Highly Accurate Chip-Based Resequencing of SARS-CoV-2 Clinical Samples.

SARS-CoV-2 has infected over 128 million people worldwide, and until a vaccine is developed and widely disseminated, vigilant testing and contact tracing are the most effective ways to slow the spread of COVID-19. Typical clinical testing only confirms the presence or absence of the virus, but rather, a simple and rapid testing procedure that sequences the entire genome would be impactful and allow for tracing the spread of the virus and variants, as well as the appearance of new variants. However, traditional short read sequencing methods are time consuming and expensive. Herein, we describe a tiled genome array that we developed for rapid and inexpensive full viral genome resequencing, and we have applied our SARS-CoV-2-specific genome tiling array to rapidly and accurately resequence the viral genome from eight clinical samples. We have resequenced eight samples acquired from patients in Wyoming that tested positive for SARS-CoV-2. We were ultimately able to sequence over 95% of the genome of each sample with greater than 99.9% average accuracy.

Using gold nanoclusters as selective luminescent probes for phosphate-containing metabolites.

Glutathione-bound gold nanoclusters (AuNCs@GSH) can emit reddish photoluminescence under illumination of ultraviolet light. The luminescence of the AuNCs@GSH is quenched when chelating with iron ions (AuNCs@GSH-Fe(3+)), presumably resulting from the effective electron transfer between the nanoclusters and iron ions. Nevertheless, we found that the luminescence of the gold nanoclusters can be restored in the presence of phosphate-containing molecules, which suggested the possibility of using AuNCs@GSH-Fe(3+) complexes as the selective luminescent switches for phosphate-containing metabolites. Phosphate-containing metabolites such as adenosine-5'-triphosphate (ATP) and pyrophosphate play an important role in biological systems. In this study, we demonstrated that the luminescence of the AuNCs@GSH-Fe(3+) is switched-on when mixing with ATP and pyrophosphate, which can readily be observed by the naked eye. It results from the high formation constants between phosphates and iron ions. When employing fluorescence spectroscopy as the detection tool, quantitative analysis for phosphate-containing metabolites such as ATP and pyrophosphate can be conducted. The linear range for ATP and pyrophosphate is 50 µM to sub-millimolar, while the limit of detection for ATP and pyrophosphate are ∼43 and ∼28 µM, respectively. Additionally, we demonstrated that the luminescence of the AuNCs@GSH-Fe(3+) can also be turned on in the presence of phosphate-containing metabolites from cell lysates and blood plasma.

Host factors do not influence the colonization or infection by fluconazole resistant Candida species in hospitalized patients.

Nosocomial yeast infections have significantly increased during the past two decades in industrialized countries, including Taiwan. This has been associated with the emergence of resistance to fluconazole and other antifungal drugs. The medical records of 88 patients, colonized or infected with Candida species, from nine of the 22 hospitals that provided clinical isolates to the Taiwan Surveillance of Antimicrobial Resistance of Yeasts (TSARY) program in 1999 were reviewed. A total of 35 patients contributed fluconazole resistant strains [minimum inhibitory concentrations (MICs) > or = 64 mg/l], while the remaining 53 patients contributed susceptible ones (MICs < or = 8 mg/l). Fluconazole resistance was more frequent among isolates of Candida tropicalis (46.5%) than either C. albicans (36.8%) or C. glabrata (30.8%). There was no significant difference in demographic characteristics or underlying diseases among patients contributing strains different in drug susceptibility.

Functional magnetic nanoparticle-based trapping and sensing approaches for label-free fluorescence detection of DNA.

In this study, a label-free fluorescence detection method for DNA was designed using functional magnetic nanoparticles (MNPs) as affinity probes. With the advantage of magnetic feature, MNP-based affinity probes can be easily manipulated for trapping and sensing target species. Two types of MNP-based nanoprobes for trapping and detecting target DNAs were fabricated. The basic strategy for this approach is the use of trapping probes to concentrate target DNAs selectively from complex samples. The detection probes are then used as fluorescence reporters to explore the level of the target species. Trapping probes were constructed by covalently immobilizing probe DNA molecules complementary to the target DNA. Detection nanoprobes were made by linking a fluorescent dye, riboflavin-5'-monophosphate (RFMP), onto the surface of the core/shell Fe(3)O(4)@Al(2)O(3) MNPs via Al-phosphate chelation. The fluorescence derived from RFMP molecules became invisible when molecules were attached onto the MNP surface. However, after phosphorylated species (e.g., DNA molecules) replaced RFMP from the surface of the RFMP-Fe(3)O(4)@Al(2)O(3) MNPs under microwave heating for 15s, the RFMP molecules released from the MNPs enhanced the fluorescence intensity in the solution. Based on the measurement of the fluorescence intensity, the level of target DNA in the samples was determined. The remaining DNA molecules on the RFMP-Fe(3)O(4)@Al(2)O(3) MNPs were characterized by using matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The detection limit for DNA was as low as 40 pM using this approach.

Functional gold nanoclusters as antimicrobial agents for antibiotic-resistant bacteria.

AIMS: Our aim was to demonstrate that lysozyme-directed generation of gold nanoclusters (Au NCs) are potential antimicrobial agents for antibiotic-resistant bacteria and broad labeling agents for pathogenic bacteria. MATERIALS & METHODS: Lysozyme is an enzyme that is capable of hydrolyzing the cell walls of bacteria. In this study, we demonstrated the generation of functional Au NCs by using lysozyme as the sequester and the reducing agent for Au precursors at 40 degrees C. In addition, to shorten the reaction time, the reaction was conducted under microwave irradiation within a short period of time for the first time. RESULTS: The bioactivity of the lysozyme on the Au NCs was retained. Therefore, the as-prepared lysozyme-Au NCs with desirable fluorescence feature were successfully employed to be broad-band labeling agents for pathogenic bacteria. Furthermore, we also demonstrated that the lysozyme-Au NCs can be used to effectively inhibit the cell growth of notorious antibiotic-resistant bacteria, including pan-drug-resistant Acinetobacter baumannii and vancomycin-resistant Enterococcus faecalis. CONCLUSION: The potential of employing the lysozyme-Au NCs for bacterial labeling and as antimicrobial agents is expected.