D-loop Dynamics and Near-Atomic-Resolution Cryo-EM Structure of Phalloidin-Bound F-Actin

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Individual-based model of spatio-temporal dynamics of mixed forest stands

This research presents the results of constructing and parameterizing an individual-based model of spatiotemporal dynamics of mixed forest stands. The model facilitates computerized experiments with forest stands having different combinations of species and age structures. These forest stands grow on temperate areas where light is the main system-forming factor that shapes and develops forest ecosystems. The model TEMFORM (TEMperate FORests Model) is developed with few equations and parameters, most of which can be estimated using standard forest inventory data. Parameterization of the model used the growth tables of a set of basic forest-forming species in Far East Russia. Simulation results of the development of the natural single- and mixed-species stands and the effects of different types of disturbances on the stand dynamics and compositions are presented.     

Dynamics of Newly Established Elk Populations

Abstract: The dynamics of newly established elk (Cervus elaphus) populations can provide insights about maximum sustainable rates of reproduction, survival, and increase. However, data used to estimate rates of increase typically have been limited to counts and rarely have included complementary estimates of vital rates. Complexities of population dynamics cannot be understood without considering population processes as well as population states. We estimated pregnancy rates, survival rates, age ratios, and sex ratios for reintroduced elk at Theodore Roosevelt National Park, North Dakota, USA; combined vital rates in a population projection model; and compared model projections with observed elk numbers and population ratios. Pregnancy rates in January (early in the second trimester of pregnancy) averaged 54.1% (SE = 5.4%) for subadults and 91.0% (SE = 1.7%) for adults, and 91.6% of pregnancies resulted in recruitment at 8 months. Annual survival rates of adult females averaged 0.96 (95% CI = 0.94-0.98) with hunting included and 0.99 (95% CI = 0.97-0.99) with hunting excluded from calculations. Our fitted model explained 99.8% of past variation in population estimates and represents a useful new tool for short-term management planning. Although we found no evidence of temporal variation in vital rates, variation in population composition caused substantial variation in projected rates of increase (Λ = 1.20-1.36). Restoring documented hunter harvests and removals of elk by the National Park Service led to a potential rate of Λ = 1.26. Greater rates of increase substantiated elsewhere were within the expected range of chance variation, given our model and estimates of vital rates. Rates of increase realized by small elk populations are too variable to support inferences about habitat quality or density dependence.     

Endophytic bacterial flora in the stem tissue of a tropical maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.) genotype: isolation,identification and enumeration

The genotypic diversity of indigenous bacterial endophytes within stem of tropical maize (Zea mays L.) was determined in field and greenhouse experiments. Strains were isolated from stem tissues of a tropical maize cultivar (PEHM-1) by trituration and surface disinfestation and their population dynamics was determined. Endophytes were found in most of the growing season at populations ranging from 1.36–6.12 × 10⁵ colony-forming units per gram fresh weight (c.f.u./gm fw) of stem. Analysis of these bacterial endophytes using Gas Chromatography—Fatty Acid Methyl Ester (GC-FAME) led to the identification of Bacillus pumilus, B. subtilis, Pseudomonas aeruginosa and P. fluorescens as the relatively more predominant group of bacterial species residing in maize stem. When the maize seedlings grown in a greenhouse were inoculated with these four isolates individually, their population densities decreased (1.6–3.1 × 10⁵ c.f.u./gm fw of stem) as compared to the field-grown maize (1.8–3.8 × 10⁵ c.f.u./gm fw of stem). The highest persistence, however, was recovered in the case of B. subtilis with a population density of 3.1 × 10⁵ c.f.u./gm fw of stem tissue on 28 days after emergence (DAE). This is the first report on population dynamics of bacterial endophytes from tropical maize and the results establish that symptomless populations of bacteria exist in the maize stem.     

Response of winter chemical defense in Alaska paper birch and green alder to manipulation of plant carbon/nutrient balance

Summary Plant carbon/nutrient balance has been implicated as an important factor in plant defensive chemistry and palatability to herbivores. We tested this hypothesis by fertilizing juvenile growth form Alaska paper birch and green alder with N, P and N-plus-P in a balanced 2x2 factorial experiment. Additionally, we shaded unfertilized plants of both species. Fertilization with N and N-plus-P increased growth of Alaska paper birch, reduced the concentration of papyriferic acid in internodes and increased the palatability of birch twigs to snowshoe hares. Shading decreased birch growth, decreased the concentration of papyriferic acid in internodes and increased twig palatability. These results indicate that the defensive chemistry and palatability of winter-dormant juvenile Alaska paper birch are sensitive to soil fertility and shade. Conversely the defensive chemistry and palatability of green alder twigs to snowshoe hares were not significantly affected by soil fertility or shade. The greater sensitivity of Alaska paper birch defensive chemistry and palatability to snowshoe hares in comparison to green alder is in agreement with the hypothesis that early successional woody plants that are adapted to high resource availability are more plastic in their chemical responses to the physical environment than are species from less favorable environments.     

Spatial and temporal variation in population trends in a long‐distance migratory bird

Aim Over the past three decades, evidence has been growing that many Afro‐Palaearctic migratory bird populations have suffered sustained and severe declines. As causes of these declines exist across both the breeding and non‐breeding season, identifying potential drivers of population change is complex. In order to explore the roles of changes in regional and local environmental conditions on population change, we examine spatial and temporal variation in population trajectories of one of Europe’s most abundant Afro‐Palaearctic summer migrants, the willow warbler, Phylloscopus trochilus. Location Britain and Ireland. Methods We use national survey data from Britain and Ireland (BBS: BTO/RSPB/JNCC Breeding Bird Survey and CBS: BWI/NPWS/Heritage Council Countryside Breeding Survey) from 1994 to 2006 to model the spatial and temporal variation in willow warbler population trends. Results Across Britain and Ireland, population trends follow a gradient from sharp declines in the south and east of England to shallow declines and/or slight increases in parts of north and west England, across Scotland and Ireland. Decreasing the spatial scale of analysis reveals variation in both the rate and spatial extent of population change within central England and the majority of Scotland. The rates of population change also vary temporally; declines in the south of England are shallower now than at the start of the time series, whereas populations further north in Britain have undergone periods of increase and decline. Main conclusion These patterns suggest that regional‐scale drivers, such as changing climatic conditions, and local‐scale processes, such as habitat change, are interacting to produce spatially variable population trends. We discuss the potential mechanisms underlying these interactions and the challenges in addressing such changes at scales relevant to migratory species.     

Rapid Analysis of Protein Structure and Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry

An automated approach for the rapid analysis of protein structure has been developed and used to study acid-induced conformational changes in human growth hormone. The labeling approach involves hydrogen/deuterium exchange (H/D-Ex) of protein backbone amide hydrogens with rapid and sensitive detection by mass spectrometry (MS). Briefly, the protein is incubated for defined intervals in a deuterated environment. After rapid quenching of the exchange reaction, the partially deuterated protein is enzymatically digested and the resulting peptide fragments are analyzed by liquid chromatography mass spectrometry (LC-MS). The deuterium buildup curve measured for each fragment yields an average amide exchange rate that reflects the environment of the peptide in the intact protein. Additional analyses allow mapping of the free energy of folding on localized segments along the protein sequence affording unique dynamic and structural information. While amide H/D-Ex coupled with MS is recognized as a powerful technique for studying protein structure and protein–ligand interactions, it has remained a labor-intensive task. The improvements in the amide H/D-Ex methodology described here include solid phase proteolysis, automated liquid handling and sample preparation, and integrated data reduction software that together improve sequence coverage and resolution, while achieving a sample throughput nearly 10-fold higher than the commonly used manual methods.