Gene silencing pathway RNA-dependent RNA polymerase of Neurospora crassa: yeast expression and crystallization of selenomethionated QDE-1 protein

The RNA-dependent RNA polymerase, QDE-1, is a component of the RNA silencing pathway in Neurospora crassa. The enzymatically active carboxy-terminal fragment QDE-1 DeltaN has been expressed in Saccharomyces cerevisiae in the presence and absence of selenomethionine (SeMet). The level of SeMet incorporation was estimated by mass spectrometry to be approximately 98%. Both native and SeMet proteins were crystallized in space group P2(1) with unit cell parameters a=101.2, b=122.5, c=114.4A, beta=108.9 degrees , and 2 molecules per asymmetric unit. The native and SeMet crystals diffract to 2.3 and 3.2A, respectively, the latter are suitable for MAD structure determination.     

Enzyme Activities and Alcohol Tolerance in Isofemale Lines of Drosophila melanogaster Originating from Different Habitats

Enzyme activity variation was studied in a Drosophila melanogaster population from two villages (Tiszafüred and Tiszaszolos) in Hungary. Two habitats (distillery and farmyard) were sampled in both villages and 8-9 isofemale lines were established from each sample with a total of 35 lines. The activities of ADH, alphaGPDH, IDH and 6PGDH were determined on starch gel after electrophoresis in 10 F1 females of each of the 35 isofemale lines. Three sublines were established from three selected isofemale lines of all four samples (altogether 36 sublines). Alcohol tolerance of the adult flies was assayed in these sublines. The activity of ADH was similar in the two habitats; so was the sensitivity to ethanol. Accordingly, no differences in adaptation to environmental ethanol were detected between the two habitats. The deviations between the two habitats in average activities and in the total variation of enzyme activities were not consistent in the two villages. These results suggest that founder effects and genetic drift are more pronounced in distilleries than selection. The association among enzyme activities varied greatly both between the two villages and between the two habitats. The two parameters of alcohol tolerance were not significantly different between the two habitats in any of the two villages.     

Adipose tissue gene expression analysis reveals changes in inflammatory, mitochondrial respiratory and lipid metabolic pathways in obese insulin-resistant subjects

Background

To elucidate gene expression associated with copy number changes, we performed a genome-wide copy number and expression microarray analysis of 25 pairs of gastric tissues.

Methods

We applied laser capture microdissection (LCM) to obtain samples for microarray experiments and profiled DNA copy number and gene expression using 244K CGH Microarray and Human Exon 1.0 ST Microarray.

Results

Obviously, gain at 8q was detected at the highest frequency (70%) and 20q at the second (63%). We also identified molecular genetic divergences for different TNM-stages or histological subtypes of gastric cancers. Interestingly, the C20orf11 amplification and gain at 20q13.33 almost separated moderately differentiated (MD) gastric cancers from poorly differentiated (PD) type. A set of 163 genes showing the correlations between gene copy number and expression was selected and the identified genes were able to discriminate matched adjacent noncancerous samples from gastric cancer samples in an unsupervised two-way hierarchical clustering. Quantitative RT-PCR analysis for 4 genes (C20orf11, XPO5, PUF60, and PLOD3) of the 163 genes validated the microarray results. Notably, some candidate genes (MCM4 and YWHAZ) and its adjacent genes such as PRKDC, UBE2V2, ANKRD46, ZNF706, and GRHL2, were concordantly deregulated by genomic aberrations.

Conclusions

Taken together, our results reveal diverse chromosomal region alterations for different TNM-stages or histological subtypes of gastric cancers, which is helpful in researching clinicopathological classification, and highlight several interesting genes as potential biomarkers for gastric cancer.     

Human CD4+ T Cell Responses to the Dog Major Allergen Can f 1 and Its Human Homologue Tear Lipocalin Resemble Each Other

Lipocalin allergens form a notable group of proteins, as they contain most of the significant respiratory allergens from mammals. The basis for the allergenic capacity of allergens in the lipocalin family, that is, the development of T-helper type 2 immunity against them, is still unresolved. As immunogenicity has been proposed to be a decisive feature of allergens, the purpose of this work was to examine human CD4⁺ T cell responses to the major dog allergen Can f 1 and to compare them with those to its human homologue, tear lipocalin (TL). For this, specific T cell lines were induced in vitro from the peripheral blood mononuclear cells of Can f 1-allergic and healthy dog dust-exposed subjects with peptides containing the immunodominant T cell epitopes of Can f 1 and the corresponding TL peptides. We found that the frequency of Can f 1 and TL-specific T cells in both subject groups was low and close to each other, the difference being about two-fold. Importantly, we found that the proliferative responses of both Can f 1 and TL-specific T cell lines from allergic subjects were stronger than those from healthy subjects, but that the strength of the responses within the subject groups did not differ between these two antigens. Moreover, the phenotype of the Can f 1 and TL-specific T cell lines, determined by cytokine production and expression of cell surface markers, resembled each other. The HLA system appeared to have a minimal role in explaining the allergenicity of Can f 1, as the allergic and healthy subjects'' HLA background did not differ, and HLA binding was very similar between Can f 1 and TL peptides. Along with existing data on lipocalin allergens, we conclude that strong antigenicity is not decisive for the allergenicity of Can f 1.     

Behavioural responses to predator chemical cues and local variation in antipredator performance in Rana temporaria tadpoles

Antipredator behaviour is an important factor influencing survival probability of prey animals, and it may evolve rapidly as a response to changes in predator regime. I studied antipredator behaviour of common frog ( Rana temporaria ) tadpoles from three populations that differ in predator regimes. In the first experiment, tadpoles obtained from four natural matings in each population were subjected to chemical cues from either European perch ( Perca fluviatilis ) or from larvae of the dragonfly Aeshna juncea . Tadpoles decreased their activity in response to both predators, but the spatial behaviour of tadpoles differed between the two predator treatments. In general, there were no differences in behaviours among the populations, but in three out of four studied behaviours there were differences between parentages within the populations suggesting that these behaviours may be genetically determined. The lack of a significant Predator×Population interaction suggests no differences in plastic antipredator behaviour among the populations, while the lack of significant Predator×Parentage interaction suggests no genetic variance within the populations for plastic antipredator behaviour. In the second experiment, tadpoles from the three populations were exposed to predation by a free-ranging A. juncea . In line with the first experiment, there were no differences in survival rate between the populations. R. temporaria tadpoles seem to rely heavily on plastic antipredator behaviour as their main response to predator chemical cues. There was very little indication of local behavioural differentiation and the possible reasons for the lack of divergence among populations are discussed.     

Pan-European δ13C values of air and organic matter from forest ecosystems

We present carbon stable isotope, δ¹³C, results from air and organic matter samples collected during 98 individual field campaigns across a network of Carboeuroflux forest sites in 2001 (14 sites) and 2002 (16 sites). Using these data, we tested the hypothesis that δ¹³C values derived from large‐scale atmospheric measurements and models, which are routinely used to partition carbon fluxes between land and ocean, and potentially between respiration and photosynthesis on land, are consistent with directly measured ecosystem‐scale δ¹³C values. In this framework, we also tested the potential of δ¹³C in canopy air and plant organic matter to record regional‐scale ecophysiological patterns. Our network estimates for the mean δ¹³C of ecosystem respired CO₂ and the related ‘discrimination’ of ecosystem respiration, δ_er and Δ_er, respectively, were ?25.6±1.9‰ and 17.8 ±2.0‰ in 2001 and ?26.6±1.5‰ and 19.0±1.6‰ in 2002. The results were in close agreement with δ¹³C values derived from regional‐scale atmospheric measurement programs for 2001, but less so in 2002, which had an unusual precipitation pattern. This suggests that regional‐scale atmospheric sampling programs generally capture ecosystem δ¹³C signals over Europe, but may be limited in capturing some of the interannual variations. In 2001, but less so in 2002, there were discernable longitudinal and seasonal trends in δ_er. From west to east, across the network, there was a general enrichment in ¹³C (～3‰ and ～1‰ for the 2 years, respectively) consistent with increasing Gorczynski continentality index for warmer and drier conditions. In 2001 only, seasonal ¹³C enrichment between July and September, followed by depletion in November (from about ?26.0‰ to ?24.5‰ to ?30.0‰), was also observed. In 2001, July and August δ_er values across the network were significantly related to average daytime vapor pressure deficit (VPD), relative humidity (RH), and, to a lesser degree, air temperature (T_a), but not significantly with monthly average precipitation (P_m). In contrast, in 2002 (a much wetter peak season), δ_er was significantly related with T_a, but not significantly with VPD and RH. The important role of plant physiological processes on δ_er in 2001 was emphasized by a relatively rapid turnover (between 1 and 6 days) of assimilated carbon inferred from time‐lag analyses of δ_er vs. meteorological parameters. However, this was not evident in 2002. These analyses also noted corresponding diurnal cycles of δ_er and meteorological parameters in 2001, indicating a rapid transmission of daytime meteorology, via physiological responses, to the δ_er signal during this season. Organic matter δ¹³C results showed progressive ¹³C enrichment from leaves, through stems and roots to soil organic matter, which may be explained by ¹³C fractionation during respiration. This enrichment was species dependent and was prominent in angiosperms but not in gymnosperms. δ¹³C values of organic matter of any of the plant components did not well represent short‐term δ_er values during the seasonal cycle, and could not be used to partition ecosystem respiration into autotrophic and heterotrophic components.     

Multiple paternity in the common frog (Rana temporaria): genetic evidence from tadpole kin groups

Very few studies have investigated the occurrence of multiple paternity and sperm competition in amphibians. We studied genetic relatedness within kin groups of tadpoles of an aquatically breeding anuran Rana temporaria using allozymes. We collected samples from 52 naturally fertilized spawn clumps produced by single females at three breeding sites in two populations. We estimated relatedness (r) within kin groups, and compared the observed genotype distributions of the tadpoles (on average 23 individuals in each group) with the expected distributions based on single mating. Average relatedness over five polymorphic loci was 0.44 and 0.43 in the two populations, the latter being significantly smaller than that expected by single mating (0.5). The number of patrilines, calculated from relatedness estimates, was 1.3 in one population and 1.4 in the other. Genotype distributions deviated significantly from the expected in half of the kin groups and at all breeding sites. The results show that egg clutches of R. temporaria commonly contain multiply sired offspring. We suggest that communal breeding may affect paternity patterns in R. temporaria as well as in anurans in general.     

Hydrology is reflected in the functioning and community composition of methanotrophs in the littoral wetland of a boreal lake

In lake ecosystems a major proportion of methane (CH(4) ) emissions originate from the littoral zone, which can have a great spatial variability in hydrology, soil quality and vegetation. Hitherto, spatial heterogeneity and the effects it has on functioning and diversity of methanotrophs in littoral wetlands have been poorly understood. A diagnostic microarray based on the particulate methane monooxygenase gene coupled with geostatistics was used to analyse spatial patterns of methanotrophs in the littoral wetland of a eutrophic boreal lake (Lake Kev?t?n, Eastern Finland). The wetland had a hydrology gradient with a mean water table varying from -8 to -25 cm. The wettest area, comprising the highest CH(4) oxidation, had the highest abundance and species richness of methanotrophs. A high water table favoured the occurrence of type Ib methanotrophs, whereas types Ia and II were found under all moisture conditions. Thus the spatial heterogeneity in functioning and diversity of methanotrophs in littoral wetlands is highly dependent on the water table, which in turn varies spatially in relation to the geomorphology of the wetland. We suggest that changes in water levels resulting from regulation of lakes and/or global change will affect the abundance, activity and diversity of methanotrophs, and consequently CH(4) emissions from such systems.