Longevity studies in GenomEUtwin.

Previous twin studies have indicated that approximately 25% of the variation in life span can be attributed to genetic factors and recent studies have also suggested a moderate clustering of extreme longevity within families. Here we discuss various definitions of extreme longevity and some analytical approaches with special attention to the challenges due to censored data. Lexis diagrams are provided for the Danish, Dutch, Finnish, Italian, Norwegian, and Swedish Twin registries hereby outlining possibilities for longevity studies within GenomEUtwin. We extend previous analyses of lifespan for the Danish 1870-1900 twin cohorts to include the new 1901-1910 cohorts, which are consistent with the previous findings. The size of the twin cohorts in GenomEUtwin and the existence of population-based, nationwide health and death registers make epidemiological studies of longevity very powerful. The combined GenomEUtwin sample will also allow detailed age-specific heritability analyses of lifespan. Finally, it will provide a resource for identifying unusual sibships (i.e., dizygotic twin pairs) where both survived to extreme ages, as a basis for discovering genetic variants of importance for extreme survival.     

Swollenin, a Trichoderma reesei protein with sequence similarity to the plant expansins, exhibits disruption activity on cellulosic materials.

Plant cell wall proteins called expansins are thought to disrupt hydrogen bonding between cell wall polysaccharides without hydrolyzing them. We describe here a novel gene with sequence similarity to plant expansins, isolated from the cellulolytic fungus Trichoderma reesei. The protein named swollenin has an N-terminal fungal type cellulose binding domain connected by a linker region to the expansin-like domain. The protein also contains regions similar to mammalian fibronectin type III repeats, found for the first time in a fungal protein. The swollenin gene is regulated in a largely similar manner as the T. reesei cellulase genes. The biological role of SWOI was studied by disrupting the swo1 gene from T. reesei. The disruption had no apparent effect on the growth rate on glucose or on different cellulosic carbon sources. Non-stringent Southern hybridization of Trichoderma genomic DNA with swo1 showed the presence of other swollenin-like genes, which could substitute for the loss of SWOI in the disruptant. The swollenin gene was expressed in yeast and Aspergillus niger var. awamori. Activity assays on cotton fibers and filter paper were performed with concentrated SWOI-containing yeast supernatant that disrupted the structure of the cotton fibers without detectable formation of reducing sugars. It also weakened filter paper as assayed by an extensometer. The SWOI protein was purified from A. niger var. awamori culture supernatant and used in an activity assay with Valonia cell walls. It disrupted the structure of the cell walls without producing detectable amounts of reducing sugars.     

Re-terrestrialization in the phylogeny of epiphytic plant lineages: Microsoroid ferns as a case study

The fern family Polypodiaceae, with over 1600 species, is not only one of the most species-rich families of ferns, but also a major contributor to the vascular epiphytic diversity throughout the tropics. Although the vast majority of species belonging to this family prefer to grow as epiphytes, several species colonize successfully rheophytic, lithophytic, and even terrestrial habitats. Here, we explore the hypothesis that non-epiphytic habitat preferences, including terrestrial growth, evolved secondarily with epiphytes being the plesiomorphic habitat preference. The results of phylogenetic analyses, based on dense taxon sampling and four chloroplast DNA regions, were integrated with divergence time estimates and ancestral character state reconstructions to test these predictions. Both fossils and secondary calibration data were incorporated to obtain divergence time estimations. The results support the prediction of multiple transitions from epiphytic/lithophytic to terrestrial/rheophytic habitats occurring mainly in the Microsoreae lineage. The change in niche preferences coincides with niche colonization opportunities created by climatic fluctuations and geographical changes during the Oligocene and Miocene periods.     

Chemotaxonomic studies onArachniodes (Dryopteridaceae) II. Phloroglucinol derivatives and taxonomic evaluation

Seven species ofArachniodes from Japan and the Philippines were examined for phloroglucinol derivatives and glandularity of rhizome and petiole bases. For comparison 3 species ofDryopteris, 2 species ofNothoperanema, 3 species ofPolystichum, 1 species ofAcrophorus and 2 species ofCtenitis were investigated as well. Phloroglucinol derivatives were detected for the first time in the following taxa:Arachniodes assamica, A. cavalerii, A. tripinnata, A. yasu-inouei, Dryopteris pulvinulifera, D. cochleata, Polystichum rigens, Acrophorus nodosus, Ctenitis setosa andC. subglandulosa. The phloroglucinols ofDryopteris, Arachniodes andPolystichum are structurally related in agreement with the taxonomic relationships of these genera. On the other hand, the less related generaAcrophorus andCtenitis contain several unknown phloroglucinols not identical with those occurring in the former genera. The phloroglucinol containing species ofArachniodes, Polystichum, Acrophorus andCtenitis contain external glands, whereasDryopteris pulvinulifera andD. cochleata have both internal and external glands. The species of the genusNothoperanema seem to completely lack phloroglucinols and glands. The phloroglucinol composition of most taxa investigated is almost constant except for that inArachnoides amabilis and its varieties,A. aristata (A. exilis) andPolystichum tsus-simense. These species show varying phloroglucinol spectra in materials collected from different geographical sources.     

Adaptations to fasting in the American mink (Mustela vison): carbohydrate and lipid metabolism

The aim of this study was to investigate whether the actively wintering American mink Mustela vison is strictly dependent on continuous food availability or if it has evolved physiological adaptations to tolerate nutritional scarcity. Fifty farm-bred male minks were divided into a fed control group and four experimental groups fasted for 2, 3, 5 or 7 days. The rate of weight loss was several-fold higher (1.5-3.2% day(-1)) in the mink than recorded previously in larger carnivores utilizing passive wintering strategies. The minks remained normoglycaemic, although their liver glycogen stores and glucose-6-phosphatase activities decreased during fasting. Adipose tissue constituted approximately 36% of their body mass after 7 days of food deprivation. Intra-abdominal fat, especially retroperitoneal but also mesenteric adipose tissue, were the most important fat depots to be hydrolyzed, but the ability of the mink to utilize its body lipids during fasting may be limited. The increased liver size, hepatic triacylglycerol accumulation and increases in the activities of plasma aminotransferases indicated liver dysfunction. Food deprivation also affected the red blood cell indices, and the blood monocyte and lymphocyte counts decreased suggesting immunosuppression during fasting. The results of the present study suggest that the mink has not evolved sophisticated adaptations to wintertime fasting.     

Metabolic responses of microbiota to diesel fuel addition in vegetated soil

The effects of trees and contamination on microbial metabolic activity, especially that of hydrocarbon degrading bacteria, were compared during phytoremediation to find which conditions increase diesel fuel removal. Diesel fuel utilisation, microbial extracellular enzyme activities and utilisation of Biolog ECO plate carbon sources by soil bacteria were determined during phytoremediation experiments consisting of two separate diesel applications. Diesel fuel removal after 28 days of second diesel application was 20–30% more than after the first application 1 year earlier. Soil microbiota utilised 26–31 of the 31 Biolog ECO plate carbon sources. Carbon source utilisation profiles indicated minor differences in microbiota in soil vegetated with pine compared to microbiota in soil vegetated with poplar. The potential maximum rates of aminopeptidase activity were 10–10² M AMC/h/g dry soil prior to and after second diesel application, except 14days after the second diesel addition, where the rates were at the scale of 10³M AMC/h/g dry soil. The potential maximum rates of esterase activity were 10³–10⁴M MUF/h/g dry soil. The presence of plants did not influence the activity of esterases. The utilisation of diesel by soil bacteria in Biolog MT2 plate assay was higher in contaminated soil, especially when vegetated, than in uncontaminated soil, measured both as lag times and maximum specific utilisation rates. MT2 plate assay detected the biological response after diesel fuel addition better than general activity methods.     

Software for quantification of labeled bacteria from digital microscope images by automated image analysis

Automated image analysis software, CellC, was developed and validated for quantification of bacterial cells from digital microscope images. CellC enables automated enumeration of bacterial cells, comparison of total count and specific count images [e.g., 4',6-diamino-2-phenylindole (DAPI) and fluorescence in situ hybridization (FISH) images], and provides quantitative estimates of cell morphology. The software includes an intuitive graphical user interface that enables easy usage as well as sequential analysis of multiple images without user intervention. Validation of enumeration reveals correlation to be better than 0.98 when total bacterial counts by CellC are compared with manual enumeration, with all validated image types. The software is freely available and modifiable: the executable files and MATLAB source codes can be obtained at www. cs. tut.fi/sgn/csb/cellc.     

Characterization of iron- and sulphide mineral-oxidizing moderately thermophilic acidophilic bacteria from an Indonesian auto-heating copper mine waste heap and a deep South African gold mine

Iron- and chalcopyrite-oxidizing enrichment cultures were obtained at 50°C from acidic, high-temperature, copper/gold mine environments in Indonesia and South Africa. Over 90% copper yield was obtained from chalcopyrite concentrate with the Indonesian enrichment in 3 months with 2% solids concentration, when pH was maintained at around 2. Neither addition of silver cations nor an enhanced nutrient concentration influenced chalcopyrite leaching. Excision and sequencing of bands from denaturing gradient gel electrophoresis of the amplified partial 16S rRNA gene showed that the enrichment cultures from different environments in South Africa and Indonesia were very simple, and similar. Chalcopyrite concentrate supported a simpler and different community than Fe²⁺. The members of the enrichment cultures were closely related to Sulfobacillus yellowstonensis and Sulfobacillus acidophilus.     

Increasing incidence of Type 1 diabetes – role for genes?

Background  

The incidence of Type 1 diabetes (T1DM) is increasing fast in many populations. The reasons for this are not known, although an increase in the penetrance of the diabetes-associated alleles, through changes in the environment, might be the most plausible mechanism. After the introduction of insulin treatment in 1930s, an increase in the pool of genetically susceptible individuals has been suggested to contribute to the increase in the incidence of Type 1 diabetes.