Contingent Conclusions: Year of Initiation Influences Ecological Field Experiments,but Temporal Replication is Rare

Interannual variation in experimental field conditions produce variability in the results of experiments monitored over multiple years, termed here “year effects.” When experimental treatments are replicated in separate years, interannual variation may influence treatment effects and produce significant treatment by initiation‐year interactions. Understanding the frequency and strength of these effects requires initiating identical experiments across years. We conducted a review of literature covering more than 500 experimental articles published in 7 journals between 1966 and 2008. Only 5% of the 276 general ecological field studies initiated experiments in multiple years. This rarity was even more evident in the journal Restoration Ecology, in which none of the 173 surveyed experimental studies initiated experiments in multiple years. In contrast, 48% of the 58 field experiments published in an agronomy journal were replicated across years. We found only 17 studies that tested treatment by initiation‐year interactions. Despite their rarity, 76% of these studies found significant interactions between treatment and initiation year. We conclude that the results of many ecological field experiments are likely to be contingent on the year in which they are implemented. We discuss the importance of treatment by initiation‐year interactions in ecology and restoration, factors that have hindered the inclusion of temporal replication in the past, and some suggestions for the appropriate design and analysis of temporally replicated experiments. We argue for more deliberate investigation of temporal contingency in ecological experimentation, especially in the field of restoration ecology, which may be particularly sensitive to treatment by initiation‐year interactions.     

Genotoxicity in the eyes of bystander cells

The controversial use of a linear, no threshold extrapolation model for low dose risk assessment has become even more so in light of the recent reports on the bystander phenomenon. The answer to the question as to which of the two phenomena, bystander versus adaptive response, is more important has practical implication in terms of low dose radiation risk assessment. In this review, genotoxicity is used as an endpoint to introduce the two phenomena, provide some insight into the mechanisms of bystander effect and to bridge the two low dose phenomena which operate in opposite directions: the bystander effect tends to exaggerate the effect at low doses, by communicating damage from hit to non-hit cells whereas the adaptive response confers resistance to a subsequent challenging dose by an initial low priming dose.     

Numerical simulation of convective and diffusive transport effects on a high-pressure-induced inactivation process

High-pressure-induced conversions, such as the inactivation of enzymes or of microorganisms, are dependent on the applied pressure and the temperature of the process. The former can be considered to be a spatially homogeneous quantity, while the latter, being a transport quantity, varies over space and time. Here we question whether the uniformity of a high-pressure conversion can be disturbed by convective and conductive heat and mass transport conditions. Enzyme inactivation is taken as a model process for a high-pressure conversion. To cover a broad range of parameters and to consider scale-up effects, the investigation is based on mathematical modeling and numerical simulation for different sizes of the pressure chamber and different solvent viscosities. Apart from viscosity, the physical properties of the enzyme solutions are assumed to be identical in all cases. Therefore, matrix effects other than that of viscosity are excluded. Moreover, the authors postulate that viscosity solely acts on the continuum mechanical scale of momentum exchange but not on the molecular scale on the inactivation kinetics. It has been found that nonuniform thermal conditions can strongly influence the result of a high-pressure process. A variation of the activity retention between 28% and 48% can be observed after 20 minutes for a 0.8-L high-pressure chamber and a matrix fluid with a viscosity comparable to that of edible oils. The same process carried out in a 6.3-L device leads to an activity retention that varies between 16% and 40%. From the analysis of the time scales for the inactivation and for hydrodynamic and thermal compensation, it can be deduced that a nonuniform activity retention has to be expected if the inactivation time scale is larger than the hydrodynamic time scale and smaller than the thermal compensation time scale.     

Preliminary observations on change of sex by the coral-inhabiting snails Coralliophila violacea (Lamarck) (Gastropoda: Coralliophilidae)

The coral-inhabiting snails, Coralliophila violacea (Lamarck), are widely distributed in the Indo–Pacific region. It has been inferred from field data that sex changes have occurred and might be influenced by neighbors. In this study, we designed a field experiment with 2 treatments, i.e. ‘single males' and ‘male–female pairings' to test the hypothesis of sex changes as well as the role of neighbors on sex changes. Snails were collected by SCUBA diving from the surface of massive coral Porites lobata in shallow waters (<6 m) in southern Taiwan. A total of 73 males and 32 females were marked and returned to the surface of a colony of the massive coral, P. lobata. After 4–5 months, a total of 25 marked males and eight marked females were recaptured. In the treatment of ‘single males', eight of 17 males had changed their sex. None of eight recaptured males in the treatment of ‘male–female pairings' had changed their sex. The occurrence of sex changes is dependent on the presence or absence of a female neighbor (P<0.05, Fisher's exact test). In this study, we have provided direct evidence of socially controlled sex changes in Coralliophila violacea.     

Transmission and scanning electron-microscopic observations on tanycytes in the mediobasal hypothalamus and the median eminence of adrenalectomized rats

Summary Tanycytes in the median eminence (ME) of the rat exhibit morphological features suggesting their possible participation in transport phenomena. After adrenalectomy, which modifies the hypothalamo-hypophyseal axis, they undergo morphological changes characterized by an accumulation of lipid droplets, an increased number of bleb-like protrusions at their apex, as well as an increased pinocytosis of intraventricularly injected horseradish peroxidase (HRP). In addition, after adrenalectomy an increased number of vacuoles appears at the level of the tubero-infundibular sulci. Their intracellular location in the tanycytes is demonstrated by an intraventricular injection of HRP. The significance of these vacuoles is discussed in relation to the hydroelectrolytic modifications associated with the state of adrenalectomy.Supported by a Fonds Lekime-Ropsy AwardSupported by grants: 20472 from the Fonds de la Recherche Scientifique Médicale; and 40025 from the Fonds National de la Recherche Scientifique     

Position-Associated GC Asymmetry of Gene Duplicates

It is well known that repositioning of a gene often exerts a strong impact on its own expression and whole development. Here we report the results of genome-wide analyses suggesting that repositioning may also radically change the evolutionary fate of gene duplicates. As an indicator of these changes, we used the GC content of gene pairs which originated by duplication. This indicator turned out to be duplicate-asymmetric, which means that genes in a pair differ significantly in GC content despite their apparent origin from a common ancestor. Such an asymmetry necessarily implies that after duplication two originally identical genes mutated in opposite directions—toward GC-rich and GC-poor content, respectively. In mammalian genomes, this trend is definitely associated with presumably methylated hypermutable CpG sites, and in a typical GC-asymmetric gene pair, its two member genes are embedded in GC-contrasting isochores. However, we unexpectedly found similar significant GC asymmetry in fish, fly, worm, and yeast. This means that neither methylation alone nor methylation in combination with isochores can be counted as a primary cause of the GC asymmetry; rather they represent specific realizations of some universal principle of genome evolution. Remarkably, genes from pairs with the greatest GC asymmetry tend to be on different chromosomes, suggesting that the mutational difference between gene duplicates is associated with translocation of a new gene to a different place in the genome, whereas GC symmetric pairs demonstrate the opposite tendency. A recently emerged extra gene copy is usually on the same chromosome as is its parent but quickly, by 0.05 substitution per synonymous site, either has perished or occupies a different chromosome. During this earliest posttranslocation period, the ratio of nonsynonymous/synonymous base substitutions is unusually high, suggesting a rapid adaptive evolution of novel functions. In a general context of evolution by gene duplication, our interpretation of this position-dependent GC asymmetry between duplicated genes is that evolution of redundant genes toward a new function has often been associated with their very early, postduplication repositioning in the genome, with a concomitant abrupt change in epigenetic control of tissue/stage-specific expression and an increase in the mutation rate. Of eight eukaryotic genomes studied, the most distinguished in this respect is the human genome.Reviewing Editor: Dr. Manyuan Long     

Lack of MHC-II expression in activated mouse T cells correlates with DNA methylation at the CIITA-PIII region

In contrast to activated human T cells, activated mouse T cells fail to express MHC class II molecules (MHC-II) at their cell surface. This is because mouse T cells hardly produce mRNA encoding the MHC-II molecules I-A and I-E, due to severely impaired expression levels upon T-cell activation of the mhc2ta gene, encoding the class II transactivator (CIITA). In humans, activated T cells express exclusively the CIITA promoter III (CIITA-PIII) isoform, which results in cell surface expression of all MHC-II isotypes (HLA-DR, -DP and -DQ). In this study, we demonstrate that methylation of CIITA-PIII contributes to the failure of mouse T cells to transcribe the mhc2ta and the resulting I-A/E genes, explaining the lack of I-A/E molecule expression at the cell surface following activation.     

Blastocysts don't go it alone. Extrinsic signals fine-tune the intrinsic developmental program of trophoblast cells

The preimplantation embryo floats freely within the oviduct and is capable of developing into a blastocyst independently of the maternal reproductive tract. While establishment of the trophoblast lineage is dependent on expression of developmental regulatory genes, further differentiation leading to blastocyst implantation in the uterus requires external cues emanating from the microenvironment. Recent studies suggest that trophoblast differentiation requires intracellular signaling initiated by uterine-derived growth factors and integrin-binding components of the extracellular matrix. The progression of trophoblast development from the early blastocyst stage through the onset of implantation appears to be largely independent of new gene expression. Instead, extrinsic signals direct the sequential trafficking of cell surface receptors to orchestrate the developmental program that initiates blastocyst implantation. The dependence on external cues could coordinate embryonic activities with the developing uterine endometrium. Biochemical events that regulate trophoblast adhesion to fibronectin are presented to illustrate a developmental strategy employed by the peri-implantation blastocyst.     

Molecular Mechanisms Involved in the Aging of the T-cell Immune Response

T-lymphocytes play a central role in the effector and regulatory mechanisms of the adaptive immune response. Upon exiting the thymus they begin to undergo a series of phenotypic and functional changes that continue throughout the lifetime and being most pronounced in the elderly. The reason postulated for this is that the dynamic processes of repeated interaction with cognate antigens lead to multiple division cycles involving a high degree of cell differentiation, senescence, restriction of the T-cell receptor (TCR) repertoire, and cell cycle arrest. This cell cycle arrest is associated with the loss of telomere sequences from the ends of chromosomes. Telomere length is reduced at each cell cycle, and critically short telomeres recruit components of the DNA repair machinery and trigger replicative senescence or apoptosis. Repetitively stimulated T-cells become refractory to telomerase induction, suffer telomere erosion and enter replicative senescence. The latter is characterized by the accumulation of highly differentiated T-cells with new acquired functional capabilities, which can be caused by aberrant expression of genes normally suppressed by epigenetic mechanisms in CD4+ or CD8+ T-cells. Age-dependent demethylation and overexpression of genes normally suppressed by DNA methylation have been demonstrated in senescent subsets of T-lymphocytes. Thus, T-cells, principally CD4+CD28^null T-cells, aberrantly express genes, including those of the KIR gene family and cytotoxic proteins such as perforin, and overexpress CD70, IFN-γ, LFA-1 and others. In summary, owing to a lifetime of exposure to and proliferation against a variety of pathogens, highly differentiated T-cells suffer molecular modifications that alter their cellular homeostasis mechanisms.