Title: “Microbial membrane lipids: opening pandora’s box under the bioinformatics light”
Membranes are composed by proteins and lipids that separate and protect the cell from the surrounding environment. Membrane lipids from Bacteria and Eukarya are structurally the same while they differ from those of Archaea. This differentiation raises unresolved questions regarding the evolution of all cell forms. Besides, the study of microbial membranes also helps in determining microbial adaptation mechanisms to environmental conditions. Here, we will dive into a journey to the bottom of a breathless sea, by using bioinformatic approaches, to determine the biological sources and evolution of the acquisition of membrane lipids.
Laura Villanueva her research fields are Geomicrobiology and Marine Microbiology in which she studies the diversity, metabolism, and evolution of marine microbes and their contribution to biogeochemical cycles. She also focusses on the study of the biological sources of organic biomarkers to make better constraints of the predictive power of these molecules to reconstruct past environmental conditions. This research addresses key questions of different disciplines such as paleoclimatology, paleobiology, (biogeo)chemistry, limnology, microbiology, metagenomics, molecular evolution, among others.
Title: “A draft human pangenome”
Reference genomes are foundational for the life sciences and underly many workflows to analyze omics data, including in genomics, epigenomics, transcriptomics, and proteomics. However, present flat reference genomes, such as GRCh38, are not adequately capturing human diversity and hence introduce reference biases. As part of the Human Pangenome Reference Consortium, we have created 47 phased, reference-quality diploid assemblies from a cohort of genetically diverse individuals. Based on alignments of the assemblies, we generated a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. Using our draft pangenome to analyse short-read data reduces small variant discovery errors by 34% and increases the number of structural variants detected per haplotype by 104% compared with GRCh38-based workfows, which enables the typing of the vast majority of structural variant alleles per sample.
Tobias Marschall is a professor at Heinrich Heine University and director of the Institute for Medical Biometry and Bioinformatics at the Medical Department. Prior to that, from 2014 to 2019, he was a professor at the Center for Bioinformatics at Saarland University and a senior researcher at the Max Planck Institute for Informatics, heading the Algorithms for Computational Genomics group. He is broadly interested in algorithms and statistical methods for computational genomics, including variant calling, haplotype phasing, structural variants single-cell genomics, genome assembly, and pangenome analyses. He contributes to a number of large-scale international projects, inluding the Human Pangenome Reference Consortium, the Telomere-to-Telomere Consortium and the Human Genome Structural Variation Consortium, where he acts as a co-chair. Tobias is an associate editor for the journal Bioinformatics.
Title: “Post-translational modifications at the interface of phage-bacteria interactions”
During phage infection, both virus and bacteria attempt to gain and/or maintain control over critical bacterial functions, through a plethora of strategies. These strategies include post-translational modifications (PTMs), as rapid and dynamic regulators of protein behavior. However, to date knowledge on the topic remains scarce and fragmented, while a more systematic investigation lies within reach. The release of AlphaFold2 and the increasing inclusivity and scale of mass spectrometry applications to new PTM types, could significantly accelerate research in the field. To date, acetylation, ADP-ribosylation and phosphorylation remain the predominant PTM-types described during phage infection. They play roles in bacterial defense (e.g. preventing phage adsorption through type IV pili glycosylation) and viral counter-defense (e.g. disarming the CRISPR-Cas system by acetylation of DNA binding residue. I will present an overview of the processes affected by lysine acetylation and our ongoing efforts to characterize the impact of Nε-lysine acetylation on methionine synthase (MetE), the enzyme ultimately in charge of synthesizing methionine in a cobalamin-independent fashion in Pseudomonas aeruginosa.
Vera van Noort is professor at the Faculty of Bioscience Engineering, KU Leuven, chair of the Leuven Centre for Bio-Science, Bio-Engineering and Bio-Technolog and program director of the POC Bioinformatics – Faculty of Bioscience Engineering, KU Leuven. Next to this, she is a guest professor of Computational Biology at the Institute for Biology at Leiden University. Her group at KU Leuven, Computational Systems Biology, is interested in understanding biological systems as a whole. They try to achieve this through computational analysis of large-scale data generated by the ever growing number of new technologies that can systematically measure the behaviour of multiple cellular components, such as biochemical activities, biophysical properties, subcellular localization and interaction. They use and develop new methods to integrate, visualize and query the large amounts of information available and in such a way come to new biological discoveries. They apply their expertise in bioinformatics, comparative genomics, proteomics data analysis and structural protein modelling to innovative research projects and relevant questions from society and industry.