Evidence for frequent recombination within species human enterovirus B based on complete genomic sequences of all thirty-seven serotypes

The species Human enterovirus B (HEV-B) in the family Picornaviridae consists of coxsackievirus A9; coxsackieviruses B1 to B6; echoviruses 1 to 7, 9, 11 to 21, 24 to 27, and 29 to 33; and enteroviruses 69 and 73. We have determined complete genome sequences for the remaining 22 HEV-B serotypes whose sequences were not represented in public databases and analyzed these in conjunction with previously available complete sequences in GenBank. Members of HEV-B were monophyletic relative to all other human enterovirus species in all regions of the genome except in the 5'-nontranslated region (NTR), where they are known to cluster with members of HEV-A. Within HEV-B, phylogenies constructed from the structural (P1) and nonstructural regions of the genome (P2 and P3) are incongruent, suggesting that recombination had occurred. Similarity plots and bootscanning analysis across the complete genome identified multiple sites at which the phylogeny of a given strain's sequence shifted, indicating potential recombination points. These points are distributed in the 5'-NTR and throughout P2 and P3, but no sites with >80% bootstrap support were identified within the capsid. Individual sequence comparisons and phylogenetic analyses suggest that members of HEV-B have recombined with one another on multiple occasions, resulting in a complex mosaic of sequences derived from multiple parental viruses in the nonstructural regions of the genome. We conclude that RNA recombination is a common mechanism for enterovirus evolution and that recombination within the nonstructural regions of the genome (P2 and P3) has been observed only among members of the same species.     

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.     

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.     

Compensating for delayed hatching reduces offspring immune response and increases life‐history costs

Organisms are exposed to multiple sources of stress in nature. When confronted with a stressful period affecting growth and development, compensatory responses allow the restoration of individual fitness, providing an important buffering mechanism against climatic and other environmental variability. However, tradeoffs between increased growth/development and other physiological traits are predicted to prevent these high growth and development rates from becoming constitutive. Here, we investigated how compensatory responses in growth and development affect immune responses. By using low temperature to stop embryonic development, we exposed moor frog Rana arvalis tadpoles to two levels of time‐constraints: non‐delayed hatching and 12‐day delayed hatching. In a common garden experiment, we recorded larval growth and development, as well as their immune response, measured as the inflammatory reaction after the injection of phytohaemagglutinin (PHA). Tadpoles originating from delayed hatching treatments had a lower immune response to PHA challenge than those from the non‐delayed hatching treatment. In general, tadpoles from the delayed hatching treatment reached metamorphosis faster and at a smaller size than control tadpoles. However, immune‐challenged tadpoles were not able to accelerate their development in response to delayed hatching. Our results indicate that 1) the innate immune response can be reduced in organisms undergoing compensatory developmental responses in growth and development and 2) compensatory capacity can be reduced when organisms are immunologically challenged. These dual findings reveal the complexity of handling multiple stressors and highlight the importance of examining the costs and limits of mounting an immune response in the context of increasing phenological instability ascribed to climate change.     

Complex patterns of geographic variation in heat tolerance and Hsp70 expression levels in the common frog Rana temporaria

1.

We tested for geographical variation in heat tolerance and Hsp70 expression levels of Rana temporaria tadpoles along a 1500 km long latitudinal gradient in Sweden.