ChromDesign Research by Clementina Altube

Documenting research, references and processes.

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ChromDesign Research Domain Map.

The four main axis of the project explain ways in which the subject of ChromDesign will be analysed and the concepts it will relate to. 

1. Researching ChromDesign 2. Capturing ChromDesign 3. Representing ChromDesign 4. Comunicating ChromDesign

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Yayoi Kusama (Japanese, b. 1929), Infinity Double Dots, 2013. Acrylic on canvas, 145.8 x 112 cm.

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Eva Fábregas exibition, “Those Things that your fingers can tell”, focused on sensory experiences. 

Credit: the artist and TIQUE

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Top:

Anni Albers, «Untitled» (1963), lithography, The Josef and Anni Albers Foundation

Bottom:

DNA fragment knotted seen with an electron microscope, captured by Steven A. Wasserman and Nicholas R. Cozzarelli.

Credit: CulturaCientifica 

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The exhibiton features mirror-glass works from the sculptor Jean-Michel Othoniel around the topic of mathematical  knots, accompanied by the film Nudos Salvajes (Wild Knots), by the mathematician Aubin Arroyo. The film is available at IMAGINARY.  

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Genes in action (1966), Will Burtin.

Credit: AIGA

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Your trust | Olafur Eliasson

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Gestalt Diagrams:

“The term “Gestalt” refers to groupings and our tendency to see patterns wherever possible. Human perception isn’t literal. We will close gaps, see motion, make partial chapes into whole ones in ways that are surprisingly predictable. Biologists who study perception refer to the <ecology> of vision— ways our visual processes favor needs or tasks essential to our survival. Such ideas counter the old “representational” approach to vision as a “picture in our heads” andreplace it with constructivist notions. We don´t simply see what it is in a mechanic way. Instead, what is seen is what is made. Instead of talking about pictures and images, we describe visual activity in terms of affordances and processes.” (Johanna Drucker (2014) Graphesis, Visual Forms of Knowledge Production.)

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Tungsten Filament

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“This photograph shows how the atoms are arranged in a crystal of tungsten.The enlargement in this picture is about 1,350,000 diameters.” Frontiers of Physics. Canadian edition. 1968.

Internet Archive

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The Electron Microscope

Transmission electron microscope (TEM):

The transmission electron microscope emits a beam of electrons directed towards the object whose image is to be magnified. A part of the electrons bounce off the sample, forming a magnified image of it.

Scanning electron microscope (SEM):

(Diagram illustrating the phenomena resulting from the interaction of highly energetic electrons with matter) 

In the scanning electron microscope (SEM) the sample is covered with a layer of thin metal, and it is scanned with electrons sent from a cannon. A detector measures the amount of electrons sent by the intensity of the sample area, being able to show figures in three dimensions, projected on a TV image.

Fluorescent Microscope:

(Yeast Cell Membranes as seen in a Fluorescent Microscope)

These techniques use these different fluorophores for analysis of cell structure at a molecular level in both live and fixed samples.

X-Ray Microscope:

X-ray microscopes are instruments that use electromagnetic radiation usually in the soft X-ray band to image objects. 

Super Resolution Microscopes:

Much current research (in the early 21st century) on optical microscope techniques is focused on development of superresolution analysis of fluorescently labelled samples. Structured illumination can improve resolution by around two to four times and techniques like stimulated emission depletion (STED) microscopy are approaching the resolution of electron microscopes.

Credit; News Medical Life Sciences

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Mapping the Epigenome.

CIRCOS is a circular visualization chart that allows the portraying of complex systems and the way they interact with one another. 

The data used (group/track) for figure elements is as follows

(C) mapping and sequencing tracks / chromosome band (ideogram)

(A) variation and repeats / snps (v126). The histogram shows the number of SNPs per 1 Mb.

(F) variation and repeats / segmental duplication. A small subset of segmental duplications are drawn, filtered by locations on chromosomes 2, 3, 7, 9. The choice of locations was motivated by the need for a visually balanced set of links.

(B) variants in genome structure catalogued by the TCAG database.

(D) locations of genes implicated in disease. Gene-to-disease mappings were done using OMIM database.

Gene-to-chromosome location mappings were done using the following data tables from UCSC

-gene and gene prediction tracks / UCSC genes

-gene and gene prediction tracks / RefSeq genes (Credit: CIRCOS)

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CONTEXT:

Pages and notes from the first research sketchbook, Clementina Altube. Barcelona, December 2020.

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EARLY STAGE RESEARCH MAP.

This map has the objective of portraying the main areas of research set on the early stages of project development. Barcelona, November 2020.

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CHROMDESIGN

ChromDesign is an organization that focuses on analysing and interpreting genomic 3D organization and its changes over time. They focus on cell biology, genomics and computational modelling to solve these challenges.

“Above all, ChromDesign believes that science communication and education is essential for the future of science. And for the future of society.” (Credit: ChromDesign)  

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CENTER OF GENOMIC REGULATION

The CRG is integrated into the Barcelona Biomedical Research Park (PRBB), together with other biomedical research institutions such as the Department of Experimental and Health Sciences (CEXS) of the UPF, the Hospital del Mar Institute of Medical Research (IMIM ), the Center for Regenerative Medicine of Barcelona (CMRB), among others.

The Centre for Genomic Regulation (CRG) is an international biomedical research institute of excellence, created in December 2000. It is a non-profit foundation funded by the Catalan Government through the Department of Business & Knowledge and the Department of Health, the Spanish Ministry of Science & Innovation, the “la Caixa” Banking Foundation, and includes the participation of Pompeu Fabra University. The mission of the CRG is to discover and advance knowledge for the benefit of society, public health and economic prosperity.

Inside the CGR of Barcelona there is mainly 2D study and representation but also with 3D technologies. Thanks to their bioinformatics departament, they process and develop their data using big-data processing programms, many times tailored for this organization.

MAIN AREAS OF INVESTIGATION:

Phenome and DNA Bioinformatics Genomics Tissue Engineering MetaGenomics Proteomics