The functional biogeography of species: Biogeographical species roles of birds in Wallacea and the West Indies

Biogeographical systems can be analyzed as networks of species and geographical units. Within such a biogeographical network, individual species may differ fundamentally in their linkage pattern, and therefore hold different topological roles. To advance our understanding of the relationship between species traits and large-scale species distribution patterns in archipelagos, we use a network approach to classify birds as one of four biogeographical species roles: peripherals, connectors, module hubs, and network hubs. These roles are based upon the position of species within the modular network of islands and species in Wallacea and the West Indies. We test whether species traits - including habitat requirements, altitudinal range-span, feeding guild, trophic level, and body length - correlate with species roles. In both archipelagos, habitat requirements, altitudinal range-span and body length show strong relations to species roles. In particular, species that occupy coastal- and open habitats, as well as habitat generalists, show higher proportions of connectors and network hubs and thus tend to span several biogeographical modules (i.e. subregions). Likewise, large body size and a wide altitudinal range-span are related to a wide distribution on many islands and across several biogeographical modules. On the other hand, species restricted to interior forest are mainly characterized as peripherals and, thus, have narrow and localized distributions within biogeographical modules rather than across the archipelago-wide network. These results suggest that the ecological amplitude of a species is highly related to its geographical distribution within and across bio geographical subregions and furthermore supports the idea that large-scale species distributions relate to distributions at the local community level. We finally discuss how our biogeographical species roles may correspond to the stages of the taxon cycle and other prominent theories of species assembly. © 2013 The Authors.

Frugivores at higher risk of extinction are the key elements of a mutualistic network

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Investigation on the catalytic roles of silver species in the selective catalytic reduction of NOx with methane

Silver impregnated H-ZSM-5 zeolite catalysts with silver loading from 3 to 15 wt.% were investigated for the selective catalytic reduction (SCR) of NOx with CH4 in the excess of oxygen. X-ray diffraction (XRD) and UV-Vis measurements established the structure of silver catalysts. A relationship between the structure of silver catalysts and their catalytic functions for the SCR of NOx by CH4 was clarified. The NO conversion to N-2 showed a S-shape dependence on the increase of Ag loading. No linear dependence of catalytic activity on the amount of silver ions in the zeolite cation sites was observed. Contrastively, the activity was significantly enhanced by the nano-sized silver particles formed on the higher Ag loading samples (greater than or equal to7 wt.%). Temperature programmed desorption (TPD) and temperature programmed reduction (TPR) studies showed that nano-silver particles provided much stronger adsorption centers for active intermediates NO3-(s) on which adsorbed NO3-(s) could be effectively reduced by the activated methane. Silver ions in the zeolite cation sites might catalyze the reaction through activation of CH4 at lower temperatures. Activated CH4 reacted with NO3-(s) adsorbed on nano-silver particles to produce N-2 and CO2. (C) 2003 Elsevier B.V. All rights reserved.

Determinants of bird species richness, endemism, and island network roles in Wallacea and the West Indies: is geography sufficient or does current and historical climate matter?

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The multifaceted roles of metabolic enzymes in the Paracoccidioides species complex

Paracoccidioides species are dimorphic fungi and are the etiologic agents of paracoccidioidomycosis, which is a serious disease that involves multiple organs. The many tissues colonized by this fungus suggest a variety of surface molecules involved in adhesion. A surprising finding is that most enzymes in the glycolytic pathway, tricarboxylic acid (TCA) cycle and glyoxylate cycle in Paracoccidioides spp. have adhesive properties that aid in interacting with the host extracellular matrix and thus act as 'moonlighting'proteins. Moonlighting proteins have multiple functions, which adds a dimension to cellular complexity and benefit cells in several ways. This phenomenon occurs in both eukaryotes and prokaryotes. For example, moonlighting proteins from the glycolytic pathway or TCA cycle can play a role in bacterial pathogenesis by either acting as proteins secreted in a conventional pathway and/or as cell surface components that facilitate adhesion or adherence. This review outlines the multifunctionality exhibited by many Paracoccidioides spp. enzymes, including aconitase, aldolase, glyceraldehyde-3-phosphate dehydrogenase, isocitratelyase, malatesynthase, triose phosphate isomerase, fumarase, and enolase. We discuss the roles that moonlighting activities play in the virulence characteristics of this fungus and several other human pathogens during their interactions with the host.

Upregulation of Reactive Oxygen Species During the Retrovirus Life Cycle and Their Roles in a Mutant of Moloney Murine Leukemia Virus, ts1-Mediated Neurodegeneration

Viral invasion of the central nervous system (CNS) and development of neurological symptoms is a characteristic of many retroviruses. The mechanism by which retrovirus infection causes neurological dysfunction has yet to be fully elucidated. Given the complexity of the retrovirus-mediated neuropathogenesis, studies using small animal models are extremely valuable. Our laboratory has used a mutant moloney murine leukemia retrovirus, ts1-mediated neurodegneration. We hypothesize that astrocytes play an important role in ts1-induced neurodegeneration since they are retroviral reservoirs and supporting cells for neurons. It has been shown that ts1 is able to infect astrocytes in vivo and in vitro. Astrocytes, the dominant cell population in the CNS, extend their end feet to endothelial cells and neuronal synapse to provide neuronal support. Signs of oxidative stress in the ts1-infected CNS have been well-documented from previous studies. After viral infection, retroviral DNA is generated from its RNA genome and integrated into the host genome. In this study, we identified the life cycle of ts1 in the infected astrocytes. During the infection, we observed reactive oxygen species (ROS) upregulations: one at low levels during the early infection phase and another at high levels during the late infection phase. Initially we hypothesized that p53 might play an important role in ts1-mediated astrocytic cell death. Subsequently, we found that p53 is unlikely to be involved in the ts1-mediated astrocytic cell death. Instead, p53 phosphorylation was increased by the early ROS upregulation via ATM, the protein encoded by the ataxia-telangiectasia (A-T) mutated gene. The early upregulation of p53 delayed viral gene expression by suppressing expression of the catalytic subunit of NADPH oxidase (NOX). We further demonstrated that the ROS upregulation induced by NOX activation plays an important role in establishing retroviral genome into the host. Inhibition of NOX decreased viral replication and delayed the onset of pathological symptoms in ts1-infected mice. These observations lead us to conclude that suppression of NOX not only prevents the establishment of the retrovirus but also decreases oxidative stress in the CNS. This study provides us with new perspectives on the retrovirus-host cell interaction and sheds light on retrovirus-induced neurodegeneration as a result of the astrocyte-neuron interaction.

Cytochrome P450 4F isoforms in different species: Identification, gene regulation and putative roles in inflammation

The cytochrome P450 4F subfamily comprises a group of enzymes that metabolize derivatives of arachidonic acid such as prostaglandins, lipoxins leukotrienes and hydroxyeicosatetraenoic acids, which are important mediators involved in the inflammatory response. Therefore, we speculate that CYP4Fs might be able to modulate the extent of the inflammation by controlling of the tissue levels of these inflammatory mediators, especially, leukotriene B4. One way to provide support for this hypothesis is to test whether the expression of CYP4Fs changes under inflammatory conditions, since these changes are required to adjust the levels of inflammatory mediators. ^ A lipopolysacchride (LPS) induced rat inflammation model was used to analyze the expressions of rat CYP4F4 and CYP4F5 in liver and kidney. LPS administration did not change the constitutive expression level of CYP4F4 and CYP4F5. In liver, the expressions of CYP4F4 and CYP4F5 decreased to 50–60% of the untreated level. The same effect of LPS on CYP4F4 and CYP4F5 expression can be mimicked in hepatocyte primary cultures treated with LPS, indicating a direct of effect of LPS on hepatocytes. LPS treatment also decreased the activity of liver microsomes towards chlorpromazine, however, antibody inhibition study revealed that liver CYP4Fs are not the only players in metabolizing chlorpromazine. To study further the underlying mechanism, CYP4F5 gene was isolated, characterized, and the promoter region was defined. ^ Accumulating evidence showed that peroxisome proliferator-activated receptors (PPARs) play an active role in inflammation. To investigate the possible role of PPARα in regulating CYP4F expression by inflammation or by clofibrate treatment, the expressions of two new mouse 4F isoforms were analyzed in PPARα knockout mice upon LPS or clofibrate challenge. A novel induction of CYP4F15 by LPS and clofibrate was observed in kidney, and this effect is totally dependent on the presence of PPARα. Renal CYP4F16 expression was not affected by LPS or clofibrate in both (+/+) and (−/−) mice. In contrast, hepatic expressions of CYP4F15 and CYP4F16 were reduced significantly in (+/+) mice, but much less in (−/−) mice, suggesting that PPARα is partially responsible for this down-regulation. Clofibrate treatment reduced the expression of CYP4F16 in liver, but has no effect on CYP4F15 and PPARα does not have a role in hepatic CYP4F expression regulated by clofibrate. In general, CYP4Fs are regulated in an isoform-, tissue- and species-specific manner. ^ A human CYP4F isoform, CYP4F11, was isolated. The genomic structure was also solved by using database mining and bioinformatics tools. Localization of CYP4F11 to chromosome 19, 16 kb upstream of CYP4F2, suggests that human CYP4F genes may form a cluster on chromosome 19. This novel human 4F is highly expressed in liver, as well as in kidney, heart and skeletal muscle. Further study of the activity and gene regulation on CYP4F11 will provide us more insights into the physiological functions of CYP4F subfamily. ^

Nrf2 activation supports cell survival during hypoxia and hypoxia/reoxygenation in cardiomyoblasts; the roles of reactive oxygen and nitrogen species

Adaptive mechanisms involving upregulation of cytoprotective genes under the control of transcription factors such as Nrf2 exist to protect cells from permanent damage and dysfunction under stress conditions. Here we explore of the hypothesis that Nrf2 activation by reactive oxygen and nitrogen species modulates cytotoxicity during hypoxia (H) with and without reoxygenation (H/R) in H9C2 cardiomyoblasts. Using MnTBap as a cell permeable superoxide dismutase (SOD) mimetic and peroxynitrite scavenger and L-NAME as an inhibitor of nitric oxide synthase (NOS), we have shown that MnTBap inhibited the cytotoxic effects of hypoxic stress with and without reoxygenation. However, L-NAME only afforded protection during H. Under reoxygenation, conditions, cytotoxicity was increased by the presence of L-NAME. Nrf2 activation was inhibited independently by MnTBap and L-NAME under H and H/R. The increased cytotoxicity and inhibition of Nrf2 activation by the presence of L-NAME during reoxygenation suggests that NOS activity plays an important role in cell survival at least in part via Nrf2-independent pathways. In contrast, O2 -• scavenging by MnTBap prevented both toxicity and Nrf2 activation during H and H/R implying that toxicity is largely dependent on O2 -.To confirm the importance of Nrf2 for myoblast metabolism, Nrf2 knockdown with siRNA reduced cell survival by 50% during 4h hypoxia with and without 2h of reoxygenation and although cellular glutathione (GSH) was depleted during H and H/R, GSH loss was not exacerbated by Nrf2 knockdown. These data support distinctive roles for ROS and RNS during H and H/R for Nrf2 induction which are important for survival independently of GSH salvage. © 2013 The Authors.

New insights into plant salt acclimation: the roles of vesicle trafficking and reactive oxygen species signalling in mitochondria and the endomembrane system

In this study, we investigated the cellular and molecular mechanisms that regulate salt acclimation. The main objective was to obtain new insights into the molecular mechanisms that control salt acclimation. Therefore, we carried out a multidisciplinary study using proteomic, transcriptomic, subcellular and physiological techniques. We obtained a Nicotiana tabacum BY-2 cell line acclimated to be grown at 258 mM NaCl as a model for this study. The proteomic and transcriptomic data indicate that the molecular response to stress (chaperones, defence proteins, etc.) is highly induced in these salt-acclimated cells. The subcellular results show that salt induces sodium compartmentalization in the cell vacuoles and seems to be mediated by vesicle trafficking in tobacco salt-acclimated cells. Our results demonstrate that abscisic acid (ABA) and proline metabolism are crucial in the cellular signalling of salt acclimation, probably regulating reactive oxygen species (ROS) production in the mitochondria. ROS may act as a retrograde signal, regulating the cell response. The network of endoplasmic reticulum and Golgi apparatus is highly altered in salt-acclimated cells. The molecular and subcellular analysis suggests that the unfolded protein response is induced in salt-acclimated cells. Finally, we propose that this mechanism may mediate cell death in salt-acclimated cells.

Quantifying the roles of competing static gears: comparative selectivity of longlines and monofilament gill nets in a multi-species fishery of the Algarve (southern Portugal)

Fishing trials with monofilament gill nets and longlines using small hooks were carried out in Algarve waters (southern Portugal) over a one-year period. Four hook sizes of "Mustad" brand, round bent, flatted sea hooks (Quality 2316 DT, numbers 15, 13, 12 and 11) and four mesh sizes of 25, 30, 35 and 40 mm (bar length) monofilament gill nets were used. Commercially valuable sea breams dominated the longline catches while small pelagics were relatively more important in the gill nets. Significant differences in the catch size frequency distributions of the two gears were found for all the most important species caught by both gears (Boops boops, Diplodus bellottii, Diplodus vulgaris, Pagellus acarne, Pagellus erythrinus, Spondyiosoma cantharus, Scomber japonicus and Scorpaena notata), with longlines catching larger fish and a wider size range than nets. Whereas longline catch size frequency distributions for most species for the different hook sizes were generally highly overlapped, suggesting little or no differences in size selectivity, gill net catch size frequency distributions clearly showed size selection. A variety of models were fitted to the gill net and hook data using the SELECT method, while the parameters of the logistic model were estimated by maximum likelihood for the longline data. The bi-normal model gave the best fits for most of the species caught with gill nets, while the logistic model adequately described hook selectivity. The results of this study show that the two static gears compete for many of the same species and have different impacts in terms of catch composition and size selectivity. This information will I;e useful for the improved management of these small-scale fisheries in which many different gears compete for scarce resources.

Difference in mosquito species (Diptera: Culicidae) and the transmission of Ross River Virus between coastline and inland areas in Brisbane, Australia

This study examined the distribution of major mosquito species and their roles in the transmission of Ross River virus (RRV) infection for coastline and inland areas in Brisbane, Australia (27°28′ S, 153°2′ E). We obtained data on the monthly counts of RRV cases in Brisbane between November 1998 and December 2001 by statistical local areas from the Queensland Department of Health and the monthly mosquito abundance from the Brisbane City Council. Correlation analysis was used to assess the pairwise relationships between mosquito density and the incidence of RRV disease. This study showed that the mosquito abundance of Aedes vigilax (Skuse), Culex annulirostris (Skuse), and Aedes vittiger (Skuse) were significantly associated with the monthly incidence of RRV in the coastline area, whereas Aedes vigilax, Culex annulirostris, and Aedes notoscriptus (Skuse) were significantly associated with the monthly incidence of RRV in the inland area. The results of the classification and regression tree (CART) analysis show that both occurrence and incidence of RRV were influenced by interactions between species in both coastal and inland regions. We found that there was an 89% chance for an occurrence of RRV if the abundance of Ae. vigifax was between 64 and 90 in the coastline region. There was an 80% chance for an occurrence of RRV if the density of Cx. annulirostris was between 53 and 74 in the inland area. The results of this study may have applications as a decision support tool in planning disease control of RRV and other mosquito-borne diseases.

Conservation and divergence of four kiwifruit SVP-like MADS-box genes suggest distinct roles in kiwifruit bud dormancy and flowering

MADS-box genes similar to Arabidopsis SHORT VEGETATIVE PHASE (SVP) have been implicated in the regulation of flowering in annual species and bud dormancy in perennial species. Kiwifruit (Actinidia spp.) are woody perennial vines where bud dormancy and out-growth affect flower development. To determine the role of SVP-like genes in dormancy and flowering of kiwifruit, four MADS-box genes with homology to Arabidopsis SVP, designated SVP1, SVP2, SVP3, and SVP4, have been identified and analysed in kiwifruit and functionally characterized in Arabidopsis. Phylogenetic analysis indicate that these genes fall into different sub-clades within the SVP-like gene group, suggesting distinct functions. Expression was generally confined to vegetative tissues, and increased transcript accumulation in shoot buds over the winter period suggests a role for these genes in bud dormancy. Down-regulation before flower differentiation indicate possible roles as floral repressors. Over-expression and complementation studies in Arabidopsis resulted in a range of floral reversion phenotypes arising from interactions with Arabidopsis MADS-box proteins, but only SVP1 and SVP3 were able to complement the svp mutant. These results suggest that the kiwifruit SVP-like genes may have distinct roles during bud dormancy and flowering.

Acoustic sensing: Roles and applications in monitoring avian biodiversity

This thesis examined the use of acoustic sensors for monitoring avian biodiversity. Acoustic sensors have the potential to significantly increase the spatial and temporal scale of ecological observations, however acoustic recordings of the environment can be opaque and complex. This thesis developed methods for analysing large volumes of acoustic data to maximise the detection of bird species, and compared the results of acoustic sensor biodiversity surveys with traditional bird survey techniques.

The roles of shared vs. Distinctive conceptual features in lexical access

Contemporary models of spoken word production assume conceptual feature sharing determines the speed with which objects are named in categorically-related contexts. However, statistical models of concept representation have also identified a role for feature distinctiveness, i.e., features that identify a single concept and serve to distinguish it quickly from other similar concepts. In three experiments we investigated whether distinctive features might explain reports of counter-intuitive semantic facilitation effects in the picture word interference (PWI) paradigm. In Experiment 1, categorically-related distractors matched in terms of semantic similarity ratings (e.g., zebra and pony) and manipulated with respect to feature distinctiveness (e.g., a zebra has stripes unlike other equine species) elicited interference effects of comparable magnitude. Experiments 2 and 3 investigated the role of feature distinctiveness with respect to reports of facilitated naming with part-whole distractor-target relations (e.g., a hump is a distinguishing part of a CAMEL, whereas knee is not, vs. an unrelated part such as plug). Related part distractors did not influence target picture naming latencies significantly when the part denoted by the related distractor was not visible in the target picture (whether distinctive or not; Experiment 2). When the part denoted by the related distractor was visible in the target picture, non-distinctive part distractors slowed target naming significantly at SOA of -150 ms (Experiment 3). Thus, our results show that semantic interference does occur for part-whole distractor-target relations in PWI, but only when distractors denote features shared with the target and other category exemplars. We discuss the implications of these results for some recently developed, novel accounts of lexical access in spoken word production.

To sonicate or not to sonicate PM filters: Reactive Oxygen Species generation upon ultrasonic irradiation

In aerosol research, a common approach for the collection of particulate matter (PM) is the use of filters in order to obtain sufficient material to undertake analysis. For subsequent chemical and toxicological analyses, in most of cases the PM needs to be extracted from the filters. Sonication is commonly used to most efficiently extract the PM from the filters. Extraction protocols generally involve 10 - 60 min of sonication. The energy of ultrasonic waves causes the formation and collapse of cavitation bubbles in the solution. Inside the collapsing cavities the localised temperatures and pressures can reach extraordinary values. Although fleeting, such conditions can lead to pyrolysis of the molecules present inside the cavitation bubbles (gases dissolved in the liquid and solvent vapours), which results in the production of free radicals and the generation of new compounds formed by reactions with these free radicals. For example, simple sonication of pure water will result in the formation of detectable levels of hydroxyl radicals. As hydroxyl radicals are recognised as playing key roles as oxidants in the atmosphere the extraction of PM from filters using sonication is therefore problematic. Sonication can result in significant chemical and physical changes to PM through thermal degradation and other reactions. In this article, an overview of sonication technique as used in aerosol research is provided, the capacity for radical generation under these conditions is described and an analysis is given of the impact of sonication-derived free radicals on three molecular probes commonly used by researchers in this field to detect Reactive Oxygen Species in PM.