U12DB: a database of orthologous U12-type spliceosomal introns

U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12-type introns of completely sequenced eukaryotic genomes in a framework that groups orthologous introns with each other. This will aid further investigations into the evolution and mechanism of U12-dependent splicing as well as assist ongoing genome annotation efforts. Public access to the U12DB is available at

The repertoire of olfactory C family G protein-coupled receptors in zebrafish: candidate chemosensory receptors for amino acids

BACKGROUND: Vertebrate odorant receptors comprise at least three types of G protein-coupled receptors (GPCRs): the OR, V1R, and V2R/V2R-like receptors, the latter group belonging to the C family of GPCRs. These receptor families are thought to receive chemosensory information from a wide spectrum of odorant and pheromonal cues that influence critical animal behaviors such as feeding, reproduction and other social interactions. RESULTS: Using genome database mining and other informatics approaches, we identified and characterized the repertoire of 54 intact "V2R-like" olfactory C family GPCRs in the zebrafish. Phylogenetic analysis – which also included a set of 34 C family GPCRs from fugu – places the fish olfactory receptors in three major groups, which are related to but clearly distinct from other C family GPCRs, including the calcium sensing receptor, metabotropic glutamate receptors, GABA-B receptor, T1R taste receptors, and the major group of V2R vomeronasal receptor families. Interestingly, an analysis of sequence conservation and selective pressure in the zebrafish receptors revealed the retention of a conserved sequence motif previously shown to be required for ligand binding in other amino acid receptors. CONCLUSION: Based on our findings, we propose that the repertoire of zebrafish olfactory C family GPCRs has evolved to allow the detection and discrimination of a spectrum of amino acid and/or amino acid-based compounds, which are potent olfactory cues in fish. Furthermore, as the major groups of fish receptors and mammalian V2R receptors appear to have diverged significantly from a common ancestral gene(s), these receptors likely mediate chemosensation of different classes of chemical structures by their respective organisms

The odorant receptor repertoire of teleost fish

BACKGROUND: Vertebrate odorant receptors comprise three types of G protein-coupled receptors: the OR, V1R and V2R receptors. The OR superfamily contains over 1,000 genes in some mammalian species, representing the largest gene superfamily in the mammalian genome. RESULTS: To facilitate an informed analysis of OR gene phylogeny, we identified the complete set of 143 OR genes in the zebrafish genome, as well as the OR repertoires in two pufferfish species, fugu (44 genes) and tetraodon (42 genes). Although the genomes analyzed here contain fewer genes than in mammalian species, the teleost OR genes can be grouped into a larger number of major clades, representing greater overall OR diversity in the fish. CONCLUSION: Based on the phylogeny of fish and mammalian repertoires, we propose a model for OR gene evolution in which different ancestral OR genes or gene families were selectively lost or expanded in different vertebrate lineages. In addition, our calculations of the ratios of non-synonymous to synonymous codon substitutions among more recently expanding OR subgroups in zebrafish implicate residues that may be involved in odorant binding

Fully Synthesizable, Rail-to-Rail Dynamic Voltage Comparator for Operation down to 0.3V

A novel rail-to-rail dynamic voltage comparator is presented in this paper. The proposed circuit is fully synthesizable, as it can be designed with automated digital design flows and standard cells, and can operate at very low voltages down to deep sub-threshold. Post-layout simulations show correct operation for rail-to-rail common-mode inputs at a supply voltage VDD down to 0.3 V. At such voltage, the input offset voltage standard deviation is less than 28 mV (8 mV) over the rail-to-rail common-mode input range (around VDD/2). The digital nature of the comparator and its ability to operate down to deep sub-threshold voltages allow its full integration with standard-cell digital circuits in terms of both design and voltage domain. The ease of design, the low area and the voltage scalability make the proposed comparator very well suited for sensor nodes, integrated circuits for the Internet of Things and related applications

A Sub-Leakage pW-Power Hz-Range Relaxation Oscillator Operating with 0.3V-1.8V Unregulated Supply

A pW-power versatile relaxation oscillator operating from sub-threshold (0.3V) to nominal voltage (1.8V) is presented, having Hz-range frequency under sub-pF capacitor. The wide voltage and low sensitivity of frequency/absorbed current to the supply allow the suppression of the voltage regulator, and direct powering from harvesters (e.g., solar cell, thermal from machines) or 1.2-1.5V batteries. A 180nm testchip exhibits a frequency of 4 Hz , 10%/V supply sensitivity at 0.3-1.8V, 8-18pA current, 4%/°C thermal drift from -20°C to 40°C

Performance enhancing strategies in sailing sports: beyond training and nutrition

Purpose. Sailing is a water sport comprising several disciplines distinguished by the type of boat and number of crew. The sailor must constantly accommodate the movement of the hull according to the weather conditions. The study aims to provide targeted guidance regarding training and nutrition for sailor athletes. Methods. Complete and effective training requires a synergistic combination of sport -specific elements and strategies designed to improve overall strength. Extensive discussion has been made of the types of workouts aimed at improving performance and preventing injury. Results. Our research findings revealed that even though sailors' training considers the development of strength, endurance, speed, balance, and coordination, which are necessary to counteract the continuous adaptations of posture to weather conditions, these athletes are exposed to the risk of injuries that predominantly affect the knee and lower back. Sailing is an aerobic/ anaerobic sport in which there are no explicit suggestions regarding the nutritional aspect and supplementation and what their contribution could be in improving performance. Conclusions. We hypothesise that targeted training paths for sailing athletes and personalisation of nutritional suggestions by timing the intake of macro- and micronutrients as well as taking specific supplements, can reduce the risk of injury and better impact recovery and performance in this discipline

Genotyping-by-sequencing resolves relationships in Polygonaceae tribe Eriogoneae

The resolution of cryptic diversity is essential for understanding the evolutionary diversification of lineages and establishing conservation priorities. We examine relationships in Eriogoneae (Polygonaceae), a diverse lineage in western North America. We ask whether Eriogonum umbellatum, a morphologically and ecologically diverse species, is monophyletic and whether its varieties represent evolutionary lineages. We use genotyping-by-sequencing to assemble a SNP dataset for 51 species in the genera Chorizanthe, Eriogonum and Sidotheca. We report a hierarchical phylogenetic analysis using maximum likelihood to estimate the evolutionary history of Eriogoneae. We illustrate admixture components for 21 populations of E. umbellatum, representing four varieties, and test for lineage structure using TreeMix. We identify strongly supported clades within Eriogoneae. Many relationships in the Eucycla + Oregonium and Latifolia clades are supported, while most relationships within the Eriogonum subg. Oligogonum clade and a clade with most Chorizanthe remain unresolved. Eriogonum congdonii resolves within the main E. umbellatum clade, while populations of three varieties of E. umbellatum are closely related to E. ursinum and are associated with serpentine soils. ADmixture and TreeMix analyses suggest E. umbellatum varieties represent evolutionary lineages. These results from SNP data are largely consistent with previous phylogenetic studies of Eriogoneae based on sequence variation. Structure within Oligogonum suggests consistent environmental association and radiation after initial colonization of serpentine. Morphology is unreliable for the infraspecific taxonomy of E. umbellatum. Additional molecular studies are needed to resolve the evolutionary relationships and ecological diversification within this species, in Oligogonum, and in Eriogoneae. © 2021 The Authors. TAXON published by John Wiley & Sons Ltd on behalf of International Association for Plant Taxonomy.We thank SGIker research support services at the University of the Basque Country, Leioa, Spain for DNA extraction and quality control, and acknowledge Centro Nacional de d-An?lisi Gen?mica in Barcelona, Spain for GBS sequencing. We thank J. Andre, N.J. Jensen and J. Steele for contributing samples and D. Marino for collaboration in nucleic acid extractions. We acknowledge the contributions of O. Lao Grueso to the?ADmixture and TreeMix analyses. We thank U.S. Forest Service employees D. Austin, J. Fedorchuk, M. Friend, J. Haas, D. Ikeda, L. Janeway, J. Nelson, D. Netz, A. Sanger, and S. Weis among others for facilitating permitting and collecting. This work was supported by funds from the Basque Government in support of the Terrestrial Plant Diversity group of the Department of Plant Biology and Ecology, University of the Basque Country, and an ERC Advanced Grant, FP7-IDEAS-ERC, ?ADAPT?, project 339941 awarded to T. Brown. We thank SGIker research support services at the University of the Basque Country, Leioa, Spain for DNA extraction and quality control, and acknowledge Centro Nacional de d‐Anàlisi Genòmica in Barcelona, Spain for GBS sequencing. We thank J. Andre, N.J. Jensen and J. Steele for contributing samples and D. Marino for collaboration in nucleic acid extractions. We acknowledge the contributions of O. Lao Grueso to the ADmixture and TreeMix analyses. We thank U.S. Forest Service employees D. Austin, J. Fedorchuk, M. Friend, J. Haas, D. Ikeda, L. Janeway, J. Nelson, D. Netz, A. Sanger, and S. Weis among others for facilitating permitting and collecting. This work was supported by funds from the Basque Government in support of the Terrestrial Plant Diversity group of the Department of Plant Biology and Ecology, University of the Basque Country, and an ERC Advanced Grant, FP7‐IDEAS‐ERC, ‘ADAPT’, project 339941 awarded to T. Brown

A novel self-cleaving viroid-like RNA identified in RNA preparations from a citrus tree is not directly associated with the plant

Viroid and viroid-like satellite RNAs are infectious, circular, non-protein coding RNAs reported in plants only so far. Some viroids (family Avsunviroidae) and viroid-like satellite RNAs share self-cleaving activity mediated by hammerhead ribozymes (HHRzs) endowed in both RNA polarity strands. Using a homology-independent method based on the search for conserved structural motifs of HHRzs in reads and contigs from high-throughput sequenced RNAseq libraries, we identified a novel small (550 nt) viroid-like RNA in a library from a Citrus reticulata tree. Such a viroid-like RNA contains a HHRz in both polarity strands. Northern blot hybridization assays showed that circular forms of both polarity strands of this RNA (tentatively named citrus transiently-associated hammerhead viroid-like RNA1 (CtaHVd-LR1)) exist, supporting its replication through a symmetric pathway of the rolling circle mechanism. CtaHVd-LR1 adopts a rod-like conformation and has the typical features of quasispecies. Its HHRzs were shown to be active during transcription and in the absence of any protein. CtaHVd-LR1 was not graft-transmissible, and after its first identification, it was not found again in the original citrus source when repeatedly searched in the following years, suggesting that it was actually not directly associated with the plant. Therefore, the possibility that this novel self-cleaving viroid-like RNA is actually associated with another organism (e.g., a fungus), in turn, transiently associated with citrus plants, is propose