Modelling the niche for a marine vertebrate: a case study incorporating behavioural plasticity,proximate threats and climate change

The integration of satellite telemetry, remotely sensed environmental data, and habitat/environmental modelling has provided for a growing understanding of spatial and temporal ecology of species of conservation concern. The Republic of Cape Verde comprises the only substantial rookery for the loggerhead turtle Caretta caretta in the eastern Atlantic. A size related dichotomy in adult foraging patterns has previously been revealed for adult sea turtles from this population with a proportion of adults foraging neritically, whilst the majority forage oceanically. Here we describe observed habitat use and employ ecological niche modelling to identify suitable foraging habitats for animals utilising these two distinct behavioural strategies. We also investigate how these predicted habitat niches may alter under the influence of climate change induced oceanic temperature rises. We further contextualise our niche models with fisheries catch data and knowledge of fisheries ‘hotspots’ to infer threat from fisheries interaction to this population, for animals employing both strategies. Our analysis revealed repeated use of coincident oceanic habitat, over multiple seasons, by all smaller loggerhead turtles, whilst larger neritic foraging turtles occupied continental shelf waters. Modelled habitat niches were spatially distinct, and under the influence of predicted sea surface temperature rises, there was further spatial divergence of suitable habitats. Analysis of fisheries catch data highlighted that the observed and modelled habitats for oceanic and neritic loggerhead turtles could extensively interact with intensive fisheries activity within oceanic and continental shelf waters of northwest Africa. We suggest that the development and enforcement of sustainable management strategies, specifically multi‐national fisheries policy, may begin to address some of these issues; however, these must be flexible and adaptive to accommodate potential range shift for this species.     

Anti-inflammatory drugs, eicosanoids and the annexin A1/FPR2 anti-inflammatory system

The action of anti-inflammatory and anti-allergic drugs on the eicosanoid system is briefly reviewed. In addition to the aspirin-like drugs, which directly inhibit the cyclo-oxygenase enzymes, other drugs such as the glucocorticoids and the cromones also inhibit the formation of eicosanoids. In the latter cases this is bought about through the release of a protein factor that acts through formyl peptide receptors on the target cell surface. Of growing interest, is the observation that this receptor is also a target for other eicosanoids, such as lipoxins and resolvins that modulate host defence systems.     

Diversity of nifH gene pools in the rhizosphere of two cultivars of sorghum (Sorghum bicolor) treated with contrasting levels of nitrogen fertilizer.

The diversity of nitrogen-fixing bacteria was assessed in the rhizospheres of two cultivars of sorghum (IS 5322-C and IPA 1011) sown in Cerrado soil amended with two levels of nitrogen fertilizer (12 and 120 kg ha(-1)). The nifH gene was amplified directly from DNA extracted from the rhizospheres, and the PCR products cloned and sequenced. Four clone libraries were generated from the nifH fragments and 245 sequences were obtained. Most of the clones (57%) were closely related to nifH genes of uncultured bacteria. NifH clones affiliated with Azohydromonas spp., Ideonella sp., Rhizobium etli and Bradyrhizobium sp. were found in all libraries. Sequences affiliated with Delftia tsuruhatensis were found in the rhizosphere of both cultivars sown with high levels of nitrogen, while clones affiliated with Methylocystis sp. were detected only in plants sown under low levels of nitrogen. Moreover, clones affiliated with Paenibacillus durus could be found in libraries from the cultivar IS 5322-C sown either in high or low amounts of fertilizer. This study showed that the amount of nitrogen used for fertilization is the overriding determinative factor that influenced the nitrogen-fixing community structures in sorghum rhizospheres cultivated in Cerrado soil.     

Bacterial and fungal communities in bulk soil and rhizospheres of aluminum-tolerant and aluminum-sensitive maize (Zea mays L.) lines cultivated in unlimed and limed Cerrado soil

Liming of acidic soils can prevent aluminum toxicity and improve crop production. Some maize lines show aluminum (Al) tolerance, and exudation of organic acids by roots has been considered to represent an important mechanism involved in the tolerance. However, there is no information about the impact of liming on the structures of bacterial and fungal communities in Cerrado soil, nor if there are differences between the microbial communities from the rhizospheres of Al-tolerant and Al-sensitive maize lines. This study evaluated the effects of liming on the structure of bacterial and fungal communities in bulk soil and rhizospheres of Al-sensitive and Al-tolerant maize (Zea mays L.) lines cultivated in Cerrado soil by PCR-DGGE, 30 and 90 days after sowing. Bacterial fingerprints revealed that the bacterial communities from rhizospheres were more affected by aluminum stress in soil than by the maize line (Al-sensitive or Al-tolerant). Differences in bacterial communities were also observed over time (30 and 90 days after sowing), and these occurred mainly in the Actinobacteria. Conversely, fungal communities from the rhizosphere were weakly affected either by liming or by the rhizosphere, as observed from the DGGE profiles. Furthermore, only a few differences were observed in the DGGE profiles of the fungal populations during plant development when compared with bacterial communities. Cloning and sequencing of 16S rRNA gene fragments obtained from dominant DGGE bands detected in the bacterial profiles of the Cerrado bulk soil revealed that Actinomycetales and Rhizobiales were among the dominant ribotypes.     

Aurora-A Kinase Is Essential for Bipolar Spindle Formation and Early Development

Aurora-A is a conserved kinase implicated in mitotic regulation and carcinogenesis. Aurora-A was previously implicated in mitotic entry and spindle assembly, although contradictory results prevented a clear understanding of the roles of Aurora-A in mammals. We developed a conditional null mutation in the mouse Aurora-A gene to investigate Aurora-A functions in primary cells ex vivo and in vivo. We show here that conditional Aurora-A ablation in cultured embryonic fibroblasts causes impaired mitotic entry and mitotic arrest with a profound defect in bipolar spindle formation. Germ line Aurora-A deficiency causes embryonic death at the blastocyst stage with pronounced cell proliferation failure, mitotic arrest, and monopolar spindle formation. Aurora-A deletion in mid-gestation embryos causes an increase in mitotic and apoptotic cells. These results indicate that murine Aurora-A facilitates, but is not absolutely required for, mitotic entry in murine embryonic fibroblasts and is essential for centrosome separation and bipolar spindle formation in vitro and in vivo. Aurora-A deletion increases apoptosis, suggesting that molecular therapies targeting Aurora-A may be effective in inducing tumor cell apoptosis. Aurora-A conditional mutant mice provide a valuable system for further defining Aurora-A functions and for predicting effects of Aurora-A therapeutic intervention.The equal partitioning of chromosomes at mitosis is critical for avoiding aneuploidy, a condition associated with spontaneous miscarriage, developmental disorders, and cancer (50). Mitosis requires coordinated completion of multiple events including nuclear envelope breakdown, chromosome condensation and congression to the metaphase plate, centrosome separation, spindle formation, chromosome-spindle attachment and error correction, sister chromatid separation, and cytokinesis. Multiple regulators, many of which are kinases, are required to ensure that each event is completed in a timely fashion and in the proper order (reviewed in reference 46). Although a number of mitotic kinases have been identified, their targets and the intricacies of mitotic signal transduction pathways are just beginning to be understood.The Aurora kinases are key mitotic regulators in eukaryotes (reviewed in reference 45). The Aurora family includes a single member in yeasts (Saccharomyces cerevisiae Ipl1p, Schizosaccharomyces pombe Ark1), two members each in Caenorhabditis elegans and Drosophila, and two or three members in vertebrates. Although originally given a variety of names, Aurora kinases in multicellular eukaryotes have subsequently been classified into A, B, and C groups based on patterns of mitotic subcellular localization and homology, which also appear to reflect functional distinctions (8, 46). Aurora-A kinases are observed at centrosomes and adjacent spindle fibers, and current evidence supports key roles in regulating protein localization and function at centrosomes, as well as regulation of the assembly, stability, and function of the mitotic spindle (reviewed in reference 43). Aurora-B kinases display “chromosomal passenger” localization, residing on mitotic chromosomes and subsequently moving to the spindle midzone after separation of sister chromatids. Aurora-B family members have been implicated in the regulation of kinetochore-spindle attachment, the spindle checkpoint, and cytokinesis (reviewed in references 1 and 8). Aurora-C kinases, which have only been identified in mammals, have a limited expression pattern and appear to have functions that overlap those of Aurora-B (7, 53).The human Aurora-A kinase (hAurA) was first identified because of its overexpression in cancer cell lines (5, 58). The hAurA gene (stk15) resides on chromosome 20q13, a region frequently amplified in human cancers (5, 58). hAurA has been dubbed an oncogene because of the fact that its overexpression transforms immortalized rodent fibroblasts (5, 70). Polymorphisms in hAurA are associated with an increased risk of colon cancer, while murine AurA (mAurA) polymorphisms confer increased susceptibility to experimentally induced skin tumors (14). The mAurA gene is frequently amplified in radiation-induced lymphomas from p53 heterozygous mice, while loss of one mAurA allele has been observed in lymphomas from p53-null mice (41). Thus, aberrant AurA expression is associated with tumorigenesis, suggesting that insight into AurA functions will lead to a better understanding of tumorigenesis mechanisms.A number of experimental observations suggest that AurA kinases are required for normal centrosome maturation and bipolar spindle assembly. The AurA ortholog in Drosophila melanogaster (Aurora) was identified in a screen for mutations that impact the centrosome cycle (21). Syncytial embryos from hypomorphic Aurora mutant females display a variety of mitotic abnormalities resulting from a failure to separate centrosomes. Aurora-null flies die at the larval stage with characteristic monopolar spindles and circular chromosome arrays in larval neuroblasts. Such monopolar spindles arise from failed centrosome separation (21). Subsequent studies of Drosophila Aurora mutant alleles revealed additional defects in centrosome maturation (including a failure to localize transforming acidic coiled-coil protein, centrosomin, and γ-tubulin at centrosomes) and in asymmetric localization of Numb protein in sensory organ precursor cells (3, 17). Similar to the case in Drosophila, disruption of the C. elegans AurA ortholog AIR-1 by RNA interference (RNAi) or mutation causes defects in centrosome maturation and monopolar spindle formation. Centrosomes undergo normal separation but collapse, leading to monopolar spindle formation (16, 24, 56). Studies of the Xenopus AurA homolog pEg2 revealed similar phenotypes after overexpression of kinase-dead mutants, antibody-mediated inhibition, or immunodepletion (18, 19, 38, 52). Furthermore, Xenopus AurA has been shown to interact with and phosphorylate Eg5, a mitotic kinesin required for bipolar spindle formation, suggesting a possible mechanism by which AurA could influence bipolar spindle formation and/or stabilization (19). Thus, existing reports from these systems are quite consistent in implicating AurA in centrosome separation and function.In contrast to the systems described above, published reports of RNAi-mediated reduction of AurA expression in mammalian cell lines have contained conflicting results about the role of AurA in mitotic entry, bipolar spindle formation, and mitotic progression. AurA RNAi in HeLa cells was reported to block or delay mitotic entry, prompting the conclusion that AurA is essential for mitotic commitment in mammalian cells (27, 36). In contrast, other AurA RNAi studies showed accumulation of mitotic cells with monopolar spindles (12, 20, 67). These discrepancies call into question the functional conservation of AurA in mammals and highlight a need for additional studies to definitively address the roles of AurA. This is particularly critical for understanding the roles of AurA in cancer and for projecting possible effects of AurA inhibitors currently in development as anticancer agents. We used gene targeting in mouse embryonic stem (ES) cells to produce a conditional null allele at the AurA locus. Here we describe cellular phenotypes of AurA deletion in primary cells in vitro and developmental phenotypes of AurA mutant mice. We show that AurA deletion in primary embryonic fibroblasts causes delayed mitotic entry with accumulation of cells in early prophase, consistent with a role for AurA in mitotic entry. Nevertheless, AurA-deficient cells that enter prometaphase arrest with monopolar spindles and eventually exit mitosis without segregating their chromosomes. Prolonged culture of AurA-deficient cells leads to polyploidy with abnormal nuclear structure. Germ line AurA deficiency causes embryonic death at the blastocyst stage with mitotic arrest and monopolar spindle formation, while AurA deletion in mid-gestation embryos causes an increased mitotic index and increased apoptosis. Together, our findings indicate that AurA is required for timely mitotic entry and bipolar spindle formation in vitro and in vivo.     

Memory T cells are uniquely resistant to melanoma-induced suppression

We have previously observed that in vivo exposure to growing melanoma tumors fundamentally alters activated T cell homeostasis by suppressing the ability of naïve T cells to undergo antigen-driven proliferative expansion. We hypothesized that exposure of T cells in later stages of differentiation to melanoma would have similar suppressive consequences. C57BL/6 mice were inoculated with media or syngeneic B16F10 melanoma tumors 8 or 60 days after infection with lymphocytic choriomeningitis virus (LCMV), and splenic populations of LCMV-specific T cells were quantified using flow cytometry 18 days after tumor inoculation. Inoculation with melanoma on post-infection day 8 potentiated the contraction of previously activated T cells. This enhanced contraction was associated with increased apoptotic susceptibility among T cells from tumor-bearing mice. In contrast, inoculation with melanoma on post-infection day 60 did not affect the ability of previously established memory T cells to maintain themselves in stable numbers. In addition, the ability of previously established memory T cells to respond to LCMV challenge was unaffected by melanoma. Following adoptive transfer into melanoma-bearing mice, tumor-specific memory T cells were significantly more effective at controlling melanoma growth than equivalent numbers of tumor-specific effector T cells. These observations suggest that memory T cells are uniquely resistant to suppressive influences exerted by melanoma on activated T cell homeostasis; these findings may have implications for T cell–based cancer immunotherapy.     

Striga hermonthica decreases photosynthesis in Zea mays through effects on leaf cell structure

Maize seedlings were grown in pots either with or without preconditionedseeds of the parasitic weed, Striga hermonthica. After between4 and 8 weeks, net photosynthesis in the leaves of maize plantsinfected with Striga decreased compared to leaves of uninfectedcontrol plants. The activities of four enzymes of photosyntheticmetabolism were, however, little affected by infection. A pulse-chaseexperiment using ¹⁴CO₂ showed that C₄ acids were the main earlyproducts of assimilation even when the rate of photosynthesiswas much decreased by infection, but more radio-activity appearedin glycine and serine than in leaves of healthy maize plants.Leaves of infected maize required longer to reach a steady rateof photosynthesis upon enclosure in a leaf chamber than leavesof uninfected plants after similar treatment. Electron microscopy of transverse sections of the leaves ofinfected maize indicated that the cell walls in the bundle sheathand vascular tissue were less robust than in leaves of healthyplants. The results suggest that infection with Striga causesan increase in the permeability of cell walls in the bundlesheath, leakage of CO₂ from the bundle sheath cells and decreasedeffectiveness of C₄ photosynthesis in host leaves. Key words: Zea mays, Striga hermonthica, photosynthesis, photorespiration, enzyme activity     

Methodological Deficits in Diagnostic Research Using ‘-Omics’ Technologies: Evaluation of the QUADOMICS Tool and Quality of Recently Published Studies

Background

QUADOMICS is an adaptation of QUADAS (a quality assessment tool for use in systematic reviews of diagnostic accuracy studies), which takes into account the particular challenges presented by ‘-omics’ based technologies. Our primary objective was to evaluate the applicability and consistency of QUADOMICS. Subsequently we evaluated and describe the methodological quality of a sample of recently published studies using the tool.

Methodology/Principal Findings

45‘-omics’- based diagnostic studies were identified by systematic search of Pubmed using suitable MeSH terms (“Genomics”, “Sensitivity and specificity”, “Diagnosis”). Three investigators independently assessed the quality of the articles using QUADOMICS and met to compare observations and generate a consensus. Consistency and applicability was assessed by comparing each reviewer''s original rating with the consensus. Methodological quality was described using the consensus rating. Agreement was above 80% for all three reviewers. Four items presented difficulties with application, mostly due to the lack of a clearly defined gold standard. Methodological quality of our sample was poor; studies met roughly half of the applied criteria (mean ± sd, 54.7±18.4%). Few studies were carried out in a population that mirrored the clinical situation in which the test would be used in practice, (6, 13.3%); none described patient recruitment sufficiently; and less than half described clinical and physiological factors that might influence the biomarker profile (20, 44.4%).

Conclusions

The QUADOMICS tool can consistently be applied to diagnostic ‘-omics’ studies presently published in biomedical journals. A substantial proportion of reports in this research field fail to address design issues that are fundamental to make inferences relevant for patient care.     

Overexpression of Spry1 in chondrocytes causes attenuated FGFR ubiquitination and sustained ERK activation resulting in chondrodysplasia

The FGF signaling pathway plays essential roles in endochondral ossification by regulating osteoblast proliferation and differentiation, chondrocyte proliferation, hypertrophy, and apoptosis. FGF signaling is controlled by the complementary action of both positive and negative regulators of the signal transduction pathway. The Spry proteins are crucial regulators of receptor tyrosine kinase-mediated MAPK signaling activity. Sprys are expressed in close proximity to FGF signaling centers and regulate FGFR-ERK-mediated organogenesis. During endochondral ossification, Spry genes are expressed in prehypertrophic and hypertrophic chondrocytes. Using a conditional transgenic approach in chondrocytes in vivo, the forced expression of Spry1 resulted in neonatal lethality with accompanying skeletal abnormalities resembling thanatophoric dysplasia II, including increased apoptosis and decreased chondrocyte proliferation in the presumptive reserve and proliferating zones. In vitro chondrocyte cultures recapitulated the inhibitory effect of Spry1 on chondrocyte proliferation. In addition, overexpression of Spry1 resulted in sustained ERK activation and increased expression of p21 and STAT1. Immunoprecipitation experiments revealed that Spry1 expression in chondrocyte cultures resulted in decreased FGFR2 ubiquitination and increased FGFR2 stability. These results suggest that constitutive expression of Spry1 in chondrocytes results in attenuated FGFR2 degradation, sustained ERK activation, and up-regulation of p21Cip and STAT1 causing dysregulated chondrocyte proliferation and terminal differentiation.     

Identification and characterization of the aspartate chemosensory receptor of Campylobacter jejuni

Campylobacter jejuni is a highly motile bacterium that responds via chemotaxis to environmental stimuli to migrate towards favourable conditions. Previous in silico analysis of the C. jejuni strain NCTC11168 genome sequence identified 10 open reading frames, tlp1‐10, that encode putative chemosensory receptors. We describe the characterization of the role and specificity of the Tlp1 chemoreceptor (Cj1506c). In vitro and in vivo models were used to determine if Tlp1 had a role in host colonization. The tlp1^‐ isogenic mutant was more adherent in cell culture, however, showed reduced colonization ability in chickens. Specific interactions between the purified sensory domain of Tlp1 and l ‐aspartate were identified using an amino acid array and saturation transfer difference nuclear magnetic resonance spectroscopy. Chemotaxis assays showed differences between migration of wild‐type C. jejuni cells and that of a tlp1^‐ isogenic mutant, specifically towards aspartate. Furthermore, using yeast two‐hybrid and three‐hybrid systems for analysis of protein–protein interactions, the cytoplasmic signalling domain of Tlp1 was found to preferentially interact with CheV, rather than the CheW homologue of the chemotaxis signalling pathway; this interaction was confirmed using immune precipitation assays. This is the first identification of an aspartate receptor in bacteria other than Escherichia coli and Salmonella enterica serovar Typhimurium.