Linking Land‐Use Scenarios,Remote Sensing and Monitoring to Project Impact of Management Decisions

Large‐scale modifications of natural ecosystems lead to mosaics of natural, semi‐natural and intensively used habitats. To improve communication in conservation planning, managers and other stakeholders need spatially explicit projections at the landscape scale of future biodiversity under different land‐use scenarios. For that purpose, we visualized the potential effect of five forest management scenarios on the avifauna of Kakamega Forest, western Kenya using different measures of bird diversity and GIS data. Future projections of bird diversity combined: (1) remotely sensed data on the spatial distribution of different forest management types; (2) field‐based data on the biodiversity of birds in the different management types; and (3) forest management scenarios that took into account possible views of various stakeholder groups. Management scenarios based on the species richness of forest specialists were very informative, because they reflected differences in the proportions of near‐natural forest types among the five scenarios. Projections based on community composition were even more meaningful, as they mirrored not only the proportions of near‐natural forest types, but also their perimeter to area ratios. This highlights that it is important to differentiate effects of the total area of available habitat and the degree of habitat fragmentation, both for species richness and community composition. Furthermore, our study shows that an approach that combines land‐use scenarios, remote sensing and field data on biodiversity can be used to visualize future biodiversity. As such, visualizations of alternative scenarios are valuable for successful communication about conservation planning considering different groups of stakeholders in species‐rich tropical forests.     

Phosphosignature Predicts Dasatinib Response in Non-small Cell Lung Cancer

Targeted drugs are less toxic than traditional chemotherapeutic therapies; however, the proportion of patients that benefit from these drugs is often smaller. A marker that confidently predicts patient response to a specific therapy would allow an individual therapy selection most likely to benefit the patient. Here, we used quantitative mass spectrometry to globally profile the basal phosphoproteome of a panel of non-small cell lung cancer cell lines. The effect of the kinase inhibitor dasatinib on cellular growth was tested against the same panel. From the phosphoproteome profiles, we identified 58 phosphorylation sites, which consistently differ between sensitive and resistant cell lines. Many of the corresponding proteins are involved in cell adhesion and cytoskeleton organization. We showed that a signature of only 12 phosphorylation sites is sufficient to accurately predict dasatinib sensitivity. Four of the phosphorylation sites belong to integrin β4, a protein that mediates cell-matrix or cell-cell adhesion. The signature was validated in cross-validation and label switch experiments and in six independently profiled breast cancer cell lines. The study supports that the phosphorylation of integrin β4, as well as eight further proteins comprising the signature, are candidate biomarkers for predicting response to dasatinib in solid tumors. Furthermore, our results show that identifying predictive phosphorylation signatures from global, quantitative phosphoproteomic data is possible and can open a new path to discovering molecular markers for response prediction.     

Multi-Biochemical Test System for Distinguishing Enteric and Other Gram-Negative Bacilli

A multi-biochemical test system consisting of nine tests, entitled Enterotube, was evaluated in parallel with conventional tests to determine its value in the identification of enteric and certain other gram-negative bacilli. The 242 bacterial strains studied were from a variety of pathological specimens and from our culture collection. When the results with individual tests represented in both test systems were compared, no discrepancies were noted in the indole test, and one discrepancy was recorded for dextrose. In 7 of 242 hydrogen sulfide tests, 3 of 242 phenylalanine tests, 22 of 242 urease tests, 15 of 242 dulcitol tests, 12 of 242 lactose tests, 27 of 217 lysine decarboxylase tests, and 5 of 242 citrate tests, the Enterotube results were contrary to those obtained with conventional methods. The lysine decarboxylase test in the Enterotube posed a problem of interpretation and readability and is not an acceptable alternative to the conventional methods. Fifteen of the strains studied were incorrectly identified by the Enterotube system and four could not be differentiated from other closely related strains. Salmonella could be identified as to group, whereas Shigella strains were frequently misidentified as Escherichia. The Enterotube method is simple and convenient, and all media are inoculated at once from a single colony.     

Structure and mechanism of the genomically encoded fosfomycin resistance protein, FosX, from Listeria monocytogenes

The fosfomycin resistance protein, FosX, catalyzes the hydration of the antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid. Genes encoding the enzyme are found in several pathogenic microorganisms. The structure and mechanism of action of the genomically encoded FosX enzyme from Listeria monocytogenes (FosXLMATCC) obtained from the American Type Culture Collection are reported. The gene harbors 31 point mutations, and as a consequence, the protein differs in 10 amino acid residues from the previously reported FosX encoded in the genome of the EGD strain of L. monocytogenes (FosXLMEGD). The FosXLMATCC enzyme is shown to catalyze the addition of water to the C1 position of the antibiotic with inversion of configuration at C1. The reaction involves Mn(II) activation of the oxirane oxygen and E44 acting as a general base. The structure of the enzyme has been determined from six different crystal forms of the protein. The structures of the enzyme without metal bound are similar but differ in the loop regions. Perhaps the most informative structure is the one with the product bound. This structure shows that the phosphonate group of the product is bound in an orientation that is different than that of fosfomycin bound to the related enzyme, FosA. The implication is that the substrate may also be bound in a different orientation in FosX. A high-resolution structure (1.44 A resolution) of the enzyme reveals a unique conformation in which the C-terminal tail of the protein coordinates to the Mn(II) center via the carboxylate of E126. The kinetic characterization of the E126Q mutant indicates that this conformation of the protein is probably not relevant to the function of the enzyme. Kinetic analysis of mutants of active site residue E44 is consistent with its proposed roll as a general base catalyst in the addition of water to the antibiotic.     

Improving DNA array data quality by minimising ‘neighbourhood’ effects

Gene expression studies using cDNA arrays require robust and sensitive detection methods. Being extremely sensitive, radioactive detection suffers from the influence of signals positioned in each other’s vicinity, the ‘neighbourhood’ effect. This limits the gene density of arrays and the quality of the results obtained. We have investigated the quantitative influence of different parameters on the ‘neighbourhood’ effect. By using a model experimental system, we could show that the effect is linear and depends only on the intensity of the hybridisation signal. We identified a common factor that can describe the influence of the neighbour spots based on their intensities. This factor is <1%, but it has to be taken into account if a high dynamic range of gene expression is to be detected. We could also derive the factor, although with less precision, from comparison of duplicate spots on arrays of 4565 different clones and replication of the hybridisation experiments. The calculated coefficient applied to our actual experimental results not only revealed previously undetected tissue or cell-specific expression differences, but also increased the dynamic range of detection. It thus provides a relatively simple way of improving DNA array data quality with few experimental modifications.     

Exotic Guavas are Foci of Forest Regeneration in Kenyan Farmland

Fruiting trees in degraded areas are attractive for frugivorous birds and may become centers of regeneration. However, a number of tree species in degraded areas are exotic species. Thus, the question arises whether these exotic species can also act as foci for forest regeneration. In the farmland adjacent to Kakamega Forest, Kenya, we investigated the frugivore assemblage in, and seed rain and seedling establishment under, 29 fruiting exotic guava trees ( Psidium guajava ) at different distances to the forest. The results show that 40 frugivorous bird species visited guava trees. All of the seed and 82 percent of the seedling species found under the treecrowns were animal dispersed, 58 and 57 percent of them late-successional species, respectively. Path analysis revealed that the abundance of frugivorous birds, seeds, and seedlings did not decrease up to a distance of 2 km from the forest. Surprisingly, the abundance of frugivorous shrubland birds, animal-dispersed seeds, and late-successional seeds showed an increase with increasing distance from forest. Even though they are exotics, fruiting guava trees may have a positive effect on forest regeneration and might prove valuable for management plans concerning forest restoration.