To identify genome-based features characteristic of the avian and human pathogen Chlamydia (C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.

After being established in 1967, the commercially available murine Leydig cell tumor line I-10 has been used in almost 50 published studies. I-10 has not been characterized, either at the chromosomal/ cytogenetic level or the genetic level, similar to many other murine tumor cell lines. In this study, we performed molecular karyotyping and multicolor banding-based molecular cytogenetics. A slightly hyperdiploid karyotype with 43 chromosomes was described. The main aberrations comprised several unbalanced translocations and three unusual rearrangements (two dicentric derivatives and one neocentric derivative). Nine regions showed copy number gains, and only five small chromosomal parts showed loss of copy numbers. A standardized translation of these imbalances in the human genome was performed, which showed a 63% overlap of the detected imbalances with testicular germ cell tumors, a 53% concordance with human spermatocytic seminomas and non-seminomas, and only a 36% overlap (approx.) of large copy number gains and losses were similar to the corresponding human Leydig cell tumors. However, no Y-chromosome was detected in this male-derived cell line. Overall, the I-10 cell line was found to be a testicular germ cell tumor model and cannot be treated as a model that is specific to human Leydig cell tumors. At best, it might be suited as a model for an early onset of Leydig cell tumors.

Iodine-based staining techniques are commonly used in histological imaging and micro-computed tomography ( $$\upmu $$ μ CT) because iodine binds to specific molecules. However, the basis for tissue-specific contrast has not yet been sufficiently explored. In this study, we analysed the human proteome at four levels: individual proteins, protein families, tissues with additional expression values for selected proteins, and organs as distinct combinations of tissues. At each level, we identified groups with high potential for iodine binding, particularly those rich in aromatic heterocyclic amino acids. We evaluated the occurrence of aromatic and non-aromatic heterocyclic and carbocyclic amino acids in 20,650 proteins, 1487 protein families, 57 tissues, and 16 organs using bioinformatic methods. This evaluation was based on curated human protein sequences and integrated expression information from the Human Protein Atlas and ProteomicsDB. At the protein level, structural proteins such as titin, nebulin, obscurin, mucin, filaggrin, and hornerin exhibited a high absolute number of aromatic heterocyclic amino acids, which could explain the high $$\upmu $$ μ CT contrast in muscle, skin, and mucosal tissues. A smaller set of proteins displayed strong relative enrichment. At the family level, the average absolute values were highest in families containing very large proteins. However, relative values highlighted sequence-level enrichment in selected enzyme- and membrane-associated families. In contrast, tissue- and organ-level enrichment showed only small, non-significant differences depending on the expression dataset, and was highly similar across groups. Furthermore, enrichment was not robustly associated with iodine staining intensity in organs. Our results provide a foundation for iodine-based tissue imaging and could serve as a starting point for future research, such as cross-species applications and the structural and functional effects of iodination.