Molecular confinement influences protein structure and enhances thermal protein stability

The sol-gel method of encapsulating proteins in a silica matrix was investigated as a potential experimental system for testing the effects of molecular confinement on the structure and stability of proteins. We demonstrate that silica entrapment (1) is fully compatible with structure analysis by circular dichroism, (2) allows conformational studies in contact with solvents that would otherwise promote aggregation in solution, and (3) generally enhances thermal protein stability. Lysozyme, alpha-lactalbumin, and metmyoglobin retained native-like solution structures following sol-gel encapsulation, but apomyoglobin was found to be largely unfolded within the silica matrix under control buffer conditions. The secondary structure of encapsulated apomyoglobin was unaltered by changes in pH and ionic strength of KCl. Intriguingly, the addition of other neutral salts resulted in an increase in the alpha-helical content of encapsulated apomyoglobin in accordance with the Hofmeister ion series. We hypothesize that protein conformation is influenced directly by the properties of confined water in the pores of the silica. Further work is needed to differentiate the steric effects of the silica matrix from the solvent effects of confined water on protein structure and to determine the extent to which this experimental system mimics the effects of crowding and confinement on the function of macromolecules in vivo.     

Molecular evidence for a new bacteriophage of Borrelia burgdorferi

We have recovered a DNase-protected, chloroform-resistant molecule of DNA from the cell-free supernatant of a Borrelia burgdorferi culture. The DNA is a 32-kb double-stranded linear molecule that is derived from the 32-kb circular plasmids (cp32s) of the B. burgdorferi genome. Electron microscopy of samples from which the 32-kb DNA molecule was purified revealed bacteriophage particles. The bacteriophage has a polyhedral head with a diameter of 55 nm and appears to have a simple 100-nm-long tail. The phage is produced constitutively at low levels from growing cultures of some B. burgdorferi strains and is inducible to higher levels with 10 microg of 1-methyl-3-nitroso-nitroguanidine (MNNG) ml(-1). In addition, the prophage can be induced with MNNG from some Borrelia isolates that do not naturally produce phage. We have isolated and partially characterized the phage associated with B. burgdorferi CA-11.2A. To our knowledge, this is the first molecular characterization of a bacteriophage of B. burgdorferi.     

Genomic characterization of the RUNX2 gene of Fugu rubripes

Inducibility of the mouse gene imap38 in the spleen has been recently described to correlate with resistance to Plasmodium chabaudi malaria. Here, we characterize the human ortholog gene himap1. The HIMAP1 34 kDa protein is localizable at the endoplasmic reticulum in transfected cells. It contains a GTP-binding domain, but it does not bind GTP, in contrast to mouse IMAP38. The himap1 gene belongs to a gene family clustered on chromosome 7q32-36 within a region highly syntenic to the mouse imap38 locus on chromosome 6B. The himap genes 1, 2, 3, and 4 display a conserved intron/exon structure. The mRNA of the himap1 gene is predominantly expressed in the spleen, in lymph nodes to a lesser extent, and only at very low levels in diverse cancer cell lines. In accordance, imap-like genes in mice and plants are associated with proliferative and apoptotic events suggesting a role in the control of cell death/survival.     

TNF receptor 1, IL-1 receptor, and iNOS genetic knockout mice are not protected from anthrax infection

Anthrax produces at least two toxins that cause an intense systemic inflammatory response, edema, shock, and eventually death. The relative contributions of various elements of the immune response to mortality and course of disease progression are poorly understood. We hypothesized that knockout mice missing components of the immune system will have an altered response to infection. Parent strain mice and knockouts were challenged with LD95 of anthrax spores (5 x 10(6)) administered subcutaneously. Our results show that all genetic knockouts succumbed to anthrax infection at the same frequency as the parent. TNF antibody delayed death but TNF receptor 1 knockout had no effect. IL-1 receptor or iNOS knockouts died sooner. Anthrax was more abundant in the injection site of TNF-alpha and iNOS knockouts compared to parent suggesting that attenuated cellular response increases rate of disease progression. With the exception of edema and necrosis at the injection site pathological changes in internal organs were not observed.     

Disruption of the Borrelia burgdorferi gac gene, encoding the naturally synthesized GyrA C-terminal domain

The C-terminal domain of the A subunit of DNA gyrase, which we term Gac, is naturally synthesized in Borrelia burgdorferi as an abundant DNA-binding protein. Full-length GyrA, which includes the C-terminal domain, is also synthesized by the spirochete and functions as a subunit of DNA gyrase. We have disrupted synthesis of Gac as an independent protein and demonstrated that it is not essential for growth in a coumarin-resistant background. We detected no alterations in DNA maintenance, condensation, or topology in B. burgdorferi lacking this small DNA-binding protein.     

Impacts of invasive plant species on riparian plant assemblages: interactions with elevated atmospheric carbon dioxide and nitrogen deposition

Resource competition is commonly invoked to explain negative effects of invasive plants on native plant abundance. If invasives out-compete natives, global changes that elevate resource availability may interact with invasives to exacerbate impacts on native communities. Indeed, evidence is accumulating that elevated CO₂ and N deposition decrease native biomass and simultaneously increase invasive biomass. However, superior competitive ability, and a relative increase in the magnitude of invasive impacts under elevated resource availability, remain to be definitively proven. Using model, multi-species, multi-individual riparian plant communities, where planting density was maintained by replacement of native with exotic individuals, we conducted a greenhouse, competition experiment using native (to the UK) and invaded communities exposed to ambient and elevated CO₂ (CO₂ experiment) or N availability (N experiment). We tested two hypotheses: (1) invasives are superior competitors to natives at ambient atmospheric CO₂ and N deposition; (2) negative effects of invasives on natives are exacerbated under elevated CO₂ or N availability. Our results provide some support for the first hypothesis: in the CO₂ experiment native biomass was significantly lower in invaded communities. In the N experiment, native biomass was unaffected by the presence of exotics but other characteristics (e.g. root:shoot ratios) were altered. Differences in light availability between the experiments may have modified the effects of the invasives on the native assemblages but our design did not permit us to determine this definitively. The hypothesis that elevated CO₂ and N availability benefit invasives at the expense of natives was not supported by our results. This may be explained either because the invasives showed minor responses to the resource manipulations or because native and exotic species were differentially limited by CO₂ and N. Our results confirm the expectation that invasives alter the characteristics of native assemblages but lead us to question whether elevated resource availability will magnify these effects.     

Electron‐Beam‐Evaporated Nickel Oxide Hole Transport Layers for Perovskite‐Based Photovoltaics

High‐quality charge carrier transport materials are of key importance for stable and efficient perovskite‐based photovoltaics. This work reports on electron‐beam‐evaporated nickel oxide (NiO_x) layers, resulting in stable power conversion efficiencies (PCEs) of up to 18.5% when integrated into solar cells employing inkjet‐printed perovskite absorbers. By adding oxygen as a process gas and optimizing the layer thickness, transparent and efficient NiO_x hole transport layers (HTLs) are fabricated, exhibiting an average absorptance of only 1%. The versatility of the material is demonstrated for different absorber compositions and deposition techniques. As another highlight of this work, all‐evaporated perovskite solar cells employing an inorganic NiO_x HTL are presented, achieving stable PCEs of up to 15.4%. Along with good PCEs, devices with electron‐beam‐evaporated NiO_x show improved stability under realistic operating conditions with negligible degradation after 40 h of maximum power point tracking at 75 °C. Additionally, a strong improvement in device stability under ultraviolet radiation is found if compared to conventional perovskite solar cell architectures employing other metal oxide charge transport layers (e.g., titanium dioxide). Finally, an all‐evaporated perovskite solar mini‐module with a NiO_x HTL is presented, reaching a PCE of 12.4% on an active device area of 2.3 cm².     

A luminescent assay for real-time measurements of receptor endocytosis in living cells

Ligand-mediated endocytosis is a key autoregulatory mechanism governing the duration and intensity of signals emanating from cell surface receptors. Due to the mechanistic complexity of endocytosis and its emerging relevance in disease, simple methods capable of tracking this dynamic process in cells have become increasingly desirable. We have developed a bioluminescent reporter technology for real-time analysis of ligand-mediated receptor endocytosis using genetic fusions of NanoLuc luciferase with various G-protein-coupled receptors (GPCRs). This method is compatible with standard microplate formats, which should decrease work flows for high-throughput screens. This article also describes the application of this technology to endocytosis of epidermal growth factor receptor (EGFR), demonstrating potential applicability of the method beyond GPCRs.     

Rainfall during parental care reduces reproductive and survival components of fitness in a passerine bird

Adverse weather conditions during parental care may have direct consequences for offspring production, but longer‐term effects on juvenile and parental survival are less well known. We used long‐term data on reproductive output, recruitment, and parental survival in northern wheatears (Oenanthe oenanthe) to investigate the effects of rainfall during parental care on fledging success, recruitment success (juvenile survival), and parental survival, and how these effects related to nestling age, breeding time, habitat quality, and parental nest visitation rates. While accounting for effects of temperature, fledging success was negatively related to rainfall (days > 10 mm) in the second half of the nestling period, with the magnitude of this effect being greater for breeding attempts early in the season. Recruitment success was, however, more sensitive to the number of rain days in the first half of the nestling period. Rainfall effects on parental survival differed between the sexes; males were more sensitive to rain during the nestling period than females. We demonstrate a probable mechanism driving the rainfall effects on reproductive output: Parental nest visitation rates decline with increasing amounts of daily rainfall, with this effect becoming stronger after consecutive rain days. Our study shows that rain during the nestling stage not only relates to fledging success but also has longer‐term effects on recruitment and subsequent parental survival. Thus, if we want to understand or predict population responses to future climate change, we need to consider the potential impacts of changing rainfall patterns in addition to temperature, and how these will affect target species' vital rates.