Tributary and Mainstem Benthic Macroinvertebrate Communities Linked By Direct Dispersal and Indirect Habitat Alteration

Benthic communities in tributary-mainstem networks might interact via downstream drift of invertebrates or material from tributaries and adult dispersal from the mainstem. Depending on the strength of these interactions, mainstem downstream communities are expected to be more similar to tributary communities due to drift or habitat alteration. Communities not connected by flow are expected to be similar due to adult dispersal but decreasing in similarity with distance from the mainstem. We investigated interactions between invertebrate communities of a 7th order river and 5th order tributary by comparing benthic community structure in the river upstream and downstream of the tributary confluence and upstream in the tributary. Non-metric multidimensional scaling showed invertebrate communities and habitat traits from river locations directly downstream of the tributary clustered tightly, intermediate between tributary and mid-channel river locations. In addition, Bray-Curtis dissimilarity increased between the mainstem and tributary with distance upstream in the tributary. Our results indicate that similarities between mainstem and tributary communities are potentially caused by direct mass effects from tributary to downstream mainstem communities by invertebrate drift and indirect mass effects by habitat restructuring via material delivery from the tributary, as well as potential effects of adult dispersal from the river on proximal tributary communities.

The strategies of the Theileria parasite: a new twist in host-pathogen interactions

Theileria parasites infect and transform cells of the ruminant immune system. Continuous proliferation and survival of Theileria-transformed cells involves the well-orchestrated activation of several host-cell signalling pathways. Constitutive NF-kappa B (nuclear factor kappa B) activation is accomplished by recruiting the IKK (I kappa B kinase) complex, a central regulator of NF-kappa B pathways, to the surface of the transforming schizont, where it becomes permanently activated. Constitutive activation of the PI-3K-PKB [phosphoinositide 3-kinase-(Akt) protein kinase B] pathway is likely to be indirect and is essential for continuous proliferation. Theileria-transformed T cells express a range of anti-apoptotic proteins that can be expected to provide protection against apoptosis induced by death receptors, as well as cellular control mechanisms that are mobilised to eliminate cells that entered a cycle of uncontrolled proliferation.

Genotype and maternal environment affect belowground interactions between Arabidopsis thaliana and its competitors

Ecological interactions between different species are not fixed, but they may depend, at least to some extent, on the particular genotypes involved as well as on the environmental conditions experienced by previous generations. We used a set of natural genotypes of Arabidopsis thaliana, that previously experienced contrasting nutrient and herbivory conditions, to test for the influences of genetic variation and maternal effects on competitive interactions between Arabidopsis and the weedy annuals Anagallis arvensis and Senecio vulgaris. We used activated carbon to discriminate between resource competition and allelopathy components of plant-plant interactions. There was a clear competitive hierarchy: Senecio > Arabidopsis > Anagallis. Although we found no evidence for allelopathic potential of Arabidopsis, our results indicate that both Anagallis and Senecio exerted negative (direct or indirect) allelopathic effects on Arabidopsis. There were significant differences among Arabidopsis genotypes in their competitive effects on both neighbor species, as well as in their response to competition. Maternal environments significantly influenced not only the growth and fitness of Arabidopsis itself, but also its competitive effect on Anagallis. We found, however, no evidence that maternal environments affected the competitive effect on Senecio or overall competitive response of Arabidopsis. Generally, resource competition played a greater role than allelopathy, and genotype effects were more important than maternal effects. Our study demonstrates that ecological interactions, such as plant competition, are complex and multi-layered, and that, in particular, the influence of genetic variation on interactions with other species should not be overlooked.

Volatiles produced by soil-borne endophytic bacteria increase plant pathogen resistance and affect tritrophic interactions

Volatile organic compounds (VOCs) released by soil microorganisms influence plant growth and pathogen resistance. Yet, very little is known about their influence on herbivores and higher trophic levels. We studied the origin and role of a major bacterial VOC, 2,3-butanediol (2,3-BD), on plant growth, pathogen and herbivore resistance, and the attraction of natural enemies in maize. One of the major contributors to 2,3-BD in the headspace of soil-grown maize seedlings was identified as Enterobacter aerogenes, an endophytic bacterium that colonizes the plants. The production of 2,3-BD by E. aerogenes rendered maize plants more resistant against the Northern corn leaf blight fungus Setosphaeria turcica. On the contrary, E. aerogenes-inoculated plants were less resistant against the caterpillar Spodoptera littoralis. The effect of 2,3-BD on the attraction of the parasitoid Cotesia marginiventris was more variable: 2,3-BD application to the headspace of the plants had no effect on the parasitoids, but application to the soil increased parasitoid attraction. Furthermore, inoculation of seeds with E. aerogenes decreased plant attractiveness, whereas inoculation of soil with a total extract of soil microbes increased parasitoid attraction, suggesting that the effect of 2,3-BD on the parasitoid is indirect and depends on the composition of the microbial community.

The Role of Glucosidase I (Cwh41p) in the Biosynthesis of Cell Wall β-1,6-Glucan Is Indirect

CWH41, a gene involved in the assembly of cell wall β-1,6-glucan, has recently been shown to be the structural gene for Saccharomyces cerevisiae glucosidase I that is responsible for initiating the trimming of terminal α-1,2-glucose residue in the N-glycan processing pathway. To distinguish between a direct or indirect role of Cwh41p in the biosynthesis of β-1,6-glucan, we constructed a double mutant, alg5Δ (lacking dolichol-P-glucose synthase) cwh41Δ, and found that it has the same phenotype as the alg5Δ single mutant. It contains wild-type levels of cell wall β-1,6-glucan, shows moderate underglycosylation of N-linked glycoproteins, and grows at concentrations of Calcofluor White (which interferes with cell wall assembly) that are lethal to cwh41Δ single mutant. The strong genetic interactions of CWH41 with KRE6 and KRE1, two other genes involved in the β-1,6-glucan biosynthetic pathway, disappear in the absence of dolichol-P-glucose synthase (alg5Δ). The triple mutant alg5Δcwh41Δkre6Δ is viable, whereas the double mutant cwh41Δkre6Δ in the same genetic background is not. The severe slow growth phenotype and 75% reduction in cell wall β-1,6-glucan, characteristic of the cwh41Δkre1Δ double mutant, are not observed in the triple mutant alg5Δcwh41Δkre1Δ. Kre6p, a putative Golgi glucan synthase, is unstable in cwh41Δ strains, and its overexpression renders these cells Calcofluor White resistant. These results demonstrate that the role of glucosidase I (Cwh41p) in the biosynthesis of cell wall β-1,6-glucan is indirect and that dolichol-P-glucose is not an intermediate in this pathway.

Recognition of diverse sequences by class I zinc fingers: asymmetries and indirect effects on specificity in the interaction between CF2II and A+T-rich elements.

The Drosophila CF2II protein, which contains zinc fingers of the Cys2His2 type and recognizes an A+T-rich sequence, behaves in cell culture as an activator of a reporter chloramphenicol acetyltransferase gene. This activity depends on C-terminal but not N-terminal zinc fingers, as does in vitro DNA binding. By site-specific mutagenesis and binding site selection, we define the critical amino acid-base interactions. Mutations of single amino acid residues at the leading edge of the recognition helix are rarely neutral: many result in a slight change in affinity for the ideal DNA target site; some cause major loss of affinity; and others change specificity for as many as two bases in the target site. Compared to zinc fingers that recognize G+C-rich DNA, CF2II fingers appear to bind to A+T-rich DNA in a generally similar manner, but with additional flexibility and amino acid-base interactions. The results illustrate how zinc fingers may be evolving to recognize an unusually diverse set of DNA sequences.

Binocular contrast interactions:Dichoptic masking is not a single process

To decouple interocular suppression and binocular summation we varied the relative phase of mask and target in a 2IFC contrast-masking paradigm. In Experiment I, dichoptic mask gratings had the same orientation and spatial frequency as the target. For in-phase masking, suppression was strong (a log-log slope of ∼1) and there was weak facilitation at low mask contrasts. Anti-phase masking was weaker (a log-log slope of ∼0.7) and there was no facilitation. A two-stage model of contrast gain control [Meese, T.S., Georgeson, M.A. and Baker, D.H. (2006). Binocular contrast vision at and above threshold. Journal of Vision, 6: 1224-1243] provided a good fit to the in-phase results and fixed its free parameters. It made successful predictions (with no free parameters) for the anti-phase results when (A) interocular suppression was phase-indifferent but (B) binocular summation was phase sensitive. Experiments II and III showed that interocular suppression comprised two components: (i) a tuned effect with an orientation bandwidth of ∼±33° and a spatial frequency bandwidth of >3 octaves, and (ii) an untuned effect that elevated threshold by a factor of between 2 and 4. Operationally, binocular summation was more tightly tuned, having an orientation bandwidth of ∼±8°, and a spatial frequency bandwidth of ∼0.5 octaves. Our results replicate the unusual shapes of the in-phase dichoptic tuning functions reported by Legge [Legge, G.E. (1979). Spatial frequency masking in human vision: Binocular interactions. Journal of the Optical Society of America, 69: 838-847]. These can now be seen as the envelope of the direct effects from interocular suppression and the indirect effect from binocular summation, which contaminates the signal channel with a mask that has been suppressed by the target. © 2007 Elsevier Ltd. All rights reserved.

Non-consumptive effects of predators in coral reef communities and the indirect consequences of marine protected areas

Predators exert strong direct and indirect effects on ecological communities by intimidating their prey. Non-consumptive effects (NCEs) of predators are important features of many ecosystems and have changed the way we understand predator-prey interactions, but are not well understood in some systems. For my dissertation research I combined a variety of approaches to examine the effect of predation risk on herbivore foraging and reproductive behaviors in a coral reef ecosystem. In the first part of my dissertation, I investigated how diet and territoriality of herbivorous fish varied across multiple reefs with different levels of predator biomass in the Florida Keys National Marine Sanctuary. I show that both predator and damselfish abundance impacted diet diversity within populations for two herbivores in different ways. Additionally, reef protection and the associated recovery of large predators appeared to shape the trade-off reef herbivores made between territory size and quality. In the second part of my dissertation, I investigated context-dependent causal linkages between predation risk, herbivore foraging behavior and resource consumption in multiple field experiments. I found that reef complexity, predator hunting mode, light availability and prey hunger influenced prey perception of threat and their willingness to feed. This research argues for more emphasis on the role of predation risk in affecting individual herbivore foraging behavior in order to understand the implications of human-mediated predator removal and recovery in coral reef ecosystems.^

Non-Consumptive Effects of Predators in Coral Reef Communities and the Indirect Consequences of Marine Protected Areas

Predators exert strong direct and indirect effects on ecological communities by intimidating their prey. Non-consumptive effects (NCEs) of predators are important features of many ecosystems and have changed the way we understand predator-prey interactions, but are not well understood in some systems. For my dissertation research I combined a variety of approaches to examine the effect of predation risk on herbivore foraging and reproductive behaviors in a coral reef ecosystem. In the first part of my dissertation, I investigated how diet and territoriality of herbivorous fish varied across multiple reefs with different levels of predator biomass in the Florida Keys National Marine Sanctuary. I show that both predator and damselfish abundance impacted diet diversity within populations for two herbivores in different ways. Additionally, reef protection and the associated recovery of large predators appeared to shape the trade-off reef herbivores made between territory size and quality. In the second part of my dissertation, I investigated context-dependent causal linkages between predation risk, herbivore foraging behavior and resource consumption in multiple field experiments. I found that reef complexity, predator hunting mode, light availability and prey hunger influenced prey perception of threat and their willingness to feed. This research argues for more emphasis on the role of predation risk in affecting individual herbivore foraging behavior in order to understand the implications of human-mediated predator removal and recovery in coral reef ecosystems.

Solid-liquid interactions in microscale structures and devices

Liquid-solid interactions become important as dimensions approach mciro/nano-scale. This dissertation focuses on liquid-solid interactions in two distinct applications: capillary driven self-assembly of thin foils into 3D structures, and droplet wetting of hydrophobic micropatterned surfaces. The phenomenon of self-assembly of complex structures is common in biological systems. Examples include self-assembly of proteins into macromolecular structures and self-assembly of lipid bilayer membranes. The principles governing this phenomenon have been applied to induce self-assembly of millimeter scale Si thin films into spherical and other 3D structures, which are then integrated into light-trapping photovoltaic (PV) devices. Motivated by this application, we present a generalized analytical study of the self-folding of thin plates into deterministic 3D shapes, through fluid-solid interactions, to be used as PV devices. This study consists of developing a model using beam theory, which incorporates the two competing components — a capillary force that promotes folding and the bending rigidity of the foil that resists folding into a 3D structure. Through an equivalence argument of thin foils of different geometry, an effective folding parameter, which uniquely characterizes the driving force for folding, has been identified. A criterion for spontaneous folding of an arbitrarily shaped 2D foil, based on the effective folding parameter, is thus established. Measurements from experiments using different materials and predictions from the model match well, validating the assumptions used in the analysis. As an alternative to the mechanics model approach, the minimization of the total free energy is employed to investigate the interactions between a fluid droplet and a flexible thin film. A 2D energy functional is proposed, comprising the surface energy of the fluid, bending energy of the thin film and gravitational energy of the fluid. Through simulations with Surface Evolver, the shapes of the droplet and the thin film at equilibrium are obtained. A critical thin film length necessary for complete enclosure of the fluid droplet, and hence successful self-assembly into a PV device, is determined and compared with the experimental results and mechanics model predictions. The results from the modeling and energy approaches and the experiments are all consistent. Superhydrophobic surfaces, which have unique properties including self-cleaning and water repelling are desired in many applications. One excellent example in nature is the lotus leaf. To fabricate these surfaces, well designed micro/nano- surface structures are often employed. In this research, we fabricate superhydrophobic micropatterned Polydimethylsiloxane (PDMS) surfaces composed of micropillars of various sizes and arrangements by means of soft lithography. Both anisotropic surfaces, consisting of parallel grooves and cylindrical pillars in rectangular lattices, and isotropic surfaces, consisting of cylindrical pillars in square and hexagonal lattices, are considered. A novel technique is proposed to image the contact line (CL) of the droplet on the hydrophobic surface. This technique provides a new approach to distinguish between partial and complete wetting. The contact area between droplet and microtextured surface is then measured for a droplet in the Cassie state, which is a state of partial wetting. The results show that although the droplet is in the Cassie state, the contact area does not necessarily follow Cassie model predictions. Moreover, the CL is not circular, and is affected by the micropatterns, in both isotropic and anisotropic cases. Thus, it is suggested that along with the contact angle — the typical parameter reported in literature quantifying wetting, the size and shape of the contact area should also be presented. This technique is employed to investigate the evolution of the CL on a hydrophobic micropatterned surface in the cases of: a single droplet impacting the micropatterned surface, two droplets coalescing on micropillars, and a receding droplet resting on the micropatterned surface. Another parameter which quantifies hydrophobicity is the contact angle hysteresis (CAH), which indicates the resistance of the surface to the sliding of a droplet with a given volume. The conventional methods of using advancing and receding angles or tilting stage to measure the resistance of the micropatterned surface are indirect, without mentioning the inaccuracy due to the discrete and stepwise motion of the CL on micropillars. A micronewton force sensor is utilized to directly measure the resisting force by dragging a droplet on a microtextured surface. Together with the proposed imaging technique, the evolution of the CL during sliding is also explored. It is found that, at the onset of sliding, the CL behaves as a linear elastic solid with a constant stiffness. Afterwards, the force first increases and then decreases and reaches a steady state, accompanied with periodic oscillations due to regular pinning and depinning of the CL. Both the maximum and steady state forces are primarily dependent on area fractions of the micropatterned surfaces in our experiment. The resisting force is found to be proportional to the number of pillars which pin the CL at the trailing edge, validating the assumption that the resistance mainly arises from the CL pinning at the trailing edge. In each pinning-and-depinning cycle during the steady state, the CL also shows linear elastic behavior but with a lower stiffness. The force variation and energy dissipation involved can also be determined. This novel method of measuring the resistance of the micropatterned surface elucidates the dependence on CL pinning and provides more insight into the mechanisms of CAH.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Endocytosis Of Tight Junctions Caveolin Nitrosylation Dependent Is Improved By Cocoa Via Opioid Receptor On Rpe Cells In Diabetic Conditions.

Retinal pigment epithelium cells, along with tight junction (TJ) proteins, constitute the outer blood retinal barrier (BRB). Contradictory findings suggest a role for the outer BRB in the pathogenesis of diabetic retinopathy (DR). The aim of this study was to investigate whether the mechanisms involved in these alterations are sensitive to nitrosative stress, and if cocoa or epicatechin (EC) protects from this damage under diabetic (DM) milieu conditions. Cells of a human RPE line (ARPE-19) were exposed to high-glucose (HG) conditions for 24 hours in the presence or absence of cocoa powder containing 0.5% or 60.5% polyphenol (low-polyphenol cocoa [LPC] and high-polyphenol cocoa [HPC], respectively). Exposure to HG decreased claudin-1 and occludin TJ expressions and increased extracellular matrix accumulation (ECM), whereas levels of TNF-α and inducible nitric oxide synthase (iNOS) were upregulated, accompanied by increased nitric oxide levels. This nitrosative stress resulted in S-nitrosylation of caveolin-1 (CAV-1), which in turn increased CAV-1 traffic and its interactions with claudin-1 and occludin. This cascade was inhibited by treatment with HPC or EC through δ-opioid receptor (DOR) binding and stimulation, thereby decreasing TNF-α-induced iNOS upregulation and CAV-1 endocytosis. The TJ functions were restored, leading to prevention of paracellular permeability, restoration of resistance of the ARPE-19 monolayer, and decreased ECM accumulation. The detrimental effects on TJs in ARPE-19 cells exposed to DM milieu occur through a CAV-1 S-nitrosylation-dependent endocytosis mechanism. High-polyphenol cocoa or EC exerts protective effects through DOR stimulation.

Inhibition Of Tumor Necrosis Factor-alpha And Cyclooxigenase-2 By Isatin: A Molecular Mechanism Of Protection Against Tnbs-induced Colitis In Rats.

Isatin, an indole alkaloid has been shown to have anti-microbial, anti-tumor and anti-inflammatory effects. Due to its findings, we evaluated whether this alkaloid would have any effect on TNBS-induced colitis. Animals (male Unib:WH rats, aged 8 weeks old) were induced colitis through a rectal administration of 2,4,6-trinitrobenzene sulphonic acid using a catheter inserted 8 cm into the rectum of the animals. The rats were divided into two major groups: non-colitic and colitic. The colitic group was sub-divided into 6 groups (10 animals per group): colitic non-treated, Isatin 3; 6; 12.5; 18.75 and 25 mg/kg. Our main results showed that the oral treatment with Isatin 6 and 25 mg/kg were capable of avoiding the increase in TNF-α, COX-2 and PGE₂ levels when compared to the colitic non-treated group. Interestingly, the same doses (6 and 25 mg/kg) were also capable of preventing the decrease in IL-10 levels comparing with the colitic non-treated group. The levels of MPO, (an indirect indicator of neutrophil presence), were also maintained lower than those of the colitic non-treated group. Isatin also prevented the decrease of SOD activity and increase of GSH-Px and GSH-Rd activity as well as the depletion of GSH levels. In conclusion, both pre-treatments (6 and 25 mg/kg) were capable of protecting the gut mucosa against the injury caused by TNBS, through the combination of antioxidant and anti-inflammatory properties, which, together, showed a protective activity of the indole alkaloid Isatin.

Contrasting Effects Of Land Use Intensity And Exotic Host Plants On The Specialization Of Interactions In Plant-herbivore Networks.

Human land use tends to decrease the diversity of native plant species and facilitate the invasion and establishment of exotic ones. Such changes in land use and plant community composition usually have negative impacts on the assemblages of native herbivorous insects. Highly specialized herbivores are expected to be especially sensitive to land use intensification and the presence of exotic plant species because they are neither capable of consuming alternative plant species of the native flora nor exotic plant species. Therefore, higher levels of land use intensity might reduce the proportion of highly specialized herbivores, which ultimately would lead to changes in the specialization of interactions in plant-herbivore networks. This study investigates the community-wide effects of land use intensity on the degree of specialization of 72 plant-herbivore networks, including effects mediated by the increase in the proportion of exotic plant species. Contrary to our expectation, the net effect of land use intensity on network specialization was positive. However, this positive effect of land use intensity was partially canceled by an opposite effect of the proportion of exotic plant species on network specialization. When we analyzed networks composed exclusively of endophagous herbivores separately from those composed exclusively of exophagous herbivores, we found that only endophages showed a consistent change in network specialization at higher land use levels. Altogether, these results indicate that land use intensity is an important ecological driver of network specialization, by way of reducing the local host range of herbivore guilds with highly specialized feeding habits. However, because the effect of land use intensity is offset by an opposite effect owing to the proportion of exotic host species, the net effect of land use in a given herbivore assemblage will likely depend on the extent of the replacement of native host species with exotic ones.

Graphene Oxide: A Carrier For Pharmaceuticals And A Scaffold For Cell Interactions.

During the last ten years, graphene oxide has been explored in many applications due to its remarkable electroconductivity, thermal properties and mobility of charge carriers, among other properties. As discussed in this review, the literature suggests that a total characterization of graphene oxide must be conducted because oxidation debris (synthesis impurities) present in the graphene oxides could act as a graphene oxide surfactant, stabilizing aqueous dispersions. It is also important to note that the structure models of graphene oxide need to be revisited because of significant implications for its chemical composition and its direct covalent functionalization. Another aspect that is discussed is the need to consider graphene oxide surface chemistry. The hemolysis assay is recommended as a reliable test for the preliminary assessment of graphene oxide toxicity, biocompatibility and cell membrane interaction. More recently, graphene oxide has been extensively explored for drug delivery applications. An important increase in research efforts in this emerging field is clearly represented by the hundreds of related publications per year, including some reviews. Many studies have been performed to explore the graphene oxide properties that enable it to deliver more than one activity simultaneously and to combine multidrug systems with photothermal therapy, indicating that graphene oxide is an attractive tool to overcome hurdles in cancer therapies. Some strategic aspects of the application of these materials in cancer treatment are also discussed. In vitro studies have indicated that graphene oxide can also promote stem cell adhesion, growth and differentiation, and this review discusses the recent and pertinent findings regarding graphene oxide as a valuable nanomaterial for stem cell research in medicine. The protein corona is a key concept in nanomedicine and nanotoxicology because it provides a biomolecular identity for nanomaterials in a biological environment. Understanding protein corona-nanomaterial interactions and their influence on cellular responses is a challenging task at the nanobiointerface. New aspects and developments in this area are discussed.