Genetic and epigenetic aspects of polyploid evolution in plants.

Polyploidy, the condition of possessing more than 2 complete chromosome sets in the same nucleus, is frequent in nature and has implications for a species' prospects for evolution. Newly formed polyploids, so-called neopolyploids, undergo a wide spectrum of genomic changes upon genome merger and duplication. Here, we review recent literature describing genomic and transcriptomic changes along the pathway from neoallopolyploid formation to the stabilization of species and diversification at the allopolyploid level. We begin by reviewing pathways of polyploid formation and discuss the effects of genome doubling and hybridization on chromosome pairing. We then review our knowledge of epigenetic changes in allopolyploids, followed by a consideration of the effects of these structural genomic and epigenetic changes on the transcriptional activity of genes in allopolyploids. We discuss the effects of changes in gene expression in polyploids with respect to current evolutionary theory. Finally, we draw attention to the general question of the relationships between genomic and transcriptomic alteration and incipient diversification among sibling polyploid lines and populations.

Neoadjuvant chemoradiotherapy with or without panitumumab in patients with wild-type KRAS, locally advanced rectal cancer (LARC): a randomized, multicenter, phase II trial SAKK 41/07.

BACKGROUND: We conducted a randomized, phase II, multicenter study to evaluate the anti-epidermal growth factor receptor (EGFR) mAb panitumumab (P) in combination with chemoradiotherapy (CRT) with standard-dose capecitabine as neoadjuvant treatment for wild-type KRAS locally advanced rectal cancer (LARC). PATIENTS AND METHODS: Patients with wild-type KRAS, T3-4 and/or N+ LARC were randomly assigned to receive CRT with or without P (6 mg/kg). The primary end-point was pathological near-complete or complete tumor response (pNC/CR), defined as grade 3 (pNCR) or 4 (pCR) histological regression by Dworak classification (DC). RESULTS: Forty of 68 patients were randomly assigned to P + CRT and 28 to CRT. pNC/CR was achieved in 21 patients (53%) treated with P + CRT [95% confidence interval (CI) 36%-69%] versus 9 patients (32%) treated with CRT alone (95% CI: 16%-52%). pCR was achieved in 4 (10%) and 5 (18%) patients, and pNCR in 17 (43%) and 4 (14%) patients. In immunohistochemical analysis, most DC 3 cells were not apoptotic. The most common grade ≥3 toxic effects in the P + CRT/CRT arm were diarrhea (10%/6%) and anastomotic leakage (15%/4%). CONCLUSIONS: The addition of panitumumab to neoadjuvant CRT in patients with KRAS wild-type LARC resulted in a high pNC/CR rate, mostly grade 3 DC. The results of both treatment arms exceeded prespecified thresholds. The addition of panitumumab increased toxicity.

Polyploidy and its effect on evolutionary success: old questions revisited with new tools.

Polyploidy, the condition of possessing more than two complete genomes in a cell, has intrigued biologists for almost a century. Polyploidy is found in many plants and some animal species and today we know that polyploidy has had a role in the evolution of all angiosperms. Despite its widespread occurrence, the direct effect of polyploidy on evolutionary success of a species is still largely unknown. Over the years many attractive hypotheses have been proposed in an attempt to assign functionality to the increased content of a duplicated genome. Among these hypotheses are the proposal that genome doubling confers distinct advantages to a polyploid and that these advantages allow polyploids to thrive in environments that pose challenges to the polyploid's diploid progenitors. This article revisits these long-standing questions and explores how the integration of recent genomic developments with ecological, physiological and evolutionary perspectives has contributed to addressing unresolved problems about the role of polyploidy. Although unsatisfactory, the current conclusion has to be that despite significant progress, there still isn't enough information to unequivocally answer many unresolved questions about cause and effect of polyploidy on evolutionary success of a species. There is, however, reason to believe that the increasingly integrative approaches discussed here should allow us in the future to make more direct connections between the effects of polyploidy on the genome and the responses this condition elicits from the organism living in its natural environment.

Prion protein as copper-binding protein at the synapse.

Various approaches have been taken to study the function of prion proteins. Biochemical methods were applied to search for a binding partner of PrPC which is attached to the cell surface by a glycosylphosphatidylinositol GPI anchor (1). The glial fibrillary acidic protein was one of the first possible binding partners to be described (2) followed by Bcl-2 (3,4), molecular chaperones (5), amyloid precursor-like protein 1 (6), the 37-kDa laminin receptor (7) and a 66-kDa membrane protein which has not been characterized in more detail (8). However, it has not been possible to show any biological significance for PrPC binding of these proteins. Based on biochemical analyses of chicken PrPC, Harris et al. (9) hypothesized that PrPC may play a role in the regulation of the expression of cholinergic receptors at the neuromuscular endplate.

Function of PrP(C) as a copper-binding protein at the synapse.

The prion protein (PrP(C)) shows cooperative copper binding of the N-terminal octarepeat (PHGGGWGO) x4. In brain homogenates, PrP(C) is found in highest concentration in synaptosomal fractions. Mice devoid of PrP(C) (Prnp0/0 mice) show synaptosomal copper concentrations diminished by 50% as compared to normal mice. PrP(C) in the synaptic cleft may serve as a copper buffer. Alternatively it may play a role in the re-uptake of copper into the presynapse or may be of structural importance for the N-terminus and thus may influence binding of PrP(C) to other proteins.

Evidence of presynaptic location and function of the prion protein.

The prion protein (PrP(C)) is a copper-binding protein of unknown function that plays an important role in the etiology of transmissible spongiform encephalopathies. Using morphological techniques and synaptosomal fractionation methods, we show that PrP(C) is predominantly localized to synaptic membranes. Atomic absorption spectroscopy was used to identify PrP(C)-related changes in the synaptosomal copper concentration in transgenic mouse lines. The synaptic transmission in the presence of H(2)O(2), which is known to be decomposed to highly reactive hydroxyl radicals in the presence of iron or copper and to alter synaptic activity, was studied in these animals. The response of synaptic activity to H(2)O(2) was found to correlate with the amount of PrP(C) expression in the presynaptic neuron in cerebellar slice preparations from wild-type, Prnp(0/0), and PrP gene-reconstituted transgenic mice. Thus, our data gives strong evidence for the predominantly synaptic location of PrP(C), its involvement in the regulation of the presynaptic copper concentration, and synaptic activity in defined conditions.

Ethylene plays multiple nonprimary roles in modulating the gravitropic response in tomato.

Ethylene is known to interact with auxin in regulating stem growth, and yet evidence for the role of ethylene in tropic responses is contradictory. Our analysis of four mutants of tomato (Lycopersicon esculentum) altered in their response to gravity, auxin, and/or ethylene revealed concentration-dependent modulation of shoot gravitropism by ethylene. Ethylene inhibitors reduce wild-type gravicurvature, and extremely low (0.0005-0.001 microliter L-1) ethylene concentrations can restore the reduced gravitropic response of the auxin-resistant dgt (diageotropica) mutant to wild-type levels. Slightly higher concentrations of ethylene inhibit the gravitropic response of all but the ethylene-insensitive nr (never-ripe) mutant. The gravitropic responses of nr and the constitutive-response mutant epi (epinastic) are slightly and significantly delayed, respectively, but otherwise normal. The reversal of shoot gravicurvature by red light in the lz-2 (lazy-2) mutant is not affected by ethylene. Taken together, these data indicate that, although ethylene does not play a primary role in the gravitropic response of tomato, low levels of ethylene are necessary for a full gravitropic response, and moderate levels of the hormone specifically inhibit gravicurvature in a manner different from ethylene inhibition of overall growth.

The cellular prion protein binds copper in vivo.

The normal cellular form of prion protein (PrPC) is a precursor to the pathogenic protease-resistant forms (PrPSc) believed to cause scrapie, bovine spongiform encephalopathy (BSE) and Creutzfeldt-Jakob disease. Its amino terminus contains the octapeptide PHGGGWGQ, which is repeated four times and is among the best-preserved regions of mammalian PrPC. Here we show that the amino-terminal domain of PrPC exhibits five to six sites that bind copper (Cu(II)) presented as a glycine chelate. At neutral pH, binding occurs with positive cooperativity, with binding affinity compatible with estimates for extracellular, labile copper. Two lines of independently derived PrPC gene-ablated (Prnp0/0) mice exhibit severe reductions in the copper content of membrane-enriched brain extracts and similar reductions in synaptosomal and endosome-enriched subcellular fractions. Prnp0/0 mice also have altered cellular phenotypes, including a reduction in the activity of copper/zinc superoxide dismutase and altered electrophysiological responses in the presence of excess copper. These findings indicate that PrPC can exist in a Cu-metalloprotein form in vivo.

Increase of intracellular free Ca2+ in microglia activated by prion protein fragment.

A synthetic peptide consisting of amino acid residues 106 to 126 of the human prion protein (PrPc) that forms fibrils in vitro is toxic to cultured neurons. We have previously shown that the neurotoxic effect of this peptide is related to microglia activation (Brown et al., 1996a). For closer insight into this process of activation, we investigated the effect of the peptide on the intracellular free Ca2+ concentration ([Ca2+]i) in cultured microglia using Fura-2. Cultured microglia from wild-type as well as from PrPc gene-ablated mice (Prn-p0/0) responded to exposure to PrP106-126 with an increase in intracellular free calcium within 30 min. We observed two types of responses. Both in wild-type and Prn-p0/0 mice about half of the tested cells presented a small and often transient calcium increase after peptide application which was found to be independent of the extracellular calcium concentration. However, a further 33% of wild-type cells showed a strong and often permanent calcium increase depending on the extracellular calcium concentration, which was only rarely observed in Prn-p0/0 cells. To determine whether the response depended on the activation state of the microglia, we also examined LPS-treated activated microglia. The character of the calcium response remained unchanged, but significantly fewer cells responded. Our findings demonstrate the earliest reaction of microglia to a PrP fragment known to date.