Characterization of the major proteins of bovine seminal fluid by two-dimensional polyacrylamide gel electrophoresis

Recently, we demonstrated that the major proteins from bovine seminal plasma BSP-A1, -A2, -A3 and -30-kDa (collectively called BSP proteins) specifically interact with choline phospholipids. These proteins coat the surface of the spermatozoa after ejaculation and are believed to play an important role in membrane modifications occurring during capacitation. In this study we determined the isoelectric point (pl) and analysed the molecular heterogeneity of BSP proteins. Total protein from bovine seminal plasma (CBSP) and purified BSP proteins were iodinated using chloramine T. Samples were reduced, denatured, separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and visualized by autoradiography. Analysis of CBSP proteins demonstrated the presence of polypeptides migrating in the pH range of 3.5–7.8 and at molecular weights (Mr) between 6 and 100 kDa. Many isoforms of each BSP protein were found when purified iodinated proteins were analysed by 2D-PAGE. BSP-A1 was found at a Mr of 16.5 kDa and in the range of pl of 4.7–5.0; BSP-A2 at 16 kDa and at a pl of 4.9–5.2; BSP-A3 at 15 kDa and at a pl of 4.8–5.2, and BSP-30-kDa at 28 kDa and at a pl of 3.9–4.6. Similar results were obtained with immunolocalization of BSP proteins after Western blot using specific antibodies. The treatment of purified iodinated BSP proteins with neuraminidase increased the pl of BSP-30-kDa to 4.8–5.0 and decreased its Mr to 25 kDa, but no change was observed for BSP-A1, -A2 and -A3. The treatment of BSP proteins with sulfatase or acid phosphatase modified neither their Mr nor their pl. Furthermore, when CBSP proteins were separated in 2D-PAGE and the gels stained for glycoproteins with dansyl hydrazine, BSP proteins were among the major glycoproteins found in the bovine seminal plasma. In conclusion, BSP proteins are acidic and have several isoforms. Furthermore, the heterogeneity of BSP-30-kDa is mainly due to its sialic acid content. © 1994 Wiley-Liss, Inc.     

Effects of fire on landscape heterogeneity in Yellowstone National Park,Wyoming

Abstract. A map of burn severity resulting from the 1988 fires that occurred in Yellowstone National Park (YNP) was derived from Landsat Thematic Mapper (TM) imagery and used to assess the isolation of burned areas, the heterogeneity that resulted from fires burning under moderate and severe burning conditions, and the relationship between heterogeneity and fire size. The majority of severely burned areas were within close proximity (50 to 200 m) to unburned or lightly burned areas, suggesting that few burned sites are very far from potential sources of propagules for plant reestablishment. Fires that occurred under moderate burning conditions early during the 1988 fire season resulted in a lower proportion of crown fire than fires that occurred under severe burning conditions later in the season. Increased dominance and contagion of burn severity classes and a decrease in the edge: area ratio for later fires indicated a slightly more aggregated burn pattern compared to early fires. The proportion of burned area in different burn severity classes varied as a function of daily fire size. When daily area burned was relatively low, the proportion of burned area in each burn severity class varied widely. When daily burned area exceeded 1250 ha, the burned area contained about 50 % crown fire, 30 % severe surface burn, and 20 % light surface burn. Understanding the effect of fire on landscape heterogeneity is important because the kinds, amounts, and spatial distribution of burned and unburned areas may influence the reestablishment of plant species on burned sites.     

Avian diversity and function across the world's most populous cities

Understanding the composition of urban wildlife communities is crucial to promote biodiversity, ecosystem function and links between nature and people. Using crowdsourced data from over five million eBird checklists, we examined the influence of urban characteristics on avian richness and function at 8443 sites within and across 137 global cities. Under half of the species from regional pools were recorded in cities, and we found a significant phylogenetic signal for urban tolerance. Site-level avian richness was positively influenced by the extent of open forest, cultivation and wetlands and avian functional diversity by wetlands. Functional diversity co-declined with richness, but groups including granivores and aquatic birds occurred even at species-poor sites. Cities in arid areas held a higher percentage of regional species richness. Our results indicate commonalities in the influence of habitat on richness and function, as well as lower niche availability, and phylogenetic diversity across the world's cities.     

Spatial patterns of trees in natural forests of East-Central Europe

The analysis of spatial patterns is one of the ways to estimate the role of competition among trees in forest dynamics. Three hypotheses concerning distribution patterns in old-growth stands were tested: (1) fine-scale spatial patterns of trees are regular; (2) patterns do not differ significantly from a random distribution, and (3) spatial patterns at larger scales are clumped because of site heterogeneity. Old-growth forest stands in Poland and the Czech Republic were analysed with a modified Ripley K function, using distribution maps of tree stems. Fine-scale spatial patterns (with distances among trees not exceeding 15 m) were usually intermediate between random and regular. Trends towards a regular distribution occurred more often among dead than among live individuals. No significant relationships between tree species were found at smaller scales; however, at larger scales (distances from 15–25 m) negative associations between some species were found. This reflects site heterogeneity rather than any direct influence of one tree species upon another.     

Abundance of white lace lerp psyllids on understorey and canopy river red gums and relationships with foliar sugars and tannins

1. Trees present herbivorous insects with the greatest diversity of resources of any plant growth form. Both ontogeny and shading can alter suitability for arboreal insect herbivores. 2. We conducted a longitudinal study of tagged ‘mature’ (>12 months old) Eucalyptus camaldulensis leaves to compare the suitability of understorey and canopy trees for the leaf senescence-inducing psyllid, Cardiaspina albitextura. We quantified sugars and tannins as possible predictors of nymphal abundance. 3. Canopy leaves hosted double the number of nymphs as understorey leaves. Variation among individual trees (understorey and canopy) was the most important source of heterogeneity explaining psyllid abundance, although relative leaf age significantly influenced oviposition on canopy leaves. The diversity of foliar sugars was higher among canopy leaves than among understorey leaves. There was significant between-tree diversity in total hydrolysable tannins (HTs) and total condensed tannins (CTs) among understorey trees but not among canopy trees. Heterogeneity among understorey and canopy trees was explained by greater diversity of ellagitannins (HTs) than of CTs. 4. Shading is detrimental to the survival of nymphs on both host types, but sugars are unlikely to explain variation in suitability. Vescalagin (an ellagitannin) was negatively correlated with the abundance of nymphs on both host types.     

Acoustic communities in an environmental gradient from native to urban areas in Central Brazil

As urban areas expand due to increasing human populations, natural habitats are diminishing in quantity and quality. We conducted a study to examine the response of diurnal acoustic communities along a gradient of environments, ranging from native to dense urban areas. We hypothesized that acoustic indices would decline with urbanization, transitioning from natural and rural areas to urban environments. We conducted the research in and around Brasília, Central Brazil. We deployed 24 digital recorders in native, rural, low-density and high-density urban areas. We employed five commonly used acoustic indices (ADI, ACI, NDSI, H and BI) to characterize the acoustic communities and represent the existing biodiversity numerically. We initially compared the index values across different land use types using a non-parametric rank sum test. Subsequently, we selected eight landscape metrics and performed a principal component analysis to summarize the surrounding matrix at each sampling point. We then employed generalized linear models to determine if the acoustic indices exhibited the anticipated variations. The results indicated significant variations in all indices among the different land use types, indicating their responsiveness to distinct acoustic communities and environmental characteristics. ADI, H and NDSI exhibited declining values from native to urban areas, while ACI and BI displayed the opposite trend. These findings underscore the influence of landscape structure on acoustic indices. Consequently, we concluded that adopting appropriate landscape planning, mainly through integrating natural and urban areas, could help preserve biodiversity in tropical urban regions.     

Semiparametric estimation of the transformation model by leveraging external aggregate data in the presence of population heterogeneity

Leveraging information in aggregate data from external sources to improve estimation efficiency and prediction accuracy with smaller scale studies has drawn a great deal of attention in recent years. Yet, conventional methods often either ignore uncertainty in the external information or fail to account for the heterogeneity between internal and external studies. This article proposes an empirical likelihood-based framework to improve the estimation of the semiparametric transformation models by incorporating information about the t-year subgroup survival probability from external sources. The proposed estimation procedure incorporates an additional likelihood component to account for uncertainty in the external information and employs a density ratio model to characterize population heterogeneity. We establish the consistency and asymptotic normality of the proposed estimator and show that it is more efficient than the conventional pseudopartial likelihood estimator without combining information. Simulation studies show that the proposed estimator yields little bias and outperforms the conventional approach even in the presence of information uncertainty and heterogeneity. The proposed methodologies are illustrated with an analysis of a pancreatic cancer study.     

Conformational analysis of protein structures derived from NMR data

A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of ?, Ψ, and χ angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline ? angles, α-helix ?, Ψ angles, ω angles, and C_α chirality. The more lightly restrained torsion angles do show increasead clustering as the number of overall experimental observations increases. ?, Ψ, and χ₁ angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 Å. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J-coupling information, stereospecific assignments, and heteronumclear techniques. A suite of programs is being developed to address the special needs of NMR-derived structures which will take into account the existence of increased mobility in solution. © 1993 Wiley-Liss, Inc.     

Application of an Escherichia coli triple reporter strain for at-line monitoring of single-cell physiology during L-phenylalanine production

Biotechnological production processes are sustainable approaches for the production of biobased components such as amino acids for food and feed industry. Scale-up from ideal lab-scale bioreactors to large-scale processes is often accompanied by loss in productivity. This may be related to population heterogeneities of cells originating from isogenic cultures that arise due to dynamic non-ideal conditions in the bioreactor. To better understand this phenomenon, deeper insights into single-cell physiologies in bioprocesses are mandatory before scale-up. Here, a triple reporter strain (3RP) was developed by chromosomally integrating the fluorescent proteins mEmerald, CyOFP1, and mTagBFP2 into the L-phenylalanine producing Escherichia coli strain FUS4 (pF81_kan) to allow monitoring of growth, oxygen availability, and general stress response of the single cells. Functionality of the 3RP was confirmed in well-mixed lab-scale fed-batch processes with glycerol as carbon source in comparison to the strain without fluorescent proteins, leading to no difference in process performance. Fluorescence levels could successfully reflect the course of related process state variables, revealed population heterogeneities during the transition between different process phases and potentially subpopulations that exhibit superior process performance. Furthermore, indications were found for noise in gene expression as regulation strategy against environmental perturbation.     

Species–energy relationships and habitat complexity in bird communities

Species–energy theory is a commonly invoked theory predicting a positive relationship between species richness and available energy. The More Individuals Hypothesis (MIH) attempts to explain this pattern, and assumes that areas with greater food resources support more individuals, and that communities with more individuals include more species. Using a large dataset for North American birds, I tested these predictions of the MIH, and also examined the effect of habitat complexity on community structure. I found qualitative support for the relationships predicted by the MIH, however, the MIH alone was inadequate for fully explaining richness patterns. Communities in more productive sites had more individuals, but they also had more even relative abundance distributions such that a given number of individuals yielded a greater number of species. Richness and evenness were also higher in structurally complex forests compared to structurally more simple grasslands when controlling for available energy.