Phosphine-Free Ruthenium Complex-Catalyzed Synthesis of Mono- or Dialkylated Acyl Hydrazides via the Borrowing Hydrogen Strategy.

Herein, we report a diaminocyclopentadienone ruthenium tricarbonyl complex-catalyzed synthesis of mono- or dialkylated acyl hydrazide compounds using the borrowing hydrogen strategy in the presence of various substituted primary and secondary alcohols as alkylating reagents. Deuterium labeling experiments confirm that the alcohols were the hydride source in this cascade process. Density functional theory (DFT) calculations unveil the origin and the threshold between the mono- and dialkylation.

Combined Effects of Temperature, Irradiance, and pH on Teleaulax amphioxeia (Cryptophyceae) Physiology and Feeding Ratio For Its Predator Mesodinium rubrum (Ciliophora)1.

The cryptophyte Teleaulax amphioxeia is a source of plastids for the ciliate Mesodinium rubrum and both organisms are members of the trophic chain of several species of Dinophysis. It is important to better understand the ecology of organisms at the first trophic levels before assessing the impact of principal factors of global change on Dinophysis spp. Therefore, combined effects of temperature, irradiance, and pH on growth rate, photosynthetic activity, and pigment content of a temperate strain of T. amphioxeia were studied using a full factorial design (central composite design 23 *) in 17 individually controlled bioreactors. The derived model predicted an optimal growth rate of T. amphioxeia at a light intensity of 400 µmol photons · m-2 · s-1 , more acidic pH (7.6) than the current average and a temperature of 17.6°C. An interaction between temperature and irradiance on growth was also found, while pH did not have any significant effect. Subsequently, to investigate potential impacts of prey quality and quantity on the physiology of the predator, M. rubrum was fed two separate prey: predator ratios with cultures of T. amphioxeia previously acclimated at two different light intensities (100 and 400 µmol photons · m-2 s-1 ). M. rubrum growth appeared to be significantly dependent on prey quantity while effect of prey quality was not observed. This multi-parametric study indicated a high potential for a significant increase of T. amphioxeia in future climate conditions but to what extent this would lead to increased occurrences of Mesodinium spp. and Dinophysis spp. should be further investigated.

Artificial iron hydrogenase made by covalent grafting of Knölker's complex into xylanase: Application in asymmetric hydrogenation of an aryl ketone in water.

We report a new artificial hydrogenase made by covalent anchoring of the iron Knölker's complex to a xylanase S212C variant. This artificial metalloenzyme was found to be able to catalyze efficiently the transfer hydrogenation of the benchmark substrate trifluoroacetophenone by sodium formate in water, yielding the corresponding secondary alcohol as a racemic. The reaction proceeded more than threefold faster with the XlnS212CK biohybrid than with the Knölker's complex alone. In addition, efficient conversion of trifluoroacetophenone to its corresponding alcohol was reached within 60 H with XlnS212CK, whereas a ≈2.5-fold lower conversion was observed with Knölker's complex alone as catalyst. Moreover, the data were rationalized with a computational strategy suggesting the key factors of the selectivity. These results suggested that the Knölker's complex was most likely flexible and could experience free rotational reorientation within the active-site pocket of Xln A, allowing it to access the subsite pocket populated by trifluoroacetophenone.

Cyclopentadienone Iron Tricarbonyl Complexes-Catalyzed Hydrogen Transfer in Water.

The development of efficient and low-cost catalytic systems is important for the replacement of robust noble metal complexes. The synthesis and application of a stable, phosphine-free, water-soluble cyclopentadienone iron tricarbonyl complex in the reduction of polarized double bonds in pure water is reported. In the presence of cationic bifunctional iron complexes, a variety of alcohols and amines were prepared in good yields under mild reaction conditions.

Identification of genetic relationships and subspecies signatures in Xylella fastidiosa.

BACKGROUND: The phytopathogenic bacterium Xylella fastidiosa was thought to be restricted to the Americas where it infects and kills numerous hosts. Its detection worldwide has been blooming since 2013 in Europe and Asia. Genetically diverse, this species is divided into six subspecies but genetic traits governing this classification are poorly understood. RESULTS: SkIf (Specific k-mers Identification) was designed and exploited for comparative genomics on a dataset of 46 X. fastidiosa genomes, including seven newly sequenced individuals. It was helpful to quickly check the synonymy between strains from different collections. SkIf identified specific SNPs within 16S rRNA sequences that can be employed for predicting the distribution of Xylella through data mining. Applied to inter- and intra-subspecies analyses, it identified specific k-mers in genes affiliated to differential gene ontologies. Chemotaxis-related genes more prevalently possess specific k-mers in genomes from subspecies fastidiosa, morus and sandyi taken as a whole group. In the subspecies pauca increased abundance of specific k-mers was found in genes associated with the bacterial cell wall/envelope/plasma membrane. Most often, the k-mer specificity occurred in core genes with non-synonymous SNPs in their sequences in genomes of the other subspecies, suggesting putative impact in the protein functions. The presence of two integrative and conjugative elements (ICEs) was identified, one chromosomic and an entire plasmid in a single strain of X. fastidiosa subsp. pauca. Finally, a revised taxonomy of X. fastidiosa into three major clades defined by the subspecies pauca (clade I), multiplex (clade II) and the combination of fastidiosa, morus and sandyi (clade III) was strongly supported by k-mers specifically associated with these subspecies. CONCLUSIONS: SkIf is a robust and rapid software, freely available, that can be dedicated to the comparison of sequence datasets and is applicable to any field of research. Applied to X. fastidiosa, an emerging pathogen in Europe, it provided an important resource to mine for identifying genetic markers of subspecies to optimize the strategies attempted to limit the pathogen dissemination in novel areas.

Room-Temperature Chemoselective Reductive Alkylation of Amines Catalyzed by a Well-Defined Iron(II) Complex Using Hydrogen.

A transition-metal frustrated Lewis pair approach has been envisaged to enhance the catalytic activity of tricarbonyl phosphine-free iron complexes in reduction of amines. A new cyclopentadienyl iron(II) tricarbonyl complex has been isolated, fully characterized, and applied in hydrogenation. This phosphine-free iron complex is the first Earth-abundant metal complex that is able to catalyze chemoselective reductive alkylation of various functionalized amines with functionalized aldehydes. Such selectivity and functionality tolerance (alkenes, esters, ketones, acetals, unprotected hydroxyl groups, and phosphines) have been demonstrated also for the first time at room temperature with an Earth-abundant metal complex. This alkylation reaction was also performed without any preliminary condensation and generated only water as a byproduct. The resulting amines provided rapid access to potential building blocks, metal ligands, or drugs. Density functional theory calculations highlighted first that the formation of the 16 electron species, via the activation of the tricarbonyl complex Fe3, was facilitated and, second, that the hydrogen cleavage did not follow the same pathway as bond breaking, usually described with the known cyclopentadienone iron tricarbonyl complexes (Fe1 and Fe4). These calculations highlighted that the new complex Fe3 does not behave as a bifunctional catalyst, in contrast to its former congeners.

Iron-Catalyzed Chemoselective Reduction of α,ß-Unsaturated Ketones.

An iron-catalyzed chemo- and diastereoselective reduction of α,ß-unsaturated ketones into the corresponding saturated ketones in mild reaction conditions is reported herein. DFT calculations and experimental work underline that transfer hydride reduction is a more facile process than hydrogenation, unveiling the fundamental role of the base.

Role of the Bridging Group in Bis-Pyridyl Ligands: Enhancing Both the Photo- and Electroluminescent Features of Cationic (IPr)CuI Complexes.

We report on the benefits of changing the bridging group X of bis-pyridyl ligands, that is, Py-X-Py where X is NH, CH2 , C(CH3 )2 , or PPh, on the photo- and electroluminescent properties of a new family of luminescent cationic H-heterocyclic carbene (NHC) copper(I) complexes. A joint experimental and theoretical study demonstrates that the bridging group affects the molecular conformation from a planar-like structure (X is NH and CH2 ) to a boat-like structure (X is C(CH3 )2 and PPh), leading to i) four-fold enhancement of the photoluminescence quantum yield (ϕem ) without affecting the thermally activated delayed fluorescence mechanism, and ii) one order of magnitude reduction of the ionic conductivity (σ) of thin films. This leads to an overall enhancement of the device efficacy and luminance owing to the increased ϕem and the use of low applied driving currents.

Large irradiation doses can improve the fast neutron/gamma discriminating capability of plastic scintillators.

When new materials appear as potential alternatives for radiation detection, several criteria have to be fulfilled. The one presented herein is the response variation to large irradiation doses of neutron/gamma discriminating plastic scintillators. Thus, several samples were exposed to high gamma doses reaching 10 kGy. They were characterized in terms of gamma spectrometry and fast neutron/gamma discrimination, prior to and after irradiation. Results show an unexpected increase of the figure of merit (FoM), which is the numerical value for n/γ discrimination performances. An in-depth investigation evaluates the physicochemical impact of such large doses within the material. The characterization includes photophysics, radiation/matter interaction and chemical analyses (EPR, 1H NMR, fluorescence spectroscopy and HRMS).

Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background.

Hybridization with introduced genetic resources is commonly practiced in ornamental plant breeding to introgress desired traits. The 19th century was a golden age for rose breeding in France. The objective here was to study the evolution of rose genetic diversity over this period, which included the introduction of Asian genotypes into Europe. A large sample of 1228 garden roses encompassing the conserved diversity cultivated during the 18th and 19th centuries was genotyped with 32 microsatellite primer pairs. Its genetic diversity and structure were clarified. Wide diversity structured in 16 genetic groups was observed. Genetic differentiation was detected between ancient European and Asian accessions, and a temporal shift from a European to an Asian genetic background was observed in cultivated European hybrids during the 19th century. Frequent crosses with Asian roses throughout the 19th century and/or selection for Asiatic traits may have induced this shift. In addition, the consistency of the results with respect to a horticultural classification is discussed. Some horticultural groups, defined according to phenotype and/or knowledge of their pedigree, seem to be genetically more consistent than others, highlighting the difficulty of classifying cultivated plants. Therefore, the horticultural classification is probably more appropriate for commercial purposes rather than genetic relatedness, especially to define preservation and breeding strategies.

Highly active phosphine-free bifunctional iron complex for hydrogenation of bicarbonate and reductive amination.

Based on a "transition metal frustrated Lewis pair" approach, a cyclopentadienone iron tricarbonyl complex has been designed and applied in the reductive amination and hydrogenation of bicarbonate. This well-defined phosphine-free complex displays the best activities reported to date for an iron complex in the reduction of bicarbonate into formate and in reductive amination.

Competitive Gold-Promoted Meyer-Schuster and oxy-Cope Rearrangements of 3-Acyloxy-1,5-enynes: Selective Catalysis for the Synthesis of (+)-(S)-γ-Ionone and (-)-(2S,6 R)-cis-γ-Irone.

We report a simple, highly stereoselective synthesis of (+)-(S)-γ-ionone and (-)-(2S,6R)-cis-γ-irone, two characteristic and precious odorants; the latter compound is a constituent of the essential oil obtained from iris rhizomes. Of general interest in this approach are the photoisomerization of an endo trisubstituted cyclohexene double bond to an exo vinyl group and the installation of the enone side chain through a [(NHC)Au(I)]-catalyzed Meyer-Schuster-like rearrangement. This required a careful investigation of the mechanism of the gold-catalyzed reaction and a judicious selection of reaction conditions. In fact, it was found that the Meyer-Schuster reaction may compete with the oxy-Cope rearrangement. Gold-based catalytic systems can promote either reaction selectively. In the present system, the mononuclear gold complex [Au(IPr)Cl], in combination with the silver salt AgSbF6 in 100:1 butan-2-one/H2O, proved to efficiently promote the Meyer-Schuster rearrangement of propargylic benzoates, whereas the digold catalyst [{Au(IPr)}2(µ-OH)][BF4] in anhydrous dichloromethane selectively promoted the oxy-Cope rearrangement of propargylic alcohols.

Long-term effects of the iron-based phosphate binder, sucroferric oxyhydroxide, in dialysis patients.

BACKGROUND: Hyperphosphatemia necessitates the use of phosphate binders in most dialysis patients. Long-term efficacy and tolerability of the iron-based phosphate binder, sucroferric oxyhydroxide (previously known as PA21), was compared with that of sevelamer carbonate (sevelamer) in an open-label Phase III extension study. METHODS: In the initial Phase III study, hemo- or peritoneal dialysis patients with hyperphosphatemia were randomized 2:1 to receive sucroferric oxyhydroxide 1.0-3.0 g/day (2-6 tablets/day; n = 710) or sevelamer 2.4-14.4 g/day (3-18 tablets/day; n = 349) for 24 weeks. Eligible patients could enter the 28-week extension study, continuing the same treatment and dose they were receiving at the end of the initial study. RESULTS: Overall, 644 patients were available for efficacy analysis (n = 384 sucroferric oxyhydroxide; n = 260 sevelamer). Serum phosphorus concentrations were maintained during the extension study. Mean ± standard deviation (SD) change in serum phosphorus concentrations from extension study baseline to Week 52 end point was 0.02 ± 0.52 mmol/L with sucroferric oxyhydroxide and 0.09 ± 0.58 mmol/L with sevelamer. Mean serum phosphorus concentrations remained within Kidney Disease Outcomes Quality Initiative target range (1.13-1.78 mmol/L) for both treatment groups. Mean (SD) daily tablet number over the 28-week extension study was lower for sucroferric oxyhydroxide (4.0 ± 1.5) versus sevelamer (10.1 ± 6.6). Patient adherence was 86.2% with sucroferric oxyhydroxide versus 76.9% with sevelamer. Mean serum ferritin concentrations increased over the extension study in both treatment groups, but transferrin saturation (TSAT), iron and hemoglobin concentrations were generally stable. Gastrointestinal-related adverse events were similar and occurred early with both treatments, but decreased over time. CONCLUSIONS: The serum phosphorus-lowering effect of sucroferric oxyhydroxide was maintained over 1 year and associated with a lower pill burden, compared with sevelamer. Sucroferric oxyhydroxide was generally well tolerated long-term and there was no evidence of iron accumulation.

MafFilter: a highly flexible and extensible multiple genome alignment files processor.

BACKGROUND: Sequence alignments are the starting point for most evolutionary and comparative analyses. Full genome sequences can be compared to study patterns of within and between species variation. Genome sequence alignments are complex structures containing information such as coordinates, quality scores and synteny structure, which are stored in Multiple Alignment Format (MAF) files. Processing these alignments therefore involves parsing and manipulating typically large MAF files in an efficient way. RESULTS: MafFilter is a command-line driven program written in C++ that enables the processing of genome alignments stored in the Multiple Alignment Format in an efficient and extensible manner. It provides an extensive set of tools which can be parametrized and combined by the user via option files. We demonstrate the software's functionality and performance on several biological examples covering Primate genomics and fungal population genomics. Example analyses involve window-based alignment filtering, feature extractions and various statistics, phylogenetics and population genomics calculations. CONCLUSIONS: MafFilter is a highly efficient and flexible tool to analyse multiple genome alignments. By allowing the user to combine a large set of available methods, as well as designing his/her own, it enables the design of custom data filtering and analysis pipelines for genomic studies. MafFilter is an open source software available at http://bioweb.me/maffilter.

Bio++: efficient extensible libraries and tools for computational molecular evolution.

Efficient algorithms and programs for the analysis of the ever-growing amount of biological sequence data are strongly needed in the genomics era. The pace at which new data and methodologies are generated calls for the use of pre-existing, optimized-yet extensible-code, typically distributed as libraries or packages. This motivated the Bio++ project, aiming at developing a set of C++ libraries for sequence analysis, phylogenetics, population genetics, and molecular evolution. The main attractiveness of Bio++ is the extensibility and reusability of its components through its object-oriented design, without compromising the computer-efficiency of the underlying methods. We present here the second major release of the libraries, which provides an extended set of classes and methods. These extensions notably provide built-in access to sequence databases and new data structures for handling and manipulating sequences from the omics era, such as multiple genome alignments and sequencing reads libraries. More complex models of sequence evolution, such as mixture models and generic n-tuples alphabets, are also included.

A phase III study of the efficacy and safety of a novel iron-based phosphate binder in dialysis patients.

Efficacy of PA21 (sucroferric oxyhydroxide), a novel calcium-free polynuclear iron(III)-oxyhydroxide phosphate binder, was compared with that of sevelamer carbonate in an open-label, randomized, active-controlled phase III study. Seven hundred and seven hemo- and peritoneal dialysis patients with hyperphosphatemia received PA21 1.0-3.0 g per day and 348 received sevelamer 4.8-14.4 g per day for an 8-week dose titration, followed by 4 weeks without dose change, and then 12 weeks maintenance. Serum phosphorus reductions at week 12 were -0.71 mmol/l (PA21) and -0.79 mmol/l (sevelamer), demonstrating non-inferiority of, on average, three tablets of PA21 vs. eight of sevelamer. Efficacy was maintained to week 24. Non-adherence was 15.1% (PA21) vs. 21.3% (sevelamer). The percentage of patients that reported at least one treatment-emergent adverse event was 83.2% with PA21 and 76.1% with sevelamer. A higher proportion of patients withdrew owing to treatment-emergent adverse events with PA21 (15.7%) vs. sevelamer (6.6%). Mild, transient diarrhea, discolored feces, and hyperphosphatemia were more frequent with PA21; nausea and constipation were more frequent with sevelamer. After 24 weeks, 99 hemodialysis patients on PA21 were re-randomized into a 3-week superiority analysis of PA21 maintenance dose in 50 patients vs. low dose (250 mg per day (ineffective control)) in 49 patients. The PA21 maintenance dose was superior to the low dose in maintaining serum phosphorus control. Thus, PA21 was effective in lowering serum phosphorus in dialysis patients, with similar efficacy to sevelamer carbonate, a lower pill burden, and better adherence.

Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control.

Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined. Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3'UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants.

NHC copper(I) complexes bearing dipyridylamine ligands: synthesis, structural, and photoluminescent studies.

We describe the synthesis of new cationic tricoordinated copper complexes bearing bidentate pyridine-type ligands and N-heterocyclic carbene as ancillary ligands. These cationic copper complexes were fully characterized by NMR, electrochemistry, X-ray analysis, and photophysical studies in different environments. Density functional theory calculations were also undertaken to rationalize the assignment of the electronic structure and the photophysical properties. These tricoordinated cationic copper complexes possess a stabilizing CH-π interaction leading to high stability in both solid and liquid states. In addition, these copper complexes, bearing dipyridylamine ligands having a central nitrogen atom as potential anchoring point, exhibit very interesting luminescent properties that render them potential candidates for organic light-emitting diode applications.

The iron-based phosphate binder PA21 has potent phosphate binding capacity and minimal iron release across a physiological pH range in vitro.

AIMS: Hyperphosphatemia in advanced chronic kidney disease (CKD) necessitates the use of phosphate binders. This in vitro study assessed phosphate binding and Fe release properties of the novel iron-based phosphate binder PA21. MATERIALS AND METHODS: Phosphate adsorption and Fe release were assessed under conditions simulating administration of PA21 on an empty stomach and full stomach across a pH range to which PA21 would be exposed during passage through the gastrointestinal (GI) tract. RESULTS: PA21 showed a robust phosphate binding capacity over the entire physiologically relevant pH range. The high binding capacity at low pH indicates that phosphate binding could begin in the stomach. Under the current experimental setting, the maximal bound phosphate to Fe ratio was 0.47 mmol P/mmol Fe. The largest amount of Fe release was observed at the lowest pH without phosphate and was much lower in the presence of phosphate. These results are in line with the formation of iron phosphate at low pH, as indicated by X-ray photoelectron spectroscopy and thermodynamic calculations. Fe release was minimal (≤ 0.35%) across pH 2.5 - 8.5. CONCLUSIONS: These studies demonstrate that PA21 has potent phosphate binding capacity and low iron release over a physiologically relevant pH range in the GI tract. These features indicate PA21 could be an effective alternative phosphate binder for CKD patients.

Blue-Light Induced Iron-Catalyzed Synthesis of γ,δ-Unsaturated Ketones.

A visible-light-induced iron-catalyzed α-alkylation of ketones with allylic and propargylic alcohols as pro-electrophiles is reported. The diaminocyclopentadienone iron tricarbonyl complex plays a dual role by harvesting light and facilitating dehydrogenation and reduction steps without the help of any exogenous photosensitizer. γ,δ-Unsaturated ketones can now be accessed through this borrowing hydrogen methodology at room temperature. Mechanistic investigations revealed that the steric hindrance on the δ-position of either the dienone or ene-ynone intermediate is the key feature to prevent or decrease the competitive 1,6-reduction (and consequently the formation of the saturated ketone) and to favor the synthesis of a set of non-conjugated enones and ynones.