of the system were evaluated by verifying the request response time between the implemented system’s agent and the client application. The results demonstrate the feasibility of monitoring the DNA extraction process over a network.

scholarly journals Development of a dry-reagent mix-based polymerase chain reaction as a novel tool for the identification of Acinetobacter species and its comparison with conventional polymerase chain reaction

2018 ◽  
Vol 10 (01) ◽  
pp. 068-072 ◽  
Author(s):  
Raghavendra D. Kulkarni ◽  
Mukti Nath Mishra ◽  
Jeevanandam Mohanraj ◽  
Arun Chandrasekhar ◽  
G S. Ajantha ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Extraction ◽  
Sensitivity And Specificity ◽  
Point Of Care ◽  
Rpob Gene ◽  
Extraction Process ◽  
Resistant Bacteria ◽  
Chain Reaction ◽  
Acinetobacter Species ◽  
Polymerase Chain

Abstract BACKGROUND: Nosocomial infections are often caused by multidrug-resistant bacteria and the incidence is increasing. Acinetobacter, a Gram-negative bacillus, is commonly associated with the use of intravascular catheterization and airway intubation. Polymerase chain reaction (PCR) for identification of Acinetobacter baumannii from samples has been standardized that use conventional wet-reagent mix. We have designed and optimized a dry-reagent mix for identification of Acinetobacter species by PCR. The dry-reagent mix can be stored at room temperature, has less chances of contamination, and thus can be used at point-of-care diagnosis. AIM AND OBJECTIVE: The present work was focused on comparing the sensitivity and specificity of dry-reagent PCR mix over conventional wet-reagent PCR mix for identification of Acinetobacter species. MATERIALS AND METHODS: Conventional wet-reagent mix based and dry-reagent mix based PCR were carried out for the DNA isolated from Acinetobacter species. The latter was also applied directly on bacterial growth without prior DNA extraction process. Equal numbers of bacterial isolates other than Acinetobacter species were also subjected to identification by the same protocols for determining the sensitivity and specificity of the test. RESULTS: The Acinetobacter species showed amplification of the target rpoB gene and the band was observed at 397 bp. The dry-reagent PCR mix results matched completely with the conventional wet-reagent PCR mix assay. All the non-Acinetobacter isolates were negative for the PCR. This indicates that the test is highly specific. The dry-reagent mix also contained an enzyme resistant to PCR inhibitors and capable of amplifying DNA directly from cells. CONCLUSION: Performance of dry-reagent PCR mix without the need for DNA extraction and preparation of a PCR mix proved to be more sensitive and reduce the handling error, minimizes the time, manual work, and skilled labor.

scholarly journals Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 146
Author(s):  
Catarina Xavier ◽  
Mayra Eduardoff ◽  
Barbara Bertoglio ◽  
Christina Amory ◽  
Cordula Berger ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Method ◽  
Fragment Size ◽  
Molecular Genetic ◽  
Extraction Methods ◽  
Degraded Dna ◽  
Size Analysis ◽  
Dna Fragments ◽  
Dna Amount

The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.

Automated DNA extraction from frozen blood using the abbott M1000™ for HLA-DRB sequencing-based typing

2003 ◽  
Vol 64 (10) ◽  
pp. S95 ◽  
Author(s):  
Jeff T. Silva ◽  
Christine Y. Wong ◽  
JoAnn L. Dileanis ◽  
Chad M. Dunn ◽  
Chaka C. Impraim
Keyword(s):  
Dna Extraction ◽  
Automated Dna Extraction

Liquid Metal Ink Enabled Rapid Prototyping of Electrochemical Sensor for Wireless Glucose Detection on the Platform of Mobile Phone

2015 ◽  
Vol 9 (4) ◽  
Author(s):  
Liting Yi ◽  
Jingjing Li ◽  
Cangran Guo ◽  
Lei Li ◽  
Jing Liu
Keyword(s):  
Liquid Metal ◽  
Mobile Phone ◽  
Detection System ◽  
Point Of Care ◽  
Low Cost ◽  
Smart Phone ◽  
Disease Diagnosis ◽  
Glucose Detection ◽  
Sensor Material ◽  
Liquid Metal Ink

Pervasive detection of blood glucose is rather critical for the real-time disease diagnosis which would provide valuable guidance for treatment planning. Here, we established a health care platform for this purpose through incorporating the glucose detection with liquid metal printed sensor and the smart phone monitoring system together. The liquid metal ink composed of bismuth indium stannic (BIS) alloy was identified as an appropriate sensor material to be quickly written or printed on polyvinyl chloride (PVC) substrate at around 59 °C to form desired electrodes. It thus eliminated the complicated procedures as usually required in conventional sensor fabrication strategies. The alloy electrodes were characterized via cyclic voltammetry to demonstrate their practical functionality. Further, unlike using the commonly adopted glucometer, a smart phone was developed as the data acquisition and display center to help improve the portability and ubiquitous virtue of the detection system. Glucose solution in different concentrations was assayed via this platform. It was shown that there is a good linear relationship between the concentration and the integral value of the curve recorded by the mobile phone, which confirms the feasibility of the present method. This quantitative point-of-care system has pervasive feature and is expected to be very useful for future low-cost electrochemical detection.

scholarly journals Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities

AMB Express ◽  
2012 ◽  
Vol 2 (1) ◽  
pp. 60 ◽  
Author(s):  
Athenia L Oldham ◽  
Heather S Drilling ◽  
Blake W Stamps ◽  
Bradley S Stevenson ◽  
Kathleen E Duncan
Keyword(s):  
Dna Extraction ◽  
Oil Production ◽  
Automated Dna Extraction ◽  
Production Facilities

Evaluation of four commercial DNA extraction kits for the detection of Microsporidia and the importance of pretreatments in DNA isolation

2018 ◽  
Vol 63 (2) ◽  
pp. 386-392
Author(s):  
Ülfet Çetinkaya ◽  
Arzuv Charyyeva ◽  
Eda Sivcan ◽  
Esra Gürbüz
Keyword(s):  
Dna Extraction ◽  
Dna Isolation ◽  
High Sensitivity ◽  
Vero Cells ◽  
Disease Diagnosis ◽  
Glass Beads ◽  
Detectable Amount ◽  
Standard Procedures ◽  
Good Concentration ◽  
Thawing Processes

Abstract Microsporidia are obligate intracellular parasitic protozoa infecting the wide variety of hosts and are commonly known as a cause of chronic diarrhea particularly in immunocompromised individuals. Molecular-based tests have high sensitivity and specificity in disease diagnosis. However, these tests’ performance relies on the isolation of DNA in a good concentration. The standard procedures of commercial DNA extraction kits are usually insufficient for this purpose due to the tough walls of spores. This study aimed to test the significance of pretreatments by glass beads and freeze-thawing processes in DNA isolation from microsporidia spores. The parasite was cultured in growing Vero cells and seven serial dilutions were prepared from the collected spores. DNA purification was performed according to different tissue kits and stool kit procedures with and without any pretreatment. Concentration of isolated DNA samples were evaluated by real-time PCR. As a result of this study, the detectable amount of spores is minimum 10 spores in each 100 μ! sample according to the different tissue kits’ standard protocols. However, according to the DNA stool mini kit, the detectable amount of spores was found to be 1,000 spores/100 μl of stool sample when pretreated with both the freeze-thawing and glass beads methods.In conclusion, the current study demonstrated that further pretreatments are an essential process for DNA extraction from the stool specimens in order to avoid possible false negativity in the diagnosis of microsporidiosis.

Multiplex sample-to-answer detection of bacteria using a pipette-actuated capillary array comb with integrated DNA extraction, isothermal amplification, and smartphone detection

Lab on a Chip ◽  
2018 ◽  
Vol 18 (18) ◽  
pp. 2854-2864 ◽  
Author(s):  
Junhou Hui ◽  
Yin Gu ◽  
Yuanshou Zhu ◽  
Yanjing Chen ◽  
Shu-juan Guo ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Point Of Care ◽  
Isothermal Amplification ◽  
Point Of Care Testing ◽  
Capillary Array

A pipette-actuated capillary array comb system controlled and detected on a smartphone-based hand-held device was developed for point-of-care testing.

scholarly journals Urine and Free Immunoglobulin Light Chains as Analytes for Serodiagnosis of Hantavirus Infection

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 809 ◽  
Author(s):  
Hepojoki ◽  
Kareinen ◽  
Strandin ◽  
Vaheri ◽  
Holthöfer ◽  
...  
Keyword(s):  
Point Of Care ◽  
Resonance Energy ◽  
Kidney Injury ◽  
Hemorrhagic Fever ◽  
Disease Diagnosis ◽  
Antibody Detection ◽  
Light Chains ◽  
Hantavirus Infection ◽  
Protein L ◽  
Donor And Acceptor

Rapid point-of-care testing is a megatrend in infectious disease diagnosis. We have introduced a homogeneous immunoassay concept, which is based on the simultaneous binding of antigen and protein L to a given immunoglobulin molecule. The complex formation is detected utilizing time-resolved Förster resonance energy transfer between antigen-attached donor and acceptor-labeled protein L, hence the name LFRET. Here, we demonstrate that urine can be used as a sample matrix in LFRET-based serodiagnostics. We studied urine samples collected during the hospitalization and recovery of patients with acute Puumala orthohantavirus (PUUV) infection. We compared PUUV antibody-specific LFRET signals in urine to those in plasma, and found excellent correlation in the test outcomes The LFRET test from urine was positive in 40/40 patients with acute PUUV infection. PUUV causes a mild form of hemorrhagic fever with renal syndrome, characterized by acute kidney injury and proteinuria. Immunofluorescence and western blotting demonstrated PUUV-IgG and -IgA in urine, however, the presence of intact immunoglobulins did not fully explain the LFRET signals. We purified free light chains (FLCs) from both urine and serum of healthy volunteers and patients with acute PUUV infection, and verified the presence of antigen-specific FLCs. Antigen-specific FLCs provide a new means for non-invasive antibody detection and disease diagnosis.

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