Improvement of binding of Puumala virus neutralization site resembling peptide with a second-generation phage library

We have previously selected a peptide insert FPCDRLSGYWERGIPSPCVR recognizing the Puumala virus (PUUV) G2-glycoprotein-specific neutralizing monoclonal antibody (MAb) 1C9 with Kd of 2.85 x 10(-8) from a random peptide library X2CX14CX2 expressed on the pIII protein of the filamentous phage fd-tet. We have now created a second-generation phage-displayed peptide library in which each amino acid of the peptide was mutated randomly to another with a certain probability. Peptides were selected for higher affinity for MAb 1C9 and for a common binding motif for MAb 4G2 having an overlapping epitope with MAb 1C9 in G2 glycoprotein. The resulting peptides were synthesized as spots on cellulose membrane. Amino acid changes which improved the reactivity of the peptides to MAb 1C9 were combined in the peptide ATCDKLFGYYERGIPLPCAL with Kd of 1.49 x 10(-9) in biosensor measurements. Our results show that the binding properties of peptides, the affinity and the specificity can be improved and the binding specificity determining amino acids and structural factors can be analyzed by combining binding assays with synthetic peptides on membrane with the use of second-generation phage display libraries.     

Intercontinental Dispersal of Bacteria and Archaea by Transpacific Winds

Microorganisms are abundant in the upper atmosphere, particularly downwind of arid regions, where winds can mobilize large amounts of topsoil and dust. However, the challenge of collecting samples from the upper atmosphere and reliance upon culture-based characterization methods have prevented a comprehensive understanding of globally dispersed airborne microbes. In spring 2011 at the Mt. Bachelor Observatory in North America (2.8 km above sea level), we captured enough microbial biomass in two transpacific air plumes to permit a microarray analysis using 16S rRNA genes. Thousands of distinct bacterial taxa spanning a wide range of phyla and surface environments were detected before, during, and after each Asian long-range transport event. Interestingly, the transpacific plumes delivered higher concentrations of taxa already in the background air (particularly Proteobacteria, Actinobacteria, and Firmicutes). While some bacterial families and a few marine archaea appeared for the first and only time during the plumes, the microbial community compositions were similar, despite the unique transport histories of the air masses. It seems plausible, when coupled with atmospheric modeling and chemical analysis, that microbial biogeography can be used to pinpoint the source of intercontinental dust plumes. Given the degree of richness measured in our study, the overall contribution of Asian aerosols to microbial species in North American air warrants additional investigation.     

Patterns in aquatic metacommunities are associated with environmental and trait heterogeneity

1. Metacommunities are structured by a combination of different ecological factors that vary in their importance depending on environmental heterogeneity and species functional equivalence. However, empirical tests of such context-dependence at regional scales are still missing.
2. We investigated associations between deterministic (e.g. environmental filtering and biotic interactions) and stochastic factors (e.g. dispersal related) and metacommunity structure of macroinvertebrates and diatoms across streams in four regions with contrasting levels of environmental and organismal trait heterogeneity.
3. Environmental filtering was most strongly associated with the region that showed moderate environmental heterogeneity and comprised communities with the highest trait heterogeneity. Associations with stochastic factors in the regions were more variable and difficult to predict. Environmental factors and the degree of genus-level association were generally more strongly associated with macroinvertebrates than with diatoms, whereas stochastic factors had consistently lower influence on macroinvertebrates.
4. These results suggest that the degree to which deterministic versus stochastic factors influence aquatic metacommunities depends on environmental and trait heterogeneity. Furthermore, organismal characteristics such as dispersal potential, habitat specialisation and sensitivity to environmental variation can also generate considerable context dependency in metacommunity structure.

     

Stream diatom assemblages as predictors of climate

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Beta diversity of stream diatoms at two hierarchical spatial scales: implications for biomonitoring

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Diatom Cooccurrence Shows Less Segregation than Predicted from Niche Modeling

Species cooccurrence patterns give significant insights into the processes shaping communities. While biotic interactions have been widely studied using cooccurrence analyses in animals and larger plants, studies about cooccurrences among micro-organisms are still relatively rare. We examined stream diatom cooccurrences in France through a national database of samples. In order to test the relative influence of environmental, biotic and spatial constraints on species’ incidence distribution, cooccurrence and nestedness patterns of real communities were compared with the patterns generated from a set of standard and environmentally constrained null models. Real communities showed a higher level of segregation than the most conservative standard null models, but a general aggregation of cooccurrences when compared to environmentally constrained null models. We did not find any evidence of limiting similarity between cooccurring species. Aggregations of species cooccurrences were associated with the high levels of nestedness. Altogether, these results suggested that biotic interactions were not structuring cooccurrences of diatom species at our study scale. Instead, the patterns were more likely to be related with colonization patterns, mass effect, and local temporal dynamics of diatom biofilms. We further highlight that the association of standard and environmentally constrained null models may give realistic insight into the cooccurrence patterns of microbial communities.     

Cholinergic deficit in Alzheimer's disease: A study based on CSF and autopsy data

Cholinesterase (ChE) activity was measured as a possible marker of cholinergic neurotransmission of the brain in CSF of 93 patients with probable Alzheimer's disease/senile dementia of the Alzheimer type (AD/SDAT) and of 29 control patients. ChE activity in CSF was decreased significantly in the AD/SDAT patients as compared to the controls. This reduction correlated significantly with the various measures of the severity of dementia. However, the reduction of ChE activity was only moderate (25–30%) even in patients with the most severe dementia and nonsignificant in patients with early symptoms of AD/SDAT. The significance of various confounding factors, which may interfere with CSF ChE measurements is discussed. Our findings seem to indicate that the deficiency of cholinergic neurons is not directly reflected in CSF and that the measurements of ChE activities in CSF are not helpful in diagnosing AD/SDAT. In the autopsy study the activities of cholineacetyltransferase (ChAT) and ChE were determined for ten brain areas of 20 AD/SDAT patients and of 14 controls. In AD/SDAT patients ChAT activity was profoundly decreased (50–85% decrease) in the cortical areas and hippocampus, but was unchanged or only mildly reduced in other subcortical brain areas. This study further confirms that the affection of cholinergic neurons is limited to projections from nucleus basalis to cortex and hippocampus, whereas other cholinergic neurons, like in striatum, seem to be relatively spared. In general, the activities of ChAT and ChE were lower in Alzheimer patients dying at younger age suggesting more severe disease process with these patients.     

Structural organization of the gene for the alpha 1 chain of human type IV collagen

The complete exon size and distribution pattern in the gene for the alpha 1 chain of human type IV collagen was determined. Clones covering 145 kilobases (kb) of genomic DNA including 100 kb of the gene itself as well as 25 kb upstream and 20 kb downstream of the gene sequences, respectively, were isolated from lambda phage and cosmid libraries. The overall gene structure was determined by endonuclease restriction mapping and R-loop analyses and all exon sizes by nucleotide sequencing. The characterized clones contained all the coding sequences except for exon 2 whose sequence was determined after its amplification by the polymerase chain reaction. There were four gaps in the intron sequences; the exact size of the gene is unknown. The entire gene is at least 100 kb in size and contains 52 exons whose size distribution is completely different from that of the genes for fibrillar collagens. In the -Gly-X-Y- coding region there are three exons of 99, 90, and 45 base pairs (bp) each and two exons of 27, 36, 42, 51, 54, 63, and 84 bp each. The rest of the exons have sizes between 71 and 192 bp in the collagenous region. About one-half of the -Gly-X-Y- repeat coding exons start with the second base for the codon of glycine, whereas the other half starts (with two exceptions) with a complete glycine codon. The distribution of split versus unsplit codons is uneven in that the first 19 exons of the gene start with a complete codon. The gene contains repetitive sequences in several regions. A 185-nucleotide segment containing 40 copies of CCT flanked by poly(C) and poly(T) sequences was shown to be located adjacent to an exon. The gene has previously been shown to be located head-to-head to the alpha 2(IV) collagen gene at the distal end of the long arm of chromosome 13, such that the first exons of the two genes are separated by as little as 42 bp (P?schl, E., Pollner, R., and Kühn, K. (1988) EMBOJ. 7,2687-2695; Soininen, R., Huotari, M., Hostikka, S. L., Prockop, D. J., and Tryggvason, K. (1988) J. Biol. Chem. 263, 17217-17220). The results demonstrate that the human alpha 1(IV) collagen gene has a structure distinctly different from the genes for fibrillar collagens and also that it is considerably larger than any collagen gene characterized to date.