Our openly available databases and software tools, the SIB Resources, allow the study of life at different scales to tackle global challenges, such as food security, pollution and pandemics. The stories on this page show examples of their impact for discoveries and innovation.
Scientific impact of the SIB Resources in 2023
14
SIB Resources, incl. 37 databases & tools
17,041
citations in the literature
>11,3
million users
9,000
mentions in patents
Elucidating the toxicity of safrole for food consumption
While its use as additive is forbidden in many countries, safrole is still present in food and feed due to its abundance in spices or herbs, giving rise to multiple safety issues.
Using Bgee, researchers could investigate interspecies differences and prioritize cats, goats and sheep as the most susceptible species to the toxicity of safrole in food, making them a priority for further investigations.
Designing stem cell-based vaccines against cancer
Stem cells share many features with cancer cells, which contribute to their respective abilities to self-renew, proliferate, and differentiate. This makes them suitable for developing cancer vaccines.
Bgee was used to single out genes whose expression in embryonic stem cells resembles that observed in tumor cell lines. The genes identified thanks to Bgee data allowed to design a vaccine reducing bladder cancer growth in mouse models.
Overcoming marine plastics pollution
Researchers discovered that a few tiny sea creatures can break down a type of plastic called PBS.
Using SwissDock, part of SwissDrugDesign, they found enzymes that might be responsible for this process and identified a particularly promising one, PBSase. This finding could contribute to a more sustainable society through further utilization of PBS.
Anticipating human-pet virus transmission
The interaction between human hosts and animal reservoirs is of crucial importance both for understanding current epidemics and for better anticipating future zoonotic pandemics.
V-pipe has been used on samples provided by VetSuisse from viral tests on companion pets living in proximity with SARS-CoV-2-infected owners. Results have helped gain a better understanding of the transmission chains between humans and their pets, and among the animals themselves.
Advancing agricultural biotechnology
Understanding how genes control plant growth is crucial for improving agricultural technology, especially in dealing with environmental changes. This knowledge helps develop crop varieties that can thrive in different conditions and continue to produce enough food for a growing population.
OMA (part of SwissOrthology) helped the identification of genes in rice and other model species which correspond to barley genes important for seed germination. This enabled researchers to explore when and where genes are expressed during germination, which ultimately could lead to barley grain improvement.
Tracing mosquito evolution to better understand disease transmission patterns
Researchers used OMA, part of SwissOrthology, as a starting point to build a complete list of similar genes found in different species of mosquitoes. This was instrumental in tracing the evolution of mosquitoes and revealing their history of host use. The findings have significant implications for understanding disease transmission patterns and informing both medical and ecological strategies.
Understanding carbon fixation processes
Cyanobacteria are special organisms that can perform photosynthesis, like plants. They could play an important role in reducing the levels of CO2 produced by humans. Understanding how they capture carbon could help us increase this process.
With the help of SWISS-MODEL, researchers were able to figure out the shape of an enzyme regulating the process. In that shape they were able to identify specific sites that control how much carbon the cynanobacteria absorb from the air.
Enhancing anti-tumour immunity
Cytotoxic T cells are powerful actors in the anticancer immune response and as such, play a key role in current successful cancer immunotherapies. However, these cells are also prone to ‘exhaustion’ in the context of chronic stimulation of the immune system in human cancer.
The authors found that high levels of the protein SNX9 plays a role in T-cell exhaustion. Using ISMARA (part of SwissRegulon) to investigate the cause of these high expression levels, they discovered that two other proteins, NFATC and NR4A1/3, are key drivers of T-cell exhaustion. This finding could help develop better treatments for cancer.
The biological processes of Autism Spectrum Disorder (ASD)
ASD is a neurodevelopmental disorder characterized by communication deficits and repetitive behavioural patterns. While genetic factors are known to play a role, a better understanding of the mechanisms in play is needed.
Using TopAnat (part of Bgee), researchers were able to pinpoint specific brain regions associated with biological processes disrupted in ASD. These are thus plausible targets for drug development.
Understanding cattle fertility
To infer if and how genes and their variants functionally affect specific traits, such as diseases or fertility, knowing in which tissue they are most expressed offers precious clues.
Bgee was used to support the hypothesis that a rare mutation of a gene in Angus bulls could lower sperm quality and thus affect their extensive use and economical importance for artificial insemination. Bgee indeed revealed that the gene, in cattle, is most highly expressed in the reproductive system.
Understanding the molecular impact of infections
To grasp the complexities of infection severity or organs affected by a viral infection, zooming in at the molecular level is needed.
ASAP, SWISSREGULON or Bgee contribute to our understanding of: the regulatory response to infection by comparing complete and single cell gene expression profiles before and after infection; how diverse viruses’ targets are (such as in long COVID) by revealing the expression of target genes in various cells and organs; or how the circadian clock affects viruses’ pathogenicity.
SwissLipids or Rhea allow insights into the metabolic dysfunctions induced by viruses such as SARS-CoV-2, or those which put patients at greater risk of developing a severe form of the disease.
Understanding the impact of air pollution
To evaluate diverse properties of molecules, scientists rely on accurate predictions at the atomic scale.
In an analysis of polluted versus clean air samples in the Maldives, SwissADME (part of SwissDrugDesign) was used to estimate the harmful properties of thousands of unknown chemicals. The study showed the importance of studying air composition at the molecular level to assess its effect on health and climate.
Designing therapeutic tools
In-depth information on 3D structures, functions and ligands of proteins, carbohydrates or lipids are crucial to investigate their function in biological processes.
Glyco@Expasy was used to prove the ability of a predicted sugar-binding protein to form a pore (i.e. to ‘punch holes’) in the membrane of cancer cells, thus opening the way to designing therapeutic molecular tools.
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Tracking the mpox (monkeypox) outbreak
Through the analysis and sharing of genomic sequences of pathogens such as bacteria and viruses, their evolution and spread can be unfolded and tracked in real time.
Nextstrain used openly shared data to provide daily updated analysis of thousands of mpox virus genomes, enabling scientists to monitor its spread during the 2022 outbreak.
Finding biological catalysts to remove environmental pollutants
To unlock the potential of enzymes as biological catalysts for a greener environment, reference databases that provide information on how these proteins work are essential.
UniProtKB/Swiss-Prot was used to identify enzymes - biological catalysts - to treat soils contaminated with pollutants like hydrocarbons, a process known as bioremediation.
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Ensuring food security
Strategies to develop agriculturally promising traits, such as resistance to drought or pests, play a key role in ensuring food security. The genetic basis of these traits in hundreds of agronomic species can be inferred using knowledge from a handful of model species thanks to orthology, which relates genes between organisms.
SwissOrthology has been leveraged as a customized database for the needs of the plant biotechnological company BASF to develop agriculturally desirable traits in crops like soybean and wheat.
Reducing chemical waste for a better environment
To unlock the potential of enzymes as biological catalysts for drugs and other desirable chemicals, reference databases that provide information on how these proteins work are essential.
RDEnzyme is a computational tool to predict pathways using enzymes for natural product synthesis. This tool employs knowledge of protein function from UniProtKB/Swiss-Prot as well as annotations from Rhea. By reducing our dependence on toxic, non-biodegradable catalysts, RDEnzyme has the potential to spark a revolution in “green catalysis,” improving not only human health and wellbeing but also the environment.
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Revealing the host-factors that are critical for infection
To examine how hosts become vulnerable to infections, zooming in at the molecular level is needed.
Several high-profile studies used STRING in their data analysis of genome-wide screens, an essential step in identifying ‘weak spots’ in the host’s genome that could facilitate the infection by SARS-CoV-2.
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