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The soil worm Enchytraeus crypticus (Oligochaeta) is an ecotoxicology model species that, until now, was without genome or transcriptome sequence information. The present research aims at studying the transcriptome of Enchytraeus crypticus, sampled from multiple test conditions, and the construction of a high-density microarray for functional genomic studies.
Over 1.5 million cDNA sequence reads were obtained representing 645 million nucleotides. After assembly, 27,296 contigs and 87,686 singletons were obtained, from which 44% and 25% are annotated as protein-coding genes, respectively, sharing homology with other animal proteomes. Concerning assembly quality, 84% of the contig sequences contain an open reading frame with a start codon while E. crypticus homologs were identified for 92% of the core eukaryotic genes. Moreover, 65% and 77% of the singletons and contigs without known homologs, respectively, were shown to be transcribed in an independent microarray experiment. An Agilent 180 K microarray platform was designed and validated by hybridizing cDNA from 4 day zinc- exposed E. crypticus to the concentration corresponding to 50% reduction in reproduction after three weeks (EC50). Overall, 70% of all probes signaled expression above background levels (mean signal + 1x standard deviation). More specifically, the probes derived from contigs showed a wider range of average intensities when compared to probes derived from singletons. In total, 522 significantly differentially regulated transcripts were identified upon zinc exposure. Several significantly regulated genes exerted predicted functions (e.g. zinc efflux, zinc transport) associated with zinc stress. Unexpectedly, the microarray data suggest that zinc exposure alters retro transposon activity in the E. crypticus genome.
An initial investigation of the E. crypticus transcriptome including an associated microarray platform for future studies proves to be a valuable resource to investigate functional genomics mechanisms of toxicity in soil environments and to annotate a potentially large number of lineage specific genes that are responsive to environmental stress conditions.
Ecotoxicogenomics, Next-generation pyrosequencing, Invertebrate, Zinc, Annelid, 454 sequencing
Transcriptome assembly and microarray construction for Enchytraeus crypticus, a model oligochaete to assess stress response mechanisms derived from soil conditions
Marta P Castro-Ferreira,1,2 Tjalf E de Boer,1 John K Colbourne,3,4 Riet Vooijs,1 Cornelis AM van Gestel,1 Nico M van Straalen,1 Amadeu MVM Soares,2 Monica JB Amorim,2 and Dick Roelofscorresponding author1
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates
Lina M. Valencia, Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Visualization, Writing - original draft, Writing - review & editing,1,* Amely Martins, Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Resources, Software,1,2 Edgardo M. Ortiz, Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Software, Validation,3 and Anthony Di Fiore, Funding acquisition, Methodology, Resources, Supervision, Visualization, Writing - original draft1 Tzen-Yuh Chiang, Editor
In the title compound, [Ir(C13H9N4)(C13H8NS)2]·3.5CDCl3, the coordination at iridium is octahedral, but with narrow ligand bite angles. The bond lengths at iridium show the expected trans influence, with the Ir—N bonds trans to C being appreciably longer than those trans to N. The chelate rings are mutually perpendicular, the interplanar angles between them all lying within 6° of 90°. All ligands are approximately planar; the maximum interplanar angles within ligands are ca 10°. The three ordered deuterochloroform molecules are all involved in C⋯D—A contacts that can be interpreted as hydrogen bonds of various types. The fourth deuterochloroform is disordered over an inversion centre.
mer-Bis[2-(1,3-benzothiazol-2-yl)phenyl-κ2 C 1,N][3-phenyl-5-(2-pyridyl)-1,2,4-triazol-1-ido-κ2 N 1,N 5]iridium(III) deuterochloroform 3.5-solvate
Peter G. Jones,a,* Andreas Freund,b Andreas Weinkauf,a Wolfgang Kowalsky,b and Hans-Hermann Johannesb
2010 Sep 1;
In vitro and in vivo inhibitory effects of 6-hydroxyrubiadin on lipopolysaccharide-induced inflammation. PUMID/DOI：DOI: 10.1080/08923973.2017.1295053 Immunopharmacol Immunotoxicol. 2017 Jun;39(3):107-116. Inflammation is a defensive response against a multitude of harmful stimuli and stress conditions such as tissue injury, and is one of the most common pathological processes of human diseases. 6-Hydroxyrubiadin, an anthraquinone isolated from Rubia cordifolia L., exhibits several bioactive properties. The aim of this study was to evaluate whether 6-hydroxyrubiadin can reduce the production of pro-inflammatory cytokines and ameliorate acute lung injury (ALI) in a mouse model. In this study, we demonstrated that 6-hydroxyrubiadin suppressed lipopolysaccharide (LPS)-induced nuclear factor-kappa B activation as well as the phosphorylation of c-Jun N-terminal kinase in RAW 264.7 macrophages. In addition, we also showed that 6-hydroxyrubiadin inhibited the expression of tumor necrosis factor (TNF)-a, interleukin (IL)-1?and IL-6 in phorbol myristate acetate (PMA)-primed U937 and RAW 264.7 cells. Furthermore, 6-hydroxyrubiadin treatment reduced the production of these cytokines in vivo and attenuated the severity of LPS-induced ALI. Thus, these results suggested that 6-hydroxyrubiadin may be a potential therapeutic candidate for the treatment of inflammation and inflammatory diseases.