Nucleo-cytoplasmic flux and intracellular mobility in single hepatocytes measured by fluorescence microphotolysis.

Fluorescence microphotolysis was used to measure nucleocytoplasmic flux in single rat hepatocytes for a series of dextrans ranging in molecular mass from 3 to 150 kd. The cytoplasmic translational diffusion coefficient DC and the nucleoplasmic diffusion coefficient DN of a 62-kd dextran were also determined. DC was approximately 2 X 10(-8) and DN approximately 3 X 10(-8) cm2/s, i.e., 1/20-1/15 of the value in free solution. The mobile fraction amounted to 0.7-0.8 in measurements of both intracellular diffusion and nucleo-cytoplasmic flux. The flux of dextrans from cytoplasm to nucleus depended inversely on molecular mass with an exclusion limit between 17 and 41 kd suggesting that the nuclear envelope has functions of a molecular sieve. Employing the Pappenheimer-Renkin equations, a functional pore radius of 50-56 A was derived. By comparison with recent measurements on isolated liver cell nuclei, large quantitative differences between the intracellularly located and the isolated nucleus were revealed.     

Stock characteristics of shovelnose sturgeon in the lower Platte River, Nebraska

The objectives of this research were to evaluate the condition, size structure, and growth of shovelnose sturgeon (Scaphirhynchus platorynchus) in the lower Platte River, Nebraska. A total of 1338 shovelnose sturgeon was collected using drifted gill and trammel nets (n = 954), trot lines (n = 340), and benthic trawls (n = 44) in the spring, summer, and autumn from four reaches: (i) Two Rivers State Park, (ii) confluence of Platte and Elkhorn rivers (iii) Louisville, Nebraska, and (iv) confluence of Platte and Missouri rivers during the spring, summer, and autumn of 2000 through 2004. Structural and condition indices were compared among reaches and years. Incremental relative stock densities (RSD) for shovelnose sturgeon sampled throughout the entire lower Platte River were: stock‐quality (1), quality‐preferred (12), preferred‐memorable (82), and memorable‐trophy (5). Proportional stock values were >99 for all years. A significance was detected in RSD categories among reaches and years with larger length‐categories observed in the upstream reaches. Mean relative weight (W_r) for all shovelnose sturgeon was 86.5, indicating a fit population. Mean W_r showed no significant differences among years, but significance was detected among reaches and RSD categories. Shovelnose sturgeon in the lower Platte River appear to be in good condition and exhibit different length‐frequency distributions longitudinally.     

The effect of Asp54 phosphorylation on the energetics and dynamics in the response regulator protein Spo0F studied by molecular dynamics

The response regulator protein Spo0F acts as an intermediate phospho‐messenger in the signal transduction pathway that controls initiation of the differentiation process of sporculation in the bacterium Bacillus subtilis. The regulatory domain of Spo0F contains a triad of three conserved aspartate residues, whereof one aspartate (Asp54) is phosphorylated. Using molecular dynamics simulations, we have studied the changes in flexibility induced by phosphorylation and estimated the free energy cost of introducing a phosphate group at this position using alchemical free energy calculations. The deduced conformational flexibility compares well with experimental NMR results. We find that the apo‐conformation of the protein explores a rough energy landscape resulting in a broad population of conformational substates. Phosphorylation of Spo0F reduces protein flexibility, and in particular, the so‐called anchor and recognition regions exhibit lower mobility relative to the apo‐conformation. Phosphorylation of Asp54 (P‐Asp54), in which the apo‐structure coordinates to the magnesium ion, results in extension of the sidechain, and depending on which carboxylate oxygen is phosphorylated, distinct interactions between P‐Asp54 and magnesium ion as well as residues in its proximity are established. However, phosphorylation does not affect the coordination number of the magnesium ion yielding, within the statistical uncertainties, the same free energy change. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

The developmental reduction of the marsupial coracoid: A case study in Monodelphis domestica

During their embryogenesis, marsupials develop a unique structure, the shoulder arch, which provides the structural and muscle‐attachment support necessary for the newborn's crawl to the teat. One of the most pronounced and important aspects of the shoulder arch is an enlarged coracoid. After marsupial newborns reach the teat, the shoulder arch is remodeled and the coracoid is reduced to a small process on the scapula. Although an understanding of marsupial coracoid reduction has the potential to provide insights into both, marsupial evolution and the origin of mammals, little is known about the morphological and cellular processes controlling this process. To remedy this situation, this study examined the morphological and cellular mechanisms behind coracoid reduction in the gray short‐tailed opossum, Monodelphis domestica. A quantitative, morphometric study of shoulder girdle development revealed that the coracoid is reduced in size relative to other aspects of the shoulder girdle by growing at a slower rate. Using a series of molecular assays for cell death, no evidence was found for programmed cell death playing a role in the reduction of coracoid size in marsupials (in contrast to hypotheses of previous researchers). Although it is likely the case that coracoid growth is reduced through a relatively lower rate of cellular proliferation, differences in proliferative rates in the coracoid and scapula were not great enough to be quantified using standard molecular assays. J. Morphol., 2010. © 2010 Wiley‐Liss, Inc.     

Computational analysis of chain flexibility and fluctuations in Rhizomucor miehei lipase.

We have performed molecular dynamics simulation of Rhizomucor miehei lipase (Rml) with explicit water molecules present. The simulation was carried out in periodic boundary conditions and conducted for 1. 2 ns in order to determine the concerted protein dynamics and to examine how well the essential motions are preserved along the trajectory. Protein motions are extracted by means of the essential dynamics analysis method for different lengths of the trajectory. Motions described by eigenvector 1 converge after approximately 200 ps and only small changes are observed with increasing simulation time. Protein dynamics along eigenvectors with larger indices, however, change with simulation time and generally, with increasing eigenvector index, longer simulation times are required for observing similar protein motions (along a particular eigenvector). Several regions in the protein show relatively large fluctuations and in particular motions in the active site lid and the segments Thr57-Asn63 and the active site hinge region Pro101-Gly104 are seen along several eigenvectors. These motions are generally associated with glycine residues, while no direct correlations are observed between these fluctuations and the positioning of prolines in the protein structure. The partial opening/closing of the lid is an example of induced fit mechanisms seen in other enzymes and could be a general mechanism for the activation of Rml.     

Consumption rates and food preferences of slugs in a calcareous grassland under current and future CO<Subscript>2</Subscript> conditions

This study explored consumption of a generalist herbivore feeding on leaf tissue of various plant species of a calcareous grassland, and tested whether consumption levels and preferences changed when plants were exposed to 5 years of in situ CO₂ enrichment. The first part of this experiment tested whether the consumption patterns of slugs (Deroceras reticulatum) observed in single-species feeding tests were altered when slugs were given a choice of food sources. Overall consumption increased 270% when slugs were given a choice, and they preferred having a choice of food sources more than they preferred having any one food source. Surprisingly, slugs consumed fewer legumes and grasses and more non-leguminous forbs when given a choice. In the second part of this experiment, feeding behaviors of slugs in response to elevated CO₂ were investigated by feeding them leaves of two legumes, one grass, and a non-leguminous forb (Trifolium medium, Lotus corniculatus, Bromus erectus, and Sanguisorba minor, respectively) in two or four species combinations. In the leguminous species mix, the non-leguminous species mix, and the combined mix (legumes and non-legumes), neither overall consumption by herbivores nor species preference was significantly altered by long-term CO₂ enrichment. In the combined species mix, slugs preferred legumes to non-legumes (P=0.012) and exhibited a weak functional group preference shift from non-legumes to legumes (P=0.089) in response to CO₂ enrichment. This is the first time such a shift has been observed, and provides evidence that there may be multiple herbivore responses to rising atmospheric CO₂ concentrations. Numerous single-species feeding tests using insects have shown that consumption by herbivores may increase when herbivores are fed plants grown in enriched CO₂ atmospheres. This study clearly demonstrates the limited applicability of non-choice feeding trials to generalist herbivores in species-rich communities. Received: 19 August 1999 / Accepted: 20 April 2000