Structure of casein micelles studied by small-angle neutron scattering

The structure of casein micelles has been studied by small-angle neutron scattering and static light scattering. Alterations in structure upon variation of pH and scattering contrast, as well as after addition of chymosin, were investigated. The experimental data were analyzed by a model in which the casein micelle consists of spherical submicelles. This model gave good agreement with the data and gave an average micellar radius of about 100–120 nm and a submicellar radius of about 7 nm both with a polydispersity of about 40–50%. The contrast variation indicated that the scattering length density of the submicelles was largest at the center of the submicelles. The submicelles were found to be closely packed, the volume fraction varying slightly with pH. Upon addition of chymosin the submicellar structure remained unchanged within the experimental accuracy. Correspondence to: S. Hansen     

Visibility conditions and diel period affect small-scale spatio-temporal behaviour of pike Esox lucius in the absence of prey and conspecifics

Pike Esox lucius in the absence of prey and conspecifics were shown to have the highest habitat-change activity during dusk and to decrease preference for complex habitats in turbid water. As the behaviours indicate routine responses in the absence of behavioural interactions, E. lucius spatio-temporal distributions should be directly affected and thereby more easily assessed and avoided by prey, with potential consequences for encounter rates.     

Spotting and validation of a genome wide oligonucleotide chip with duplicate measurement of each gene

The quality of DNA microarray based gene expression data relies on the reproducibility of several steps in a microarray experiment. We have developed a spotted genome wide microarray chip with oligonucleotides printed in duplicate in order to minimise undesirable biases, thereby optimising detection of true differential expression. The validation study design consisted of an assessment of the microarray chip performance using the MessageAmp and FairPlay labelling kits. Intraclass correlation coefficient (ICC) was used to demonstrate that MessageAmp was significantly more reproducible than FairPlay. Further examinations with MessageAmp revealed the applicability of the system. The linear range of the chips was three orders of magnitude, the precision was high, as 95% of measurements deviated less than 1.24-fold from the expected value, and the coefficient of variation for relative expression was 13.6%. Relative quantitation was more reproducible than absolute quantitation and substantial reduction of variance was attained with duplicate spotting. An analysis of variance (ANOVA) demonstrated no significant day-to-day variation.     

Plio-Pleistocene climate change and geographic heterogeneity in plant diversity–environment relationships

Plio‐Pleistocene climate change may have induced geographic heterogeneity in plant species richness–environment relationships in Europe due to greater in situ species survival and speciation rates in southern Europe. We formulate distinct hypotheses on how Plio‐Pleistocene climate change may have affected richness–topographic heterogeneity and richness–water‐energy availability relationships, causing steeper relationships in southern Europe. We investigated these hypotheses using data from Atlas Florae Europaeae on the distribution of 3069 species and geographically weighted regression (GWR). Our analyses showed that plant species richness generally increased with topographic heterogeneity (ln‐transformed altitudinal range) and actual evapotranspiration (AET). We also found evidence for strong geographic heterogeneity in the species richness–environment relationship, with a greater increase in species richness with increasing topographic heterogeneity in southern Europe (mean standardized local slope 0.610±0.245 SD in southern Europe, but only 0.270±0.175 SD in northern Europe). However, the local AET slopes were, at most, weakly different between the two regions, and their pattern did not conform to predictions, as there was a band of high local slopes across southern‐central northern Europe. This band broadly matches the transition between the temperate and boreal zones and may simply reflect the fact that few species tolerate the boreal climate. We discuss the potential explanations for the contrasting findings for the two richness–environment relationships. In conclusion, we find support for the idea that Plio‐Pleistocene climate change may sometimes affect current species richness–environment relationships via its effects on regional species pools. However, further studies integrating information on species ages and clade differentiation rates will be needed to substantiate this interpretation. On a general level, our results indicate that although strong richness–environment relationships are often found in macroecological studies, these can be contingent upon the historical constraints on the species pool.     

Geography,topography, and history affect realized‐to‐potential tree species richness patterns in Europe

Environmental conditions and biotic interactions are generally thought to influence local species richness. However, immigration and the evolutionary and historical factors that shape regional species pools should also contribute to determining local species richness because local communities arise by assembly from regional species pools. Using the European tree flora as our study system, we implemented a novel approach to assess the relative importance of local and regional mechanisms that control local species richness. We first identified species pools that tolerate particular local environments and quantified the proportion of the pool that is present locally, i.e. the realized/potential (R/P) richness ratio. Because no consensus exists on how to estimate potential richness, we estimated it using three different approaches. Using these three estimates separately and in a combined ensemble estimate, we then analyzed the effects of potential drivers on R/P richness ratios. We predicted that the R/P richness ratio would 1) increase with decreasing distance from glacial refugia (accessibility), 2) and be generally low in geographically fragmented southern Europe because of dispersal limitation; 3) increase with actual evapotranspiration because greater availability of water and energy promotes local population persistence; and 4) increase with topographic heterogeneity because it promotes local species coexistence and facilitates long‐term species survival. There was considerable variation among the three R/P richness ratio estimates, but we found consistent support for a negative effect of regional geographic fragmentation and a positive topographic effect. We also identified fairly broad support for the predicted effect of accessibility. We conclude that local tree assemblages in Europe often fail to realize a large proportion of the potential richness held in the regional species pool, partially reflecting their geographical, historical, and environmental circumstances. The dispersal‐related effects of geographic fragmentation and accessibility exemplify regional controls that combine with local ecological sorting to determine local species richness.     

Crystal structure of a transfer‐ribonucleoprotein particle that promotes asparagine formation

Four out of the 22 aminoacyl‐tRNAs (aa‐tRNAs) are systematically or alternatively synthesized by an indirect, two‐step route requiring an initial mischarging of the tRNA followed by tRNA‐dependent conversion of the non‐cognate amino acid. During tRNA‐dependent asparagine formation, tRNA^Asn promotes assembly of a ribonucleoprotein particle called transamidosome that allows channelling of the aa‐tRNA from non‐discriminating aspartyl‐tRNA synthetase active site to the GatCAB amidotransferase site. The crystal structure of the Thermus thermophilus transamidosome determined at 3 Å resolution reveals a particle formed by two GatCABs, two dimeric ND‐AspRSs and four tRNAs^Asn molecules. In the complex, only two tRNAs are bound in a functional state, whereas the two other ones act as an RNA scaffold enabling release of the asparaginyl‐tRNA^Asn without dissociation of the complex. We propose that the crystal structure represents a transient state of the transamidation reaction. The transamidosome constitutes a transfer‐ribonucleoprotein particle in which tRNAs serve the function of both substrate and structural foundation for a large molecular machine.     

Radioresponsiveness at low doses: hyper-radiosensitivity and increased radioresistance in mammalian cells

The rationale for and importance of research on effects after radiation at "low doses" are outlined. Such basic radiobiological studies on induction of repair enzymes, protective mechanisms, priming, and hypersensitivity are certainly all relevant to treatment of cancer (see Section 1, Studies at low doses - relevance to cancer treatment). Included are examples from many groups, using various endpoints to address the possibility of an induced resistance, which has been compared to the adaptive response [M.C. Joiner, P. Lambin, E.P. Malaise, T. Robson, J.E. Arrand, K.A. Skov, B. Marples, Hypersensitivity to very low single radiation doses: its relationship to the adaptive response and induced radioresistance, Mutat. Res. 358 (1996) 171-183.]. This is not intended to be an exhaustive review--rather a re-introduction of concepts such as priming and a short survey of molecular approaches to understanding induced resistance. New data on the response of HT29 cells after treatment (priming) with co-cultured activated neutrophils are included, with protection against X-rays (S1). Analysis of previously published results in various cells lines in terms of increased radioresistance (IRR)/intrinsic sensitivity are presented which complement a study on human tumour lines [P. Lambin, E.P. Malaise, M.C. Joiner, Might intrinsic radioresistance of human tumour cells be induced by radiation?, Int. Radiat. Biol. 69 (1996) 279-290].It is not feasible to extrapolate to low doses from studies at high doses. The biological responses probably vary with dose, LET, and have variable time frames. The above approaches may lead to new types of treatment, or additional means to assess radioresponsiveness of tumours. Studies in many areas of biology would benefit from considerations of different dose regions, as the biological responses vary with dose. There may also be some implications in the fields of radiation protection and carcinogenesis, and the extensions of concepts of hyper-radiosensitivity (HRS)/IRR extended to radiation exposure are considered in Section 2, Possible relevance of IRR concepts to radiation exposure (space). More knowledge on inducible responses could open new approaches for protection and means to assess genetic predisposition. Many endpoints are used currently--clonogenic survival, mutagenesis, chromosome aberrations and more direct--proteins/genes/functions/repair/signals, as well as different biological systems. Because of scant knowledge of the relevant aspects at low doses, such as inducible/protective mechanisms, threshold, priming, dose-rate effects, LET within one system, it is still too early to draw conclusions in the area of radiation exposure. Technological advances may permit much needed studies at low doses in the areas of both treatment and protection.     

Crystal structure of the covalent intermediate of amylosucrase from Neisseria polysaccharea

The alpha-retaining amylosucrase from the glycoside hydrolase family 13 performs a transfer reaction of a glucosyl moiety from sucrose to an acceptor molecule. Amylosucrase has previously been shown to be able to use alpha-D-glucopyranosyl fluoride as a substrate, which suggested that it could also be used for trapping the reaction intermediate for crystallographic studies. In this paper, the crystal structure of the acid/base catalyst mutant, E328Q, with a covalently bound glucopyranosyl moiety is presented. Sucrose cocrystallized crystals were soaked with alpha-D-glucopyranosyl fluoride, which resulted in the trapping of a covalent intermediate in the active site of the enzyme. The structure is refined to a resolution of 2.2 A and showed that binding of the covalent intermediate resulted in a backbone movement of 1 A around the location of the nucleophile, Asp286. This structure reveals the first covalent intermediate of an alpha-retaining glycoside hydrolase where the glucosyl moiety is identical to the expected biologically relevant entity. Comparison to other enzymes with anticipated glucosylic covalent intermediates suggests that this structure is a representative model for such intermediates. Analysis of the active site shows how oligosaccharide binding disrupts the putative nucleophilic water binding site found in the hydrolases of the GH family 13. This reveals important parts of the structural background for the shift in function from hydrolase to transglycosidase seen in amylosucrase.