Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses
Background The unique and complex paleoclimatic and paleogeographic events which affected the Mediterranean Sea since late Miocene deeply influenced the distribution and evolution of marine organisms and shaped their genetic structure. Following the Messinian salinity crisis and the sea-level fluctuations during the Pleistocene, several Mediterranean marine species developed deep genetic differentiation, and some underwent rapid radiation. Here, we consider two of the most prioritized groups for conservation in the light of their evolutionary history: sharks and rays (elasmobranchs). This paper deals with a comparative multispecies analysis of phylogeographic structure and historical demography in two pairs of sympatric, phylogenetically- and ecologically-related elasmobranchs, two scyliorhinid catsharks (Galeus melastomus, Scyliorhinus canicula) and two rajid skates (Raja clavata, Raja miraletus). Sampling and experimental analyses were designed to primarily test if the Sicilian Channel can be considered as effective eco-physiological barrier for Mediterranean demersal sympatric elasmobranchs. Methods The phylogeography and the historical demography of target species were inferred by analysing the nucleotide variation of three mitochondrial DNA markers (i.e., partial sequence of COI, NADH2 and CR) obtained from a total of 248 individuals sampled in the Western and Eastern Mediterranean Sea as well as in the adjacent northeastern Atlantic Ocean. Phylogeographic analysis was performed by haplotype networking and testing spatial genetic differentiation of samples (i.e., analysis of molecular variance and of principal components). Demographic history of Mediterranean populations was reconstructed using mismatch distribution and Bayesian Skyline Plot analyses. Results No spatial genetic differentiation was identified in either catshark species, while phylogeographic structure of lineages was identified in both skates, with R. miraletus more structured than R. clavata. However, such structuring of skate lineages was not consistent with the separation between Western and Eastern Mediterranean. Sudden demographic expansions occurred synchronously during the upper Pleistocene (40,000–60,000 years ago) in both skates and G. melastomus, likely related to optimal environmental conditions. In contrast, S. canicula experienced a slow and constant increase in population size over the last 350,000 years. Discussion The comparative analysis of phylogeographic and historical demographic patterns for the Mediterranean populations of these elasmobranchs reveals that historical phylogeographic breaks have not had a large impact on their microevolution. We hypothesize that interactions between environmental and ecological/physiological traits may have been the driving force in the microevolution of these demersal elasmobranch species in the Mediterranean rather than oceanographic barriers.
Ferrari et al. (2018) Natural history and molecular evolution of demersal Mediterranean sharks and skates inferred by comparative phylogeographic and demographic analyses. PeerJ 6:e5560 https://doi.org/10.7717/peerj.5560
Functional significance of cuckoo Cuculus canorus calls: responses of conspecifics, hosts and non-hosts
Male cuckoos Cuculus canorus produce calls that differ in number of syllables depending on environmental conditions and presence of male and female conspecifics. Why different males produce so repeatable calls that vary greatly in duration among males remains an open question. We used playback of cuckoo calls with few or many syllables (hereafter short and long calls), and woodpigeon calls (a control that also produces few or many syllables), predicting that playback of longer cuckoo calls should attract more male cuckoos (if males with such calls are dominant and successfully out-compete other males due to intraspecific competition), and attract more hosts mobbing male cuckoos (cuckoos with such calls and their females attract more hosts because of an increased risk of parasitism). Because cuckoos differentially parasitize hosts away from human habitation, we also tested whether the number of syllables in cuckoo calls differed with distance from buildings. Playback showed significant effects of number of syllables in cuckoo calls, but not woodpigeon Columba palumbus calls, with an additional effect of distance from human habitation decreasing the response to playback. These findings are consistent with the hypothesis that longer cuckoo calls, especially played back near human habitation, attract more conspecifics and hosts than shorter calls. To the best of knowledge this is the first study showing that cuckoo call response modified both other cuckoo individuals, as well as hosts response.
Tryjanowski et al. (2018) Functional significance of cuckoo Cuculus canorus calls: responses of conspecifics, hosts and non-hosts. PeerJ 6:e5302 https://doi.org/10.7717/peerj.5302
Neuroblastomas in Eastern China: a retrospective series study of 275 cases in a regional center
Purpose Most studies on neuroblastoma (NB) have been conducted in Western countries or Japan. The objective of our study was to analyze clinical and pathological features, MYCN status, surgical methods, and prognosis in Chinese NB patients. Methods A retrospective, single-center case series study of 275 NBs was implemented. Clinical manifestations, pathological features, MYCN status, and surgical treatment were analyzed. Log-rank test and Cox hazards models were used to assess overall survivals (OSs). Results The cohort consisted of 105 females and 170 males, with an age range of five days to 15 years. MYCN amplification was detected in 21.5% of all cases. The median OS was 15.0 months for MYCN amplified group. The five-year OS rates were 70.8% and 18.3% for MYCN unamplified and amplified groups, respectively, and the comparison of Kaplan–Meier curves for these two groups showed statistical significance (P < .001 by log-rank test). Gross total resection (GTR, n = 111) and subtotal resection (STR, n = 58) were administered in 169 patients at stages 3 and 4 who received chemotherapy and the comparison of Kaplan–Meier curves for different groups in these patients had statistical significance (STR vs. GTR, P = .009; MYCN unamplified vs. amplified, P < .001 by log-rank test, respectively).The multivariate survival analyses showed statistical significance (STR vs. GTR, P = .047; MYCN unamplified vs. amplified, P = .001 by Cox regression model). Conclusions MYCN amplification is an independently adverse prognostic factor in Chinese NB patients at stages 3 and 4 and GTR is associated with improved OS compared with STR in these patients.
Ma et al. (2018) Neuroblastomas in Eastern China: a retrospective series study of 275 cases in a regional center. PeerJ 6:e5665 https://doi.org/10.7717/peerj.5665
60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3
The processes of association and dissociation of ribosomal subunits are of great importance for the protein biosynthesis. The mechanistic details of these processes, however, are not well known. In bacteria, upon translation termination, the ribosome dissociates into subunits which is necessary for its further involvement into new initiation step. The dissociated state of the ribosome is maintained by initiation factor 3 (IF3) which binds to free small subunits and prevents their premature association with large subunits. In this work, we have exchanged IF3 in Escherichia coli cells by its ortholog from Saccharomyces cerevisiae mitochondria (Aim23p) and showed that yeast protein cannot functionally substitute the bacterial one and is even slightly toxic for bacterial cells. Our in vitro experiments have demonstrated that Aim23p does not split E. coli ribosomes into subunits. Instead, it fixes a state of ribosomes characterized by sedimentation coefficient about 60S which is not a stable structure but rather reflects a shift of dynamic equilibrium between associated and dissociated states of the ribosome. Mitochondria-specific terminal extensions of Aim23p are necessary for “60S state” formation, and molecular modeling results point out that these extensions might stabilize the position of the protein on the bacterial ribosome.
Levitskii et al. (2018) 60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3. PeerJ 6:e5620 https://doi.org/10.7717/peerj.5620
Zooming into plant-flower visitor networks: an individual trait-based approach
Understanding how ecological communities are structured is a major goal in ecology. Ecological networks representing interaction patterns among species have become a powerful tool to capture the mechanisms underlying plant-animal assemblages. However, these networks largely do not account for inter-individual variability and thus may be limiting our development of a clear mechanistic understanding of community structure. In this study, we develop a new individual-trait based approach to examine the importance of individual plant and pollinator functional size traits (pollinator thorax width and plant nectar holder depth) in mutualistic networks. We performed hierarchical cluster analyses to group interacting individuals into classes, according to their similarity in functional size. We then compared the structure of bee-flower networks where nodes represented either species identity or trait sets. The individual trait-based network was almost twice as nested as its species-based equivalent and it had a more symmetric linkage pattern resulting from of a high degree of size-matching. In conclusion, we show that by constructing individual trait-based networks we can reveal important patterns otherwise difficult to observe in species-based networks and thus improve our understanding of community structure. We therefore recommend using both trait-based and species-based approaches together to develop a clearer understanding of the properties of ecological networks.
Rumeu et al. (2018) Zooming into plant-flower visitor networks: an individual trait-based approach. PeerJ 6:e5618 https://doi.org/10.7717/peerj.5618
Insomnia and intellect mask the positive link between schizotypal traits and creativity
Background Schizotypy is a set of personality traits that resemble the signs and symptoms of schizophrenia in the general population, and it is associated with various subclinical mental health problems, including sleep disturbances. Additionally, dimensions of schizotypy show specific but weak associations with creativity. Given that creativity demands cognitive control and mental health, and that sleep disturbances negatively impact cognitive control, we predicted that positive, impulsive and disorganised schizotypy will demonstrate stronger associations with indicators of creativity, if the effect of mental health, insomnia, and intellect are statistically controlled. Methods University students (N = 182) took part in the study. Schizotypy was assessed with the shortened Oxford-Liverpool Inventory of Feelings and Experiences (sO-LIFE). Creative achievements were measured with the Creative Achievement Questionnaire (CAQ), divergent thinking was assessed with the ‘Just suppose’ task, and remote association problem solving was tested with Compound Remote Associate (CRA) problems. Mental health was assessed with the 12-item version of the General Health Questionnaire (GHQ-12), and insomnia was examined with the Athens Insomnia Scale (AIS). Verbal short term memory was measured with the forward digit span task, and intellect was assessed with the Rational-Experiential Inventory (REI). Multiple linear regressions were performed to examine the relationship between creativity and schizotypy. Indicators of creativity were the dependent variables. In the first block, dimensions of schizotypy, age, gender and smoking were entered, and in the second block, the models were extended with mental health, insomnia, verbal short term memory, and intellect. Results Positive schizotypy positively predicted real-life creative achievements, independently from the positive effect of intellect. Follow-up analyses revealed that positive schizotypy predicted creative achievements in art, while higher disorganised schizotypy was associated with creative achievements in science (when intellect was controlled for). Furthermore, disorganised schizotypy positively predicted remote association problem solving performance, if insomnia and verbal short term memory were statistically controlled. No dimension of schizotypy was significantly associated with divergent thinking. Discussion In line with previous findings, positive schizotypy predicted real-life creative achievements. The positive effects of disorganised schizotypy might be explained in terms of the simultaneous involvement of enhanced semantic priming and cognitive control in problem solving. We speculate that the lack of associations between divergent thinking and schizotypy might be related to instruction effects. Our study underscores the relevance of sleep impairment to the psychosis-spectrum, and refines our knowledge about the adaptive aspects of schizotypy in the general population.
Polner et al. (2018) Insomnia and intellect mask the positive link between schizotypal traits and creativity. PeerJ 6:e5615 https://doi.org/10.7717/peerj.5615
Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales
Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.
Speth et al. (2018) Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. PeerJ 6:e5614 https://doi.org/10.7717/peerj.5614
Effects of income and residential area on survival of patients with head and neck cancers following radiotherapy: working age individuals in Taiwan
Objectives The five-year survival rate of head and neck cancer (HNC) after radiotherapy (RT) varies widely from 35% to 89%. Many studies have addressed the effect of socioeconomic status and urban dwelling on the survival of HNC, but a limited number of studies have focused on the survival rate of HNC patients after RT. Materials and methods During the period of 2000–2013, 40,985 working age individuals (20 < age < 65 years) with HNC patients treated with RT were included in this study from a registry of patients with catastrophic illnesses maintained by the Taiwan National Health Insurance Research Database (NHIRD). Results The cumulative survival rate of HNC following RT in Taiwan was 53.2% (mean follow-up period, 3.75 ± 3.31 years). The combined effects of income and geographic effect on cumulative survival rates were as follows: high income group > medium income group > low income group and northern > central > southern > eastern Taiwan. Patients with moderate income levels had a 36.9% higher risk of mortality as compared with patients with high income levels (hazard ratio (HR) = 1.369; p < 0.001). Patients with low income levels had a 51.4% greater risk of mortality than patients with high income levels (HR = 1.514, p < 0.001). Conclusion In Taiwan, income and residential area significantly affected the survival rate of HNC patients receiving RT. The highest income level group had the best survival rate, regardless of the geographic area. The difference in survival between the low and high income groups was still pronounced in more deprived areas.
Lai et al. (2018) Effects of income and residential area on survival of patients with head and neck cancers following radiotherapy: working age individuals in Taiwan. PeerJ 6:e5591 https://doi.org/10.7717/peerj.5591
The influence of sample distribution on growth model output for a highly-exploited marine fish, the Gulf Corvina (Cynoscion othonopterus)
Estimating the growth of fishes is critical to understanding their life history and conducting fisheries assessments. It is imperative to sufficiently sample each size and age class of fishes to construct models that accurately reflect biological growth patterns, but this may be a challenging endeavor for highly-exploited species in which older fish are rare. Here, we use the Gulf Corvina (Cynoscion othonopterus), a vulnerable marine fish that has been persistently overfished for two decades, as a model species to compare the performance of several growth models. We fit the von Bertalanffy, Gompertz, logistic, Schnute, and Schnute–Richards growth models to length-at-age data by nonlinear least squares regression and used simple indicators to reveal biased data and ensure our results were biologically feasible. We then explored the consequences of selecting a biased growth model with a per-recruit model that estimated female spawning-stock-biomass-per-recruit and yield-per-recruit. Based on statistics alone, we found that the Schnute–Richards model described our data best. However, it was evident that our data were biased by a bimodal distribution of samples and underrepresentation of large, old individuals, and we found the Schnute–Richards model output to be biologically implausible. By simulating an equal distribution of samples across all age classes, we found that sample distribution distinctly influenced model output for all growth models tested. Consequently, we determined that the growth pattern of the Gulf Corvina was best described by the von Bertalanffy growth model, which was the most robust to biased data, comparable across studies, and statistically comparable to the Schnute–Richards model. Growth model selection had important consequences for assessment, as the per-recruit model employing the Schnute–Richards model fit to raw data predicted the stock to be in a much healthier state than per-recruit models employing other growth models. Our results serve as a reminder of the importance of complete sampling of all size and age classes when possible and transparent identification of biased data when complete sampling is not possible.
Bolser et al. (2018) The influence of sample distribution on growth model output for a highly-exploited marine fish, the Gulf Corvina (Cynoscion othonopterus). PeerJ 6:e5582 https://doi.org/10.7717/peerj.5582
The role of miRNAs 34a, 146a, 320a and 542 in the synergistic anticancer effects of methyl 2-(5-fluoro-2-hydroxyphenyl)-1H- benzo[d]imidazole-5-carboxylate (MBIC) with doxorubicin in breast cancer cells
Combination Index (CI) analysis suggested that MBIC and doxorubicin synergistically inhibited up to 97% of cell proliferation in ER+/PR+MCF-7 and triple negative MDA-MB-231 breast cancer cell lines. Moreover, treatment of the breast cancer cells with the combined drugs resulted in lower IC50 values in contrast to the individual drug treatment. Small noncoding microRNAs (miRNA) may function as non-mutational gene regulators at post-transcriptional level of protein synthesis. In the present study, the effect of the combined treatment of MBIC and doxorubicin on the expression level of several miRNAs including miR-34a, miR-146a, miR-320a and miR-542 were evaluated in MCF-7 and MDA-MB-231 breast cancer cell lines. These miRNAs have the potential to alter the protein level of survivin, the anti-apoptotic protein and reduce the metastatic activity in human breast cancer cell lines by interfering with the nuclear accumulation of NF-κB. Our results demonstrated the several fold changes in expression of miRNAs, which is drug and cell line dependent. This finding demonstrated a functional synergistic network between miR-34a, miR-320a and miR-542 that are negatively involved in post-transcriptional regulation of survivin in MCF-7 cells. While in MDA-MB-231 cells, changes in expression level of miR-146a was correlated with inhibition of the nuclear translocation of NF-κB. The overall result suggested that alteration in protein level and location of survivin and NF-κB by miR-34a, miR-320a, miR-146a and miR-542, remarkably influenced the synergistic enhancement of combined MBIC and doxorubicin in treatment of aggressive and less aggressive human breast cancer cell lines.
Hasanpourghadi et al. (2018) The role of miRNAs 34a, 146a, 320a and 542 in the synergistic anticancer effects of methyl 2-(5-fluoro-2-hydroxyphenyl)-1H- benzo[d]imidazole-5-carboxylate (MBIC) with doxorubicin in breast cancer cells. PeerJ 6:e5577 https://doi.org/10.7717/peerj.5577