Oceanographic and atmospheric phenomena influence the abundance of whale sharks at Ningaloo Reef, Western Australia

Seasonal observations of whale shark abundance recorded by ecotourist operators at Ningaloo Reef, Western Australia from 1999 to 2004 were compared with weekly regional and global oceanographic and atmospheric variables, including average sea surface temperatures, along-shelf wind shear, sea level and the Southern Oscillation Index (SOI). Estimates of these physical variables were derived from either ground-based data or from remote sensing instruments. A generalised linear mixed-effects modelling (GLMM) approach with random sampling and model simulation was used to determine the relationships between the number of whale sharks and all model variants of the environmental parameters, using information-theoretic weights of evidence to rank models. SOI and wind shear had the most support for explaining the deviance in weekly whale shark abundance at Ningaloo Reef during a season. The SOI and wind shear variables positively influenced whale shark abundance such that more sharks were sighted when the Southern Oscillation was stronger and along-shelf winds were increasingly prevalent. This may reflect changes in the strength of oceanographic processes such as the Leeuwin Current (in response to the Southern Oscillation) and wind/current driven upwelling which may affect the abundance of whale sharks transported to the region and/or the availability of their prey by driving productivity changes.     

Aggregations of juvenile whale sharks (<Emphasis Type="Italic">Rhincodon typus</Emphasis>) in the Gulf of Tadjoura,Djibouti

A total of 23 whale sharks were identified over a 5 d period in the Arta Bay region of the Gulf of Tadjora, Djibouti. Most of the sharks aggregating in this area were small (<4 m TL) males. Individuals were identified using photographs of distinctive scars and spot and stripe patterns on the sides of the animals. Of these, 65% had scarring that was attributable to boat or propeller strikes. Most of the whale sharks we encountered were feeding on dense accumulations of plankton in shallow water just off (10–200 m) the shoreline. This food source may account for the aggregation of sharks in this area. One 3 m male shark was tagged with an ARGOS (Splash) satellite tag for 9 d. During this time the shark traversed to the shoreline on the opposite side of the Gulf (a distance of 14 km) and then returned to the Arta Bay area before retracing his path to the other shore. The shark spent most of the daylight hours at the surface, while at night dives were more frequent, deeper and for longer durations.

To go or not to go with the flow: Environmental influences on whale shark movement patterns

Seven whale sharks were tracked using satellite-linked tags from Ningaloo Reef, off northern Western Australia, following tagging in April and June 2002 and April-May 2005. We investigated how the movements of those whale shark tracks were influenced by geostrophic surface currents during sequential one-week periods by using a passive diffusion model parameterised with observed starting locations of the sharks and weekly maps of surface current velocity and direction (derived from altimetry). We compared the outputs from the passive diffusion model and maps of chlorophyll-a concentration (SeaWiFs/MODIS) and with the actual tracks of the sharks using GIS and generalized linear mixed-effects models (GLMM). The GLMM indicated very little support for passive diffusion with sea-surface ocean currents influencing whale shark distributions in the north eastern Indian Ocean. Moreover, the sharks' movements correlated only weakly with the spatial distribution of sea-surface chlorophyll-a concentrations. The seven whale sharks had average swimming speeds comparable with those recorded in other satellite tracking studies of this species. Swimming speeds of the seven sharks were similar to those reported in previous studies and up to three times greater than the maximum sea-surface current velocities that the sharks encountered while traversing into lower southerly latitudes (moving northward towards the equator). Our results indicate that whale sharks departing from Ningaloo travel actively and independently of near-surface currents where they spend most of their time despite additional metabolic costs of this behaviour.     

Evaluation of FT-IR spectroscopy as a tool to quantify bacteria in binary mixed cultures

Fourier-transform infrared (FT-IR) spectroscopy is known as a high-resolution method for the rapid identification of pure cultures of microorganisms. Here, we evaluated FT-IR as a method for the quantification of bacterial populations in binary mixed cultures consisting of Pseudomonas putida and Rhodococcus ruber. A calibration procedure based on Principal Component Regression was developed for estimating the ratio of the bacterial species. Data for method calibration were gained from pure cultures and artificially assembled communities of known ratios of the two member populations. Moreover, to account for physiological variability, FT-IR measurements were performed with organisms sampled at different growth phases. Measurements and data analyses were subsequently applied to growing mixed cultures revealing that growth of R. ruber was almost completely suppressed in co-culture with P. putida. Population ratios obtained by fatty acid analysis as an independent reference method were in high agreement with the FT-IR derived ratios.     

Seasonal dynamics of entomopathogenic nematodes of the genera Steinernema and Heterorhabditis as a response to abiotic factors and abundance of insect hosts

The seasonal dynamics of entomopathogenic nematodes (EPNs) of the genus Steinernema and Heterorhabditis were studied during one season in meadow and oak wood habitats, in the vicinity of Ceské Budejovice, Czech Republic. The influences of soil temperature, moisture, and abundance of suitable hosts on EPN dynamics were investigated. The host range of these nematodes, in both habitats was also observed. A total of four EPN species were found in both habitats. Steinernema affine was the dominant species both in oak wood and in meadow. Additionally, the oak wood habitat was inhabited by S. kraussei and S. weiseri; the meadow habitat by Heterorhabditis bacteriophora. The mean abundance of total EPN community was 28,000ind./m(2) in oak wood and 11,000ind./m(2) in meadow. The seasonal dynamics of entomopathogenic nematodes in both habitats were characterized by high nematode densities in the beginning of the season, followed by a rapid decrease, and then stabilization. EPN abundances did not show any apparent correlation with soil temperature and moisture, but they were negatively correlated with the abundance of suitable insect hosts. Inter- and intraspecific competition for limited nutrients (hosts) probably played a major role in EPN seasonal dynamics. Broad host range of entomopathogenic nematodes in both habitats was predominantly represented by dipteran and coleopteran larvae. Most common hosts belonged to the families Asilidae, Bibionidae, and Empididae (Diptera), as well as Carabidae and Curculionidae (Coleoptera).     

MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: Application to the identification of Lupinus nodulating strains

Genus Bradyrhizobium includes slow growing bacteria able to nodulate different legumes as well as species isolated from plant tumours. The slow growth presented by the members of this genus and the phylogenetic closeness of most of its species difficults their identification. In the present work we applied for the first time Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to the analysis of Bradyrhizobium species after the extension of MALDI Biotyper 2.0 database with the currently valid species of this genus. With this methodology it was possible to identify strains belonging to phylogenetically closely related species of genus Bradyrhizobium allowing the discrimination among species with rrs gene identities higher than 99%. The application of MALDI-TOF MS to strains isolated from nodules of different Lupinus species in diverse geographical locations allowed their correct identification when comparing with the results of rrs gene and ITS analyses. The nodulation of Lupinus gredensis, an endemic species of the west of Spain, by B. canariense supports the European origin of this species.     

Demography, reproduction, and dormancy along altitudinal gradients in three intermountain Allium species with contrasting abundance and distribution

Little is known about the variation in demographics, flower number, fruit set, and summer dormancy in Allium species native to the Intermountain West region of the United States. The purpose of this study was to investigate demographic patterns, summer dormancy traits, and variation in reproductive characteristics among habitats. Three populations of each of three species, Allium acuminatum, A. brandegei, and A. passeyi, were studied along an altitudinal gradient in northern Utah, USA, from 2004 to 2006. Demographic data were collected from individuals in permanent plots established in each population. Individual flowering plants were periodically monitored and used to calculate reproductive characteristics. Leaf area measurements throughout the 2005 growing season and soil temperature sensors were used to assess the relationship between habitat and dormancy characteristics. Populations of the widely distributed species, A. acuminatum and A. brandegei, were dominated by individuals in seedling and flowering stages while the restricted A. passeyi had populations containing a majority of individuals in the post-seedling, but non-flowering stage-class. There was a strong directional trend in A. acuminatum reproductive traits, with flower number and fruit set decreasing with increasing elevation. The mid-elevation A. brandegei populations were reproductively more successful than the high and low-elevation populations. The high-elevation A. passeyi population had more flowers per plant and higher fruit set in comparison to the lower elevation populations. The onset of summer dormancy as indicated by the timing of leaf senescence, was associated with high soil temperatures specific to each species. In general, the timing of leaf senescence was later in higher elevation populations in all species. A smaller proportion of non-flowering individuals in A. acuminatum and A. brandegei may indicate a high seedling mortality rate or a shorter juvenile phase in comparison to A. passeyi. The A. passeyi populations exhibit demographic characteristics of rare taxa; low seed production and low seedling recruitment. The high number of non-flowering plants in A. passeyi likely includes many reproductively mature individuals which are influenced by the unique habitat and environment of this species. Temperature is likely the key environmental cue inducing summer dormancy in all three species.     

Fortnightly periodicity in the abundance of diatom and dinoflagellate taxa at a coastal study site

From 3 July to 15 September 2000, plankton samples were collected roughly every 2 days at three stations within 1.5 km from shore at Sunset Bay, OR. In these samples we enumerated Coscinodiscus-like diatoms, Protoperidinium spp., and the potentially toxic phytoplankter, Pseudo-nitzschia spp. Using time series analysis, the abundance of these phytoplankters was compared to wind stress, tidal range, and sea surface temperature (SST). SST was significantly cross-correlated with wind stress (lower SST occurred during upwelling favorable winds) and maximum daily tidal range (cold and warm anomalies in SST occurred around the neap and spring tides, respectively). We found no significant cross-correlations between wind stress (upwelling vs. downwelling winds) and the abundance of any of the taxa. Significant cross-correlations were found between phytoplankton abundances and the maximum daily tidal range (peak concentrations occurred between the neap and spring tides) and SST (peak concentrations occurred during periods of warmer SST). We hypothesize that this pattern of abundance may be caused by shoreward transport of offshore phytoplankton populations by internal tidal waves.     

Genomic DNA macroarrays as a tool for analysis of gene expression in Leishmania

Gene-array technologies have been applied in a wide number of organisms to study gene expression profiling under several physiological and experimental conditions. Gene-array implementations combined with the information arising from emerging genome sequencing projects are expected to be in the near future a major tool to characterize genes involved in different processes. So far, gene expression profile studies in trypanosomatids have been performed in microarrays that use a glass support to immobilize fragments of genomic DNA followed by fluorescent detection. Here, we wanted to test the potential of genomic DNA macroarrays of Leishmania infantum using nylon membranes and radioactive detection. Nylon macroarrays present a number of advantages since the processing of the membranes is based on standard Southern blotting protocols familiar to molecular biologists, and the data acquisition equipment is available to most research institutions. Nylon macroarrays were employed to search for genes showing increased mRNA abundance during an axenic differentiation of L. infantum promastigotes to amastigotes. Several clones were rescued and, after validation by Northern blot assays, these L. infantum sequences were used to screen the Leishmania major gene database. The L. major contigs with high homology to the L. infantum sequences allowed a consistent identification of the regulated genes.     

Antioxidant dehydrotocopherols as a new chemical character of Stemona species

From the roots of various Stemona species four new dehydrotocopherols (chromenols) were isolated and their structures and stereochemistry elucidated by spectroscopic methods. The double bond between C-3 and C-4 proved to be a typical chemical character of the genus found in most of the species. Various C-methylations of the aromatic ring reflect differences in methyltransferase activities and agreed with the current species delimitations showing an exclusive accumulation of dehydro-delta-tocopherol for the Stemona tuberosa group, whereas different provenances of Stemona curtisii were characterized by dehydro-gamma-tocopherol accompanied by small amounts of dehydro-alpha-tocopherol. From Stemona collinsae all four tocopherols were isolated with a clear preponderance of dehydro-delta-tocopherol accompanied by smaller amounts of the rare dehydro-beta-tocopherol. Stemona burkillii and a group of unidentified species showed a weak accumulation trend towards dehydro-alpha-tocopherol, whereas Stemona cochinchinensis and especially Stemona kerrii clearly differed by a preponderance of chromanol derivatives. In Stemona cf. pierrei no tocopherols could be detected at all. Based on TLC tests and microplate assays with the free radical 2,2-diphenyl-1-picrylhydrazyl (DPPH*) the antioxidant capacities of all chromenol derivatives were comparable with that of alpha-tocopherol showing no significant differences among each other, except for a more rapid kinetic behaviour of the 5,7,8-methylated dehydro-alpha-tocopherol.     

3-hydroxypropionic acid as a nematicidal principle in endophytic fungi

3- Hydroxypropionic acid was isolated by bioactivity-guided fractionation of extracts obtained from submerged cultures of several endophytic fungi isolated from above-ground plant organs. This compound showed selective nematicidal activity against the plant-parasitic nematode Meloidogyne incognita with LD50 values of 12.5-15 microg/ml. Activity against the saprophytic Caenorhabditis elegans was fivefold lower. No antimicrobial, cytotoxic or phytotoxic effects were observed. Propionic acid and D- and L-lactic acids were not active against either nematode species. Based on morphological features and ITS, 18S and 28S rDNA analyses, the producing strains were identified as Phomopsis phaseoli isolated from the leaf of a tropical tree, and four strains of Melanconium betulinum isolated from twigs of Betula pendula and B. pubescens in Germany. This is the first report of 3-hydroxypropionic acid in fungi, and of the nematicidal activity of this metabolite.     

Feruloyl esterases as a tool for the release of phenolic compounds from agro-industrial by-products

Agro-industrial by-products are a potential source of added-value phenolic acids with promising applications in the food and pharmaceutical industries. Here two purified feruloyl esterases from Aspergillus niger, FAEA and FAEB were tested for their ability to release phenolic acids such as caffeic acid, p-coumaric acid and ferulic acid from coffee pulp, apple marc and wheat straw. Their hydrolysis activity was evaluated and compared with their action on maize bran and sugar beet pulp. The specificity of both enzymes against natural and synthetic substrates was evaluated; particular attention was paid to quinic esters and lignin monomers. The efficiency of both enzymes on model substrates was studied. We show the ability of these enzymes to hydrolyze quinic esters and ester linkages between phenolic acids and lignin monomer.     

Composite Cucurbita pepo plants with transgenic roots as a tool to study root development

Background and Aims

In most plant species, initiation of lateral root primordia occurs above the elongation zone. However, in cucurbits and some other species, lateral root primordia initiation and development takes place in the apical meristem of the parental root. Composite transgenic plants obtained by Agrobacterium rhizogenes-mediated transformation are known as a suitable model to study root development. The aim of the present study was to establish this transformation technique for squash.

Methods

The auxin-responsive promoter DR5 was cloned into the binary vectors pKGW-RR-MGW and pMDC162-GFP. Incorporation of 5-ethynyl-2′-deoxyuridine (EdU) was used to evaluate the presence of DNA-synthesizing cells in the hypocotyl of squash seedlings to find out whether they were suitable for infection. Two A. rhizogenes strains, R1000 and MSU440, were used. Roots containing the respective constructs were selected based on DsRED1 or green fluorescent protein (GFP) fluorescence, and DR5::Egfp-gusA or DR5::gusA insertion, respectively, was verified by PCR. Distribution of the response to auxin was visualized by GFP fluorescence or β-glucuronidase (GUS) activity staining and confirmed by immunolocalization of GFP and GUS proteins, respectively.

Key Results

Based on the distribution of EdU-labelled cells, it was determined that 6-day-old squash seedlings were suited for inoculation by A. rhizogenes since their root pericycle and the adjacent layers contain enough proliferating cells. Agrobacterium rhizogenes R1000 proved to be the most virulent strain on squash seedlings. Squash roots containing the respective constructs did not exhibit the hairy root phenotype and were morphologically and structurally similar to wild-type roots.

Conclusions

The auxin response pattern in the root apex of squash resembled that in arabidopsis roots. Composite squash plants obtained by A. rhizogenes-mediated transformation are a good tool for the investigation of root apical meristem development and root branching.     

Facultative scavenging as a survival strategy of entomopathogenic nematodes

Entomopathogenic nematodes cannot be considered only as parasitic organisms. With dead Galleria mellonella larvae, we demonstrated that these nematodes use scavenging as an alternative survival strategy. We consider scavenging as the ability of entomopathogenic nematodes to penetrate, develop and produce offspring in insects which have been killed by causes other than the nematode-bacteria complex. Six Steinernema and two Heterorhabditis species scavenged but there were differences among them in terms of frequency of colonisation and in the time after death of G. mellonella larvae that cadavers were penetrated. The extremes of this behaviour were represented by Steinernema glaseri which was able to colonise cadavers which had been freeze-killed 240 h earlier and Heterorhabditis indica which only colonised cadavers which had been killed up to 72 h earlier. Also, using an olfactometer, we demonstrated that entomopathogenic nematodes were attracted to G. mellonella cadavers.     

Carnivory in plants as a beneficial trait in wetlands

A new hypothesis for the benefit of carnivory in plants (i.e., an alternative to aerenchyma for avoiding hypoxia) is evaluated. Root porosity and root depth were quantified in eight carnivorous plant species and 48 non-carnivorous species within a nutrient-poor wet pine savanna in south Mississippi, USA. Carnivorous and non-carnivorous plant species were contrasted with respect to their indication of wetlands, open habitats, and habitats with nutrient-poor soils. We used path analysis, multiplicative regression, and a field experiment to test hypotheses of the effects of soil moisture/hypoxia on the abundance of carnivorous and non-carnivorous plants. All carnivorous plant species produced non-porous roots (or no roots), which were shallower than the average for non-carnivorous plants (6.9 ± 0.95 cm vs. 11.9 ± 0.96 cm), even after correcting for plant size. Root porosity in non-carnivorous species (mean = 22%) was positively correlated with root depth (r = 0.6). Despite lacking porous roots, carnivorous plants were four times more indicative of wetland habitats than were the non-carnivorous species encountered in the wetland studied here. Carnivorous plants, along with non-carnivorous plants with well-developed aerenchyma, were positively associated with the wettest microsites and were more negatively affected by elevating the substrate than were non-carnivorous plants with low-porosity roots. Non-carnivorous plants with shallow roots, while less indicative of wetlands and less abundant in wet microsites of the wet pine savanna than were carnivorous plants, were no less indicative of nutrient-poor soils than were carnivorous plants. Results supported the hypothesis that carnivory is advantageous in wet soils and disadvantageous in drier (including mesic) soils and are more indicative of wetland conditions than of low soil fertility.     

A survey of ancient conserved non-coding elements in the PAX6 locus reveals a landscape of interdigitated cis-regulatory archipelagos

Biological differences between cell types and developmental processes are characterised by differences in gene expression profiles. Gene-distal enhancers are key components of the regulatory networks that specify the tissue-specific expression patterns driving embryonic development and cell fate decisions, and variations in their sequences are a major contributor to genetic disease and disease susceptibility. Despite advances in the methods for discovery of putative cis-regulatory sequences, characterisation of their spatio-temporal enhancer activities in a mammalian model system remains a major bottle-neck. We employed a strategy that combines gnathostome sequence conservation with transgenic mouse and zebrafish reporter assays to survey the genomic locus of the developmental control gene PAX6 for the presence of novel cis-regulatory elements. Sequence comparison between human and the cartilaginous elephant shark (Callorhinchus milii) revealed several ancient gnathostome conserved non-coding elements (agCNEs) dispersed widely throughout the PAX6 locus, extending the range of the known PAX6 cis-regulatory landscape to contain the full upstream PAX6-RCN1 intergenic region. Our data indicates that ancient conserved regulatory sequences can be tested effectively in transgenic zebrafish even when not conserved in zebrafish themselves. The strategy also allows efficient dissection of compound regulatory regions previously assessed in transgenic mice. Remarkable overlap in expression patterns driven by sets of agCNEs indicates that PAX6 resides in a landscape of multiple tissue-specific regulatory archipelagos.     

Eya 1 acts as a critical regulator for specifying the metanephric mesenchyme

Although it is well established that the Gdnf-Ret signal transduction pathway initiates metanephric induction, no single regulator has yet been identified to specify the metanephric mesenchyme or blastema within the intermediate mesoderm, the earliest step of metanephric kidney development and the molecular mechanisms controlling Gdnf expression are essentially unknown. Previous studies have shown that a loss of Eya 1 function leads to renal agenesis that is a likely result of failure of metanephric induction. The studies presented here demonstrate that Eya 1 specifies the metanephric blastema within the intermediate mesoderm at the caudal end of the nephrogenic cord. In contrast to its specific roles in metanephric development, Eya 1 appears dispensable for the formation of nephric duct and mesonephric tubules. Using a combination of null and hypomorphic Eya 1 mutants, we now demonstrated that approximately 20% of normal Eya 1 protein level is sufficient for establishing the metanephric blastema and inducing the ureteric bud formation but not for its normal branching. Using Eya 1, Gdnf, Six 1 and Pax 2 mutant mice, we show that Eya 1 probably functions at the top of the genetic hierarchy controlling kidney organogenesis and it acts in combination with Six 1 and Pax 2 to regulate Gdnf expression during UB outgrowth and branching. These findings uncover an essential function for Eya 1 as a critical determination factor in acquiring metanephric fate within the intermediate mesoderm and as a key regulator of Gdnf expression during ureteric induction and branching morphogenesis.     

A model to explain the origin of a parasite sex-specific population structure

A discrete time model was built to understand the origin of the sex-specific population structure of the human blood fluke, Schistosoma mansoni. We have estimated both male/female individual ratio and male/female genotype ratio of this parasite taking into account all the experimental published values on differential male and female life-history traits all along the life cycle. We considered in our model male and female life-history traits when both separated and together. The model showed that both male/female individual ratio and male/female genotype ratio of S. mansoni adults are biased toward males in each combination. This bias was more important in male/female genotype ratio than in the male/female individual ratio for the same initial values of cercarial development success. This model could explain the sex specific population structure of this parasite. Firstly, we showed that the male-biased individual ratio finds its origin in the vertebrate host. Secondly, we showed that the male-biased genotype ratio originates prior to any interrelationship between adult worms and could generate by itself a sex-specific genetic structure.