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.     

Bacteriophage ϕ6 nucleocapsid surface protein 8 interacts with virus-specific membrane vesicles containing major envelope protein 9

Enveloped double-stranded RNA (dsRNA) bacterial virus Pseudomonas phage ϕ6 has been developed into an advanced assembly system where purified virion proteins and genome segments self-assemble into infectious viral particles, inferring the assembly pathway. The most intriguing step is the membrane assembly occurring inside the bacterial cell. Here, we demonstrate that the middle virion shell, made of protein 8, associates with the expanded viral core particle and the virus-specific membrane vesicle.     

Spatial graphs as templates for habitat networks in boreal landscapes

Network topology serves as a useful model for biological systems at various scales. Contrary to many biological systems, spatial reference is crucial for habitat networks. Boreal forest landscapes provide a wide gradient of spatial patterns and, thus, unique network structures. Assuming forest-dwelling organisms in general aim to minimize travel distances during foraging, dispersal, etc., linear links across the landscape matrix constitute expected movement routes among forested areas in boreal landscapes. We quantified the number and length of links in a set of 57 boreal forest landscapes for four hierarchically nested graphs in order to compare the incremental changes in characteristics of resulting graph measures. The forest cover graphs consisted of the same set of forest patches, and hierarchical link types extracted from real landscapes: nearest neighbour graph (NN), minimum spanning tree (MST), Gabriel graph (GG) and minimum planar graph (MPG). Most of the links in graphs were NN and GG links. Commonly links were 100–200?m in length, but link lengths particularly in the GG and MPG shorten when the proportion of forest in landscapes increased. Most nodes had 3–5 links each, but the number of links per node depended on node size and the proportion of forest cover. GG and MPG graphs retain the topology of the underlying node layout. Changes in node pattern alter the NN and MST graphs more than GG and MPG. Variation in regional network topologies is likely to affect connectivity patterns in a landscape and, thus, many ecological processes that occur at a local scale. An appropriate network analysis enables the discovery and comparison of distinctive network patterns. Understanding network topologies provide practical tools for land use planning and biodiversity management of broader areas that target functional habitat networks.     

An amino-indazole scaffold with spectrum selective kinase inhibition of FLT3, PDGFRα and kit

Here we describe the synthesis and characterization of a number of 3-amino-1H-indazol-6-yl-benzamides that were designed to target the 'DFG-out' conformation of the kinase activation loop. Several compounds such as 4 and 11 exhibit single-digit nanomolar EC(50)s against FLT3, c-Kit and the gatekeeper T674M mutant of PDGFRα.     

Context dependency and metacommunity structuring in boreal headwater streams

We studied the relative importance of spatial and environmental factors as determinants of algal, bryophyte, and macroinvertebrate metacommunities in two boreal drainage basins differing in spatial extent. We used eigenfunction spatial analysis to model the spatial relationships among sites and distance‐based redundancy analysis to partition the variability in biotic communities between the spatial filters generated through spatial eigenfunction analysis and the environmental factors measured in the field. In the smaller study area, each metacommunity was structured mostly by environmental factors. This was evidenced by the fact that either the pure environmental effect was significant or environmental factors were strongly spatially structured. In the larger study area, only pure environmental effects were significant. These findings suggest that the environmental control prevails in boreal headwater streams. However, our findings also suggest that the specific details of the community‐environment and community–space relationships are dependent on the focal organism group and drainage basin.