The evolutionarily conserved Arabidopsis thaliana F-box protein AtFBP7 is required for efficient translation during temperature stress

In eukaryotes, E3 ubiquitin ligases (E3s) mediate the ubiquitylation of proteins that are destined for degradation by the ubiquitin-proteasome system. In SKP1/CDC53/F-box protein (SCF)-type E3 complexes, the interchangeable F-box protein confers specificity to the E3 ligase through direct physical interactions with the degradation substrate. The vast majority of the approximately 700 F-box proteins from the plant model organism Arabidopsis thaliana remain to be characterized. Here, we investigate the previously uncharacterized and evolutionarily conserved Arabidopsis F-box protein 7 (AtFBP7), which is encoded by a unique gene in Arabidopsis (At1g21760). Several apparent fbp7 loss-of-function alleles do not have an obvious phenotype. AtFBP7 is ubiquitously expressed and its expression is induced after cold and heat stress. When following up on a reported co-purification of the eukaryotic elongation factor-2 (eEF-2) with YLR097c, the apparent budding yeast orthologue of AtFBP7, we discovered a general defect in protein biosynthesis after cold and heat stress in fbp7 mutants. Thus, our findings suggest that AtFBP7 is required for protein synthesis during temperature stress.     

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.     

Impact of feed supplementation with antimicrobial agents on growth performance of broiler chickens, Clostridium perfringens and enterococcus counts, and antibiotic resistance phenotypes and distribution of antimicrobial resistance determinants in Escherichia coli isolates

The effects of feed supplementation with the approved antimicrobial agents bambermycin, penicillin, salinomycin, and bacitracin or a combination of salinomycin plus bacitracin were evaluated for the incidence and distribution of antibiotic resistance in 197 commensal Escherichia coli isolates from broiler chickens over 35 days. All isolates showed some degree of multiple antibiotic resistance. Resistance to tetracycline (68.5%), amoxicillin (61.4%), ceftiofur (51.3%), spectinomycin (47.2%), and sulfonamides (42%) was most frequent. The levels of resistance to streptomycin, chloramphenicol, and gentamicin were 33.5, 35.5, and 25.3%, respectively. The overall resistance levels decreased from day 7 to day 35 (P < 0.001). Comparing treatments, the levels of resistance to ceftiofur, spectinomycin, and gentamicin (except for resistance to bacitracin treatment) were significantly higher in isolates from chickens receiving feed supplemented with salinomycin than from the other feeds (P < 0.001). Using a DNA microarray analysis capable of detecting commonly found antimicrobial resistance genes, we characterized 104 tetracycline-resistant E. coli isolates from 7- to 28-day-old chickens fed different growth promoters. Results showed a decrease in the incidence of isolates harboring tet(B), bla(TEM), sulI, and aadA and class 1 integron from days 7 to 35 (P < 0.01). Of the 84 tetracycline-ceftiofur-resistant E. coli isolates, 76 (90.5%) were positive for bla(CMY-2). The proportions of isolates positive for sulI, aadA, and integron class 1 were significantly higher in salinomycin-treated chickens than in the control or other treatment groups (P < 0.05). These data demonstrate that multiantibiotic-resistant E. coli isolates can be found in broiler chickens regardless of the antimicrobial growth promoters used. However, the phenotype and the distribution of resistance determinants in E. coli can be modulated by feed supplementation with some of the antimicrobial agents used in broiler chicken production.     

Genetic diversity in a collection of Italian long storage tomato landraces as revealed by SNP markers array

Tomato (Solanum lycopersicum L.) is one of the most important crops worldwide. In this study, we used 7720 genome-wide SNPs to characterize the genetic diversity within a tomato germplasm collection enriched with 64 accessions from southern Italy of the so called “da serbo” type i.e. drought-tolerant and long storage landraces. Notwithstanding the relatively small collection area, 1575 (20.4%) polymorphic SNPs, mostly on Chr11, detected considerable levels of genetic variation. Maximum parsimony analysis of genetic distance revealed four main clusters and clearly separated most “da serbo” landraces from the outgroups. One of the clusters grouped the landraces from the Mount Vesuvius area, though no further indications of a geographic-specific structure were found. STRUCTURE analysis confirmed the presence of four genetic groups within the collection, with admixture between them. A survey of non-synonymous SNPs highlighted several mutations in genes related to stress tolerance and fruit maturation/quality. Overall, our results suggest possible exchange of “da serbo” genetic material between southern Italy regions and indicate that the long storage “da serbo” germplasm could be a promising reservoir of peculiar alleles for traits of interest.     

Raw material criticality assessment as a complement to environmental life cycle assessment: Examining methods for product‐level supply risk assessment

The diversity of raw materials used in modern products, compounded by the risk of supply disruptions—due to uneven geological distribution of resources, along with socioeconomic factors like production concentration and political (in)stability of raw material producing countries—has drawn attention to the subject of raw material “criticality.” In this article, we review the state of the art regarding the integration of criticality assessment, herein termed “product‐level supply risk assessment,” as a complement to environmental life cycle assessment. We describe and compare three methods explicitly developed for this purpose—Geopolitical Supply Risk (GeoPolRisk), Economic Scarcity Potential (ESP), and the Integrated Method to Assess Resource Efficiency (ESSENZ)—based on a set of criteria including considerations of data sources, uncertainties, and other contentious methodological aspects. We test the methods on a case study of a European‐manufactured electric vehicle, and conclude with guidance for appropriate application and interpretation, along with opportunities for further methodological development. Although the GeoPolRisk, ESP, and ESSENZ methods have several limitations, they can be useful for preliminary assessments of the potential impacts of raw material supply risks on a product system (i.e., “outside‐in” impacts) alongside the impacts of a product system on the environment (i.e., “inside‐out” impacts). Care is needed to not overlook critical raw materials used in small amounts but nonetheless important to product functionality. Further methodological development could address regional and firm‐level supply risks, multiple supply‐chain stages, and material recycling, while improving coverage of supply risk characterization factors.     

Sex Distribution of Study Samples Reported in American Society of Biomechanics Annual Meeting Abstracts

Background

Study samples should be appropriately selected to maximize generalizability of results. Excluding one sex from studies of conditions that affect both sexes is problematic and has received attention as a public policy issue in the United States, resulting in legislation and recommendations made by the National Institutes of Health to address this deficiency of study designs. It is unknown to what extent biomechanical studies have inappropriately excluded one sex. The objective of this study was to provide objective data on this question.

Methods

A retrospective review of random samples of abstracts presented at American Society of Biomechanics annual meetings from 1983 to 2013 was conducted to assess reporting of sex of study samples and whether the study samples were approximately balanced with respect to sex.

Findings

We did not find a statistically significant increasing trend in the percentage of abstracts reporting sex over time. However, increasing trends were noted in the percentage of abstracts including both sexes (p < 0.05) and percentage of abstracts having an “approximately balanced” study sample containing 50 ± 20% females (p > 0.05). In 2013 the percentage of abstracts reporting studies having approximately balanced study samples was only 28%, far from the ideal level of 100%.

Interpretation

While there has been modest change since 1983, there remains significant room for improvement in the reporting and composition of experimental studies reported at American Society of Biomechanics annual meetings.     

Comparative rates of sialylation by recombinant trans-sialidase and inhibitor properties of synthetic oligosaccharides from Trypanosoma cruzi mucins-containing galactofuranose and galactopyranose

The mucin-like glycoproteins of Trypanosoma cruzi have novel O-linked oligosaccharides that are acceptors of sialic acid in the trans-sialidase (TcTS) reaction. The transference of sialic acid from host glycoconjugates to the mucins is involved in infection and pathogenesis. The O-linked chains may contain galactofuranose in addition to the acceptor galactopyranose units. Thus far, the galactofuranose form was found in the mucins of strains belonging to the less infective lineage. The acceptor properties of the chemically synthesized oligosaccharides were now studied in order to correlate their structure with the ability to act as substrates. Recombinant TcTS and sialyllactose as donor were used. The reactions were followed by HPAEC-PAD. The K(m) values were calculated for the free sugars, the sugar alditols and the benzyl glycosides. All the compounds showed to be good acceptors of sialic acid. Thus, the introduction of galactofuranose in the mucins of the strains of lineage 1 would not be responsible for the diminished virulence of the strains. The oligosaccharides and derivatives inhibited the transfer of sialic acid to the substrate N-acetyllactosamine with IC(50) values between 0.6 and 4 mM.     

The DELLA domain of GA INSENSITIVE mediates the interaction with the GA INSENSITIVE DWARF1A gibberellin receptor of Arabidopsis

Gibberellic acid (GA) promotes seed germination, elongation growth, and flowering time in plants. GA responses are repressed by DELLA proteins, which contain an N-terminal DELLA domain essential for GA-dependent proteasomal degradation of DELLA repressors. Mutations of or within the DELLA domain of DELLA repressors have been described for species including Arabidopsis thaliana, wheat (Triticum aestivum), maize (Zea mays), and barley (Hordeum vulgare), and we show that these mutations confer GA insensitivity when introduced into the Arabidopsis GA INSENSITIVE (GAI) DELLA repressor. We also demonstrate that Arabidopsis mutants lacking the three GA INSENSITIVE DWARF1 (GID1) GA receptor genes are GA insensitive with respect to GA-promoted growth responses, GA-promoted DELLA repressor degradation, and GA-regulated gene expression. Our genetic interaction studies indicate that GAI and its close homolog REPRESSOR OF ga1-3 are the major growth repressors in a GA receptor mutant background. We further demonstrate that the GA insensitivity of the GAI DELLA domain mutants is explained in all cases by the inability of the mutant proteins to interact with the GID1A GA receptor. Since we found that the GAI DELLA domain alone can mediate GA-dependent GID1A interactions, we propose that the DELLA domain functions as a receiver domain for activated GA receptors.