Capture

The piece consists of an interactive multimedia ‘game’ which requires the player to conceal themselves and remain still and silent to allow a landscape to grow and move. The work was curated for public display in the show The Image Looks Back, at RMIT Gallery, Melbourne, in Spring 2020, as part of the biennale PHOTO2020. The work was the product of a team comprising Adam Brown, Tabea Iseli and Alan Warburton, and won the 2018 Post-Photography Prototyping Prize, organised by Fotomuseum Winterthur, the Photographers’ Gallery, London and the Julius Baer Foundation. The piece was built in 24 hours, in a ‘hackathon’ involving competing teams selected by a panel of experts. It combined team members’ individual skills in games design, photography and CGI modelling

Untersuchung von Renaturierungskonzepten am Seeufer Gals, Bielersee

Analyse des ökologischen Aufwertungspotentials am Seeufer Gals (Bielersee, Schweiz), welche mithilfe einer hydrodynamisch- numerischen Modellierung mit der Software MIKE 21 und Bestimmung von Makrophyten vorgenommen wurde. Unter der Annahme von zwei unterschiedlich starken Windszenarien wurden die windinduzierten signifikanten Wellenhöhen und die welleninduzierten Strömungen für verschiedene Varianten simuliert. Die Ergebnisse der Modellierungen zeigten, ob die in den Varianten geplanten Massnahmen eine Reduzierung der Wellenhöhen und der Strömungen verursachen. Das Hauptziel war, Bedingungen zu schaffen, welche den Habitatsansprüchen von Makrophyten zusagen und somit eine Neuansiedlung von Makrophytenarten an dem Seeufer Gals möglich machen und gleichzeitig die Wellenbelastung auf das Ufer zu verringern, um eine fortschreitende Erosion zu vermeiden. Mithilfe einiger Massnahmen konnten erfolgsversprechende Ergebnisse erzielt werden, die zu einer Verbesserung der aktuellen Situation führen würden. Es wurde ebenfalls gezeigt, dass Makrophyten für die Beurteilung eine bedeutende Rolle spielen, doch eine Bewertung nur anhand von ihnen sehr schwierig ist, da sie nicht nur auf Wellen- und Strömungsbedingungen, sondern auf weitere Faktoren und zudem extrem schnell auf deren Veränderungen reagieren. Die Studie wurde im Rahmen einer Masterarbeit an der TU Dresden im Landschaftswerk Biel-Seeland durchgeführt

Indexing Strategies for Rapid Searches of Short Words in Genome Sequences

Searching for matches between large collections of short (14–30 nucleotides) words and sequence databases comprising full genomes or transcriptomes is a common task in biological sequence analysis. We investigated the performance of simple indexing strategies for handling such tasks and developed two programs, fetchGWI and tagger, that index either the database or the query set. Either strategy outperforms megablast for searches with more than 10,000 probes. FetchGWI is shown to be a versatile tool for rapidly searching multiple genomes, whose performance is limited in most cases by the speed of access to the filesystem. We have made publicly available a Web interface for searching the human, mouse, and several other genomes and transcriptomes with oligonucleotide queries

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.

The huge genetic diversity of circulating viruses is a challenge for diagnostic assays for emerging or rare viral diseases. High-throughput technology offers a new opportunity to explore the global virome of patients without preconception about the culpable pathogens. It requires a solid reference dataset to be accurate. Virosaurus has been designed to offer a non-biased, automatized and annotated database for clinical metagenomics studies and diagnosis. Raw viral sequences have been extracted from GenBank, and cleaned up to remove potentially erroneous sequences. Complete sequences have been identified for all genera infecting vertebrates, plants and other eukaryotes (insect, fungus, etc.). To facilitate the analysis of clinically relevant viruses, we have annotated all sequences with official and common virus names, acronym, genotypes, and genomic features (linear, circular, DNA, RNA, etc.). Sequences have been clustered to remove redundancy at 90% or 98% identity. The analysis of clustering results reveals the state of the virus genetic landscape knowledge. Because herpes and poxviruses were under-represented in complete genomes considering their potential diversity in nature, we used genes instead of complete genomes for those in Virosaurus

Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

Hen egg-white lysozyme has long been the paradigm for enzymatic glycosyl hydrolysis with retention of configuration, with a protonated carboxylic acid and a deprotonated carboxylate participating in general acid-base catalysis. In marked contrast, the retaining chitin degrading enzymes from glycosyl hydrolase families 18 and 20 all have a single glutamic acid as the catalytic acid but lack a nucleophile on the enzyme. Both families have a catalytic (βα)8-barrel domain in common. X-ray structures of three different chitinolytic enzymes complexed with substrates or inhibitors identify a retaining mechanism involving a protein acid and the carbonyl oxygen atom of the substrate’s C2 N-acetyl group as the nucleophile. These studies unambiguously demonstrate the distortion of the sugar ring toward a sofa conformation, long postulated as being close to that of the transition state in glycosyl hydrolysis.

MAR-Mediated transgene integration into permissive chromatin and increased expression by recombination pathway engineering.

Untargeted plasmid integration into mammalian cell genomes remains a poorly understood and inefficient process. The formation of plasmid concatemers and their genomic integration has been ascribed either to non-homologous end-joining (NHEJ) or homologous recombination (HR) DNA repair pathways. However, a direct involvement of these pathways has remained unclear. Here, we show that the silencing of many HR factors enhanced plasmid concatemer formation and stable expression of the gene of interest in Chinese hamster ovary (CHO) cells, while the inhibition of NHEJ had no effect. However, genomic integration was decreased by the silencing of specific HR components, such as Rad51, and DNA synthesis-dependent microhomology-mediated end-joining (SD-MMEJ) activities. Genome-wide analysis of the integration loci and junction sequences validated the prevalent use of the SD-MMEJ pathway for transgene integration close to cellular genes, an effect shared with matrix attachment region (MAR) DNA elements that stimulate plasmid integration and expression. Overall, we conclude that SD-MMEJ is the main mechanism driving the illegitimate genomic integration of foreign DNA in CHO cells, and we provide a recombination engineering approach that increases transgene integration and recombinant protein expression in these cells. Biotechnol. Bioeng. 2017;114: 384-396. © 2016 The Authors. Biotechnology and Bioengineering published by Wiley Periodicals, Inc

Baccharis dracunculifolia, the main source of green propolis, exhibits potent antioxidant activity and prevents oxidative mitochondrial damage

Baccharis dracunculifolia DC (Asteraceae) is the main botanical source used by honeybees to produce Brazilian green propolis whose hepatoprotective properties have been already described. in this work we investigated the protective effects of the glycolic extract of B. dracunculifolia (GEBd) against oxidative stress in isolated rat liver mitochondria (RLM). the GEBd was prepared by fractionated percolation using propylene glycol as solvent. the total phenols and flavonoids, which are substances with recognized antioxidant action, were quantified in GEBd and the phytochemical analysis was carried out by HPLC. GEBd exhibited significant scavenger activity towards DPPH radicals and superoxide anions in a concentration-dependent manner, and also a Fe2+ chelating activity. GEBd decreased the basal H2O2 generation and the Fe2+- or t-BuOOH-induced ROS production in isolated mitochondria. Lipid oxidation of mitochondrial membranes, protein thiol groups and GSH oxidation were also prevented by GEBd. This shows that B. dracunculifolia exhibit potent antioxidant activity protecting liver mitochondria against oxidative damage and such action probably contribute to the antioxidant and hepatoprotective effects of green propolis. (C) 2011 Elsevier B.V. All rights reserved.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Univ Mogi das Cruzes UMC, Ctr Interdisciplinar Invest Bioquim CIIB, Mogi Das Cruzes, SP, BrazilUniv Estadual Paulista UNESP, Inst Quim, São Paulo, BrazilFac Ciencias Farmaceut Ribeirao Preto FCFRP USP, São Paulo, BrazilUniversidade Federal de São Paulo UNIFESP, Dept Bioquim, São Paulo, BrazilUniv Fed ABC UFABC, Ctr Ciencias Nat & Humanas CCNH, Santo Andre, SP, BrazilUniversidade Federal de São Paulo UNIFESP, Dept Bioquim, São Paulo, BrazilFAPESP: 2008/01724-4FAPESP: 2008/07246-7CNPq: 301672/2009-1CNPq: 136255/2009-4Web of Scienc

Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing.

The activation, or maturation, of dendritic cells (DCs) is crucial for the initiation of adaptive T-cell mediated immune responses. Research on the molecular mechanisms implicated in DC maturation has focused primarily on inducible gene-expression events promoting the acquisition of new functions, such as cytokine production and enhanced T-cell-stimulatory capacity. In contrast, mechanisms that modulate DC function by inducing widespread gene-silencing remain poorly understood. Yet the termination of key functions is known to be critical for the function of activated DCs. Genome-wide analysis of activation-induced histone deacetylation, combined with genome-wide quantification of activation-induced silencing of nascent transcription, led us to identify a novel inducible transcriptional-repression pathway that makes major contributions to the DC-maturation process. This silencing response is a rapid primary event distinct from repression mechanisms known to operate at later stages of DC maturation. The repressed genes function in pivotal processes--including antigen-presentation, extracellular signal detection, intracellular signal transduction and lipid-mediator biosynthesis--underscoring the central contribution of the silencing mechanism to rapid reshaping of DC function. Interestingly, promoters of the repressed genes exhibit a surprisingly high frequency of PU.1-occupied sites, suggesting a novel role for this lineage-specific transcription factor in marking genes poised for inducible repression