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1.
Cell ; 184(15): 3899-3914.e16, 2021 07 22.
Article in English | MEDLINE | ID: mdl-34237254

ABSTRACT

The impact of the microbiome on HIV disease is widely acknowledged although the mechanisms downstream of fluctuations in microbial composition remain speculative. We detected rapid, dynamic changes in translocated microbial constituents during two years after cART initiation. An unbiased systems biology approach revealed two distinct pathways driven by changes in the abundance ratio of Serratia to other bacterial genera. Increased CD4 T cell numbers over the first year were associated with high Serratia abundance, pro-inflammatory innate cytokines, and metabolites that drive Th17 gene expression signatures and restoration of mucosal integrity. Subsequently, decreased Serratia abundance and downregulation of innate cytokines allowed re-establishment of systemic T cell homeostasis promoting restoration of Th1 and Th2 gene expression signatures. Analyses of three other geographically distinct cohorts of treated HIV infection established a more generalized principle that changes in diversity and composition of translocated microbial species influence systemic inflammation and consequently CD4 T cell recovery.


Subject(s)
Gastrointestinal Microbiome , HIV Infections/immunology , HIV Infections/microbiology , Antiretroviral Therapy, Highly Active , Biodiversity , CD4-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/immunology , Chemokines/blood , Cohort Studies , Glycolysis , HIV Infections/blood , HIV Infections/drug therapy , Humans , Inflammation/genetics , Inflammation/pathology , Mitochondria/metabolism , Monocytes/metabolism , Nucleic Acids/blood , Principal Component Analysis , Serratia/physiology , Th1 Cells/immunology , Th2 Cells/immunology , Transcription, Genetic , Uganda , Viral Load/immunology
2.
Proc Natl Acad Sci U S A ; 116(33): 16240-16249, 2019 08 13.
Article in English | MEDLINE | ID: mdl-31358642

ABSTRACT

Rapid and reliable detection of ultralow-abundance nucleic acids and proteins in complex biological media may greatly advance clinical diagnostics and biotechnology development. Currently, nucleic acid tests rely on enzymatic processes for target amplification (e.g., PCR), which have many inherent issues restricting their implementation in diagnostics. On the other hand, there exist no protein amplification techniques, greatly limiting the development of protein-based diagnosis. We report a universal biomolecule enrichment technique termed hierarchical nanofluidic molecular enrichment system (HOLMES) for amplification-free molecular diagnostics using massively paralleled and hierarchically cascaded nanofluidic concentrators. HOLMES achieves billion-fold enrichment of both nucleic acids and proteins within 30 min, which not only overcomes many inherent issues of nucleic acid amplification but also provides unprecedented enrichment performance for protein analysis. HOLMES features the ability to selectively enrich target biomolecules and simultaneously deplete nontargets directly in complex crude samples, thereby enormously enhancing the signal-to-noise ratio of detection. We demonstrate the direct detection of attomolar nucleic acids in urine and serum within 35 min and HIV p24 protein in serum within 60 min. The performance of HOLMES is comparable to that of nucleic acid amplification tests and near million-fold improvement over standard enzyme-linked immunosorbent assay (ELISA) for protein detection, being much simpler and faster in both applications. We additionally measured human cardiac troponin I protein in 9 human plasma samples, and showed excellent agreement with ELISA and detection below the limit of ELISA. HOLMES is in an unparalleled position to unleash the potential of protein-based diagnosis.


Subject(s)
Blood Proteins/isolation & purification , Nanotechnology/trends , Nucleic Acids/isolation & purification , Pathology, Molecular/methods , Blood Proteins/chemistry , Enzyme-Linked Immunosorbent Assay , HIV Core Protein p24/blood , HIV Core Protein p24/isolation & purification , HIV Core Protein p24/urine , Humans , Microfluidic Analytical Techniques/methods , Nucleic Acid Amplification Techniques/methods , Nucleic Acids/blood , Nucleic Acids/urine , Troponin I/blood , Troponin I/isolation & purification
3.
Pak J Pharm Sci ; 35(1(Special)): 375-380, 2022 Jan.
Article in English | MEDLINE | ID: mdl-35236651

ABSTRACT

To investigate the effect analysis and preventive effects of nucleic acid testing combined with enzyme-linked immunosorbent assay (ELISA) on blood-borne diseases. This study included 72335 blood samples that were collected in our hospital from March 2019 to March 2020. All the samples were tested for anti HIV (AIDS antibody), anti HCV (hepatitis C antibody), HBsAg (hepatitis B surface antigen) and anti TP (syphilis antibody) in blood respectively with two manufacturers' reagents. The results of anti HIV, anti HCV, HBsAg and anti TP of all samples were analyzed, and blood samples with 0.7< sample test value / critical value (s / CO) < 3.0 were tested by ELISA and negative blood samples were tested by ELISA and nucleic acid testing. Then we analyzed the results of nucleic acid testing. 610 blood samples failed to pass the test of anti HIV, anti HCV, HBsAg and anti TP ELISA, accounting for 0.84% of the total numbers, including 100 blood samples with 1.0 3.0, 338 blood samples with 0.7< s/CO <1.0 and 71725 blood samples were qualified. We used nucleic acid testing to test 71725 qualified samples tested by ELISA and then there were 50 samples with positive HBV-DNA , accounting for 0.07% (50 / 71725), no one with positive HIV-RNA and positive HCV-RNA, accounting for 0.00% (0/71725). The positive rate of blood samples with HBsAg 0.7

Subject(s)
Blood-Borne Infections/diagnosis , Enzyme-Linked Immunosorbent Assay/methods , Nucleic Acids/blood , Adult , Female , Humans , Immunosorbent Techniques , Male , Middle Aged , Young Adult
4.
Int J Mol Sci ; 22(18)2021 Sep 16.
Article in English | MEDLINE | ID: mdl-34576168

ABSTRACT

Although treatment outcomes of glioblastoma, the most malignant central nervous system (CNS) tumor, has improved in the past decades, it is still incurable, and survival has only slightly improved. Advances in molecular biology and genetics have completely transformed our understanding of glioblastoma. Multiple classifications and different diagnostic methods were made according to novel molecular markers. Discovering tumor heterogeneity only partially explains the ineffectiveness of current anti-proliferative therapies. Dynamic heterogeneity secures resistance to combined oncotherapy. As tumor growth proceeds, new therapy-resistant sub clones emerge. Liquid biopsy is a new and promising diagnostic tool that can step up with the dynamic genetic change. Getting a 'real-time' picture of a specific tumor, anti-invasion and multi-target treatment can be designed. During invasion to the peri-tumoral brain tissue, glioma cells interact with the extracellular matrix components. The expressional levels of these matrix molecules give a characteristic pattern, the invasion spectrum, which possess vast diagnostical, predictive and prognostic information. It is a huge leap forward combating tumor heterogeneity and searching for novel therapies. Using the invasion spectrum of a tumor sample is a novel tool to distinguish between histological subtypes, specifying the tumor grades or different prognostic groups. Moreover, new therapeutic methods and their combinations are under trial. These are crucial steps towards personalized oncotherapy.


Subject(s)
Glioblastoma/therapy , Glioma/therapy , Aged , Biomarkers, Tumor/blood , Brain/metabolism , Brain Neoplasms/blood , Epigenesis, Genetic/genetics , Exosomes/metabolism , Female , Humans , Immunotherapy , Liquid Biopsy/methods , Male , Middle Aged , Nucleic Acids/blood , Prognosis
5.
Cochrane Database Syst Rev ; 8: CD011871, 2019 Aug 01.
Article in English | MEDLINE | ID: mdl-31425612

ABSTRACT

BACKGROUND: Early diagnosis of leptospirosis may contribute to the effectiveness of antimicrobial therapy and early outbreak recognition. Nucleic acid and antigen detection tests have the potential for early diagnosis of leptospirosis. With this systematic review, we assessed the sensitivity and specificity of nucleic acid and antigen detection tests. OBJECTIVES: To determine the diagnostic test accuracy of nucleic acid and antigen detection tests for the diagnosis of human symptomatic leptospirosis. SEARCH METHODS: We searched electronic databases including MEDLINE, Embase, the Cochrane Library, and regional databases from inception to 6 July 2018. We did not apply restrictions to language or time of publication. SELECTION CRITERIA: We included diagnostic cross-sectional studies and case-control studies of tests that made use of nucleic acid and antigen detection methods in people suspected of systemic leptospirosis. As reference standards, we considered the microscopic agglutination test alone (which detects antibodies against leptospirosis) or in a composite reference standard with culturing or other serological tests. Studies were excluded when the controls were healthy individuals or when there were insufficient data to calculate sensitivity and specificity. DATA COLLECTION AND ANALYSIS: At least two review authors independently extracted data from each study. We used the revised Quality Assessment of Diagnostic Accuracy Studies tool (QUADAS-2) to assess risk of bias. We calculated study-specific values for sensitivity and specificity with 95% confidence intervals (CI) and pooled the results in a meta-analysis when appropriate. We used the bivariate model for index tests with one positivity threshold, and we used the hierarchical summary receiver operating characteristic model for index tests with multiple positivity thresholds. As possible sources of heterogeneity, we explored: timing of index test, disease prevalence, blood sample type, primers or target genes, and the real-time polymerase chain reaction (PCR) visualisation method. These were added as covariates to the meta-regression models. MAIN RESULTS: We included 41 studies evaluating nine index tests (conventional PCR (in short: PCR), real-time PCR, nested PCR, PCR performed twice, loop-mediated isothermal amplification, enzyme-linked immunosorbent assay (ELISA), dot-ELISA, immunochromatography-based lateral flow assay, and dipstick assay) with 5981 participants (1834 with and 4147 without leptospirosis). Methodological quality criteria were often not reported, and the risk of bias of the reference standard was generally considered high. The applicability of findings was limited by the frequent use of frozen samples. We conducted meta-analyses for the PCR and the real-time PCR on blood products.The pooled sensitivity of the PCR was 70% (95% CI 37% to 90%) and the pooled specificity was 95% (95% CI 75% to 99%). When studies with a high risk of bias in the reference standard domain were excluded, the pooled sensitivity was 87% (95% CI 44% to 98%) and the pooled specificity was 97% (95% CI 60% to 100%). For the real-time PCR, we estimated a summary receiver operating characteristic curve. To illustrate, a point on the curve with 85% specificity had a sensitivity of 49% (95% CI 30% to 68%). Likewise, at 90% specificity, sensitivity was 40% (95% CI 24% to 59%) and at 95% specificity, sensitivity was 29% (95% CI 15% to 49%). The median specificity of real-time PCR on blood products was 92%. We did not formally compare the diagnostic test accuracy of PCR and real-time PCR, as direct comparison studies were lacking. Three of 15 studies analysing PCR on blood products reported the timing of sample collection in the studies included in the meta-analyses (range 1 to 7 days postonset of symptoms), and nine out of 16 studies analysing real-time PCR on blood products (range 1 to 19 days postonset of symptoms). In PCR studies, specificity was lower in settings with high leptospirosis prevalence. Other investigations of heterogeneity did not identify statistically significant associations. Two studies suggested that PCR and real-time PCR may be more sensitive on blood samples collected early in the disease stage. Results of other index tests were described narratively. AUTHORS' CONCLUSIONS: The validity of review findings are limited and should be interpreted with caution. There is a substantial between-study variability in the accuracy of PCR and real-time PCR, as well as a substantial variability in the prevalence of leptospirosis. Consequently, the position of PCR and real-time PCR in the clinical pathway depends on regional considerations such as disease prevalence, factors that are likely to influence accuracy, and downstream consequences of test results. There is insufficient evidence to conclude which of the nucleic acid and antigen detection tests is the most accurate. There is preliminary evidence that PCR and real-time PCR are more sensitive on blood samples collected early in the disease stage, but this needs to be confirmed in future studies.


Subject(s)
Antibodies, Bacterial/immunology , Leptospira/immunology , Leptospirosis/diagnosis , Nucleic Acids/blood , Polymerase Chain Reaction/methods , Enzyme-Linked Immunosorbent Assay/methods , Humans , Leptospirosis/blood , ROC Curve , Sensitivity and Specificity
6.
Sensors (Basel) ; 19(23)2019 Nov 29.
Article in English | MEDLINE | ID: mdl-31795306

ABSTRACT

Information about the characteristics of measuring chips according to their storage conditions is of great importance for clinical diagnosis. In our present work, we have studied the capability of chips to detect nanowire biosensors when they are either freshly prepared or have been stored for either one or two years in a clean room. Potential to detect DNA oligonucleotides (oDNAs)-synthetic analogues of microRNAs (miRNAs) 198 and 429 that are associated with the development of prostate cancer (PCa)-in buffer solution was demonstrated using a nanowire biosensor based on silicon-on-insulator structures (SOI-NW biosensor). To provide biospecific detection, nanowire surfaces were sensitized with oligonucleotide probes (oDNA probes) complimentary to the known sequences of miRNA 183 and 484. In this study it is demonstrated that freshly prepared SOI-NW biosensor chips with n-type conductance and immobilized oDNA probes exhibit responses to the addition of complimentary oDNAs in buffer, leading to decreases in chips' conductance at a concentration of 3.3 × 10-16 M. The influence of storage time on the characteristics of SOI-NW biosensor chips is also studied herein. It is shown that a two-year storage of the chips leads to significant changes in their characteristics, resulting in "inverse" sensitivity toward negatively charged oDNA probes (i.e., through an increase in chips' conductance). It is concluded that the surface layer makes the main contribution to conductance of the biosensor chip. Our results indicate that the detection of target nucleic acid molecules can be carried out with high sensitivity using sensor chips after long-term storage, but that changes in their surface properties, which lead to inversed detection signals, must be taken into account. Examples of the applications of such chips for the detection of cancer-associated microRNAs in plasma samples of patients with diagnosed prostate cancer are given. The results obtained herein are useful for the development of highly sensitive nanowire-based diagnostic systems for the revelation of (prostate) cancer-associated microRNAs in human plasma.


Subject(s)
Biomarkers, Tumor/blood , Biosensing Techniques/methods , MicroRNAs/blood , Prostatic Neoplasms/blood , Humans , Male , Nanowires/chemistry , Nucleic Acids/blood , Nucleic Acids/isolation & purification , Silicon/chemistry
7.
Forensic Sci Med Pathol ; 15(3): 332-341, 2019 Sep.
Article in English | MEDLINE | ID: mdl-31054024

ABSTRACT

Postmortem diagnosis of extreme-weather-related deaths is a challenging forensic task. Here, we present a state-of-the-art study that employed attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy in combination with Chemometrics for postmortem diagnosis of fatal hypothermia/hyperthermia by biochemical investigation of plasma in rats. The results of principal component analysis (PCA) and spectral analysis revealed that plasma samples from the fatal hypothermia, fatal hyperthermia, and control groups, are substantially different from each other based on the spectral variations associated with the lipid, carbohydrate and nucleic acid components. Two partial least squares-discriminant analysis (PLS-DA) classification models (hypothermia-nonhypothermia and hyperthermia-nonhyperthermia binary models) with a 100% accuracy rate were constructed. Subsequently, internal cross-validation was performed to assess the robustness of these two models, which resulted in 98.1 and 100% accuracy. Ultimately, classification predictions of 42 unknown plasma samples were performed by these two models, and both models achieved 100% accuracy. Additionally, our results demonstrated that hemolysis and postmortem hypothermic/hyperthermic effects did not weaken the prediction ability of these two classification models. In summary, this work demonstrates ATR-FTIR spectroscopy's great potential for postmortem diagnosis of fatal hypothermia/hyperthermia.


Subject(s)
Fever/diagnosis , Hypothermia/diagnosis , Plasma/chemistry , Spectroscopy, Fourier Transform Infrared , Animals , Biomarkers/blood , Blood Glucose/analysis , Blood Proteins/analysis , Carbohydrates/blood , Discriminant Analysis , Fatty Acids/blood , Fever/blood , Forensic Pathology/methods , Hypothermia/blood , Lipids/blood , Nucleic Acids/blood , Principal Component Analysis , Rats, Sprague-Dawley
8.
Anal Chem ; 90(12): 7221-7229, 2018 06 19.
Article in English | MEDLINE | ID: mdl-29761701

ABSTRACT

Nucleic acid amplification tests (NAATs) provide high diagnostic accuracy for infectious diseases and quantitative results for monitoring viral infections. The majority of NAATs require complex equipment, cold chain dependent reagents, and skilled technicians to perform the tests. This largely confines NAATs to centralized laboratories and can significantly delay appropriate patient care. Low-cost, point-of-care (POC) NAATs are especially needed in low-resource settings to provide patients with diagnosis and treatment planning in a single visit to improve patient care. In this work, we present a rapid POC NAAT with integrated sample preparation and amplification using electrokinetics and paper substrates. We use simultaneous isotachophoresis (ITP) and recombinase polymerase amplification (RPA) to rapidly extract, amplify, and detect target nucleic acids from serum and whole blood in a paper-based format. We demonstrate simultaneous ITP and RPA can consistently detect 5 copies per reaction in buffer and 10 000 copies per milliliter of human serum with no intermediate user steps. We also show preliminary extraction and amplification of DNA from whole blood samples. Our test is rapid (results in less than 20 min) and made from low-cost materials, indicating its potential for detecting infectious diseases and monitoring viral infections at the POC in low resource settings.


Subject(s)
Isotachophoresis , Nucleic Acid Amplification Techniques , Nucleic Acids/blood , Nucleic Acids/isolation & purification , Humans , Isotachophoresis/instrumentation , Nucleic Acid Amplification Techniques/instrumentation , Nucleic Acids/genetics , Paper , Point-of-Care Systems
9.
Ann Hematol ; 97(12): 2447-2454, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30056581

ABSTRACT

The recently introduced Revised International Staging System (R-ISS) for multiple myeloma (MM) integrates albumin, ß2 microglobulin, lactate dehydrogenase (LDH) with high-risk cytogenetic aberrations (CA), i.e., t(4;14) and t(14;16) and del17p using fluorescent in situ hybridization (FISH). We evaluated utility of nucleic acid-based tests of multiplex ligation-based probe amplification (MLPA) and quantitative real-time polymerase chain reaction (qRT-PCR) to define the CA and the R-ISS categories as per this approach were evaluated for their ability to predict outcome in terms of response, progression-free (PFS), and overall survival (OS). In this study (n = 180), 17 (9.4%), 118 (65.6%), and 45 (25%) patients were assigned to R-ISS1, R-ISS2, and R-ISS3 categories with statistically significant differences in median PFS (p = 0.02) and OS (p < 0.001).On univariate analysis, serum creatinine, LDH, 17p deletion, chromosome 1q gain, and response after first induction therapy were associated with statistically significant differences (p < 0.05) in PFS and in addition, age> 65 years and use of triplet therapy with OS. On multivariate analysis, only serum creatinine, LDH, and response after first induction therapy retained significance for predicting PFS and in addition, use of triplet therapy retained significance for the OS. The proposed nucleic acid-based algorithm using qRT-PCR and MLPA for R-ISS is resource-effective in terms of small quantities of sample required; feasibility of batch processing and reduced overall cost for the total number of regions evaluated and retained the prognostic significance of R-ISS, making it suitable for clinical practice for molecular characterization of MM.


Subject(s)
Algorithms , Chromosome Aberrations , Multiple Myeloma , Multiplex Polymerase Chain Reaction , Nucleic Acids , Real-Time Polymerase Chain Reaction , Adult , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Multiple Myeloma/blood , Multiple Myeloma/diagnosis , Multiple Myeloma/genetics , Neoplasm Staging , Nucleic Acids/blood , Nucleic Acids/genetics
10.
Microbiol Immunol ; 60(4): 228-33, 2016 Apr.
Article in English | MEDLINE | ID: mdl-26876770

ABSTRACT

Streptococcus suis infection induces formation of neutrophil extracellular traps (NETs) in vitro; however, the contribution of NETs-mediated killing to the pathogenesis of S. suis in vivo is yet to be elicited. The findings of the present study indicated that extracellular DNA fiber can be induced in a murine model in response to S. suis infection. A nuclease that destroys their structure was used to evaluate the role of NETs on S. suis infection. Treatment with nuclease resulted in a greater bacteria load and higher serum TNF-α concentrations in response to S. suis infection, indicating that NETs structure played an essential role in S. suis clearance and inflammation. Furthermore, nuclease treatment resulted in more severe clinical signs during and higher mortality from S. suis infection. These findings indicated that NETs structure contributes to protection against S. suis infection.


Subject(s)
Extracellular Traps/immunology , Neutrophils/immunology , Streptococcal Infections/immunology , Streptococcal Infections/microbiology , Streptococcus suis/immunology , Animals , Bacterial Load , Deoxyribonucleases/pharmacology , Female , Host-Pathogen Interactions , Mice , Mice, Inbred C57BL , Microscopy, Fluorescence , Nucleic Acids/blood , Random Allocation , Streptococcal Infections/pathology , Streptococcal Infections/therapy , Streptococcus suis/drug effects , Streptococcus suis/enzymology , Streptococcus suis/genetics , Tumor Necrosis Factor-alpha/blood
11.
Adv Exp Med Biol ; 924: 201-215, 2016.
Article in English | MEDLINE | ID: mdl-27753044

ABSTRACT

Researchers working in industrial laboratories as well as in academic laboratories discussed topics related to the use of extracellular nucleic acids in different fields. These included areas like non-invasive prenatal diagnosis, the application of different methods for the analysis and characterization of patients with benign and malignant diseases and technical aspects associated with extracellular nucleic acids. In addition, the possibilities and chances for a cooperation of researchers working in different worlds, i.e. academia and industry, were discussed.


Subject(s)
Academic Medical Centers/methods , Industry/methods , Laboratory Personnel , Molecular Diagnostic Techniques/methods , Nucleic Acids/genetics , Research Personnel , Congresses as Topic , Disease/genetics , Extracellular Space/genetics , Humans , Neoplasms/diagnosis , Neoplasms/genetics , Nucleic Acids/analysis , Nucleic Acids/blood
12.
Adv Exp Med Biol ; 924: 53-60, 2016.
Article in English | MEDLINE | ID: mdl-27753019

ABSTRACT

Liquid profiling is a traditional concept in laboratory diagnostics using patterns of blood-derived biochemical molecules for disease detection and characterization. Beyond protein and cellular parameters, molecular biomarkers at the DNA, RNA and miRNA level have been developed as promising diagnostic tools in metabolic and malignant diseases as new technologies for ultrasensitive profiling of nucleic acids in blood and body fluids became available. In cancer disease, they are successfully applied for the stratification of patients for individually tailored therapies, treatment monitoring and the sensitive detection of minimal residual disease. Due to its minimally invasive nature, blood-based qualitative and quantitative determinations of targeted and global molecular changes can be applied serially and complement well-established molecular tissue diagnostics. Interdisciplinary interaction between laboratory medicine, pathology and human genetics will speed up the development of liquid nucleic acid profiling as a most valuable tool for precision medicine.


Subject(s)
Biomarkers, Tumor/genetics , Molecular Diagnostic Techniques/methods , Neoplasms/genetics , Nucleic Acids/genetics , Biomarkers, Tumor/blood , DNA, Neoplasm/blood , DNA, Neoplasm/genetics , Humans , MicroRNAs/blood , MicroRNAs/genetics , Molecular Targeted Therapy/methods , Neoplasms/diagnosis , Neoplasms/drug therapy , Nucleic Acids/blood , Precision Medicine/methods , RNA, Neoplasm/blood , RNA, Neoplasm/genetics , Sensitivity and Specificity
13.
Adv Exp Med Biol ; 924: 91-95, 2016.
Article in English | MEDLINE | ID: mdl-27753025

ABSTRACT

The quantitative and qualitative differences of circulating nucleic acids (cirNAs) between healthy and diseased individuals have motivated researchers to utilize these differences in the diagnosis and prognosis of various pathologies. The position maintained here is that reviewing the rather neglected early work associated with cirNAs and extracellular vesicles (EVs) is required to fully describe the nature of cirNAs. This review consists of an empirically up-to-date schematic summary of the major events that developed and integrated the concepts of heredity, genetic information and cirNAs. This reveals a clear pattern implicating cirNA as a homeostatic entity or messenger of genetic information. The schematic summary paints a picture of how cirNAs may serve as homeostatic genetic entities that promote synchrony of both adaptation and damage in tissues and organs depending on the source of the message.


Subject(s)
Exosomes/genetics , Extracellular Vesicles/genetics , Homeostasis , Nucleic Acids/genetics , Biological Evolution , Cytoplasmic Structures/metabolism , DNA/blood , DNA/genetics , DNA/metabolism , Humans , Lipopolysaccharides/metabolism , Nucleic Acids/blood , Nucleic Acids/metabolism , RNA/blood , RNA/genetics , RNA/metabolism
14.
Cancer Invest ; 33(3): 78-85, 2015 Mar.
Article in English | MEDLINE | ID: mdl-25647443

ABSTRACT

Pancreatic cancer is a highly aggressive disease with rapid invasion and early encasement of blood vessels. Hence, levels of circulating nucleic acids and tumor-associated mutations in them may have clinical importance. We analyzed the levels of circulating tumor DNA and oncogenic k-ras mutation in plasma of patients with pancreatic cancer and correlated their levels with survival and clinicopathological parameters. Higher levels of plasma DNA (>62 ng/mL) was found to associate significantly with lower overall survival time (p=.002), presence of vascular encasement (p=.030) and metastasis (p=.001). However, k-ras mutation status did not correlate with any of the clinicopathological parameters or survival. We conclude that circulating DNA in plasma can be an important predictor of prognosis in pancreatic cancer.


Subject(s)
Nucleic Acids/blood , Pancreatic Neoplasms/blood , Pancreatic Neoplasms/genetics , Female , Humans , Male , Middle Aged , Mutation , Neoplasm Metastasis , Pancreatic Neoplasms/pathology , Prognosis , Survival Analysis , Pancreatic Neoplasms
15.
Analyst ; 140(23): 7876-85, 2015 Dec 07.
Article in English | MEDLINE | ID: mdl-26332289

ABSTRACT

Visual detection of nucleic acid biomarkers is a simple and convenient approach to point-of-care applications. However, issues of sensitivity and the handling of complex bio-fluids have posed challenges. Here we report on a visual method detecting nucleic acids using Mie scattering of polystyrene microparticles and the magnetophoretic effect. Magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) were surface-functionalised with oligonucleotide probes, which can hybridise with target oligonucleotides in juxtaposition and lead to the formation of MMPs-targets-PMPs sandwich structures. Using an externally applied magnetic field, the magnetophoretic effect attracts the sandwich structure to the sidewall, which reduces the suspended PMPs and leads to a change in the light transmission via the Mie scattering. Based on the high extinction coefficient of the Mie scattering (∼3 orders of magnitude greater than that of the commonly used gold nanoparticles), our results showed the limit of detection to be 4 pM using a UV-Vis spectrometer or 10 pM by direct visual inspection. Meanwhile, we also demonstrated that this method is compatible with multiplex assays and detection in complex bio-fluids, such as whole blood or a pool of nucleic acids, without purification in advance. With a simplified operation procedure, low instrumentation requirement, high sensitivity and compatibility with complex bio-fluids, this method provides an ideal solution for visual detection of nucleic acids in resource-limited settings.


Subject(s)
Chemistry Techniques, Analytical/methods , Magnetics , Nucleic Acids/analysis , Animals , Coloring Agents/chemistry , Nanoparticles/chemistry , Nucleic Acids/blood , Polymorphism, Single Nucleotide , Polystyrenes/chemistry
16.
Crit Rev Clin Lab Sci ; 51(4): 200-31, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24878357

ABSTRACT

This review focuses on the promising potential of nucleic acids in body fluids such as blood and urine as diagnostic, prognostic, predictive and monitoring biomarkers in urologic malignancies. The tremendous progress in the basic knowledge of molecular processes in cancer, as shown in the companion review on nucleic acid-based biomarkers in tissue of urologic tumors, provides a strong rationale for using these molecular changes as non-invasive markers in body fluids. The changes observed in body fluids are an integrative result, reflecting both tissue changes and processes occurring in the body fluids. The availability of sensitive methods has only recently made possible detailed studies of DNA- and RNA-based markers in body fluids. In addition to these biological aspects, methodological aspects of the determination of nucleic acids in body fluids, i.e. pre-analytical, analytical and post-analytical issues, are particularly emphasized. The characteristic changes of RNA (differential mRNA and miRNA expression) and DNA (concentrations, integrity index, mutations, microsatellite and methylation alterations) in serum/plasma and urine samples of patients suffering from the essential urologic cancers of the prostate, bladder, kidney and testis are summarized and critically discussed below. To translate the promising results into clinical practice, laboratory scientists and clinicians have to collaborate to resolve the challenges of harmonized and feasible pre-analytical and analytical conditions for the selected markers and to validate these markers in well-designed and sufficiently powered multi-center studies.


Subject(s)
Biomarkers, Tumor , Nucleic Acids , Urologic Neoplasms , Biomarkers, Tumor/blood , Biomarkers, Tumor/urine , Humans , Nucleic Acids/blood , Nucleic Acids/urine , Prognosis , Urologic Neoplasms/blood , Urologic Neoplasms/diagnosis , Urologic Neoplasms/urine
17.
Anal Chem ; 86(15): 7264-8, 2014 Aug 05.
Article in English | MEDLINE | ID: mdl-24945850

ABSTRACT

We report on our efforts to create an on-chip system to simultaneously purify and fractionate nucleic acids and proteins from complex samples using isotachophoresis (ITP). We have developed this technique to simultaneously extract extracellular DNA and proteins from human blood serum samples and deliver these to two separate output reservoirs on a chip. The purified DNA is compatible with quantitative polymerase chain reaction (qPCR), and proteins can be extracted so as to exclude albumin, the most abundant protein in serum. We describe significant remaining challenges in making this bidirectional method a robust and efficient technique. These challenges include managing channel surface adsorption of proteins, identifying the cause of observed reductions in low molecular weight proteins, and dealing with nonspecific binding of proteins and DNA.


Subject(s)
Blood Proteins/isolation & purification , Isotachophoresis/methods , Nucleic Acids/isolation & purification , Electrophoresis, Polyacrylamide Gel , Humans , Nucleic Acids/blood
18.
J Clin Microbiol ; 52(4): 1232-4, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24452173

ABSTRACT

Magnetic beads offer superior impurity removal and nucleic acid selection over older extraction methods. The performances of nucleic acid extraction of biothreat agents in blood or buffer by easyMAG, MagNA Pure, EZ1 Advanced XL, and Nordiag Arrow were evaluated. All instruments showed excellent performance in blood; however, the easyMAG had the best precision and versatility.


Subject(s)
Automation, Laboratory/methods , Biological Warfare Agents , Microbiological Techniques/methods , Nucleic Acids/blood , Nucleic Acids/isolation & purification , Humans , Microbiological Techniques/instrumentation
19.
Mol Ecol Resour ; 24(6): e13979, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38780145

ABSTRACT

Collecting and preserving biological samples in the field, particularly in remote areas in tropical forests, prior to laboratory analysis is challenging. Blood samples in many cases are used for nucleic acid-based species determination, genomics or pathogen research. In most cases, maintaining a cold chain is impossible and samples remain at ambient temperature for extended periods of time before controlled storage conditions become available. Dried blood spot (DBS) storage, blood stored on cellulose-based paper, has been widely applied to facilitate sample collection and preservation in the field for decades. However, it is unclear how long-term storage on this substrate affects nucleic acid concentration and integrity. We analysed nucleic acid quality from DBS stored on Whatman filter paper no. 3 and FTA cards for up to 15 years in comparison to cold-chain stored samples using four nucleic acid extraction methods. We examined the ability to identify viral sequences from samples of 12 free-ranging primates in the Amazon forest, using targeted hybridization capture, and determined if mitochondrial genomes could be retrieved. The results suggest that even after extended periods of storage, DBS will be suitable for some genomic applications but may be of limited use for viral pathogen research, particularly RNA viruses.


Subject(s)
Dried Blood Spot Testing , Specimen Handling , Animals , Specimen Handling/methods , Dried Blood Spot Testing/methods , Time Factors , Nucleic Acids/blood , Nucleic Acids/isolation & purification , Nucleic Acids/genetics , Preservation, Biological/methods
20.
Shock ; 61(6): 848-854, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38662595

ABSTRACT

ABSTRACT: Background: Inorganic polyphosphate (polyP) is a procoagulant polyanion. We assessed the impact of polyP inhibition on thrombin generation after trauma using the novel polyP antagonists, macromolecular polyanion inhibitor 8 (MPI 8), and universal heparin reversal agent 8 (UHRA-8). Methods: Plasma thrombin generation (calibrated automated thrombogram, CAT), in 56 trauma patients and 39 controls +/- MPI 8 and UHRA-8 (50 µg/mL), was expressed as lag time (LT, minutes), peak height (PH, nM), and time to peak (ttPeak, minutes), with change in LT (ΔLT) and change in ttPeak (ΔttPeak) quantified. Results expressed in median and quartiles [Q1, Q3], Wilcoxon matched-pairs testing, P < 0.05 significant. Results: Trauma patients had greater baseline PH than controls (182.9 [121.0, 255.2]; 120.5 [62.1, 174.8], P < 0.001). MPI 8 treatment prolonged LT and ttPeak in trauma (7.20 [5.88, 8.75]; 6.46 [5.45, 8.93], P = 0.020; 11.28 [8.96, 13.14]; 11.00 [8.95, 12.94], P = 0.029) and controls (7.67 [6.67, 10.50]; 6.33 [5.33, 8.00], P < 0.001; 13.33 [11.67, 15.33]; 11.67 [10.33, 13.33], P < 0.001). UHRA-8 treatment prolonged LT and ttPeak and decreased PH in trauma (9.09 [7.45, 11.33]; 6.46 [5.45, 8.93]; 14.02 [11.78, 17.08]; 11.00 [8.95, 12.94]; 117.4 [74.5, 178.6]; 182.9 [121.0, 255.2]) and controls (9.83 [8.00, 12.33]; 6.33 [5.33, 8.00]; 16.67 [14.33, 20.00]; 11.67 [10.33, 13.33]; 55.3 [30.2, 95.9]; 120.5 [62.1, 174.8]), all P < 0.001. Inhibitor effects were greater for controls (greater ΔLT and ΔttPeak for both inhibitors, P < 0.001). Conclusion: PolyP inhibition attenuates thrombin generation, though to a lesser degree in trauma than in controls, suggesting that polyP contributes to accelerated thrombin generation after trauma.


Subject(s)
Polyphosphates , Thrombin , Wounds and Injuries , Humans , Thrombin/metabolism , Male , Adult , Wounds and Injuries/blood , Wounds and Injuries/drug therapy , Female , Middle Aged , Nucleic Acids/blood
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