Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution
Transient Receptor Potential cation channel, subfamily Melastatin, member 8 (TRPM8) is involved in detection of cold temperature, different noxious compounds and in execution of thermo- as well as chemo-sensitive responses at cellular levels. Here we explored the molecular evolution of TRPM8 by analyzing sequences from various species. We elucidate that several regions of TRPM8 had different levels of selection pressure but the 4th–5th transmembrane regions remain highly conserved. Analysis of synteny suggests that since vertebrate origin, TRPM8 gene is linked with SPP2, a bone morphogen. TRPM8, especially the N-terminal region of it, seems to be highly variable in human population. We found 16,656 TRPM8 variants in 1092 human genomes with top variations being SNPs, insertions and deletions. A total of 692 missense mutations are also mapped to human TRPM8 protein of which 509 seem to be delateroiours in nature as supported by Polyphen V2, SIFT and Grantham deviation score. Using a highly specific antibody, we demonstrate that TRPM8 is expressed endogenously in the testis of rat and sperm cells of different vertebrates ranging from fish to higher mammals. We hypothesize that TRPM8 had emerged during vertebrate evolution (ca 450 MYA). We propose that expression of TRPM8 in sperm cell and its role in regulating sperm function are important factors that have guided its molecular evolution, and that these understandings may have medical importance.
Majhi et al. (2015) Expression of temperature-sensitive ion channel TRPM8 in sperm cells correlates with vertebrate evolution. PeerJ 3:e1310 https://doi.org/10.7717/peerj.1310
Antityrosinase activity of Euphorbia characias extracts
Tyrosinase is a well-known key enzyme in melanin biosynthesis and its inhibitors have become increasingly important because of their potential use as hypopigmenting agents. In the present study, the anti-melanogenic effect of aqueous and ethanolic extracts from Euphorbia characias leaves, stems, and flowers in cell-free and cellular systems was examined. All the extracts showed inhibitory effects against mushroom tyrosinase with leaf extracts exhibiting the lowest IC50 values of 24 and 97 µg/mL for aqueous and ethanolic extracts respectively. Enzyme kinetic analysis indicated that leaf aqueous extract acts as a mixed type inhibitor, while ethanolic extract shows a competitive inhibition effect on mushroom tyrosinase using L-DOPA as substrate. In addition, the inhibitory effect of leaf extracts on tyrosinase activity and melanin production was examined in murine melanoma B16F10 cells. Cellular tyrosinase activity as well as levels of melanin synthesis are reduced in a dose-dependent manner by extracts in cells treated with α-melanocyte stimulating hormone (α-MSH). The effects are comparable, and sometimes even better, than that of kojic acid, a well known tyrosinase inhibitor used for reference. All these results suggest that E. characias could be a great source of the natural inhibitors from tyrosinase and has the potential to be used as a whitening agent in therapeutic fields.
Pintus et al. (2015) Antityrosinase activity of Euphorbia characias extracts. PeerJ 3:e1305 https://doi.org/10.7717/peerj.1305
Validation experiments on finite element models of an ostrich (Struthio camelus) cranium
The first finite element (FE) validation of a complete avian cranium was performed on an extant palaeognath, the ostrich (Struthio camelus). Ex-vivo strains were collected from the cranial bone and rhamphotheca. These experimental strains were then compared to convergence tested, specimen-specific finite element (FE) models. The FE models contained segmented cortical and trabecular bone, sutures and the keratinous rhamphotheca as identified from micro-CT scan data. Each of these individual materials was assigned isotropic material properties either from the literature or from nanoindentation, and the FE models compared to the ex-vivo results. The FE models generally replicate the location of peak strains and reflect the correct mode of deformation in the rostral region. The models are too stiff in regions of experimentally recorded high strain and too elastic in regions of low experimentally recorded low strain. The mode of deformation in the low strain neurocranial region is not replicated by the FE models, and although the models replicate strain orientations to within 10° in some regions, in most regions the correlation is not strong. Cranial sutures, as has previously been found in other taxa, are important for modifying both strain magnitude and strain patterns across the entire skull, but especially between opposing the sutural junctions. Experimentally, we find that the strains on the surface of the rhamphotheca are much lower than those found on nearby bone. The FE models produce much higher principal strains despite similar strain ratios across the entirety of the rhamphotheca. This study emphasises the importance of attempting to validate FE models, modelling sutures and rhamphothecae in birds, and shows that whilst location of peak strain and patterns of deformation can be modelled, replicating experimental data in digital models of avian crania remains problematic.
Cuff et al. (2015) Validation experiments on finite element models of an ostrich (Struthio camelus) cranium. PeerJ 3:e1294 https://doi.org/10.7717/peerj.1294
Under which conditions can introverts achieve happiness? Mediation and moderation effects of the quality of social relationships and emotion regulation ability on happiness
Personality traits have been directly associated with happiness. One consistent finding is a strong link between extraversion and happiness: extraverts are happier than introverts. Although happy introverts exist, it is currently unclear under what conditions they can achieve happiness. The present study analyzes, generally, how the quality of social relationships and emotion regulation ability influence happiness and, specifically, how these factors can lead introverts to be happy. In the present study, 1,006 participants aged 18–80 (42% males) completed measures of extraversion, neuroticism, quality of social relationships, emotion regulation ability, and happiness. We found that extraverts had significantly higher happiness, quality of social relationships and emotion regulation ability scores than introverts. In addition, people with high quality social relationships or high emotion regulation ability were happier. Serial mediation analyses indicated that greater levels of extraversion were associated with greater happiness, with small effect size, via two indirect mechanisms: (a) higher quality of social relationships, and (b) higher quality of social relationships followed serially by higher emotion regulation ability. We also found a moderating effect due to the three-way interaction of extraversion, quality of social relationships, and emotion regulation ability: introverts were happier when they had high scores for these two variables, though the effect size was small. These results suggest that the quality of social relationships and emotion regulation ability are relevant to our understanding of complex associations between extraversion and happiness.
Cabello et al. (2015) Under which conditions can introverts achieve happiness? Mediation and moderation effects of the quality of social relationships and emotion regulation ability on happiness. PeerJ 3:e1300 https://doi.org/10.7717/peerj.1300
Promoting an active form of learning out-of-class via answering online “study questions” leads to higher than expected exam scores in General Biology
A rising need for workers in science, technology, engineering and mathematics (STEM) fields has fueled interest in improving teaching within STEM disciplines. Numerous studies have demonstrated the benefits of active learning approaches on student learning outcomes. However, many of these studies have been conducted in experimental, rather than real-life class, settings. In addition, most of these studies have focused on in-class active learning exercises. This study tested the effects of answering questions outside of class on exam performance for General Biology students at the University of Minnesota. An online database of 1,020 multiple-choice questions covering material from the first half of the course was generated. Students in seven course sections (with an average of ∼265 students per section) were given unlimited access to the online study questions. These students made extensive use of the online questions, with students answering an average of 1,323 questions covering material from the half of the semester for which the questions were available. After students answered a set of questions, they were shown the correct answers for those questions. More specific feedback describing how to arrive at the correct answer was provided for the 73% of the questions for which the correct answers were not deemed to be self-explanatory. The extent to which access to the online study questions improved student learning outcomes was assessed by comparing the performance on exam questions of students in the seven course sections with access to the online study questions with the performance of students in course sections without access to the online study questions. Student performance was analyzed for a total of 89 different exams questions that were not included in the study questions, but that covered the same material covered by the study questions. Each of these 89 questions was used on one to five exams given to students in course sections that had access to the online study questions and on three to 77 exams given to students in sections that lacked such access. Data from over 1,800 students in sections with access to the online study questions show that those students scored a statistically significant average of 6.6% points higher on the exam questions analyzed than students in sections without access to the study questions. This difference was greater than the average amount necessary to raise students’ exam grades by one grade (e.g., from a “B-” to a “B”). In addition, there was a higher correlation between number of questions answered and success on exam questions on material related to the study questions than between number of questions answered and success on exam questions on material unrelated to the study questions. The online study question system required substantial effort to set up, but required minimal effort to maintain and was effective in significantly raising average exam scores for even very large course sections.
Gibson (2015) Promoting an active form of learning out-of-class via answering online “study questions” leads to higher than expected exam scores in General Biology. PeerJ 3:e1322 https://doi.org/10.7717/peerj.1322
Interdisciplinary, interinstitutional and international collaboration of family medicine researchers in Taiwan
The family medicine researches flourished worldwide in the past decade. However, the collaborative patterns of family medicine publications had not been reported. Our study analyzed the collaborative activity of family medicine researchers in Taiwan. We focused on the types of collaboration among disciplines, institutions and countries. We searched “family medicine” AND “Taiwan” in address field from Web of Science and documented the disciplines, institutions and countries of all authors. We analyzed the collaborative patterns of family medicine researchers in Taiwan from 2010 to 2014. The journal’s impact factor of each article in the same publication year was also retrieved. Among 1,217 articles from 2010 to 2014, interdisciplinary collaboration existed in 1,185 (97.3%) articles, interinstitutional in 1,012 (83.2%) and international in 142 (11.7%). Public health was the most common collaborative discipline. All international researches were also interdisciplinary and interinstitutional. The United States (75 articles), the United Kingdom (21) and the People’s Republic of China (20) were the top three countries with which family medicine researchers in Taiwan had collaborated. We found a high degree of interdisciplinary and interinstitutional collaboration of family medicine researches in Taiwan. However, the collaboration of family medicine researchers in Taiwan with family medicine colleagues of other domestic or foreign institutions was insufficient. The future direction of family medicine studies could focus on the promotion of communication among family medicine researchers.
Lin et al. (2015) Interdisciplinary, interinstitutional and international collaboration of family medicine researchers in Taiwan. PeerJ 3:e1321 https://doi.org/10.7717/peerj.1321
Anvi’o: an advanced analysis and visualization platform for ‘omics data
Advances in high-throughput sequencing and ‘omics technologies are revolutionizing studies of naturally occurring microbial communities. Comprehensive investigations of microbial lifestyles require the ability to interactively organize and visualize genetic information and to incorporate subtle differences that enable greater resolution of complex data. Here we introduce anvi’o, an advanced analysis and visualization platform that offers automated and human-guided characterization of microbial genomes in metagenomic assemblies, with interactive interfaces that can link ‘omics data from multiple sources into a single, intuitive display. Its extensible visualization approach distills multiple dimensions of information about each contig, offering a dynamic and unified work environment for data exploration, manipulation, and reporting. Using anvi’o, we re-analyzed publicly available datasets and explored temporal genomic changes within naturally occurring microbial populations through de novo characterization of single nucleotide variations, and linked cultivar and single-cell genomes with metagenomic and metatranscriptomic data. Anvi’o is an open-source platform that empowers researchers without extensive bioinformatics skills to perform and communicate in-depth analyses on large ‘omics datasets.
Eren et al. (2015) Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3:e1319 https://doi.org/10.7717/peerj.1319
Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria
Fertilizer application is a common anthropogenic alteration to terrestrial systems. Increased nutrient input can impact soil microbial diversity or function directly through altered soil environments, or indirectly through plant-microbe feedbacks, with potentially important effects on ecologically-important plant-associated mutualists. We investigated the impacts of plant fertilizer, containing all common macro and micronutrients on symbiotic nitrogen-fixing bacteria (rhizobia), a group of bacteria that are important for plant productivity and ecosystem function. We collected rhizobia nodule isolates from natural field soil that was treated with slow-release plant fertilizer over a single growing season and compared phenotypic traits related to free-living growth and host partner quality in these isolates to those of rhizobia from unfertilized soils. Through a series of single inoculation assays in controlled glasshouse conditions, we found that isolates from fertilized field soil provided legume hosts with higher mutualistic benefits. Through growth assays on media containing variable plant fertilizer concentrations, we found that plant fertilizer was generally beneficial for rhizobia growth. Rhizobia isolated from fertilized field soil had higher growth rates in the presence of plant fertilizer compared to isolates from unfertilized field soil, indicating that plant fertilizer application favoured rhizobia isolates with higher abilities to utilize fertilizer for free-living growth. We found a positive correlation between growth responses to fertilizer and mutualism benefits among isolates from fertilized field soil, demonstrating that variable plant fertilizer induces context-dependent genetic correlations, potentially changing the evolutionary trajectory of either trait through increased trait dependencies. Our study shows that short-term application is sufficient to alter the composition of rhizobia isolates in the population or community, either directly though changes in the soil chemistry or indirectly through altered host legume feedbacks, and is potentially a strong selective agent acting on natural rhizobia populations.
Simonsen et al. (2015) Short-term fertilizer application alters phenotypic traits of symbiotic nitrogen fixing bacteria. PeerJ 3:e1291 https://doi.org/10.7717/peerj.1291
Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs
In a number of recent studies we used computer modeling to investigate the evolution of muscle leverage (moment arms) and function in extant and extinct archosaur lineages (crocodilians, dinosaurs including birds and pterosaurs). These studies sought to quantify the level of disparity and convergence in muscle moment arms during the evolution of bipedal and quadrupedal posture in various independent archosaur lineages, and in doing so further our understanding of changes in anatomy, locomotion and ecology during the group’s >250 million year evolutionary history. Subsequent work by others has led us to re-evaluate our models, which revealed a methodological error that impacted on the results obtained from the abduction–adduction and long-axis rotation moment arms in our published studies. In this paper we present corrected abduction–adduction and long axis rotation moment arms for all our models, and evaluate the impact of this new data on the conclusions of our previous studies. We find that, in general, our newly corrected data differed only slightly from that previously published, with very few qualitative changes in muscle moments (e.g., muscles originally identified as abductors remained abductors). As a result the majority of our previous conclusions regarding the functional evolution of key muscles in these archosaur groups are upheld.
Bates et al. (2015) Comments and corrections on 3D modeling studies of locomotor muscle moment arms in archosaurs. PeerJ 3:e1272 https://doi.org/10.7717/peerj.1272
Competition from native hydrophytes reduces establishment and growth of invasive dense-flowered cordgrass (Spartina densiflora)
Experimental studies to determine the nature of ecological interactions between invasive and native species are necessary for conserving and restoring native species in impacted habitats. Theory predicts that species boundaries along environmental gradients are determined by physical factors in stressful environments and by competitive ability in benign environments, but little is known about the mechanisms by which hydrophytes exclude halophytes and the life history stage at which these mechanisms are able to operate. The ongoing invasion of the South American Spartina densiflora in European marshes is causing concern about potential impacts to native plants along the marsh salinity gradient, offering an opportunity to evaluate the mechanisms by which native hydrophytes may limit, or even prevent, the expansion of invasive halophytes. Our study compared S. densiflora seedling establishment with and without competition with Phragmites australis and Typha domingensis, two hydrophytes differing in clonal architecture. We hypothesized that seedlings of the stress tolerant S. densiflora would be out-competed by stands of P. australis and T. domingensis. Growth, survivorship, biomass patterns and foliar nutrient content were recorded in a common garden experiment to determine the effect of mature P. australis and T. domingensis on the growth and colonization of S. densiflora under fresh water conditions where invasion events are likely to occur. Mature P. australis stands prevented establishment of S. densiflora seedlings and T. domingensis reduced S. densiflora establishment by 38%. Seedlings grown with P. australis produced fewer than five short shoots and all plants died after ca. 2 yrs. Our results showed that direct competition, most likely for subterranean resources, was responsible for decreased growth rate and survivorship of S. densiflora. The presence of healthy stands of P. australis, and to some extent T. domingensis, along river channels and in brackish marshes may prevent the invasion of S. densiflora by stopping the establishment of its seedlings.
Abbas et al. (2015) Competition from native hydrophytes reduces establishment and growth of invasive dense-flowered cordgrass (Spartina densiflora). PeerJ 3:e1260 https://doi.org/10.7717/peerj.1260