Modeling heterogeneity in nest survival data

Current statistical methods for estimating nest survival rates assume that nests are identical in their propensity to succeed. However, there are several biological reasons to question this assumption. For example, experience of the nest builder, number of nest helpers, genetic fitness of individuals, and site effects may contribute to an inherent disparity between nests with respect to their daily mortality rates. Ignoring such heterogeneity can lead to incorrect survival estimates. Our results show that constant survival models can seriously underestimate overall survival in the presence of heterogeneity. This paper presents a flexible random-effects approach to model heterogeneous nest survival data. We illustrate our methods through data on redwing blackbirds.     

Distribution of actin bundles in Bowman's capsule of rat kidney

In this study we define the distribution of actin bundle arrangement in Bowman's capsule of rat renal corpuscles. Parietal cells of Bowman's capsule were examined by conventional light microscopy, electron microscopy and confocal microscopy. Within each parietal cell individual actin bundles are arranged in a parallel fashion running the length of the cell. Computer reconstructions obtained using confocal microscopy clearly show the lengths of actin bundles to be arranged, on a capsule level, end-to-end, at angles and perpendicular to bundles in adjacent cells. The bundles stain positively for non-muscle myosin and vinculin. The presence and arrangement of actin bundles in parietal cells is consistent with a role in reinforcing capsule structure.     

Cellular pathology of Parkinson’s disease: astrocytes,microglia and inflammation

Parkinsons disease (PD) is a frequent neurological disorder of the basal ganglia, which is characterized by the progressive loss of dopaminergic neurons mainly in the substantia nigra pars compacta (SNpc). Inflammatory processes have been shown to be associated with the pathogenesis of PD. Activated microglia, as well as to a lesser extent reactive astrocytes, are found in the area associated with cell loss, possibly contributing to the inflammatory process by the release of pro-inflammatory prostaglandins or cytokines. Further deleterious factors released by activated microglia or astrocytes are reactive oxygen species. On the other hand, they may mediate neuroprotective properties by the release of trophic factors or the uptake of glutamate. In this review, we will discuss the different aspects of activated glial cells and potential mechanisms that mediate or protect against cell loss in PD.     

Classic toxin-induced animal models of Parkinson’s disease: 6-OHDA and MPTP

Neurological disorders in humans can be modeled in animals using standardized procedures that recreate specific pathogenic events and their behavioral outcomes. The development of animal models of Parkinsons disease (PD) is important to test new neuroprotective agents and strategies. Such animal models of PD have to mimic, at least partially, a Parkinson-like pathology and should reproduce specific features of the human disease. PD is characterized by massive degeneration of dopaminergic neurons in the substantia nigra, the loss of striatal dopaminergic fibers and a dramatic reduction of the striatal dopamine levels. The formation of cytoplasmic inclusion bodies (Lewy bodies) in surviving dopaminergic neurons represents the most important neuropathological feature of PD. Furthermore, the massive striatal dopamine deficiency causes easily detectable motor deficits in PD patients, including bradykinesia, rigidity, and resting tremor, which are the cardinal symptoms of PD. Over the years, a broad variety of experimental models of PD were developed and applied in diverse species. This review focuses on the two most common classical toxin-induced PD models, the 6-hydroxy-dopamine (6-OHDA model) and the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model. Both neurotoxins selectively and rapidly destroy catecholaminergic neurons, whereas in humans the PD pathogenesis follows a progressive course over decades. This discrepancy reflects one important and principal point of weakness related to most animal models. This review discusses the most important properties of 6-OHDA and MPTP, their modes of administration, and critically examines advantages and limitations of selected animal models. The new genetic and environmental toxin models of PD (e.g. rotenone, paraquat, maneb) are discussed elsewhere in this special issue.This work was supported by grants from the Deutsche Forschungsgemeinschaft.     

Silica deposition in relation to ageing of leaf tissues in Sasa veitchii (Carriere) Rehder (Poaceae: Bambusoideae)

BACKGROUND AND AIMS: Silica deposition is one of the important characteristics of plants in the family Poaceae. There have been many investigations into the distribution, deposition and physiological functions of silica in this family. Two hypotheses on silica deposition have been proposed based on these studies. First, that silica deposition occurs passively as a result of water uptake by plants, and second, that silica deposition is controlled positively by plants. To test these two apparently contradictory hypotheses, silica deposition in relation to the ageing of leaf tissues in Sasa veitchii was investigated. METHODS: Tissues were examined using a light microscope and a scanning electron microscope equipped with an energy dispersive X-ray microanalyser. KEY RESULTS: The deposition process differed depending on cell type. In mesophyll tissue, fusoid cells deposited large amounts of silica depending on leaf age after maturation, while chlorenchyma cells deposited little. In epidermal tissue, comprised of eight cell types, only silica cells deposited large amounts of silica during the leaf's developmental process and none after maturation. Bulliform cells, micro-hairs and prickle hairs deposited silica densely and continuously after leaf maturation. Cork cells, guard cells, long cells and subsidiary cells deposited silica at low levels. CONCLUSIONS: The significance of these observations is discussed in relation to the two hypotheses proposed for silica deposition in Poaceae. The results of the present study clearly indicate that both hypotheses are compatible with each other dependent on cell types.     

Effect of viscoelastic relaxation on moisture transport in foods. Part I: Solution of general transport equation

Within the framework of continuum mechanics, Singh et al. [1] developed an integro-differential equation, which applies to both Darcian (Fickian) and non-Darcian (non-Fickian) modes of fluid transport in swelling biological systems. A dimensionless form of the equation was obtained and transformed from moving Eulerian to the stationary Lagrangian coordinates. Here a solution scheme for the transport equation is developed to predict moisture transport and viscoelastic stresses in spheroidal biopolymeric materials. The equation was solved numerically and results used for predicting drying and sorption curves, moisture profiles, and viscoelastic stresses in soybeans. The Lagrangian solution was obtained by assembling together several schemes: the finite element method was used to discretize the equation in space; non-linearity was addressed using the Newton-Raphson method; the Volterra term was handled via a time integration scheme of Patlashenko et al. [2] and the Galerkin rule was used to solve the time-differential term. The solution obtained in Lagrangian coordinates was transformed back to the Eulerian coordinates. In part II of this sequence we present the numerical results.Revised version: 5 October 2003     

Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

We have studied the potential of mean force of two peptides, one known to adopt a beta-hairpin and the other an alpha-helical conformation in solution. These peptides are, respectively, residues 41-56 of the C-terminus (GEWTYDDATKTFTVTE) of the B1 domain of protein G and the 13 residue C-peptide (KETAAAKFERQHM) of ribonuclease A. Extensive canonical ensemble sampling has been performed using a parallel replica exchange method. The effective potential employed in this work consists of the OPLS all-atom force field (OPLS-AA) and an analytical generalized Born (AGB) implicit solvent model including a novel nonpolar solvation free energy estimator (NP). An additional dielectric screening parameter has been incorporated into the AGBNP model. In the case of the beta-hairpin, the nonpolar solvation free energy estimator provides the necessary effective interactions for the collapse of the hydrophobic core (W43, Y45, F52, and V54), which the more commonly used surface-area-dependent nonpolar model does not provide. For both the beta-hairpin and the alpha-helix, increased dielectric screening reduces the stability of incorrectly formed salt bridges, which tend to disrupt the formation of the hairpin and helix, respectively. The fraction of beta-hairpin and alpha-helix content we obtained using the AGBNP model agrees well with experimental results. The thermodynamic stability of the beta-hairpin from protein G and the alpha-helical C-peptide from ribonuclease A as modeled with the OPLS-AA/AGBNP effective potential reflects the balance between the nonpolar effective potential terms, which drive compaction, and the polar and hydrogen bonding terms, which promote secondary structure formation.