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The capacity of human induced pluripotent stem cells (hiPSCs) for indefinite self-renewal warrants their application in disease modeling, drug discovery, toxicity assays and efficacy screening. However, their poor proliferation ability, inability to adhere to surfaces without Matrigel coating and tendency to spontaneously differentiate in vitro hinder the application of hiPSCs in these fields. Here we study the ability to culture hiPSCs inside 200 ​nL droplets on the droplet microarray (DMA) platform. We demonstrate that (1) hiPSCs can attach to the Matrigel (MG)-free surface of DMA and show good viability after 24 h culture; (2) hiPSC do not spontaneously differentiate when cultured on the MG-free surface of DMAs; (3) culturing of hiPSCs in 200 ​nL as compared to 2 ​mL culture leads to higher expression of the Nanog pluripotency marker. Overall, the results demonstrate the possibility to culture undifferentiated hiPSCs in 200 ​nL droplets on DMA, thereby opening the possibility for high-throughput screenings of hiPSCs with various factors without compromising the results through the involvement of animal-derived materials, such as Matrigel., Graphical abstract Image 1

Highlights • Developed a high-throughput microarray for anti-microbial susceptibility testing (AST). • Demonstrated that the feasibility of the AST against clinical isolates of MRSA. • Platform is a low sample volume, rapid, high-throughput alternative to traditional assays., We describe the development of a novel, high-throughput, nano-scale microarray platform for antimicrobial susceptibility testing (AST). The platform allows to process 480 samples at 50 nL volume on a single chip, analyze by fluorescence read-out with an easy dunk-and-rinse step, and the ability to process multiple samples and chips simultaneously. We demonstrate the applicability of this chip for culturing community acquired methicillin resistant Staphylococcus aureus (CA-MRSA), and perform AST against clinical isolates of CA-MRSA. The chip platform holds promise for an impact in microbial biotechnology as an attractive high-throughput, lower sample volume and quicker alternative to conventional AST such as the traditional broth microdilution or the newer automated systems.

Alternative splicing is a highly regulated process which generates transcriptome and proteome diversity through the skipping or inclusion of exons within gene loci. Identification of aberrant alternative splicing associated with human diseases has become feasible with the development of new genomic technologies and powerful bioinformatics. We have previously reported genome-wide gene alterations in the neocortex of a well-characterized cohort of Alzheimer's disease (AD) patients and matched elderly controls using a commercial exon microarray platform [1]. Here, we provide detailed description of analyses aimed at identifying differential alternative splicing events associated with AD.

The interest towards extracellular vesicles (EVs) has grown exponentially over the last few years; being involved in intercellular communication and serving as reservoirs for biomarkers for tumors, they have a great potential for liquid biopsy development, possibly replacing many costly and invasive tissue biopsies. Here we propose, for the first time, the use of a Si/SiO2 interferometric, microarray platform for multiparametric intact EVs analysis combining label-free EVs mass quantitation and high sensitivity fluorescence based phenotyping. Label free interferometric measurement allows to quantify the amount of vesicles captured by printed antibodies while, on the same chip, EVs are also detected by fluorescence in a sandwich immunoassay. The proposed method simultaneously detects, quantify and phenotype intact EVs in a microarray format.

Publisher Summary This chapter focuses on DNA microarray-based large-scale gene expression studies in the nervous system concentrating on the choice of microarray platform, data analysis, and interpretation. Microarray experiments start with array design and synthesis. The purity and quality of the starting RNA has a significant effect on the results of microarray experiments, so it is essential that all the steps of RNA isolation be carried out with maximum care and speed. In addition, choosing the appropriate array slides is essential. The chapter proposes several data analysis and interpretation steps found prerequisite for most microarray experiments. Several bioinformatic approaches are available that facilitate the data interpretation and further hypothesis building. The potential presence of false positives and false negatives in a microarray experiment requires validating a subset of the information (genes) identified by microarray analysis. The analytical tools are becoming more standardized and statistical thresholds are more accepted. Bioinformatic mining of the data and functional confirmation remains an important challenge and is one of the exciting areas of progress.