A comparison of immobilized pH gradient isoelectric focusing and strong-cation-exchange chromatography as a first dimension in shotgun proteomics

Recently, we have developed a high-resolution two-dimensional separation strategy for the analysis of complex peptide mixtures. This methodology employs isoelectric focusing of peptides on immobilized pH gradient (IPG) gels in the first dimension, followed by reversed-phase chromatography in the second dimension, and subsequent tandem mass spectrometry analysis. The traditional approach to this mixture problem employs strong-cation-exchange (SCX) chromatography in the first dimension. Here, we present a direct comparison of these two first-dimensional techniques using complex protein samples derived from the testis of Rattus norvegicus. It was found that the use of immobilized pH gradients (narrow range pH 3.5-4.5) for peptide separation in the first dimension yielded 13% more protein identifications than the optimized off-line SCX approach (employing the entire pI range of the sample). In addition, the IPG technique allows for a much more efficient use on mass spectrometer analysis time. Separation of a tryptic digest derived from a rat testis sample on a narrow range pH gradient (over the 3.5-4.5 pH range) yielded 7626 and 2750 peptides and proteins, respectively. Peptide and protein identification was performed with high confidence using SEQUEST in combination with a data filtering program employing pI and statistical based functions to remove false-positives from the data.     

Spatial patterns in the distribution of European springtails (Hexapoda: Collembola)

Using a large database on the spatial distribution of European springtails (Collembola) we investigated how range sizes and range distribution across European countries and major islands vary. Irrespective of ecological guild, islands tended to contain more endemic species than mainland countries. Nestedness and species co‐occurrence analysis based on country species lists revealed latitudinal and longitudinal gradients of species occurrences across Europe. Species range sizes were much more coherent and had fewer isolated occurrences than expected from a null model based on random colonization. We did not detect clear postglacial colonization trajectories that shaped the faunal composition across Europe. Our results are consistent with a multiregional postglacial colonization. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 498–506.     

Water interaction in paper cellulose fibres as investigated by NMR pulsed field gradient

In this paper, water diffusion coefficients were measured using NMR pulsed field gradient, on a variety of paper materials made from predominantly cellulose fibre and nanofibres, derived from wood, with different dimensions, internal porosity, and chemical composition. The moisture content ranged from 0.2 to 1.2 g of water/g of dry fibre. Diffusion measurements were made both in the plane and through the thickness of the sheet. All data was generally well fitted by a simple two component diffusion model. For moisture contents less than 0.55 and 0.85 g/g for measurements in the plane and through the thickness, respectively, it was found that both diffusion components increased approximately linearly with moisture content, with the faster diffusion coefficient being approximately five times larger than the smaller. The water appeared, within errors, to be evenly split between two components. The measured diffusion coefficients were not affected by fibre dimensions, internal structure or chemical composition, but were consistently higher when measured in the plane.     

The latitudinal position of peak marine diversity in living and fossil biotas

Aim Peak marine taxonomic diversity has only rarely occurred at or near the equator during the Phanerozoic Eon, in contrast to the present‐day pattern. This fundamental difference is difficult to reconcile because the latitude at which peak diversity occurs for living marine taxa has not yet been explicitly determined at a broad taxonomic and spatial scale. Here, we attempt to determine this value in order to compare the contemporary and fossil patterns directly. Location Our data are global in coverage. Methods We used a literature compilation of 149 present‐day marine latitudinal diversity gradients. We summed the number of marine taxa that exhibited peak diversity within 10° latitudinal bins. In addition, we recorded locality data, general habitat (benthic/pelagic), and the taxonomic level of the study organisms. Results We found that peak diversity for most sampled marine taxa currently occurs between 10° and 20° N, even after correcting for a Northern Hemisphere sampling bias. Moreover, this peak position is a global phenomenon: it is found across habitats and higher taxa, within all sampled ocean basins, and on both sides of the Atlantic and Pacific oceans. Benthic taxa, which dominate our data, exhibit one peak at 10°–20° N, while pelagic taxa exhibit a peak at 10°–20° N and an additional peak at 10°–20° S, producing a distinct trough at the equator. Main conclusions Our data indicate that peak marine diversity for many taxa is currently within 10°–20° N rather than at the equator, and that this is not likely to result from either undersampling at lower latitudes or the pattern being dominated by a particular taxon. Possible explanations may include a coincidence with the intertropical convergence zone, a mid‐domain effect, abundant shallow marine habitat, or high ocean temperatures at latitudes nearest the equator. Regardless of its exact cause, the position of peak diversity should be considered a fundamental feature of the latitudinal diversity gradient that must be accounted for within attempts to explain the latter’s existence.     

Sources of variation in larval parasitism of two sympatrically outbreaking birch forest defoliators

1. Studies of insect communities rarely support the parasitoid–host regulation hypothesis. Spatio‐temporal variation in parasitoid prevalence due to complex food web interactions or abiotic factors may prevent parasitoids from regulating hosts. 2. We examined the relative contribution of spatial (altitude) and temporal (years) sources to total variation in parasitoid prevalence rates in outbreaks of Epirrita autumnata Borkhausen and Operophtera brumata Linnaeus populations. We tested whether prevalence rates of generalist parasitoids were correlated between sympatric host populations and to what extent any of the parasitoids were host density dependent. 3. Four larval parasitoids (two specialists and two generalists) exhibited significantly structured spatio‐temporal dynamics over years and altitudes. The prevalence rates of one of the generalists were spatio‐temporally correlated between the two host species, while for the other they were not. 4. Three parasitoids showed tendencies for direct or delayed positive density dependence as expected from numerical and functional responses to their hosts. However, the effects were weak and minute compared to the variation attributed to year and altitude. 5. We conclude that unknown aspects of the larval parasitoid ecology that co‐vary with altitude and year in the study system dominate their prevalence dynamics and thus act to hinder density‐dependent responses that could potentially regulate host populations.     

Sexually selected skin colour is heritable and related to fecundity in a non-human primate

Sexual selection promotes the prevalence of heritable traits that increase an individual''s reproductive rate. Despite theoretically strong directional selection, sexually selected traits can show inter-individual variation. Here, we investigate whether red skin ornamentation, a rare example of a male mammalian trait involved in mate attraction, influences fecundity and is heritable in rhesus macaques (Macaca mulatta), and explore the mechanisms that are involved in maintaining trait variation. Interestingly, the trait is expressed by and is attractive to both sexes. We collected facial images of 266 free-ranging individuals and modelled skin redness and darkness to rhesus macaque vision. We used 20 years of genetic parentage data to calculate selection gradients on the trait and perform heritability analyses. Results show that males who were both darkly coloured and high-ranking enjoyed higher fecundity. Female skin redness was positively linked to fecundity, although it remains unclear whether this influences male selectiveness. Heritability explained 10–15% of the variation in redness and darkness, and up to 30% for skin darkness when sexes are considered separately, suggesting sex-influenced inheritance. Our results suggest that inter-individual variation is maintained through condition-dependence, with an added effect of balancing selection on male skin darkness, providing rare evidence for a mammalian trait selected through inter-sexual selection.     

Leveraging remote learning during the Covid‐19 pandemic to enhance student understanding of biodiversity

We evaluated whether individual nature‐based ecological (NBE) study used in tandem with group collaboration enhanced undergraduate student understanding of ecological concepts and pro‐environmental perceptions. In response to the Covid‐19 pandemic, we developed a multiweek unit on the latitude diversity gradient (LDG) for fully online instruction that leveraged the unique situation of students learning in disparate geographic locations. Student understanding of the LDG and pro‐environmental perceptions were assessed with surveys administered both pre‐ and post‐activity in an introductory‐level biology laboratory course. Student understanding of the geographic location where biodiversity is the highest was high prior to the start of the laboratory unit and exhibited only a small improvement after the unit. In contrast, students’ higher order thinking around the LDG was enhanced by the lab activity. Student environmental perceptions shifted toward ecocentric views and away from anthropocentric views after the laboratory unit. The greatest gains in ecological understanding and shifts toward ecocentric viewpoints occurred in the group of students who visited their field sites most often. Our results provide further evidence as to the value of NBE for the introductory biology laboratory, even in an online learning setting. The lab unit described in this study provides a potential approach to teaching ecology in an online format that could easily be adapted to fit the needs of a particular curriculum.     

Mass transfer effects on the reaction rate for heterogeneously distributed immobilized yeast cells

Here we examine the efficiency of different immobilized cell gradients applied to immobilized Saccharomyces cerevisiae fermenting glucose to ethanol. We developed a simulation model to fully study the competing effects of mass transfer hindrance and kinetics. It is based on a diffusion-reaction model and can be used to analyze the different cell concentration profiles inside an immobilized gel bead, in terms of effectiveness factors, productivity, and mass flux. The internal diffusion coefficient, which varies with the local cell concentration, as well as the external mass transfer, is taken into account when describing the efficiency. Although the diffusion hindrance is greater at higher cell concentrations, high cell concentration is still advantageous in the present case because the increase in reaction rate outweighs the diffusion hindrance. Thus, high cell concentrations contribute to increased productivity. The influence of the cell concentration gradient on the efficiency of the beads is negligible. Within the range of cell profiles studied it has been established that the location of the cells within the bead is of lesser importance. However, a steep cell gradient increases the importance of the external mass transfer.