Nerding for Newbies 2014 A Summer School in Computers & Programming

Recruiting students to informatics can be a challenge, particularly when itcomes to recruiting female students. The Department of Informatics at theUniversity of Bergen has had severe problems with both recruitment andretention of female students.As part of an effort to raise interest in computers and programming ingeneral, and among women in particular, we organised a two-week summerschool where students could learn a range of subject including programming,Linux, electronics, statistics and other basic computer geek skills – in short,Nerding for Newbies. In this paper, we discuss the organisation of the summerschool, our teaching methods and our experiences

Control of Neural Stem Cell Survival by Electroactive Polymer Substrates

Stem cell function is regulated by intrinsic as well as microenvironmental factors, including chemical and mechanical signals. Conducting polymer-based cell culture substrates provide a powerful tool to control both chemical and physical stimuli sensed by stem cells. Here we show that polypyrrole (PPy), a commonly used conducting polymer, can be tailored to modulate survival and maintenance of rat fetal neural stem cells (NSCs). NSCs cultured on PPy substrates containing different counter ions, dodecylbenzenesulfonate (DBS), tosylate (TsO), perchlorate (ClO4) and chloride (Cl), showed a distinct correlation between PPy counter ion and cell viability. Specifically, NSC viability was high on PPy(DBS) but low on PPy containing TsO, ClO4 and Cl. On PPy(DBS), NSC proliferation and differentiation was comparable to standard NSC culture on tissue culture polystyrene. Electrical reduction of PPy(DBS) created a switch for neural stem cell viability, with widespread cell death upon polymer reduction. Coating the PPy(DBS) films with a gel layer composed of a basement membrane matrix efficiently prevented loss of cell viability upon polymer reduction. Here we have defined conditions for the biocompatibility of PPy substrates with NSC culture, critical for the development of devices based on conducting polymers interfacing with NSCs

Conjugated Polymers, Amyloid Detection and Assembly of Biomolecular Nanowires

The research field of conjugated polymers has grown due to the optical and electronic properties of the material, useful in applications such as solar cells and printed electronics, but also in biosensors and for interactions with biomolecules. In this thesis conjugated polymers have been used in two related topics; to detect conformational changes in proteins and to assemble the polymers with biomolecules into nanowires. Within biosensing, conjugated polymers have been used for detection of a wide range of biological events, such as DNA hybridization or enzymatic activity, utilizing both electronic and optical changes in the polymer. Here the focus has been to use the polymers as optical probes to discriminate between native and misfolded protein, as well as to follow the misfolding processes in vitro. The understanding and detection of protein misfolding, for example amyloid fibril formation, is a topic of growing importance. The misfolding process is strongly associated with several devastating diseases such as Alzheimer’s disease, Parkinson’s disease and Bovine Spongiform Encephalopathy (BSE). We have developed detection schemes for discrimination between proteins in the native or amyloid fibril state based on luminescent polythiophene derivatives. Through a synthesis strategy based on polymerization of trimer blocks rather than of monomers, polythiophene derivatives with higher optical signal specificity for amyloid-like fibrils were obtained. Self-assembly of nanowires containing conjugated polymers is a route to generate structures of unique opto-electrical characteristics without the need for tedious topdown processes. Biomolecules can have nanowire geometries of extraordinary aspect ratio and functionalities. The DNA molecule is the most well known and exploited of these. In this thesis work the more stable amyloid fibril has been used as a template to organize conjugated polymers. Luminescent, semi-conducting, conjugated polymers have been incorporated in and assembled onto amyloid fibrils. Using luminescence quenching we have demonstrated that the conjugated material can retain the electro-activity after the incorporation process. Furthermore, the amyloid fibril/conjugated polymer hybrid structures can be organized on surfaces by the means of molecular combing and soft lithography. In the process of generating self-assembled biomolecular nanowires functionalized with conjugated polymers, we have shown a new synthesis strategy for a water-soluble highly conducting polythiophene derivative. This material, PEDOT-S, has shown affinity for amyloid fibrils, but can also be very useful in conventional opto-electronic polymer-based devices

Sorption of Neuropsychopharmaca in Microfluidic Materials for In Vitro Studies

Sorption (i.e., adsorption and absorption) of small-molecule compounds to polydimethylsiloxane (PDMS) is a widely acknowledged phenomenon. However, studies to date have largely been conducted under atypical conditions for microfluidic applications (lack of perfusion, lack of biological fluids, etc.), especially considering biological studies such as organs-on-chips where small-molecule sorption poses the largest concern. Here, we present an in-depth study of small-molecule sorption under relevant conditions for microphysiological systems, focusing on a standard geometry for biological barrier studies that find application in pharmacokinetics. We specifically assess the sorption of a broad compound panel including 15 neuropsychopharmaca at in vivo concentration levels. We consider devices constructed from PDMS as well as two material alternatives (off-stoichiometry thiol–ene–epoxy, or tape/polycarbonate laminates). Moreover, we study the much neglected impact of peristaltic pump tubing, an essential component of the recirculating systems required to achieve in vivo-like perfusion shear stresses. We find that the choice of the device material does not have a significant impact on the sorption behavior in our barrier-on-chip-type system. Our PDMS observations in particular suggest that excessive compound sorption observed in prior studies is not sufficiently described by compound hydrophobicity or other suggested predictors. Critically, we show that sorption by peristaltic tubing, including the commonly utilized PharMed BPT, dominates over device sorption even on an area-normalized basis, let alone at the typically much larger tubing surface areas. Our findings highlight the importance of validating compound dosages in organ-on-chip studies, as well as the need for considering tubing materials with equal or higher care than device materials.QC 20211020</p

Generation of Human iPSC-Derived Astrocytes with a mature star-shaped phenotype for CNS modeling

The generation of astrocytes from human induced pluripotent stem cells has been hampered by either prolonged diferentiation—spanning over two months—or by shorter protocols that generate immature astrocytes, devoid of salient matureastrocytic traits pivotal for central nervous system (CNS) modeling. We directed stable hiPSC-derived neuroepithelial stemcells to human iPSC-derived Astrocytes (hiAstrocytes) with a high percentage of star-shaped cells by orchestrating anastrocytic-tuned culturing environment in 28 days. We employed RT-qPCR and ICC to validate the astrocytic commitmentof the neuroepithelial stem cells. To evaluate the infammatory phenotype, we challenged the hiAstrocytes with the proinfammatory cytokine IL-1β (interleukin 1 beta) and quantitatively assessed the secretion profle of astrocyte-associatedcytokines and the expression of intercellular adhesion molecule 1 (ICAM-1). Finally, we quantitatively assessed the capacityof hiAstrocytes to synthesize and export the antioxidant glutathione. In under 28 days, the generated cells express canonicaland mature astrocytic markers, denoted by the expression of GFAP, AQP4 and ALDH1L1. In addition, the notion of a maturephenotype is reinforced by the expression of both astrocytic glutamate transporters EAAT1 and EAAT2. Thus, hiAstrocyteshave a mature phenotype that encompasses traits critical in CNS modeling, including glutathione synthesis and secretion,upregulation of ICAM-1 and a cytokine secretion profle on a par with human fetal astrocytes. This protocol generates amultifaceted astrocytic model suitable for in vitro CNS disease modeling and personalized medicine.QC 20220503</p

Data for “<b>Modeling subarachnoid hemorrhage </b><b><i>in vitro</i></b><b>: an exploratory analysis of brain microvascular endothelial cells gene expression modulation by astrocytes”</b>

Submitted to Fluids and Barriers of the CNS</p

Single molecular imaging and spectroscopy of conjugated polyelectrolytes decorated on stretched aligned DNA

DNA is the prototype template for building nanoelectronic devices by self-assembly. The electronic functions are made possible by coordinating electronic polymer chains to DNA. This paper demonstrates two methods for fabrication of aligned and ordered DNA nanowires complexed with conjugated polyelectrolytes (CPEs). The complex can be formed either in solution prior to stretching or after stretching of the bare DNA on a surface. Molecular combing was used to stretch the complexes on surface energy patterned surfaces, and PMMA for the bare DNA. Single molecular spectroscopy, in fluorescence, and microscopy, in atomic force microscopy, give evidence for coordination of the short CPE chains to the aligned DNA