Foraging in Non-Native Environments: Comparison of Nile Tilapia and Three Co-Occurring Native Centrarchids in Invaded Coastal Mississippi Watersheds

We examined the diet of the alien Nile tilapia and bluegill, redear sunfish, and largemouth bass over a two-year period in coastal Mississippi. Nile tilapia diet was visually separated from the three natives based on group-average linkage cluster analysis. Sequential two-way nested analysis of similarities indicted there was no season effect (Global R = 0.026, P = 24.3%), but there was a moderate size class effect (Global R = 0.457, P = 0.1%) and a strong species effect (Global R = 0.876, P = 0.1%). Pairwise tests indicated species fed on different components of and locations within the environment, with bluegill, redear sunfish and largemouth bass (all R ≤ 0.683, P = 0.1%) having the most similar dietary components and Nile tilapia (all R ≥ 0.953, P = 0.1%) having the most distinct. Multivariate dispersion indicated that largemouth bass (1.425) and bluegill (1.394) had the most diverse diets compared to redear sunfish (0.906) and Nile tilapia (0.918). Similarities of percentages indicated that diets were separated based on prey: bluegill and redear sunfish consumed chironomids and insects; largemouth bass consumed fish and insects; and Nile tilapia fed most often on sediment resources such as nematodes, rotifers, bryozoans and hydrozoans. Nile tilapia had the highest frequency of mud, sand and detritus in their stomachs, suggesting they fed directly on bottom sediments. These data and the fact that Nile tilapia has a 1.3–7.6 times longer intestine on average than its body length, support our contention that this alien species feeds at the base of the food web and is well adapted to survive and proliferate in non-native environments.     

Photonic crystal nanostructures for optical biosensing applications

We present the design, fabrication and optical investigation of photonic crystal (PhC) nanocavity drop filters for use as optical biosensors. The resonant cavity mode wavelength and Q-factor are studied as a function of the ambient refractive index and as a function of adsorbed proteins (bovine serum albumin) on the sensor surface. Experiments were performed by evanescent excitation of the cavity mode via a PhC waveguide. This in turn is coupled to a ridge waveguide that allows the introduction of a fluid flow cell on a chip. A response of ∂λ/∂c=(4.54±0.66)×10⁵ nm/M is measured leading to a measured detection limit as good as  fg or  pg/mm²in the sensitive area.     

Hierarchical spatial modeling of additive and dominance genetic variance for large spatial trial datasets

Summary .  This article expands upon recent interest in Bayesian hierarchical models in quantitative genetics by developing spatial process models for inference on additive and dominance genetic variance within the context of large spatially referenced trial datasets. Direct application of such models to large spatial datasets are, however, computationally infeasible because of cubic-order matrix algorithms involved in estimation. The situation is even worse in Markov chain Monte Carlo (MCMC) contexts where such computations are performed for several iterations. Here, we discuss approaches that help obviate these hurdles without sacrificing the richness in modeling. For genetic effects, we demonstrate how an initial spectral decomposition of the relationship matrices negate the expensive matrix inversions required in previously proposed MCMC methods. For spatial effects, we outline two approaches for circumventing the prohibitively expensive matrix decompositions: the first leverages analytical results from Ornstein–Uhlenbeck processes that yield computationally efficient tridiagonal structures, whereas the second derives a modified predictive process model from the original model by projecting its realizations to a lower-dimensional subspace, thereby reducing the computational burden. We illustrate the proposed methods using a synthetic dataset with additive, dominance, genetic effects and anisotropic spatial residuals, and a large dataset from a Scots pine ( Pinus sylvestris L.) progeny study conducted in northern Sweden. Our approaches enable us to provide a comprehensive analysis of this large trial, which amply demonstrates that, in addition to violating basic assumptions of the linear model, ignoring spatial effects can result in downwardly biased measures of heritability.     

In silico feasibility of novel biodegradation pathways for 1,2,4-trichlorobenzene

Background  

Bioremediation offers a promising pollution treatment method in the reduction and elimination of man-made compounds in the environment. Computational tools to predict novel biodegradation pathways for pollutants allow one to explore the capabilities of microorganisms in cleaning up the environment. However, given the wealth of novel pathways obtained using these prediction methods, it is necessary to evaluate their relative feasibility, particularly within the context of the cellular environment.     

Evolution of competence and DNA uptake specificity in the Pasteurellaceae

Background  

Many bacteria can take up DNA, but the evolutionary history and function of natural competence and transformation remain obscure. The sporadic distribution of competence suggests it is frequently lost and/or gained, but this has not been examined in an explicitly phylogenetic context. Additional insight may come from the sequence specificity of uptake by species such as Haemophilus influenzae, where a 9 bp uptake signal sequence (USS) repeat is both highly overrepresented in the genome and needed for efficient DNA uptake. We used the distribution of competence genes and DNA uptake specificity in H. influenzae 's family, the Pasteurellaceae, to examine the ancestry of competence.     

Occult pulmonary haemorrhage in leukaemia.

Through gleeding into the lung parenchyma is responsible for morbidity and mortality in patients with leukaemia pulmonary haemorrhage is seldom diagnosed during life. We diagnosed occult pulmonary haemorrhage in five leukaemic patients with unexplained infiltrates on chest roetgenograms by examining alveolar macrophages retrieved by bronchopulmonary lavage. Macrophage haemosiderin content was greatly increased in the patients with pulmonary haemorrhage as compared to normal and thrombocytopenic control subjects. Haemoglobin and intact erythrocytes in alveolar macrophages were taken as evidence of recent haemorrhage. Intrapulmonary bleeding may occur often in patients with leukaemia, and bronchopulmonary lavage offers a safe approach to diagnosis and allows for concomitant identification of pulmonary infection.     

Functional analysis of the proteasome regulatory particle

We have developed S. cerevisiae as a model system for mechanistic studies of the 26S proteasome. The subunits of the yeast 19S complex, or regulatory particle (RP), have been defined, and are closely related to those of mammalian proteasomes. The multiubiquitin chain binding subunit (S5a/Mcb1/Rpn10) was found, surprisingly, to be nonessential for the degradation of a variety of ubiquitin-protein conjugates in vivo. Biochemical studies of proteasomes from rpn10 mutants revealed the existence of two structural subassemblies within the RP, the lid and the base. The lid and the base are both composed of 8 subunits. By electron microscopy, the base and the lid correspond to the proximal and distal masses of the RP, respectively. The base is sufficient to activate the 20S core particle for degradation of peptides, but the lid is required for ubiquitin-dependent degradation. The lid subunits share sequence motifs with components of the COP9/signalosome complex, suggesting that these functionally diverse particles have a common evolutionary ancestry. Analysis of equivalent point mutations in the six ATPases of the base indicate that they have well-differentiated functions. In particular, mutations in one ATPase gene, RPT2, result in an unexpected defect in peptide hydrolysis by the core particle. One interpretation of this result is that Rpt2 participates in gating of the channel through which substrates enter the core particle.     

Rad23 and Rpn10 serve as alternative ubiquitin receptors for the proteasome

The selective recognition of ubiquitin conjugates by proteasomes is a key step in protein degradation. The receptors that mediate this step have yet to be clearly defined although specific candidates exist. Here we show that the proteasome directly recognizes ubiquitin chains through a specific subunit, Rpn10, and also recognizes chains indirectly through Rad23, a reversibly bound proteasome cofactor. Both binding events can be observed in purified biochemical systems. A block substitution in the chain-binding ubiquitin interacting motif of RPN10 when combined with a null mutation in RAD23 results in a synthetic defect in protein degradation consistent with the view that the direct and indirect recognition modes function to some extent redundantly in vivo. Rad23 and the deubiquitinating enzyme Ubp6 both bind proteasome subunit Rpn1 through N-terminal ubiquitin-like domains. Surprisingly, Rad23 and Ubp6 do not compete with each other for proteasome binding. Thus, Rpn1 may act as a scaffold to assemble on the proteasome multiple proteins that act to either bind or hydrolyze multiubiquitin chains.     

Ubiquitin depletion as a key mediator of toxicity by translational inhibitors

Cycloheximide acts at the large subunit of the ribosome to inhibit translation. Here we report that ubiquitin levels are critical for the survival of Saccharomyces cerevisiae cells in the presence of cycloheximide: ubiquitin overexpression confers resistance to cycloheximide, while a reduced ubiquitin level confers sensitivity. Consistent with these findings, ubiquitin is unstable in yeast (t(1/2) = 2 h) and is rapidly depleted upon cycloheximide treatment. Cycloheximide does not noticeably enhance ubiquitin turnover, but serves principally to block ubiquitin synthesis. Cycloheximide also induces UBI4, the polyubiquitin gene. The cycloheximide-resistant phenotype of ubiquitin overexpressors is also characteristic of partial-loss-of-function proteasome mutants. Ubiquitin is stabilized in these mutants, which may account for their cycloheximide resistance. Previous studies have reported that ubiquitin is destabilized in the absence of Ubp6, a proteasome-associated deubiquitinating enzyme, and that ubp6 mutants are hypersensitive to cycloheximide. Consistent with the model that cycloheximide-treated cells are ubiquitin deficient, the cycloheximide sensitivity of ubp6 mutants can be rescued either by ubiquitin overexpression or by mutations in proteasome subunit genes. These results also show that ubiquitin wasting in ubp6 mutants is proteasome mediated. Ubiquitin overexpression rescued cells from additional translational inhibitors such as anisomycin and hygromycin B, suggesting that ubiquitin depletion may constitute a widespread mechanism for the toxicity of translational inhibitors.     

Bioavailability of selenium from meat and broccoli as determined by retention and distribution of 75Se

The concentration of selenium (Se), an essential nutrient, is variable in foods, depending, in part, on how and where foods are produced; some foods accumulate substantial amounts of Se when produced on high-Se soils. The chemical form of Se also differs among foods. Broccoli is a Se-accumulating plant that contains many methylated forms of Se, and Se bioavailability from broccoli has been reported to be low. Red meats such as pork or beef could accumulate Se when the animal is fed high-Se diets, and Se from such meats has been reported to be highly bioavailable for selenoprotein synthesis. In a further attempt to characterize the utilization of Se from broccoli and meats such as pork or beef, we have fed rats diets adequate (0.1 μg Se/g diet) in Se or high in Se (1.5 μg S/g diet), with the Se source being either high-Se broccoli or beef. Rats were then given test meals of broccoli or pork intrinsically labeled with ⁷⁵Se. When dietary Se was nutritionally adequate (0.1 μg/g diet), more ⁷⁵Se from pork than broccoli was retained in tissues; however, there were no significant differences in whole-body retention when dietary Se was high (1.5 μg/g diet). A significantly greater percentage of ⁷⁵Se from broccoli than pork was excreted in the urine and dietary Se did not affect urinary excretion of broccoli ⁷⁵Se, but the amount excreted from pork varied directly with dietary Se intake. Radiolabeled ⁷⁵Se derived from pork effectively labeled selenoproteins in all tissues examined, but ⁷⁵Se from broccoli was undetectable in selenoproteins. These differences in retention and distribution of Se from broccoli or pork are consistent with reported differences in bioavailability of Se from beef and broccoli. They also suggest that there are fewer differences in bioavailability when Se is consumed in supranutritional amounts.