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Pirlo R.K.,National Research Council Research Associate | Wu P.,Southern Oregon University | Liu J.,Center for Biomolecular Science and Engineering | Ringeisen B.,U.S. Navy
Biotechnology and Bioengineering | Year: 2012

Two major challenges in tissue engineering are mimicking the native cell-cell arrangements of tissues and maintaining viability of three-dimension (3D) tissues thicker than 300μm. Cell printing and prevascularization of engineered tissues are promising approaches to meet these challenges. However, the printing technologies used in biofabrication must balance the competing parameters of resolution, speed, and volume, which limit the resolution of thicker 3D structures. We suggest that high-resolution conformal printing techniques can be used to print 2D patterns of vascular cells onto biopaper substrates which can then be stacked to form a thicker tissue construct. Towards this end we created 1cm×1cm×300μm biopapers to be used as the transferable, stackable substrate for cell printing. 3.6% w/v poly-lactide-co-glycolide was dissolved in chloroform and poured into molds filled with NaCl crystals. The salt was removed with DI water and the scaffolds were dried and loaded with a Collagen Type I or Matrigel™. SEM of the biopapers showed extensive porosity and gel loading throughout. Biological laser printing (BioLP™) was used to deposit human umbilical vein endothelial cells (HUVEC) in a simple intersecting pattern to the surface of the biopapers. The cells differentiated and stretched to form networks preserving the printed pattern. In a separate experiment to demonstrate "stackability," individual biopapers were randomly seeded with HUVECs and cultured for 1 day. The mechanically stable and viable biopapers were then stacked and cultured for 4 days. Three-dimensional confocal microscopy showed cell infiltration and survival in the compound multilayer constructs. These results demonstrate the feasibility of stackable "biopapers" as a scaffold to build 3D vascularized tissues with a 2D cell-printing technique. © 2011 Wiley Periodicals, Inc. Source

Franks A.E.,University of Massachusetts Amherst | Nevin K.P.,University of Massachusetts Amherst | Glaven R.H.,University of Massachusetts Amherst | Glaven R.H.,Center for Biomolecular Science and Engineering | Lovley D.R.,University of Massachusetts Amherst
ISME Journal | Year: 2010

Further insight into the metabolic status of cells within anode biofilms is essential for understanding the functioning of microbial fuel cells and developing strategies to optimize their power output. Cells throughout anode biofilms of Geobacter sulfurreducens reduced the metabolic stains: 5-cyano-2,3-ditolyl tetrazolium chloride and Redox Green, suggesting metabolic activity throughout the biofilm. To compare the metabolic status of cells growing close to the anode versus cells in the outer portion of the anode biofilm, anode biofilms were encased in resin and sectioned into inner (0-20 m from anode surface) and outer (30-60 m) fractions. Transcriptional analysis revealed that, at a twofold threshold, 146 genes had significant (P>0.05) differences in transcript abundance between the inner and outer biofilm sections. Only 1 gene, GSU0093, a hypothetical ATP-binding cassette transporter, had significantly higher transcript abundances in the outer biofilm. Genes with lower transcript abundance in the outer biofilm included genes for ribosomal proteins and NADH dehydrogenase, suggesting lower metabolic rates. However, differences in transcript abundance were relatively low (>threefold) and the expression of genes for the tricarboxylic acid cycle enzymes was not significantly lower. Lower expression of genes involved in stress responses in the outer biofilm may reflect the development of low pH near the surface of the anode. The results of this study suggest that cells throughout the biofilm are metabolically active and can potentially contribute to current production. The microtoming/microarray strategy described here may be useful for evaluating gene expression with depth in a diversity of microbial biofilms. © 2010 International Society for Microbial Ecology. All Rights Reserved. Source

Paz I.,Technion - Israel Institute of Technology | Kosti I.,Technion - Israel Institute of Technology | Ares Jr. M.,Cellular and Developmental Biology | Cline M.,Center for Biomolecular Science and Engineering | Mandel-Gutfreund Y.,Technion - Israel Institute of Technology
Nucleic Acids Research | Year: 2014

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5' and 3' UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. © 2014 The Author(s). Source

Edwankar C.R.,University of Wisconsin - Milwaukee | Edwankar R.V.,University of Wisconsin - Milwaukee | Deschamps J.R.,Center for Biomolecular Science and Engineering | Cook J.M.,University of Wisconsin - Milwaukee
Angewandte Chemie - International Edition | Year: 2012

All five: The first total synthesis of the C2-symmetric indole alkaloid 1 involved a late-stage thallium(III) acetate-mediated intermolecular oxidative coupling to construct the C9-C9' bond with complete regio- and stereocontrol. The formation of a single atropodiastereomer in this critical step arises from internal asymmetric induction. The first total synthesis of four other monomeric sarpagine indole alkaloids is also described. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Source

Zerbino D.R.,Center for Biomolecular Science and Engineering
Current Protocols in Bioinformatics | Year: 2010

The Velvet de novo assembler was designed to build contigs and eventually scaffolds from short-read sequencing data. This protocol describes how to use Velvet, interpret its output, and tune its parameters for optimal results. It also covers practical issues such as configuration, using the VelvetOptimiser routine, and processing colorspace data. Copyright © 2010 John Wiley & Sons, Inc. Source

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