Insights into the evolutionary process of genome degradation

Studies of noncoding and pseudogene sequence diversity, particularly in Rickettsia, have begun to reveal the basic principles of genome degradation in microorganisms. Increasingly, studies of genes and genomes suggest that there has been an extensive amount of horizontal gene transfer among microorganisms. As this inflow of genetic material does not seem generally to have resulted in genome size expansions, however, degenerative processes must be at the very least as widespread as horizontal gene transfer. The basic principles of gene degradation and elimination that are being explored in Rickettsia are likely to be of major importance for our understanding of how microbial genomes evolve.     

Reproductive tactics under severe egg predation: an eider’s dilemma

Parental defence against predators may increase offspring survival but entail other costs. Egg predation is frequent early in the laying sequence of the common eider, which differs in this and in several other ways from most other waterfowl. We test the hypothesis that permanent presence at the nest from the second or third egg is an adaptation for reducing egg predation in eiders. Two other alternative hypotheses for lower predation at later nest stages are early predation loss of the most vulnerable nests and seasonal decrease in predation risk. Analyses of predation rates at the one-egg and later stages refute these two alternatives. Early nest attendance by eider females is estimated to increase clutch survival by about 20% in four-egg and 35% in five-egg clutches, albeit probably at a cost of smaller clutch size.     

Size and temperature dependent foraging capacities and metabolism: consequences for winter starvation mortality in fish

The foraging related capacities, energy requirements and the ability of individuals to withstand starvation are strongly dependent on body size and temperature. In this study, we estimated size-dependent foraging rates and critical resource density (CRD) in small Arctic char ( Salvelinus alpinus ) under winter conditions and compared these with previous observations under summer conditions. We investigated if starvation mortality is size-dependent in the laboratory, and we assessed the potential for winter growth and the occurrence and size dependency of winter mortality both in a large scale pond experiment and in natural lakes. The efficiency of foraging on macroinvertebrates increased with size but was lower at 4 than 12°C, still CRD was lower at 4 than 12°C as metabolic rates decreased faster than foraging efficiency with temperature. When starved, small char died before large and at rates which suggest that YOY char need to feed during winter to avoid starvation. Results from both our pond experiment and field study indicate that survival of YOY char over winter is high, despite severe winter conditions, because YOY char are able to feed and grow during winter. In seasonal environments with declining resources, the size scaling and temperature dependency of foraging and metabolic demands may provide conditions which can favour either small or large individuals. This size advantage dichotomy relates to that larger individual's by having a higher CRD are more likely to start starving, but once resource levels are below CRD for all size classes, small individuals starve to death at a higher rate. Negative size-dependent winter mortality from starvation is suggested to be more pronounced in species that are not adapted to feed at low temperatures and in species feeding on zooplankton, since zooplankton abundance, in contrast to macroinvertebrate abundance, is generally low during winter.     

Sexual selection and mate choice

The past two decades have seen extensive growth of sexual selection research. Theoretical and empirical work has clarified many components of pre- and postcopulatory sexual selection, such as aggressive competition, mate choice, sperm utilization and sexual conflict. Genetic mechanisms of mate choice evolution have been less amenable to empirical testing, but molecular genetic analyses can now be used for incisive experimentation. Here, we highlight some of the currently debated areas in pre- and postcopulatory sexual selection. We identify where new techniques can help estimate the relative roles of the various selection mechanisms that might work together in the evolution of mating preferences and attractive traits, and in sperm-egg interactions.     

A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins

Time-resolved X-ray scattering has emerged as a powerful technique for studying the rapid structural dynamics of small molecules in solution. Membrane-protein-catalyzed transport processes frequently couple large-scale conformational changes of the transporter with local structural changes perturbing the uptake and release of the transported substrate. Using light-driven halide ion transport catalyzed by halorhodopsin as a model system, we combine molecular dynamics simulations with X-ray scattering calculations to demonstrate how small-molecule time-resolved X-ray scattering can be extended to the study of membrane transport processes. In particular, by introducing strongly scattering atoms to label specific positions within the protein and substrate, the technique of time-resolved wide-angle X-ray scattering can reveal both local and global conformational changes. This approach simultaneously enables the direct visualization of global rearrangements and substrate movement, crucial concepts that underpin the alternating access paradigm for membrane transport proteins.     

Studies of crystallinity of Scots pine and Norway spruce cellulose

The variation in the mass fraction of crystalline cellulose (crystallinity of wood), the intrinsic crystallinity of cellulose, and the thickness of cellulose crystallites in early wood of Norway spruce [Picea abies (L.) Karst.], and Scots pine (Pinus sylvestris L.) grown in Finland were studied using wide angle X-ray scattering and nuclear magnetic resonance spectroscopy. The mass fraction of crystalline cellulose in wood increased slightly with the distance from the pith and was about 30±4% in mature wood of both species. The crystallinity of cellulose and the thickness of cellulose crystallites were almost constant for both species. The crystallinity of cellulose was 52±3% for both species and the average thickness of the cellulose crystallites was 32±1 Å and 31±1 Å for Norway spruce and Scots pine, respectively. The mass fraction of cellulose in wood, calculated from the crystallinity values, increased with the distance from the pith for both species.     

Estimating the frequency of Asian cytochrome B haplotypes in standard European and local Spanish pig breeds

Mitochondrial DNA has been widely used to perform phylogenetic studies in different animal species. In pigs, genetic variability at the cytochrome B gene and the D-loop region has been used as a tool to dissect the genetic relationships between different breeds and populations. In this work, we analysed four SNP at the cytochrome B gene to infer the Asian (A1 and A2 haplotypes) or European (E1 and E2 haplotypes) origins of several European standard and local pig breeds. We found a mixture of Asian and European haplotypes in the Canarian Black pig (E1, A1 and A2), German Piétrain (E1, A1 and A2), Belgian Piétrain (E1, A1), Large White (E1 and A1) and Landrace (E1 and A1) breeds. In contrast, the Iberian (Guadyerbas, Ervideira, Caldeira, Campanario, Puebla and Torbiscal strains) and the Majorcan Black pig breeds only displayed the E1 haplotype. Our results show that the introgression of Chinese pig breeds affected most of the major European standard breeds, which harbour Asian haplotypes at diverse frequencies (15–56%). In contrast, isolated local Spanish breeds, such as the Iberian and Majorcan Black pig, only display European cytochrome B haplotypes, a feature that evidences that they were not crossed with other Chinese or European commercial populations. These findings illustrate how geographical confinement spared several local Spanish breeds from the extensive introgression event that took place during the 18th and 19th centuries in Europe.     

Characterization of 111In and 177Lu-labeled antibodies binding to CD44v6 using a novel automated radioimmunoassay

Targeted cancer therapies rely on bifunctional molecules, typically a protein that specifically recognizes tumor cells and a toxic component which is linked to the protein. Therefore, development of such therapies includes detailed characterizations of protein-cell interactions in order to find a good targeting agent. Knowledge of factors such as antibody-antigen specificity, as well as cellular uptake, retention and affinity of the antibody are necessary in order to be successful.In this paper, we have used a novel instrument, LigandTracer Yellow, to characterize the interactions of (111)In and (177)Lu-labeled monoclonal antibodies (MAbs) with CD44v6. Uptake studies with varying specific radioactivity of the chimeric MAb U36 and with an irrelevant antibody for the CD44v6 receptor verified the reliability of the method, as well as the specificity of the antibody-receptor binding. Uptake, retention, and affinity were very similar for the (111)In and (177)Lu-labeled conjugate, and were in line with earlier studies using manual methods. The fact that no adverse effects from labeling were seen, together with the high retention, could make these conjugates promising candidates for imaging and therapy of certain cancer types in the future. The novel LigandTracer technology reduced the workload and reagent spending while providing data with superior time resolution. The obtained results were in agreement with previously reported findings. In addition the real-time detection and higher time resolution made more detailed studies of the interactions possible.     

Voltage-induced gating of the mechanosensitive MscL ion channel reconstituted in a tethered lipid bilayer membrane

The mechanosensitive (MS) ion channel is gated by changes in bilayer deformation. It is functional without the presence of any other proteins and gating of the channel has been successfully achieved using conventional patch clamping techniques where a voltage has been applied together with a pressure over the membrane. Here, we have for the first time analyzed the large conducting (MscL) channel in a supported membrane using only an external electrical field. This was made possible using a newly developed technique utilizing a tethered lipid bilayer membrane (tBLM), which is part of an engineered microelectronic array chip. Single ion channel activity characteristic for MscL was obtained, albeit with lower conductivity. The ion channel was gated using solely a transmembrane potential of 300 mV. Computations demonstrate that this amount of membrane potential induces a membrane tension of 12 dyn/cm, equivalent to that calculated to gate the channel in patch clamp from pressure-induced stretching of the bilayer. These results strengthen the supposition that the MscL ion channel gates in response to stress in the lipid membrane rather than pressure across it. Furthermore, these findings illustrate the possibility of using the MscL as a release valve for engineered membrane devices; one step closer to mimicking the true function of the living cell.