PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Shaping ability of the profile 25/0.06 and protaper F2 in rotary motion, and reciproc in simulated canals
items: Comparing enzyme activity modifier equations through the development of global data fitting templates in Excel
items: Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene
items: Evidence for the Cretaceous shark Cretoxyrhina mantelli feeding on the pterosaur Pteranodon from the Niobrara Formation
items: Exploring the mechanistic link between corticosterone and insulin-like growth factor-1 in a wild passerine bird
items: Populations and assemblages living on the edge: dung beetles responses to forests-pasture ecotones
items: Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage
items: Acute effects of contract-relax proprioceptive neuromuscular facilitation stretching of hip abductors and adductors on dynamic balance
items: The influence of maternal body mass index and physical activity on select cardiovascular risk factors of preadolescent Hispanic children
items: Isolation and identification of pathogenic fungi and oomycetes associated with beans and cowpea root diseases in Oman

Shaping ability of the profile 25/0.06 and protaper F2 in rotary motion, and reciproc in simulated canals
type: item
type: AcademicArticle
description: Background Since the introduction of nickel–titanium (Ni–Ti) instruments to dentistry, a wide variety of Ni–Ti instruments have become commercially available. These Ni–Ti instruments are expensive, which limits their usage in developing countries and forces practitioners to use instruments repeatedly. Another problem is the possible prion cross-contamination associated with the multiple usage of endodontic instruments. In addition, the use of these instruments requires new skills and experience. In this article, the shaping capacities of two conventional rotary file systems, ProFile 25/0.06 and ProTaper F2, were reviewed and compared with the Reciproc single-file system. Methods A total of 45 simulated canals with 40° curvature, in clear resin blocks, were prepared using conventional rotary systems consisting of ProFile orifice shaping (OS) #3 and final flaring #25/.06, Reciproc R25, and ProTaper shaping file SX and finishing file F2. Pre-and post-instrumentation images were analyzed at ten different levels, using AutoCAD 2007 software. The measurement positions were defined in 1-mm intervals: positions 0–3 established the apical part, positions 4–6 constituted the middle part, and positions 7–10 established the coronal part of the canal. The amount of removed resin, the transportation, instrumentation time, change in working length (WL), instrumentation fractures, and the presence of ledge were evaluated. Data were analyzed using ANOVA, Kruskal–Wallis and independent t-test (p < 0.001). Results ProFile removed the least resin (p < 0.001) and caused less transportation than Reciproc and ProTaper, in total (p < 0.001). ProTaper caused more transportation ProFile and Reciproc in the apical part (p < 0.000). Reciproc caused more transportation than ProTaper and ProFile (p < 0.001), and the transportation tendency toward the inner aspect of the curvature in the middle part. Reciproc caused the less transportation than ProFile and ProTaper in the coronal part. The transp…
format: application/pdf
format: text/html
creator: Gül Çelik
creator: Murat Maden
creator: Ahmet Savgat
creator: Hikmet Orhan
subject: Dentistry
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.6109
publisher: PeerJ Inc.
rights: © 2018 Çelik et al.
abstract: Background Since the introduction of nickel–titanium (Ni–Ti) instruments to dentistry, a wide variety of Ni–Ti instruments have become commercially available. These Ni–Ti instruments are expensive, which limits their usage in developing countries and forces practitioners to use instruments repeatedly. Another problem is the possible prion cross-contamination associated with the multiple usage of endodontic instruments. In addition, the use of these instruments requires new skills and experience. In this article, the shaping capacities of two conventional rotary file systems, ProFile 25/0.06 and ProTaper F2, were reviewed and compared with the Reciproc single-file system. Methods A total of 45 simulated canals with 40° curvature, in clear resin blocks, were prepared using conventional rotary systems consisting of ProFile orifice shaping (OS) #3 and final flaring #25/.06, Reciproc R25, and ProTaper shaping file SX and finishing file F2. Pre-and post-instrumentation images were analyzed at ten different levels, using AutoCAD 2007 software. The measurement positions were defined in 1-mm intervals: positions 0–3 established the apical part, positions 4–6 constituted the middle part, and positions 7–10 established the coronal part of the canal. The amount of removed resin, the transportation, instrumentation time, change in working length (WL), instrumentation fractures, and the presence of ledge were evaluated. Data were analyzed using ANOVA, Kruskal–Wallis and independent t-test (p < 0.001). Results ProFile removed the least resin (p < 0.001) and caused less transportation than Reciproc and ProTaper, in total (p < 0.001). ProTaper caused more transportation ProFile and Reciproc in the apical part (p < 0.000). Reciproc caused more transportation than ProTaper and ProFile (p < 0.001), and the transportation tendency toward the inner aspect of the curvature in the middle part. Reciproc caused the less transportation than ProFile and ProTaper in the coronal part. The transp…
bibliographic citation: Çelik et al. (2018) Shaping ability of the profile 25/0.06 and protaper F2 in rotary motion, and reciproc in simulated canals. PeerJ 6:e6109 https://doi.org/10.7717/peerj.6109
date submitted: 2018-03-06
date accepted: 2018-11-14
issued: 2018-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Çelik
  given name: Gül
author list: Agent
  family name: Maden
  given name: Murat
author list: Agent
  family name: Savgat
  given name: Ahmet
author list: Agent
  family name: Orhan
  given name: Hikmet
doi: 10.7717/peerj.6109
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-14
copyright: ©2018 Çelik et al.
attribution name: Çelik et al.

Comparing enzyme activity modifier equations through the development of global data fitting templates in Excel
type: item
type: AcademicArticle
description: The classical way of defining enzyme inhibition has obscured the distinction between inhibitory effect and the inhibitor binding constant. This article examines the relationship between the simple binding curve used to define biomolecular interactions and the standard inhibitory term (1 + ([I]∕Ki)). By understanding how this term relates to binding curves which are ubiquitously used to describe biological processes, a modifier equation which distinguishes between inhibitor binding and the inhibitory effect, is examined. This modifier equation which can describe both activation and inhibition is compared to standard inhibitory equations with the development of global data fitting templates in Excel and via the global fitting of these equations to simulated and previously published datasets. In both cases, this modifier equation was able to match or outperform the other equations by providing superior fits to the datasets. The ability of this single equation to outperform the other equations suggests an over-complication of the field. This equation and the template developed in this article should prove to be useful tools in the study of enzyme inhibition and activation.
format: application/pdf
format: text/html
creator: Ryan Walsh
subject: Biochemistry
subject: Computational Biology
subject: Mathematical Biology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.6082
publisher: PeerJ Inc.
rights: © 2018 Walsh
abstract: The classical way of defining enzyme inhibition has obscured the distinction between inhibitory effect and the inhibitor binding constant. This article examines the relationship between the simple binding curve used to define biomolecular interactions and the standard inhibitory term (1 + ([I]∕Ki)). By understanding how this term relates to binding curves which are ubiquitously used to describe biological processes, a modifier equation which distinguishes between inhibitor binding and the inhibitory effect, is examined. This modifier equation which can describe both activation and inhibition is compared to standard inhibitory equations with the development of global data fitting templates in Excel and via the global fitting of these equations to simulated and previously published datasets. In both cases, this modifier equation was able to match or outperform the other equations by providing superior fits to the datasets. The ability of this single equation to outperform the other equations suggests an over-complication of the field. This equation and the template developed in this article should prove to be useful tools in the study of enzyme inhibition and activation.
bibliographic citation: Walsh (2018) Comparing enzyme activity modifier equations through the development of global data fitting templates in Excel. PeerJ 6:e6082 https://doi.org/10.7717/peerj.6082
date submitted: 2017-07-18
date accepted: 2018-11-07
issued: 2018-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Walsh
  given name: Ryan
doi: 10.7717/peerj.6082
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-14
copyright: ©2018 Walsh
attribution name: Walsh

Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene
type: item
type: AcademicArticle
description: Bacterial endosymbionts of aquatic invertebrates remain poorly studied. This is at least partly due to a lack of suitable techniques and primers for their identification. We designed a pair of non-degenerate primers which enabled us to amplify a fragment of ca. 500 bp of the 16S rRNA gene from various known bacterial endosymbiont species. By using this approach, we identified four bacterial endosymbionts, two endoparasites and one uncultured bacterium in seven, taxonomically diverse, freshwater crustacean hosts from temporary waters across a wide geographical area. The overall efficiency of our new WOLBSL and WOLBSR primers for amplification of the bacterial 16S rRNA gene was 100%. However, if different bacterial species from one sample were amplified simultaneously, sequences were illegible, despite a good quality of PCR products. Therefore, we suggest using our primers at the first stage of bacterial endosymbiont identification. Subsequently, genus specific primers are recommended. Overall, in the era of next-generation sequencing our method can be used as a first simple and low-cost approach to identify potential microbial symbionts associated with freshwater crustaceans using simple Sanger sequencing. The potential to detected bacterial symbionts in various invertebrate hosts in such a way will facilitate studies on host-symbiont interactions and coevolution.
format: application/pdf
format: text/html
creator: Monika Mioduchowska
creator: Michał Jan Czyż
creator: Bartłomiej Gołdyn
creator: Adrianna Kilikowska
creator: Tadeusz Namiotko
creator: Tom Pinceel
creator: Małgorzata Łaciak
creator: Jerzy Sell
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
subject: Genetics
subject: Freshwater Biology
description: doi:10.7717/peerj.6039
publisher: PeerJ Inc.
rights: © 2018 Mioduchowska et al.
abstract: Bacterial endosymbionts of aquatic invertebrates remain poorly studied. This is at least partly due to a lack of suitable techniques and primers for their identification. We designed a pair of non-degenerate primers which enabled us to amplify a fragment of ca. 500 bp of the 16S rRNA gene from various known bacterial endosymbiont species. By using this approach, we identified four bacterial endosymbionts, two endoparasites and one uncultured bacterium in seven, taxonomically diverse, freshwater crustacean hosts from temporary waters across a wide geographical area. The overall efficiency of our new WOLBSL and WOLBSR primers for amplification of the bacterial 16S rRNA gene was 100%. However, if different bacterial species from one sample were amplified simultaneously, sequences were illegible, despite a good quality of PCR products. Therefore, we suggest using our primers at the first stage of bacterial endosymbiont identification. Subsequently, genus specific primers are recommended. Overall, in the era of next-generation sequencing our method can be used as a first simple and low-cost approach to identify potential microbial symbionts associated with freshwater crustaceans using simple Sanger sequencing. The potential to detected bacterial symbionts in various invertebrate hosts in such a way will facilitate studies on host-symbiont interactions and coevolution.
bibliographic citation: Mioduchowska et al. (2018) Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene. PeerJ 6:e6039 https://doi.org/10.7717/peerj.6039
date submitted: 2018-07-19
date accepted: 2018-10-30
issued: 2018-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mioduchowska
  given name: Monika
author list: Agent
  family name: Czyż
  given name: Michał Jan
author list: Agent
  family name: Gołdyn
  given name: Bartłomiej
author list: Agent
  family name: Kilikowska
  given name: Adrianna
author list: Agent
  family name: Namiotko
  given name: Tadeusz
author list: Agent
  family name: Pinceel
  given name: Tom
author list: Agent
  family name: Łaciak
  given name: Małgorzata
author list: Agent
  family name: Sell
  given name: Jerzy
doi: 10.7717/peerj.6039
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-14
copyright: ©2018 Mioduchowska et al.
attribution name: Mioduchowska et al.

Evidence for the Cretaceous shark Cretoxyrhina mantelli feeding on the pterosaur Pteranodon from the Niobrara Formation
type: item
type: AcademicArticle
description: A cervical vertebra of the large, pelagic pterodactyloid pterosaur Pteranodon sp. from the Late Cretaceous Niobrara Formation of Kansas, USA is significant for its association with a tooth from the large lamniform shark, Cretoxyrhina mantelli. Though the tooth does not pierce the vertebral periosteum, the intimate association of the fossils—in which the tooth is wedged below the left prezygapophysis—suggests their preservation together was not mere chance, and the specimen is evidence of Cretoxyrhina biting Pteranodon. It is not possible to infer whether the bite reflects predatory or scavenging behaviour from the preserved material. There are several records of Pteranodon having been consumed by other fish, including other sharks (specifically, the anacoracid Squalicorax kaupi), and multiple records of Cretoxyrhina biting other vertebrates of the Western Interior Seaway, but until now interactions between Cretoxyrhina and Pteranodon have remained elusive. The specimen increases the known interactions between large, pelagic, vertebrate carnivores of the Western Interior Seaway of North America during the Late Cretaceous, in addition to bolstering the relatively small fossil record representing pterosaurian interactions with other species.
format: application/pdf
format: text/html
creator: David W.E. Hone
creator: Mark P. Witton
creator: Michael B. Habib
subject: Paleontology
description: doi:10.7717/peerj.6031
publisher: PeerJ Inc.
rights: © 2018 Hone et al.
abstract: A cervical vertebra of the large, pelagic pterodactyloid pterosaur Pteranodon sp. from the Late Cretaceous Niobrara Formation of Kansas, USA is significant for its association with a tooth from the large lamniform shark, Cretoxyrhina mantelli. Though the tooth does not pierce the vertebral periosteum, the intimate association of the fossils—in which the tooth is wedged below the left prezygapophysis—suggests their preservation together was not mere chance, and the specimen is evidence of Cretoxyrhina biting Pteranodon. It is not possible to infer whether the bite reflects predatory or scavenging behaviour from the preserved material. There are several records of Pteranodon having been consumed by other fish, including other sharks (specifically, the anacoracid Squalicorax kaupi), and multiple records of Cretoxyrhina biting other vertebrates of the Western Interior Seaway, but until now interactions between Cretoxyrhina and Pteranodon have remained elusive. The specimen increases the known interactions between large, pelagic, vertebrate carnivores of the Western Interior Seaway of North America during the Late Cretaceous, in addition to bolstering the relatively small fossil record representing pterosaurian interactions with other species.
bibliographic citation: Hone et al. (2018) Evidence for the Cretaceous shark Cretoxyrhina mantelli feeding on the pterosaur Pteranodon from the Niobrara Formation. PeerJ 6:e6031 https://doi.org/10.7717/peerj.6031
date submitted: 2018-09-18
date accepted: 2018-10-30
issued: 2018-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hone
  given name: David W.E.
author list: Agent
  family name: Witton
  given name: Mark P.
author list: Agent
  family name: Habib
  given name: Michael B.
doi: 10.7717/peerj.6031
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-14
copyright: ©2018 Hone et al.
attribution name: Hone et al.

Exploring the mechanistic link between corticosterone and insulin-like growth factor-1 in a wild passerine bird
type: item
type: AcademicArticle
description: Background Physiological regulators of life history trade-offs need to be responsive to sudden changes of resource availability. When homeostasis is challenged by unpredictable stressors, vertebrates respond through a set of physiological reactions, which can promote organismal survival. Glucocorticoids have been traditionally recognized as one of the main regulators of the physiological stress response, but the role of an evolutionarily more conserved pathway, the hypothalamic-pituitary-somatotropic (HPS) axis producing insulin-like growth factor-1 (IGF-1) has received much less attention. Although IGF-1 is known to affect several life history traits, little is known about its role in the physiological stress response and it has never been studied directly in adult wild animals. Methods In this study, we combined field observations with a controlled experiment to investigate how circulating levels of IGF-1 change in response to stress and whether this change is due to concomitant change in glucocorticoids in a free-living songbird, the bearded reedling Panurus biarmicus. We used a standard capture-restraint protocol in field observation, in which we took first and second (stress induced: 15 minutes later) samples. In a follow-up experiment, we used a minimally invasive oral corticosterone manipulation. Results We showed that corticosterone levels significantly increased while IGF-1 levels significantly decreased during capture and handling stress. However, change in corticosterone levels were not related to change in IGF-1 levels. We found that experimentally elevated corticosterone levels did not affect IGF-1 levels. Discussion Our results are the first to highlight that circulating IGF-1 levels are responsive to stress independently from glucocorticoids and suggest that the HPS axis is an autonomous physiological pathway that may play an important role as regulator of life-history decisions.
format: application/pdf
format: text/html
creator: Zsófia Tóth
creator: Jenny Q. Ouyang
creator: Ádám Z. Lendvai
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.5936
publisher: PeerJ Inc.
rights: © 2018 Tóth et al.
abstract: Background Physiological regulators of life history trade-offs need to be responsive to sudden changes of resource availability. When homeostasis is challenged by unpredictable stressors, vertebrates respond through a set of physiological reactions, which can promote organismal survival. Glucocorticoids have been traditionally recognized as one of the main regulators of the physiological stress response, but the role of an evolutionarily more conserved pathway, the hypothalamic-pituitary-somatotropic (HPS) axis producing insulin-like growth factor-1 (IGF-1) has received much less attention. Although IGF-1 is known to affect several life history traits, little is known about its role in the physiological stress response and it has never been studied directly in adult wild animals. Methods In this study, we combined field observations with a controlled experiment to investigate how circulating levels of IGF-1 change in response to stress and whether this change is due to concomitant change in glucocorticoids in a free-living songbird, the bearded reedling Panurus biarmicus. We used a standard capture-restraint protocol in field observation, in which we took first and second (stress induced: 15 minutes later) samples. In a follow-up experiment, we used a minimally invasive oral corticosterone manipulation. Results We showed that corticosterone levels significantly increased while IGF-1 levels significantly decreased during capture and handling stress. However, change in corticosterone levels were not related to change in IGF-1 levels. We found that experimentally elevated corticosterone levels did not affect IGF-1 levels. Discussion Our results are the first to highlight that circulating IGF-1 levels are responsive to stress independently from glucocorticoids and suggest that the HPS axis is an autonomous physiological pathway that may play an important role as regulator of life-history decisions.
bibliographic citation: Tóth et al. (2018) Exploring the mechanistic link between corticosterone and insulin-like growth factor-1 in a wild passerine bird. PeerJ 6:e5936 https://doi.org/10.7717/peerj.5936
date submitted: 2018-06-06
date accepted: 2018-10-15
issued: 2018-12-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tóth
  given name: Zsófia
author list: Agent
  family name: Ouyang
  given name: Jenny Q.
author list: Agent
  family name: Lendvai
  given name: Ádám Z.
doi: 10.7717/peerj.5936
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-14
copyright: ©2018 Tóth et al.
attribution name: Tóth et al.

Populations and assemblages living on the edge: dung beetles responses to forests-pasture ecotones
type: item
type: AcademicArticle
description: Edge effects alter insect biodiversity in several ways. However, we still have a limited understanding on simultaneous responses of ecological populations and assemblages to ecotones, especially in human modified landscapes. We analyze edge effects on dung beetle populations and assemblages between livestock pastures and native temperate forests (Juniperus and pine-oak forests (POFs)) to describe how species abundances and assemblage parameters respond to edge effects through gradients in forest-pasture ecotones. In Juniperus forest 13 species avoided the ecotones: six species showed greater abundance in forest interior and seven in pasturelands, while the other two species had a neutral response to the edge. In a different way, in POF we found five species avoiding the edge (four with greater abundance in pastures and only one in forest), two species had a neutral response, and two showed a unimodal pattern of abundance near to the edge. At the assemblage level edge effects are masked, as species richness, diversity, functional richness, functional evenness, and compositional incidence dissimilarity did not vary along forest-pasture ecotones. However, total abundance and functional divergence showed higher values in pastures in one of the two sampling localities. Also, assemblage similarity based on species’ abundance showed a peak near to the edge in POF. We propose that conservation efforts in human-managed landscapes should focus on mitigating current and delayed edge effects. Ecotone management will be crucial in livestock dominated landscapes to conserve regional biodiversity and the environmental services carried out by dung beetles.
format: application/pdf
format: text/html
creator: Ana Paola Martínez-Falcón
creator: Gustavo A. Zurita
creator: Ilse J. Ortega-Martínez
creator: Claudia E. Moreno
subject: Biodiversity
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.6148
publisher: PeerJ Inc.
rights: © 2018 Martínez-Falcón et al.
abstract: Edge effects alter insect biodiversity in several ways. However, we still have a limited understanding on simultaneous responses of ecological populations and assemblages to ecotones, especially in human modified landscapes. We analyze edge effects on dung beetle populations and assemblages between livestock pastures and native temperate forests (Juniperus and pine-oak forests (POFs)) to describe how species abundances and assemblage parameters respond to edge effects through gradients in forest-pasture ecotones. In Juniperus forest 13 species avoided the ecotones: six species showed greater abundance in forest interior and seven in pasturelands, while the other two species had a neutral response to the edge. In a different way, in POF we found five species avoiding the edge (four with greater abundance in pastures and only one in forest), two species had a neutral response, and two showed a unimodal pattern of abundance near to the edge. At the assemblage level edge effects are masked, as species richness, diversity, functional richness, functional evenness, and compositional incidence dissimilarity did not vary along forest-pasture ecotones. However, total abundance and functional divergence showed higher values in pastures in one of the two sampling localities. Also, assemblage similarity based on species’ abundance showed a peak near to the edge in POF. We propose that conservation efforts in human-managed landscapes should focus on mitigating current and delayed edge effects. Ecotone management will be crucial in livestock dominated landscapes to conserve regional biodiversity and the environmental services carried out by dung beetles.
bibliographic citation: Martínez-Falcón et al. (2018) Populations and assemblages living on the edge: dung beetles responses to forests-pasture ecotones. PeerJ 6:e6148 https://doi.org/10.7717/peerj.6148
date submitted: 2018-08-31
date accepted: 2018-11-21
issued: 2018-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Martínez-Falcón
  given name: Ana Paola
author list: Agent
  family name: Zurita
  given name: Gustavo A.
author list: Agent
  family name: Ortega-Martínez
  given name: Ilse J.
author list: Agent
  family name: Moreno
  given name: Claudia E.
doi: 10.7717/peerj.6148
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-13
copyright: © 2018 Martínez-Falcón et al.
attribution name: Martínez-Falcón et al.

Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage
type: item
type: AcademicArticle
description: Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55–75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.
format: application/pdf
format: text/html
creator: Prapatsorn Areesirisuk
creator: Narongrit Muangmai
creator: Kirati Kunya
creator: Worapong Singchat
creator: Siwapech Sillapaprayoon
creator: Sorravis Lapbenjakul
creator: Watcharaporn Thapana
creator: Attachai Kantachumpoo
creator: Sudarath Baicharoen
creator: Budsaba Rerkamnuaychoke
creator: Surin Peyachoknagul
creator: Kyudong Han
creator: Kornsorn Srikulnath
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.6121
publisher: PeerJ Inc.
rights: © 2018 Areesirisuk et al.
abstract: Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55–75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.
bibliographic citation: Areesirisuk et al. (2018) Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage. PeerJ 6:e6121 https://doi.org/10.7717/peerj.6121
date submitted: 2018-07-30
date accepted: 2018-11-15
issued: 2018-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Areesirisuk
  given name: Prapatsorn
author list: Agent
  family name: Muangmai
  given name: Narongrit
author list: Agent
  family name: Kunya
  given name: Kirati
author list: Agent
  family name: Singchat
  given name: Worapong
author list: Agent
  family name: Sillapaprayoon
  given name: Siwapech
author list: Agent
  family name: Lapbenjakul
  given name: Sorravis
author list: Agent
  family name: Thapana
  given name: Watcharaporn
author list: Agent
  family name: Kantachumpoo
  given name: Attachai
author list: Agent
  family name: Baicharoen
  given name: Sudarath
author list: Agent
  family name: Rerkamnuaychoke
  given name: Budsaba
author list: Agent
  family name: Peyachoknagul
  given name: Surin
author list: Agent
  family name: Han
  given name: Kyudong
author list: Agent
  family name: Srikulnath
  given name: Kornsorn
doi: 10.7717/peerj.6121
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-13
copyright: ©2018 Areesirisuk et al.
attribution name: Areesirisuk et al.

Acute effects of contract-relax proprioceptive neuromuscular facilitation stretching of hip abductors and adductors on dynamic balance
type: item
type: AcademicArticle
description: Background Balance control has been shown to play a fundamental role both in everyday life and many athletic activities. An important component of balance control is the somatosensory information gained from muscle spindles and Golgi tendon organs. The changes in the muscle-tendon unit stiffness could alter the ability to detect and respond promptly to changes of an unstable environment. One of the procedures affecting muscle stiffness is stretching, and contract-relax PNF stretching (CRS) is considered as one of the safest and most effective techniques. So far, there are no studies on the impact of CRS of hip adductor and abductor muscles on body balance. These muscle groups are responsible for maintaining mediolateral balance which is of particular interest, since it is more affected by ageing and disease and since its deterioration has been associated with an increased risk of falling. In light of the above, the aim of the present study was to investigate the effects of a single dose of contract-relax proprioceptive neuromuscular facilitation stretching of hip adductors and abductors on mediolateral dynamic balance. Methods The study involved 45 healthy individuals (age 19–23 years) assigned to the intervention group (IG) or the control group (CG). Balance testing was carried out before (Pre) and immediately after CRS in the intervention group or after 5-minute rest in the control group (Post). There were performed three repetitions of the CRS targeting the adductor and abductor muscles of the hip. Results Statistically significant differences between Pre and Post condition were observed only in the intervention group. The values of all measured variables defining the body’s dynamic balance were significantly lower immediately after the applied CRS, which indicates an improved body balance: Global Index (p = 0.0001), total area of sway (p = 0.0001), external area of sway (p = 0.00004), external time (p = 0.0004) and reaction time (p = 0.0003). Conclusions A singl…
format: application/pdf
format: text/html
creator: Rafał Szafraniec
creator: Krystyna Chromik
creator: Amanda Poborska
creator: Adam Kawczyński
subject: Neuroscience
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.6108
publisher: PeerJ Inc.
rights: © 2018 Szafraniec et al.
abstract: Background Balance control has been shown to play a fundamental role both in everyday life and many athletic activities. An important component of balance control is the somatosensory information gained from muscle spindles and Golgi tendon organs. The changes in the muscle-tendon unit stiffness could alter the ability to detect and respond promptly to changes of an unstable environment. One of the procedures affecting muscle stiffness is stretching, and contract-relax PNF stretching (CRS) is considered as one of the safest and most effective techniques. So far, there are no studies on the impact of CRS of hip adductor and abductor muscles on body balance. These muscle groups are responsible for maintaining mediolateral balance which is of particular interest, since it is more affected by ageing and disease and since its deterioration has been associated with an increased risk of falling. In light of the above, the aim of the present study was to investigate the effects of a single dose of contract-relax proprioceptive neuromuscular facilitation stretching of hip adductors and abductors on mediolateral dynamic balance. Methods The study involved 45 healthy individuals (age 19–23 years) assigned to the intervention group (IG) or the control group (CG). Balance testing was carried out before (Pre) and immediately after CRS in the intervention group or after 5-minute rest in the control group (Post). There were performed three repetitions of the CRS targeting the adductor and abductor muscles of the hip. Results Statistically significant differences between Pre and Post condition were observed only in the intervention group. The values of all measured variables defining the body’s dynamic balance were significantly lower immediately after the applied CRS, which indicates an improved body balance: Global Index (p = 0.0001), total area of sway (p = 0.0001), external area of sway (p = 0.00004), external time (p = 0.0004) and reaction time (p = 0.0003). Conclusions A singl…
bibliographic citation: Szafraniec et al. (2018) Acute effects of contract-relax proprioceptive neuromuscular facilitation stretching of hip abductors and adductors on dynamic balance. PeerJ 6:e6108 https://doi.org/10.7717/peerj.6108
date submitted: 2018-03-07
date accepted: 2018-11-14
issued: 2018-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szafraniec
  given name: Rafał
author list: Agent
  family name: Chromik
  given name: Krystyna
author list: Agent
  family name: Poborska
  given name: Amanda
author list: Agent
  family name: Kawczyński
  given name: Adam
doi: 10.7717/peerj.6108
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-13
copyright: ©2018 Szafraniec et al.
attribution name: Szafraniec et al.

The influence of maternal body mass index and physical activity on select cardiovascular risk factors of preadolescent Hispanic children
type: item
type: AcademicArticle
description: Background Maternal obesity and physical inactivity have been identified as correlates of overweight and obesity and physical inactivity in older preadolescents; however, no study has explored this relationship in Hispanic preadolescents. Furthermore, the relation between maternal physical activity (PA) and blood pressure (BP) in Hispanic preadolescents has not been examined. Purpose This study aimed to assess the associations between Hispanic mothers’ PA and body mass index (BMI) and their preadolescents’ PA, screen time, BP, and BMI. Methods Data of 118 mother-child (aged 2–10 years) dyads enrolled in a cross-sectional study of metabolic syndrome in Hispanic preadolescents at a community health center in Johnson City, TN were used. Parent and child questionnaires were used to ascertain mothers’ BMI and PA and preadolescents’ PA and screen time. Preadolescents’ height, weight, and BP were measured. Multiple logistic regression was used to examine the association between child and maternal variables, adjusting for mother’s education and the child’s sex and age. Results Pradolescents of obese mothers were more likely than preadolescents of mothers with normal weight to engage in less than three days of at least 60 min of vigorous PA per week (OR: 6.47, 95% CI [1.61–26.0]). Preadolescents whose mothers did not engage in moderate PA were more likely to engage in less than three days of at least 60 min of vigorous PA per week (OR: 2.92, CI [1.18–7.24]); and have elevated BP (OR: 2.50, 95% CI [1.02–4.53]) than preadolescents whose mothers engaged in moderate PA. Discussion Our results show a negative relationship between maternal obesity and preadolescent PA, and a positive relationship between lower maternal PA and elevated BP and lower PA in Hispanic preadolescents. This suggests that interventions aimed at improving Hispanic preadolescents’ PA and BP may use maternal PA and maternal BMI (for preadolescent PA) as a modification strategy to improve health in Hispanic pr…
format: application/pdf
format: text/html
creator: Basil A. Alhassan
creator: Ying Liu
creator: Deborah Slawson
creator: Jonathan M. Peterson
creator: Jo-Ann Marrs
creator: William A. Clark
creator: Arsham Alamian
subject: Epidemiology
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.6100
publisher: PeerJ Inc.
rights: © 2018 Alhassan et al.
abstract: Background Maternal obesity and physical inactivity have been identified as correlates of overweight and obesity and physical inactivity in older preadolescents; however, no study has explored this relationship in Hispanic preadolescents. Furthermore, the relation between maternal physical activity (PA) and blood pressure (BP) in Hispanic preadolescents has not been examined. Purpose This study aimed to assess the associations between Hispanic mothers’ PA and body mass index (BMI) and their preadolescents’ PA, screen time, BP, and BMI. Methods Data of 118 mother-child (aged 2–10 years) dyads enrolled in a cross-sectional study of metabolic syndrome in Hispanic preadolescents at a community health center in Johnson City, TN were used. Parent and child questionnaires were used to ascertain mothers’ BMI and PA and preadolescents’ PA and screen time. Preadolescents’ height, weight, and BP were measured. Multiple logistic regression was used to examine the association between child and maternal variables, adjusting for mother’s education and the child’s sex and age. Results Pradolescents of obese mothers were more likely than preadolescents of mothers with normal weight to engage in less than three days of at least 60 min of vigorous PA per week (OR: 6.47, 95% CI [1.61–26.0]). Preadolescents whose mothers did not engage in moderate PA were more likely to engage in less than three days of at least 60 min of vigorous PA per week (OR: 2.92, CI [1.18–7.24]); and have elevated BP (OR: 2.50, 95% CI [1.02–4.53]) than preadolescents whose mothers engaged in moderate PA. Discussion Our results show a negative relationship between maternal obesity and preadolescent PA, and a positive relationship between lower maternal PA and elevated BP and lower PA in Hispanic preadolescents. This suggests that interventions aimed at improving Hispanic preadolescents’ PA and BP may use maternal PA and maternal BMI (for preadolescent PA) as a modification strategy to improve health in Hispanic pr…
bibliographic citation: Alhassan et al. (2018) The influence of maternal body mass index and physical activity on select cardiovascular risk factors of preadolescent Hispanic children. PeerJ 6:e6100 https://doi.org/10.7717/peerj.6100
date submitted: 2018-03-19
date accepted: 2018-11-12
issued: 2018-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alhassan
  given name: Basil A.
author list: Agent
  family name: Liu
  given name: Ying
author list: Agent
  family name: Slawson
  given name: Deborah
author list: Agent
  family name: Peterson
  given name: Jonathan M.
author list: Agent
  family name: Marrs
  given name: Jo-Ann
author list: Agent
  family name: Clark
  given name: William A.
author list: Agent
  family name: Alamian
  given name: Arsham
doi: 10.7717/peerj.6100
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-13
copyright: ©2018 Alhassan et al.
attribution name: Alhassan et al.

Isolation and identification of pathogenic fungi and oomycetes associated with beans and cowpea root diseases in Oman
type: item
type: AcademicArticle
description: The purpose of this study was to characterize fungal and oomycete species associated with root diseases of Phaseolus vulgaris, Vigna unguiculata, V. radiata and Vicia faba in Oman. Root samples were collected from plants suffering from weakened growth and yellowing symptoms. Fungal species were isolated on 2.5% potato dextrose agar amended with 10 mg l−1 rifampicin and 200 mg l−1 of ampicillin and identification was based on sequences of the internal transcribed spacer region of the ribosomal RNA gene (ITS rRNA), glycerol-3-phosphate dehydrogenase (GPDH), translation elongation factor-1 alpha (TEF), beta-tubulin (TUB), calmodulin (CMD), actin (ACT). Isolations yielded 204 fungal isolates belonging to nine different genera, with most isolates belonging to Alternaria and Fusarium. Molecular identification revealed that the isolates belong to 20 fungal species, the most dominant of which was Alternaria alternata. Pathogenicity tests were conducted on each plant species. The inoculations on P. vulgaris revealed that Pythium aphanidermatum induced rotting, damping-off and wilt symptoms while Fusarium equiseti induced yellowing symptoms on the leaves. Rhizoctonia solani produced lesions and root rot on Vigna unguiculata while Curvularia muehlenbeckiae and Curvularia caricae-papayae produced root lesions on the roots of V. unguiculata and V. radiata, respectively. Alternaria alternata produced brown symptoms on the tap root of Vicia faba. P. aphanidermatum resulted in a significant reduction in the fresh weight, dry weight and shoot length of Phaseolus vulgaris. The study shows that several fungal species can be found associated with the roots of beans and Vigna unguiculata in Oman and can result in varying disease symptoms. This is the first report of root lesions produced by Curvularia muehlenbeckiae on the roots of V. unguiculata and by C. caricae-papayae on V. radiata worldwide.
format: application/pdf
format: text/html
creator: Asma Al-Jaradi
creator: Issa Al-Mahmooli
creator: Rhonda Janke
creator: Sajeewa Maharachchikumbura
creator: Nadiya Al-Saady
creator: Abdullah M. Al-Sadi
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.6064
publisher: PeerJ Inc.
rights: © 2018 Al-Jaradi et al.
abstract: The purpose of this study was to characterize fungal and oomycete species associated with root diseases of Phaseolus vulgaris, Vigna unguiculata, V. radiata and Vicia faba in Oman. Root samples were collected from plants suffering from weakened growth and yellowing symptoms. Fungal species were isolated on 2.5% potato dextrose agar amended with 10 mg l−1 rifampicin and 200 mg l−1 of ampicillin and identification was based on sequences of the internal transcribed spacer region of the ribosomal RNA gene (ITS rRNA), glycerol-3-phosphate dehydrogenase (GPDH), translation elongation factor-1 alpha (TEF), beta-tubulin (TUB), calmodulin (CMD), actin (ACT). Isolations yielded 204 fungal isolates belonging to nine different genera, with most isolates belonging to Alternaria and Fusarium. Molecular identification revealed that the isolates belong to 20 fungal species, the most dominant of which was Alternaria alternata. Pathogenicity tests were conducted on each plant species. The inoculations on P. vulgaris revealed that Pythium aphanidermatum induced rotting, damping-off and wilt symptoms while Fusarium equiseti induced yellowing symptoms on the leaves. Rhizoctonia solani produced lesions and root rot on Vigna unguiculata while Curvularia muehlenbeckiae and Curvularia caricae-papayae produced root lesions on the roots of V. unguiculata and V. radiata, respectively. Alternaria alternata produced brown symptoms on the tap root of Vicia faba. P. aphanidermatum resulted in a significant reduction in the fresh weight, dry weight and shoot length of Phaseolus vulgaris. The study shows that several fungal species can be found associated with the roots of beans and Vigna unguiculata in Oman and can result in varying disease symptoms. This is the first report of root lesions produced by Curvularia muehlenbeckiae on the roots of V. unguiculata and by C. caricae-papayae on V. radiata worldwide.
bibliographic citation: Al-Jaradi et al. (2018) Isolation and identification of pathogenic fungi and oomycetes associated with beans and cowpea root diseases in Oman. PeerJ 6:e6064 https://doi.org/10.7717/peerj.6064
date submitted: 2018-05-21
date accepted: 2018-11-03
issued: 2018-12-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al-Jaradi
  given name: Asma
author list: Agent
  family name: Al-Mahmooli
  given name: Issa
author list: Agent
  family name: Janke
  given name: Rhonda
author list: Agent
  family name: Maharachchikumbura
  given name: Sajeewa
author list: Agent
  family name: Al-Saady
  given name: Nadiya
author list: Agent
  family name: Al-Sadi
  given name: Abdullah M.
doi: 10.7717/peerj.6064
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-13
copyright: ©2018 Al-Jaradi et al.
attribution name: Al-Jaradi et al.

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