In vitro homology search array comprehensively reveals highly conserved genes and their functional characteristics in non-sequenced species

<p>Abstract</p> <p>Background</p> <p>With the increase in genomic and transcriptomic data produced by the recent advancements in next generation sequencers and microarrays, it is now easier than ever to conduct large-scale comparative genomic studies for familiar species. However, there are more than ten million species on earth, and the study of all remaining species is not realistic in terms of cost and time. There have been a number of attempts at using microarrays for cross-species hybridization; however, those approaches only utilized the same probes for each species or different probes designed from orthologous genes. To establish easier and cheaper methods for the large-scale comparative genomic study of non-sequenced species, we developed an <it>in vitro</it> homology search array with the aid of a bioinformatic approach to probe design.</p> <p>Results</p> <p>To perform large-scale genomic comparisons of non-sequenced species, we chose squid, one of the most intelligent species among Protostomes, for comparison with human genes. We designed a microarray using human single copy genes and conducted microarray experiments with mRNAs extracted from the squid. Multi-copy genes could not be detected using the microarray in this study because their sequence similarity caused cross-hybridization. A search for squid homologous genes among human genes revealed that 68% of the human probes tested showed the expression of squid homolog genes and 95 genes were confirmed to be expressed highly in squid. Functional classification analysis showed that these highly expressed genes comprise DNA binding proteins, which are under pressure of DNA level mutation and, consequently, show high similarity at the nucleotide level.</p> <p>Conclusions</p> <p>Our array could detect homologous genes in squids and humans in spite of the distant phylogenic relationships between the species. This experimental method will be useful for identifying homologs in non-sequenced species, for the development of genetic resources and for the collection of information on biodiversity, particularly when using the genome of sibling or closely related species.</p

Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis

To clarify the establishment process of coral-algal symbiotic relationships, coral transcriptome changes during increasing algal symbiont densities were examined in juvenile corals following inoculation with the algae Symbiodinium goreaui (clade C) and S. trenchii (clade D), and comparison of their transcriptomes with aposymbiotic corals by RNA-sequencing. Since Symbiodinium clades C and D showed very different rates of density increase, comparisons were made of early onsets of both symbionts, revealing that the host behaved differently for each. RNA-sequencing showed that the number of differentially-expressed genes in corals colonized by clade D increased ca. two-fold from 10 to 20 days, whereas corals with clade C showed unremarkable changes consistent with a slow rate of density increase. The data revealed dynamic metabolic changes in symbiotic corals. In addition, the endocytosis pathway was also upregulated, while lysosomal digestive enzymes and the immune system tended to be downregulated as the density of clade D algae increased. The present dataset provides an enormous number of candidate symbiosis-related molecules that exhibit the detailed process by which coral-algal endosymbiosis is established

Rapid changes in plaque composition and morphology after intensive lipid lowering therapy: study with serial coronary CT angiography.

Although intensive lipid lowering by statins can enhance plaque stability, few data exist regarding how early statins change plaque composition and morphology in clinical setting. Therefore, to examine early changes in plaque composition and morphology by intensive lipid lowering with statins, we evaluate coronary plaques from acute coronary syndrome (ACS) before and 3 weeks after lipid lowering by coronary CT angiography. We enrolled 110 patients with suspected ACS and underwent coronary CT. We defined plaque as unstable when CT number of plaque1.10. Rosuvastatin (5 mg/day) or atorvastatin (20 mg/day) were introduced to reduce low density lipoprotein cholesterol (LDL-C). Then, CT was again performed by the same condition 3 weeks after lipid lowering therapy. Total 10 patients (8 men, mean age 72.0 years), in whom informed consent regarding serial CT examination was obtained, were analyzed. Among them, 4 patients who denied to have intensive lipid lowering were served as controls. In remaining 6 patients, LDL-C reduced from 129.5±26.9 mg/dl to 68.5±11.1 mg/dl after statin treatment. Under these conditions, CT number of the targeted plaque significantly increased from 16.0±15.9 to 50.8±35.0 HU (p<0.05) and remodeling index decreased from 1.22±0.11 to 1.11±0.06 (p<0.05), although these values substantially unchanged in controls. These results demonstrate that MDCT-determined plaque composition as well as volume could be changed within 3 weeks after intensive lipid lowering. This may explain acute effects of statins in treatment of acute coronary syndrome

Vasopressin-oxytocin–type signaling is ancient and has a conserved water homeostasis role in euryhaline marine planarians

Vasopressin/oxytocin (VP/OT)–related peptides are essential for mammalian antidiuresis, sociosexual behavior, and reproduction. However, the evolutionary origin of this peptide system is still uncertain. Here, we identify orthologous genes to those for VP/OT in Platyhelminthes, intertidal planarians that have a simple bilaterian body structure but lack a coelom and body-fluid circulatory system. We report a comprehensive characterization of the neuropeptide derived from this VP/OT-type gene, identifying its functional receptor, and name it the “platytocin” system. Our experiments with these euryhaline planarians, living where environmental salinities fluctuate due to evaporation and rainfall, suggest that platytocin functions as an “antidiuretic hormone” and also organizes diverse actions including reproduction and chemosensory-associated behavior. We propose that bilaterians acquired physiological adaptations to amphibious lives by such regulation of the body fluids. This neuropeptide-secreting system clearly became indispensable for life even without the development of a vascular circulatory system or relevant synapses

A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis

Background:Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.Findings:To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ∼17–kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ∼656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ∼70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ∼99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.Conclusions:Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians

Explosive nucleosynthesis in the neutrino-driven aspherical supernova explosion of a non-rotating 15M⊙M_{\odot} star with solar metallicity

We investigate explosive nucleosynthesis in a non-rotating 15$M_\odot$ star with solar metallicity that explodes by a neutrino-heating supernova (SN) mechanism aided by both standing accretion shock instability (SASI) and convection. To trigger explosions in our two-dimensional hydrodynamic simulations, we approximate the neutrino transport with a simple light-bulb scheme and systematically change the neutrino fluxes emitted from the protoneutron star. By a post-processing calculation, we evaluate abundances and masses of the SN ejecta for nuclei with the mass number $\le 70$ employing a large nuclear reaction network. Aspherical abundance distributions, which are observed in nearby core-collapse SN remnants, are obtained for the non-rotating spherically-symmetric progenitor, due to the growth of low-mode SASI. Abundance pattern of the supernova ejecta is similar to that of the solar system for models whose masses ranges (0.4-0.5) \Ms of the ejecta from the inner region (\le 10,000\km) of the precollapse core. For the models, the explosion energies and the \nuc{Ni}{56} masses are $\simeq 10^{51} \rm erg$ and (0.05-0.06) \Ms, respectively; their estimated baryonic masses of the neutron star are comparable to the ones observed in neutron-star binaries. These findings may have little uncertainty because most of the ejecta is composed by matter that is heated via the shock wave and has relatively definite abundances. The abundance ratios for Ne, Mg, Si and Fe observed in Cygnus loop are well reproduced with the SN ejecta from an inner region of the 15\Ms progenitor.Comment: 15 pages, 1 table, 17 figures, accepted for publication in Astrophyscal Journa

Determination of Early and Late Endothelial Progenitor Cells in Peripheral Circulation and Their Clinical Association with Coronary Artery Disease

金沢大学医薬保健研究域医学系The clinical implications of early and late endothelial progenitor cells (EPCs) in coronary artery disease (CAD) remain unclear. We investigated endothelial dysfunction in CAD by simultaneously examining early and late EPC colony formation and gene expression of specific surface markers in EPCs. EPCs were extracted from a total of 83 subjects with (n=47) and without (n=36) CAD. Early and late EPC colonies were formed from mononuclear cells extracted from peripheral blood. We found that fewer early EPC colonies were produced in the CAD group (7.2 ± 3.l/well) than those in the control group (12.4 ± 1.4/well, p<0.05), and more late EPC colonies were produced in the CAD group (0.8 ± 0.2/well) than those in the control group (0.25 ± 0.02/well, p<0.05). In the CAD group, the relative expression of CD31 and KDR of early and late EPCs was lower than in the control group. These results demonstrate that CAD patients could have increased late EPC density and that early and late EPCs in CAD patients exhibited immature endothelial characteristics. We suggest that changes in EPC colony count and gene expression of endothelial markers may have relation with development of CAD. © 2015 Shotoku Tagawa et al