Larval fish assemblage recovery: a reflection of environmental change in a large degraded river

Estuaries are globally important to fisheries but face many anthropogenic stressors that reduce water quality and degrade benthic habitat. The Maumee River estuary has been degraded by industrial contaminants, high sediment and nutrient loads, channelization and elimination of surrounding wetlands, lessening its value as spawning habitat for fishes of Lake Erie. Regulation and better management practices (BMPs) in the watershed have improved the water quality in this estuary, which should result in a response of the biotic community. We compared recent (2010/2011) larval fish assemblage data to similar data from the 1970s (1976/1977) in order to identify changes due to improved water and habitat quality. Family‐level diversity was greater in recent study years compared to the 1970s and family richness increased from 6 to 10. In addition, the abundance of lithophilic spawning fishes was significantly greater in the recent study years. Increased diversity and family richness were consistent with increased water quality in the Maumee River whereas the observed increase in abundance of lithophilic spawners was consistent with an increase in the amount or quality of benthic habitat used by species in these families for spawning. Better wastewater management and agricultural practices in coastal watersheds can benefit the early life stages of fishes, thus benefitting coastal fisheries. Furthermore, larval fish assemblages may be useful indicators of biological integrity because of their sensitivities to environmental change. Routine sampling of estuarine larval fish assemblages could provide practitioners with insight into ecosystem changes and measure the response of the biotic community to restoration.     

Comparative whole-genome hybridization reveals genomic islands in Brucella species

Brucella species are responsible for brucellosis, a worldwide zoonotic disease causing abortion in domestic animals and Malta fever in humans. Based on host preference, the genus is divided into six species. Brucella abortus, B. melitensis, and B. suis are pathogenic to humans, whereas B. ovis and B. neotomae are nonpathogenic to humans and B. canis human infections are rare. Limited genome diversity exists among Brucella species. Comparison of Brucella species whole genomes is, therefore, likely to identify factors responsible for differences in host preference and virulence restriction. To facilitate such studies, we used the complete genome sequence of B. melitensis 16M, the species highly pathogenic to humans, to construct a genomic microarray. Hybridization of labeled genomic DNA from Brucella species to this microarray revealed a total of 217 open reading frames (ORFs) altered in five Brucella species analyzed. These ORFs are often found in clusters (islands) in the 16M genome. Examination of the genomic context of these islands suggests that many are horizontally acquired. Deletions of genetic content identified in Brucella species are conserved in multiple strains of the same species, and genomic islands missing in a given species are often restricted to that particular species. These findings suggest that, whereas the loss or gain of genetic material may be related to the host range and virulence restriction of certain Brucella species for humans, independent mechanisms involving gene inactivation or altered expression of virulence determinants may also contribute to these differences.     

Semiparametric modeling of longitudinal measurements and time-to-event data--a two-stage regression calibration approach

SUMMARY: In this article we investigate regression calibration methods to jointly model longitudinal and survival data using a semiparametric longitudinal model and a proportional hazards model. In the longitudinal model, a biomarker is assumed to follow a semiparametric mixed model where covariate effects are modeled parametrically and subject-specific time profiles are modeled nonparametrially using a population smoothing spline and subject-specific random stochastic processes. The Cox model is assumed for survival data by including both the current measure and the rate of change of the underlying longitudinal trajectories as covariates, as motivated by a prostate cancer study application. We develop a two-stage semiparametric regression calibration (RC) method. Two variations of the RC method are considered, risk set regression calibration and a computationally simpler ordinary regression calibration. Simulation results show that the two-stage RC approach performs well in practice and effectively corrects the bias from the naive method. We apply the proposed methods to the analysis of a dataset for evaluating the effects of the longitudinal biomarker PSA on the recurrence of prostate cancer.     

Emerging perspectives in store-operated Ca2+ entry: roles of Orai, Stim and TRP

Depletion of intracellular Ca2+ stores induces Ca2+ influx across the plasma membrane through store-operated channels (SOCs). This store-operated Ca2+ influx is important for the replenishment of the Ca2+ stores, and is also involved in many signaling processes by virtue of the ability of intracellular Ca2+ to act as a second messenger. For many years, the molecular identities of particular SOCs, as well as the signaling mechanisms by which these channels are activated, have been elusive. Recently, however, the mammalian proteins STIM1 and Orai1 were shown to be necessary for the activation of store-operated Ca2+ entry in a variety of mammalian cells. Here we present molecular, pharmacological, and electrophysiological properties of SOCs, with particular focus on the roles that STIM1 and Orai1 may play in the signaling processes that regulate various pathways of store-operated entry.     

Quantitative determination by real-time PCR of four vaginalLactobacillus species,Gardnerella vaginalisandAtopobium vaginaeindicates an inverse relationship betweenL. gasseriandL. iners

Background  

Most studies of the vaginal microflora have been based on culture or on qualitative molecular techniques. Here we applied existing real-time PCR formats forLactobacillus crispatus,L. gasseriandGardnerella vaginalisand developed new formats forAtopobium vaginae,L. inersandL. jenseniito obtain a quantitative non culture-based determination of these species in 71 vaginal samples from 32 pregnant and 28 non-pregnant women aged between 18 and 45 years.     

Mouthpart morphology and feeding behavior of the invasive kudzu bug,Megacopta cribraria (Hemiptera: Plataspidae)

The invasive kudzu bug, Megacopta cribraria, was first reported in North America in 2009 and has subsequently spread through most of the southeastern United States, causing yield loss in soybean. Since detection in the USA, research has focused mainly on managing this newly established pest, but many important characteristics of the pest's mouthpart morphology and feeding behavior are unknown. Qualitative and quantitative comparisons of nymph and adult mouthparts and sensilla were made through scanning electron microscopy and light microscopy, and feeding behavior was examined using electropenetrography (EPG) and paraffin histology. Morphologies observed were similar to what has previously been reported for other piercing–sucking hemipterans. The relationship between rostrum length and body size (pronotum width and dorsal length) exhibited negative allometry. Rostrum length exhibited an isometric relationship with interocular width. Adult females (n=9) probed soybean stems 1.3±0.8 times in 9 h, with an average probe time of 2.3±1.3 h. EPG waveforms were characterized and correlated with behavior. Salivary sheaths were shown to terminate in the vascular tissue; four of five sheaths terminated in the phloem. This is the first time that the feeding behavior of a member of the Plataspidae has been recorded using EPG. Results add to our current limited knowledge of plataspid mouthpart morphology and provide a baseline for further research on the feeding behaviors of M. cribraria and other soybean‐feeding hemipterans.     

Demographic controls of aboveground forest biomass across North America

Ecologists have limited understanding of how geographic variation in forest biomass arises from differences in growth and mortality at continental to global scales. Using forest inventories from across North America, we partitioned continental‐scale variation in biomass growth and mortality rates of 49 tree species groups into (1) species‐independent spatial effects and (2) inherent differences in demographic performance among species. Spatial factors that were separable from species composition explained 83% and 51% of the respective variation in growth and mortality. Moderate additional variation in mortality (26%) was attributable to differences in species composition. Age‐dependent biomass models showed that variation in forest biomass can be explained primarily by spatial gradients in growth that were unrelated to species composition. Species‐dependent patterns of mortality explained additional variation in biomass, with forests supporting less biomass when dominated by species that are highly susceptible to competition (e.g. Populus spp.) or to biotic disturbances (e.g. Abies balsamea).     

Distinct requirements for Pot1 in limiting telomere length and maintaining chromosome stability

The fission yeast Pot1 (protection of telomeres) protein binds to the single-stranded extensions at the ends of telomeres, where its presence is critical for the maintenance of linear chromosomes. Homologs of Pot1 have been identified in a wide variety of eukaryotes, including plants, animals, and humans. We now show that Pot1 plays dual roles in telomere length regulation and chromosome end protection. Using a series of Pot1 truncation mutants, we have defined distinct areas of the protein required for chromosome stability and for limiting access to telomere ends by telomerase. We provide evidence that a large portion of Pot1, including the N-terminal DNA binding domain and amino acids close to the C terminus, is essential for its protective function. C-terminal Pot1 fragments were found to exert a dominant-negative effect by displacing endogenous Pot1 from telomeres. Reducing telomere-bound Pot1 in this manner resulted in dramatic lengthening of the telomere tract. Upon further reduction of Pot1 at telomeres, the opposite phenotype was observed: loss of telomeric DNA and chromosome end fusions. Our results demonstrate that cells must carefully regulate the amount of telomere-bound Pot1 to differentiate between allowing access to telomerase and catastrophic loss of telomeres.