PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation
items: Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii
items: Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
items: Defensive behaviors of the Oriental armyworm Mythimna separata in response to different parasitoid species (Hymenoptera: Braconidae)
items: A Miocene breeding ground of an extinct baleen whale (Cetacea: Mysticeti)
items: Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon
items: Histological characterization of denticulate palatal plates in an Early Permian dissorophoid
items: Effects of linear and daily undulating periodized resistance training programs on measures of muscle hypertrophy: a systematic review and meta-analysis
items: The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae)
items: Structural dynamics in the host-parasitoid system of the pine needle gall midge (Thecodiplosis japonensis) during invasion

Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation
type: item
type: AcademicArticle
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 …
format: application/pdf
format: text/html
creator: Jakub Cieslak
creator: Lukasz Wodas
creator: Alicja Borowska
creator: Ernest G. Cothran
creator: Anas M. Khanshour
creator: Mariusz Mackowski
subject: Agricultural Science
subject: Conservation Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.3714
publisher: PeerJ Inc.
rights: © 2017 Cieslak et al.
abstract: 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 …
bibliographic citation: Cieslak et al. (2017) Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation. PeerJ 5:e3714 https://doi.org/10.7717/peerj.3714
date submitted: 2017-03-16
date accepted: 2017-07-28
issued: 2017-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cieslak
  given name: Jakub
author list: Agent
  family name: Wodas
  given name: Lukasz
author list: Agent
  family name: Borowska
  given name: Alicja
author list: Agent
  family name: Cothran
  given name: Ernest G.
author list: Agent
  family name: Khanshour
  given name: Anas M.
author list: Agent
  family name: Mackowski
  given name: Mariusz
doi: 10.7717/peerj.3714
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-24
copyright: ©2017 Cieslak et al.
attribution name: Cieslak et al.

Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii
type: item
type: AcademicArticle
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 fun…
format: application/pdf
format: text/html
creator: Muhammad Y. Ali
creator: Ana Pavasovic
creator: Lalith K. Dammannagoda
creator: Peter B. Mather
creator: Peter J. Prentis
subject: Aquaculture, Fisheries and Fish Science
subject: Genetics
subject: Genomics
subject: Marine Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.3623
publisher: PeerJ Inc.
rights: © 2017 Ali et al.
abstract: 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 fun…
bibliographic citation: Ali et al. (2017) Comparative molecular analyses of select pH- and osmoregulatory genes in three freshwater crayfish Cherax quadricarinatus, C. destructor and C. cainii. PeerJ 5:e3623 https://doi.org/10.7717/peerj.3623
date submitted: 2016-12-09
date accepted: 2017-07-08
issued: 2017-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ali
  given name: Muhammad Y.
author list: Agent
  family name: Pavasovic
  given name: Ana
author list: Agent
  family name: Dammannagoda
  given name: Lalith K.
author list: Agent
  family name: Mather
  given name: Peter B.
author list: Agent
  family name: Prentis
  given name: Peter J.
doi: 10.7717/peerj.3623
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-24
copyright: ©2017 Ali et al.
attribution name: Ali et al.

Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño
type: item
type: AcademicArticle
description: Background Gene 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. Methods Allele 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. Results A 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. Discussion Prior 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 …
format: application/pdf
format: text/html
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
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.3737
publisher: PeerJ Inc.
rights: © 2017 Aguilar-Rangel et al.
abstract: Background Gene 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. Methods Allele 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. Results A 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. Discussion Prior 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 …
bibliographic citation: Aguilar-Rangel et al. (2017) Allele specific expression analysis identifies regulatory variation associated with stress-related genes in the Mexican highland maize landrace Palomero Toluqueño. PeerJ 5:e3737 https://doi.org/10.7717/peerj.3737
date submitted: 2017-06-22
date accepted: 2017-08-04
issued: 2017-08-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Aguilar-Rangel
  given name: M. Rocío
author list: Agent
  family name: Chávez Montes
  given name: Ricardo A.
author list: Agent
  family name: González-Segovia
  given name: Eric
author list: Agent
  family name: Ross-Ibarra
  given name: Jeffrey
author list: Agent
  family name: Simpson
  given name: June K.
author list: Agent
  family name: Sawers
  given name: Ruairidh J.H.
doi: 10.7717/peerj.3737
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-23
copyright: ©2017 Aguilar-Rangel et al.
attribution name: Aguilar-Rangel et al.

Defensive behaviors of the Oriental armyworm Mythimna separata in response to different parasitoid species (Hymenoptera: Braconidae)
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Jincheng Zhou
creator: Ling Meng
creator: Baoping Li
subject: Animal Behavior
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.3690
publisher: PeerJ Inc.
rights: © 2017 Zhou et al.
abstract: 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.
bibliographic citation: Zhou et al. (2017) Defensive behaviors of the Oriental armyworm Mythimna separata in response to different parasitoid species (Hymenoptera: Braconidae). PeerJ 5:e3690 https://doi.org/10.7717/peerj.3690
date submitted: 2017-05-04
date accepted: 2017-07-24
issued: 2017-08-23
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Jincheng
author list: Agent
  family name: Meng
  given name: Ling
author list: Agent
  family name: Li
  given name: Baoping
doi: 10.7717/peerj.3690
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-23
copyright: ©2017 Zhou et al.
attribution name: Zhou et al.

A Miocene breeding ground of an extinct baleen whale (Cetacea: Mysticeti)
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Cheng-Hsiu Tsai
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.3711
publisher: PeerJ Inc.
rights: © 2017 Tsai
abstract: 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.
bibliographic citation: Tsai (2017) A Miocene breeding ground of an extinct baleen whale (Cetacea: Mysticeti). PeerJ 5:e3711 https://doi.org/10.7717/peerj.3711
date submitted: 2017-05-09
date accepted: 2017-07-28
issued: 2017-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tsai
  given name: Cheng-Hsiu
doi: 10.7717/peerj.3711
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-22
copyright: ©2017 Tsai
attribution name: Tsai

Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Sarah M. Engle
creator: Justin J. Crowder
creator: Sheldon G. Watts
creator: Christopher J. Indovina
creator: Samuel Z. Coffey
creator: Eric M. Rubenstein
subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.3728
publisher: PeerJ Inc.
rights: © 2017 Engle et al.
abstract: 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.
bibliographic citation: Engle et al. (2017) Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon. PeerJ 5:e3728 https://doi.org/10.7717/peerj.3728
date submitted: 2017-06-20
date accepted: 2017-08-02
issued: 2017-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Engle
  given name: Sarah M.
author list: Agent
  family name: Crowder
  given name: Justin J.
author list: Agent
  family name: Watts
  given name: Sheldon G.
author list: Agent
  family name: Indovina
  given name: Christopher J.
author list: Agent
  family name: Coffey
  given name: Samuel Z.
author list: Agent
  family name: Rubenstein
  given name: Eric M.
doi: 10.7717/peerj.3728
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-22
copyright: ©2017 Engle et al.
attribution name: Engle et al.

Histological characterization of denticulate palatal plates in an Early Permian dissorophoid
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Bryan M. Gee
creator: Yara Haridy
creator: Robert R. Reisz
subject: Paleontology
subject: Histology
description: doi:10.7717/peerj.3727
publisher: PeerJ Inc.
rights: © 2017 Gee et al.
abstract: 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.
bibliographic citation: Gee et al. (2017) Histological characterization of denticulate palatal plates in an Early Permian dissorophoid. PeerJ 5:e3727 https://doi.org/10.7717/peerj.3727
date submitted: 2017-06-21
date accepted: 2017-08-02
issued: 2017-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gee
  given name: Bryan M.
author list: Agent
  family name: Haridy
  given name: Yara
author list: Agent
  family name: Reisz
  given name: Robert R.
doi: 10.7717/peerj.3727
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-22
copyright: ©2017 Gee et al.
attribution name: Gee et al.

Effects of linear and daily undulating periodized resistance training programs on measures of muscle hypertrophy: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background Periodization 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 Methods A 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). Results The 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). Conclusions The 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.
format: application/pdf
format: text/html
creator: Jozo Grgic
creator: Pavle Mikulic
creator: Hrvoje Podnar
creator: Zeljko Pedisic
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.3695
publisher: PeerJ Inc.
rights: © 2017 Grgic et al.
abstract: Background Periodization 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 Methods A 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). Results The 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). Conclusions The 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.
bibliographic citation: Grgic et al. (2017) Effects of linear and daily undulating periodized resistance training programs on measures of muscle hypertrophy: a systematic review and meta-analysis. PeerJ 5:e3695 https://doi.org/10.7717/peerj.3695
date submitted: 2017-04-14
date accepted: 2017-07-25
issued: 2017-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grgic
  given name: Jozo
author list: Agent
  family name: Mikulic
  given name: Pavle
author list: Agent
  family name: Podnar
  given name: Hrvoje
author list: Agent
  family name: Pedisic
  given name: Zeljko
doi: 10.7717/peerj.3695
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-22
copyright: ©2017 Grgic et al.
attribution name: Grgic et al.

The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae)
type: item
type: AcademicArticle
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 th…
format: application/pdf
format: text/html
creator: Fabrizio Ghiselli
creator: Liliana Milani
creator: Mariangela Iannello
creator: Emanuele Procopio
creator: Peter L. Chang
creator: Sergey V. Nuzhdin
creator: Marco Passamonti
subject: Zoology
description: doi:10.7717/peerj.3692
publisher: PeerJ Inc.
rights: © 2017 Ghiselli et al.
abstract: 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 th…
bibliographic citation: Ghiselli et al. (2017) The complete mitochondrial genome of the grooved carpet shell, Ruditapes decussatus (Bivalvia, Veneridae). PeerJ 5:e3692 https://doi.org/10.7717/peerj.3692
date submitted: 2017-05-19
date accepted: 2017-07-25
issued: 2017-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ghiselli
  given name: Fabrizio
author list: Agent
  family name: Milani
  given name: Liliana
author list: Agent
  family name: Iannello
  given name: Mariangela
author list: Agent
  family name: Procopio
  given name: Emanuele
author list: Agent
  family name: Chang
  given name: Peter L.
author list: Agent
  family name: Nuzhdin
  given name: Sergey V.
author list: Agent
  family name: Passamonti
  given name: Marco
doi: 10.7717/peerj.3692
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-22
copyright: © 2017 Ghiselli et al.
attribution name: Ghiselli et al.

Structural dynamics in the host-parasitoid system of the pine needle gall midge (Thecodiplosis japonensis) during invasion
type: item
type: AcademicArticle
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.
format: application/pdf
format: text/html
creator: Won Il Choi
creator: Mun-Jang Jeon
creator: Young-Seuk Park
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Evolutionary Studies
subject: Biosphere Interactions
description: doi:10.7717/peerj.3610
publisher: PeerJ Inc.
rights: © 2017 Choi et al.
abstract: 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.
bibliographic citation: Choi et al. (2017) Structural dynamics in the host-parasitoid system of the pine needle gall midge (Thecodiplosis japonensis) during invasion. PeerJ 5:e3610 https://doi.org/10.7717/peerj.3610
date submitted: 2016-07-05
date accepted: 2017-07-03
issued: 2017-08-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Won Il
author list: Agent
  family name: Jeon
  given name: Mun-Jang
author list: Agent
  family name: Park
  given name: Young-Seuk
doi: 10.7717/peerj.3610
volume: 5
issn: 2167-8359
publication name: PeerJ
publication date: 2017-08-22
copyright: ©2017 Choi et al.
attribution name: Choi et al.

PeerJ
type: Periodical
uri: PeerJ
issn: 2167-8359