Predicting polygynous settlement while incorporating varying female competitive strength

The rationale behind the polygyny threshold model is that thebreeding situation quality (BSQ) males have to offer femalesvaries, and that differences in BSQ offset females' costs ofsharing with other females, thus favoring polygynous settling.It predicts that the first chosen territories become polygynousfirst, and that breeding success of secondary and contemporarymonogamous females is similar. This is not generally found.Testing of the polygyny threshold model (PTM) assumes that femalesare equal competitors and distribute ideally free around availablebreeding resources, a condition probably not often met. If sharinga male is costly, and competitors differ in quality, weakerindividuals should experience degrees of competitive exclusion.Setting female competitive abilities proportional to arrivalorder, we use an individual-based interference-competition modelto examine settlement patterns. Shifts in the ratio of variancein interfemale competitiveness to interterritorial differencesin BSQ result in various settlement patterns, with differentpredictions concerning settlement order and fitness returns.We find support for the novel predictions from data on northernlapwing (Vanellus vanellus), starling (Sturnus vulgaris), piedflycatcher (Ficedula hypoleuca), and blue tit (Parus caeruleus).We suggest that before testing polygyny predictions, an evaluationof the settlement sequence should be made, which may help togenerate more accurate predictions. We argue that violationof the "equal female" assumption may explain much of the discrepancybetween predictions and empirical findings in previous testsof the PTM, and that secondary females in general have lowersuccess than do monogamous breeders because they are of lowerquality.     

Tensile properties of Arabidopsis cell walls depend on both a xyloglucan cross-linked microfibrillar network and rhamnogalacturonan II-borate complexes

The mechanical properties of plant organs depend upon anatomical structure, cell-cell adhesion, cell turgidity, and the mechanical properties of their cell walls. By testing the mechanical responses of Arabidopsis mutants, it is possible to deduce the contribution that polymers of the cell wall make to organ strength. We developed a method to measure the tensile parameters of the expanded regions of turgid or plasmolyzed dark-grown Arabidopsis hypocotyls and applied it to the fucose biosynthesis mutant mur1, the xyloglucan glycosyltransferase mutants mur2 and mur3, and the katanin mutant bot1. Hypocotyls from plants grown in the presence of increasing concentrations of dichlorobenzonitrile, an inhibitor of cellulose synthesis, were considerably weakened, indicating the validity of our approach. In order of decreasing strength, the hypocotyls of mur2 > bot1 and mur1 > mur3 were each found to have reduced strength and a proportionate reduction in modulus compared with wild type. The tensile properties of the hypocotyls and of the inflorescence stems of mur1 were rescued by growth in the presence of high concentrations of borate, which is known to cross-link the pectic component rhamnogalacturonan II. From comparison of the mechanical responses of mur2 and mur3, we deduce that galactose-containing side chains of xyloglucan make a major contribution to overall wall strength, whereas xyloglucan fucosylation plays a comparatively minor role. We conclude that borate-complexed rhamnogalacturonan II and galactosylated xyloglucan contribute to the tensile strength of cell walls.     

Purification,localization, and expression of human intestinal alkaline sphingomyelinase

Sphingomyelin (SM) metabolism in the gut may have an impact on colon cancer development. In this study, we purified alkaline sphingomyelinase (alk-SMase) from human intestinal content, and studied its location in the mucosa, expression in colon cancer, and function on colon cancer cells. The enzyme was purified by a series of chromatographies. The molecular mass of the enzyme is 60 kDa, optimal pH is 8.5, and isoelectric point is 6.6. Under optimal conditions, 1 mg of the enzyme hydrolyzed 11 mM SM per hour. The properties of the enzyme are similar to those of rat intestinal alk-SMase but not to those of bacterial neutral SMase. Immunogold electronmicroscopy identified the enzyme on the microvillar membrane in endosome-like structures and in the Golgi complexes of human enterocytes. The expression and the activity of the enzyme were decreased in parallel in human colon cancer tissues compared with the adjacent normal tissue. The enzyme inhibited DNA biosynthesis and cell proliferation dose dependently and caused a reduction of SM in HT29 cells. Intestinal alk-SMase is localized in the enterocytes, down-regulated in human colon cancer, and may have antiproliferative effects on colon cancer cells.     

Implementation and application of a versatile clustering tool for tandem mass spectrometry data

High-throughput proteomics experiments typically generate large amounts of peptide fragmentation mass spectra during a single experiment. There is often a substantial amount of redundant fragmentation of the same precursors among these spectra, which is usually considered a nuisance. We here discuss the potential of clustering and merging redundant spectra to turn this redundancy into a useful property of the dataset. To this end, we have created the first general-purpose, freely available open-source software application for clustering and merging MS/MS spectra. The application also introduces a novel approach to calculating the similarity of fragmentation mass spectra that takes into account the increased precision of modern mass spectrometers, and we suggest a simple but effective improvement to single-linkage clustering. The application and the novel algorithms are applied to several real-life proteomic datasets and the results are discussed. An analysis of the influence of the different algorithms available and their parameters is given, as well as a number of important applications of the overall approach.     

Sea surface temperature dictates movement and habitat connectivity of Atlantic cod in a coastal fjord system

While movements of organisms have been studied across a myriad of environments, information is often lacking regarding spatio‐seasonal patterning in complex temperate coastal systems. Highly mobile fish form an integral part of marine food webs providing linkages within and among habitats, between patches of habitats, and at different life stages. We investigated how movement, activity, and connectivity patterns of Atlantic cod (Gadus morhua) are influenced by dynamic environmental conditions. Movement patterns of 39 juvenile and subadult Atlantic cod were assessed in two coastal sites in the Swedish Skagerrak for 5 months. We used passive acoustic telemetry and network analysis to assess seasonal and spatial movement patterns of cod and their relationships to different environmental factors, using statistical correlations, analysis of recurrent spatial motifs, and generalized linear mixed models. Temperature, in combination with physical barriers, precludes significant connectivity (complex motifs) within the system. Sea surface temperature had a strong influence on connectivity (node strength, degree, and motif frequency), where changes from warmer summer waters to colder winter waters significantly reduced movement activity of fish. As the seasons changed, movement of fish gradually decreased from large‐scale (km) linkages in the summer to more localized movement patterns in the winter (limited to 100s m). Certain localized areas, however, were identified as important for connectivity throughout the whole study period, likely due to these multiple‐habitat areas fulfilling functions required for foraging and shelter. This study provides new knowledge regarding inshore movement dynamics of juvenile and subadult Atlantic cod that use complex, coastal fjord systems. The findings show that connectivity, seasonal patterns in particular, should be carefully considered when selecting conservation areas to promote marine stewardship.     

Estimation of cell numbers of methanotrophic bacteria in boreal peatlands based on analysis of specific phospholipid fatty acids

Abstract: Concentrations of two phospholipid fatty acids (PLFAs) specific for methane-oxidizing bacteria (16:1 ω8 and 18:1 ω8), were used to estimate the biomass and cell numbers of this group of bacteria in two Sphagnum-dominated boreal peatlands. Concentration ranges of 16:1 ω8 and 18:1 ω8 were 0.0–73 and 1.0–486 pmol g⁻¹ of wet peat, respectively. Concentrations in the peat of each fatty acid were positively correlated with the potential methane oxidation activity ( V _max), which was used as an independent estimate of methanotrophic biomass. This correlation suggests that the two PLFAs are good biomarkers for the population of methanotrophic bacteria in peatlands. Concentrations of the two PLFAs were transformed to cell numbers using conversion factors for the cell content of PLFAs, average cell volume and percentage of cellular dry matter. The total cell number of methanotrophic bacteria in peat samples from a range of sites and depths ranged between 0.3 and 51 × 10⁶ cells g⁻¹ of wet peat, with similar proportions of type I and type II methanotrophic bacteria in most samples. Within particular peat profiles, numbers of methanotrophic bacteria were highest around the level of the water table, implying that the supplies of methane and oxygen largely determine the biomass distribution of methanotrophic bacteria in this type of peatlands.     

PTP-3 phosphatase promotes intramolecular folding of SYD-2 to inactivate kinesin-3 UNC-104 in neurons

UNC-104 is the Caenorhabditis elegans homolog of kinesin-3 KIF1A known for its fast shuffling of synaptic vesicle protein transport vesicles in axons. SYD-2 is the homolog of liprin-α in C. elegans known to activate UNC-104; however, signals that trigger SYD-2 binding to the motor remain unknown. Because SYD-2 is a substrate of PTP-3/LAR PTPR, we speculate a role of this phosphatase in SYD–2-mediated motor activation. Indeed, coimmunoprecipitation assays revealed increased interaction between UNC-104 and SYD-2 in ptp-3 knockout worms. Intramolecular FRET analysis in living nematodes demonstrates that SYD-2 largely exists in an open conformation state in ptp-3 mutants. These assays also revealed that nonphosphorylatable SYD-2 (Y741F) exists predominately in folded conformations, while phosphomimicking SYD-2 (Y741E) primarily exists in open conformations. Increased UNC-104 motor clustering was observed along axons likely as a result of elevated SYD-2 scaffolding function in ptp-3 mutants. Also, both motor velocities as well as cargo transport speeds were visibly increased in neurons of ptp-3 mutants. Lastly, epistatic analysis revealed that PTP-3 is upstream of SYD-2 to regulate its intramolecular folding.     

The effect of induced heat waves on Pinus taeda and Quercus rubra seedlings in ambient and elevated CO(2) atmospheres

Here, we investigated the effect of different heat-wave intensities applied at two atmospheric CO(2) concentrations ([CO(2) ]) on seedlings of two tree species, loblolly pine (Pinus taeda) and northern red oak (Quercus rubra). Seedlings were assigned to treatment combinations of two levels of [CO(2) ] (380 or 700?μmol?mol(-1) ) and four levels of air temperature (ambient, ambient +3°C, or 7-d heat waves consisting of a biweekly +6°C heat wave, or a monthly +12°C heat wave). Treatments were maintained throughout the growing season, thus receiving equal heat sums. We measured gas exchange and fluorescence parameters before, during and after a mid-summer heat wave. The +12°C heat wave, significantly reduced net photosynthesis (A(net) ) in both species and [CO(2) ] treatments but this effect was diminished in elevated [CO(2) ]. The decrease in A(net) was accompanied by a decrease in F(v) '/F(m) ' in P.?taeda and Φ(PSII) in Q.?rubra. Our findings suggest that, if soil moisture is adequate, trees will experience negative effects in photosynthetic performance only with the occurrence of extreme heat waves. As elevated [CO(2) ] diminished these negative effects, the future climate may not be as detrimental to plant communities as previously assumed.     

Pr is a member of a restricted class of σ70-dependent promoters that lack a recognizable ?10 element

The Pr promoter is the first verified member of a class of bacterial σ⁷⁰-promoters that only possess a single match to consensus within its −10 element. In its native context, the activity of this promoter determines the ability of Pseudomonas putida CF600 to degrade phenolic compounds, which provides proof-of-principle for the significance of such promoters. Lack of identity within the −10 element leads to non-detection of Pr-like promoters by current search engines, because of their bias for detection of the −10 motif. Here, we report a mutagenesis analysis of Pr that reveals strict sequence requirements for its activity that includes an essential −15 element and preservation of non-consensus bases within its −35 and −10 elements. We found that highly similar promoters control plasmid- and chromosomally- encoded phenol degradative systems in various Pseudomonads. However, using a purpose-designed promoter-search algorithm and activity analysis of potential candidate promoters, no bona fide Pr-like promoter could be found in the entire genome of P. putida KT2440. Hence, Pr-like σ⁷⁰-promoters, which have the potential to be a widely distributed class of previously unrecognized promoters, are in fact highly restricted and remain in a class of their own.