Global topology analysis of the Escherichia coli inner membrane proteome

The protein complement of cellular membranes is notoriously resistant to standard proteomic analysis and structural studies. As a result, membrane proteomes remain ill-defined. Here, we report a global topology analysis of the Escherichia coli inner membrane proteome. Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins. By constraining a topology prediction algorithm with this data, we derived high-quality topology models for the 601 proteins, providing a firm foundation for future functional studies of this and other membrane proteomes. We also estimated the overexpression potential for 397 green fluorescent protein fusions; the results suggest that a large fraction of all inner membrane proteins can be produced in sufficient quantities for biochemical and structural work.     

Emulsion properties of sunflower (Helianthus annuus) proteins

Emulsions were made with sunflower protein isolate (SI), helianthinin, and sunflower albumins (SFAs). Emulsion formation and stabilization were studied as a function of pH and ionic strength and after heat treatment of the proteins. The emulsions were characterized with respect to average droplet size, surface excess, and the occurrence of coalescence and/or droplet aggregation. Sunflower proteins were shown to form stable emulsions, with the exception of SFAs at neutral and alkaline pH values. Droplet aggregation occurred in emulsions made with SI, helianthinin, and SFAs. Droplet aggregation and subsequent coalescence of emulsions made with SFAs could be prevented at pH 3. Calcium was found to cause droplet aggregation of emulsions made with helianthinin, at neutral and alkaline pH values. Treatments that increase conformational flexibility of the protein molecule improved the emulsion properties of sunflower proteins.     

Auswirkungen der durch oxidative Ammonolyse chemisch veränderten Braunkohle auf die Bodenbiologie

In Langzeit-Inkubationsversuchen wurden die Auswirkungen abgestufter Mengen von chemisch veränderter (N-modifizierter) Braunkohle auf die mikrobiologischen und enzymatischen Unsatzleistungen in verschiedenen Kippsubstraten geprüft. Die Untersuchungsbefunde charakterisieren diesen Humusdüngestoff als ein dauerhaft wirksames organisches Bodenverbesserungsmittel mit N-Düngewirkung, das die bodenmikrobiologischen Aktivitäten verbessert.     

Tree Species Diversity in Community Managed and National Park Forests in the Mid-Hills of Central Nepal

Community forestry is expanding in developing countries but there is limited knowledge of, and contradictory findings about, its contribution to biodiversity conservation. This study aims at increasing the understanding of tree species diversity in community forests compared to National Parks. A forest inventory was carried out in four community forests and one National Park in the mid-hills of central Nepal. The study found that community forestry has contributed to high tree species diversity where forest management communities have interests in multiple species, but most community forests are moving toward promoting limited timber yielding species that have high economic value. Linking community forestry with economic incentives for conserving multiple tree species could therefore be a strategy to conserve biodiversity outside of protected areas.     

Microspectroscopy as applied to the study of wood molecular structure

Microspectroscopy gives access to spatially resolved information on the molecular structure and chemical composition of a material. For a highly heterogeneous and anisotropic material like wood, such information is essential when assessing structure/property relationships such as moisture-induced dimensional changes, decay resistance or mechanical properties. It is, however, important to choose the right technique for the purpose at hand and to apply it in a suitable way if any new insights are to be gained. This review presents and compares three different microspectroscopic techniques: infrared, Raman and ultraviolet. Issues such as sample preparation, spatial resolution, data acquisition and extraction of knowledge from the spectral data are discussed. Additionally, an overview of applications in wood science is given for each method. Lastly, current trends and challenges within microspectroscopy of wood are discussed.     

Expression of trefoil factor genes in the duodenum and colon of dogs with inflammatory bowel disease and healthy dogs

Trefoil factors (TFF) are small peptides produced by goblet cells, which are crucial for epithelial restitution. In humans with inflammatory bowel disease (IBD), TFF expression is up-regulated as part of an unspecific repair mechanism. The goal of this study was to assess TFF gene expression in the gastrointestinal tract from dogs with IBD compared to healthy controls. Preliminary assessment by PCR revealed TFF1 and 3 expression in the small and large intestine, whereas TFF2 was amplified only in the stomach. Subsequent RT-qPCR (with relative quantification against 3 reference genes) on endoscopic duodenal (IBD n = 22, healthy controls n = 18) and colonic (IBD n = 12, controls n = 11) biopsies revealed that TFF1 expression was significantly up-regulated in the duodenum from IBD dogs (Mann–Whitney p = 0.001), whereas TFF3 expression was significantly lower in IBD colon compared to controls (t-test p = 0.018).This study demonstrates evidence for dysregulation of TFF gene expression in canine IBD. Up-regulation of TFF1 could signify ectopic expression as a compensatory repair-mechanism, whereas down-regulation of TFF3 could contribute to defective epithelial barrier function, respectively. Whether this is a cause or consequence of IBD could not be established.     

Preparation and comparative release characteristics of three anthocyanin encapsulation systems

Bilberries (Vaccinium myrtillus L.) and their major polyphenolic constituents, anthocyanins, have preventive activities inter alia against colon cancer and inflammatory bowel diseases. However, anthocyanins are sensitive to environmental conditions; thus their bioavailability in the gastrointestinal tract is an important determinant of their in vivo activity. In the study reported here, the potential benefits of encapsulating an anthocyanin rich bilberry extract (BE) on anthocyanin stability were investigated. Nonencapsulated BE and three different BE loaded microcapsule systems were incubated in simulated gastric fluid (SGF) and fed state simulated intestinal fluid (FeSSIF). After exposure to these media, released anthocyanins were identified and quantified by HPLC with UV/Vis detection. Although a rapid release of anthocyanins was observed within the first 20 min, encapsulation of anthocyanins doubled the amount of available anthocyanins after 150 min of incubation. These results illustrate the ability of encapsulation to inhibit early degradation of anthocyanins in the intestinal system.     

Genetic variation among <Emphasis Type="Italic">Fusarium</Emphasis> isolates from onion,and resistance to <Emphasis Type="Italic">Fusarium</Emphasis> basal rot in related <Emphasis Type="Italic">Allium</Emphasis> species

The aim of this research was to study levels of resistance to Fusarium basal rot in onion cultivars and related Allium species, by using genetically different Fusarium isolates. In order to select genetically different isolates for disease testing, a collection of 61 Fusarium isolates, 43 of them from onion (Allium cepa), was analysed using amplified fragment length polymorphism (AFLP) markers. Onion isolates were collected in The Netherlands (15 isolates) and Uruguay (9 isolates), and received from other countries and fungal collections (19 isolates). From these isolates, 29 were identified as F. oxysporum, 10 as F. proliferatum, whereas the remaining four isolates belonged to F. avenaceum and F. culmorum. The taxonomic status of the species was confirmed by morphological examination, by DNA sequencing of the elongation factor 1-α gene, and by the use of species-specific primers for Fusarium oxysporum, F. proliferatum, and F. culmorum. Within F. oxysporum, isolates clustered in two clades suggesting different origins of F. oxysporum forms pathogenic to onion. These clades were present in each sampled region. Onion and six related Allium species were screened for resistance to Fusarium basal rot using one F. oxysporum isolate from each clade, and one F. proliferatum isolate. High levels of resistance to each isolate were found in Allium fistulosum and A. schoenoprasum accessions, whereas A. pskemense, A. roylei and A. galanthum showed intermediate levels of resistance. Among five A. cepa cultivars, ‘Rossa Savonese’ was also intermediately resistant. Regarding the current feasibility for introgression, A. fistulosum, A. roylei and A. galanthum were identified as potential sources for the transfer of resistance to Fusarium into onion.     

Urea fertilisation affected soil organic matter dynamics and microbial community structure in pasture soils of Southern Ecuador

In the mountain rainforest region of the South Ecuadorian Andes natural forests have often been converted to pastures by slash-and-burn practice. With advanced pasture age the pasture grasses are increasingly replaced by the tropical bracken leading to the abandonment of the sites. To improve pasture productivity a fertilisation experiment with urea was established. The effects of urea on soil organic matter (SOM) mineralisation and microbial community structure in top soil (0–5 cm depth) of an active and abandoned pasture site have been investigated in laboratory incubation experiments. Either ¹⁴C- or ¹⁵N-labelled urea (74 mg urea-N kg⁻¹ dw soil) was added to track the fate of ¹⁴C into CO₂ or microbial biomass and that of ¹⁵N into the KCl-extractable NH₄-N or NO₃-N or microbial biomass pool. The soil microbial community structure was assessed using phospholipid fatty acid analysis (PLFA). In a second experiment two levels of ¹⁴C-labelled urea (74 and 110 mg urea-N kg⁻¹ dw soil) were added to soil from 5 to 10 cm depth of the respective sites. Urea fertilisation accelerated the mineralisation of SOC directly after addition up to 17% compared to the non-fertilised control after 14 days of incubation. The larger the amount of N potentially available per unit of microbial biomass N the larger was the positive priming effect. Since in average 80% of the urea-C had been mineralised already 1 day after amendment, the priming effect was strong enough to cause a net loss of soil C. Although the structure of the microbial community was significantly different between sites, urea fertilisation induced the same alteration in microbial community composition: towards a relative lower abundance of PLFA marker characteristic of Gram-positive bacteria and a higher one of those typical of Gram-negative bacteria and fungi. This change was positively correlated with the increase in NH₄, NO₃ and DON availability. In addition to the activation of different microbial groups the abolishment of energy limitation of the microbes seemed to be an important mechanism for the enhanced mineralisation of SOM.