title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1722 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Intervention effects of five cations and their correction on hemolytic activity of tentacle extract from the jellyfish Cyanea capillata link: https://peerj.com/articles/3338 last-modified: 2017-05-09 description: Cations have generally been reported to prevent jellyfish venom-induced hemolysis through multiple mechanisms by spectrophotometry. Little attention has been paid to the potential interaction between cations and hemoglobin, potentially influencing the antagonistic effect of cations. Here, we explored the effects of five reported cations, La3+, Mn2+, Zn2+, Cu2+ and Fe2+, on a hemolytic test system and the absorbance of hemoglobin, which was further used to measure their effects on the hemolysis of tentacle extract (TE) from the jellyfish Cyanea capillata. All the cations displayed significant dose-dependent inhibitory effects on TE-induced hemolysis with various dissociation equilibrium constant (Kd) values as follows: La3+ 1.5 mM, Mn2+ 93.2 mM, Zn2+ 38.6 mM, Cu2+ 71.9 μM and Fe2+ 32.8 mM. The transparent non-selective pore blocker La3+ did not affect the absorbance of hemoglobin, while Mn2+ reduced it slightly. Other cations, including Zn2+, Cu2+ and Fe2+, greatly decreased the absorbance with Kd values of 35.9, 77.5 and 17.6 mM, respectively. After correction, the inhibitory Kd values were 1.4 mM, 45.8 mM, 128.5 μM and 53.1 mM for La3+, Zn2+, Cu2+ and Fe2+, respectively. Mn2+ did not inhibit TE-induced hemolysis. Moreover, the inhibitory extent at the maximal given dose of all cations except La3+ was also diminished. These corrected results from spectrophotometry were further confirmed by direct erythrocyte counting under microscopy. Our results indicate that the cations, except for La3+, can interfere with the absorbance of hemoglobin, which should be corrected when their inhibitory effects on hemolysis by jellyfish venoms are examined. The variation in the inhibitory effects of cations suggests that the hemolysis by jellyfish venom is mainly attributed to the formation of non-selective cation pore complexes over other potential mechanisms, such as phospholipases A2 (PLA2), polypeptides, protease and oxidation. Blocking the pore-forming complexes may be a primary strategy to improve the in vivo damage and mortality from jellyfish stings due to hemolytic toxicity. creator: Hui Zhang creator: Qianqian Wang creator: Liang Xiao creator: Liming Zhang uri: https://doi.org/10.7717/peerj.3338 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Zhang et al. title: Divergent effect of fluoxetine on the response to physical or chemical stressors in zebrafish link: https://peerj.com/articles/3330 last-modified: 2017-05-09 description: Fluoxetine is a selective serotonin reuptake inhibitor that increases serotonin concentration in the central nervous system and modulates various systems, including the control of sympathetic outflow and the hypothalamus–pituitary–adrenal. However, it is not yet established whether fluoxetine can modulate the responses to stressors stimulants (physical or chemical) that trigger cortisol response in zebrafish. We demonstrate that fluoxetine blunts the response to physical stress, but not to chemical stress. creator: Murilo S. Abreu creator: Ana Cristina V.V. Giacomini creator: Gessi Koakoski creator: Angelo L.S. Piato creator: Leonardo J.G. Barcellos uri: https://doi.org/10.7717/peerj.3330 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Abreu et al. title: Social relationships enhance the time spent eating and intake of a novel diet in pregnant Hanwoo (Bos taurus coreanae) heifers link: https://peerj.com/articles/3329 last-modified: 2017-05-09 description: The objective of this study was to evaluate the effects of social relationships on the feed intake, eating behavior, and growth, upon exposure to a novel diet, in Hanwoo (Bos taurus coreanae) heifers during pregnancy. Twenty-four pregnant Hanwoo heifers, averaging 438 ± 27.8 kg in weight, 21 months in age, and 194 ± 8.5 days in pregnancy, were involved in a two-month (eight weeks) experiment. The heifers were randomly assigned to either the single housing group (SG; one individual per pen, n = 12), or the paired housing group (PG; two individuals per pen, n = 12). All pens were of the same size (5 × 5 m) and provided with one feed bin, which automatically recorded the individual feed intake and eating behavior. As the experiment began, the diet of the heifers was switched from a total mixed ration (TMR; 250 g/kg ryegrass straw and 750 g/kg concentrate mix) to a forage-only diet (mixed hay cubes composed of 500 g/kg alfalfa, 250 g/kg timothy, and 250 g/kg blue grass hay). The heifers were fed ad libitum twice a day. The individual feed intake and eating behavior were recorded daily throughout the experiment, and body weights (BWs) were measured every four weeks before the morning feeding. PG animals visited the feed bin 22% less often than SG. PG, however, stayed 39% longer in the feed bin and consumed 40% more feed per visit, compared with SG. Consequently, PG heifers spent 23% more time in eating and had 16% more daily dry matter intake than SG during the experiment. Average daily gain during the experimental period tended to be greater in PG than in SG. When pregnant Hanwoo heifers encountered a novel diet, social relationships (i.e., presence of a pen-mate) enhanced their time spent eating and feed intake. Social interactions, even with an unfamiliar individual, may be helpful for pregnant Hanwoo heifers cope with a diet challenge compared to solitary situation. creator: Dong-Han Shin creator: Hyun-Min Kang creator: Seongwon Seo uri: https://doi.org/10.7717/peerj.3329 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Shin et al. title: Student evaluations of teaching: teaching quantitative courses can be hazardous to one’s career link: https://peerj.com/articles/3299 last-modified: 2017-05-09 description: Anonymous student evaluations of teaching (SETs) are used by colleges and universities to measure teaching effectiveness and to make decisions about faculty hiring, firing, re-appointment, promotion, tenure, and merit pay. Although numerous studies have found that SETs correlate with various teaching effectiveness irrelevant factors (TEIFs) such as subject, class size, and grading standards, it has been argued that such correlations are small and do not undermine the validity of SETs as measures of professors’ teaching effectiveness. However, previous research has generally used inappropriate parametric statistics and effect sizes to examine and to evaluate the significance of TEIFs on personnel decisions. Accordingly, we examined the influence of quantitative vs. non-quantitative courses on SET ratings and SET based personnel decisions using 14,872 publicly posted class evaluations where each evaluation represents a summary of SET ratings provided by individual students responding in each class. In total, 325,538 individual student evaluations from a US mid-size university contributed to theses class evaluations. The results demonstrate that class subject (math vs. English) is strongly associated with SET ratings, has a substantial impact on professors being labeled satisfactory vs. unsatisfactory and excellent vs. non-excellent, and the impact varies substantially depending on the criteria used to classify professors as satisfactory vs. unsatisfactory. Professors teaching quantitative courses are far more likely not to receive tenure, promotion, and/or merit pay when their performance is evaluated against common standards. creator: Bob Uttl creator: Dylan Smibert uri: https://doi.org/10.7717/peerj.3299 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Uttl and Smibert title: A public dataset of running biomechanics and the effects of running speed on lower extremity kinematics and kinetics link: https://peerj.com/articles/3298 last-modified: 2017-05-09 description: BackgroundThe goals of this study were (1) to present the set of data evaluating running biomechanics (kinematics and kinetics), including data on running habits, demographics, and levels of muscle strength and flexibility made available at Figshare (DOI: 10.6084/m9.figshare.4543435); and (2) to examine the effect of running speed on selected gait-biomechanics variables related to both running injuries and running economy.MethodsThe lower-extremity kinematics and kinetics data of 28 regular runners were collected using a three-dimensional (3D) motion-capture system and an instrumented treadmill while the subjects ran at 2.5 m/s, 3.5 m/s, and 4.5 m/s wearing standard neutral shoes.ResultsA dataset comprising raw and processed kinematics and kinetics signals pertaining to this experiment is available in various file formats. In addition, a file of metadata, including demographics, running characteristics, foot-strike patterns, and muscle strength and flexibility measurements is provided. Overall, there was an effect of running speed on most of the gait-biomechanics variables selected for this study. However, the foot-strike patterns were not affected by running speed.DiscussionSeveral applications of this dataset can be anticipated, including testing new methods of data reduction and variable selection; for educational purposes; and answering specific research questions. This last application was exemplified in the study’s second objective. creator: Reginaldo K. Fukuchi creator: Claudiane A. Fukuchi creator: Marcos Duarte uri: https://doi.org/10.7717/peerj.3298 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Fukuchi et al. title: Pollen extracts and constituent sugars increase growth of a trypanosomatid parasite of bumble bees link: https://peerj.com/articles/3297 last-modified: 2017-05-09 description: Phytochemicals produced by plants, including at flowers, function in protection against plant diseases, and have a long history of use against trypanosomatid infection. Floral nectar and pollen, the sole food sources for many species of insect pollinators, contain phytochemicals that have been shown to reduce trypanosomatid infection in bumble and honey bees when fed as isolated compounds. Nectar and pollen, however, consist of phytochemical mixtures, which can have greater antimicrobial activity than do single compounds. This study tested the hypothesis that pollen extracts would inhibit parasite growth. Extracts of six different pollens were tested for direct inhibitory activity against cell cultures of the bumble bee trypanosomatid gut parasite Crithidia bombi. Surprisingly, pollen extracts increased parasite growth rather than inhibiting it. Pollen extracts contained high concentrations of sugars, mainly the monosaccharides glucose and fructose. Experimental manipulations of growth media showed that supplemental monosaccharides (glucose and fructose) increased maximum cell density, while a common floral phytochemical (caffeic acid) with inhibitory activity against other trypanosomatids had only weak inhibitory effects on Crithidia bombi. These results indicate that, although pollen is essential for bees and other pollinators, pollen may promote growth of intestinal parasites that are uninhibited by pollen phytochemicals and, as a result, can benefit from the nutrients that pollen provides. creator: Evan C. Palmer-Young creator: Lucy Thursfield uri: https://doi.org/10.7717/peerj.3297 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Palmer-Young and Thursfield title: Analysis of RecA-independent recombination events between short direct repeats related to a genomic island and to a plasmid in Escherichia coli K12 link: https://peerj.com/articles/3293 last-modified: 2017-05-09 description: RecA-independent recombination events between short direct repeats, leading to deletion of the intervening sequences, were found to occur in two genetic models in the Escherichia coli K12 background. The first model was a small E. coli genomic island which had been shown to be mobile in its strain of origin and, when cloned, also in the E. coli K12 context. However, it did not encode a site-specific recombinase as mobile genomic islands usually do. It was then deduced that the host cells should provide the recombination function. This latter was searched for by means of a PCR approach to detect the island excision in E. coli K12 mutants affected in a number of recombination functions, including the 16 E. coli K12 site-specific recombinases, the RecET system, and multiple proteins that participate in the RecA-dependent pathways of homologous recombination. None of these appeared to be involved in the island excision. The second model, analyzed in a RecA deficient context, was a plasmid construction containing a short direct repeat proceeding from Saccharomyces cerevisiae, which flanked the cat gene. The excision of this gene by recombination of the DNA repeats was confirmed by PCR and through the detection, recovery and characterization of the plasmid deleted form. In sum, we present new evidence on the occurrence of RecA-independent recombination events in E. coli K12. Although the mechanism underlying these processes is still unknown, their existence suggests that RecA-independent recombination may confer mobility to other genetic elements, thus contributing to genome plasticity. creator: María F. Azpiroz creator: Magela Laviña uri: https://doi.org/10.7717/peerj.3293 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Azpiroz and Laviña title: Toward a better understanding of the mechanisms of symbiosis: a comprehensive proteome map of a nascent insect symbiont link: https://peerj.com/articles/3291 last-modified: 2017-05-09 description: Symbiotic bacteria are common in insects and can affect various aspects of their hosts’ biology. Although the effects of insect symbionts have been clarified for various insect symbiosis models, due to the difficulty of cultivating them in vitro, there is still limited knowledge available on the molecular features that drive symbiosis. Serratia symbiotica is one of the most common symbionts found in aphids. The recent findings of free-living strains that are considered as nascent partners of aphids provide the opportunity to examine the molecular mechanisms that a symbiont can deploy at the early stages of the symbiosis (i.e., symbiotic factors). In this work, a proteomic approach was used to establish a comprehensive proteome map of the free-living S. symbiotica strain CWBI-2.3T. Most of the 720 proteins identified are related to housekeeping or primary metabolism. Of these, 76 were identified as candidate proteins possibly promoting host colonization. Our results provide strong evidence that S. symbiotica CWBI-2.3T is well-armed for invading insect host tissues, and suggest that certain molecular features usually harbored by pathogenic bacteria are no longer present. This comprehensive proteome map provides a series of candidate genes for further studies to understand the molecular cross-talk between insects and symbiotic bacteria. creator: François Renoz creator: Antoine Champagne creator: Hervé Degand creator: Anne-Marie Faber creator: Pierre Morsomme creator: Vincent Foray creator: Thierry Hance uri: https://doi.org/10.7717/peerj.3291 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Renoz et al. title: Network science meets respiratory medicine for OSAS phenotyping and severity prediction link: https://peerj.com/articles/3289 last-modified: 2017-05-09 description: Obstructive sleep apnea syndrome (OSAS) is a common clinical condition. The way that OSAS risk factors associate and converge is not a random process. As such, defining OSAS phenotypes fosters personalized patient management and population screening. In this paper, we present a network-based observational, retrospective study on a cohort of 1,371 consecutive OSAS patients and 611 non-OSAS control patients in order to explore the risk factor associations and their correlation with OSAS comorbidities. To this end, we construct the Apnea Patients Network (APN) using patient compatibility relationships according to six objective parameters: age, gender, body mass index (BMI), blood pressure (BP), neck circumference (NC) and the Epworth sleepiness score (ESS). By running targeted network clustering algorithms, we identify eight patient phenotypes and corroborate them with the co-morbidity types. Also, by employing machine learning on the uncovered phenotypes, we derive a classification tree and introduce a computational framework which render the Sleep Apnea Syndrome Score (SASScore); our OSAS score is implemented as an easy-to-use, web-based computer program which requires less than one minute for processing one individual. Our evaluation, performed on a distinct validation database with 231 consecutive patients, reveals that OSAS prediction with SASScore has a significant specificity improvement (an increase of 234%) for only 8.2% sensitivity decrease in comparison with the state-of-the-art score STOP-BANG. The fact that SASScore has bigger specificity makes it appropriate for OSAS screening and risk prediction in big, general populations. creator: Stefan Mihaicuta creator: Mihai Udrescu creator: Alexandru Topirceanu creator: Lucretia Udrescu uri: https://doi.org/10.7717/peerj.3289 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Mihaicuta et al. title: Direct evidence of megamammal-carnivore interaction decoded from bone marks in historical fossil collections from the Pampean region link: https://peerj.com/articles/3117 last-modified: 2017-05-09 description: Pleistocene South American megafauna has traditionally attracted the interest of scientists and the popular media alike. However, ecological interactions between the species that inhabited these ecosystems, such as predator-prey relationships or interspecific competition, are poorly known. To this regard, carnivore marks imprinted on the fossil bones of megamammal remains are very useful for deciphering biological activity and, hence, potential interspecific relationships among taxa. In this article, we study historical fossil collections housed in different European and Argentinean museums that were excavated during the 19th and early 20th centuries in the Pampean region, Argentina, in order to detect carnivore marks on bones of megamammals and provide crucial information on the ecological relationships between South American taxa during the Pleistocene. Our results indicate that the long bones of megafauna from the Pampean region (e.g., the Mylodontidae and Toxodontidae families) exhibit carnivore marks. Furthermore, long bones of medium-sized species and indeterminate bones also present punctures, pits, scores and fractures. Members of the large-carnivore guild, such as ursids, canids and even felids, are recognised as the main agents that inflicted the marks. We hypothesize that the analysed carnivore marks represent the last stages of megaherbivore carcass exploitation, suggesting full consumption of these animals by the same or multiple taxa in a hunting and/or scavenging scenario. Moreover, our observations provide novel insights that help further our understanding of the palaeoecological relationships of these unique communities of megamammals. creator: Karina Vanesa Chichkoyan creator: Borja Figueirido creator: Margarita Belinchón creator: José Luis Lanata creator: Anne-Marie Moigne creator: Bienvenido Martínez-Navarro uri: https://doi.org/10.7717/peerj.3117 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chichkoyan et al.