Genetic and sequence analysis of an 8.7-kilobase Pseudomonas denitrificans fragment carrying eight genes involved in transformation of precorrin-2 to cobyrinic acid.

A 8.7-kilobase DNA fragment carrying Pseudomonas denitrificans cob genes has been sequenced. The nucleotide sequence and the genetic analysis revealed that this fragment carries eight different cob genes (cobF to cobM). Six of these genes have the characteristics of translationally coupled genes. cobI has been identified as S-adenosyl-L-methionine (SAM):precorrin-2 methyltransferase structural gene because the encoded protein has the same NH2 terminus and molecular weight as those of the purified enzyme. From protein homology with CobA and CobI, two SAM-dependent methyltransferases of the cobalamin pathway, it is proposed that cobF, cobJ, cobL, and cobM code for other methyltransferases involved in the cobalamin pathway. In addition, purified CobF protein has affinity for SAM, as expected for a SAM-dependent methyltransferase. Accumulation of cobalamin precursors in Agrobacterium tumefaciens mutants complemented by any of these eight genes suggest that, apart from cobI, whose function is identified, the products of all these genes are implicated in the conversion of precorrin-3 into cobyrinic acid.     

Assay and purification of S-adenosyl-L-methionine:precorrin-2 methyltransferase from Pseudomonas denitrificans.

S-Adenosyl-L-methionine:precorrin-2 methyltransferase (SP2MT), which catalyzes the C-20 methylation of precorrin-2 to precorrin-3, was purified to homogeneity from extracts of a recombinant strain of Pseudomonas denitrificans derived from a cobalamin-overproducing strain. Ammonium sulfate fractionation followed by chromatography on DEAE-Trisacryl, hydroxyapatite, and Mono Q HR purified the enzyme about 110-fold, with a 28% yield. For enzyme purification and characterization, a coupled-enzyme assay was developed which generated in situ the highly oxygen-sensitive substrate, precorrin-2, from delta-aminolevulinic acid. Evidence is given that the chemically reduced form of sirohydrochlorin (dihydrosirohydrochlorin) is methylated at C-20 to precorrin-3 by pure SP2MT. No subsequent SP2MT-dependent methylation reaction of precorrin-3 was detected. The native enzyme has an apparent molecular weight of 53,000, as estimated by gel filtration, and consists of two identical subunits of Mr 26,000, as estimated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Stepwise Edman degradation provided the N-terminal sequence of the first 17 amino acids.     

Largest reported groups for the Indo‐Pacific bottlenose dolphin (Tursiops aduncus) found in Algoa Bay,South Africa: Trends and potential drivers

This study investigates how group size of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) changes temporally, spatially, and/or with predominant behavior at two discreet sites along the Eastern Cape coastline of South Africa: Algoa Bay and the Wild Coast. The mean group size of bottlenose dolphins was large with an average of 52 animals. Significantly larger groups were observed in Algoa Bay ( = 60, range = 1–600) than off the Wild Coast ( = 32.9, range = 1–250). In Algoa Bay, the mean group size increased significantly over the study period, from an average 18 animals in 2008 to 76 animals in 2016. Additionally, the largest average and maximum group sizes ever reported both in South Africa and worldwide, were recorded in Algoa Bay (maximum group size = 600). Neither season nor behavior had a significant effect on mean group size at both sites. Similarly environmental variables such as the depth and substrate type also had no influence on group size. It remains unclear which ecological drivers, such as predation risk and food availability, are leading to the large groups observed in this area, and further research on abundance and distribution of both predators and prey is necessary.     

Small-scale experiments aimed at optimization of large-scale production of the microalga <Emphasis Type="Italic">Rhodomonas salina</Emphasis>

The cryptophyte Rhodomonas is an important feed item for live feed organisms in aquaculture and although large-scale cultivation of Rhodomonas in photobioreactors (PBRs) is feasible, the production needs to be optimized through further studies of specific factors. Through small-scale experiments, several factors relevant for an on-going large-scale production of Rhodomonas were studied and the results presented here provide a useful insight on factors that can help future large-scale production. The content of polyunsaturated fatty acids (PUFAs) and the temporal sedimentation was compared in five strains of Rhodomonas. Strain K-1487 (R. salina) was chosen as the most suitable for cultivation in PBRs due to a good biochemical content of PUFAs and low cell sedimentation. The f/2 growth medium used for cultivation was modified by excluding CoCl₂ which did not affect either growth rate or cell content of the PUFAs, DHA, EPA, and ARA. Furthermore, the growth medium was modified by adding the nitrogen source as ammonium (NH₄⁺), nitrate (NO₃^?), urea, or combinations of these, with NH₄⁺ yielding a significantly higher growth rate of 1.30?±?0.07 day^?1. The seawater used for cultivation was exposed to three types of treatments which gave no significant difference in the growth rate: (1) filtration (0.2 μm)?+?autoclaving, (2) filtration (0.2 μm)?+?UV-radiation, and (3) filtration (0.2 μm). Finally, the results for growth rates of inocula at initial densities ranging from 2000 to 200,000 cells mL^?1 showed that growth rate decreased with increasing density but a final density of 10⁶ cells mL^?1 was obtained fastest with the highest initial density. With the present findings, several barriers for effective cultivation of Rhodomonas are solved and future large-scale production has become a great step closer.     

mvmapper: Interactive spatial mapping of genetic structures

Characterizing genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata are not always easily integrated into these methods in a user‐friendly fashion. Here, we present a deployable Python‐based web‐tool, mvmapper , for visualizing and exploring results of multivariate analyses in geographic space. This tool can be used to map results of virtually any multivariate analysis of georeferenced data, and routines for exporting results from a number of standard methods have been integrated in the R package adegenet , including principal components analysis (PCA), spatial PCA, discriminant analysis of principal components, principal coordinates analysis, nonmetric dimensional scaling and correspondence analysis. mvmapper 's greatest strength is facilitating dynamic and interactive exploration of the statistical and geographic frameworks side by side, a task that is difficult and time‐consuming with currently available tools. Source code and deployment instructions, as well as a link to a hosted instance of mvmapper , can be found at https://popphylotools.github.io/mvMapper/ .     

Theoretical study of the geometrical and electronic structures and thermochemistry of spherophanes

A set of supramolecular cage-structures—spherophanes—was studied at the density functional B3LYP level. Full geometrical structure optimisations were made with 6–31G and 6–31G(d) basis sets followed by frequency calculations, and electronic energies were evaluated at B3LYP/6–31++G(d,p). Three different symmetries were considered: C1, Ci, and Oh. It was found that the bonds between the benzene rings are very long to allow π-electron delocalisation between them. These spherophanes show portal openings of 2.596 Å in Spher1, 4.000 Å in Meth2, 3.659 Å in Oxa3, and 4.412 Å in Thia4. From the point of view of potential host–guest interaction studies, it should also be noted that the atoms nearest to the centre of the cavities are carbons bonded to X groups. These supramolecules seem to exhibit relatively large gap HOMO?LUMO: 2.89 eV(Spher1), 5.26 eV(Meth2), 5.73 eV(Oxa3), and 4.82 eV(Thia4). The calculated ΔH°_f (298.15 K) values at B3LYP/6–31G(d) are (in kcal mol^?1) 750.98, 229.78, ?10.97, and 482.49 for Spher1, Meth2, Oxa3, and Thia4, respectively. Using homodesmotic reactions, relative to Spher1, the spherophanes Meth2, Oxa3, and Thia4 are less strained by ?399.13 kcal mol^?1, ?390.40 kcal mol^?1, and ?411.38 kcal mol^?1, respectively. Their infrared and ¹³C NMR calculated spectra are reported.     

Telomeric trans-silencing: an epigenetic repression combining RNA silencing and heterochromatin formation

The study of P-element repression in Drosophila melanogaster led to the discovery of the telomeric Trans-Silencing Effect (TSE), a repression mechanism by which a transposon or a transgene inserted in subtelomeric heterochromatin (Telomeric Associated Sequence or TAS) has the capacity to repress in trans in the female germline, a homologous transposon, or transgene located in euchromatin. TSE shows variegation among egg chambers in ovaries when silencing is incomplete. Here, we report that TSE displays an epigenetic transmission through meiosis, which involves an extrachromosomal maternally transmitted factor. We show that this silencing is highly sensitive to mutations affecting both heterochromatin formation (Su(var)205 encoding Heterochromatin Protein 1 and Su(var)3–7) and the repeat-associated small interfering RNA (or rasiRNA) silencing pathway (aubergine, homeless, armitage, and piwi). In contrast, TSE is not sensitive to mutations affecting r2d2, which is involved in the small interfering RNA (or siRNA) silencing pathway, nor is it sensitive to a mutation in loquacious, which is involved in the micro RNA (or miRNA) silencing pathway. These results, taken together with the recent discovery of TAS homologous small RNAs associated to PIWI proteins, support the proposition that TSE involves a repeat-associated small interfering RNA pathway linked to heterochromatin formation, which was co-opted by the P element to establish repression of its own transposition after its recent invasion of the D. melanogaster genome. Therefore, the study of TSE provides insight into the genetic properties of a germline-specific small RNA silencing pathway.     

A pilot study of IL-1 inhibition by anakinra in acute gout

Monosodium urate crystals stimulate monocytes and macrophages to release IL-1β through the NALP3 component of the inflammasome. The effectiveness of IL-1 inhibition in hereditary autoinflammatory syndromes with mutations in the NALP3 protein suggested that IL-1 inhibition might also be effective in relieving the inflammatory manifestations of acute gout. The effectiveness of IL-1 inhibition was first evaluated in a mouse model of monosodium urate crystal-induced inflammation. IL-1 inhibition prevented peritoneal neutrophil accumulation but TNF blockade had no effect. Based on these findings, we performed a pilot, open-labeled study (trial registration number ISRCTN10862635) in 10 patients with gout who could not tolerate or had failed standard antiinflammatory therapies. All patients received 100 mg anakinra daily for 3 days. All 10 patients with acute gout responded rapidly to anakinra. No adverse effects were observed. IL-1 blockade appears to be an effective therapy for acute gouty arthritis. The clinical findings need to be confirmed in a controlled study.     

Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain

Prolyl-tRNA synthetases (ProRSs) are unique among synthetases in that they have diverse architectures, notably the variable presence of a cis-editing domain homologous to the freestanding deacylase proteins YbaK and ProX. Here, we describe crystal structures of two bacterial ProRSs from the pathogen Enterococcus faecalis, which possesses an editing domain, and from Rhodopseudomonas palustris, which does not. We compare the overall structure and binding mode of ATP and prolyl-adenylate with those of the archael/eukaryote-type ProRS from Thermus thermophilus. Although structurally more homologous to YbaK, which preferentially hydrolyzes Cys-tRNA(Pro), the editing domain of E. faecalis ProRS possesses key elements similar to ProX, with which it shares the activity of hydrolyzing Ala-tRNA(Pro). The structures give insight into the complex evolution of ProRSs, the mechanism of editing, and structural differences between prokaryotic- and eukaryotic-type ProRSs that can be exploited for antibiotic design.