Manual / Issue 11 / Repair

Manual, a journal about art and its making. Repair. Can we find in the detail, in the stitch and the weave, an ecology of care, a model for activating new forms of life, ones that might reject or reimagine an economic and cultural order based on novelty, disposability, and the monadic self? Can they help us learn to live together in a broken world? —Brian Goldberg and Kate Irvin, from the preface to Issue 11 This volume complemented the exhibition Repair and Design Futures, on view at the RISD Museum October 5, 2018 through June 30, 2019. Softcover, 96 pages. Published 2018 by the RISD Museum. Manual 11 (Repair) contributors include Markus Berger, Gina Borromeo, Linda Catano, Thomas Denenberg, Daniel Eatock, Brian Goldberg, Ramiro Gomez, Kate Irvin, Anna Rose Keefe, Olivia Laing, Steven Lubar, Roberto Lugo, Lisa Z. Morgan, Maureen C. O’Brien, Barry Schwabsky, Sharma Shields, Jessica Urick, and Liliane Wong.https://digitalcommons.risd.edu/risdmuseum_journals/1037/thumbnail.jp

Nucleosome Chiral Transition under Positive Torsional Stress in Single Chromatin Fibers

Using magnetic tweezers to investigate the mechanical response of single chromatin fibers, we show that fibers submitted to large positive torsion transiently trap positive turns, at a rate of one turn per nucleosome. A comparison with the response of fibers of tetrasomes (the (H3-H4)2 tetramer bound with ~50 bp of DNA) obtained by depletion of H2A-H2B dimers, suggests that the trapping reflects a nucleosome chiral transition to a metastable form built on the previously documented righthanded tetrasome. In view of its low energy, <8 kT, we propose this transition is physiologically relevant and serves to break the docking of the dimers on the tetramer which in the absence of other factors exerts a strong block against elongation of transcription by the main RNA polymerase.Comment: 33 pages (double spacing), 7 figure

Study of the methylation status of the desmoplakin gene and its role in the onset of arrhythmogenic cardiomyopathy

[ES] La miocardiopatía arritmogénica (MCA) es una enfermedad genética rara (OMIM #107970; ORPHA247) con una prevalencia de entre 1:1000 y 1:5000. Se caracteriza por la sustitución progresiva del miocardio por tejido fibroadiposo y puede debutar directamente con muerte súbita. Se conocen 16 genes cuyas mutaciones pueden ser causantes de MCA, siendo más frecuentes las mutaciones en genes desmosómicos (desmoplaquina-DSP, placofilina-2, desmocolina-2, desmogleína-2 y placoglobina). El patrón de herencia de estos genes es con frecuencia autosómico dominante, tiene una penetrancia incompleta y una expresividad variable. La epigenética modula la producción proteica pero el estudio del tejido clave en la MCA plantea limitaciones éticas en tanto en cuanto supone tener que realizar una biopsia endomiocárdica asumiendo potenciales riesgos de complicaciones. Por ello, decidimos verificar si el frotis bucal (fácilmente accesible, barato y sin riesgos) puede actuar como como espejo de lo que sucede en el corazón. Más concretamente, desde un punto de vista bibliográfico evaluamos si el estado los promotores de los genes causantes de la enfermedad son metilables. De entre ellos seleccionamos el gen DSP para el estudio de su metilación por pirosecuenciación en la muestra disponible en humanos, pues es uno de los que tenemos familias bien caracterizadas en la consulta de Cardiopatías Familiares. Se reclutaron 13 portadores de mutación en DSP sin expresión del fenotipo de MCA, 25 pacientes MCA y 11 familiares sanos. Gracias a la actividad trasplantadora del centro en el que se realizó el trabajo, se reclutaron 7 pacientes con muestra pareada de frotis bucal y miocardio obtenidos al acudir a recibir un trasplante cardíaco por insuficiencia cardíaca terminal, independientemente del diagnóstico de base. Se analizaron 4 regiones del gen que comprendían 14 sitios metilables de una isla CpG y un shore localizada en el promotor del gen. Este estudio se realizó en queratinocitos bucales como biomarcador de fenotipo subrogado de la MCA. Dada la situación de alerta sanitaria quedó pendiente la validación de los resultados downstream mediante la cuantificación del mRNA de DSP en dichas muestras para correlacionar el nivel de metilación y de expresión del gen en cada una de las muestras recogidas.[EN] Arrhythmogenic cardiomyopathy (ACM) is a rare genetic disease (OMIM # 107970; ORPHA247) with a prevalence of between 1:1000 and 1:5000. It is characterized by the progressive replacement of the myocardium by fibrofatty tissue and can debut directly with sudden death. Mutations in 16 genes were identified as the cause of ACM with mutations being more frequent in desmosomal genes (desmoplakin-DSP, placophilin-2, desmocollin-2, desmoglein-2 and plakoglobin). The inheritance pattern of these genes is often autosomal dominant, has incomplete penetrance, and variable expressivity. Epigenetics modulates protein production, but the study of the heart tissue in ACM poses ethical limitations as it involves having to perform an endomyocardial biopsy, assuming potential risks of complications. Therefore, we decided to verify if oral keratinocytes (easily accessible, cheap and without risks) can act as a substitute of what happens in the heart. From a bibliographic point of view, we evaluated whether the state of the promoters of the genes causing the disease are methylable. From among them, we selected the DSP gene for the study of its methylation by pyrosequencing in the sample available in humans, since we have well-characterized families in the Family Heart Disease consultation. 13 DSP mutation carriers without expression of the ACM phenotype, 25 ACM patients and 11 healthy family members were recruited. Thanks to the transplantation activity of the center where the work was carried out, we recruited 7 patients with a paired sample of oral keratinocytes and myocardial tissue, regardless of the underlying diagnosis. 4 regions of the gene were analyzed that comprised 14 methylatable sites of a CpG island and shore located in the gene promoter. This study was carried out in oral keratinocytes as a surrogate phenotype biomarker of ACM. Given the health alert situation, the validation of the downstream results by quantifying the DSP mRNA in said samples are pending to correlate the level of methylation and gene expression in each of the samples collected.Este trabajo fue parcialmente financiado con ayudas de investigación del Instituto de Salud Carlos III, FEDER “Unión Europea”, "Una forma de hacer Europa” [PI18/01582; CIBERCV, Biobanco La Fe PT17/0015/0043] y el Memorial Nacho Barberá.Lin Wong, L. (2020). Estudio del estado de metilación del gen de desmoplaquina y su papel en el desarrollo de la miocardiopatía arritmogénica. Universitat Politècnica de València. http://hdl.handle.net/10251/151332TFG

In silico analysis of 16S ribosomal RNA gene sequencing‐based methods for identification of medically important anaerobic bacteria

This study is the first study that provides useful guidelines to clinical microbiologists and technicians on the usefulness of full 16S rRNA sequencing, 5′‐end 527‐bp 16S rRNA sequencing and the existing MicroSeq full and 500 16S rDNA bacterial identification system (MicroSeq, Perkin‐Elmer Applied Biosystems Division, Foster City, California, USA) databases for the identification of all existing medically important anaerobic bacteria. Full and 527‐bp 16S rRNA sequencing are able to identify 52–63% of 130 Gram‐positive anaerobic rods, 72–73% of 86 Gram‐negative anaerobic rods and 78% of 23 anaerobic cocci. The existing MicroSeq databases are able to identify only 19–25% of 130 Gram‐positive anaerobic rods, 38% of 86 Gram‐negative anaerobic rods and 39% of 23 anaerobic cocci. These represent only 45–46% of those that should be confidently identified by full and 527‐bp 16S rRNA sequencing. To improve the usefulness of MicroSeq, bacterial species that should be confidently identified by full and/or 527‐bp 16S rRNA sequencing but not included in the existing MicroSeq databases should be included

MP1 Homologue-Based Multilocus Sequence System for Typing the Pathogenic Fungus Penicillium marneffei: a Novel Approach Using Lineage-Specific Genes▿

A highly reproducible and discriminative typing system is essential for better understanding of the epidemiology of Penicillium marneffei, the most important thermal dimorphic fungus causing respiratory, skin, and systemic mycosis in Southeast Asia. The sequences of 11 housekeeping genes were identical among 10 strains of P. marneffei, but those of MP1 and its 13 homologues, a novel superfamily of mannoproteins in the subdivision Pezizomycotina of Ascomycetes, mostly species of Penicillium and Aspergillus, showed significant variations. Therefore, a multilocus sequence typing (MLST) system for P. marneffei was constructed using MP1 (549 bp) and the four of its homologues (MPLP4 [337 bp], MPLP7 [347 bp], MPLP10 [546 bp], and MPLP13 [422 bp]) that showed the greatest variations. Among the 2,201 bp of the five loci, 183 polymorphic sites were observed in 44 strains of P. marneffei. The median number of alleles at each locus was five (range, 5 [MPLP4, MPLP7, and MPLP13] to 15 [MPLP10]). Four of the five genes had nonsynonymous substitution/synonymous substitution (dn/ds) ratios of >1. A total of 35 different sequence types (STs) were assigned to the 44 P. marneffei isolates, with 28 of the 35 STs identified only once. The discriminatory power was 0.9884. MP1 and its homologues were better than housekeeping genes for MLST in P. marneffei. Due to their more rapid evolutionary rates, lineage-specific genes may be better candidates than housekeeping genes for sequence-based typing, especially in microbes that evolve slowly or have evolved recently