A Comparison of DNA-DNA Hybridization Kinetics in Complex Media on Planar and Nanostructured Electrodes.

A comprehensive investigation into how nanostructures alter real-time DNA hybridization kinetics in both buffer and complex media and under a wide range of probe and target concentrations is currently lacking. In response, we use a real-time, wash-free, and in situ assay to study DNA hybridization kinetics by performing continuous electrochemical measurements in different media. We investigated the differences in hybridization kinetics under three regimes of probe density (low, medium, and high) and over three orders of magnitude of target concentrations (0.01-1 µM). Additionally, we compared the performance of planar and nanostructured electrodes in buffer, blood, urine, and saliva. Our experiments indicate that adding nanostructures to the transducer surface is only effective under a specific probe/target concentration regime. Additionally, we found that direct electrochemical readout is possible in the examined physiological media, with measurements in blood showing the highest and saliva showing the lowest signal magnitudes compared to buffer.

A universal bacterial sensor created by integrating a light modulating aptamer complex with photoelectrochemical signal readout.

Photoelectrochemical (PEC) signal transduction is of great interest for ultrasensitive biosensing; however, signal-on PEC assays that do not require target labeling remain elusive. In this work, we developed a signal-on biosensor that uses nucleic acids to modulate PEC currents upon target capture. Target presence removes a biorecognition probe from a DNA duplex carrying a gold nanoparticle, bringing the gold nanoparticle in direct contact to the photoelectrode and increasing the PEC current. This assay was used to develop a universal bacterial detector by targeting peptidoglycan using an aptamer, demonstrating a limit-of-detection of 82 pg/mL (13 pM) in buffer and 239 pg/mL (37 pM) in urine for peptidoglycan and 1913 CFU/mL forEscherichia coliin urine. When challenged with a panel of unknown targets, the sensor identified samples with bacterial contamination versus fungi. The versatility of the assay was further demonstrated by analyzing DNA targets, which yielded a limit-of-detection of 372 fM.

Liquid NanoBiosensors Enable One-Pot Electrochemical Detection of Bacteria in Complex Matrices.

There is a need for point-of-care bacterial sensing and identification technologies that are rapid and simple to operate. Technologies that do not rely on growth cultures, nucleic acid amplification, step-wise reagent addition, and complex sample processing are the key for meeting this need. Herein, multiple materials technologies are integrated for overcoming the obstacles in creating rapid and one-pot bacterial sensing platforms. Liquid-infused nanoelectrodes are developed for reducing nonspecific binding on the transducer surface; bacterium-specific RNA-cleaving DNAzymes are used for bacterial identification; and redox DNA barcodes embedded into DNAzymes are used for binding-induced electrochemical signal transduction. The resultant single-step and one-pot assay demonstrates a limit-of-detection of 102 CFU mL-1 , with high specificity in identifying Escherichia coli amongst other Gram positive and negative bacteria including Klebsiella pneumoniae, Staphylococcus aureus, and Bacillus subtilis. Additionally, this assay is evaluated for analyzing 31 clinically obtained urine samples, demonstrating a clinical sensitivity of 100% and specify of 100%. When challenging this assay with nine clinical blood cultures, E. coli-positive and E. coli-negative samples can be distinguished with a probability of p < 0.001.

Electrochemical DNAzyme-based biosensors for disease diagnosis.

DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.

DNAzyme-Immobilizing Microgel Magnetic Beads Enable Rapid, Specific, Culture-Free, and Wash-Free Electrochemical Quantification of Bacteria in Untreated Urine.

Rapid, ultrasensitive, and specific detection and identification of bacteria in unprocessed clinical specimens is critically needed to enable point-of-care diagnosis of infectious diseases. However, existing systems require sample processing and/or analyte enrichment for direct bacterial analysis in clinical samples, which significantly adds to the assay time and complexity. Herein, we integrate RNA-cleaving DNAzymes specific to Escherichia coli (E. coli) and programmed for electrochemical signal transduction, multifunctional microgel magnetic beads for immobilizing the DNAzyme into a hydrated and three-dimensional scaffold, and hierarchical electrodes for ultrasensitive electrochemical readout to achieve rapid bacterial analysis in undiluted and unprocessed urine collected from symptomatic patients suspected of having urinary tract infections (UTIs). The microgel magnetic bead assay enables highly efficient conjugation and hydration of the immobilized DNAzymes, resulting in low limits-of-detection of 6 CFU/mL in buffer and 138 CFU/mL in unprocessed urine with high specificity against multiple urinary pathogens within a 1 hour assay time. The assay successfully identifies which patients are infected with E. coli as the causative organism for their UTI symptoms, indicating the clinical relevance of this assay.

Thrombocytopenia Associated With Teicoplanin Use: A Retrospective Observational Study.

BACKGROUND: Contradictory studies reporting vast heterogeneity in the teicoplanin-induced thrombocytopenia (TIT) incidence exist. OBJECTIVE: To identify the incidence of TIT associated with teicoplanin dosing range (6-12 mg/kg/dose) and the risk factors of TIT. METHODS: This retrospective observational study included adult patients who received teicoplanin for ≥3 consecutive days over a period of 3.5 years. Thrombocytopenia was defined as a platelet count of <100 × 103/µL coupled with at least a 25% drop from the baseline count. The TIT incidence was assessed using the adverse drug reaction probability scale (Naranjo scale). RESULTS: Data from 482 patients who received teicoplanin and met the predefined inclusion criteria were included in the analyses. The cohort presented a mean age of 53.5 ± 19 years, where 72.4% were male, and 49.2% exhibited normal baseline renal function. Teicoplanin was most commonly used for bacteremia (n = 134), and the most common isolated pathogen being Staphylococcus aureus (n = 221). The TIT incidence was 4.6% (the possible and probable category using the Naranjo scale; 22/482). The median time to first platelet count dropped to <100 × 103/µL after teicoplanin initiation was 5 (interquartile range [IQR], 3-10) days and 8 (IQR, 5-14) days till the maximum platelet count dropped. None of the tested patient variables were found to be independently associated with an increased risk of thrombocytopenia. CONCLUSION AND RELEVANCE: The overall TIT incidence was low across our study cohort, including critically ill patients. Our study results may aid in the optimal monitoring of such serious teicoplanin-induced adverse effects.

Two-Step Competitive Hybridization Assay: A Method for Analyzing Cancer-Related microRNA Embedded in Extracellular Vesicles.

With an increased understanding of the role of microRNAs (miRNAs) in cancer evolution, there is a growing interest in the use of these non-coding nucleic acids in cancer diagnosis, prognosis, and treatment monitoring. miRNAs embedded in extracellular vesicles (EVs) are of particular interest given that circulating EVs carry cargo that are strongly correlated to their cells of origin such as tumor cells while protecting them from degradation. As such, there is a tremendous interest in new simple-to-operate vesicular microRNA analysis tools for widespread use in performing liquid biopsies. Herein, we present a two-step competitive hybridization assay that is rationally designed to translate low microRNA concentrations to large electrochemical signals as the measured signal is inversely proportional to the microRNA concentration. Using this assay, with a limit-of-detection of 122 aM, we successfully analyzed vesicular miRNA 200b from prostate cancer cell lines and human urine samples, demonstrating the expected lower expression levels of miRNA 200b in the EVs from prostate cancer cells and in the prostate cancer patient's urine samples compared to healthy patients and non-tumorigenic cell lines, validating the suitability of our approach for clinical analysis.

Association between TNF-α, Interleukin-18 Polymorphisms and Risk of Hepatocellular Carcinoma in Egyptian patients.

OBJECTIVE: To evaluate the association of gene polymorphisms of the SNP of TNF-α gene -238G>A and IL-18 gene-607C>A with the development of hepatocellular carcinoma among Egyptian patients. METHODS: One hundred and fifty patients were allocated to this study; eighty patients with hepatocellular carcinoma (Group A), seventy cancer-free HCV age, and sex-matched patients (Group B). We analyzed two Single nucleotide polymorphisms (SNPs) (TNF-α-238G>A and IL-18-607C>A) by real-time polymerase chain reaction using sequence-specific primers (PCR-SSP). RESULTS: Significant higher risk of HCC was associated with genotype IL-18-607AA (p <0.001), OR: 5(2.188-11.47), allele IL-18 -607/A (P=0.001), OR: 2.1(1.32-3.3). A significant association was found between the size of HFL in the HCC group and different genotypes of IL18 genes (P=0.013) where 62.5% of patients with tumor size >5 cm carried the risky (AA) genotype on the other hand the SNP of TNF-α gene -238G>A showed no statistically significant association between the two groups. CONCLUSION: The SNP -607C>A in the IL18 gene was associated with increased HCC risk in Egyptian patients suggesting its use as a potential diagnostic non-invasive tool that allows to identify a new group of HCC patients at an earlier stage.
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Roadmap to the Bioanalytical Testing of COVID-19: From Sample Collection to Disease Surveillance.

The disease caused by SARS-CoV-2, coronavirus disease 2019 (COVID-19), has led to a global pandemic with tremendous mortality, morbidity, and economic loss. The current lack of effective vaccines and treatments places tremendous value on widespread screening, early detection, and contact tracing of COVID-19 for controlling its spread and minimizing the resultant health and societal impact. Bioanalytical diagnostic technologies have played a critical role in the mitigation of the COVID-19 pandemic and will continue to be foundational in the prevention of the subsequent waves of this pandemic along with future infectious disease outbreaks. In this Review, we aim at presenting a roadmap to the bioanalytical testing of COVID-19, with a focus on the performance metrics as well as the limitations of various techniques. The state-of-the-art technologies, mostly limited to centralized laboratories, set the clinical metrics against which the emerging technologies are measured. Technologies for point-of-care and do-it-yourself testing are rapidly emerging, which open the route for testing in the community, at home, and at points-of-entry to widely screen and monitor individuals for enabling normal life despite of an infectious disease pandemic. The combination of different classes of diagnostic technologies (centralized and point-of-care and relying on multiple biomarkers) are needed for effective diagnosis, treatment selection, prognosis, patient monitoring, and epidemiological surveillance in the event of major pandemics such as COVID-19.

Frequency of rs731236 (Taql), rs2228570 (Fok1) of Vitamin-D Receptor (VDR) gene in Emirati healthy population.

Vitamin D is getting more attention everyday due to its importance in maintaining bone and calcium homeostasis, cellular proliferation, differentiation and immune response. Vitamin D is derived from diet or elicited in the skin by the activation of 7-dehydrocholesterol, which is an inert molecule that must be activated by ultraviolet light to form pre-vitamin D3. Recent studies connected the gene encoding for vitamin D (VDR) to the genetic control of bone mass and other diseases. As VDR SNPs have been associated with several disorders and diseases, it's important to investigate the allelic and genotypic distribution among populations. The aim of this study is to determine the frequency of rs731236 (Taq1) and rs2228570 (Fok1) variants in healthy Emirati individuals and compare their genotype and allele distribution with other populations. In this study 282 (female, 187; male, 95) unrelated healthy UAE nationals were involved. Two hundreds and eight two DNA samples been collected to genotype rs731236 (Taq1) and rs2228570 (Fok1) VDR SNPs. Our results indicate that the distribution of the alleles and genotypes of rs731236 (Taq1) and rs2228570 (Fok1) vary considerably in different populations. In the Emirati population the distribution of rs731236 (Taq1) and rs2228570 (Fok1) were AA 38%, AG 42%, GG 20% and AA 27%, AG 42%, GG 31% respectively. The Emirati population genotype and allele distribution of rs731236 (Taq1) and rs2228570 (Fok1) had no difference with Caucasians from USA and France. However, there was significant difference with Asian populations.

Evaluation of squamous cell carcinoma antigen-immunoglobulin M complex (SCCA-IGM) and alpha-L-fucosidase (AFU) as novel diagnostic biomarkers for hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) surveillance lacks a reliable biomarker. Alpha-fetoprotein (AFP) is the most widely used. However, not all HCCs secrete AFP. AFP may be elevated with cirrhosis in the absence of HCC. Serum alpha-L-fucosidase (AFU) and squamous cell carcinoma antigen-immunoglobulin M complex (SCCA-IgM) were found to be useful markers in diagnosing HCC. SCCA-IgM and AFU were assessed by ELISA technique; AFP was measured by enzyme chemiluminescence in serum of 40 patients with HCC, 30 patients with liver cirrhosis, and 20 healthy control participants to compare their accuracy in early diagnosis of HCC. Serum SCCA-IgM and AFU levels were significantly elevated in HCC group compared to cirrhotic group (P value<0.001 and <0.001, respectively). Receiver operating characteristic curve showed the optimal cutoff value for SCCA-IgM was 233 AU/ml with sensitivity 87.5% and specificity 66% and for AFU was 25 U/L with sensitivity 87.5% and specificity 98%. AFP cutoff value was 48 ng/mL with sensitivity of 70% and specificity of 53.3%. The simultaneous determination of AFP and SCCA-IgM activity increased the sensitivity to 92.5% and specificity to 62.1%. There were positive significant correlations between SCCA-IgM and each of AFU (r=0.296, P=0.005) and AFP (r=0.284, P=0.007) and no correlation between AFP and AFU. All markers did not correlate with the tumor size or affected by the Child score. The significant difference between SCCA-IgM and AFU levels among HCC and cirrhotic patients suggests their use as potential diagnostic tools and allows identifying a new group of HCC patients even in the absence of elevated AFP.