Bioimaging – the real-time visualisation of living organisms, ranging from single cells to small animals – is opening up new avenues for cutting-edge multidisciplinary research worldwide, largely due to the expansion of groundbreaking open access databases.
Bioimaging is a data-intensive process; a single lab can record petabytes of information every day.
According to Dr. Christopher Wood, director of Mexico’s Laboratorio Nacional de Microscopía Avanzada (LNMA), new findings in the field are increasingly coming from re-analysing old data to answer new questions.
When Wood first arrived in Mexico in 2002, bioimaging research – which covers a wide range of disciplines, from astrobiology to zoology – was largely the remit of well-established individuals with access to specialist facilities. The national funding agency, CONACYT, would sponsor individual laboratories to conduct and publish their research, and was able to provide some equipment on request. For scientists not attached to a laboratory equipped with high-tech microscopes, access was limited to a few sites scattered around the country.
In an effort to upgrade Mexico’s scientific infrastructure, CONACYT committed to funding a national core facility for bioimaging in 2011. The LNMA opened its doors to the public shortly after, in January 2013, and the lab has since grown to occupy two additional premises: one at Centro Médico Nacional Siglo XXI in Mexico City – the country’s primary clinical research hospital – and another at the CICESE research institute in Ensenada.
Diff-Nanores Cells Montage of diffraction limited and super resolution image of fibroblast cell Gaston Contreras, Adán Guerrero, UNAM
Wood’s lab serves as a core facility for Mexican bioimaging – a lab that provides affordable access to anyone wishing to use specialized microscopes. The LNMA team is also working to pioneer open access microscopy databases for Mexico and Latin America as a whole, in order to level the playing field for bioimaging scientists in the region and ensure that their research keeps pace with global scientific progress.
When it comes to reanalysing existing data, the main concern is standardization – for science to be credible, it has to include precise details of how, when and why data was collected. Unlike with genome sequencing, researchers cannot simply send their samples to specialist facilities and wait for the results; examining specimens must be done firsthand. Core facility staff can make sure that the right metadata is recorded for each sample – an essential requirement if users plan to submit their results to major databases.
“It’s not just about the equipment – we also have highly trained specialized technicians and researchers who can guide the users into getting the best results, and the kind of results they need from their experiments,” explains Dr. Wood.
Worldwide, the most ambitious and widely used bioimage databases are currently managed by the European Molecular Biology Laboratory (EMBL) in Germany. Submitted images go through a strict screening process to make sure each has enough identifying information for the database to be highly searchable. Scientists contribute to these databases on a purely voluntary basis, but Dr. Wood estimates that at some point during the next decade a tipping point will be reached, after which funding agencies and publications will begin to insist on data being made publically available. Having a Latin American database management hub would streamline the process for researchers working in the region.
In terms of replicating this system, the LNMA are still at the proof of principle stage. Networks must be established, expertise exchanged and job roles created before the project can properly get off the ground. To this end, the lab has received help from the Chan-Zuckerberg Initiative, established in 2015. While they have a wide remit, the fund places a particular focus on frontier science – including biomedical imaging. “The Initiative has given a huge boost to the discipline of bioimaging,” says Dr. Wood.
Rather than directly funding experiments or equipment, the CZI funds the development of global networks for communication, training and collaboration. The latest round of grants went to community-building projects based in Latin American, ex-Soviet and African countries. Two of the awarded projects are being supervised by the LNMA; the first is a partnership between Mexican and Argentinian biomedical scientists with the intention of building capacity for new nanoscopic technology.
The second Mexican project to secure funding aims to build connections closer to home. “One of the things we haven’t done as well as we should have until now in Mexico is to actually develop a Mexican bioimaging community,” says Dr. Wood. “And so we’ll be organising a series of twelve workshops over three years in different bases.” The schedule includes visits to microscopy centres in Merida, Ensenada, Leon, CDMX and Queretaro, with assistance provided by educational and government institutions. Each workshop on advanced bioimaging techniques will be accompanied by a separate outreach event for schools or the general public, focusing on low-cost microscopes.
Arabidopsis root GFP labelled Arabidopsis root with starch granules. Arturo Guevara, Chris Wood, UNAM
Dr. Wood emphasises that he and the LNMA faculty are simply custodians of a public facility, with a mandate to make bioimaging more accessible. “It depersonalizes the science. It’s not about great individuals – it democratizes access and makes it a bit more horizontal. Anyone with two hundred pesos in their pocket can have an hour on our microscopes,” he explains. Should the databases he envisages be created, they would represent another major step towards democratizing science in Mexico and the rest of Latin America.
Sita Bates for Times Media Mexico
