Microcalorimetric study of elongation factor Tu from Thermus thermophilus in nucleotide-free,GDP and GTP forms and in the presence of elongation factor Ts

Elongation factor (EF) Tu undergoes profound nucleotide-dependent conformational changes in its functional cycle. The thermodynamic parameters of the different Thermus thermophilus EF-Tu forms, its domains I, II/III and III, were determined by microcalorimetry. Thermal transitions of the EF-Tu.GDP and EF-Tu.guanosine-5'-[beta,gamma-imido]triphosphate have a cooperative two-state character. Nucleotide removal affected the cooperativity of the thermal transition of EF-Tu. Microcalorimetric measurements of nucleotide-free EF-Tu and its separated domains showed that domains II/III have the main stabilizing role for the whole protein. Despite the fact that strong interactions between elongation factors Tu and Ts from T. thermophilus at 20 degrees C exist, the thermal transition of neither protein in the complex was significantly affected.     

Extensive linkage disequilibrium in small human populations in Eurasia

The extent of linkage disequilibrium (LD) was studied in two small food-gathering populations—Evenki and Saami—and two larger food-producing populations—Finns and Swedes—in northern Eurasia. In total, 50 single-nucleotide polymorphisms (SNPs) from five genes were genotyped using real-time pyrophosphate DNA sequencing, whereas 14 microsatellites were genotyped in two X-chromosomal regions. In addition, hypervariable region I of the mtDNA was sequenced to shed light on the demographic history of the populations. The SNP data, as well as the microsatellite data, reveal extensive levels of LD in Evenki and Saami when compared to Finns and Swedes. mtDNA-sequence variation is compatible with constant population size over time in Evenki and Saami but indicates population expansion in Finns and Swedes. Furthermore, the similarity between Finns and Swedes in SNP allele- and haplotype-frequency distributions indicate that these two populations may share a recent common origin. These findings suggest that populations such as the Evenki and the Saami, rather than the Finns, may be particularly suited for the initial coarse mapping of common complex diseases.     

Large-scale chromatin fibers of living cells display a discontinuous functional organization

We investigated the chromatin organization of living cells with a combination of recently developed approaches for histone and DNA labeling. Nucleosomal DNA was labeled with a histone H2B-GFP (green fluorescent protein) fusion protein and the chromatin organization of living HeLa cells was analyzed by high resolution confocal microscopy. Within the perinuclear and perinucleolar regions chromatin was organized into large-scale fibers of 2 to 8 microm in length and 300 to 500 nm in diameter. Within the nuclear interior we observed similar large-scale fibers, but in addition focal as well as diffuse forms of organization. Comparison with standard labeling and detection procedures revealed major differences in the chromatin organization observed. Chromatin organization revealed by the distribution of histone H2B-GFP was directly compared with the functional organization of chromatin by Cy3-dUTP labeling of DNA replicating at a specific time. DNA regions replicating at a specific time display characteristic physical and functional properties. Analysis of Cy3-labeled foci revealed that they are associated with all three forms of chromatin organization (fibrillar, focal and diffuse). In particular, Cy3-labeled foci appeared as discontinuous regions of large-scale fibers. These results demonstrate that large-scale chromatin fibers have discontinuous functional characteristics.     

Molecular studies on the colonization of the Madeiran archipelago by house mice

To study the colonization history of the house mouse (Mus musculus domesticus) on the Madeiran archipelago, complete mitochondrial D-loop sequences were obtained for 44 individuals from Madeira, Porto Santo and Ilhas Desertas. Altogether, 19 D-loop haplotypes were identified which formed part of a single clade in a phylogeny incorporating haplotypes from elsewhere in the range of M. m. domesticus, indicating that the Madeiras were colonized from a single source. Similarities between the sequences found in the Madeiras and those in Scandinavia and northern Germany suggest that northern Europe was the source area, and there is the intriguing possibility that the Vikings may have accidentally brought house mice to the archipelago. However, there is no record of Vikings visiting the Madeiras; on historical grounds, Portugal is the most likely source area for Madeiran mice and further molecular data from Portugal are needed to rule out that possibility.     

Anthropological and palaeopathological analysis of the human remains from three "Tombs of the Nobles" of the necropolis of Thebes-west, upper Egypt

During several recent excavation campaigns at the necropolis of Sheikh-Abd-el-Gurna, Thebes-West, Upper Egypt, we investigated the human remains of three "Tombs of the Nobles" totalling at least 273 individuals. The investigation covered the human material (skeletons and mummy residues) from the tombs TT-84, TT-85 and TT-95. These tombs had been built in the New Kingdom (approx. 1500-1000 B.C.) and used until the Late period (up to 330 BC). All samples were analyzed macroscopically, isolated findings were further investigated by endoscopic and radiological techniques. The at least 273 individuals covered an age range from newborns to senile individuals with a main age of death between 20 and 40 years of age. The rate of infants and subadults was at 20.2% of all individuals and there was a slight male predominance comprising 54.5% of the adults. In this population a fairly high rate of pathological lesions was seen. Thus, dental conditions generally were poor with a high degree of dental abrasion, an also high rate of carious dental lesions (affecting between 13.8% and 27.7% of the yaws) and consequently a significant number of dental abscesses (mean 15.9%). Residues of trauma were observed in a considerable number of individuals ranging between 12.3% and 22.6% depending on the burial place (mean 15.8%). Inflammatory bone reactions (except the dental abscesses) were present to variable extent, in some locations ranging up to 6.8% of the cases (mean 5.1%). In addition, we noted several cases showing cribra orbitalia (mean 29.2%) and porotic hyperostosis (15.4% of cases), mild to severe osteopenia (7.5%) and in several cases subperiosteal new bone formation suggestive of chronic vitamin D-deficiency ("scurvy") (9.5%). The data support the notion of a significant impairment of living conditions in a high number of individuals. The rates of osteoarthrotic joint alterations were considerably variable depending on the burial places (between 1.9% and 18.5%) providing insight into the physical activities of subpopulations in different locations of the burial places. Similarly, the rate of spondylosis showed also variable extent ranging between 12% and 66.1% of vertebral bodies. In general, our analysis provides evidences that the living conditions in the ancient Egyptian population of one of the main necropoles of Thebes analyzed in this study were quite poor. This is somewhat in contrast to the usually assumed high standard of living of the socially higher population of the capital of ancient Egypt.     

Study Design for Assessing Species Environment Relationships and Developing Indicator Systems for Ecological Changesin Floodplains – The Approach of the RIVA Project

In this article the study design and data sampling of the RIVA project – “Development and Testing of a Robust Indicator System for Ecological Changes in Floodplain Systems” – are described. The project was set up to improve existing approaches to study species environment relationships as a basis for the development of indicator systems and predictive models. Periodically flooded grassland was used as a model system. It is agriculturally used at a level of intermediate intensity and is the major habitat type along the Middle Elbe, Germany. We chose a main study area to analyse species environment relationships and two reference sites for testing the transferability of the results. Using a stratified random sampling scheme, we distributed 36 study plots across the main study site and 12 plots each within the reference sites. In each of the study plots, hydrological and soil variables were measured and plants, molluscs, and carabid beetles were sampled. Hoverflies were collected on a subset of the sampling plots. A brief summary of first results is then provided. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Bioindication and Functional Response in Floodplain Systems: Where to from Here?

We synthesise the results of the papers in this Special Issue, place them within the context of current trends in floodplain research, and outline promising new avenues that emerge from the contributions. The indication system presented complements existing approaches by focussing on a quantitative indication of environmental parameters. A promising research line that emerges is an extension of the systematic comparison of taxonomic groups with contrasting traits in terms of their performance as quantitative indicators for different environmental parameters. The studies show similarities and dissimilarities in the traits explaining the functional response of plants, molluscs, carabids, and syrphids to site conditions but trait databases and studies on additional taxa are required before broad generalisations can be made. The rigorous study design developed for the RIVA project, of which all contributions in this Special Issue are a part, not only was essential for an improvement of the understanding of species environment relationships and the role biological traits play for it, it also provides a baseline for assessing future change as part of long‐term ecological monitoring of floodplains. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)