Effect of Biofilm Formation by Bacillus subtilis natto on Menaquinone-7 Biosynthesis

Bacillus subtilis natto is the key microorganism for the industrial production of menaquinone-7. The fermentation of this bacterium in static culture is associated with biofilm formation. The objective of this study was to determine the effect of biofilm formation on menaquinone-7 production to develop a suitable bio-reactor for the production of menaquinone-7. In the static culture, menaquinone-7 biosynthesis showed a linear correlation with biofilm formation (R ² = 0.67) and cell density (R ² = 0.7). The amount of biofilm, cell density and menaquinone-7 formation were a function of nutrient and processing conditions. Glycerol, soy peptone, and yeast extract mixture and 40 °C were found to be the optimum nutrients and temperature for accelerating both biofilm and menaquinone-7 biosynthesis in static culture. However, glucose, mixture of soy peptone and yeast extract and 45 °C were found to be the optima for cell density. As compared to the static culture, the biofilm formation was significantly inhibited when a shaken fermentation was used. However, shaking caused only a small decrease on menaquinone-7 production. These results demonstrate that the biofilm formation is not essential for menaquinone-7 biosynthesis. This study underlines the feasibility of using large scale stirred fermentation process for menaquinone-7 production.     

Conformational Ensembles of Antibodies Determine Their Hydrophobicity

A major challenge in the development of antibody biotherapeutics is their tendency to aggregate. One root cause for aggregation is exposure of hydrophobic surface regions to the solvent. Many current techniques predict the relative aggregation propensity of antibodies via precalculated scales for the hydrophobicity or aggregation propensity of single amino acids. However, those scales cannot describe the nonadditive effects of a residue’s surrounding on its hydrophobicity. Therefore, they are inherently limited in their ability to describe the impact of subtle differences in molecular structure on the overall hydrophobicity. Here, we introduce a physics-based approach to describe hydrophobicity in terms of the hydration free energy using grid inhomogeneous solvation theory (GIST). We apply this method to assess the effects of starting structures, conformational sampling, and protonation states on the hydrophobicity of antibodies. Our results reveal that high-quality starting structures, i.e., crystal structures, are crucial for the prediction of hydrophobicity and that conformational sampling can compensate errors introduced by the starting structure. On the other hand, sampling of protonation states only leads to good results when combined with high-quality structures, whereas it can even be detrimental otherwise. We conclude by pointing out that a single static homology model may not be adequate for predicting hydrophobicity.     

Linking radial growth patterns and moderate‐severity disturbance dynamics in boreal old‐growth forests driven by recurrent insect outbreaks: A tale of opportunities,successes, and failures

In boreal landscapes, emphasis is currently placed on close‐to‐nature management strategies, which aim to maintain the biodiversity and ecosystem services related to old‐growth forests. The success of these strategies, however, depends on an accurate understanding of the dynamics within these forests. While moderate‐severity disturbances have recently been recognized as important drivers of boreal forests, little is known about their effects on stand structure and growth. This study therefore aimed to reconstruct the disturbance and postdisturbance dynamics in boreal old‐growth forests that are driven by recurrent moderate‐severity disturbances. We studied eight primary old‐growth forests in Québec, Canada, that have recorded recurrent and moderately severe spruce budworm (Choristoneura fumiferana [Clem.]) outbreaks over the 20th century. We applied an innovative dendrochronological approach based on the combined study of growth patterns and releases to reconstruct stand disturbance and postdisturbance dynamics. We identified nine growth patterns; they represented trees differing in age, size, and canopy layer. These patterns highlighted the ability of suppressed trees to rapidly fill gaps created by moderate‐severity disturbances through a single and significant increase in radial growth and height. Trees that are unable to attain the canopy following the disturbance tend to remain in the lower canopy layers, even if subsequent disturbances create new gaps. This combination of a low stand height typical of boreal forests, periodic disturbances, and rapid canopy closure often resulted in stands constituted mainly of dominant and codominant trees, similar to even‐aged forests. Overall, this study underscored the resistance of boreal old‐growth forests owing to their capacity to withstand repeated moderate‐severity disturbances. Moreover, the combined study of growth patterns and growth release demonstrated the efficacy of such an approach for improving the understanding of the fine‐scale dynamics of natural forests. The results of this research will thus help develop silvicultural practices that approximate the moderate‐severity disturbance dynamics observed in primary and old‐growth boreal forests.     

When to sample in an inaccessible landscape: a case study with carabids from the Allgäu (northern Alps) (Coleoptera, Carabidae)

While pitfall trapping is generally accepted as the standard method for sampling carabid beetles, this method has rarely been used in mountain ecosystems, mainly due to the high labour intensity it involves. As part of a research project in the German Alps, we investigated the phenologic appearance of adult carabid beetles in mountain ecosystems along with the consequences of possible reductions in sampling periods. Our results show that an early activity peak among carabids is predominant in mountain ecosystems. However, there are differences among species: the main group of species showed the highest activity directly after snow melt, a second group showed a delayed activity peak and a small third group had no clear peak at all. Based on this study, we recommend two fortnightly sampling periods as a minimum for a sampling programme: one immediately after snow melt, and a second sampling period after a pause of two weeks.     

Susceptibility of clinical Staphylococcus aureus isolates to innate defense antimicrobial peptides

Antimicrobial peptides (AMPs) are effector molecules of innate immunity. To determine whether AMP susceptibility of S. aureus varies according to different types of infection, 102 isolates from patients with S. aureus bacteremia or recurrent skin and soft tissue infection, and colonizing isolates were investigated. Using microbroth dilution assays we found a narrow range of MICs of human β-defensin-3, cathelicidin LL-37 and bovine indolicidin without significant differences between the groups. Colony-forming unit (CFU) assays revealed minor differences in bactericidal activity with slightly but not significantly higher CFU reduction in colonizing isolates. These data do not support a role for differential AMP susceptibility in vitro as a major determinant of S. aureus invasive infection.     

Aestivation in Pieris brassicae (L.) affects the parasitoid load caused by Cotesia glomerata (L.)

The large white butterfly Pieris brassicae (L.) (Lepidoptera: Pieridae) undergoes a unique aestivation in southern Spain. Its pupae remain dormant for three months in summer, emerging in early September. Its main parasitoid, Cotesia glomerata (L.) (Hymenoptera: Braconidae), shows no such diapause behavior and is thus deprived of its main host for this period and has to switch to less suitable host species. To study the effect the aestivation has on the parasitoids, caterpillars were collected from the region in May and September and levels of parasitization were determined. Results show that parasitoid attacks decrease clearly after the summer diapause. The number of parasitized butterfly clutches in September was only one third as the number in May and the infestation rate of an attacked clutch decreased by 55% after aestivation. The distribution of brood sizes of C. glomerata showed clear signs of superparasitism before but not after the diapause. Therefore, the butterfly generation after summer diapause has to deal with distinctly diminished numbers of parasitoids. This increases the survival rate of the caterpillar and thus improves the fitness of the butterfly.     

Purification and properties of antimicrobial peptides from skin secretions of the Eritrea clawed frog Xenopus clivii (Pipidae)

Five peptides with antimicrobial activity were isolated from norepinephrine-stimulated skin secretions of the tetraploid frog Xenopus clivii Peracca, 1898 (Pipidae). Characterization of the peptides demonstrated that they are structurally similar to magainins (2 peptides), caerulein-precursor fragments, CPF (2 peptides), and xenopsin-precursor fragments, XPF (1 peptide) that have been previously isolated from other species of the genus Xenopus. The magainins and the XPF peptide were active only against the Gram-negative microorganism Escherichia coli whereas the CPF peptides were also active against the Gram-positive Staphylococcus aureus. The most abundant antimicrobial peptide in the secretions, CPF-C1 (GFGSLLGKALRLG ANVL.NH(2)) inhibited the growth of the Gram-negative bacteria Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa (MIC≤25μM) suggesting potential for development into an anti-infective agent for use against these emerging antibiotic-resistant pathogens.     

Regulation of cathepsin G reduces the activation of proinsulin-reactive T cells from type 1 diabetes patients

Autoantigenic peptides resulting from self-proteins such as proinsulin are important players in the development of type 1 diabetes mellitus (T1D). Self-proteins can be processed by cathepsins (Cats) within endocytic compartments and loaded to major histocompatibility complex (MHC) class II molecules for CD4(+) T cell inspection. However, the processing and presentation of proinsulin by antigen-presenting cells (APC) in humans is only partially understood. Here we demonstrate that the processing of proinsulin by B cell or myeloid dendritic cell (mDC1)-derived lysosomal cathepsins resulted in several proinsulin-derived intermediates. These intermediates were similar to those obtained using purified CatG and, to a lesser extent, CatD, S, and V in vitro. Some of these intermediates polarized T cell activation in peripheral blood mononuclear cells (PBMC) from T1D patients indicative for naturally processed T cell epitopes. Furthermore, CatG activity was found to be elevated in PBMC from T1D patients and abrogation of CatG activity resulted in functional inhibition of proinsulin-reactive T cells. Our data suggested the notion that CatG plays a critical role in proinsulin processing and is important in the activation process of diabetogenic T cells.