Microhabitat use and feeding strategies of the Pied Flycatcher and the Willow Warbler in their West-African winter quarters compared with resident species

Salewski, V. 2000. Microhabitat use and feeding strategies of the Pied Flycatcher and the Willow Warbler in their West-African winter quarters compared with resident species. Ostrich 71 (1 & 2): 191–193.

Habitat choice, microhabitat and foraging behaviour of the palaearctic Pied Flycatcher and Willow Warbler are described in their West-African wintering areas and are compared with those of resident species. The migrants were more flexible in habitat choice and foraging techniques, but in general did not feed in more open habitat.     

Decoupling litter barrier and soil moisture influences on the establishment of an invasive grass

Background and aims

Through recruitment, plants establish in novel environments. Recruitment also is the stage where plants undergo the highest mortality. We investigate the recruitment niche for Microstegium vimineum, an annual grass from East Asia spreading throughout eastern North American forests.

Methods

Current observational and greenhouse research indicates that M. vimineum recruitment may be inhibited by leaf litter and promoted by soil moisture; we use field studies to experimentally test how these factors influence M. vimineum germination, seedling survival and reproduction. Specifically, we introduce M. vimineum seeds into forest microhabitats with experimentally varied levels of soil moisture and leaf litter.

Results

Soil moisture increases M. vimineum germination regardless of leaf litter thickness and ameliorates seedling mortality in deep leaf litter. Seed production per m² increases with watering, reflecting higher germination and survival, whereas per capita seed production increases with leaf litter thickness, reflecting density-dependent limits on seed production.

Conclusions

The interactive effects of varied levels of soil moisture and leaf litter thickness on key M. vimineum life history stages highlight the need to consider multiple drivers, such as rainfall and local forest disturbance, when assessing how soil properties influence the establishment of invasive plants.     

Effect of Multimerization on Membrane Association of Rous Sarcoma Virus and HIV-1 Matrix Domain Proteins

In most retroviruses, plasma membrane (PM) association of the Gag structural protein is a critical step in viral assembly, relying in part on interaction between the highly basic Gag MA domain and the negatively charged inner leaflet of the PM. Assembly is thought to begin with Gag dimerization followed by multimerization, resulting in a hexameric lattice. To directly address the role of multimerization in membrane binding, we fused the MA domains of Rous sarcoma virus (RSV) and HIV-1 to the chemically inducible dimerization domain FK506-binding protein (FKBP) or to the hexameric protein CcmK4 from cyanobacteria. The cellular localization of the resulting green fluorescent protein (GFP)-tagged chimeric proteins was examined by fluorescence imaging, and the association of the proteins with liposomes was quantified by flotation in sucrose gradients, following synthesis in a reticulocyte extract or as purified proteins. Four lipid compositions were tested, representative of liposomes commonly reported in flotation experiments. By themselves, GFP-tagged RSV and HIV-1 MA proteins were largely cytoplasmic, but both hexamerized proteins were highly concentrated at the PM. Dimerization led to partial PM localization for HIV-1 MA. These in vivo effects of multimerization were reproduced in vitro. In flotation analyses, the intact RSV and HIV-1 Gag proteins were more similar to multimerized MA than to monomeric MA. RNA is reported to compete with acidic liposomes for HIV-1 Gag binding, and thus we also examined the effects of RNase treatment or tRNA addition on flotation. tRNA competed with liposomes in the case of some but not all lipid compositions and ionic strengths. Taken together, our results further underpin the model that multimerization is critical for PM association of retroviral Gag proteins. In addition, they suggest that the modulation of membrane binding by RNA, as previously reported for HIV-1, may not hold for RSV.     

Biomarkers Reveal Diverse Microbial Communities in Black Smoker Sulfides from Turtle Pits (Mid-Atlantic Ridge,Recent) and Yaman Kasy (Russia,Silurian)

The steep biogeochemical gradients near deep sea hydrothermal vents provide various niches for microbial life. Here we present biosignatures of such organisms enclosed in a modern and an ancient hydrothermal sulfide deposit (Turtle Pits, Mid-Atlantic Ridge, Recent; Yaman Kasy, Russia, Silurian). In the modern sulfide we found high amounts of specific bacterial and archaeal biomarkers with δ¹³C values between ?8 and ?37‰ VPDB. Our data indicate the presence of thermophilic members of the autotrophic Aquificales using the reductive tricarboxylic acid (rTCA) cycle as well as of methanogenic and chemolithoheterotrophic Archaea. In the ancient sample, most potential biomarkers of thermophiles were obscured by compounds derived from allochthonous organic matter (OM), except for an acyclic C₄₀ biphytane and its C₃₉ breakdown product. Both samples contained high amounts of unresolved complex mixtures (UCM) of hydrocarbons. Apparently, OM in the sulfides had to withstand high thermal stress, indicated by highly mature hopanes, steranes, and cheilanthanes with up to 41 carbon atoms.     

Organic Carbon Degradation in Anoxic Organic-Rich Shelf Sediments: Biogeochemical Rates and Microbial Abundance

Identifying and explaining bottlenecks in organic carbon mineralization and the persistence of organic matter in marine sediments remain challenging. This study aims to illuminate the process of carbon flow between microorganisms involved in the sedimentary microbial food chain in anoxic, organic-rich sediments of the central Namibian upwelling system, using biogeochemical rate measurements and abundances of Bacteroidetes, Gammaproteobacteria, and sulfate-reducing bacteria at two sampling stations. Sulfate reduction rates decreased by three orders of magnitude in the top 20 cm at one sampling station (280 nmol cm^?3 d^?1 – 0.1 nmol cm^?3 d^?1) and by a factor of 7 at the second station (65 nmol cm^?3 d^?1 – 9.6 nmol cm^?3 d^?1). However, rates of enzymatic hydrolysis decreased by less than a factor of three at both sampling stations for the polysaccharides laminarin (23 nmol cm^?3 d^?1– 8 nmol cm^?3 d^?1 and 22 nmol cm^?3 d^?1– 10 nmol cm^?3 d^?1) and pullulan (11 nmol cm^?3 d^?1– 4 nmol cm^?3 d^?1 and 8 nmol cm^?3 d^?1– 6 nmol cm^?3 d^?1). Increasing imbalance between carbon turnover by hydrolysis and terminal oxidation with depth, the steep decrease in cell specific activity of sulfate reducing bacteria with depth, low concentrations of volatile fatty acids (less than 15 μM), and persistence of dissolved organic carbon, suggest decreasing bioavailability and substrate limitation with depth.     

Lipid Segregation and Membrane Budding Induced by the Peripheral Membrane Binding Protein Annexin A2

The formation of dynamic membrane microdomains is an important phenomenon in many signal transduction and membrane trafficking events. It is driven by intrinsic properties of membrane lipids and integral as well as membrane-associated proteins. Here we analyzed the ability of one peripherally associated membrane protein, annexin A2 (AnxA2), to induce the formation of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P₂)-rich domains in giant unilamellar vesicles (GUVs) of complex lipid composition. AnxA2 is a cytosolic protein that can bind PI(4,5)P₂ and other acidic phospholipids in a Ca²⁺-dependent manner and that has been implicated in cellular membrane dynamics in endocytosis and exocytosis. We show that AnxA2 binding to GUVs induces lipid phase separation and the recruitment of PI(4,5)P₂, cholesterol and glycosphingolipids into larger clusters. This property is observed for the full-length monomeric protein, a mutant derivative comprising the C-terminal protein core domain and for AnxA2 residing in a heterotetrameric complex with its intracellular binding partner S100A10. All AnxA2 derivatives inducing PI(4,5)P₂ clustering are also capable of forming interconnections between PI(4,5)P₂-rich microdomains of adjacent GUVs. Furthermore, they can induce membrane indentations rich in PI(4,5)P₂ and inward budding of these membrane domains into the lumen of GUVs. This inward vesiculation is specific for AnxA2 and not shared with other PI(4,5)P₂-binding proteins such as the pleckstrin homology (PH) domain of phospholipase Cδ1. Together our results indicate that annexins such as AnxA2 can efficiently induce membrane deformations after lipid segregation, a mechanism possibly underlying annexin functions in membrane trafficking.     

Rule-based modeling and simulations of the inner kinetochore structure

Background

Combinatorial complexity is a central problem when modeling biochemical reaction networks, since the association of a few components can give rise to a large variation of protein complexes. Available classical modeling approaches are often insufficient for the analysis of very large and complex networks in detail. Recently, we developed a new rule-based modeling approach that facilitates the analysis of spatial and combinatorially complex problems. Here, we explore for the first time how this approach can be applied to a specific biological system, the human kinetochore, which is a multi-protein complex involving over 100 proteins.

Results

Applying our freely available SRSim software to a large data set on kinetochore proteins in human cells, we construct a spatial rule-based simulation model of the human inner kinetochore. The model generates an estimation of the probability distribution of the inner kinetochore 3D architecture and we show how to analyze this distribution using information theory. In our model, the formation of a bridge between CenpA and an H3 containing nucleosome only occurs efficiently for higher protein concentration realized during S-phase but may be not in G1. Above a certain nucleosome distance the protein bridge barely formed pointing towards the importance of chromatin structure for kinetochore complex formation. We define a metric for the distance between structures that allow us to identify structural clusters. Using this modeling technique, we explore different hypothetical chromatin layouts.

Conclusions

Applying a rule-based network analysis to the spatial kinetochore complex geometry allowed us to integrate experimental data on kinetochore proteins, suggesting a 3D model of the human inner kinetochore architecture that is governed by a combinatorial algebraic reaction network. This reaction network can serve as bridge between multiple scales of modeling. Our approach can be applied to other systems beyond kinetochores.