In electroreceptive jawed fishes and amphibians, individual lateral line placodes form lines of neuromasts on the head containing mechanosensory hair cells, flanked by fields of ampullary organs containing electroreceptors-modified hair cells that respond to weak electric fields. Extensively shared gene expression between neuromasts and ampullary organs suggests that conserved molecular mechanisms are involved in their development, but a few transcription factor genes are restricted either to the developing electrosensory or mechanosensory lateral line. Here, we used CRISPR/Cas9-mediated mutagenesis in G0-injected sterlet embryos (Acipenser ruthenus, a sturgeon) to test the function of three such genes. We found that the 'hair cell' transcription factor gene Atoh1 is required for both hair cell and electroreceptor differentiation in sterlet, and for Pou4f3 and Gfi1 expression in both neuromasts and ampullary organs. These data support the conservation of developmental mechanisms between hair cells and electroreceptors. Targeting ampullary organ-restricted Neurod4 did not yield any phenotype, potentially owing to redundancy with other Neurod genes that we found to be expressed in sterlet ampullary organs. After targeting mechanosensory-restricted Foxg1, ampullary organs formed within neuromast lines, suggesting that FoxG1 normally represses their development, whether directly or indirectly. We speculate that electrosensory organs may be the 'default' developmental fate of lateral line primordia in electroreceptive vertebrates.

• Klíčová slova
• Acipenser ruthenus, Atoh1, Foxg1, ampullary organs, developmental biology, lateral line, neuromasts, sterlet sturgeon,
• MeSH
• buněčná diferenciace MeSH
• forkhead transkripční faktory * metabolismus   genetika   MeSH
• proudový orgán * embryologie   metabolismus   MeSH
• rybí proteiny * metabolismus   genetika   MeSH
• ryby * embryologie   genetika   MeSH
• transkripční faktory bHLH * metabolismus   genetika   MeSH
• vláskové buňky * fyziologie   MeSH
• vývojová regulace genové exprese MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• forkhead transkripční faktory * MeSH
• rybí proteiny * MeSH
• transkripční faktory bHLH * MeSH

Tetradesmus sp. strain 198 is a microalga with potential for the biotechnological production of carotenoids. In this study, we have sequenced the genome, obtaining a total contig-level genome assembly length of 149 Mbp. The BUSCO completeness was 91%, the N50 was 783 kbp, and the total number of annotated genes was 19,841.

• Klíčová slova
• dryland, green algae,
• Publikační typ
• časopisecké články MeSH

Spongin is a fundamental biopolymer that has played a crucial role in the skeletogenesis of keratosan sponges for over 800 million years. This biomaterial had so far remained chemically unidentified and believed to be an enigmatic type of halogenated collagen-keratin-based bioelastomer. Here we show collagen I and III as the main structural components of spongin. Proteomics, 13C solid state NMR and Raman spectroscopy confirm the identity of collagenous domains in spongin with collagen from mammals. Using an HPLC-MS analysis, we found halogenated di- and tri-tyrosines as crosslinking agents in spongin. Using molecular dynamics modeling, we solvated the crystal structures of collagen mimetic peptides for type I and type III collagens in four different systems, including selected brominated crosslinks. The results underscore the complex interplay between the collagen structures and crosslinks, raising intriguing questions about the molecular mechanisms underlying collagen chemistry within spongin as an ancient biocomposite.

• MeSH
• biopolymery chemie   MeSH
• kolagen typ III * chemie   metabolismus   MeSH
• kolagen typu I * chemie   metabolismus   MeSH
• magnetická rezonanční spektroskopie MeSH
• Porifera * chemie   metabolismus   MeSH
• proteomika MeSH
• Ramanova spektroskopie MeSH
• savci metabolismus   MeSH
• simulace molekulární dynamiky MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biopolymery MeSH
• kolagen typ III * MeSH
• kolagen typu I * MeSH
• spongin MeSH Prohlížeč

The lateral line system enables fishes and aquatic-stage amphibians to detect local water movement via mechanosensory hair cells in neuromasts, and many species to detect weak electric fields via electroreceptors (modified hair cells) in ampullary organs. Both neuromasts and ampullary organs develop from lateral line placodes, but the molecular mechanisms underpinning ampullary organ formation are understudied relative to neuromasts. This is because the ancestral lineages of zebrafish (teleosts) and Xenopus (frogs) independently lost electroreception. We identified Bmp5 as a promising candidate via differential RNA-seq in an electroreceptive ray-finned fish, the Mississippi paddlefish (Polyodon spathula; Modrell et al., 2017, eLife 6: e24197). In an experimentally tractable relative, the sterlet sturgeon (Acipenser ruthenus), we found that Bmp5 and four other Bmp pathway genes are expressed in the developing lateral line, and that Bmp signalling is active. Furthermore, CRISPR/Cas9-mediated mutagenesis targeting Bmp5 in G0-injected sterlet embryos resulted in fewer ampullary organs. Conversely, when Bmp signalling was inhibited by DMH1 treatment shortly before the formation of ampullary organ primordia, supernumerary ampullary organs developed. These data suggest that Bmp5 promotes ampullary organ development, whereas Bmp signalling via another ligand(s) prevents their overproduction. Taken together, this demonstrates opposing roles for Bmp signalling during ampullary organ formation.

• Klíčová slova
• Acipenser ruthenus, Bmp, ampullary organs, developmental biology, lateral line, neuromasts, sterlet sturgeon, sterlet sturgeon (acipenser ruthenus),
• MeSH
• kostní morfogenetické proteiny * metabolismus   genetika   MeSH
• proudový orgán * embryologie   metabolismus   růst a vývoj   MeSH
• rybí proteiny * metabolismus   genetika   MeSH
• ryby * embryologie   genetika   MeSH
• signální transdukce * MeSH
• vývojová regulace genové exprese MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• kostní morfogenetické proteiny * MeSH
• rybí proteiny * MeSH

Listeria monocytognes is an emerging pathogen responsible for the serious foodborne disease, listeriosis. The commensal gut microbiota is the first line of defense against pathogen internalization. The gut microbiome can be modified by prebiotic substrates, which are frequently added to food products and dietary supplements. Prebiotics should selectively support the growth of beneficial microbes and thus improve host health. Nevertheless, little is known about their effect on the growth of L. monocytogenes. The aim of this study was to evaluate the growth ability of four L. monocytogenes strains, representing the most common serotypes, on prebiotic oligosaccharides (beta-(1,3)-D-glucan, inulin, fructooligosaccharides, galactooligosaccharides, lactulose, raffinose, stachyose and 2'-fucosyllactose and a mixture of human milk oligosaccharides) as a sole carbon source. The results showed that only beta-(1,3)-D-glucan was metabolized by L. monocytogenes. These cell culture data suggest that beta-(1,3)-D-glucan may not be selectively utilized by healthy commensal bacteria, and its role in intestinal pathogen growth warrants further exploration in vivo.

• Klíčová slova
• Listeria monocytogenes, beta-(1,3)-D-glucan, oligosaccharides, pathogen growth, prebiotics,
• Publikační typ
• časopisecké články MeSH

In electroreceptive jawed vertebrates, embryonic lateral line placodes give rise to electrosensory ampullary organs as well as mechanosensory neuromasts. Previous reports of shared gene expression suggest that conserved mechanisms underlie electroreceptor and mechanosensory hair cell development and that electroreceptors evolved as a transcriptionally related "sister cell type" to hair cells. We previously identified only one transcription factor gene, Neurod4, as ampullary organ-restricted in the developing lateral line system of a chondrostean ray-finned fish, the Mississippi paddlefish (Polyodon spathula). The other 16 transcription factor genes we previously validated in paddlefish were expressed in both ampullary organs and neuromasts. Here, we used our published lateral line organ-enriched gene-set (arising from differential bulk RNA-seq in late-larval paddlefish), together with a candidate gene approach, to identify 25 transcription factor genes expressed in the developing lateral line system of a more experimentally tractable chondrostean, the sterlet (Acipenser ruthenus, a small sturgeon), and/or that of paddlefish. Thirteen are expressed in both ampullary organs and neuromasts, consistent with conservation of molecular mechanisms. Seven are electrosensory-restricted on the head (Irx5, Irx3, Insm1, Sp5, Satb2, Mafa and Rorc), and five are the first-reported mechanosensory-restricted transcription factor genes (Foxg1, Sox8, Isl1, Hmx2 and Rorb). However, as previously reported, Sox8 is expressed in ampullary organs as well as neuromasts in a catshark (Scyliorhinus canicula), suggesting the existence of lineage-specific differences between cartilaginous and ray-finned fishes. Overall, our results support the hypothesis that ampullary organs and neuromasts develop via largely conserved transcriptional mechanisms, and identify multiple transcription factors potentially involved in the formation of electrosensory versus mechanosensory lateral line organs.

• Klíčová slova
• ampullary organ, electrosensory, lateral line organs, mechanosensory, neuromast, paddlefish, sterlet, sturgeon,
• Publikační typ
• časopisecké články MeSH

BACKGROUND: While web-based tools such as BLAST have made identifying conserved gene homologs appear easy, genes with variable sequences pose significant challenges. Functionally important noncoding RNAs (ncRNA) often show low sequence conservation due to genetic variations, including insertions and deletions. Rather than conserved sequences, these RNAs possess highly conserved structural features across a broad phylogenetic range. Such features can be identified using the covariance models approach, which combines sequence alignment with a secondary RNA structure consensus. However, running standard implementation of that approach (Infernal) requires advanced bioinformatics knowledge compared to user-friendly web services like BLAST. The issue is partially addressed by RNAcentral, which can be used to search for homologs across a broad range of ncRNA sequence collections from diverse organisms but not across the genome assemblies. RESULTS: Here, we present GERONIMO, which conducts evolutionary searches across hundreds of genomes in a fully automated way. It provides results extended with taxonomy context, as summary tables and visualizations, to facilitate analysis for user convenience. Additionally, GERONIMO supplements homologous sequences with genomic regions to analyze promoter motifs or gene collinearity, enhancing the validation of results. CONCLUSION: GERONIMO, built using Snakemake, has undergone extensive testing on hundreds of genomes, establishing itself as a valuable tool in the identification of ncRNA homologs across diverse taxonomic groups. Consequently, GERONIMO facilitates the investigation of the evolutionary patterns of functionally significant ncRNA players, whose understanding has previously been limited to individual organisms and close relatives.

• Klíčová slova
• Snakemake, evolution, high-throughput pipeline, sequence homology searches,
• MeSH
• algoritmy * MeSH
• fylogeneze MeSH
• genomika MeSH
• nekódující RNA genetika   chemie   MeSH
• RNA * MeSH
• sekvenční seřazení MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• nekódující RNA MeSH
• RNA * MeSH

The frameshift hypothesis is a widely accepted model of bird wing evolution. This hypothesis postulates a shift in positional values, or molecular-developmental identity, that caused a change in digit phenotype. The hypothesis synthesized developmental and paleontological data on wing digit homology. The "most anterior digit" (MAD) hypothesis presents an alternative view based on changes in transcriptional regulation in the limb. The molecular evidence for both hypotheses is that the MAD expresses Hoxd13 but not Hoxd11 and Hoxd12. This digit I "signature" is thought to characterize all amniotes. Here, we studied Hoxd expression patterns in a phylogenetic sample of 18 amniotes. Instead of a conserved molecular signature in digit I, we find wide variation of Hoxd11, Hoxd12, and Hoxd13 expression in digit I. Patterns of apoptosis, and Sox9 expression, a marker of the phalanx-forming region, suggest that phalanges were lost from wing digit IV because of early arrest of the phalanx-forming region followed by cell death. Finally, we show that multiple amniote lineages lost phalanges with no frameshift. Our findings suggest that the bird wing evolved by targeted loss of phalanges under selection. Consistent with our view, some recent phylogenies based on dinosaur fossils eliminate the need to postulate a frameshift in the first place. We suggest that the phenotype of the Archaeopteryx lithographica wing is also consistent with phalanx loss. More broadly, our results support a gradualist model of evolution based on tinkering with developmental gene expression.

• Klíčová slova
• apoptosis, evo-devo, frameshift theory, bird, reptile, hox genes, limb development, phalanx-forming region,
• MeSH
• dinosauři * anatomie a histologie   MeSH
• fylogeneze MeSH
• končetiny MeSH
• křídla zvířecí * MeSH
• ptáci genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Butyrate is formed in the gut during bacterial fermentation of dietary fiber and is attributed numerous beneficial effects on the host metabolism. We aimed to develop a method for the assessment of functional capacity of gut microbiota butyrate synthesis based on the qPCR quantification of bacterial gene coding butyryl-CoA:acetate CoA-transferase, the key enzyme of butyrate synthesis. In silico, we identified bacteria possessing but gene among human gut microbiota by searching but coding sequences in available databases. We designed and validated six sets of degenerate primers covering all selected bacteria, based on their phylogenetic nearness and sequence similarity, and developed a method for gene abundance normalization in human fecal DNA. We determined but gene abundance in fecal DNA of subjects with opposing dietary patterns and metabolic phenotypes-lean vegans (VG) and healthy obese omnivores (OB) with known fecal microbiota and metabolome composition. We found higher but gene copy number in VG compared with OB, in line with higher fecal butyrate content in VG group. We further found a positive correlation between the relative abundance of target bacterial genera identified by next-generation sequencing and groups of but gene-containing bacteria determined by specific primers. In conclusion, this approach represents a simple and feasible tool for estimation of microbial functional capacity.

• Klíčová slova
• butyrate, functional capacity, gut microbiota,
• MeSH
• bakteriální geny * MeSH
• butyráty metabolismus   MeSH
• DNA bakterií genetika   MeSH
• dospělí MeSH
• feces mikrobiologie   MeSH
• fenotyp MeSH
• fylogeneze MeSH
• genová dávka MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• neparametrická statistika MeSH
• obezita mikrobiologie   MeSH
• polymerázová řetězová reakce * MeSH
• reprodukovatelnost výsledků MeSH
• střevní mikroflóra genetika   MeSH
• vegani MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mladý dospělý MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• butyráty MeSH
• DNA bakterií MeSH

Understanding how context (e.g., host species, environmental conditions) drives disease susceptibility is an essential goal of disease ecology. We hypothesized that in bat white-nose syndrome (WNS), species-specific host-pathogen interactions may partly explain varying disease outcomes among host species. We characterized bat and pathogen transcriptomes in paired samples of lesion-positive and lesion-negative wing tissue from bats infected with Pseudogymnoascus destructans in three parallel experiments. The first two experiments analyzed samples collected from the susceptible Nearctic Myotis lucifugus and the less-susceptible Nearctic Eptesicus fuscus, following experimental infection and hibernation in captivity under controlled conditions. The third experiment applied the same analyses to paired samples from infected, free-ranging Myotis myotis, a less susceptible, Palearctic species, following natural infection and hibernation (n = 8 sample pairs/species). Gene expression by P. destructans was similar among the three host species despite varying environmental conditions among the three experiments and was similar within each host species between saprophytic contexts (superficial growth on wings) and pathogenic contexts (growth in lesions on the same wings). In contrast, we observed qualitative variation in host response: M. lucifugus and M. myotis exhibited systemic responses to infection, while E. fuscus up-regulated a remarkably localized response. Our results suggest potential phylogenetic determinants of response to WNS and can inform further studies of context-dependent host-pathogen interactions.

• Klíčová slova
• Eptesicus fuscus, Myotis lucifugus, Myotis myotis, Pseudogymnoascus destructans, Disease ecology, emerging infectious diseases, host–pathogen interactions, susceptibility, virulence,
• MeSH
• Ascomycota genetika   patogenita   MeSH
• Chiroptera klasifikace   mikrobiologie   MeSH
• dermatomykózy mikrobiologie   veterinární   MeSH
• druhová specificita MeSH
• fylogeneze MeSH
• interakce hostitele a patogenu genetika   MeSH
• křídla zvířecí mikrobiologie   patologie   MeSH
• nos mikrobiologie   patologie   MeSH
• stanovení celkové genové exprese * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH