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.     

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.     

Trees and/or networks to display intraspecific DNA sequence variation?

Phylogenetic trees and networks are both used in the scientific literature to display DNA sequence variation at the intraspecific level. Should we rather use trees or networks? I argue that the process of inferring the most parsimonious genealogical relationships among a set of DNA sequences should be dissociated from the problem of displaying this information in a graph. A network graph is probably more appropriate than a strict consensus tree if many alternative, equally most parsimonious, genealogies are to be included. Within the maximum parsimony framework, current phylogenetic inference and network‐building algorithms are both unable to guarantee the finding of all most parsimonious (MP) connections. In fact, each approach can find MP connections that the other does not. Although it should be possible to improve at least the maximum parsimony approach, current implementations of these algorithms are such that it is advisable to use both approaches to increase the probability of finding all possible MP connections among a set of DNA sequences.     

Reversible and irreversible modifications ofβ-lactoglobulin upon exposure to heat

Modifications in the exposure to the solvent of hydrophobic residues, changes in their organization into surface hydrophobic patches, and alterations in the dimerization equilibrium of-lactoglobulin upon thermal treatment at neutralpH were studied. Exposure of tryptophan residues was temperature dependent and was essentially completed on the time scale of seconds. Reorganization of generic hydrophobic protein patches on the protein surface was monitored through binding of 1,8-anilinonaphthalenesulfonate, and was much slower than changes in tryptophan exposure. Different phases in surface hydrophobicity changes were related to the swelling and the subsequent collapse of the protein, which formed a metastable swollen intermediate. Heat treatment of-lactoglobulin also resulted in the formation of soluble oligomeric aggregates. The aggregation process was studied as a function of temperature, demonstrating that (i) dimer dissociation was a necessary step in a sequential polymerization mechanism and (ii) cohesion of hydrophobic patches was the major driving force for aggregation.     

The CTLA-4 +49 A/G and ?318 C/T polymorphisms and susceptibility to asthma: a meta-analysis

The aim of this study was to explore whether cytotoxic T lymphocyte antigen-4 (CTLA-4) +49 A/G, and -318 C/T polymorphisms confer susceptibility to asthma. A meta-analysis was conducted on the associations between the CTLA-4 +49 A/G, and -318 C/T polymorphisms and asthma using; (1) allele contrast, (2) the recessive model, (3) the dominant model, and (4) the additive model. Eight studies on the CTLA-4 polymorphisms and asthma involving 2,330 patients with asthma and 1,743 control subjects were included in this meta-analysis. The meta-analysis revealed an association between asthma and the CTLA-4 +49 A/G polymorphism under the dominant model in Asians (OR = 0.758, 95 % CI = 0.599-0.958, p = 0.020). Stratification by age indicated an association between the CTLA-4 +49 GG+GA genotype and asthma in children (OR = 0.690, 95 % CI = 0.497-0.957, p = 0.026), but not in adults (OR = 0.837, 95 % CI = 0.598-1.172, p = 0.300). Furthermore, stratification by atopy status indicated an association between the CTLA-4 +49 G allele and atopic asthma (OR = 0.639, 95 % CI = 0.464-0.881, p = 0.006), but not non-atopic asthma (OR = 0.706, 95 % CI = 0.385-1.294, p = 0.266). There was no association between asthma and the CTLA-4 -318 C/T polymorphism for the whole population, or when stratified by ethnicity, age, or atopy status. This meta-analysis demonstrates that the CTLA-4 +49 A/G polymorphism confers susceptibility to asthma in Asians, children, patients with atopy status, but there was no association between the CTLA-4 -318 C/T polymorphism and asthma susceptibility.     

Are the diatoms Navicula sp. and Thalassiosira fluviatilis suitable to be fed to the benthic harpacticoid copepod Tisbe biminiensis?

The objective of this study was to compare the influence of the diets of two diatoms, Navicula sp. (benthic) and Thalassiosira fluviatilis (planctonic), on the development, fecundity and survival of the harpacticoid copepod Tisbe biminiensis. In order to determine the optimal concentration of food, 35 egg-bearing females were submitted to six algal concentrations and controls (without food). After 24 h, the content of the recipients was fixed with 4% formalin and then fecal pellets produced by each female were counted and measured. The larval development was studied by surveying 50 nauplii on each diet individually until the adult stage, at intervals of 6 h. The cast exoskeletons were removed to count the number of segments and for measurement. The fecundity was obtained counting the naupliar production every 48 h of groups containing 10 females in different algal concentrations in both diets. The diet influence on fecundity was tested by submitting four groups of 10 females fed on optimal algal concentrations based on the fecal pellet experiments. In the Navicula sp. concentration of 0.4 μg Chl-a/ml, considered to be optimal for fecal pellets production, the diatoms were shown toxic, resulting in a low survival rate and inhibiting the egg production of copepods. The optimal concentration considering fecundity was estimated to be 0.1 μg Chl-a/ml for both diets. Copepods fed on Navicula sp. presented a faster development rate and higher naupliar production compared to copepods fed on T. fluviatilis. Size and survival did not vary significantly among diets. The algal concentration interfered significantly in the reproductive success of females. Both very low and very high algal concentrations reduced reproductive success. Concluding, the benthic diatom Navicula sp. was more favorable to the copepod T. biminiensis than the planktonic diatom T. fluviatilis.     

Papillomaviruses—to vaccination and beyond

High risk human papillomavirus (HPV) types 16 and 18 DNAs were initially identified in 1983-1984. Subsequently the DNA of several other high risk HPV types has been identified. HPV 16 is present in more than 50% of cervical cancer biopsies, and HPV 18 is close to 20%. Some geographic variations exist in the prevalence of HPV high risk types: e.g. HPV 45 is more frequently observed in equatorial Africa, whereas types 58 and 52 have been more often found in East Asia. Molecular as well as epidemiological studies demonstrate that high risk HPV are indeed the causative agents for cervical cancer, they are also involved in other anogenital cancers, and in 25-30% of oropharyngeal carcinomas. Some of the mechanistic aspects are discussed in this review.     

Expression of Oct4 in HCC and modulation to wnt/β-catenin and TGF-β signal pathways

Hepatocellular carcinoma (HCC) is considered as a disease of dysfunction of the stem cells. Studies on stem cells have demonstrated that Oct4 plays a pivotal role in embryo regulation. In order to understand the role of Oct4 in HCC and the relationship among Oct4 and wnt/β-catenin and TGF-β signal pathways, we have detected the expression of Oct4, Nanog, Sox2, STAT3 as well as the genes in wnt/β-catenin, and TGF-β families in HCC cell lines and in tumor specimens from HCC patients. The authors found that Oct4 was expressed in all of the four HCC cell lines and the tumor specimens from HCC patients. Some other genes were also expressed in them with different level including Nanog, Sox2, STAT3 and TCF3, wnt10b, β-catenin, ELF, Smad3 and Smad4. The ability of the clone formation and migration of the HepG2 decreased after Oct4 was knockdowned. Silencing of Oct4 and TCF3 in HCC cell line HepG2 revealed that there were complicated relationships among Oct4, wnt/β-catenin family and TGF-β family genes. Knockdowning Oct4 reduced the expression of TGF-β family genes ELF, Smad3, Smad4 and wnt/β-catenin family genes, wnt10b, and β-catenin but increased TCF3. In reverse, knockdowning TCF3 led to the increased expression of Oct4 and TGF-β family genes. In conclusion, the expression of Oct4 in HCC may play an important role as in stem cell. Because Oct4 improves not only the function of wnt/β-catenin, but also the TGF-β signal pathways, the significance of its expression in HCC might be more complicated than we evinced before.     

Global and Local Concerns: What Attitudes and Beliefs Motivate Farmers to Mitigate and Adapt to Climate Change?

In response to agriculture''s vulnerability and contribution to climate change, many governments are developing initiatives that promote the adoption of mitigation and adaptation practices among farmers. Since most climate policies affecting agriculture rely on voluntary efforts by individual farmers, success requires a sound understanding of the factors that motivate farmers to change practices. Recent evidence suggests that past experience with the effects of climate change and the psychological distance associated with people''s concern for global and local impacts can influence environmental behavior. Here we surveyed farmers in a representative rural county in California''s Central Valley to examine how their intention to adopt mitigation and adaptation practices is influenced by previous climate experiences and their global and local concerns about climate change. Perceived changes in water availability had significant effects on farmers'' intention to adopt mitigation and adaptation strategies, which were mediated through global and local concerns respectively. This suggests that mitigation is largely motivated by psychologically distant concerns and beliefs about climate change, while adaptation is driven by psychologically proximate concerns for local impacts. This match between attitudes and behaviors according to the psychological distance at which they are cognitively construed indicates that policy and outreach initiatives may benefit by framing climate impacts and behavioral goals concordantly; either in a global context for mitigation or a local context for adaptation.     

Clinical and immunological aspects of autoantibodies to RA33/hnRNP-A/B proteins — A link between RA,SLE and MCTD

Heterogeneous nuclear ribonucleoprotein (hnRNP) complexes are major constituents of the spliceosome. They are composed of approximately 30 different proteins which can bind to nascent pre-mRNA. Among these, the hnRNP-A/B proteins form a subgroup of highly related proteins consisting of two adjacent RNA binding domains (RBD) within the N-terminal parts, whereas the C-terminal halves contain almost 50% glycine residues. These proteins, in particular A2/RA33, are targeted by autoantibodies from patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), and mixed connective tissue disease (MCTD). In SLE anti-hnRNP antibodies frequently occur together with antibodies to U1 small nuclear RNP (U1-snRNP) and Sm, other proteins of the spliceosome. Preliminary epitope mapping studies have revealed major antibody binding sites in the RNA binding regions for all three diseases. Nevertheless, there is some indication of disease specific epitope recognition. Studies in animal models have demonstrated anti-RA33/hnRNP-A/B antibodies in lupus-prone mouse strains.Thus, autoantibodies to the spliceosomal hnRNP-A/B proteins are a common feature of RA, SLE, and MCTD. However, these diseases differ in their reactivities to other spliceosomal proteins, especially anti-U1 snRNP and Sm. Therefore, anti-RA33/hnRNP-A/B autoantibodies are not only valuable diagnostic markers but may also allow additional insights into the pathogenesis of rheumatic autoimmune diseases.Abbreviations AS ankylosing spondylitis - hnRNP heterogeneous nuclear ribonucleoprotein - MCTD mixed connective tissue disease - PSA psoriatic arthropathy - RA rheumatoid arthritis - RBD RNA binding domain - SLE systemic lupus erythematosus - snRNP small nuclear ribonucleoprotein     

Thyroid hormone and cardiac repair/regeneration: from Prometheus myth to reality?

Nature's models of repair and (or) regeneration provide substantial evidence that a natural healing process may exist in the heart. The potential for repair and (or) regeneration has been evolutionarily conserved in mammals, and seems to be restricted to the early developmental stages. This window of regeneration is reactivated during the disease state in which fetal gene reprogramming occurs in response to stress. Analogies exist between the damaged and developing heart, indicating that a regulatory network that drives embryonic heart development may control aspects of heart repair and (or) regeneration. In this context, thyroid hormone (TH), which is a critical regulator of the maturation of the myocardium, appears to have a reparative role later in adult life. Changes in TH - thyroid hormone receptor (TR) homeostasis govern the return of the injured myocardium to the fetal phenotype. Accordingly, TH can induce cardiac repair and (or) regeneration by reactivating developmental gene programming. As a proof of concept in humans, TH is found to be an independent determinant of functional recovery and mortality after myocardial infarction. The potential of TH to regenerate and (or) repair the ischemic myocardium is now awaited to be tested in clinical trials.     

Lung epithelial-C/EBPβ contributes to LPS-induced inflammation and its suppression by formoterol

Muscle mass is related to higher bone mass and a reduction in fracture risk. However, the interactions between muscle tissues and bone metabolism are incompletely understood and there might be some humoral factors that are produced in muscle tissues and exhibit bone anabolic activity. We therefore investigated the role of FAM5C in osteoblast differentiation and the interactions between muscle and bone. A reduction of endogenous FAM5C by siRNA reduced the levels of osterix, alkaline phosphatase (ALP) and osteocalcin (OCN) mRNA as well as the levels of type 1 collagen and β-catenin in mouse osteoblastic MC3T3-E1 cells and mouse calvarial osteoblasts, although FAM5C overexpression significantly antagonized the levels of osterix, ALP and OCN mRNA induced by bone morphogenetic protein-2 in C2C12 cells. The conditioned medium from FAM5C-overexpressed and -suppressed C2C12 cells increased and decreased the levels of osterix, ALP and OCN mRNA in MC3T3-E1 cells, respectively. In conclusion, the present study is the first to show that FAM5C enhances osteoblast differentiation in differentiated osteoblasts, and that the effects of the conditioned medium from FAM5C-modulated myoblastic cells were positively correlated with the effects of FAM5C on osteoblast phenotype in osteoblasts. FAM5C might be an important humoral bone anabolic factor produced from muscle cells.     

The KDEL receptor couples to Gαq/11 to activate Src kinases and regulate transport through the Golgi

Membrane trafficking involves large fluxes of cargo and membrane across separate compartments. These fluxes must be regulated by control systems to maintain homoeostasis. While control systems for other key functions such as protein folding or the cell cycle are well known, the mechanisms that control secretory transport are poorly understood. We have previously described a signalling circuit operating at the Golgi complex that regulates intra-Golgi trafficking and is initiated by the KDEL receptor (KDEL-R), a protein previously known to mediate protein recycling from the Golgi to the endoplasmic reticulum (ER). Here, we investigated the KDEL-R signalling mechanism. We show that the KDEL-R is predicted to fold like a G-protein-coupled receptor (GPCR), and that it binds and activates the heterotrimeric signalling G-protein Gα(q/11) which, in turn, regulates transport through the Golgi complex. These findings reveal an unexpected GPCR-like mode of action of the KDEL-R and shed light on a core molecular control mechanism of intra-Golgi traffic.     

Preparation and characterization of novel pyrrol-3-ones attached to α/β-amino acids, esters and amides

Summary. Various α/β amino acid derivatives 5 were attached to compounds 3 to yield 2,3-dihydro-1H-pyrrol-3-ones amino acids derivatives 6. This rare heterocyclic amino acid skeleton including the pyrrolo[1,2-b][1,3]oxazol moiety was also successfully prepared in the esteric form. The structure of the new compounds was characterized by spectroscopic methods.     

TNF/LTα double knockout mice display abnormal inflammatory and regenerative responses to acute and chronic liver injury

Following acute liver injury, hepatocytes divide to facilitate regeneration. However, during chronic injury, hepatocyte proliferation is typically blocked and repair is mediated through liver progenitor (oval) cells. Signalling of the p55 tumour necrosis factor (TNF) receptor is central to these processes. Two ligands for p55 are known: TNF and lymphotoxin-alpha (LT). However, one study suggests that another exists that mediates liver injury following viral challenge. We have therefore investigated whether ligands other than TNF and LT are required for liver regeneration following either acute or chronic injury. Wild-type and double TNF/LT knockout (TNF^–/–LT^–/–) mice were subjected to either partial hepatectomy (PHx) or a choline-deficient ethionine-supplemented (CDE) diet. Proliferating hepatocytes, oval cells and inflammatory cells were identified and quantified in liver sections by immunohistochemistry. Liver inflammatory cells were characterised by cell surface antigen expression. Liver damage and mortality were monitored. Both hepatocyte and oval cell proliferation was reduced in TNF^–/–LT^–/– mice. Lymphocyte clusters were evident in all TNF^–/–LT^–/– livers and were heterogeneous, comprising B and T lymphocytes. PHx evoked liver inflammation in TNF^–/–LT^–/– but not wild-type mice, whereas no difference was apparent between genotypes in CDE experiments. Thus, TNF/LT signalling mediates liver regeneration involving both hepatocytes and progenitor cells. The hyper-inflammatory response following PHx in TNF^–/–LT^–/– animals, which is absent following CDE-induced injury, demonstrates that the two forms of liver injury evoke discrete inflammatory responses and provides a model in which such differences can be examined further.