TY - GEN AB - Predicted frameshift and nonsense mutations in Chlamydial pan-genome. For the analysis of putative pseudogenes, events located less than 60 bp. away from gene end or present in a single genome from the corresponding OG were excluded. (CSV 600 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9783 TI - Additional file 10 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Frameshift and nonsense mutations near homopolymeric tracts of OG1 genes. Only 374 genes with typical length and domain composition were considered. (CSV 6 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9897 TI - Additional file 20 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Distribution of OGs with mosaic phyletic patterns across species (complete genomes only). (CSV 7 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9890 TI - Additional file 15 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Distribution of OGs with mosaic phyletic patterns across species (all genomes). (CSV 10 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9892 TI - Additional file 16 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Summary of peripheral genesa phyletic patterns and tree concordance. (CSV 26 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9893 TI - Additional file 17 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Orthologous families (OFs) derived by MCL clustering of OGs. (CSV 189 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9894 TI - Additional file 18 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Additional information on proteins from OG1. (CSV 30 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9895 TI - Additional file 19 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - GEN AB - Summary of the analysed genomes. (CSV 24 kb) AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 9896 TI - Additional file 1 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction ER - TY - JOUR AB - Intra-organ communication guides morphogenetic processes that are essential for an organ to carry out complex physiological functions. In the heart, the growth of the myocardium is tightly coupled to that of the endocardium, a specialized endothelial tissue that lines its interior. Several molecular pathways have been implicated in the communication between these tissues including secreted factors, components of the extracellular matrix, or proteins involved in cell-cell communication. Yet, it is unknown how the growth of the endocardium is coordinated with that of the myocardium. Here, we show that an increased expansion of the myocardial atrial chamber volume generates higher junctional forces within endocardial cells. This leads to biomechanical signaling involving VE-cadherin, triggering nuclear localization of the Hippo pathway transcriptional regulator Yap1 and endocardial proliferation. Our work suggests that the growth of the endocardium results from myocardial chamber volume expansion and ends when the tension on the tissue is relaxed. AU - Bornhorst, Dorothee AU - Xia, Peng AU - Nakajima, Hiroyuki AU - Dingare, Chaitanya AU - Herzog, Wiebke AU - Lecaudey, Virginie AU - Mochizuki, Naoki AU - Heisenberg, Carl-Philipp J AU - Yelon, Deborah AU - Abdelilah-Seyfried, Salim ID - 6899 IS - 1 JF - Nature communications TI - Biomechanical signaling within the developing zebrafish heart attunes endocardial growth to myocardial chamber dimensions VL - 10 ER - TY - JOUR AB - Background Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria. Results We report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system. Conclusions This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity. AU - Sigalova, Olga M. AU - Chaplin, Andrei V. AU - Bochkareva, Olga AU - Shelyakin, Pavel V. AU - Filaretov, Vsevolod A. AU - Akkuratov, Evgeny E. AU - Burskaia, Valentina AU - Gelfand, Mikhail S. ID - 6898 IS - 1 JF - BMC Genomics TI - Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction VL - 20 ER -