Selection of control genes for quantitative RT-PCR based on microarray data

Use of internal reference gene(s) is necessary for adequate quantification of target gene expression by RT-PCR. Herein, we elaborated a strategy of control gene selection based on microarray data and illustrated it by analyzing endomyocardial biopsies with acute cardiac rejection and infection. Using order statistics and binomial distribution we evaluated the probability of finding low-varying genes by chance. For analysis, the microarray data were divided into two sample subsets. Among the first 10% of genes with the lowest standard deviations, we found 14 genes common to both subsets. After normalization using two selected genes, high correlation was observed between expression of target genes evaluated by microarray and RT-PCR, and in independent dataset by RT-PCR (r = 0.9, p < 0.001). In conclusion, we showed a simple and reliable strategy of selection and validation of control genes for RT-PCR from microarray data that can be easily applied for different experimental designs and tissues.     

Is local adaptation in Mimulus guttatus caused by trade‐offs at individual loci?

Local adaptation is considered to be the result of fitness trade‐offs for particular phenotypes across different habitats. However, it is unclear whether such phenotypic trade‐offs exist at the level of individual genetic loci. Local adaptation could arise from trade‐offs of alternative alleles at individual loci or by complementary sets of loci with different fitness effects of alleles in one habitat but selective neutrality in the alternative habitat. To evaluate the genome‐wide basis of local adaptation, we performed a field‐based quantitative trait locus (QTL) mapping experiment on recombinant inbred lines (RILs) created from coastal perennial and inland annual races of the yellow monkeyflower (Mimulus guttatus) grown reciprocally in native parental habitats. Overall, we detected 19 QTLs affecting one or more of 16 traits measured in two environments, most of small effect. We identified 15 additional QTL effects at two previously identified candidate QTLs [DIV ERGENCE (DIV)]. Significant QTL by environment interactions were detected at the DIV loci, which was largely attributable to genotypic differences at a single field site. We found no detectable evidence for trade‐offs for any one component of fitness, although DIV2 showed a trade‐off involving different fitness traits between sites, suggesting that local adaptation is largely controlled by non‐overlapping loci. This is surprising for an outcrosser, implying that reduced gene flow prevents the evolution of individuals adapted to multiple environments. We also determined that native genotypes were not uniformly adaptive, possibly reflecting fixed mutational load in one of the populations.     

THE BIOLOGY OF SPECIATION

Since Darwin published the “Origin,” great progress has been made in our understanding of speciation mechanisms. The early investigations by Mayr and Dobzhansky linked Darwin's view of speciation by adaptive divergence to the evolution of reproductive isolation, and thus provided a framework for studying the origin of species. However, major controversies and questions remain, including: When is speciation nonecological? Under what conditions does geographic isolation constitute a reproductive isolating barrier? and How do we estimate the “importance” of different isolating barriers? Here, we address these questions, providing historical background and offering some new perspectives. A topic of great recent interest is the role of ecology in speciation. “Ecological speciation” is defined as the case in which divergent selection leads to reproductive isolation, with speciation under uniform selection, polyploid speciation, and speciation by genetic drift defined as “nonecological.” We review these proposed cases of nonecological speciation and conclude that speciation by uniform selection and polyploidy normally involve ecological processes. Furthermore, because selection can impart reproductive isolation both directly through traits under selection and indirectly through pleiotropy and linkage, it is much more effective in producing isolation than genetic drift. We thus argue that natural selection is a ubiquitous part of speciation, and given the many ways in which stochastic and deterministic factors may interact during divergence, we question whether the ecological speciation concept is useful. We also suggest that geographic isolation caused by adaptation to different habitats plays a major, and largely neglected, role in speciation. We thus provide a framework for incorporating geographic isolation into the biological species concept (BSC) by separating ecological from historical processes that govern species distributions, allowing for an estimate of geographic isolation based upon genetic differences between taxa. Finally, we suggest that the individual and relative contributions of all potential barriers be estimated for species pairs that have recently achieved species status under the criteria of the BSC. Only in this way will it be possible to distinguish those barriers that have actually contributed to speciation from those that have accumulated after speciation is complete. We conclude that ecological adaptation is the major driver of reproductive isolation, and that the term “biology of speciation,” as proposed by Mayr, remains an accurate and useful characterization of the diversity of speciation mechanisms.     

野黄瓜与栽培黄瓜正反交异源四倍体序列消除的初步研究

不同分类群的异源多倍体在二倍化过程中, 正反交序列消除往往表现出不同特征, 暗示了在不同物种中, 核质互作在多倍体进化过程的作用不同。利用13对EcoRI-NN/MseI-NNN选择性引物, 对野黄瓜Cucumis hystrix (2n=24)与栽培黄瓜C. sativus (2n=14)的正反交F1、异源四倍体及二倍体亲本DNA进行AFLP分析。结果表明: 杂交后代基因组的杂合性诱发了F1与异源四倍体广泛的序列消除; 细胞质可能会影响部分亲本序列消除的频率, 但是正反交在序列消除频率上差异不显著, 并且在序列消除时间(均始于F1代)及消除类型上也表现出一致性, 表明核质互作并不是影响序列消除的主要因素; 实验还发现, 正反交不能影响序列的倾向性丢失, 染色体数少的黄瓜条带易发生丢失。     

Controlling death--compromising life: chronic disease, prognostication, and the new biotechnologies

Within the modern culture of control, patients and physicians seek to actively shape the uncertainty of prognostications concerning the course of disease and the anticipated effects of therapeutic and surgical interventions. This article discusses the results of a three-year ethnographic study of persons with cystic fibrosis (CF) who undergo double-lung transplant. It draws on interviews with a difficult-to-access patient group, adult CF sufferers, and investigates their dilemmas with regard to having or not having a double-lung transplant. It situates their decisions within a complex framework: the denial of death and disability in technological modernity, the consequent emphasis on cure and saving life at any cost, rather than the management of chronic illness, the extent to which health and illness constitute identity, and the problems of CF patients conceiving their life narrative when life will be short. This framework produces two key questions: Do patient beliefs in the progress narratives of medicine overshadow other considerations, and are biotechnologies such as organ transplant a calculated gamble on a better life or an uncertain reliance on biomedical expertise? I argue that risk interpretation is heavily influenced by the constant introduction of new therapeutics that intersect with social technologies of normalization to strongly influence patient decisions concerning the pursuit of high-risk surgeries such as organ transplant, surgeries that sometimes hasten a patient's decline and death.     

Interactive effects of past and present environments on overwintering success-a reciprocal transplant experiment

Life-history traits are influenced by environmental factors throughout the lifespan of an individual. The relative importance of past versus present environment on individual fitness, therefore, is a relevant question in populations that face the challenge of temporally varying environment. We studied the interacting effects of past and present density on body mass, condition, and survival in enclosure populations of the bank vole (Myodes glareolus) using a reciprocal transplant design. In connection with the cyclic dynamics of natural vole populations, our hypothesis was that individuals born in low-density enclosures would do better overwintering in low-density enclosures than in high-density enclosures and vice versa. Our results show that the effect of summer (past) density was strong especially on survival and body mass. The response of body mass to summer density was negative in both winter (present) density groups, whereas the response of survival probability was nonlinear and differed between the winter density groups. In particular, our data show a trend for higher overwintering success of individuals originating from the lowest summer densities in low winter density and vice versa. We therefore conclude that the capacity of individuals to respond to a change in density was constrained by the delayed density-dependent effects of environment experienced in the past. These effects have the potential to contribute to vole population dynamics. Possible mechanisms mediating the effects of past environment into present performance include both intrinsic and environmental factors.     

Understanding niche shifts: using current and historical data to model the invasive redlegged earth mite,Halotydeus destructor

Aim Niche conservatism is key to understanding species responses to environmental stress such as climate change or arriving in new geographical space such as biological invasion. Halotydeus destructor is an important agricultural pest in Australia and has been the focus of extensive surveys that suggest this species has undergone a niche shift to expand its invasive range inland to hotter and drier environments. We employ modern correlative modelling methods to examine niche conservatism in H. destructor and highlight ecological differences between historical and current distributions. Location Australia and South Africa. Methods We compile comprehensive distribution data sets for H. destructor, representing the native range in South Africa, its invasive range in Australia in the 1960s (40 yr post‐introduction) and its current range in Australia. Using MAXENT, we build correlative models and reciprocally project them between South Africa and Australia and investigate range expansion with models constructed for historical and current data sets. We use several recently developed model exploration tools to examine the climate similarity between native and invasive ranges and subsequently examine climatic variables that limit distributions. Results The invasive niche of H. destructor in Australia transgresses the native niche in South Africa, and the species has expanded in Australia beyond what is predicted from the native distribution. Our models support the notion that H. destructor has undergone a more recent range shift into hotter and drier inland areas of Australia since establishing a stable distribution in the 1960s. Main conclusions Our use of historical and current data highlights that invasion is an ongoing dynamic process and demonstrates that once a species has reached an established range, it may still expand at a later stage. We also show that model exploration tools help understand factors influencing the range of invasive species. The models generate hypotheses about adaptive shifts in H. destructor.     

Expression and identification of folate-sensitive fragile sites in British Suffolk sheep (<Emphasis Type="Italic">Ovis aries</Emphasis>)

An investigation to understand the dynamics and biological significance of fragile site expression, and identification of 5-fluorodeoxyuridine (FUdR) induced chromosomal gaps/breaks, were carried out in an experimental flock of 45 Suffolk sheep. The statistical comparison revealed, highly significant variation in the frequency of chromosomal fragile site expression between control and FUdR cultures. Mean (± S.D.) values for cells with gaps and breaks, or aberrant cell count (AC), and the number of aberrations (NoA) per animal were 2.02 ± 0.34, 2.42 ± 0.48, 13.26 ± 0.85 and 21.87 ± 1.88 (P < 0.01) in control and FUdR cultures, respectively. The comparison of age revealed nonsignificant variation between control and FUdR cultures. The G-band analysis of fragile site data revealed gaps in 29 autosomal and two X-chromosomal bands in the control cultures, whereas FUdR treated cultures scored 78 unstable bands in autosomes of which 56 were significantly fragile. X-chromosomes expressed breaks and gaps in six G-negative bands and five of them (Xq13, Xq15, Xq17, Xq24 and Xq26) were significantly fragile. The distribution comparison of autosomal fragile sites between sex groups did not reveal any significant variation. Female X-chromosomes were significantly more fragile than the male X-chromosomes. The distribution comparison for age groups (lambs versus adults) revealed significantly higher number of fragile bands in adults. Comparison of published data on reciprocal translocations in sheep with the fragile-site data obtained in this study indicated that the break sites of both phenomena were correlated. Similarities were also found between fragile sites and breakpoints of evolutionary significance in family Bovidae.     

Niche differentiation between diploid and hexaploid <Emphasis Type="Italic">Aster amellus</Emphasis>

The maintenance of separated diploid and polyploid populations within a contact zone is possible due to both prezygotic and postzygotic isolation mechanisms. Niche differentiation between two cytotypes may be an important prezygotic isolating mechanism and can be studied using reciprocal transplant experiments. We investigated niche differentiation between diploid and hexaploid Aster amellus in their contact zone in the Czech Republic. Diploid populations are confined to habitats with low productivity, whereas hexaploid populations occur in habitats with both low and high productivity. Thus, we chose three diploid populations and six hexaploid populations, three in each of the two different habitat types. We analyzed habitat characteristics and carried out reciprocal transplant experiments in the field using both seeds and adult plants. Sites of diploid and hexaploid populations differed significantly in vegetation and soil properties. The mean number of juveniles was higher at sites of home ploidy level than at sites of foreign ploidy level, suggesting niche differentiation between the two cytotypes. On the other hand, transplanted adult plants survived at all sites and juvenile plants were able to establish at some sites of the foreign cytotype. Furthermore, the mean number of juveniles, survival, and flowering percentages were higher at home sites than at foreign sites, indicating local adaptation. We conclude that niche differentiation between the two cytotypes and local adaptation within each cytotype may contribute to the maintenance of diploid and hexaploid populations of A. amellus in their contact zone. Moreover, further factors, such as differences in flowering phenology and exclusion of minority cytotypes, should also be considered.