MICRO AND NANO-FLUIDICS FOR DNA MOLECULES APPLICATIONS

Master'sMASTER OF SCIENC

High-Sensitive Detection and Quantitative Analysis of Thyroid-Stimulating Hormone Using Gold-Nanoshell-Based Lateral Flow Immunoassay Device

Au nanoparticles (AuNPs) have been used as signal reporters in colorimetric lateral flow immunoassays (LFAs) for decades. However, it remains a major challenge to significantly improve the detection sensitivity of traditional LFAs due to the low brightness of AuNPs. As an alternative approach, we overcome this problem by utilizing 150 nm gold nanoshells (AuNSs) that were engineered by coating low-density silica nanoparticles with a thin layer of gold. AuNSs are dark green, have 14 times larger surface area, and are approximately 35 times brighter compared to AuNPs. In this study, we used detection of thyroid-stimulating hormone (TSH) in a proof-of-concept assay. The limit of detection (LOD) with AuNS-based LFA was 0.16 µIU/mL, which is 26 times more sensitive than the conventional colorimetric LFA that utilizes AuNP as a label. The dynamic range of the calibration curve was 0.16–9.5 µIU/mL, making it possible to diagnose both hyperthyroidism (5 µIU/mL) using AuNS-based LFA. Thus, the developed device has a strong potential for early screening and diagnosis of diseases related to the thyroid hormone

Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene

Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug- resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation

Laser-Patternable Graphene Field Emitters for Plasma Displays

This paper presents a plasma display device (PDD) based on laser-induced graphene nanoribbons (LIGNs), which were directly fabricated on polyimide sheets. Superior field electron emission (FEE) characteristics, viz. a low turn-on field of 0.44 V/μm and a large field enhancement factor of 4578, were achieved for the LIGNs. Utilizing LIGNs as a cathode in a PDD showed excellent plasma illumination characteristics with a prolonged plasma lifetime stability. Moreover, the LIGN cathodes were directly laser-patternable. Such superior plasma illumination performance of LIGN-based PDDs has the potential to make a significant impact on display technology

Facilitated sequence assembly using densely labeled optical DNA barcodes:A combinatorial auction approach

<div><p>The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.</p></div

A three-dimensional Mn3O4 network supported on a nitrogenated graphene electrocatalyst for efficient oxygen reduction reaction in alkaline media

Developing low cost oxygen reduction catalysts that perform with high efficiency is highly desirable for the commercial success of environmentally friendly energy conversion devices such as fuel cells and metal-air batteries. In this work a three-dimensional, 3D, self-assembled Mn3O4 hierarchical network has been grown on nitrogen doped reduced graphene oxide (NrGO), by a facile and controllable electrodeposition process and its electrocatalytic performance for oxygen reduction reaction (ORR) has been assessed. The directly electrodeposited MnOx on a glassy carbon electrode (GCE) exhibits little electrocatalytic activity, whereas the integrated Mn3O4/NrGO catalyst is more ORR active than the NrGO. The resulting electrode architecture exhibits an "apparent" four-electron oxygen reduction pathway involving a dual site reduction mechanism due to the synergetic effect between Mn3O4 and NrGO. The 3D Mn3O4/NrGO hierarchical architecture exhibits improved durability and methanol tolerance, far exceeding the commercial Pt/C. The enhanced ORR performance of the room temperature electrodeposited Mn3O4 nanoflake network integrated with NrGO reported here offers a new pathway for designing advanced catalysts for energy conversion and storage.</p

Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach

Large-scale genomic alterations play an important role in disease, gene expression, andchromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensityprofiles (DNA barcodes) along single DNA molecules and is a technique well-suited fordetecting such alterations. For sparsely-labelled barcodes, the possibility to detect largegenomic alterations has been investigated extensively, while densely-labelled barcodeshave not received as much attention. In this work, we introduce HMMSV, a hidden Markovmodel (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach usingsimulated data-sets with 5 different types of SVs, and combinations thereof, and demon-strate that the method reaches a true positive rate greater than 80% for randomly generatedbarcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV fur-ther leads to larger true positive rates. For a real data-set with experimental barcodes onbacterial plasmids, we successfully detect matching barcode pairs and SVs without any par-ticular assumption of the types of SVs present. Instead, our method effectively goes throughall possible combinations of SVs. Since ODM works on length scales typically not reachablewith other techniques, our methodology is a promising tool for identifying arbitrary combina-tions of genomic alterations