title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1693 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: The extracellular vesicles secreted by lung cancer cells in radiation therapy promote endothelial cell angiogenesis by transferring miR-23a link: https://peerj.com/articles/3627 last-modified: 2017-08-25 description: Angiogenesis is an important factor contributing to the radioresistance of lung cancer. However, the associated mechanisms underlying radiotherapy-induced pro-angiogenesis are unclear. Here, we demonstrated that Extracellular vesicles (EVs) derived from cultured cells in vitro enhanced HUVEC proliferation and migration, and the enhancement effect became more obvious when HUVECs were treated with EV derived from A549 or H1299, two lung cancer cell lines. Additionally, the pro-angiogenesis effect induced by EV could be strengthened when the lung cancer cells were exposed to X-ray irradiation. Furthermore, we verified that the downregulation of PTEN plays a vital role in this process. By evaluating the changes in the levels of microRNAs(miRNAs) targeting PTEN in EV, we found that miR-23a was significantly upregulated and mediated a decrease in PTEN. A luciferase reporter gene transfer experiment demonstrated that PTEN was the direct target of miR-23a, and the kinetics of PTEN expression were opposite to those of miR-23a. Our results show that the miR-23a/PTEN pathway plays an important role in EV-induced angiogenesis. These findings implicate the miR-23a/PTEN axis as a novel therapeutic target for lung cancer radiotherapy. creator: Yongfa Zheng creator: Liang Liu creator: Cong Chen creator: Pingpo Ming creator: Qin Huang creator: Changhu Li creator: Dedong Cao creator: Ximing Xu creator: Wei Ge uri: https://doi.org/10.7717/peerj.3627 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zheng et al. title: Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation link: https://peerj.com/articles/3714 last-modified: 2017-08-24 description: The Polish Primitive Horse (PPH, Konik) is a Polish native horse breed managed through a conservation program mainly due to its characteristic phenotype of a primitive horse. One of the most important goals of PPH breeding strategy is the preservation and equal development of all existing maternal lines. However, until now there was no investigation into the real genetic diversity of 16 recognized PPH dam lines using mtDNA sequence variation. Herein, we describe the phylogenetic relationships between the PPH maternal lines based upon partial mtDNA D-loop sequencing of 173 individuals. Altogether, 19 mtDNA haplotypes were detected in the PPH population. Five haplotypes were putatively novel while the remaining 14 showed the 100% homology with sequences deposited in the GenBank database, represented by both modern and primitive horse breeds. Generally, comparisons found the haplotypes conformed to 10 different recognized mtDNA haplogroups (A, B, E, G, J, M, N, P, Q and R). A multi-breed analysis has indicated the phylogenetic similarity of PPH and other indigenous horse breeds derived from various geographical regions (e.g., Iberian Peninsula, Eastern Europe and Siberia) which may support the hypothesis that within the PPH breed numerous ancestral haplotypes (found all over the world) are still present. Only in the case of five maternal lines (Bona, Dzina I, Geneza, Popielica and Zaza) was the segregation of one specific mtDNA haplotype observed. The 11 remaining lines showed a higher degree of mtDNA haplotype variability (2–5 haplotypes segregating in each line). This study has revealed relatively high maternal genetic diversity in the small, indigenous PPH breed (19 haplotypes, overall HapD = 0.92). However, only some traditionally distinguished maternal lines can be treated as genetically pure. The rest show evidence of numerous mistakes recorded in the official PPH pedigrees. This study has proved the importance of maternal genetic diversity monitoring based upon the application of molecular mtDNA markers and can be useful for proper management of the PPH conservation program in the future. creator: Jakub Cieslak creator: Lukasz Wodas creator: Alicja Borowska creator: Ernest G. Cothran creator: Anas M. Khanshour creator: Mariusz Mackowski uri: https://doi.org/10.7717/peerj.3714 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Cieslak et al. title: Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii link: https://peerj.com/articles/3623 last-modified: 2017-08-24 description: Systemic acid-base balance and osmotic/ionic regulation in decapod crustaceans are in part maintained by a set of transport-related enzymes such as carbonic anhydrase (CA), Na+/K+-ATPase (NKA), H+-ATPase (HAT), Na+/K+/2Cl− cotransporter (NKCC), Na+/Cl−/HCO${}_{3}^{-}$3− cotransporter (NBC), Na+/H+ exchanger (NHE), Arginine kinase (AK), Sarcoplasmic Ca+2-ATPase (SERCA) and Calreticulin (CRT). We carried out a comparative molecular analysis of these genes in three commercially important yet eco-physiologically distinct freshwater crayfish, Cherax quadricarinatus, C. destructor and C. cainii, with the aim to identify mutations in these genes and determine if observed patterns of mutations were consistent with the action of natural selection. We also conducted a tissue-specific expression analysis of these genes across seven different organs, including gills, hepatopancreas, heart, kidney, liver, nerve and testes using NGS transcriptome data. The molecular analysis of the candidate genes revealed a high level of sequence conservation across the three Cherax sp. Hyphy analysis revealed that all candidate genes showed patterns of molecular variation consistent with neutral evolution. The tissue-specific expression analysis showed that 46% of candidate genes were expressed in all tissue types examined, while approximately 10% of candidate genes were only expressed in a single tissue type. The largest number of genes was observed in nerve (84%) and gills (78%) and the lowest in testes (66%). The tissue-specific expression analysis also revealed that most of the master genes regulating pH and osmoregulation (CA, NKA, HAT, NKCC, NBC, NHE) were expressed in all tissue types indicating an important physiological role for these genes outside of osmoregulation in other tissue types. The high level of sequence conservation observed in the candidate genes may be explained by the important role of these genes as well as potentially having a number of other basic physiological functions in different tissue types. creator: Muhammad Y. Ali creator: Ana Pavasovic creator: Lalith K. Dammannagoda creator: Peter B. Mather creator: Peter J. Prentis uri: https://doi.org/10.7717/peerj.3623 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ali et al. title: Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño link: https://peerj.com/articles/3737 last-modified: 2017-08-23 description: BackgroundGene regulatory variation has been proposed to play an important role in the adaptation of plants to environmental stress. In the central highlands of Mexico, farmer selection has generated a unique group of maize landraces adapted to the challenges of the highland niche. In this study, gene expression in Mexican highland maize and a reference maize breeding line were compared to identify evidence of regulatory variation in stress-related genes. It was hypothesised that local adaptation in Mexican highland maize would be associated with a transcriptional signature observable even under benign conditions.MethodsAllele specific expression analysis was performed using the seedling-leaf transcriptome of an F1 individual generated from the cross between the highland adapted Mexican landrace Palomero Toluqueño and the reference line B73, grown under benign conditions. Results were compared with a published dataset describing the transcriptional response of B73 seedlings to cold, heat, salt and UV treatments.ResultsA total of 2,386 genes were identified to show allele specific expression. Of these, 277 showed an expression difference between Palomero Toluqueño and B73 alleles under benign conditions that anticipated the response of B73 cold, heat, salt and/or UV treatments, and, as such, were considered to display a prior stress response. Prior stress response candidates included genes associated with plant hormone signaling and a number of transcription factors. Construction of a gene co-expression network revealed further signaling and stress-related genes to be among the potential targets of the transcription factors candidates.DiscussionPrior activation of responses may represent the best strategy when stresses are severe but predictable. Expression differences observed here between Palomero Toluqueño and B73 alleles indicate the presence of cis-acting regulatory variation linked to stress-related genes in Palomero Toluqueño. Considered alongside gene annotation and population data, allele specific expression analysis of plants grown under benign conditions provides an attractive strategy to identify functional variation potentially linked to local adaptation. creator: M. Rocío Aguilar-Rangel creator: Ricardo A. Chávez Montes creator: Eric González-Segovia creator: Jeffrey Ross-Ibarra creator: June K. Simpson creator: Ruairidh J.H. Sawers uri: https://doi.org/10.7717/peerj.3737 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Aguilar-Rangel et al. title: Defensive behaviors of the Oriental armyworm Mythimna separata in response to different parasitoid species (Hymenoptera: Braconidae) link: https://peerj.com/articles/3690 last-modified: 2017-08-23 description: This study examined defensive behaviors of Mythimna separata (Lepidoptera: Noctuidae) larvae varying in body size in response to two parasitoids varying in oviposition behavior; Microplitis mediator females sting the host with the ovipositor after climbing onto it while Meteorus pulchricornis females make the sting by standing at a close distance from the host. Mythimna separata larvae exhibited evasive (escaping and dropping) and aggressive (thrashing) behaviors to defend themselves against parasitoids M. mediator and M. pulchricornis. Escaping and dropping did not change in probability with host body size or parasitoid species. Thrashing did not vary in frequency with host body size, yet performed more frequently in response to M. mediator than to M. pulchricornis. Parasitoid handling time and stinging likelihood varied depending not only on host body size but also on parasitoid species. Parasitoid handling time increased with host thrashing frequency, similar in slope for both parasitoids yet on a higher intercept for M. mediator than for M. pulchricornis. Handling time decreased with host size for M. pulchricornis but not for M. mediator. The likelihood of realizing an ovipositor sting decreased with thrashing frequency of both small and large hosts for M. pulchricornis, while this was true only for large hosts for M. mediator. Our results suggest that the thrashing behavior of M. separata larvae has a defensive effect on parasitism, depending on host body size and parasitoid species with different oviposition behaviors. creator: Jincheng Zhou creator: Ling Meng creator: Baoping Li uri: https://doi.org/10.7717/peerj.3690 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhou et al. title: A Miocene breeding ground of an extinct baleen whale (Cetacea: Mysticeti) link: https://peerj.com/articles/3711 last-modified: 2017-08-22 description: Locating breeding sites is definitely a key to understanding the ecological requirements and maintaining the sustainability of populations/species. Here I re-examined published specimens of an extinct baleen whale, Parietobalaena yamaokai, from the lower part of Itahashi Formation (16.1–15.6 Ma, Middle Miocene) in Shobara, Hiroshima, Japan. A critical and previously unnoticed feature, the open suture between the supraoccipital and exoccipital, in one specimen indicates the preservation of a very young individual–under six months old and even close to a new-born calf. Given the occurrence of a new-born whale and relatively abundant assemblage of Parietobalaena yamaokai, I propose a previously hidden and unknown breeding ground for the extinct baleen whale, P. yamaokai, in the Middle Miocene of Shobara (16.1–15.6 Ma), Hiroshima. Discovery of paleo-breeding sites of extinct populations/species should further help us to understand biological extinctions from a long-term perspective as conservation paleobiology aims to offer new insights into policy making for conserving endangered populations/species. creator: Cheng-Hsiu Tsai uri: https://doi.org/10.7717/peerj.3711 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Tsai title: Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon link: https://peerj.com/articles/3728 last-modified: 2017-08-22 description: Conserved homologues of the Hrd1 ubiquitin ligase target for degradation proteins that persistently or aberrantly engage the endoplasmic reticulum translocon, including mammalian apolipoprotein B (apoB; the major protein component of low-density lipoproteins) and the artificial yeast protein Deg1-Sec62. A complete understanding of the molecular mechanism by which translocon-associated proteins are recognized and degraded may inform the development of therapeutic strategies for cholesterol-related pathologies. Both apoB and Deg1-Sec62 are extensively post-translationally modified. Mass spectrometry of a variant of Deg1-Sec62 revealed that the protein is acetylated at the N-terminal methionine and two internal lysine residues. N-terminal and internal acetylation regulates the degradation of a variety of unstable proteins. However, preventing N-terminal and internal acetylation had no detectable consequence for Hrd1-mediated proteolysis of Deg1-Sec62. Our data highlight the importance of empirically validating the role of post-translational modifications and sequence motifs on protein degradation, even when such elements have previously been demonstrated sufficient to destine other proteins for destruction. creator: Sarah M. Engle creator: Justin J. Crowder creator: Sheldon G. Watts creator: Christopher J. Indovina creator: Samuel Z. Coffey creator: Eric M. Rubenstein uri: https://doi.org/10.7717/peerj.3728 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Engle et al. title: Histological characterization of denticulate palatal plates in an Early Permian dissorophoid link: https://peerj.com/articles/3727 last-modified: 2017-08-22 description: Denticles are small, tooth-like protrusions that are commonly found on the palate of early tetrapods. Despite their widespread taxonomic occurrence and similar external morphology to marginal teeth, it has not been rigorously tested whether denticles are structurally homologous to true teeth with features such as a pulp cavity, dentine, and enamel, or if they are bony, tooth-like protrusions. Additionally, the denticles are known to occur not only on the palatal bones but also on a mosaic of small palatal plates that is thought to have covered the interpterygoid vacuities of temnospondyls through implantation in a soft tissue covering; however, these plates have never been examined beyond a simple description of their position and external morphology. Accordingly, we performed a histological analysis of these denticulate palatal plates in a dissorophoid temnospondyl in order to characterize their microanatomy and histology. The dentition on these palatal plates has been found to be homologous with true teeth on the basis of both external morphology and histological data through the identification of features such as enamel and a pulp cavity surrounded by dentine. In addition, patterns of tooth replacement and ankylosis support the hypothesis of structural homology between these tiny teeth on the palatal plates and the much larger marginal dentition. We also provide the first histological characterization of the palatal plates, including documentation of abundant Sharpey’s fibres that provide a direct line of evidence to support the hypothesis of soft tissue implantation. Finally, we conducted a survey of the literature to determine the taxonomic distribution of these plates within Temnospondyli, providing a broader context for the presence of palatal plates and illustrating the importance of maintaining consistency in nomenclature. creator: Bryan M. Gee creator: Yara Haridy creator: Robert R. Reisz uri: https://doi.org/10.7717/peerj.3727 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Gee et al. 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.