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It has been a busy term for the 49Women in Science Committee, which was formed five years ago after identifying the need for supports and guidance for young women pursuing a career in STEM. Our fall 2022 student event was held on-campus on October 13. Students had the privilege of listening to guest speaker Dr. Fiona Brinkman, SFU professor in Bioinformatics and head of the Brinkman Lab. She shared her educational and career journey, inspiring those in attendance with what is possible.
How Honduras managed to carry out genomic sequencing for the first time
June 2023
When microbiologist Soany Ávilez was selected to implement the genomic sequencing of the SARS-CoV-2 virus in Honduras, she was amazed. In the wake of the pandemic, Soany had started working at the National Virology Laboratory in 2020 performing PCR tests. At that time, genomic sequencing to detect circulating variants of the virus that causes COVID-19 was carried out outside the country. But a project to provide Honduras with the capabilities to do it in situ and obtain faster results was being developed with technical support from the Pan American Health Organization (PAHO) and financial support from the United States Government.
Although she lacked knowledge on the subject, Soany remembers that she longed for the opportunity to work in sequencing. "When they chose us (her and her partner Karla Romero) to implement sequencing in the country and move the area forward, I couldn't believe it," she says.
Genomic surveillance allows us to know the evolution of viruses and other pathogens as they change over time. Knowing those changes or mutations that can modify its transmissibility and severity, allows us to guide public health measures. During the pandemic, it was a key strategy to monitor the behavior of SARS-CoV-2 and a technique that is being integrated into the surveillance of other pathogens.
Karla Romero, the other microbiologist in charge of genomic surveillance, acknowledges that the implementation of sequencing in Honduras has been "a great challenge" that required a lot of "sacrifice and commitment" both inside and outside the laboratory.
The sequencing area had to be created from scratch. In 2022, the authorities selected and conditioned a space within the National Virology Laboratory. With the support of PAHO, a sequencer, supplies, reagents, and furniture were purchased, and Soany and Karla were trained in bioinformatics and genomic sequencing at the Gorgas Memorial Institute in Panama.
“All with the aim of strengthening the capacities for genomic surveillance of SARS-CoV-2 and other pathogens in Honduras,” says Gabriela Rodriguez Segura, coordinator of the PAHO Project for the Consolidation of Genomic Sequencing Capacities in Honduras. Before these capacities were created at the local level, samples to determine the variants circulating in the country were sent to the laboratories of the Regional Network for Genomic Surveillance of COVID-19 (COVIGEN) created by PAHO to support countries without capacity to carry out sequencing in its territory.
In March 2023, the effort paid off and excitement took over the National Virology Laboratory when, after several attempts, the first sequencing of SARS-COV-2 in the country was successfully carried out. “We couldn't believe it,” says Soany. "We feel very happy because it was a great challenge and the result made us feel fulfilled."
On March 21, 2023, the results were obtained and it was the first time that the XBB sublineage of the omicron variant was detected in the country and by Honduran health professionals. For Karla, the key was “not to give up in the face of the biggest challenge”.
"It is a milestone for the country that genomic sequencing is being carried out," says Dr. Mitzi Castro, head of the National Health Surveillance Laboratory of Honduras. “It is a historic moment because we are starting from here to carry out future genomic surveillance of other pathogens of sanitary interest to the country,” she adds.
According to Dr. Castro, the country now has state-of-the-art technology. "The laboratory is at the forefront, and that is a success and a source of pride, for which we thank all those who have contributed their bit so that Honduras is not left behind."
My bioinformatics photograph, Pipeline 2, centre top.
The Hospital for Sick Children website. For promotional purposes only.
An scheme that represents the relation between new emergent knowledge areas at the Bioinformatics and Computational Biology sphere.
Elements of Bioinformatics:
Yet another PTEP (Periodic Table of the Elements Parody). I often love
these, but this one is truly exceptional, because I love
bioinformatics tools, also. Now, yes, there are more bioinformatics
and genomics tools, but this is the cream of the crop, the best ones,
compiled into an interactive visual structure that facilitates easy
browsing by category and clear relationship for types of tools. The
largest grouping of tools are the open source tools, and the smallest
are commercial tools. Bravo, bravo! When you mouse over the "Key to
Tool Type", whichever category your mouse is on is highlighted across
all groupings. Click on an elemental symbol, and you get more
detailed information about the tool represented by that two-letter
code, including authors, operating system, year created, publication,
download (or more info) link, licensing. Excellent structure for the
metadata. Color me impressed, and delighted to find this awesome
useful tool.
Content Workflow 2010 is an exciting one day event detailing strategies for professionals -- in information management, knowledge management and IT, R&D, medical affairs, and publishing -- to inject high-value STM content into the workflow of knowledge workers when and where they need it, and exploring critical information about global copyright compliance.
Figure 2 from Inhibition of Antiapoptotic BCL-XL, BCL-2, and MCL-1 Proteins by Small Molecule Mimetics Published in Cancer Informatics
Clockwise from top left, Hannah Lawrence, executive administrator; Jorge Andrade, director of bioinformatics; Caitlin Pike, communication specialist; Samuel Volchenboum, director; Brad Orr, senior project manager; Plamen Martinov, directory of systems and security; and Suzi Birz, HIPAA consultant at the Center for Research Informatics in McGiffert Hall Monday, Sept. 16, 2013. (Photo by Robert Kozloff)
iMAL, Brussels, May 2014
William Latham is a computer art pioneer, internationally known for his organic artworks based on the processes of evolution. Up to 1993, he was a Research Fellow at The IBM UK Scientific Centre. He then founded Computer Artworks Ltd, a game studio that produced the video game The THING. Since 2007, Latham is Professor of Computer Art at Goldsmiths, where he applies his evolutionary rule-based approach to the domain of protein folding, scientific visualization and gamification in collaboration with the Bioinformatics department, neuroscientists and Prof. Frederic Leymarie.
Shearing typically occurs along coastal marshes when strong storms rip away the plants at the marsh edge. Because oiled shoreline sediment is in a weakened state and less able to securely hold plants in place, some Louisiana marshes that were heavily oiled following Deepwater Horizon are experiencing more shearing than usual. The loss of vegetation adversely affects the entire marsh ecosystem. Patrick Rayle uses metabarcoding methods to examine differences in meiofauna biodiversity in oiled and unoiled Louisiana marshes that have experienced shearing. His research can help us better understand how meiofauna communities respond to these co-occurring stressors. He also wants to help answer questions about whether losing the marsh edges through erosion will diminish the diversity of this unique intertidal ecosystem. Patrick is a master’s student with the Louisiana State University AgCenter’s Department of Entomology and a GoMRI Scholar with the project A Study of Horse Fly (Tabanidae) Populations and Their Food Web Dynamics as Indicators of the Effects of Environmental Stress on Coastal Marsh Health.
Photo Caption: Patrick Rayle, a master’s student at Louisiana State University AgCenter, sets up a sample transect at a marsh site that has not experienced shearing.
Photo Credit: Claudia Husseneder.
Read More: gulfresearchinitiative.org/grad-student-rayle-examines-ch...