Christian Anthon

A New Tripodal Ligand System with Steric and Electronic Modularity for Uranium Coordination Chemistry

The synthesis of a potentially redox active tripodal ligand containing a tris(aryloxide) functionalized mesitylene anchor, (((tBu)ArOH)(3)mes) (1), and its metalation with low-valent uranium to form [(((tBu)ArO)(3)mes)U] (1-U) is reported. The results from characterization by X-ray crystallography, spectroscopic studies, and computational analysis, as well as initial reactivity studies, support a +3 uranium oxidation state. Comparison to the previously synthesized complex, [(((tBu)ArO)(3)tacn)U] (2-U), featuring the redox-innocent triazacyclononane anchor reveals that changing the anchor from the flexible triazacyclononane to a rigid mesityl fragment increases the structural flexibility of the aryloxide substituents in complexes of 1. The synthesis and crystal structures of uranium(IV) amide complexes of 1-U and 2-U are discussed.

Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae

BackgroundMicroRNAs (miRNAs) are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level during the latest years, functional annotation is sparse. Actinobacillus pleuropneumoniae (APP) causes serious lung infections in pigs. Severe damage to the lungs, in many cases deadly, is caused by toxins released by the bacterium and to some degree by host mediated tissue damage. However, understanding of the role of microRNAs in the course of this infectious disease in porcine is still very limited.ResultsIn this study, the RNA extracted from visually unaffected and necrotic tissue from pigs infected with Actinobacillus pleuropneumoniae was subjected to small RNA deep sequencing. We identified 169 conserved and 11 candidate novel microRNAs in the pig. Of these, 17 were significantly up-regulated in the necrotic sample and 12 were down-regulated. The expression analysis of a number of candidates revealed microRNAs of potential importance in the innate immune response. MiR-155, a known key player in inflammation, was found expressed in both samples. Moreover, miR-664-5p, miR-451 and miR-15a appear as very promising candidates for microRNAs involved in response to pathogen infection.ConclusionsThis is the first study revealing significant differences in composition and expression profiles of miRNAs in lungs infected with a bacterial pathogen. Our results extend annotation of microRNA in pig and provide insight into the role of a number of microRNAs in regulation of bacteria induced immune and inflammatory response in porcine lung.

Tools and data services registry: a community effort to document bioinformatics resources

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

RAIN: RNA-protein Association and Interaction Networks

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain

Gender and Obesity Specific MicroRNA Expression in Adipose Tissue from Lean and Obese Pigs.

Obesity is a complex condition that increases the risk of life threatening diseases such as cardiovascular disease and diabetes. Studying the gene regulation of obesity is important for understanding the molecular mechanisms behind the obesity derived diseases and may lead to better intervention and treatment plans. MicroRNAs (miRNAs) are short non-coding RNAs regulating target mRNA by binding to their 3’UTR. They are involved in numerous biological processes and diseases, including obesity. In this study we use a mixed breed pig model designed for obesity studies to investigate differentially expressed miRNAs in subcutaneous adipose tissue by RNA sequencing (RNAseq). Both male and female pigs are included to explore gender differences. The RNAseq study shows that the most highly expressed miRNAs are in accordance with comparable studies in pigs and humans. A total of six miRNAs are differentially expressed in subcutaneous adipose tissue between the lean and obese group of pigs, and in addition gender specific significant differential expression is observed for a number of miRNAs. The differentially expressed miRNAs have been verified using qPCR. The results of these studies in general confirm the trends found by RNAseq. Mir-9 and mir-124a are significantly differentially expressed with large fold changes in subcutaneous adipose tissue between lean and obese pigs. Mir-9 is more highly expressed in the obese pigs with a fold change of 10 and a p-value < 0.001. Mir-124a is more highly expressed in the obese pigs with a fold change of 114 and a p-value < 0.001. In addition, mir-124a is significantly higher expressed in abdominal adipose tissue in male pigs with a fold change of 119 and a p-value < 0.05. Both miRNAs are also significantly higher expressed in the liver of obese male pigs where mir-124a has a fold change of 12 and mir-9 has a fold change of 1.6, both with p-values < 0.05.

Heterobimetallic Nitride Complexes from Terminal Chromium(V) Nitride Complexes: Hyperfine Coupling Increases with Distance†

Terminal nitride complexes of rhenium, osmium and molybdenum can form complexes with either alkylating agents, Lewis acidic metal halides, or low-valent, coordinatively unsaturated metal complexes. The few reactions of this type with a first-row transition-metal complex are limited to vanadium. Recently, the nitride chemistry of the chromium(V) cation has been significantly expanded by introduction of a preparative route which is based on nitrogen transfer from [Mn(N)(salen)] (salen=N,N’-bis(salicylidene)ethylenediamine) to the chromium(V) cation. With a range of chromium nitride complexes at hand we have investigated their reactivity and found that nucleophilicity is a general property which can be observed during formation of imide complexes with, for example, the trityl cation, tris(pentafluorophenyl)boron, and methyl triflate. In addition we report that terminal chromium(V) nitride complexes coordinate through the nitride ligand to low-valent complexes of the platinum metals. These compounds are possible precursors to bimetallic nitride phases which are gaining in importance as heterogeneous catalysts in, for example, the Haber–Bosch process. Solutions of terminal chromium nitride complexes in noncoordinating solvents treated with electrophiles such as B(C6F5)3 or C(C6H5)3 + quickly yield intensely colored orangered or green solutions. The reactions proceed cleanly as shown by EPR spectra which display a signal from a single S= =2 spin species. Similar reactivity was observed in reactions with either [Rh(cod)Cl]2 or cis-[PtCl2(dmso)2] (cod= 1,5cyclooctadiene, dmso= dimethyl sulfoxide). Structures of some of these systems, characterized by single-crystal X-ray diffraction, are shown in Scheme 1. Experimental and crystallographic details such as ORTEP drawings andmetric parameters of complexes 1–5 (Scheme 1) are available in the Supporting Information (Tables S1 and S1a). Inspection of the structures reveals a number of general aspects: there is a strong propensity for the chromium center to increase its coordination number from five to six upon coordination of the nitride ligand. This propensity is expected and a consequence of the trans influence of either an imide or a bridging nitride ligand which is significantly lower than that of a terminal nitride ligand. Accompanying this, the displacement of Cr out of the plane spanned by the equatorial ligators is diminished from about 0.5 to about 0.2 . The Cr N bond length is elongated from 1.55 in the terminal nitride complexes to approximately 1.60–1.62 in the functionalized systems. Comparison of structure 1 with that of [Cr(N)(salen)] reveals that the metal–salen ligand bonds are significantly shorter when the nitride ligand is functionalized, as expected when two ligands compete for electron donation. However, for the systems derived from [Cr(N)(dbm)2] the situation is less clear (dbm= dibenzoylmethanolate). In complex 2 all the Cr–dbm bonds are longer than in the parent terminal nitride complex, while they are shorter or similar within the limits of uncertainty in complex 5. The B N and C N bonds in 1, 4, and 5 are unexceptional but the N Rh and N Pt bond lengths in 2 and 3 are at about 1.970 and 1.906 , respectively, and very short; the first value belongs to the top 5% of the shortest Rh N bonds and the second belongs to the top 1% of the shortest Pt N bonds. Table 1 compares the Pt N bond of 3 with Pt N bonds of other cis[PtCl2(dmso)L] structures. Scheme 1. Schematic representation of the chromium(V) imide and chromium(V) bridging-nitride complexes.

Structured RNAs and synteny regions in the pig genome

BackgroundAnnotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals.ResultsWe present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 de novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific de novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog).ConclusionsWe have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at http://rth.dk/resources/rnannotator/susscr102/version1.02.

Quality Assessment of Domesticated Animal Genome Assemblies

The era of high-throughput sequencing has made it relatively simple to sequence genomes and transcriptomes of individuals from many species. In order to analyze the resulting sequencing data, high-quality reference genome assemblies are required. However, this is still a major challenge, and many domesticated animal genomes still need to be sequenced deeper in order to produce high-quality assemblies. In the meanwhile, ironically, the extent to which RNA seq and other next-generation data is produced frequently far exceeds that of the genomic sequence. Furthermore, basic comparative analysis is often affected by the lack of genomic sequence. Herein, we quantify the quality of the genome assemblies of 20 domesticated animals and related species by assessing a range of measurable parameters, and we show that there is a positive correlation between the fraction of mappable reads from RNAseq data and genome assembly quality. We rank the genomes by their assembly quality and discuss the implications for genotype analyses.

RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure

Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence.

Bridging Kohn–Sham DFT and the Angular Overlap Model. Ligand-Field Parameters and Bond Covalencies in Tetrahedral Complexes

Kohn–Sham density functional theory (DFT), constrained by the average-of-configuration computations, allows the valence shell of regular tetrahedral chlorido complexes of a complete series of 3d transition metal ions to be orbitally compared. The concept of classificational parentage provides a handle on the discussion of the energetic ordering of all the valence orbitals and illuminates an almost identical ordering for all the systems. Only the participation of the metal 4s orbital in bonding causes a few minor fluctuations. The partially filled ‘3d’ molecular orbitals sit in an energy window framed by completely filled ‘ligand orbitals’ on the low-energy side and an empty metal ‘4s’ orbital on the high-energy side. Regular tetrahedral symmetry requires the halides to be linearly ligating and this property is stable within the ‘experimental’ uncertainty for small distortions. By lowering the symmetry towards the planar configuration, keeping the equivalence of the ligands stable, the information content of the computations was doubled and the angular overlap energy parameters referring to the individual ligands obtained. The orbital energies of the partially filled shell depend linearly on the Angular Overlap Model (AOM) parameters eλ, the slope being the sum of the squares of the single-ligand λ angular overlaps (λ = σ and π). Mulliken population analysis shows the contents of the appropriate ligand orbitals in the ‘d’ orbitals to vary in parallel with the molecular orbital AOM energies and to increase pronouncedly with the oxidation number z. Results for tetraoxidoferrate(vi) show a remarkable resemblance with the chloride complexes of even the divalent metal ions. However, although the bonding orbitals are more π-bonding, the totally symmetrical bonding orbitals use M_4s less in the oxido complex. The sensitivity of covalency and spectroscopic energy parameters towards radial distortions are examined and show Werner-type complexes and the high-valent FeO42– to behave somewhat differently.