En route to a genome-based classification of Archaea and Bacteria?

Given the considerable promise whole-genome sequencing offers for phylogeny and classification, it is surprising that microbial systematics and genomics have not yet been reconciled. This might be due to the intrinsic difficulties in inferring reasonable phylogenies from genomic sequences, particularly in the light of the significant amount of lateral gene transfer in prokaryotic genomes. However, recent studies indicate that the species tree and the hierarchical classification based on it are still meaningful concepts, and that state-of-the-art phylogenetic inference methods are able to provide reliable estimates of the species tree to the benefit of taxonomy. Conversely, we suspect that the current lack of completely sequenced genomes for many of the major lineages of prokaryotes and for most type strains is a major obstacle in progress towards a genome-based classification of microorganisms. We conclude that phylogeny-driven microbial genome sequencing projects such as the Genomic Encyclopaedia of Archaea and Bacteria (GEBA) project are likely to rectify this situation.     

How to regulate a gene: to repress or to activate?

Gene-expression responses to an input can depend on growth conditions; in this issue, Sasson et al. (2012) show that this dependence is lower when the input results in a high degree of promoter occupancy.     

Some ecophysiological and historical approaches to species richness and calcicole/calcifuge behaviour — contribution to a debate

Species richness in vascular plants was related to the plants’ calcifuge or calcicole behaviour using documentation from forests and open-land vegetation at about one thousand sites in the southern parts of Sweden. It is concluded that vegetation of strongly acid soils (pH-KCl < 4.5) have fewer vascular plant species than comparable vegetation of other soils, whereas there are no consistent differences in species richness between slightly-moderately acid and calcareous sites. Low species richness is particularly related to high concentrations of Al³⁺ and H⁺ ions (either soil solution concentrations or concentrations of exchangeable ions), not to a lack of calcium carbonate. The majority of plant species are able to render the sparingly soluble phosphate, iron and manganese compounds of high-pH soils available, but they are unable to tolerate much Al³⁺ or H⁺. Acidicole (calcifuge) species have developed the power of tolerating Al³⁺ and H⁺, which may be considered a secondary property of plants, but they have lost the power of solubilizing critical mineral nutrients in high-pH soils. The reasons why these ecophysiological properties are inversely related in the current flora are obscure, difficult to account for experimentally and a main ecological problem. In areas with cool-temperate climates the flora was partly or mainly extinguished by the Pleistocene glaciations. Comparatively fewer calcifuge than calcicole species have, since then, had enough time to develop, and the number of calcifuges is lower, in spite of the fact that most natural and seminatural soils of these areas are nowadays acidic.     

CCN2/decorin interactions: a novel approach to combating fibrosis?

CCN2 (connective tissue growth factor, CTGF), a member of the CCN family is overexpressed in fibrotic disease and is essential for the development of experimental fibrosis. Drugs targeting CCN2 action may therefore prove to be useful anti-fibrotic approaches. CCN2 acts via integrins and heparan sulfate-containing proteoglycans (HSPGs). In a recent study, Vial and colleagues (2011) show that decorin can bind CCN2. A peptide corresponding to the leucine rich repeats peptide 12 region of decorin can neutralize CCN2-mediated activity on C2C12 cells in vitro. Thus it is conceivable that this peptide could be used in the future as a novel antifibrotic approach.     

Senescence: a telomeric limit to immortality or a cellular response to physiologic stresses?

Cells entering a state of senescence undergo a irreversible cell cycle arrest, associated by a set of functional and morphological changes. Senescence occurs following telomeres shortening (replicative senescence) or exposure to other acute or chronic physiologic stress signals (a phenomenon termed stasis: stress or aberrant signaling-induced senescence). In this review, I discuss the pathways of cellular senescence, the mechanisms involved and the role that these pathways have in regulating the initiation and progression of cancer. Telomere-initiated senescence or loss of telomere function trigger focal recruitement of protein sensors of the DNA double-strand breaks leading to the activation of the DNA damage checkpoint responses and the tumour suppressor gene product, p53, which in turn induces the cell-cycle inhibitor, p21(WAF1). Loss of p53 and pRb function allows continued cell division despite increasing telomere dysfunction and eventually entry into telomere crisis. Immortalisation is an essential prerequisite for the formation of a tumour cell. Therefore, a developing tumour cell must circumvent at least two proliferative barriers--cellular senescence and crisis--to achieve neoplastic transformation. These barriers are regulated by telomere shortening and by the p16(INK4a)/Rb and p53 tumour suppressor pathways. Elucidation of the genes and emerging knowledge about the regulatory mechanisms that lead to senescence and determine the pattern of gene expression in senescent cells may lead to more effective treatments for cancer.     

Intra-Golgi transport: a way to a new paradigm?

The morpho-functional principles of intra-Golgi transport are, surprisingly, still not clear, which is in marked contrast to our advanced knowledge of the underlying molecular machineries. Recently, the conceptual and technological hindrances that had delayed progress in this area have been disappearing, and a cluster of powerful morphological techniques has been revealing new glimpses of the organization of traffic in intact cells. Here, we discuss the new concepts around the present models of intra-Golgi transport.     

How does a Psittacanthus robustus Mart. population structure relate to a Vochysia thyrsoidea Pohl. host population?

Distribution of parasitic plants is directly linked with the distribution of host species and behavioral patterns of seed dispersers. Psittacanthus robustus (Loranthaceae) is a neotropical hemiparasite that mainly colonizes species of the family Vochysiaceae. Vochysia thyrsoidea is the main host of P. robustus and is commonly found in areas of cerrado rupestre (rocky savanna), an abundant vegetation in our study site. We conducted the study in the ecological park Parque Ecológico Quedas do Rio Bonito (PEQRB), over an area of 2.82 ha of cerrado rupestre. The objective of this work was to investigate population structure, parasitic behavior (mistletoe grip height and circumference of host branch), and spatial distribution of Psittacanthus robustus on a population of Vochysia thyrsoidea. We sampled 267 V. thyrsoidea individuals and found that the population had a random distribution pattern. Seventy-nine individuals (29.6% of the sample population) hosted the hemiparasite, to a total of 193 P. robustus individuals. The number of mistletoe individuals per host plant ranged between 1 and 12. The V. thyrsoidea individuals most infested with mistletoes were those reaching greater heights. The correlation between height of host plant and preferred grip height was highly significant, with the preferred grip height being the uppermost portions of host plants. The crown size of P. robustus individuals ranged between 10 and 230 cm. The main disperser of P. robustus fruit was found to be swallow-tanager Tersina viridis viridis. Its activities led to a clumped pattern of spatial distribution of the hemiparasite along with higher infestation in larger trees.     

The BOS™ as a species-specific method to deliver baits to wild boar in a Mediterranean area

The impact of wild boar Sus scrofa and feral pigs on ecosystems and human activities is of interest worldwide. Bait-delivered pharmaceuticals such as contraceptives or disease vaccines are increasingly advocated to assist the management of such impacts. We evaluated the Boar-Operated-System (BOS?) to deliver baits to wild boar in a Mediterranean area with a large community of potential nontarget species. In a pre-trial phase (BOS? open), both wild boar and 12 nontarget species (wildlife and livestock) visited the BOS? and eight species consumed the baits. In the trial phase, when the BOS? were closed, only wild boar consumed baits. From pre-trial to trial, the rate of visits by nontarget species to the BOS? decreased significantly, but that of wild boar did not change. We observed that crested porcupines Hystrix cristata prevented the wild boar from using BOS?. We confirmed the effectiveness of BOS? to deliver baits selectively to wild boar in a Mediterranean area.     

Ecology – a science put to use

There is no lack of pretext for reviewing historically how ecologists have striven to gain the respect of scholars in their own and other fields, and to demonstrate the wider public-utility of their science. If self-serving, in terms of securing the scope and resources required to advance their studies in ecology, such activities have also been encouraged, and indeed commissioned, in the belief that a greater awareness and understanding of the natural world is essential for human wellbeing. Illustrative material is drawn from the British experience.     

How to kill a mocking bug?

All metazoans have evolved means to protect themselves from threats present in the environment: injuries, viruses, fungi, bacteria and other parasites. Insect protection includes innate physical barriers and both cellular and humoral responses. The insect innate immune response, best characterized in Drosophila melanogaster, is a rapid broad response, triggered by pathogen-associated molecular patterns (PAMPs) recognition, which produces a limited range of effectors that does not alter upon continued pathogen exposure and lacks immunological memory. The Drosophila response, particularly its humoral response, has been investigated by both low and high-throughput methods. Three signalling pathways conserved between insects and mammals have been implicated in this response: Toll (equivalent to mammalian TLR), Imd (equivalent to TNFalpha) and Hop (equivalent to JAK/STAT). This review provides an entry point to the insect immune system literature outlining the main themes in D. melanogaster bacterial pathogen detection and humoral and cellular immune responses. The Drosophila immune response is compared with other insects and the mammalian immune system.     

Root gravitropism: a complex response to a simple stimulus?

Roots avoid depleting their immediate environment of essential nutrients by continuous growth. Root growth is directed by environmental cues, including gravity. Gravity sensing occurs mainly in the columella cells of the root cap. Upon reorientation within the gravity field, the root-cap amyloplasts sediment, generating a physiological signal that promotes the development of a curvature at the root elongation zones. Recent molecular genetic studies in Arabidopsis have allowed the identification of genes that play important roles in root gravitropism. Among them, the ARG1 gene encodes a DnaJ-like protein involved in gravity signal transduction, whereas the AUX1 and AGR1 genes encode proteins involved in polar auxin transport. These studies have important implications for understanding the intra- and inter-cellular signaling processes that underlie root gravitropism.     

Switching TGFβ from a tumor suppressor to a tumor promoter

TGFβ acts as a potent tumor suppressor and tumor promoter in a context dependent manner. Tumor suppressive functions include inhibition of cell proliferation, induction of apoptosis and regulation of autophagy. As tumors develop they switch their response to TGFβ and utilise this factor as a potent promoter of cell motility, invasion, metastasis and tumor stem cell maintenance. These multifactorial tumor influencing actions of TGFβ involve regulation of an increasing number of signal transduction pathways employing a diverse range of signaling molecules. Understanding the molecular mechanisms of how tumor cells respond to TGFβ and switch their response to this cytokine during disease progression is vital for both the development and the informed use of potentially powerful TGFβ targeted therapeutics.     

Stasipatric speciation: resurrecting a system to bury a hypothesis?

The process of speciation remains a fundamental topic in evolutionary biology. Numerous models of speciation have been proposed and they are as diverse and colourful as the scientists who conceived them ( Coyne & Orr 2004 ). One of the more controversial theories has been the ‘stasipatric speciation’ model, proposed by the pioneering and influential cytogeneticist Michael White and his co‐workers ( White 1968 ; White et al. 1967 ). This is one of a number of speciation models whereby chromosomal rearrangements drive the speciation process. The inspiration for the theory of stasipatric speciation came from White’s karyotypic analyses of a group of Australian grasshoppers of the genus Vandiemenella ( White et al. 1967 ) ( Fig. 1 ). It has been exactly three decades since the last scientific publication on this group of grasshoppers, over which time the molecular revolution dramatically altered the landscape of evolutionary genetics. Kawakami and colleagues have successfully resurrected the Vandiemenella system ( Kawakami et al. 2009a, 2007 ) and in this issue they have applied modern molecular‐based techniques to reassess the validity of the stasipatric speciation model for this historically important group ( Kawakami et al. 2009b ).

Figure 1 Open in figure viewer PowerPoint The grasshopper (Vandiemenella viatica) that inspired Michael White to develop the stasipatric speciation model (photograph by Remko Leijs).