Project description:Conventional food-web theory assumes that nutrients from dissolved organic matter are transferred to aquatic vertebrates via long nutrient pathways involving multiple eukaryotic species as intermediary nutrient transporters. Here, using larvae of the salamander Hynobius retardatus as a model system, we provide experimental evidence of a shortcut nutrient pathway by showing that H. retardatus larvae can use dissolved amino acids for their growth without eukaryotic mediation. First, to explore which amino acids can promote larval growth, we kept individual salamander larvae in one of eight different high-concentration amino acid solutions, or in control water from which all other eukaryotic organisms had been removed. We thus identified five amino acids (lysine, threonine, serine, phenylalanine, and tyrosine) as having the potential to promote larval growth. Next, using 15N-labelled amino acid solutions, we demonstrated that nitrogen from dissolved amino acids was found in larval tissues. These results suggest that salamander larvae can take up dissolved amino acids from environmental water to use as an energy source or a growth-promoting factor. Thus, aquatic vertebrates as well as aquatic invertebrates may be able to use dissolved organic matter as a nutrient source.
Project description:Sera were acquired from the Sjogren's International Collaborative Clinical Alliance (SICCA) biorepository and were assayed for IgG autoantibodies. The autoantigen array was performed to identify the specific autoantibodies that were enriched in pSS patients.
Project description:Biodiversity genomics of small metazoa: high quality de novo genomes from single specimens of field-collected and ethanol-preserved springtails
Project description:BackgroundAlthough the overlap of transcriptional units occurs frequently in eukaryotic genomes, its evolutionary and biological significance remains largely unclear. Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm).ResultsFor all analyzed species the observed number of overlapping genes is always lower than expected assuming functional neutrality, suggesting that gene overlap is negatively selected. The comparison to the random distribution also shows that retained overlaps do not exhibit random features: antiparallel overlaps are significantly enriched, while overlaps lying on the same strand and those involving coding sequences are highly underrepresented. We confirm that overlap is mostly species-specific and provide evidence that it frequently originates through the acquisition of terminal, non-coding exons. Finally, we show that overlapping genes tend to be significantly co-expressed in a breast cancer cDNA library obtained by 454 deep sequencing, and that different overlap types display different patterns of reciprocal expression.ConclusionOur data suggest that overlap between protein-coding genes is selected against in Metazoa. However, when retained it may be used as a species-specific mechanism for the reciprocal regulation of neighboring genes. The tendency of overlaps to involve non-coding regions of the genes leads to the speculation that the advantages achieved by an overlapping arrangement may be optimized by evolving regulatory non-coding transcripts.
Project description:Protein reference databases are a critical part of producing efficient proteomic analyses. However, the method for constructing clean, efficient, and comprehensive protein reference databases is lacking. Existing methods either do not have contamination control procedures, or these methods rely on a three-frame and/or six-frame translation that sharply increases the search space and harms MS results. Herein we propose a framework for constructing a customized comprehensive proteomic reference database (CCPRD) from draft genomes and deep sequencing transcriptomes. Its effectiveness is demonstrated by incorporating the proteomes of nematocysts from endoparasitic cnidarian: myxozoans. By applying customized contamination removal procedures, contaminations in omic data were successfully identified and removed. This is an effective method that does not result in over-decontamination. This can be shown by comparing the CCPRD MS results with an artificially-contaminated database and another database with removed contaminations in genomes and transcriptomes added back. CCPRD outperformed traditional frame-based methods by identifying 35.2%-50.7% more peptides and 35.8%-43.8% more proteins, with a maximum 84.6% in size reduction. A BUSCO analysis showed that the CCPRD maintained a relatively high level of completeness compared to traditional methods. These results confirm the superiority of the CCPRD over existing methods in peptide and protein identification numbers, database size, and completeness. By providing a general framework for generating the reference database, the CCPRD, which does not need a high-quality genome, can potentially be applied to any organisms and significantly contribute to proteomic research.
Project description:Canonical RNA processing in mammalian mitochondria necessitates that tRNAs are recognised by nucleases to release flanking transcripts. However, not all mitochondrial transcripts are punctuated by tRNAs, and the mechanism and factors involved in their processing has remained unsolved. Here, we demonstrate that phosphatase activity of the carbon catabolite repressor 4 domain containing family member ANGEL2 is required for the hydrolysis of 3′ phosphates, resulting from non-canonical processing. Interaction studies in Drosophila further identify that members of the FAST kinase domain containing protein family are involved in the formation of these 3′ phosphates. Our results therefore resolve the mechanism of RNA processing in metazoan mitochondria, by defining the outstanding non-canonical processing mechanism.
Project description:Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation [Pires-daSilva & Sommer, Nat. Rev. Genet. 4, 39-49 (2003)]. Remarkably, in contrast to the large number of transcription factors present in animal genomes, only a few of these pathways operate during development [Sanz-Ezquerro, Münsterberg & Stricker, Front. Cell Dev. Biol. 5, 76 (2017)]. Moreover, most of them have been largely conserved during metazoan evolution [Babonis & Martindale, Philos. Trans. R. Soc. B 372, 20150477 (2017)]. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. Here, we show that gain of interconnectivity between signaling pathways, and the GRNs they control, may have critically contributed to the origin of vertebrates. We perturbed the retinoic acid, Wnt, FGF and Nodal signaling pathways during gastrulation in the invertebrate chordate amphioxus and zebrafish and compared the effects on gene expression and cis-regulatory elements (CREs). We found that multiple developmental genes gain response to these pathways through vertebrate-specific CREs. Moreover, in contrast to amphioxus, many of these CREs responded to multiple pathways in zebrafish, which reflects their high interconnectivity. Furthermore, we found that vertebrate-specific cell types are more enriched in highly interconnected genes than tissues with more ancient origin. Thus, the increase of CREs in vertebrates integrating inputs from different signaling pathways probably contributed to gene expression complexity and to the formation of new cell types and morphological novelties in this lineage.