title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1681 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of linear and daily undulating periodized resistance training programs on measures of muscle hypertrophy: a systematic review and meta-analysis link: https://peerj.com/articles/3695 last-modified: 2017-08-22 description: BackgroundPeriodization is an important component of resistance training programs. It is meant to improve adherence to the training regimen, allow for constant progression, help in avoiding plateaus, and reduce occurrence and severity of injuries. Previous findings regarding the effects of different periodization models on measures of muscle hypertrophy are equivocal. To provide a more in-depth look at the topic, we undertook a systematic review of the literature and a meta-analysis of intervention trials comparing the effects of linear periodization (LP) and daily undulating periodization (DUP) resistance training programs on muscle hypertrophy.Materials and MethodsA comprehensive literature search was conducted through PubMed/MEDLINE, Scopus, Web of Science, SPORTDiscus, Networked Digital Library of Theses and Dissertations (NDLTD) and Open Access Theses and Dissertations (OATD).ResultsThe pooled standardized mean difference (Cohen’s d) from 13 eligible studies for the difference between the periodization models on muscle hypertrophy was −0.02 (95% confidence interval [−0.25, 0.21], p = 0.848).ConclusionsThe meta-analysis comparing LP and DUP indicated that the effects of the two periodization models on muscle hypertrophy are likely to be similar. However, more research is needed in this area, particularly among trained individuals and clinical populations. Future studies may benefit from using instruments that are more sensitive for detecting changes in muscle mass, such as ultrasound or magnetic resonance imaging. creator: Jozo Grgic creator: Pavle Mikulic creator: Hrvoje Podnar creator: Zeljko Pedisic uri: https://doi.org/10.7717/peerj.3695 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Grgic et al. title: The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae) link: https://peerj.com/articles/3692 last-modified: 2017-08-22 description: Despite the large number of animal complete mitochondrial genomes currently available in public databases, knowledge about mitochondrial genomics in invertebrates is uneven. This paper reports, for the first time, the complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus, also known as the European clam. Ruditapes decussatus is morphologically and ecologically similar to the Manila clam Ruditapes philippinarum, which has been recently introduced for aquaculture in the very same habitats of Ruditapes decussatus, and that is replacing the native species. Currently the production of the European clam is almost insignificant, nonetheless it is considered a high value product, and therefore it is an economically important species, especially in Portugal, Spain and Italy. In this work we: (i) assembled Ruditapes decussatus mitochondrial genome from RNA-Seq data, and validated it by Sanger sequencing; (ii) analyzed and characterized the Ruditapes decussatus mitochondrial genome, comparing its features with those of other venerid bivalves; (iii) assessed mitochondrial sequence polymorphism (SP) and copy number variation (CNV) of tandem repeats across 26 samples. Despite using high-throughput approaches we did not find evidence for the presence of two sex-linked mitochondrial genomes, typical of the doubly uniparental inheritance of mitochondria, a phenomenon known in ∼100 bivalve species. According to our analyses, Ruditapes decussatus is more genetically similar to species of the Genus Paphia than to the congeneric Ruditapes philippinarum, a finding that bolsters the already-proposed need of a taxonomic revision. We also found a quite low genetic variability across the examined samples, with few SPs and little variability of the sequences flanking the control region (Largest Unassigned Regions (LURs). Strikingly, although we found low nucleotide variability along the entire mitochondrial genome, we observed high levels of length polymorphism in the LUR due to CNV of tandem repeats, and even a LUR length heteroplasmy in two samples. It is not clear if the lack of genetic variability in the mitochondrial genome of Ruditapes decussatus is a cause or an effect of the ongoing replacement of Ruditapes decussatus with the invasive Ruditapes philippinarum, and more analyses, especially on nuclear sequences, are required to assess this point. creator: Fabrizio Ghiselli creator: Liliana Milani creator: Mariangela Iannello creator: Emanuele Procopio creator: Peter L. Chang creator: Sergey V. Nuzhdin creator: Marco Passamonti uri: https://doi.org/10.7717/peerj.3692 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Ghiselli et al. title: Structural dynamics in the host-parasitoid system of the pine needle gall midge (Thecodiplosis japonensis) during invasion link: https://peerj.com/articles/3610 last-modified: 2017-08-22 description: The structural dynamics of host–parasitoid populations play a key role in the mechanism of natural community development with invasive species. Species invading new habitats experience coevolution with their newly acquired natural enemies, and their population dynamics are driven by a complex interaction between biological and environmental factors. We examined the biological and environmental factors which potentially influence a community of parasitoids throughout the 25-year invasion history of the pine needle gall midge (PNGM), Thecodiplosis japonensis, an important pest of pines in eastern Asia. We found that differences in establishment sequence and competitive ability among the parasitoids attacking this species determined the parasitoid community’s structure and dynamics. In particular, the timing for the initial establishment of the host–parasitoid association, incomplete superiority in competition among parasitoids, and indirect competition by a combination of the parasitoids were important factors for determining community’s structure and dynamics. Finally, the history of change in the community composition could be explained by the phenology differences in its member species, mediated by environmental factors. creator: Won Il Choi creator: Mun-Jang Jeon creator: Young-Seuk Park uri: https://doi.org/10.7717/peerj.3610 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Choi et al. title: A demographic history of a population of howler monkeys (Alouatta palliata) living in a fragmented landscape in Mexico link: https://peerj.com/articles/3547 last-modified: 2017-08-22 description: Long-term field studies are critical for our understanding of animal life history and the processes driving changes in demography. Here, we present long-term demographic data for the northernmost population of mantled howler monkeys (Alouatta palliata) residing in a highly anthropogenically fragmented landscape in Los Tuxtlas, Mexico. We carried out 454 monthly group visits to 10 groups of mantled howler monkeys between 2000 and 2011. The population remained relatively stable over the 11-year study period, with an overall increase in the total number of individuals. Birth rates and inter-birth intervals were comparable to those of howler monkeys at non-fragmented sites, suggesting that living in a fragmented landscape did not affect the reproductive output of our study population. Moreover, despite the landscape, dispersal events were commonplace, including many secondary dispersals (individuals emigrating from groups that they had previously immigrated into). Finally, we found a marked effect of seasonality on the dynamics of our study population. In particular, the period of lowest temperatures and resource scarcity between November and March was associated with higher mortality and reproductive inhibition, while the period of resource abundance between April and May was associated with the majority of conceptions and weaning of offspring. This, in turn, could be influencing dispersal patterns in our study area, as male howler monkeys seem to time some of their immigrations into new groups to coincide with the start of the period of higher fertility, while females preferentially joined new groups several months before the onset of this period. These data have important implications for the conservation and management of howler monkeys in fragmented landscapes, as well as for our understanding of the effect of seasonality over howler monkey dispersal, reproduction and survival. creator: Jurgi Cristóbal Azkarate creator: Jacob C. Dunn creator: Cristina Domingo Balcells creator: Joaquim Veà Baró uri: https://doi.org/10.7717/peerj.3547 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cristóbal Azkarate et al. title: The effects of allogenic stem cells in a murine model of hind limb diabetic ischemic tissue link: https://peerj.com/articles/3664 last-modified: 2017-08-21 description: BackgroundDiabetes is one of the major risk factors for peripheral arterial disease. In patients in whom surgery cannot be performed, cell therapy may be an alternative treatment. Since time is crucial for these patients, we propose the use of allogenic mesenchymal cells.MethodsWe obtained mesenchymal cells derived from the fat tissue of a healthy Sprague-Dawley rat. Previous diabetic induction with streptozotocin in 40 male Sprague-Dawley rats, ligation plus left iliac and femoral artery sections were performed as a previously described model of ischemia. After 10 days of follow-up, macroscopic and histo-pathological analysis was performed to evaluate angiogenic and inflammatory parameters in the repair of the injured limb. All samples were evaluated by the same blind researcher. Statistical analysis was performed using the SPSS v.11.5 program (P < 0.05).ResultsSeventy percent of the rats treated with streptozotocin met the criteria for diabetes. Macroscopically, cell-treated rats presented better general and lower ischemic clinical status, and histologically, a better trend towards angiogenesis, greater infiltration of type 2 macrophages and a shortening of the inflammatory process. However, only the inflammatory variables were statistically significant. No immunological reaction was observed with the use of allogeneic cells.DiscussionThe application of allogeneic ASCs in a hind limb ischemic model in diabetic animals shows no rejection reactions and a reduction in inflammatory parameters in favor of better repair of damaged tissue. These results are consistent with other lines of research in allogeneic cell therapy. This approach might be a safe, effective treatment option that makes it feasible to avoid the time involved in the process of isolation, expansion and production of the use of autologous cells. creator: Jesús Álvarez García creator: Soledad García Gómez-Heras creator: Luis Riera del Moral creator: Carlota Largo creator: Damián García-Olmo creator: Mariano García-Arranz uri: https://doi.org/10.7717/peerj.3664 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Álvarez García et al. title: Population structure of Bathymodiolus manusensis, a deep-sea hydrothermal vent-dependent mussel from Manus Basin, Papua New Guinea link: https://peerj.com/articles/3655 last-modified: 2017-08-21 description: Deep-sea hydrothermal vents in the western Pacific are increasingly being assessed for their potential mineral wealth. To anticipate the potential impacts on biodiversity and connectivity among populations at these vents, environmental baselines need to be established. Bathymodiolus manusensis is a deep-sea mussel found in close association with hydrothermal vents in Manus Basin, Papua New Guinea. Using multiple genetic markers (cytochrome C-oxidase subunit-1 sequencing and eight microsatellite markers), we examined population structure at two sites in Manus Basin separated by 40 km and near a potential mining prospect, where the species has not been observed. No population structure was detected in mussels sampled from these two sites. We also compared a subset of samples with B. manusensis from previous studies to infer broader population trends. The genetic diversity observed can be used as a baseline against which changes in genetic diversity within the population may be assessed following the proposed mining event. creator: Andrew D. Thaler creator: William Saleu creator: Jens Carlsson creator: Thomas F. Schultz creator: Cindy L. Van Dover uri: https://doi.org/10.7717/peerj.3655 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Thaler et al. title: Assessing the utility of urinary and fecal cortisol as an indicator of stress in golden snub-nosed monkeys (Rhinopithecus roxellana) link: https://peerj.com/articles/3648 last-modified: 2017-08-21 description: Cortisol concentration (CC) is often used as a stress indicator in animals, as high CC is associated with elevated stress levels. During field research, non-invasive methods of measuring CC, such as collection of urine and feces, are superior to using blood samples when monitoring free-ranging animals’ stress levels. However, due to different metabolic pathways, whether CC can be detected in urine and feces to reliably assess stress varies across species. Therefore, it is important to ascertain whether urine and fecal samples are a reliable source for determining CCs and to determine a suitable sampling regime. In this study, we subjected three captive adult golden snub-nosed monkeys (Rhinopithecus roxellana) to a high-stress situation (capture and injection). Urine and feces were collected for four days before and for four days after the manipulations for laboratory analysis. Immunoreactive CC was detected with a commercial enzyme immunoassay (EIA) kit and showed distinct rises. Peak CC values in urine were detected within 5 h, while peak fecal CC ranged between 5 and 24 hours post-interference. These results provide evidence that CC in urine and feces can be used to assess stress levels in the golden snub-nosed monkey. The optimal time frame to collect urinary and fecal samples for CC analysis is within one day of a potential stressful event. creator: Haochun Chen creator: Hui Yao creator: Wanji Yang creator: Penglai Fan creator: Zuofu Xiang uri: https://doi.org/10.7717/peerj.3648 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Chen et al. title: Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species link: https://peerj.com/articles/3640 last-modified: 2017-08-21 description: The molecular mechanisms that allow generalist parasitoids to exploit many, often very distinct hosts are practically unknown. The wasp Aphidius ervi, a generalist koinobiont parasitoid of aphids, was introduced from Europe into Chile in the late 1970s to control agriculturally important aphid species. A recent study showed significant differences in host preference and host acceptance (infectivity) depending on the host A. ervi were reared on. In contrast, no genetic differentiation between A. ervi populations parasitizing different aphid species and aphids of the same species reared on different host plants was found in Chile. Additionally, the same study did not find any fitness effects in A. ervi if offspring were reared on a different host as their mothers. Here, we determined the effect of aphid host species (Sitobion avenae versus Acyrthosiphon pisum reared on two different host plants alfalfa and pea) on the transcriptome of adult A. ervi females. We found a large number of differentially expressed genes (between host species: head: 2,765; body: 1,216; within the same aphid host species reared on different host plants: alfalfa versus pea: head 593; body 222). As expected, the transcriptomes from parasitoids reared on the same host species (pea aphid) but originating from different host plants (pea versus alfalfa) were more similar to each other than the transcriptomes of parasitoids reared on a different aphid host and host plant (head: 648 and 1,524 transcripts; body: 566 and 428 transcripts). We found several differentially expressed odorant binding proteins and olfactory receptor proteins in particular, when we compared parasitoids from different host species. Additionally, we found differentially expressed genes involved in neuronal growth and development as well as signaling pathways. These results point towards a significant rewiring of the transcriptome of A. ervi depending on aphid-plant complex where parasitoids develop, even if different biotypes of a certain aphid host species (A. pisum) are reared on the same host plant. This difference seems to persist even after the different wasp populations were reared on the same aphid host in the laboratory for more than 50 generations. This indicates that either the imprinting process is very persistent or there is enough genetic/allelic variation between A. ervi populations. The role of distinct molecular mechanisms is discussed in terms of the formation of host fidelity. creator: Gabriel I. Ballesteros creator: Jürgen Gadau creator: Fabrice Legeai creator: Angelica Gonzalez-Gonzalez creator: Blas Lavandero creator: Jean-Christophe Simon creator: Christian C. Figueroa uri: https://doi.org/10.7717/peerj.3640 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ballesteros et al. title: A systematic review of differential rate of use of the word “evolve” across fields link: https://peerj.com/articles/3639 last-modified: 2017-08-21 description: BackgroundAlthough evolution is the driving force behind many of today’s major public health and agriculture issues, both journalists and scientific researchers often do not use the term “evolve” in discussions of these topics.MethodsIn a total of 1,066 articles and 716 papers selected from 25 US newspapers and 34 scientific journals, we assess usage of the word “evolve” and its substitute words in the contexts of cancer tumor drug resistance, HIV drug resistance, mosquito insecticide resistance, and weed pesticide resistance.ResultsWe find significant differences in the use of “evolve” among fields and sources. “Evolve” is used most when discussing weed pesticide resistance (25.9% in newspapers, 52.4% in journals) and least when discussing cancer tumor drug resistance (3.9% in newspapers, 9.8% in journals). On average, scientific journals use “evolve” more often (22.2%) than newspapers (7.8%). Different types of journals (general science, general clinical, cancer specific, and drug resistance specific) show significantly different “evolve” usages when discussing cancer tumor drug resistance.DiscussionWe examine potential explanations of these findings, such as the relatively recent framing of cancer in evolutionary terms, before looking at consequences of low “evolve” usage and of differential “evolve” usage across fields. Use of the word “evolve” may not reflect current understanding of the problems we examine. However, given that our ability to tackle resistance issues relies upon accurate understandings of what causes and exacerbates resistance, use of the word “evolve” when called for may help us confront these issues in the future. creator: Nina Singh creator: Matthew T. Sit creator: Marissa K. Schutte creator: Gabriel E. Chan creator: Jeyson E. Aldana creator: Diana Cervantes creator: Clyde H. Himmelstein creator: Pamela J. Yeh uri: https://doi.org/10.7717/peerj.3639 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Singh et al. title: RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers link: https://peerj.com/articles/3631 last-modified: 2017-08-21 description: Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer. creator: Van L.T. Hoang creator: Lisa N. Tom creator: Xiu-Cheng Quek creator: Jean-Marie Tan creator: Elizabeth J. Payne creator: Lynlee L. Lin creator: Sudipta Sinnya creator: Anthony P. Raphael creator: Duncan Lambie creator: Ian H. Frazer creator: Marcel E. Dinger creator: H. Peter Soyer creator: Tarl W. Prow uri: https://doi.org/10.7717/peerj.3631 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hoang et al.