title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1347 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Chronic intake of high-dose of blueberry leaf extract does not augment the harmful effects of ethanol in rats link: https://peerj.com/articles/6989 last-modified: 2019-06-07 description: Excessive alcohol consumption is a risk factor for liver diseases. Enhancement of alcohol metabolism could be an effective strategy to prevent these adverse effects since it promotes the clearance of ethanol and acetaldehyde from the serum. Polyphenol-rich products have shown to protect against alcohol-related liver damage. Blueberry leaves have attracted attention as they are rich polyphenols such as proantocyanidins and chlorogenic acid. In this study, we investigated the effects of a high dose of blueberry leaf extract (BLEx) on alcohol metabolism during chronic intake of ethanol. Seven-week old Sprague-Dawley (SD) rats were divided into four groups: normal liquid diet group (NLD), normal liquid diet + BLEx group (NLD + BLEx), alcohol liquid diet group (ALD), and alcohol liquid diet + BLEx (ALD + BLEx). Then, rats were fed experimental diet for 5 weeks and at the end of feeding period, body weight, food intake, liver weight, indices of liver injury, expression and activity of alcohol metabolism-related and anti-oxidative enzymes, and levels of carbonyl protein, triglyceride (TG), and total cholesterol (T-Chol) were measured. Body weight and food intake decreased, whereas liver aldehyde dehydrogenase (ALDH) activity, liver microsomal cytochrome P450 2E1 (CYP2E1) protein and mRNA expression, and heme oxygenase 1 (HO-1) mRNA expression were upregulated by ethanol intake. Dietary BLEx, however, did not affect any of these ethanol-related changes. Indices of liver injury, expression and activity of other alcohol metabolism-related enzymes, liver carbonyl protein, TG, and T-Chol levels were not altered by ethanol and BLEx. Thus, chronic BLEx intake does not ameliorate the harmful effects of ethanol. creator: Kaede Yamasaki creator: Kazuhiro Sugamoto creator: Teruaki Arakawa creator: Kazuo Nishiyama creator: Masao Yamasaki uri: https://doi.org/10.7717/peerj.6989 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yamasaki et al. title: Digital dissection of the pelvis and hindlimb of the red-legged running frog, Phlyctimantis maculatus, using Diffusible Iodine Contrast Enhanced computed microtomography (DICE μCT) link: https://peerj.com/articles/7003 last-modified: 2019-06-07 description: BackgroundThe current study applies both traditional and Diffusible Iodine Contrast Enhanced computed microtomography (DICE µCT) techniques to reveal the musculoskeletal anatomy of Phlyctimantis maculatus. DICE µCT has emerged as a powerful tool to visualise intricate musculoskeletal anatomy. By generating 3D digital models, anatomical analyses can be conducted non-destructively, preserving the in situ 3D topography of the system, therefore eliminating some of the drawbacks associated with traditional methods. We aim to describe the musculature of the spine, pelvis, and hindlimb, compare the musculoskeletal anatomy and pelvic morphology of P. maculatus with functionally diverse frogs, and produce 3D digital anatomy reference data.MethodAn adult frog was stained using an aqueous Lugol’s solution and scanned in a SkyScan1176 in vivo µCT scanner. Scan images were reconstructed, resampled, and digitally segmented to produce a 3D model. A further adult female frog was dissected traditionally for visualisation of tendinous insertions.ResultsOur work revealed three main findings: (1) P. maculatus has similar gross muscular anatomy to Rana catesbeiana (bullfrog) but is distinct from those species that exhibit ancestral traits (leopelmids) and those that are highly specialised (pipids), (2) P. maculatus’s pelvic anatomy best fits the description of Emerson’s walking/hopping pelvic morphotype IIA, and (3) a split in the semimembranosus and gracilis major muscles is consistent with the reported myology in other anuran species.DiscussionWhile DICE µCT methods were instrumental in characterising the 3D anatomy, traditional dissection was still required to visualise important structures such as the knee aponeurosis, tendinous insertions, and fasciae. Nonetheless, the anatomical data presented here marks the first detailed digital description of an arboreal and terrestrial frog. Further, our digital model presents P. maculatus as a good frog model system and as such has formed a crucial platform for further functional analysis within the anuran pelvis and hindlimb. creator: Amber J. Collings creator: Christopher T. Richards uri: https://doi.org/10.7717/peerj.7003 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Collings and Richards title: Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach link: https://peerj.com/articles/7015 last-modified: 2019-06-07 description: The genome-scale metabolic model of a lipid-overproducing strain of Mucor circinelloides WJ11 was developed. The model (iNI1159) contained 1,159 genes, 648 EC numbers, 1,537 metabolites, and 1,355 metabolic reactions, which were localized in different compartments of the cell. Using flux balance analysis (FBA), the iNI1159 model was validated by predicting the specific growth rate. The metabolic traits investigated by phenotypic phase plane analysis (PhPP) showed a relationship between the nutrient uptake rate, cell growth, and the triacylglycerol production rate, demonstrating the strength of the model. A putative set of metabolic reactions affecting the lipid-accumulation process was identified when the metabolic flux distributions under nitrogen-limited conditions were altered by performing fast flux variability analysis (fastFVA) and relative flux change. Comparative analysis of the metabolic models of the lipid-overproducing strain WJ11 (iNI1159) and the reference strain CBS277.49 (iWV1213) using both fastFVA and coordinate hit-and-run with rounding (CHRR) showed that the flux distributions between these two models were significantly different. Notably, a higher flux distribution through lipid metabolisms such as lanosterol, zymosterol, glycerolipid and fatty acids biosynthesis in iNI1159 was observed, leading to an increased lipid production when compared to iWV1213. In contrast, iWV1213 exhibited a higher flux distribution across carbohydrate and amino acid metabolisms and thus generated a high flux for biomass production. This study demonstrated that iNI1159 is an effective predictive tool for the pathway engineering of oleaginous strains for the production of diversified oleochemicals with industrial relevance. creator: Nattapat Isarankura Na Ayudhya creator: Kobkul Laoteng creator: Yuanda Song creator: Asawin Meechai creator: Wanwipa Vongsangnak uri: https://doi.org/10.7717/peerj.7015 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Isarankura Na Ayudhya et al. title: Antioxidant enzyme cycling over reproductive lunar cycles in Pocillopora damicornis link: https://peerj.com/articles/7020 last-modified: 2019-06-07 description: The impacts of continued degradation of watersheds on coastal coral reefs world-wide is alarming, and action addressing anthropogenic stressors and subsequent rehabilitation of watersheds and adjacent reefs is an urgent priority. The aim of this study is to develop and improve the use of antioxidant enzymes as bioindicators of stress in coral species. In order to fully develop such tools, it is necessary to first understand baseline cycling of these enzymes within coral tissues. Due to inherent links between reproduction and oxidative stress, these aims may be facilitated by sampling coral tissues over reproductively-linked lunar cycles to determine variations from baseline. By developing a greater understanding of biochemical markers of stress in corals, specifically antioxidant defense enzymes catalase (CAT), glutathione reductase (GR), glutathione peroxidase (GPx), and superoxide dismutase (SOD) in Hawaiian Pocillopora damicornis, we have provided molecular tools that identify thresholds of stress on coral reefs. Our results suggest that the coral reproductive state is a significant factor affecting the activity of antioxidant enzymes. Specifically, CAT and GR display maximum activity during peak reproductive state. Whereas significant maximal Se-independent GPx and SOD activity was measured during off-peak reproductive cycles. Such insight into the cyclical variation of the activity of these enzymes should be applied towards differentiating the influence of natural biological activity cycling in diagnostic tests identifying the effects of different physical environmental factors and chemical pollutants on coral health. Through the development and application of these molecular biomarkers of stress, we look to improve our ability to identify problems at the sub-lethal level, when action can be taken to mitigate a/biotic impacts. creator: James W.A. Murphy creator: Abby C. Collier creator: Robert H. Richmond uri: https://doi.org/10.7717/peerj.7020 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Murphy et al. title: The complete chloroplast genome of Fagus crenata (subgenus Fagus) and comparison with F. engleriana (subgenus Engleriana) link: https://peerj.com/articles/7026 last-modified: 2019-06-07 description: This study reports the whole chloroplast genome of Fagus crenata (subgenus Fagus), a foundation tree species of Japanese temperate forests. The genome has a total of 158,227 bp containing 111 genes, including 76 protein-coding genes, 31 tRNA genes and 4 ribosomal RNA genes. Comparison with the only other published Fagus chloroplast genome, F. engeleriana (subgenus Engleriana) shows that the genomes are relatively conserved with no inversions or rearrangements observed while the proportion of nucleotide sites differing between the two species was equal to 0.0018. The six most variable regions were, in increasing order of variability, psbK-psbI, trnG-psbfM, rpl32, trnV, ndhI-ndh and ndhD-psaC. These highly variable chloroplast regions in addition to 160 chloroplast microsatellites identified (of which 46 were variable between the two species) will provide useful genetic resources for studies of the inter- and intra-specific genetic structure and diversity of this important northern hemisphere tree genus. creator: James R. P. Worth creator: Luxian Liu creator: Fu-Jin Wei creator: Nobuhiro Tomaru uri: https://doi.org/10.7717/peerj.7026 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Worth et al. title: The influence of pharmacologically-induced affective states on attention bias in sheep link: https://peerj.com/articles/7033 last-modified: 2019-06-07 description: When an individual attends to certain types of information more than others, the behavior is termed an attention bias. The occurrence of attention biases in humans and animals can depend on their affective states. Based on evidence from the human literature and prior studies in sheep, we hypothesized that an attention bias test could discriminate between pharmacologically-induced positive and negative affective states in sheep. The test measured allocation of attention between a threat and a positive stimulus using key measures of looking time and vigilance. Eighty 7-year-old Merino ewes were allocated to one of four treatment groups; Anxious (m-chlorophenylpiperazine), Calm (diazepam), Happy (morphine) and Control (saline). Drugs were administered 30 min prior to attention bias testing. The test was conducted in a 4 × 4.2 m arena with high opaque walls. An approximately life-size photograph of a sheep was positioned on one wall of the arena (positive stimulus). A small window with a retractable opaque cover was positioned on the opposite wall, behind which a dog was standing quietly (threat). The dog was visible for 3 s after a single sheep entered the arena, then the window was covered and the dog was removed. Sheep then remained in the arena for 3 min while behaviors were recorded. Key behaviors included time looking toward the dog wall or photo wall, duration of vigilance behavior and latency to become non-vigilant. In contrast with our hypothesis, no significant differences were found between treatment groups for duration of vigilance or looking behaviors, although Anxious sheep tended to be more vigilant than Control animals (P < 0.1) and had a longer latency to become non-vigilant (P < 0.001). A total of 24 of 80 animals were vigilant for the entire test duration. This censoring of data may explain why no differences were detected between groups for vigilance duration. Overall, a lack of difference between groups may suggest the test cannot discriminate positive and negative states in sheep. We suggest that the censoring of vigilance duration data, the use of insufficient drug doses, the potential influence of background noise and the age of the sheep may explain a lack of difference between groups. Due to these potential effects, it remains unclear whether the attention bias test can detect positive states in sheep. creator: Jessica E. Monk creator: Caroline Lee creator: Sue Belson creator: Ian G. Colditz creator: Dana L.M. Campbell uri: https://doi.org/10.7717/peerj.7033 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Monk et al. title: Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting link: https://peerj.com/articles/7055 last-modified: 2019-06-07 description: BackgroundAlthough pathogenic Gram-negative bacteria lack their own ubiquitination machinery, they have evolved or acquired virulence effectors that can manipulate the host ubiquitination process through structural and/or functional mimicry of host machinery. Many such effectors have been identified in a wide variety of bacterial pathogens that share little sequence similarity amongst themselves or with eukaryotic ubiquitin E3 ligases.MethodsTo allow identification of novel bacterial E3 ubiquitin ligase effectors from protein sequences we have developed a machine learning approach, the SVM-based Identification and Evaluation of Virulence Effector Ubiquitin ligases (SIEVE-Ub). We extend the string kernel approach used previously to sequence classification by introducing reduced amino acid (RED) alphabet encoding for protein sequences.ResultsWe found that 14mer peptides with amino acids represented as simply either hydrophobic or hydrophilic provided the best models for discrimination of E3 ligases from other effector proteins with a receiver-operator characteristic area under the curve (AUC) of 0.90. When considering a subset of E3 ubiquitin ligase effectors that do not fall into known sequence based families we found that the AUC was 0.82, demonstrating the effectiveness of our method at identifying novel functional family members. Feature selection was used to identify a parsimonious set of 10 RED peptides that provided good discrimination, and these peptides were found to be located in functionally important regions of the proteins involved in E2 and host target protein binding. Our general approach enables construction of models based on other effector functions. We used SIEVE-Ub to predict nine potential novel E3 ligases from a large set of bacterial genomes. SIEVE-Ub is available for download at https://doi.org/10.6084/m9.figshare.7766984.v1 or https://github.com/biodataganache/SIEVE-Ub for the most current version. creator: Jason E. McDermott creator: John R. Cort creator: Ernesto S. Nakayasu creator: Jonathan N. Pruneda creator: Christopher Overall creator: Joshua N. Adkins uri: https://doi.org/10.7717/peerj.7055 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 McDermott et al. title: Reduced thermal variability in cities and its impact on honey bee thermal tolerance link: https://peerj.com/articles/7060 last-modified: 2019-06-07 description: Urbanization is one of the most significant land cover transformations, and while climate alteration is one of its most cited ecological consequences we have very limited knowledge on its effect on species’ thermal responses. We investigated whether changes in environmental thermal variability caused by urbanization influence thermal tolerance in honey bees (Apis mellifera) in a semi-arid city in central Mexico. Ambient environmental temperature and honey bee thermal tolerance were compared in urban and rural sites. Ambient temperature variability decreased with urbanization due to significantly higher nighttime temperatures in urban compared to rural sites and not from differences in maximum daily temperatures. Honey bee thermal tolerance breadth [critical thermal maxima (CTmax)—critical thermal minima (CTmin)] was narrower for urban bees as a result of differences in cold tolerance, with urban individuals having significantly higher CTmin than rural individuals, and CTmax not differing among urban and rural individuals. Honey bee body size was not correlated to thermal tolerance, and body size did not differ between urban and rural individuals. We found that honey bees’ cold tolerance is modified through acclimation. Our results show that differences in thermal variability along small spatial scales such as urban-rural gradients can influence species’ thermal tolerance breadths. creator: Karina Sánchez-Echeverría creator: Ignacio Castellanos creator: Luis Mendoza-Cuenca creator: Iriana Zuria creator: Gerardo Sánchez-Rojas uri: https://doi.org/10.7717/peerj.7060 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sánchez-Echeverría et al. title: Impact of body weight gain on hepatic metabolism and hepatic inflammatory cytokines in comparison of Shetland pony geldings and Warmblood horse geldings link: https://peerj.com/articles/7069 last-modified: 2019-06-07 description: BackgroundNon-alcoholic fatty liver disease is known as determining part of human obesity. The impact of body weight (BW) gain on liver metabolism has not been extensively investigated yet.ObjectivesTo investigate hepatic alterations caused by increasing BW in ponies and horses.AnimalsA total of 19 non-obese equines (10 Shetland ponies, geldings; nine Warmblood horses, geldings).MethodsAnimals received 200% of their metabolizable maintenance energy requirements for 2 years. Serum alkaline phosphatase, glutamate dehydrogenase (GLDH), aspartate aminotransferase (AST), and gamma-glutamyl transferase activities and bile acids were analyzed several times during 2 years of hypercaloric diet. Hepatic lipid content and hepatic levels of the interleukin (IL)-6, tumor necrosis factor α (TNFα), cluster of differentiation (CD) 68, IL-1β, lipoprotein lipase (LPL), fatty acid-binding protein 1, chemerin and nuclear factor-κB mRNAs were assessed at the start of the study and after 1 and 2 years of excess energy intake.ResultsThe mean (±SD) BW gain recorded during 2 years of excess energy intake was 29.9 ± 19.4% for ponies and 17 ± 6.74% for horses. The hepatic lipid content was not profoundly affected by increasing BW. Levels of the IL-6, TNFα, CD68 and IL-1β mRNAs did not change during BW gain. Levels of the chemerin mRNA increased significantly in both breeds (ponies: P = 0.02; horses: P = 0.02) in response to BW gain. Significant differences in serum GLDH and AST activities, serum bile acid concentrations and hepatic levels of the LPL mRNA were observed between ponies and horses at the end of the study.ConclusionsChemerin might represent an interesting marker for future equine obesity research. Interestingly, steatosis caused by increasing BW may occur later in the development of obesity in equines than in humans. Additionally, the hepatic metabolism exhibits differences between ponies and horses, which may explain in part the greater susceptibility of ponies to obesity-associated metabolic dysregulations. creator: Carola Schedlbauer creator: Dominique Blaue creator: Martin Gericke creator: Matthias Blüher creator: Janine Starzonek creator: Claudia Gittel creator: Walter Brehm creator: Ingrid Vervuert uri: https://doi.org/10.7717/peerj.7069 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Schedlbauer et al. title: Sprint interval exercise versus continuous moderate intensity exercise: acute effects on tissue oxygenation, blood pressure and enjoyment in 18–30 year old inactive men link: https://peerj.com/articles/7077 last-modified: 2019-06-07 description: BackgroundSprint interval training (SIT) can be as effective, or more effective, than continuous moderate intensity exercise (CMIE) for improving a primary risk factor for cardiometabolic disease, low cardiorespiratory fitness (CRF). However, there has been no direct comparison in inactive individuals, of the acute effects of a session of SIT with a work-matched session of CMIE on local oxygen utilisation, which is a primary stimulus for increasing CRF. Furthermore, post-exercise blood pressure (BP) and enjoyment, if symptomatic and low, respectively, have implications for safety and adherence to exercise and have not been compared between these specific conditions. It was hypothesised that in young inactive men, local oxygen utilisation would be higher, while post-exercise BP and enjoyment would be lower for SIT, when compared to CMIE.MethodsA total of 11 inactive men (mean ± SD; age 23 ± 4 years) completed a maximal ramp-incremental exercise test followed by two experiment conditions: (1) SIT and (2) work-matched CMIE on a cycle ergometer on separate days. Deoxygenated haemoglobin (∆HHb) in the pre-frontal cortex (FH), gastrocnemius (GN), left vastus lateralis (LVL) and the right vastus lateralis (RVL) muscles, systemic oxygen utilisation (VO2), systolic (SBP) and diastolic (DBP) blood pressure and physical activity enjoyment scale (PACES) were measured during the experiment conditions.ResultsDuring SIT, compared to CMIE, ∆HHb in FH (p = 0.016) and GN (p = 0.001) was higher, while PACES (p = 0.032) and DBP (p = 0.043) were lower. No differences in SBP and ∆HHb in LVL and RVL were found between conditions.ConclusionsIn young inactive men, higher levels of physiological stress occurred during SIT, which potentially contributed to lower levels of post-exercise DBP and enjoyment, when compared to CMIE. creator: Yuri Kriel creator: Christopher D. Askew creator: Colin Solomon uri: https://doi.org/10.7717/peerj.7077 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kriel et al.