Molecular architecture of the ribosome‐bound Hepatitis C Virus internal ribosomal entry site RNA

Internal ribosomal entry sites (IRESs) are structured cis‐acting RNAs that drive an alternative, cap‐independent translation initiation pathway. They are used by many viruses to hijack the translational machinery of the host cell. IRESs facilitate translation initiation by recruiting and actively manipulating the eukaryotic ribosome using only a subset of canonical initiation factor and IRES transacting factors. Here we present cryo‐EM reconstructions of the ribosome 80S‐ and 40S‐bound Hepatitis C Virus (HCV) IRES. The presence of four subpopulations for the 80S•HCV IRES complex reveals dynamic conformational modes of the complex. At a global resolution of 3.9 Å for the most stable complex, a derived atomic model reveals a complex fold of the IRES RNA and molecular details of its interaction with the ribosome. The comparison of obtained structures explains how a modular architecture facilitates mRNA loading and tRNA binding to the P‐site. This information provides the structural foundation for understanding the mechanism of HCV IRES RNA‐driven translation initiation.     

Demographic and clinical variables affecting mid‐ to late‐life trajectories of plasma ceramide and dihydroceramide species

It has been increasingly recognized at the basic science level that perturbations in ceramide metabolism are associated with the development and progression of many age‐related diseases. However, the translation of this work to the clinic has lagged behind. Understanding the factors longitudinally associated with plasma ceramides and dihydroceramides (DHCer) at the population level and how these lipid levels change with age, and by sex, is important for the clinical development of future therapeutics and biomarkers focused on ceramide metabolism. We, therefore, examined factors cross‐sectionally and longitudinally associated with plasma concentrations of ceramides and DHCer among Baltimore Longitudinal Study of Aging participants (n = 992; 3960 total samples), aged 55 years and older, with plasma at a mean of 4.1 visits (range 2–6). Quantitative analyses were performed on a high‐performance liquid chromatography‐coupled electrospray ionization tandem mass spectrometer. Linear mixed models were used to assess the relationships between plasma ceramide and DHCer species and demographics, diseases, medications, and lifestyle factors. Women had higher plasma concentrations of most ceramide and DHCer species and showed steeper trajectories of age‐related increases compared to men. Ceramides and DHCer were more associated with waist–hip ratio than body mass index. Plasma cholesterol and triglycerides, prediabetes, and diabetes were associated with ceramides and DHCer, but the relationship showed specificity to the acyl chain length and saturation. These results demonstrate the importance of examining the individual species of ceramides and DHCer, and of establishing whether intra‐individual age‐ and sex‐specific changes occur in synchrony to disease onset and progression.     

Differential Growth of and Nanoscale TiO2 Accumulation in Tetrahymena thermophila by Direct Feeding versus Trophic Transfer from Pseudomonas aeruginosa

Nanoscale titanium dioxide (TiO₂) is increasingly used in consumer goods and is entering waste streams, thereby exposing and potentially affecting environmental microbes. Protozoans could either take up TiO₂ directly from water and sediments or acquire TiO₂ during bactivory (ingestion of bacteria) of TiO₂-encrusted bacteria. Here, the route of exposure of the ciliated protozoan Tetrahymena thermophila to TiO₂ was varied and the growth of, and uptake and accumulation of TiO₂ by, T. thermophila were measured. While TiO₂ did not affect T. thermophila swimming or cellular morphology, direct TiO₂ exposure in rich growth medium resulted in a lower population yield. When TiO₂ exposure was by bactivory of Pseudomonas aeruginosa, the T. thermophila population yield and growth rate were lower than those that occurred during the bactivory of non-TiO₂-encrusted bacteria. Regardless of the feeding mode, T. thermophila cells internalized TiO₂ into their food vacuoles. Biomagnification of TiO₂ was not observed; this was attributed to the observation that TiO₂ appeared to be unable to cross the food vacuole membrane and enter the cytoplasm. Nevertheless, our findings imply that TiO₂ could be transferred into higher trophic levels within food webs and that the food web could be affected by the decreased growth rate and yield of organisms near the base of the web.     

Tailoring host immune responses to Listeria by manipulation of virulence genes -- the interface between innate and acquired immunity

Although attenuated strains of microbial pathogens have triggered vaccine development from its origin, the role of virulence factors in determining host immunity has remained largely unexplored. Using the murine listeriosis model, we investigated whether the induction and expansion of protective and inflammatory T cell responses may be modified by selective manipulation of virulence genes. We intentionally deleted specific genes of Listeria monocytogenes, including those encoding the positive regulatory factor (prfA), hemolysin (hly), the actin nucleator (actA), and phospholipase B (plcB). The resulting strains showed decisive differences in their immunogenic properties. In particular, we identified a double-deletion mutant that retained Listeria's profound ability to induce protective CD8(+) T cells, but that is strongly attenuated and exhibits a significantly reduced ability to induce CD4(+) T cell-mediated inflammation. We conclude that this mutant, L. monocytogenes DeltaactADeltaplcB, is at present the most promising mutant for a bacterial vaccine vector and is able to safely induce potent CD8(+) T cell-mediated immunity.     

The development of rating of perceived exertion-based tests of physical working capacity

The purpose of the present study was to use ratings of perceived exertion (RPE) from the Borg (6-20) and OMNI-Leg (0-10) scales to determine the Physical Working Capacity at the Borg and OMNI thresholds (PWC(BORG) and PWC(OMNI)). PWC(BORG) and PWC(OMNI) were compared with other fatigue thresholds determined from the measurement of heart rate (the Physical Working Capacity at the Heart Rate Threshold: PWC(HRT)), and oxygen consumption (the Physical Working Capacity at the Oxygen Consumption Threshold, PWC(VO2)), as well as the ventilatory threshold (VT). Fifteen men and women volunteers (mean age +/- SD = 22 +/- 1 years) performed an incremental test to exhaustion on an electronically braked ergometer for the determination of VO2 peak and VT. The subjects also performed 4 randomly ordered workbouts to exhaustion at different power outputs (ranging from 60 to 206W) for the determination of PWC(BORG), PWC(OMNI), PWC(HRT), and PWC(VO2). The results indicated that there were no significant mean differences among the fatigue thresholds: PWC(BORG) (mean +/- SD = 133 +/- 37W; 67 +/- 8% of VO2 peak), PWC(OMNI) (137 +/- 44W; 68 +/- 9% of VO2 peak), PWC(HRT) (135 +/- 36W; 68 +/- 8% of VO2 peak), PWC(VO2) (145 +/- 41W; 72 +/- 7% of VO2 peak) and VT (131 +/- 45W; 66 +/- 8% of VO2 peak). The results of this study indicated that the mathematical model used to estimate PWC(HRT) and PWC(VO2) can be applied to ratings of perceived exertion to determine PWC(BORG) and PWC(OMNI) during cycle ergometry. Salient features of the PWC(BORG) and PWC(OMNI) tests are that they are simple to administer and require the use of only an RPE scale, a stopwatch, and a cycle ergometer. Furthermore, the power outputs at the PWC(BORG) and PWC(OMNI) may be useful to estimate the VT noninvasively and without the need for expired gas analysis.     

RNA primary sequence or secondary structure in the translational initiation region controls expression of two variant interferon-beta genes in Escherichia coli

Efficient expression in Escherichia coli (E. coli) of the human interferon-beta gene (IFN-beta) gene and of a chemically synthesized IFN-beta gene variant (506 base pairs; synIFN-beta) adapted to the E. coli codon usage, both fused to the E. coli atpE ribosome-binding site, is controlled either by primary sequence or by mRNA secondary-structure in the translational initiation region. High level expression of the natural human atpE/IFN-beta gene fusion is governed by the nucleotide composition preceding the initiator codon AUG. A single U----C exchange in the -2 or -1 position preceding the initiator codon AUG reduces the translational efficiency from 18% of total cellular protein to only 8% or 4%, respectively, while both U----C substitutions reduce IFN-beta expression below 1%. These sequence alterations interfere with efficient ribosome binding as revealed by toeprinting. They provide further evidence for the influence of the anticodon-flanking regions of tRNA(fMet) upon the initiation rate of translation. In contrast, translation of the synthetic variant atpE/synIFN-beta gene fusion is controlled by a moderately stable stem-loop structure (delta G = -4 kcal/mol; 37 degrees C) located within the coding region and overlapping the 30 S ribosomal subunit attachment site. That the stability of the hairpin interferes with the initiation of translation is inferred from site-directed mutagenesis and toeprint analyses. mRNA half-life in these variants is positively correlated with the rate of translation and involves two major endonucleolytic cleavage site 5'-upstream of the Shine-Dalgarno region.     

Interactions of donor sources and media influence the histo‐morphological quality of full‐thickness skin models

Human artificial skin models are increasingly employed as non‐animal test platforms for research and medical purposes. However, the overall histopathological quality of such models may vary significantly. Therefore, the effects of manufacturing protocols and donor sources on the quality of skin models built‐up from fibroblasts and keratinocytes derived from juvenile foreskins is studied. Histo‐morphological parameters such as epidermal thickness, number of epidermal cell layers, dermal thickness, dermo‐epidermal adhesion and absence of cellular nuclei in the corneal layer are obtained and scored accordingly. In total, 144 full‐thickness skin models derived from 16 different donors, built‐up in triplicates using three different culture conditions were successfully generated. In univariate analysis both media and donor age affected the quality of skin models significantly. Both parameters remained statistically significant in multivariate analyses. Performing general linear model analyses we could show that individual medium‐donor‐interactions influence the quality. These observations suggest that the optimal choice of media may differ from donor to donor and coincides with findings where significant inter‐individual variations of growth rates in keratinocytes and fibroblasts have been described. Thus, the consideration of individual medium‐donor‐interactions may improve the overall quality of human organ models thereby forming a reproducible test platform for sophisticated clinical research.     

Loureirophonte psammophila,a new species of Laophontidae T. Scott, 1904 (Copepoda: Harpacticoida) from Baja California,Mexico

Loureirophonte psammophila n. sp. was collected from coarse sediments of a beach near La Paz, Baja California, Mexico. The species belongs to the subterranea-group as defined by Fiers (1993). It differs from the other representative of the group, L. subterranea (Lang, 1965) in the presence of an outer dentiform process on 2nd segment of the antennula, the chaetotaxy of P.2–P.5 and the 1-segmented male endopodite P.4. A map with the distribution of the eleven species known so far is provided.