Expanded host and geographic range of tadpole associations with the Severe Perkinsea Infection group

Severe Perkinsea infection is an emerging disease of amphibians, specifically tadpoles. Disease presentation correlates with liver infections of a subclade of Perkinsea (Alveolata) protists, named Pathogenic Perkinsea Clade (PPC). Tadpole mortality events associated with PPC infections have been reported across North America, from Alaska to Florida. Here, we investigate the geographic and host range of PPC associations in seemingly healthy tadpoles sampled from Panama, a biogeographic provenance critically affected by amphibian decline. To complement this work, we also investigate a mortality event among Hyla arborea tadpoles in captive-bred UK specimens. PPC SSU rDNA was detected in 10 of 81 Panama tadpoles tested, and H. arborea tadpoles from the UK. Phylogenies of the Perkinsea SSU rDNA sequences demonstrate they are highly similar to PPC sequences sampled from mortality events in the USA, and phylogenetic analysis of tadpole mitochondrial SSU rDNA demonstrates, for the first time, PPC associations in diverse hylids. These data provide further understanding of the biogeography and host range of this putative pathogenic group, factors likely to be important for conservation planning.     

Separating Population Structure from Population History: A Cladistic Analysis of the Geographical Distribution of Mitochondrial DNA Haplotypes in the Tiger Salamander, Ambystoma Tigrinum

Nonrandom associations of alleles or haplotypes with geographical location can arise from restricted gene flow, historical events (fragmentation, range expansion, colonization), or any mixture of these factors. In this paper, we show how a nested cladistic analysis of geographical distances can be used to test the null hypothesis of no geographical association of haplotypes, test the hypothesis that significant associations are due to restricted gene flow, and identify patterns of significant association that are due to historical events. In this last case, criteria are given to discriminate among contiguous range expansion, long-distance colonization, and population fragmentation. The ability to make these discriminations depends critically upon an adequate geographical sampling design. These points are illustrated with a worked example: mitochondrial DNA haplotypes in the salamander Ambystoma tigrinum. For this example, prior information exists about restricted gene flow and likely historical events, and the nested cladistic analyses were completely concordant with this prior information. This concordance establishes the plausibility of this nested cladistic approach, but much future work will be necessary to demonstrate robustness and to explore the power and accuracy of this procedure.     

Optimum associations of tester strains for maximum detection of mutagenic compounds in the Ames test

The Ames test is now widely used as a short-term test for the detection of mutagens. Different strains are available with various genetic characteristics, and in the past decade various authors have recommended different associations of strains to give maximum detection potential. However, few studies have been done to compare the sensitivity of individual strains towards a wide range of compounds in a single study. In order to define the best association of strains for screening or regulatory purpose, we have tested 103 direct mutagens (reference genotoxins or in-house compounds) on 7 strains of Salmonella typhimurium: TA1535, TA1537, TA1538, TA97, TA98, TA100 and TA102. 126 different associations of strains have been studied in terms of sensitivity and percentage overlap. Optimum associations of 2, 3, 4 or 5 strains included strains both with and without plasmid pKM101. However, the specificity of detection is greatly diminished by the presence of plasmid pKM101 in the strain, as shown by the high degree of overlap in associations constituted entirely of strains containing the plasmid. The association of strains TA1538 and TA100 detected 86% of the chemicals tested and is therefore recommended for large-scale screening. A rate of detection of 100% was obtained when 6 strains were used. The best associations of 4 and 5 strains, which detected 97 and 99% chemicals respectively, all contained strains TA1537, TA1538 and TA102. Finally, the associations of 4 strains (TA1537, TA1538, TA100, TA102) or 5 strains (TA1535, TA1537, TA1538, TA97, TA102) seemed well adapted to the optimum detection of mutagenic compounds.     

Loss of DNA recombinational repair enzymes in the initial stages of genome degeneration

Many obligate intracellular pathogens and symbionts undergo genome degeneration during long-term association with eukaryotic hosts; however, very little is known about genome changes that occur in the initial stages of such intracellular associations. By focusing on a clade of bacteria that have recently established symbiotic associations with insect hosts, we have identified events that may contribute to the reduction and degeneration of symbiont genomes. Unlike virtually all other bacteria, the obligate symbionts of maize and rice weevils each display substantial sequence divergence between multiple copies of their rDNA genes, resulting from a reduction in the efficacy of recombinational gene conversion, coincident with the inactivation of the recombinational repair gene recF in the common ancestor of both symbionts. The maize weevil endosymbiont also lacks a functional recA, resulting in further reduction in the efficacy of gene conversion between paralogous rDNAs and in a novel IS-mediated deletion in a 23S rDNA gene. Similar events may be pervasive during the evolution of symbiosis because symbiont genomes typically lack recombinational repair genes and have reduced numbers of ribosomal operons.     

Accounting for multiplicity in the evaluation of "signals" obtained by data mining from spontaneous report adverse event databases

Surveillance of drug products in the marketplace continues after approval, to identify rare potential toxicities that are unlikely to have been observed in the clinical trials carried out before approval. This surveillance accumulates large numbers of spontaneous reports of adverse events along with other information in spontaneous report databases. Recently developed empirical Bayes and Bayes methods provide a way to summarize the data in these databases, including a quantitative measure of the strength of the reporting association between the drugs and the events. Determining which of the particular drug-event associations, of which there may be many tens of thousands, are real reporting associations and which random noise presents a substantial problem of multiplicity because the resources available for medical and epidemiologic followup are limited. The issues are similar to those encountered with the evaluation of microarrays, but there are important differences. This report compares the application of a standard empirical Bayes approach with micorarray-inspired methods for controlling the False Discovery Rate, and a new Bayesian method for the resolution of the multiplicity problem to a relatively small database containing about 48,000 reports. The Bayesian approach appears to have attractive diagnostic properties in addition to being easy to interpret and implement computationally.     

SHR5: a novel plant receptor kinase involved in plant-N2-fixing endophytic bacteria association

Endophytic nitrogen-fixing bacteria have been isolated from graminaceous plants such as maize, rice, and sugarcane. They are thought to promote plant growth, not only by fixing nitrogen, but also by the production of plant hormones. The molecular mechanisms involved in this interaction are not yet clear. In this work, the identification of a receptor-like kinase (RLK), named SHR5, which may participate in signal transduction involved in the establishment of plant-endophytic bacteria interaction is described for the first time. SHR5 seems to be part of a novel subclass of RLKs present in a wide range of plant species. The expression of this gene is down-regulated in sugarcane plants associated exclusively with beneficial endophytic bacteria and is not a general response caused by micro-organisms or abiotic stress. In addition, more successful sugarcane-endophytic bacteria associations have a more pronounced decrease in SHR5 expression, suggesting that SHR5 mRNA levels in plant cells are inversely related to the efficiency of the association.     

The Euprymna scolopes-Vibrio fischeri symbiosis: a biomedical model for the study of bacterial colonization of animal tissue

The diversity of microorganisms found in the marine environment reflects the immense size, range of physical conditions and energy sources, and evolutionary age of the sea. Because associations with living animal tissue are an important and ancient part of the ecology of many microorganisms, it is not surprising that the study of marine symbioses (including both cooperative and pathogenic interactions) has produced numerous discoveries of biotechnological and biomedical significance. The association between the bioluminescent bacterium Vibrio fischeri and the sepiolid squid Euprymna scolopes has emerged as a productive model system for the investigation of the mechanisms by which cooperative bacteria initiate colonization of specific host tissues. The results of the last decade of research on this system have begun to reveal surprising similarities between this association and the pathogenic associations of disease-causing Vibrio species, including those of interest to human health and aquaculture. Studies of the biochemical and molecular events underlying the development of the squid-vibrio symbiosis can be expected to continue to increase our understanding of the factors controlling both benign and pathogenic bacterial associations.     

Trace fossil associations related to facies of an upper Ordovician low wave energy shoreface and shelf, Oslo-Asker district, Norway

Three trace fossil associations have been identified from facies interpreted as low wave energy upper, middle and lower shoreface deposits, transitional shoreface/shelf deposits and open epicontinental shelf deposits. These were developed in pre-regressive, regressive and transgressive phases associated with eustatic sea level changes caused by the upper Ordovician glaciation. The three associations are the Skolithos-Diplocraterion association, the Diplichnites-Phycodes association and the Thalassinoides association. The Skolithos-Diplocraterion association inhabited upper, middle and lower shoreface environments, the Diplichnites-Phycodes association a lowermost shoreface environment and the Thalassinoides association inhabited offshore epicontinental shelf environmcnts. The Skolithos-Diplocraferion and Diplichnites-Phycodes associations bear strong affinities with previously described Skolithos ichnofacies assemblages (indicating shoreline environments) and the Cruziana ichnofacies forms (indicating shallow water environments down to wave base) respectively. The Thalassinoides assemblage, however, closely compares with assemblages described from Mesozoic epicontinental shelf sequences. Trace fossil diversity achieves a maximum in the lowermost shoreface environment and reduces in deeper water and shallower water environments. This accords with diversity patterns identified in analogous Jurassic epicontinental palaeonvironments. The stratigraphic distribution of some trace fossil association boundaries accords with those of contemporary body fossil associations. However, several body fossil associations are included within the volume of distribution of a single trace fossil assemblage. □ Trace fossil association, shoreface and shelf, Oslo district, upper Ordovician.     

Commensal association of the common kingfisher with foraging Eurasian otters

Positive interactions between birds and mammals are a fascinating aspect of animal behaviour. Feeding associations may consist of local enhancement or facilitation, and in the latter case, of commensalism or mutualism depending on the benefits received by the facilitator. We report here on a previously undescribed feeding association between piscivorous birds and Eurasian otters Lutra lutra. In Spain, common kingfisher Alcedo atthis and grey heron Ardea cinerea were observed closely following foraging otters and benefited from feeding opportunities provided by these. Behavioural observations of otters in central Spain (28.4 hr; 19 days) revealed that an association with kingfishers occurred in 33% of otter foraging events (n = 92). Simultaneous observations in northern Spain (14.2 hr; 16 days) showed an association between otters and kingfishers or grey herons in 41.6% and 11.7% of otter foraging events (n = 77), respectively. The association probability between kingfishers and otters increased significantly when otters foraged closer to the shore and on small fish rather than other prey (crayfish or large fish). Birds fed on prey remain left by the feeding otters, on small fish captured by otters when these were satiated and playing, or on prey displaced by otters. Our observations are consistent with facilitation and commensalism: piscivorous birds gained feeding opportunities provided by the otters, with no apparent costs or benefits to the latter. Similar feeding associations have been described between other species of otters and piscivorous birds (kingfishers, herons, egrets, storks) in Asia, South America and Southern Africa, but had not yet been described in Europe. The occurrence of piscivorous bird–otter associations in different species and regions suggests that this commensalism may be often overlooked but widespread. We have shown that the association can be frequent and is context‐dependent, with benefits for associating birds depending on otters´ behaviour and targeted prey.     

植物种间联结研究内容与方法评述

植物种间联结是植物群落重要的数量和结构特征之一,是植物群落结构形成和演化的基础。研究种间联结,对于植物群落的稳定与演替、植被的恢复与重建等具有重要的理论意义和应用价值。为了便于探讨种间联结的形成机制,本文评述了种间联结的研究内容、计算方法及其影响因素,同时指出了现研究存在的问题及今后的研究方向。植物种间联结受多方面因素影响,既有人为取样尺度的影响,又有环境与生物自身的因素。在群落演替的不同阶段,种间联结性往往有所不同。为此,可采用多尺度排序法分析不同尺度格局上复杂的种间联结关系,重点加强植物"利他作用"及入侵种种间联结的研究。在Fisher精确检验的基础上,结合Pearson相关系数和Spearman秩相关系数来检验种对间的相关性,并利用生态位理论或从植物生理、分子遗传的角度研究密度主导的种间联结的变化,可以准确揭示植物种间的内在关联性。     

Hunting patterns and geographic profiling of white shark predation

Interspecific associations can arise for varied reasons including reduced predation risk and improved foraging success. In the case of bird–primate associations, birds typically appear to follow primate groups to harvest insects flushed by primates' movements. However, while previous studies have linked temporal changes in bird–primate associations to environmental conditions, few have assessed the additional effects of bird activity patterns and primate group behaviour and none have disentangled their potentially interdependent effects. Here, we test the hypothesis that foraging opportunities can drive interspecific associations in a previously undescribed bird–primate association between rock kestrels Falco rupicolus and chacma baboons Papio ursinus in central Namibia. Data were collected from two baboon groups and associated kestrels using instantaneous scan sampling during full-day follows over a 7-month field period, and analysed using generalized linear mixed models. We found that kestrel associations with baboons vary with season, show diurnal cycles and are more frequent when the baboons are in open desert habitat, engaged in travel foraging and in a large group. These patterns are statistically independent and consistent with the hypothesis that the kestrel–baboon association is driven by the foraging opportunities acquired by the kestrels. As the baboons do not appear to gain any benefits nor incur any costs from the association, we conclude that the kestrels are likely to be commensal with the baboons.     

Association study of MIA3 rs17465637 polymorphism with cardiovascular disease in rheumatoid arthritis patients

Rheumatoid arthritis (RA) is a complex polygenic inflammatory disease associated with accelerated atherosclerosis. Melanoma inhibitor protein 3 (MIA3) is required for the export of collagen VlI (COL7A1) from the endoplasmic reticulum and it appears to be a tumor suppressor of malignant melanoma. Genome-wide association studies have described an association between MIA3 rs17465637 A/C polymorphisms and coronary artery disease and myocardial infarction. Because of that, we assessed the MIA3 rs17465637 polymorphism in 1505 RA Spanish patients stratified according to the presence/absence of cardiovascular (CV) disease. Also, a subgroup of patients without CV events was assessed for the presence of subclinical atherosclerosis using carotid ultrasound to establish carotid intima-media wall thickness and carotid plaques and brachial ultrasonography to determine the presence of endothelial dysfunction by flow-mediated endothelium-dependent and independent vasodilatation. MIA3 rs17465637 allele A showed a trend for association with the presence of carotid plaques (odds ratio 1.56, 95% confidence interval [0.96-2.51]; p=0.07). However, apart from an association of the MIA3 rs17465637 A allele with the risk of CV events in RA patients with dyslipidemia (p=0.018), no other significant associations were found between the presence of MIA3 rs17465637 A allele and the risk of suffering CV events or other surrogate markers of atherosclerosis. In conclusion, our results suggest a potential association of the MIA3 rs17465637 with CV disease in dyslipidemic patients with RA. However, additional studies are required to better establish the role of the MIA3 gene in mechanisms leading to the accelerated atherogenesis observed in RA.     

Predation risk and the interspecific association of two Brazilian Atlantic forest primates in Cabruca agroforest

Forming interspecific associations is one of many strategies adopted by primates in order to avoid predation. In addition to improved predator detection and avoidance, benefits of interspecific associations relate to improved foraging efficiency. In this study we tested these two hypotheses explaining associations between the endangered golden-headed lion tamarin, Leontopithecus chrysomelas and the sympatric Wied's marmoset, Callithrix kuhlii. We estimated predation risk by recording the number of encounters between lion tamarins and potential predators in cabruca agroforest (shaded cacao plantation) and in mosaic forest (a mix of cabruca, primary and secondary forest). To evaluate if the association between the two species was related to foraging benefits we recorded the number of associations between the two species when the lion tamarins were eating and when they were not eating. To test if the association occurred to improve predator detection and avoidance, we evaluated if associations between the species were more frequent in areas with higher predation risk and during the part of the day when predation risk is higher. We also compared the number of associations 3 months before birth events and 3 months after, when the lion tamarins are more susceptible to predation. Predation risk, mainly by raptors, was significantly higher in cabruca than in mosaic forest (0.17 and 0.05 encounters with predators per hour of observation, respectively). Associations were significantly more frequent after birth events and during the part of the day when predation risk was also higher (5-6 am until noon). We did not observe any direct evidence of foraging-related advantages of interspecific associations for the lion tamarins. The tamarins did not associate more when they were foraging. Our findings suggest that lion tamarins are more exposed to predation in cabruca than in mosaic forest and associations between lion tamarins and Wied's marmosets are related to predation avoidance.     

Comprehensive evaluation of apolipoprotein H gene (APOH) variation identifies novel associations with measures of lipid metabolism in GENOA

Apolipoprotein H (apoH, also named beta-2 glycoprotein I) is found on several classes of lipoproteins, and is involved in the activation of lipoprotein lipase in lipid metabolism. We have comprehensively investigated the association of variation in the apoH gene (APOH) with lipid traits in hepatic cholesterol transport, dietary cholesterol transport (DCT), and reverse cholesterol transport (RCT). Our study population consisted of families from the Genetic Epidemiology Network of Arteriopathy multicenter study that include African Americans, Mexican Americans, and European Americans. We individually tested 36 single-nucleotide polymorphisms (SNPs) that span the APOH locus, including nonsynonymous variants that result in known apoH charge isoforms. In addition, we constructed haplotypes from SNPs in the 5' promoter region that comprise cis-acting regulatory elements, as well as haplotypes for multiple amino acid substitutions. We found point-wise significant associations of APOH variants with various lipid measures in the three racial groups. The strongest associations were found for DCT traits (triglyceride and apoE levels) in Mexican Americans with a nonsynonymous variant (SNP 14917, Cys306Gly) that may alter apoH protein folding in a region involved in phospholipid binding. In conclusion, family-based analyses of APOH variants have identified associations with measures of lipid metabolism in three American racial groups.     

Ichnology of deep‐sea fan overbank deposits of the Ganei slates (Eocene,Switzerland)— a classical flysch trace fossil locality studied first by Oswald Heer

Ganei (Switzerland) is a classical locality for trace fossils. At this site, Heer (1877) described a large number of trace fossils, several of which were new taxa. The trace fossils occur in thin‐bedded turbidites in which the basal divisions of the Bouma sequence are typically absent; the turbidites are assigned to the Ganei Slates and are Eocene in age. They are interpreted to have been deposited in an overbank environment within an upper to middle fan area distal to a channel. Two trace‐fossil associations occur: the first (I) is characterized by bulldozing organisms producing biodeformational structures, Scolica, and Nereites irregularis; the second (II) association shows a distinct tiering pattern with near‐surface graphoglyptids and a mixed layer with simple tubes such as cf. Palaeophycus and Planolites, plus patterned tubes such as Nereites cirrinalis, and Chondrites. Deeper turbidite layers were colonized by Chondrites and Gyro‐phyllites. All trace fossils show a normal size spectrum compared to previously studied trace‐fossil associations, so the degree of oxygenation probably did not influence the composition of either trace‐fossil association. Seafloor sediment was probably soft and did not affect the trace‐fossil associations. Sedimentation rate and event frequency did not change and are estimated to have been in a range of 5–10 cm/1000 years and 2–5 events per 1000 years, respectively. The composition of trace‐fossil associations I and II is therefore interpreted to have been controlled by the benthic food content being higher for trace‐fossil association I than for II.     

Analytical approaches to measuring cospeciation of host and parasites: through a glass, darkly

Studies of cophylogenetic associations between hosts and parasites have become increasingly common. Historically, congruence between host and parasite phylogenies has been seen as evidence for cospeciation. Analyses of such coevolutionary relationships, however, are made extremely difficult by the complex interplay of cospeciation, host switching, sorting (extinction), duplication (intrahost speciation) and inertia (lack of parasite speciation) events, all of which may produce incongruence between host and parasite phylogenies. Here we review several methods of analysing cospeciation. We illustrate these methods with an example from a Procellariiformes (seabird) and chewing louse (Halipeurus) association.     

Functional characterization of kurtz, a Drosophila non-visual arrestin, reveals conservation of GPCR desensitization mechanisms

The arrestins are a family of molecules that terminate signaling from many different G protein-coupled receptors, by inhibiting the association between receptor and downstream effectors. We recently employed a human betaarrestin2-GFP fusion protein to explore the dynamics of different neuropeptide receptors in Drosophila and have previously used a betaarrestin translocation assay to identify ligands at orphan receptors. Here, we report that the Drosophila arrestin encoded by kurtz functions in a similar fashion and can be employed to investigate GPCR-arrestin associations. Specifically, a GFP-krz fusion protein, upon co-expression with various Drosophila peptide receptors, an amine receptor, and a mammalian peptide receptor translocates to the plasma membrane in specific response to ligand application. This molecular phenotype is exhibited in a mammalian cell line as well as in a Drosophila cell line. Notably, the details of receptor-arrestin associations in terms of endocytotic patterns are functionally conserved between the mammalian arrestins and kurtz. Furthermore, we report that kurtz mutants exhibit hypersensitivity to osmotic stress, implicating GPCR desensitization as an important feature of the endocrine events that shape this stress response.     

Magnesium and the Risk of Cardiovascular Events: A Meta-Analysis of Prospective Cohort Studies

Background

Prospective studies that have examined the association between dietary magnesium intake and serum magnesium concentrations and the risk of cardiovascular disease (CVD) events have reported conflicting findings. We undertook a meta-analysis to evaluate the association between dietary magnesium intake and serum magnesium concentrations and the risk of total CVD events.

Methodology/Principal Findings

We performed systematic searches on MEDLINE, EMBASE, and OVID up to February 1, 2012 without limits. Categorical, linear, and nonlinear, dose-response, heterogeneity, publication bias, subgroup, and meta-regression analysis were performed. The analysis included 532,979 participants from 19 studies (11 studies on dietary magnesium intake, 6 studies on serum magnesium concentrations, and 2 studies on both) with 19,926 CVD events. The pooled relative risks of total CVD events for the highest vs. lowest category of dietary magnesium intake and serum magnesium concentrations were 0.85 (95% confidence interval 0.78 to 0.92) and 0.77 (0.66 to 0.87), respectively. In linear dose-response analysis, only serum magnesium concentrations ranging from 1.44 to 1.8 mEq/L were significantly associated with total CVD events risk (0.91, 0.85 to 0.97) per 0.1 mEq/L (P_nonlinearity = 0.465). However, significant inverse associations emerged in nonlinear models for dietary magnesium intake (P_nonlinearity = 0.024). The greatest risk reduction occurred when intake increased from 150 to 400 mg/d. There was no evidence of publication bias.

Conclusions/Significance

There is a statistically significant nonlinear inverse association between dietary magnesium intake and total CVD events risk. Serum magnesium concentrations are linearly and inversely associated with the risk of total CVD events.     

To be or not to be social: foraging associations of free-ranging dogs in an urban ecosystem

Canids display a wide diversity of social systems, from solitary to pairs to packs, and hence, they have been extensively used as model systems to understand social dynamics in natural habitats. Among canids, the dog can show various levels of social organization due to the influence of humans on their lives. Though the dog is known as man’s best friend and has been studied extensively as a pet, studies on the natural history, ecology and behavior of dogs in a natural habitat are rare. Here, we report results of an extensive population-level study conducted through one-time censuses in urban India to understand the foraging associations of free-ranging dogs. We built a model to test if the observed groups could have been formed through random associations while foraging. Our modeling results suggest that the dogs, like all efficient scavengers, tend to forage singly but also form random uncorrelated groups. A closer inspection of the group compositions, however, reveals that the foraging associations are non-random events. The tendency of adults to associate with the opposite sex in the mating season and of juveniles to stay close to adults in the non-mating season drives the population towards specific aggregation. Hence we conclude that to be or not to be social is a matter of choice for the free-ranging dogs, and not a matter of chance.