The postcranial skeleton of Boreogomphodon (Cynodontia: Traversodontidae) from the Upper Triassic of North Carolina, USA and the comparison with other traversodontids
Postcranial remains of Boreogomphodon from the Upper Triassic of North Carolina are described and compared to those of other known traversodontid cynodonts. The postcranial skeleton of Boreogomphodon is characterized by four sacral ribs, simple ribs lacking costal plates, the extension of the scapular neck below the acromion process, a short scapular facet on the procoracoid, a concave anterior margin of the procoracoid, humerus entepicondyle with smooth corner, and the presence of a fifth distal carpal. Four types of ribs are identified among traversodontids: ‘normal’ form, tubercular rib, costal plate, and Y-shaped rib. Fossorial behavior is suggested for traversodontids with elaborate costal plates. Within Traversodontidae, the procoracoid is relatively small; the anterior process of the iliac blade extends anteroventrally to different degrees in different taxa, which facilitates retraction of the femur; and the limb bones show allometric growth in terms of length and width.
Liu et al. (2017) The postcranial skeleton of Boreogomphodon (Cynodontia: Traversodontidae) from the Upper Triassic of North Carolina, USA and the comparison with other traversodontids. PeerJ 5:e3521 https://doi.org/10.7717/peerj.3521
The role of polycarbonate monomer bisphenol-A in insulin resistance
Bisphenol A (BPA) is a synthetic unit of polycarbonate polymers and epoxy resins, the types of plastics that could be found in essentially every human population and incorporated into almost every aspect of the modern human society. BPA polymers appear in a wide range of products, from liquid storages (plastic bottles, can and glass linings, water pipes and tanks) and food storages (plastics wraps and containers), to medical and dental devices. BPA polymers could be hydrolyzed spontaneously or in a photo- or temperature-catalyzed process, providing widespread environmental distribution and chronic exposure to the BPA monomer in contemporary human populations. Bisphenol A is also a xenoestrogen, an endocrine-disrupting chemical (EDC) that interferes with the endocrine system mimicking the effects of an estrogen and could potentially keep our endocrine system in a constant perturbation that parallels endocrine disruption arising during pregnancy, such as insulin resistance (IR). Gestational insulin resistance represents a natural biological phenomenon of higher insulin resistance in peripheral tissues of the pregnant females, when nutrients are increasingly being directed to the embryo instead of being stored in peripheral tissues. Gestational diabetes mellitus may appear in healthy non-diabetic females, due to gestational insulin resistance that leads to increased blood sugar levels and hyperinsulinemia (increased insulin production from the pancreatic beta cells). The hypothesis states that unnoticed and constant exposure to this environmental chemical might potentially lead to the formation of chronic low-level endocrine disruptive state that resembles gestational insulin resistance, which might contribute to the development of diabetes. The increasing body of evidence supports the major premises of this hypothesis, as exemplified by the numerous publications examining the association of BPA and insulin resistance, both epidemiological and mechanistic. However, to what extent BPA might contribute to the development of diabetes in the modern societies still remains unknown. In this review, I discuss the chemical properties of BPA and the sources of BPA contamination found in the environment and in human tissues. I provide an overview of mechanisms for the proposed role of bisphenol A in insulin resistance and diabetes, as well as other related diseases, such as cardiovascular diseases. I describe the transmission of BPA effects to the offspring and postulate that gender related differences might originate from differences in liver enzyme levels, such as UDP-glucuronosyltransferase, which is involved in BPA processing and its elimination from the organism. I discuss the molecular mechanisms of BPA action through nuclear and membrane-bound ER receptors, non-monotonic dose response, epigenetic modifications of the DNA and propose that chronic exposure to weak binders, such as BPA, may mimic the effects of strong binders, such as estrogens.
Pjanic (2017) The role of polycarbonate monomer bisphenol-A in insulin resistance. PeerJ 5:e3809 https://doi.org/10.7717/peerj.3809
Allele specific expression and methylation in the bumblebee, Bombus terrestris
The social hymenoptera are emerging as models for epigenetics. DNA methylation, the addition of a methyl group, is a common epigenetic marker. In mammals and flowering plants methylation affects allele specific expression. There is contradictory evidence for the role of methylation on allele specific expression in social insects. The aim of this paper is to investigate allele specific expression and monoallelic methylation in the bumblebee, Bombus terrestris. We found nineteen genes that were both monoallelically methylated and monoallelically expressed in a single bee. Fourteen of these genes express the hypermethylated allele, while the other five express the hypomethylated allele. We also searched for allele specific expression in twenty-nine published RNA-seq libraries. We found 555 loci with allele-specific expression. We discuss our results with reference to the functional role of methylation in gene expression in insects and in the as yet unquantified role of genetic cis effects in insect allele specific methylation and expression.
Lonsdale et al. (2017) Allele specific expression and methylation in the bumblebee, Bombus terrestris. PeerJ 5:e3798 https://doi.org/10.7717/peerj.3798
Heterologous expression of Plasmodium vivax apical membrane antigen 1 (PvAMA1) for binding peptide selection
Background Plasmodium is an obligate intracellular parasite. Apical membrane antigen 1 (AMA1) is the most prominent and well characterized malarial surface antigen that is essential for parasite-host cell invasion, i.e., for sporozoite to invade and replicate within hepatocytes in the liver stage and merozoite to penetrate and replicate within erythrocytes in the blood stage. AMA1 has long served as a potent antimalarial drug target and is a pivotal vaccine candidate. A good understanding of the structure and molecular function of this Plasmodium protein, particularly its involvement in host-cell adhesion and invasion, is of great interest and hence it offers an attractive target for the development of novel therapeutics. The present study aims to heterologous express recombinant Plasmodium AMA1 ectodomain of P. vivax (rPvAMA1) for the selection of binding peptides. Methods The rPvAMA1 protein was heterologous expressed using a tag-free Profinity eXactTM system and codon optimized BL21-Codon Plus (DE3)-RIL Escherichia coli strain and further refolded by dialysis for renaturation. Binding peptides toward refolded rPvAMA1 were panned using a Ph.D.-12 random phage display library. Results The rPvAMA1 was successfully expressed and refolded with three phage-displayed dodecapeptides designated as PdV1 (DLTFTVNPLSKA), PdV2 (WHWSWWNPNQLT), and PdV3 (TSVSYINNRHNL) with affinity towards rPvAMA1 identified. All of them exhibited positive binding signal to rPvAMA1 in both direct phage assays, i.e., phage ELISA binding assay and Western blot binding assay. Discussion Phage display technology enables the mapping of protein-protein interactions based on a simple principle that a library of phage particles displaying peptides is used and the phage clones that bind to the target protein are selected and identified. The binding sites of each selected peptides toward PvAMA1 (Protein Data Bank, PDB ID: 1W8K) were in silico predicted using CABS-dock web server. In this case, the binding peptides provide a valuable starting point for the development of peptidomimetic as antimalarial antagonists directed at PvAMA1.
Chew et al. (2017) Heterologous expression of Plasmodium vivax apical membrane antigen 1 (PvAMA1) for binding peptide selection. PeerJ 5:e3794 https://doi.org/10.7717/peerj.3794
Calcitonin receptor expression in medullary thyroid carcinoma
Background Calcitonin expression is a well-established marker for medullary thyroid carcinoma (MTC); yet the role of calcitonin receptor (CTR), its seven-transmembrane G-protein coupled receptor, remains to be established in C-cells derived thyroid tumors. The aim of this work was to investigate CTR expression in MTC and to correlate such expression with clinicopathological features in order to evaluate its possible role as a prognostic indicator of disease aggressiveness and outcome. Methods Calcitonin receptor expression was analyzed in a series of 75 MTCs by immunohistochemistry, and by qPCR mRNA quantification in specimens from four patients. Statistical tests were used to evaluate the correlation between CTR expression and the clinicopathological and molecular characteristics of patients and tumors. Results Calcitonin receptor expression was detected in 62 out of 75 samples (82.7%), whereas 13 of the 75 samples (17.3%) were completely negative. CTR expression was significantly associated with expression of cytoplasmatic phosphatase and tensin homologue deleted on chromosome 10 and osteopontin, as well as with wild type RET/RAS genes and absence of tumor stroma, suggesting that CTR expression do not associate with clinicopathological signs of worse prognosis. Discussion Calcitonin receptor expression appears to be associated in MTC with more differentiated status of the neoplastic cells.
Cappagli et al. (2017) Calcitonin receptor expression in medullary thyroid carcinoma. PeerJ 5:e3778 https://doi.org/10.7717/peerj.3778
Constructing three emotion knowledge tests from the invariant measurement approach
Background Psychological constructionist models like the Conceptual Act Theory (CAT) postulate that complex states such as emotions are composed of basic psychological ingredients that are more clearly respected by the brain than basic emotions. The objective of this study was the construction and initial validation of Emotion Knowledge measures from the CAT frame by means of an invariant measurement approach, the Rasch Model (RM). Psychological distance theory was used to inform item generation. Methods Three EK tests—emotion vocabulary (EV), close emotional situations (CES) and far emotional situations (FES)—were constructed and tested with the RM in a community sample of 100 females and 100 males (age range: 18–65), both separately and conjointly. Results It was corroborated that data-RM fit was sufficient. Then, the effect of type of test and emotion on Rasch-modelled item difficulty was tested. Significant effects of emotion on EK item difficulty were found, but the only statistically significant difference was that between “happiness” and the remaining emotions; neither type of test, nor interaction effects on EK item difficulty were statistically significant. The testing of gender differences was carried out after corroborating that differential item functioning (DIF) would not be a plausible alternative hypothesis for the results. No statistically significant sex-related differences were found out in EV, CES, FES, or total EK. However, the sign of d indicate that female participants were consistently better than male ones, a result that will be of interest for future meta-analyses. Discussion The three EK tests are ready to be used as components of a higher-level measurement process.
Delgado et al. (2017) Constructing three emotion knowledge tests from the invariant measurement approach. PeerJ 5:e3755 https://doi.org/10.7717/peerj.3755
In rats fed high-energy diets, taste, rather than fat content, is the key factor increasing food intake: a comparison of a cafeteria and a lipid-supplemented standard diet
Background Food selection and ingestion both in humans and rodents, often is a critical factor in determining excess energy intake and its related disorders. Methods Two different concepts of high-fat diets were tested for their obesogenic effects in rats; in both cases, lipids constituted about 40% of their energy intake. The main difference with controls fed standard lab chow, was, precisely, the lipid content. Cafeteria diets (K) were self-selected diets devised to be desirable to the rats, mainly because of its diverse mix of tastes, particularly salty and sweet. This diet was compared with another, more classical high-fat (HF) diet, devised not to be as tasty as K, and prepared by supplementing standard chow pellets with fat. We also analysed the influence of sex on the effects of the diets. Results K rats grew faster because of a high lipid, sugar and protein intake, especially the males, while females showed lower weight but higher proportion of body lipid. In contrast, the weight of HF groups were not different from controls. Individual nutrient’s intake were analysed, and we found that K rats ingested large amounts of both disaccharides and salt, with scant differences of other nutrients’ proportion between the three groups. The results suggest that the key differential factor of the diet eliciting excess energy intake was the massive presence of sweet and salty tasting food. Conclusions The significant presence of sugar and salt appears as a powerful inducer of excess food intake, more effective than a simple (albeit large) increase in the diet’s lipid content. These effects appeared already after a relatively short treatment. The differential effects of sex agree with their different hedonic and obesogenic response to diet.
Oliva et al. (2017) In rats fed high-energy diets, taste, rather than fat content, is the key factor increasing food intake: a comparison of a cafeteria and a lipid-supplemented standard diet. PeerJ 5:e3697 https://doi.org/10.7717/peerj.3697
Awareness about antibiotic resistance in a self-medication user group from Eastern Romania: a pilot study
Background Awareness about antibiotic resistance depends on the attitudes and information about antibiotic resistance of both patients and physicians. Persons who practice self-medication are at high risk of also self-medicating with antibiotics. The purpose of the present study was to evaluate the awareness about antibiotic resistance by investigating the practice in a group of self-medication users in a sample of adults in Romania and the variables associated with such practice. Material and Methods A cross-sectional self-filled questionnaire based study was conducted from December 2016 through January 2017 amongst 218 self-medication users (SMUG). The attitudes, the level of knowledge, the perceptions, about antibiotic use (ABU) and about antibiotic resistance (ABR) were compared to a reference group represented by medical residents group in their specialty training (MRG) considered to have a higher level of knowledge and awareness about ABU and ABR. Results The response rate was 87.2% in the SMUG group and 100% in the MRG group. The SMUG group reported self-medication practices for antibiotics with a high frequency at any time in life (72%), but with a very low frequency from the month previous to the date of the study (12%), comparative with the MRG group (75% and 7%, respectively). The multivariate logistic regression analysis showed that self-medication with antibiotics at any time in life in the SMUG group could be predicted by the answers to two questions regarding the practices and knowledge about ABU (Q13 and Q20). On the other hand, in the MRG group, a question about ABR perception (Q23), could be predictor for self-medication with antibiotics. Self-medication with antibiotics in the month previous to the date of the study in the SMUG group could be predicted with three questions: one about ABU practice (Q14), one about ABR perception (Q26) and one referring to ABR knowledge (Q28). On the other hand, in the MRG group, a question about ABR knowledge (Q32) could be predictor for self-medication with antibiotics. The reduced awareness about ABR in the SMUG group, is revealed by the reduced number of subjects (38%), who did not know that missing an antibiotic dose during a medical treatment contributes to ABR, comparative with the MRG group (84%). Indirectly, low ABR awareness in the SMUG group is revealed by the confusion about the appropriate use of antibiotics in bacterial or viral infections (that antibiotics are not used against viruses). Conclusions The findings from our study on the awareness about antibiotic resistance in the SMUG group might help the policy makers and regulatory authorities to develop educational programs directed to change the perceptions and attitudes about the appropriate use of antibiotics in order to diminish self-medication practices with antibiotics.
Topor et al. (2017) Awareness about antibiotic resistance in a self-medication user group from Eastern Romania: a pilot study. PeerJ 5:e3803 https://doi.org/10.7717/peerj.3803
Automated classification of tropical shrub species: a hybrid of leaf shape and machine learning approach
Plants play a crucial role in foodstuff, medicine, industry, and environmental protection. The skill of recognising plants is very important in some applications, including conservation of endangered species and rehabilitation of lands after mining activities. However, it is a difficult task to identify plant species because it requires specialized knowledge. Developing an automated classification system for plant species is necessary and valuable since it can help specialists as well as the public in identifying plant species easily. Shape descriptors were applied on the myDAUN dataset that contains 45 tropical shrub species collected from the University of Malaya (UM), Malaysia. Based on literature review, this is the first study in the development of tropical shrub species image dataset and classification using a hybrid of leaf shape and machine learning approach. Four types of shape descriptors were used in this study namely morphological shape descriptors (MSD), Histogram of Oriented Gradients (HOG), Hu invariant moments (Hu) and Zernike moments (ZM). Single descriptor, as well as the combination of hybrid descriptors were tested and compared. The tropical shrub species are classified using six different classifiers, which are artificial neural network (ANN), random forest (RF), support vector machine (SVM), k-nearest neighbour (k-NN), linear discriminant analysis (LDA) and directed acyclic graph multiclass least squares twin support vector machine (DAG MLSTSVM). In addition, three types of feature selection methods were tested in the myDAUN dataset, Relief, Correlation-based feature selection (CFS) and Pearson’s coefficient correlation (PCC). The well-known Flavia dataset and Swedish Leaf dataset were used as the validation dataset on the proposed methods. The results showed that the hybrid of all descriptors of ANN outperformed the other classifiers with an average classification accuracy of 98.23% for the myDAUN dataset, 95.25% for the Flavia dataset and 99.89% for the Swedish Leaf dataset. In addition, the Relief feature selection method achieved the highest classification accuracy of 98.13% after 80 (or 60%) of the original features were reduced, from 133 to 53 descriptors in the myDAUN dataset with the reduction in computational time. Subsequently, the hybridisation of four descriptors gave the best results compared to others. It is proven that the combination MSD and HOG were good enough for tropical shrubs species classification. Hu and ZM descriptors also improved the accuracy in tropical shrubs species classification in terms of invariant to translation, rotation and scale. ANN outperformed the others for tropical shrub species classification in this study. Feature selection methods can be used in the classification of tropical shrub species, as the comparable results could be obtained with the reduced descriptors and reduced in computational time and cost.
Murat et al. (2017) Automated classification of tropical shrub species: a hybrid of leaf shape and machine learning approach. PeerJ 5:e3792 https://doi.org/10.7717/peerj.3792
Greater reproductive investment, but shorter lifespan, in agrosystem than in natural-habitat toads
Global amphibian decline is due to several factors: habitat loss, anthropization, pollution, emerging diseases, and global warming. Amphibians, with complex life cycles, are particularly susceptible to habitat alterations, and their survival may be impaired in anthropized habitats. Increased mortality is a well-known consequence of anthropization. Life-history theory predicts higher reproductive investment when mortality is increased. In this work, we compared age, body size, and different indicators of reproductive investment, as well as prey availability, in natterjack toads (Epidalea calamita) from agrosystems and adjacent natural pine groves in Southwestern Spain. Mean age was lower in agrosystems than in pine groves, possibly as a consequence of increased mortality due to agrosystem environmental stressors. Remarkably, agrosystem toads were larger despite being younger, suggesting accelerated growth rate. Although we detected no differences in prey availability between habitats, artificial irrigation could shorten aestivation in agrosystems, thus increasing energy trade. Moreover, agrosystem toads exhibited increased indicators of reproductive investment. In the light of life-history theory, agrosystem toads might compensate for lesser reproductive events—due to shorter lives—with a higher reproductive investment in each attempt. Our results show that agrosystems may alter demography, which may have complex consequences on both individual fitness and population stability.
Zamora-Camacho et al. (2017) Greater reproductive investment, but shorter lifespan, in agrosystem than in natural-habitat toads. PeerJ 5:e3791 https://doi.org/10.7717/peerj.3791