Biology subjects

Barf, L.-M.

Publications and source records attributed to Barf, L.-M..

4 recordsLinked to original sources

bioRxiv2025

Proteomic study for the prediction of μCT imaging with iodine

Iodine-based staining techniques are commonly used in histological imaging and micro-computed tomography ({micro}CT) due to iodines affinity for binding to specific molecules. However, the basis for tissue-specific contrast has not yet been sufficiently explored. In this study, we analyse the human proteome at four different levels: individual proteins, protein families, tissues with additional expression values for selected proteins, and organs as a distinct combination of different tissues. At each level, we try to identify proteins/groups with high potential for iodine binding, especially those rich in aromatic heterocyclic amino acids. Using bioinformatic methods, we evaluate the occurrence of aromatic/non-aromatic heterocyclic, carbocyclic, and the remaining 15 amino acids in 20,650 proteins, 1,487 families, 57 tissues, and 16 organs. At the protein level, structural proteins such as titin, nebulin, obscurin, mucin, filaggrin and hornerin have a high absolute number of aromatic heterocyclic amino acids, which could explain the high {micro}CT contrast in muscle, skin and mucosal tissues. At the next level, however, structural families (such as the Laminin-family) rank significantly lower in comparison. These results are reflected in tissues and organs for which protein expression is available. Here, no significant correlations between the enrichment of heterocycles and the intensity of iodine staining can be observed. Furthermore, the enrichment of amino acids in each tissue/organ is relatively similar and shows no significant difference. Our results provide a general basis for iodine-based tissue imaging and serve as a potential starting point for future research, e.g. for cross-species applications and for the structural and functional effects of iodination.

biochemistry↗

bioRxiv2025

Multiple losses of ecdysone receptor genes in nematodes: an alternative evolutionary scenario of molting regulation

Molting is a hallmark feature of ecdysozoans, including arthropods, tardigrades, and nematodes. Ecdysone hormones play a crucial role in regulating the molting process of different ecdysozoan taxa. Interestingly, despite this highly conserved function of ecdysone, the model nematode Caenorhabditis elegans has lost the ecdysone receptor (ECR) genes and their molting appears to be ecdysone-independent. The loss of ecr has only been reported in Caenorhabditis within ecdysozoans, and the evolutionary background behind this loss has remained enigmatic. Here, we show that loss of ecr is not exceptional in Caenorhabditis, but has occurred at least three times in Rhabditina and Tylenchina nematodes. Our genome-wide analysis of 160 nematode species revealed multiple losses of ecr and its typical heterodimer partner usp during nematode evolution. Furthermore, using transcriptomic, pharmacological, and in silico/ in vivo protein interaction analyses, we identified two factors that potentially underlie and buffer the loss of ECR gene/function: (1) molting regulation by an alternative nuclear receptor HR3 (NHR-23) and (2) a lineage-specific expansion of nuclear receptors in the ecr-deficient taxa. Taken together, this study shows how key regulators of ecdysozoan molting can be altered during evolution. We propose a novel scenario for the evolution of molting regulation in nematodes.

evolutionary biology↗

bioRxiv2023

Pangenome calculation beyond the species level using RIBAP: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise ILPs

Pangenome analysis is a computational method for identifying genes that are present or absent from a group of genomes, which helps to understand evolutionary relationships and to identify essential genes. While current state-of-the-art approaches for calculating pangenomes comprise various software tools and algorithms, these methods can have limitations such as low sensitivity, specificity, and poor performance on specific genome compositions. A common task is the identification of core genes, i.e., genes that are present in (almost) all input genomes. However, especially for species with high sequence diversity, e.g., higher taxonomic orders like genera or families, identifying core genes is challenging for current methods. We developed RIBAP (Roary ILP Bacterial core Annotation Pipeline) to specifically address these limitations. RIBAP utilizes an integer linear programming (ILP) approach that refines the gene clusters initially predicted by the pangenome pipeline Roary. Our approach performs pairwise all-versus-all sequence similarity searches on all annotated genes for the input genomes and translates the results into an ILP formulation. With the help of these ILPs, RIBAP has successfully handled the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, even when genomes of different species are part of the analysis. We compared the results of RIBAP with other established and recent pangenome tools (Roary, Panaroo, PPanGGOLiN) and showed that RIBAP identifies all-encompassing core gene sets, especially at the genus level. RIBAP is freely available as a Nextflow pipeline under the GPL3 license: https://github.com/hoelzer-lab/ribap.

bioinformatics↗

bioRxiv2022

Extensive genomic divergence among 61 strains of Chlamydia psittaci

Chlamydia (C.) psittaci, the causative agent of avian chlamydiosis and human psittacosis, is a genetically heterogeneous species. Its broad host range includes parrots and many other birds, but occasionally also humans (via zoonotic transmission), ruminants, horses, swine and rodents. To assess whether there are genetic markers associated with host tropism we comparatively analyzed whole-genome sequences of 61 C. psittaci strains. Initially, poorly assembled genomes in public databases were subjected to clean-up, reassembly and polishing. Multiple sequence alignment of the genome sequences revealed four major clades within this species. Clade 1 represents the most recent lineage comprising 40/61 strains and contains 9/10 of the psittacine strains, including type strain 6BC, and 10/13 of human isolates. Clades 2-4 carry strains from different non-psittacine hosts. We found that clade membership correlates with classification schemes based on SNP types, ompA genotypes, multilocus sequence types as well as plasticity zone (PZ) structure and host preference. Genome analysis also revealed that i) sequence variation in the major outer membrane porin OmpA can result in 3D structural changes of immunogenic domains, ii) past host change of Clade 3 and 4 strains could be associated with loss of MAC/perforin in the PZ, rather than the large cytotoxin, iii) the distinct phylogeny of atypical strains (Clades 3 and 4) is also reflected in their repertoire of inclusion proteins (Inc family) and polymorphic membrane proteins (Pmps). Altogether, our study identified a number of genomic features that can be correlated with the phylogeny and host preference of C. psittaci strains.

genomics↗