Inhibition of methanogenesis and its reversal during biogas formation from cattle manure

The composition of volatile fatty acids in the biogas digester based on cattle manure as substrate and stabilised at 25°C showed that it contained 87–88% branched chain fatty acids, comprising of isobutyric and isovaleric acids, in comparison to 38 % observed in the digester operating at 35°C. Mixed cellulolytic cultures equilibrated at 25°C (C-25) and 35‡C (C-35) showed similar properties, but rates of hydrolysis were three times higher than that observed in a standard biogas digester. The proportion of isobutyric and isovaleric were drastically reduced when C-25 was grown with glucose or filter paper as substrates. The volatile fatty acids recovered from C-25 (at 25°C) inhibited growth of methanogens on acetate, whereas that from C-35 was not inhibitory. The inhibitory effects were due to the branched chain fatty acids and were observed with isobutyric acid at concentrations as low as 50 ppm. Addition of another micro-organismRhodotorula selected for growth on isobutyric completely reversed this inhibition. Results indicate that the aceticlastic methanogens are very sensitive to inhibition by branched chain fatty acids and reduction in methane formation in biogas digester at lower temperature may be due to this effect.     

Correspondence of vegetation boundaries to redox barriers in a Northern European moraine plain

Little attention has been devoted to the investigation of the formation and functioning of ecotones at the interfaces between the upland and riparian zones. The margins of riparian mires act as redox geochemical barriers. Such biogeochemical hot spots retain elements that have leached from upland soils, favouring the growth of mesomorphic plants in hydromorphic soils. This paper aims to clarify the correspondence of vegetation borders to horizontal redox barriers of a Northern European moraine plain in Estonia.24 random transects were surveyed on the moraine plain, sampled across sharp soil moisture boundaries as proxies of redox barriers. The shifts in vegetation perpendicular to the boundaries were investigated. Curves of Euclidean distance were computed by moving a 20 m split-window along transects. The curves showed peaks of high dissimilarity a few metres below the redox barriers in the sites of natural soil moisture. In artificially drained sites, the relict redox barriers poorly corresponded to the vegetation borders. We conclude that in the studied moraine plain, the vegetation boundaries between riparian mires and uplands correspond to the redox barriers. The same can be set as a hypothesis for Northern European moraine plains. Related ecotones can be observed on the footslopes, revealing redox barrier in the landscape and related hot spots in cultural landscapes. In field margins, the redox barriers and corresponding ecotones occur below cultivation terraces. The ecotones may represent functional boundaries for delineating wetlands. Man-made drainage removes soil redox barriers and corresponding vegetation boundaries, making the landscape uniform and therefore vulnerable to disturbances. As a management implication, footslope ecotones should be preserved in their natural condition.     

Structural similarity of YbeD protein from Escherichia coli to allosteric regulatory domains

Lipoic acid is an essential prosthetic group in several metabolic pathways. The biosynthetic pathway of protein lipoylation in Escherichia coli involves gene products of the lip operon. YbeD is a conserved bacterial protein located in the dacA-lipB intergenic region. Here, we report the nuclear magnetic resonance structure of YbeD from E. coli. The structure includes a beta alpha beta beta alpha beta fold with two alpha-helices on one side of a four-strand antiparallel beta-sheet. The beta 2-beta 3 loop shows the highest sequence conservation and is likely functionally important. The beta-sheet surface contains a patch of conserved hydrophobic residues, suggesting a role in protein-protein interactions. YbeD shows striking structural homology to the regulatory domain from d-3-phosphoglycerate dehydrogenase, hinting at a role in the allosteric regulation of lipoic acid biosynthesis or the glycine cleavage system.     

Using remote sensing to model tree species distribution in Peruvian lowland Amazonia

Species distribution models for Amazonian trees have mostly been produced at scales and resolutions that are too broad and coarse for practical use in either conservation or forestry. On the other hand, several studies have shown that elevation and the medium‐resolution remote sensing data available via Landsat imagery can be successfully used to detect differences in plant species composition in Amazonia. Therefore, it seems likely that the same data can also be used to predict geographical distributions of individual taxa. Here we use remotely sensed data and a maximum entropy algorithm (MaxEnt) to generate landscape‐scale distribution models at 30‐m‐resolution for five economically important timber tree genera (Apuleia, Amburana, Crepidospermum, Dipteryx, and Manilkara). Individual Landsat Thematic Mapper bands and normalized difference vegetation index yielded acceptable model performance, and the use of averaging filters (3 × 3 and 5 × 5 pixel low‐pass filters) improved model performance further. Including elevation as a predictor also improved model performance for all the genera. Our results suggest that it is possible to use Landsat bands and elevation as predictors for modeling the potential distribution of tree species in lowland Amazonia at a fine enough resolution to facilitate the practical management of forest resources.     

Evolution of Dispersal in a Structured Metapopulation Model in Discrete Time

In this article, a structured metapopulation model in discrete time with catastrophes and density-dependent local growth is introduced. The fitness of a rare mutant in an environment set by the resident is defined, and an efficient method to calculate fitness is presented. With this fitness measure evolutionary analysis of this model becomes feasible. This article concentrates on the evolution of dispersal. The effect of catastrophes, dispersal cost, and local dynamics on the evolution of dispersal is investigated. It is proved that without catastrophes, if all population–dynamical attractors are fixed points, there will be selection for no dispersal. A new mechanism for evolutionary branching is also found: Even though local population sizes approach fixed points, catastrophes can cause enough temporal variability, so that evolutionary branching becomes possible.     

Structural model of the BCL-w-BID peptide complex and its interactions with phospholipid micelles

A peptide corresponding to the BH3 region of the proapoptotic protein, BID, could be bound in the cleft of the antiapoptotic protein, BCL-w. This binding induced major conformational rearrangements in both the peptide and protein components of the complex and led to the displacement and unfolding of the BCL-w C-terminal alpha-helix. The structure of BCL-w with a bound BID-BH3 peptide was determined using NMR spectroscopy and molecular docking. These studies confirmed that a region of 16 residues of the BID-BH3 peptide is responsible for its strong binding to BCL-w and BCL-x(L). The interactions of BCL-w and the BID-BH3 peptide complex with dodecylphosphocholine micelles were characterized and showed that the conformational change of BCL-w upon lipid binding occurred at the same time as the release and unfolding of the BH3 peptide.     

C-terminal Peptides of Tissue Factor Pathway Inhibitor Are Novel Host Defense Molecules

Tissue factor pathway inhibitor (TFPI) inhibits tissue factor-induced coagulation, but may, via its C terminus, also modulate cell surface, heparin, and lipopolysaccharide interactions as well as participate in growth inhibition. Here we show that C-terminal TFPI peptide sequences are antimicrobial against the Gram-negative bacteria Escherichia coli and Pseudomonas aeruginosa, Gram-positive Bacillus subtilis and Staphylococcus aureus, as well as the fungi Candida albicans and Candida parapsilosis. Fluorescence studies of peptide-treated bacteria, paired with analysis of peptide effects on liposomes, showed that the peptides exerted membrane-breaking effects similar to those seen for the “classic” human antimicrobial peptide LL-37. The killing of E. coli, but not P. aeruginosa, by the C-terminal peptide GGLIKTKRKRKKQRVKIAYEEIFVKNM (GGL27), was enhanced in human plasma and largely abolished in heat-inactivated plasma, a phenomenon linked to generation of antimicrobial C3a and activation of the classic pathway of complement activation. Furthermore, GGL27 displayed anti-endotoxic effects in vitro and in vivo in a mouse model of LPS shock. Importantly, TFPI was found to be expressed in the basal layers of normal epidermis, and was markedly up-regulated in acute skin wounds as well as wound edges of chronic leg ulcers. Furthermore, C-terminal fragments of TFPI were associated with bacteria present in human chronic leg ulcers. These findings suggest a new role for TFPI in cutaneous defense against infections.     

Structure of the archaeal translation initiation factor aIF2 beta from Methanobacterium thermoautotrophicum: implications for translation initiation

aIF2 beta is the archaeal homolog of eIF2 beta, a member of the eIF2 heterotrimeric complex, implicated in the delivery of Met-tRNA(i)(Met) to the 40S ribosomal subunit. We have determined the solution structure of the intact beta-subunit of aIF2 from Methanobacterium thermoautotrophicum. aIF2 beta is composed of an unfolded N terminus, a mixed alpha/beta core domain and a C-terminal zinc finger. NMR data shows the two folded domains display restricted mobility with respect to each other. Analysis of the aIF2 gamma structure docked to tRNA allowed the identification of a putative binding site for the beta-subunit in the ternary translation complex. Based on structural similarity and biochemical data, a role for the different secondary structure elements is suggested.     

Synthesis and pharmacological evaluation of N-substituted 2-(2-oxo-2H-chromen-4-yloxy)propanamide as cyclooxygenase inhibitors

A series of novel N-substituted 2-(2-oxo-2H-chromen-4-yloxy)propanamide derivatives were synthesized via converting the readily available 4-hydroxy coumarin to the corresponding ethyl 2-(2-oxo-2H-chromen-4-yloxy)propanoate followed by hydrolysis and then reacting with different substituted amines. The molecular structures of two representative compounds, that is, 3 and 5l were confirmed by single crystal X-ray diffraction study. All the compounds synthesized were evaluated for their cyclooxygenase (COX) inhibiting properties in vitro. The compound 5i showed balanced selectivity towards COX-2 over COX-1 inhibition and good docking scores when docked into the COX-2 protein.