scholarly journals 3C Based DNA Hybridization Method for Chromosomal Translocation Screening

2021 ◽  
Author(s):  
Moloud Absalan ◽  
Zahra Jabbarpour ◽  
Mohammad Hossein Ghahremani ◽  
Elaheh Motevaseli ◽  
Fatemeh Mahmoudian ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Colorimetric Assay ◽  
Chromosomal Translocation ◽  
High Specificity ◽  
Thiol Group ◽  
Dna Probes ◽  
Lymphocytic Leukemia ◽  
Diagnostic Tools ◽  
Color Intensity ◽  
Specificity And Sensitivity

Abstract Background: DNA probes have been widely used as diagnostic tools for chromosomal translocations in malignancies. PCR-based methods often fail to detect translocations such as MYC/TRD in chronic lymphocytic leukemia. In addition, microscopic techniques cannot be helpful due to size detection limitations. This study sought to design a screening tool using immobilized ssDNA probes on a nitrocellulose membrane followed by 3C library fragments hybridization. Results: Hence, we focused on developing a suitable 27 bp specific probe for the juxtaposed region of MYC and TRD. Colloidal gold nanoparticles (AuNP) functionalized translocation fragments of the MYC gene with a thiol group (MYC-AuNP-probe). Then TRD-probes were immobilized on nitrocellulose surface to detect TRD/MYC translocation in the SKW3 cells. Hybridization between DNA probes and 3C-library fragments of SKW3 cells was determined by color intensity. Optimal hybridization of the 3C library sample of the cell line to TRD-probe and MYC-AuNP-probe showed higher color intensity due to their convenient proximity to the juxtaposed region compared with normal cells. Conclusions: Our results demonstrated that DNA hybridization colorimetric assay could be a helpful technique in chromosomal rearrangements screening. Accordingly, the combination of 3C based techniques and DNA-DNA hybridization can identify cancer cells with high specificity and sensitivity.

scholarly journals 3C based DNA hybridization method for chromosomal translocation screening

2021 ◽  
Author(s):  
Moloud Absalan ◽  
Zahra Jabbarpour ◽  
Mohammad Hossein Ghahremani ◽  
Elahe Motevaseli ◽  
Fatemeh Mahmoudian ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Colorimetric Assay ◽  
Chromosomal Translocation ◽  
High Specificity ◽  
Thiol Group ◽  
Dna Probes ◽  
Lymphocytic Leukemia ◽  
Diagnostic Tools ◽  
Color Intensity ◽  
Specificity And Sensitivity

Abstract Background DNA probes have been widely used as diagnostic tools for chromosomal translocations in malignancies. PCR-based methods often fail to detect translocations such as MYC/TRD in chronic lymphocytic leukemia. In addition, microscopic techniques cannot be helpful due to size detection limitations. This study sought to design a screening tool using immobilized ssDNA probes on a nitrocellulose membrane followed by 3C library fragments hybridization. Results Hence, we focused on developing a suitable 27 bp specific probe for the juxtaposed region of MYC and TRD. Colloidal gold nanoparticles (AuNP) functionalized translocation fragments of the MYC gene with a thiol group (MYC-AuNP-probe). Then TRD-probes were immobilized on nitrocellulose surface to detect TRD/MYC translocation in the SKW3 cells. Hybridization between DNA probes and 3C-library fragments of SKW3 cells was determined by color intensity. Optimal hybridization of the 3C library sample of the cell line to TRD-probe and MYC-AuNP-probe showed higher color intensity due to their convenient proximity to the juxtaposed region compare with normal cells. Conclusions Our results demonstrated that DNA hybridization colorimetric assay could be a helpful technique in chromosomal rearrangements screening. Accordingly, the combination of 3C based techniques and DNA-DNA hybridization can identify cancer cells with high specificity and sensitivity.

scholarly journals Validation and performance of a quantitative IgG assay for the screening of SARS-CoV-2 antibodies

2020 ◽  
Author(s):  
Ana M. Espino ◽  
Petraleigh Pantoja ◽  
Carlos A. Sariol
Keyword(s):  
Drug Administration ◽  
Vaccine Development ◽  
High Specificity ◽  
Diagnostic Tools ◽  
Predictive Values ◽  
Federal Drug Administration ◽  
Current Period ◽  
Specificity And Sensitivity ◽  
And Performance ◽  
Development And Validation

AbstractThe current COVID-19 epidemic imposed an unpreceded challenge to the scientific community in terms of treatment, epidemiology, diagnosis, social interaction, fiscal policies and many other areas. The development of accurate and reliable diagnostic tools (high specificity and sensitivity) is crucial in the current period, the near future and in the long term. These assays should provide guidance to identify immune presumptive protected persons, potential plasma, and/or B cell donors and vaccine development among others. Also, such assays will be contributory in supporting prospective and retrospective studies to identify the prevalence and incidence of COVID-19 and to characterize the dynamics of the immune response. As of today, only thirteen serological assays have received the Emergency Use Authorization (EUA) by the U.S. Federal Drug Administration (FDA). In this work we describe the development and validation of a quantitative IgG enzyme-linked immunoassay (ELISA) using the recombinant SARS-CoV-2 Spike Protein S1 domain, containing the receptor-binding domain (RBD), showing 98% sensitivity, 98.9% specificity and positive and negative predictive values of 100% and 99.2%, respectively. The assay showed to be useful to test for SARS-CoV-2 IgG antibodies in plasma samples from COVID-19-recovered subjects as potential donors for plasmapheresis. This assay is currently under review by the Federal Drug Administration for an Emergency Use Authorization request (Submission Number EUA201115).

Graphene-Based Hall Effect Biosensor for Improved Specificity and Sensitivity of Label-Free DNA Detection

NANO ◽  
2020 ◽  
Vol 15 (07) ◽  
pp. 2050088
Author(s):  
Naiyuan Cui ◽  
Fei Wang ◽  
Hanyuan Ding
Keyword(s):  
Hall Effect ◽  
Dna Hybridization ◽  
Chemical Vapor ◽  
High Specificity ◽  
Label Free ◽  
Complementary Dna ◽  
Mismatched Dna ◽  
Specificity And Sensitivity ◽  
Label Free Detection ◽  
Detection Of Biomolecules

There is a broad interest in using graphene or graphene oxide (GO) sheets as a transducer for selective and label-free detection of biomolecules such as DNA, tumor marker, biological ions, etc. Here, a chemical vapor deposition (CVD) graphene-based Hall effect biosensor used for ultrasensitive label-free detection of DNA via DNA hybridization is reported. Hall effect measurements based on the Van der Pauw method are used to perform single-base sequence selective detection of DNA on graphene sheets, which are prepared by CVD. The mobility decreases and the sheet resistance increases with the adding of either complementary or one-base mismatched DNA to the graphene device. The hole carrier concentration of the graphene devices increases apparently with the addition of complementary DNA while it is hardly affected by the one-base mismatched DNA. The detection limit as low as 1[Formula: see text]pM was realized with a linear range from 1[Formula: see text]pM to 100[Formula: see text]nM. Moreover, the Hall effect biosensor was able to distinguish the complementary DNA from one-base mismatched DNA with a high specificity of [Formula: see text]6.2 which is almost two orders of magnitude higher than that of the previously reported graphene biosensors based on DNA–DNA hybridization.

scholarly journals Immunoglobulin AMG Anti Natural Disaccharide Octyl - Leprosy IDRI Diagnostic (NDO-LID) Serologic Test for Leprosy Diagnosis: a Pilot Study

2019 ◽  
Author(s):  
Bayu Bijaksana Rumondor ◽  
Anisha Callista Prakoeswa ◽  
Meva Nareza Trianita ◽  
I. Iswahyudi ◽  
Nanny Herwanto ◽  
...  
Keyword(s):  
Clinical Signs ◽  
Public Health Problem ◽  
High Specificity ◽  
Diagnostic Tools ◽  
Great Promise ◽  
Serologic Test ◽  
Diagnostic Potential ◽  
Specificity And Sensitivity ◽  
Leprosy Patients ◽  
Antibody Titers

Leprosy remains a public health problem in Indonesia. Diagnostic tools have been developed in order to aid early diagnosis and prompt treatment. Phenolic glycolipid (PGL)-1 has been considered as a good candidate for leprosy diagnosis but has been found to have several limitations. More recently, the conjugation between natural disaccharide octyl (NDO) and leprosy IDRI diagnostic (LID)-1, known as NDO-LID, shows great promise because of its high specificity and sensitivity and its ability to detect leprosy before any clinical signs are present. The test incorporates the detection of IgM antibodies towards NDO and IgG antibodies towards LID-1. This study aimed to show the profile of IgM, IgG, and IgAMG antibody titers against NDO-LID to further discover its diagnostic potential. Sera from eight new leprosy patients from Surabaya, Indonesia were evaluated using ELISA detecting levels of IgG, IgM and IgAMG antibodies against NDO-LID antigen. Skin slit biopsy was also taken for smear and histopathology test. This study shows that the titer levels IgAMG anti NDO-LID were consistent with the results from smear and were consistently higher compared to IgM or IgG titer alone. IgAMG might have the potential to improve the sensitivity of NDO-LID serologic tests but further investigation is needed.

Nanofluorescence Probes to Detect miR-192/Integrin Alpha 1 and Their Correlations with Retinoblastoma

2021 ◽  
Vol 17 (11) ◽  
pp. 2176-2185
Author(s):  
Yu Gao ◽  
Hongjun Zhang ◽  
Shaofei Zhao ◽  
Daotong He ◽  
Cao Gu
Keyword(s):  
Physicochemical Properties ◽  
Cell Lines ◽  
High Specificity ◽  
Dna Probes ◽  
Infiltration Capacity ◽  
Promoting Effect ◽  
Specificity And Sensitivity ◽  
Early Biomarker ◽  
Apoptosis Level

We developed a novel nanostructure DNA probe for the in situ detection of ITGA1 and miR-192 in retinoblastoma (RB) and to study the correlation between ITGA1 and miR-192 expression and RB development. ITGA1 and miR-192 nanostructure DNA probes were carried by silica particles and coated by dioleoyl-trimethy-lammonium-propane, which enhances their organizational compatibility and infiltration capacity. This probe has stable physicochemical properties and high specificity and sensitivity to detect ITGA1 and miR-192 in situ both in RB cell lines and RB tissues. Using ITGA1 and miR-192 nanostructure DNA probes in RB tissue and cell lines, we found that the expression of ITAG1 drastically increased, but to the contrary, miR-192 was not expressed. After transfection, ITGA1 and miR-192 were overexpressed or silenced in RB116 cells, and we found that ITGA1 could effectively increase the activity and invasion of this RB cell line and reduce its apoptosis level, while miR-192 antagonized this tumor-promoting effect. Therefore, miR-192 can be used as an early biomarker of RB, and ITGA1 may be a new prognostic marker and therapeutic target for the treatment of RB.

Prospective Application of Aptamer-based Assays and Therapeutics in Bloodstream Infections

2020 ◽  
Vol 20 (10) ◽  
pp. 831-840
Author(s):  
Weibin Li
Keyword(s):  
Pathogenic Bacteria ◽  
Genetic Diagnosis ◽  
Bloodstream Infections ◽  
High Specificity ◽  
Peptide Sequence ◽  
High Morbidity ◽  
Specificity And Sensitivity ◽  
Prospective Application ◽  
Small Molecule Therapeutics

Sepsis is still a severe health problem worldwide with high morbidity and mortality. Blood bacterial culture remains the gold standard for the detection of pathogenic bacteria in bloodstream infections, but it is time-consuming, and both the sophisticated equipment and well-trained personnel are required. Immunoassays and genetic diagnosis are expensive and limited to specificity and sensitivity. Aptamers are single-stranded deoxyribonucleic acid (ssDNA) and ribonucleic acid (RNA) oligonucleotide or peptide sequence generated in vitro based on the binding affinity of aptamer-target by a process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). By taking several advantages over monoclonal antibodies and other conventional small-molecule therapeutics, such as high specificity and affinity, negligible batch-to-batch variation, flexible modification and production, thermal stability, low immunogenicity and lack of toxicity, aptamers are presently becoming promising novel diagnostic and therapeutic agents. This review describes the prospective application of aptamerbased laboratory diagnostic assays and therapeutics for pathogenic bacteria and toxins in bloodstream infections.

scholarly journals SARS-CoV-2 specific antibody and neutralization assays reveal the wide range of the humoral immune response to virus

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Mikail Dogan ◽  
Lina Kozhaya ◽  
Lindsey Placek ◽  
Courtney Gunter ◽  
Mesut Yigit ◽  
...  
Keyword(s):  
Specific Antibody ◽  
Neutralizing Antibodies ◽  
Vaccine Development ◽  
High Specificity ◽  
Spike Protein ◽  
Humoral Immune ◽  
Specificity And Sensitivity ◽  
Wide Range ◽  
Specific Igg ◽  
Negative Controls

AbstractDevelopment of antibody protection during SARS-CoV-2 infection is a pressing question for public health and for vaccine development. We developed highly sensitive SARS-CoV-2-specific antibody and neutralization assays. SARS-CoV-2 Spike protein or Nucleocapsid protein specific IgG antibodies at titers more than 1:100,000 were detectable in all PCR+ subjects (n = 115) and were absent in the negative controls. Other isotype antibodies (IgA, IgG1-4) were also detected. SARS-CoV-2 neutralization was determined in COVID-19 and convalescent plasma at up to 10,000-fold dilution, using Spike protein pseudotyped lentiviruses, which were also blocked by neutralizing antibodies (NAbs). Hospitalized patients had up to 3000-fold higher antibody and neutralization titers compared to outpatients or convalescent plasma donors. Interestingly, some COVID-19 patients also possessed NAbs against SARS-CoV Spike protein pseudovirus. Together these results demonstrate the high specificity and sensitivity of our assays, which may impact understanding the quality or duration of the antibody response during COVID-19 and in determining the effectiveness of potential vaccines.

scholarly journals Highly Sensitive Fluorescent Detection of Acetylcholine Based on the Enhanced Peroxidase-Like Activity of Histidine Coated Magnetic Nanoparticles

Nanomaterials ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1207
Author(s):  
Hong Jae Cheon ◽  
Quynh Huong Nguyen ◽  
Moon Il Kim
Keyword(s):  
Magnetic Nanoparticles ◽  
High Sensitivity ◽  
High Specificity ◽  
Choline Oxidase ◽  
Fluorescent Detection ◽  
One Pot ◽  
Site Structure ◽  
Specificity And Sensitivity ◽  
Highly Sensitive ◽  
Peroxidase Mimics

Inspired by the active site structure of natural horseradish peroxidase having iron as a pivotal element with coordinated histidine residues, we have developed histidine coated magnetic nanoparticles (His@MNPs) with relatively uniform and small sizes (less than 10 nm) through one-pot heat treatment. In comparison to pristine MNPs and other amino acid coated MNPs, His@MNPs exhibited a considerably enhanced peroxidase-imitating activity, approaching 10-fold higher in catalytic reactions. With the high activity, His@MNPs then were exploited to detect the important neurotransmitter acetylcholine. By coupling choline oxidase and acetylcholine esterase with His@MNPs as peroxidase mimics, target choline and acetylcholine were successfully detected via fluorescent mode with high specificity and sensitivity with the limits of detection down to 200 and 100 nM, respectively. The diagnostic capability of the method is demonstrated by analyzing acetylcholine in human blood serum. This study thus demonstrates the potential of utilizing His@MNPs as peroxidase-mimicking nanozymes for detecting important biological and clinical targets with high sensitivity and reliability.

scholarly journals Identification of sixteen novel candidate genes for late onset Parkinson’s disease

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Alessandro Gialluisi ◽  
Mafalda Giovanna Reccia ◽  
Nicola Modugno ◽  
Teresa Nutile ◽  
Alessia Lombardi ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Candidate Genes ◽  
Rare Variants ◽  
Late Onset ◽  
High Specificity ◽  
Diagnostic Tools ◽  
Multi Stage ◽  
Whole Exome ◽  
Family Based

Abstract Background Parkinson’s disease (PD) is a neurodegenerative movement disorder affecting 1–5% of the general population for which neither effective cure nor early diagnostic tools are available that could tackle the pathology in the early phase. Here we report a multi-stage procedure to identify candidate genes likely involved in the etiopathogenesis of PD. Methods The study includes a discovery stage based on the analysis of whole exome data from 26 dominant late onset PD families, a validation analysis performed on 1542 independent PD patients and 706 controls from different cohorts and the assessment of polygenic variants load in the Italian cohort (394 unrelated patients and 203 controls). Results Family-based approach identified 28 disrupting variants in 26 candidate genes for PD including PARK2, PINK1, DJ-1(PARK7), LRRK2, HTRA2, FBXO7, EIF4G1, DNAJC6, DNAJC13, SNCAIP, AIMP2, CHMP1A, GIPC1, HMOX2, HSPA8, IMMT, KIF21B, KIF24, MAN2C1, RHOT2, SLC25A39, SPTBN1, TMEM175, TOMM22, TVP23A and ZSCAN21. Sixteen of them have not been associated to PD before, were expressed in mesencephalon and were involved in pathways potentially deregulated in PD. Mutation analysis in independent cohorts disclosed a significant excess of highly deleterious variants in cases (p = 0.0001), supporting their role in PD. Moreover, we demonstrated that the co-inheritance of multiple rare variants (≥ 2) in the 26 genes may predict PD occurrence in about 20% of patients, both familial and sporadic cases, with high specificity (> 93%; p = 4.4 × 10− 5). Moreover, our data highlight the fact that the genetic landmarks of late onset PD does not systematically differ between sporadic and familial forms, especially in the case of small nuclear families and underline the importance of rare variants in the genetics of sporadic PD. Furthermore, patients carrying multiple rare variants showed higher risk of manifesting dyskinesia induced by levodopa treatment. Conclusions Besides confirming the extreme genetic heterogeneity of PD, these data provide novel insights into the genetic of the disease and may be relevant for its prediction, diagnosis and treatment.

scholarly journals Serum MicroRNA Signature as a Diagnostic and Therapeutic Marker in Patients with Psoriatic Arthritis

2020 ◽  
Vol 47 (12) ◽  
pp. 1760-1767
Author(s):  
Sarah M. Wade ◽  
Trudy McGarry ◽  
Siobhan C. Wade ◽  
Ursula Fearon ◽  
Douglas J. Veale
Keyword(s):  
Psoriatic Arthritis ◽  
Characteristic Curve ◽  
High Specificity ◽  
Serum Samples ◽  
Rna Molecules ◽  
Serum Mirna ◽  
Serum Microrna ◽  
Specificity And Sensitivity ◽  
European League Against Rheumatism ◽  
Noninvasive Markers

ObjectiveMicroRNA (miRNA) are small endogenous regulatory RNA molecules that have emerged as potential therapeutic targets and biomarkers in autoimmunity. Here, we investigated serum miRNA levels in patients with psoriatic arthritis (PsA) and further assessed a serum miRNA signature in therapeutic responder versus nonresponder PsA patients.MethodsSerum samples were collected from healthy controls (HC; n = 20) and PsA patients (n = 31), and clinical demographics were obtained. To examine circulatory miRNA in serum from HC and PsA patients, a focused immunology miRNA panel was analyzed utilizing a miRNA Fireplex assay (FirePlex Bioworks Inc.). MiRNA expression was further assessed in responders versus nonresponders according to the European League Against Rheumatism response criteria.ResultsSix miRNA (miR-221-3p, miR-130a-3p, miR-146a-5p, miR-151-5p, miR-26a-5p, and miR-21-5p) were significantly higher in PsA compared to HC (all P < 0.05), with high specificity and sensitivity determined by receiver-operating characteristic curve analysis. Analysis of responder versus nonresponders demonstrated higher baseline levels of miR-221-3p, miR-130a-3p, miR-146a-5p, miR-151-5p, and miR-26a-5p were associated with therapeutic response.ConclusionThis study identified a 6-serum microRNA signature that could be attractive candidates as noninvasive markers for PsA and may help to elucidate the disease pathogenesis.

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