A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic,phylogenetic, and phenotypic criteria

The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA–DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G + C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of “aerotolerant campylobacters” as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].     

Enhanced ozone exposure of European beech (Fagus sylvatica) stimulates nitrogen mobilization from leaf litter and nitrogen accumulation in the soil

Abstract

In a lysimeter study with young beech trees, the effects of elevated ozone concentration on the decomposition and fate of nitrogen in ¹⁵N‐labeled leaf litter were analyzed after one growing season. Nitrogen in the litter was dominated by a relatively inert, residual fraction, but easily decomposable nitrogen was present in substantial amounts. Nitrogen loss was significantly higher at twice‐ambient ozone which was largely attributed to an enhanced mobilization of residual nitrogen. Enhanced mobilization of nitrogen from litter at twice‐ambient ozone exposure resulted in additional ¹⁵N incorporation into the soil down to 30 cm depth. Only 0.41–0.62% of the nitrogen in the litter was incorporated into plant material at both ozone concentrations. Twice‐ambient ozone exposure changed the distribution of the nitrogen taken up from litter inside the beech trees in favor of the shoot, where it may have been used in biosynthetic processes required for defense reactions.     

Quantitative Structure-Activity Relationship Study on Some Dihydropteridine Reductase Inhibitors

Abstract

The dihydropteridine reductase (DHPR) inhibitory potencies of some 4-phenyltetrahydropyridines, 4-phenylpiperidines, and 4-phenylpyridines, are analyzed in relation to their physicochemical and molecular properties. They are found to have significant correlation with Hammett constant s and the van der Waals volume V_w. The correlation is linear with s and parabolic with V_w. Hence, it is argued that DHPR inhibition involves dispersion interaction and is enhanced by electron donation from the substituents but hindered by steric effects produced by large substituents. It is also found that these electronic and steric effects are significant only when they are produced by substituents being at specific position in the molecules.     

A combination of genome-wide association study and selection signature analysis dissects the genetic architecture underlying bone traits in chickens

The bones of chicken play an important role in supporting and protecting the body. The growth and development of bones have a substantial influence on the health and production performance in chickens. However, genetic architecture underlying chicken bone traits is not well understood. The objectives of this study are to dissect the genetic basis of bone traits in chickens and to identify valuable genes and genetic markers for chicken breeding. We performed a combination of genome-wide association study (GWAS) and selection signature analysis (fixation index values and nucleotide diversity ratios) in an F₂ crossbred experimental population with different genetic backgrounds (broiler × layer) to identify candidate genes and significant variants related to femur, shank, keel length, chest width, metatarsal claw weight, metatarsal length, and metatarsal circumference. A total of 545 individuals were genotyped based on the whole genome re-sequencing method (26 F₀ individuals were re-sequenced at 10 × coverage; 519 F₂ individuals were re-sequenced at 3 × coverage). A total of 2 028 112 single-nucleotide polymorphisms (SNPs) remained to carry out analysis after quality control and imputation. The integration of GWAS and selection signature analysis indicated that all significant SNPs responsible for bone traits were mainly localized on chicken chromosomes 1, 4, and 27. Finally, we identified 21 positional candidate genes that might regulate chicken bone growth and development, including LRCH1, RB1, FNDC3A, MLNR, CAB39L, FOXO1, LHFP, TRPC4, POSTN, SMAD9, RBPJ, PPARGC1A, SLIT2, NCAPG, NKX3-2, CPZ, SPOP, NGFR, SOST, ZNF652, and HOXB3. Additionally, an array of uncharacterized genes was identified. The findings provide an in-depth understanding of the genetic architecture of chicken bone traits and offer a molecular basis for applying genomics in practical chicken breeding.     

Profil parasitologique de deux formes de schistosomiase (formes urinaire et intestinale) dans dix sites du Burkina Faso (pays d’Afrique sub-saharienne)

In spite of great progress in schistosomiasis control during the last decade in Burkina Faso, this disease remains a public health concern in the country. Indeed, our study consisted of the analysis of parasitological data related to Schistosoma haematobium and Schistosoma mansoni and in malacological investigations. The prevalence rate of Schistosoma haematobium varies from 3.3% to 50.4% and from 3.3% to 39.1% for Schistosoma mansoni, but only in the western part of Burkina Faso. Schoolboys are more infested than girls, but the phenomenon is reversed in adults. Biomphalaria pfeifferi, Bulinus truncatus, Bulinus senegalensis and Bulinus globosus were collected during this study. Thus, the behavioral factors as well as the dynamics and the distribution of the intermediate mollusks play a major role in the persistence of the disease.     

Topographic,morphologic and developmental characterization of the nucleus loci coerulei in the chicken

Summary Golgi- and fluorescence-histochemical studies in the chicken show the presence of a sharply delimited group of aminergic neurons beneath the floor of the fourth ventricle at the mesen-metencephalic boundary. According to the observations reported in other avian species a homology can be established between the mammalian locus coeruleus (LC) and this fluorescent cell mass of the chicken brainstem. Golgi studies revealed an isodendritic pattern of ramification of the neurons in this nucleus.In addition, a developmental study on the morphological maturation of the LC in the chick embryo was carried out by means of the histochemical-fluorescence method for biogenic amines and the rapid Golgi method. The time of the first onset of catecholamine synthesis and storage has been shown to correspond to the 9th day of incubation (stage HH 35), just when these cells display a well-established and peculiar dendritic pattern. All maturational events in the LC of the chick embryo thus occur earlier than in the fetal rat brain, the prenatal development of which is accomplished in a period of comparable length.This investigation was partly supported by grants from the Italian National Research Council (CNR) No. 79.01890.04 and No. 80.00442.04     

Power analysis of statistical methods for comparing treatment differences from limiting dilution assays

Summary Six different statistical methods for comparing limiting dilution assays were evaluated, using both real data and a power analysis of simulated data. Simulated data consisted of a series of 12 dilutions for two treatment groups with 24 cultures per dilution and 1,000 independent replications of each experiment. Data within each replication were generated by Monte Carlo simulation, based on a probability model of the experiment. Analyses of the simulated data revealed that the type I error rates for the six methods differed substantially, with only likelihood ratio and Taswell's weighted mean methods approximating the nominal 5% significance level. Of the six methods, likelihood ratio and Taswell's minimum Chi-square exhibited the best power (least probability of type II errors). Taswell's weighted mean test yielded acceptable type I and type II error rates, whereas the regression method was judged unacceptable for scientific work.     

Intrageneric amplification of horse microsatellite markers with emphasis on the Przewalski's horse (E. pmewalskii)

Primer sequences flanking 13 microsatellite loci isolated from the domestic horse (E. caballus) were successfully used to amplify homologous loci in the Przewalski's horse (E. przewalskii). The results demonstrate that the level of polymorphism at all 13 loci in the Przewalski's horse was comparable to that in the domestic horse and the overall exclusion probability in the Przewalski's horse was calculated to be 0.9994. The results suggest that it should be possible to use E. caballus-derived microsatellite markers to provide parentage verification and additional valuable information to the captive management of E. przewalskii. The ability to amplify corresponding loci in the remaining five species of the genus was also confirmed, illustrating the general application of markers isolated from the domestic horse to the evaluation of polymorphism in the other six species of the genus.     

Association of single nucleotide polymorphisms in the microRNA miR‐1596 locus with residual feed intake in chickens

MicroRNAs are an abundant class of small non‐coding RNAs that regulate gene expression. Genetic variations in microRNA sequences may be associated with phenotype differences by influencing the expression of microRNAs and/or their targets. This study identified two single nucleotide polymorphisms (SNPs) in the genomic region of the microRNA miR‐1596 locus of chicken. Of the two SNPs, one was 95 bp upstream of miR‐1596 (g.5678784A>T) and the other was in the middle of the sequence producing the mature microRNA gga‐miR‐1596‐3p (g.5678944A>G). Genotypic distribution of the two SNPs had large differences among 12 chicken breeds (lines), especially between the fast‐growing commercial lines and the slow‐growing Chinese indigenous breeds for the g.5678784A>T SNP. Only the g.5678784A>T SNP was significantly associated with residual feed intake (RFI) in the F₂ population derived from a fast‐growing and a slow‐growing broiler as well as in the pure Huiyang bearded chicken. The birds with the AA genotype of the g.5678784A>T SNP had lower RFI and higher expression of the mature gga‐miR‐1596‐3p microRNA of miR‐1596 than did those with the other genotypes of the same SNP. We also found that the expression of the mature gga‐miR‐1596‐3p microRNA of miR‐1596 was significantly associated with RFI. These findings suggest that miR‐1596 can become a candidate gene related to RFI, and its genetic variation may contribute to changes in RFI by altering expression levels of the mature gga‐miR‐1596‐3p microRNA in chicken.     

Ionic liquid-enabled synthesis,cholinesterase inhibitory activity,and molecular docking study of highly functionalized tetrasubstituted pyrrolidines

A small library of novel spiropyrrolidine heterocyclic hybrids has been prepared regioselectively in 1-butyl-3-methylimidazoliumbromide ([bmim]Br) with good to excellent yields using a [3+2] cycloaddition reaction. These synthesized compounds were evaluated as potential agents for treating Alzheimer’s disease. Compound 4b showed the most potent activity, with an IC₅₀ of 7.9 ± 0.25 µM against acetylcholinesterase (AChE). The inhibition mechanisms for the most active compounds on AChE and butyrylcholinesterase (BChE) receptors were elucidated using molecular docking simulations.