PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe
items: Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars
items: In vivo antioxidant activity of mackerel (Scomber japonicus) muscle protein hydrolysate
items: Modulation of corticomotor excitability in response to distal focal cooling
items: Species turnover in plants does not predict turnover in flower-visiting insects
items: Application of insect-proof nets in pesticide-free rice creates an altered microclimate and differential agronomic performance
items: Shell variability in the stem turtles Proterochersis spp.
items: Non-invasive monitoring of glucocorticoid metabolite concentrations in urine and faeces of the Sungazer (Smaug giganteus)
items: Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae)
items: Biochemical and growth responses of silver maple (Acer saccharinum L.) to sodium chloride and calcium chloride

Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe
type: item
type: AcademicArticle
description: Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
format: application/pdf
format: text/html
creator: Beatriz Roncero-Ramos
creator: M. Ángeles Muñoz-Martín
creator: Sonia Chamizo
creator: Lara Fernández-Valbuena
creator: Diego Mendoza
creator: Elvira Perona
creator: Yolanda Cantón
creator: Pilar Mateo
subject: Biodiversity
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.6169
publisher: PeerJ Inc.
rights: © 2019 Roncero-Ramos et al.
abstract: Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
bibliographic citation: Roncero-Ramos et al. (2019) Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe. PeerJ 7:e6169 https://doi.org/10.7717/peerj.6169
date submitted: 2018-07-11
date accepted: 2018-11-27
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roncero-Ramos
  given name: Beatriz
author list: Agent
  family name: Muñoz-Martín
  given name: M. Ángeles
author list: Agent
  family name: Chamizo
  given name: Sonia
author list: Agent
  family name: Fernández-Valbuena
  given name: Lara
author list: Agent
  family name: Mendoza
  given name: Diego
author list: Agent
  family name: Perona
  given name: Elvira
author list: Agent
  family name: Cantón
  given name: Yolanda
author list: Agent
  family name: Mateo
  given name: Pilar
doi: 10.7717/peerj.6169
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Roncero-Ramos et al.
attribution name: Roncero-Ramos et al.

Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars
type: item
type: AcademicArticle
description: MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified and characterized a total of 18 miR169 family members in banana (Musa acuminata L.) based on small RNA sequencing. The banana miR169 family clustered into two groups based on miRNA evolutionary analysis. Multiple sequence alignment indicated a high degree of sequence conservation in miRNA169 family members across 28 plant species. Computational target prediction algorithms were used to identify 25 targets of miR169 family members in banana. These targets were enriched in various metabolic pathways that include the following molecules: glycine, serine, threonine, pentose, glycerolipids, nucleotide sugars, starch, and sucrose. Through miRNA transcriptomic analysis, we found that ma-miR169a and ma-miR169b displayed high expression levels, whereas the other 16 ma-miR169 members exhibited low expression in the HG and Baxi banana cultivars. Further experiments indicate that there were negative relationships between ma-miR169a, ma-miR169b and their targets basing on their expression levels to Foc4 (Fusarium oxysporum f. sp. cubense tropical race 4) infection in resistant cultivars. But they were low expressed in susceptive cultivars. These results suggested that the expression levels of ma-miR169a and ma-miR169b were consistent with the resistance degree of the banana cultivars to Foc4. The analysis presented here constitutes a starting point to understand ma-miR169-mediated Fusarium wilt resistance at the transcriptional level in banana and predicts possible candidate targets for the genetic improvement of banana resistance to Foc4.
format: application/pdf
format: text/html
creator: Shun Song
creator: Yi Xu
creator: Dongmei Huang
creator: Muhammad Aleem Ashraf
creator: Jingyang Li
creator: Wei Hu
creator: Zhiqiang Jin
creator: Changying Zeng
creator: Fenling Tang
creator: Biyu Xu
creator: Huicai Zeng
creator: Yujia Li
creator: Jianghui Xie
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6209
publisher: PeerJ Inc.
rights: © 2018 Song et al.
abstract: MicroRNAs (miRNAs) play an important role in plant resistance to pathogen infections. However, little is known about the role of miRNAs in banana Fusarium wilt, which is the most economically devastating disease in banana production. In the present study, we identified and characterized a total of 18 miR169 family members in banana (Musa acuminata L.) based on small RNA sequencing. The banana miR169 family clustered into two groups based on miRNA evolutionary analysis. Multiple sequence alignment indicated a high degree of sequence conservation in miRNA169 family members across 28 plant species. Computational target prediction algorithms were used to identify 25 targets of miR169 family members in banana. These targets were enriched in various metabolic pathways that include the following molecules: glycine, serine, threonine, pentose, glycerolipids, nucleotide sugars, starch, and sucrose. Through miRNA transcriptomic analysis, we found that ma-miR169a and ma-miR169b displayed high expression levels, whereas the other 16 ma-miR169 members exhibited low expression in the HG and Baxi banana cultivars. Further experiments indicate that there were negative relationships between ma-miR169a, ma-miR169b and their targets basing on their expression levels to Foc4 (Fusarium oxysporum f. sp. cubense tropical race 4) infection in resistant cultivars. But they were low expressed in susceptive cultivars. These results suggested that the expression levels of ma-miR169a and ma-miR169b were consistent with the resistance degree of the banana cultivars to Foc4. The analysis presented here constitutes a starting point to understand ma-miR169-mediated Fusarium wilt resistance at the transcriptional level in banana and predicts possible candidate targets for the genetic improvement of banana resistance to Foc4.
bibliographic citation: Song et al. (2018) Identification and characterization of miRNA169 family members in banana (Musa acuminata L.) that respond to fusarium oxysporum f. sp. cubense infection in banana cultivars. PeerJ 6:e6209 https://doi.org/10.7717/peerj.6209
date submitted: 2018-08-27
date accepted: 2018-12-04
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Song
  given name: Shun
author list: Agent
  family name: Xu
  given name: Yi
author list: Agent
  family name: Huang
  given name: Dongmei
author list: Agent
  family name: Ashraf
  given name: Muhammad Aleem
author list: Agent
  family name: Li
  given name: Jingyang
author list: Agent
  family name: Hu
  given name: Wei
author list: Agent
  family name: Jin
  given name: Zhiqiang
author list: Agent
  family name: Zeng
  given name: Changying
author list: Agent
  family name: Tang
  given name: Fenling
author list: Agent
  family name: Xu
  given name: Biyu
author list: Agent
  family name: Zeng
  given name: Huicai
author list: Agent
  family name: Li
  given name: Yujia
author list: Agent
  family name: Xie
  given name: Jianghui
doi: 10.7717/peerj.6209
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: © 2018 Song et al.
attribution name: Song et al.

In vivo antioxidant activity of mackerel (Scomber japonicus) muscle protein hydrolysate
type: item
type: AcademicArticle
description: Pacific chub mackerel (Scomber japonicus) is an important fish throughout the world, especially in East Asian countries, including Korea, China, and Japan. Protein hydrolysates from marine sources are commonly used as nutritional supplements, functional ingredients, and flavor enhancers in the food, beverage, and pharmaceutical industries. Antioxidants isolated from fish are relatively easy to prepare, are cost effective, and have no reported side effects. Hence, the present study aimed to investigate the in vivo antioxidant activities of mackerel muscle protein hydrolysate (MMPH) prepared using Protamex. The in vivo bioactivities of MMPH were investigated in alcoholic fatty liver mice (C57BL/6). Serum alanine aminotransferase and aspartate aminotransferase levels were comparable in test and control mice, whereas serum triglyceride and lipid peroxidation levels significantly (p < 0.05; p < 0.001) decreased after administration of MMPH (100–500 mg kg−1), especially at a concentration of 100 mg kg−1. A significant (p < 0.05) reduction in xanthine oxidase activity was observed in all groups treated with MMPH (100–500 mg kg−1), as compared with the control group. Significantly (p < 0.05) higher superoxide dismutase (SOD) activity/protein expression and regulated catalase (CAT) activity/protein expression levels were observed in groups administered MMPH (100–500 mg kg−1), especially at a concentration of 100 mg kg−1. These results show that the abundant amino acids of S. japonicus play an important role in the cytosol of the liver cells by directly participating in the expression of xanthine oxidase and the detoxifying SOD and CAT proteins, thereby enhancing antioxidant ability and ultimately, inhibiting lipid peroxidation. This study demonstrated that muscle protein hydrolysate from S. japonicus has strong antioxidant activities.
format: application/pdf
format: text/html
creator: Khawaja Muhammad Imran Bashir
creator: Md. Mohibbullah
creator: Jeong Hyeon An
creator: Ji-Yeon Choi
creator: Yong-Ki Hong
creator: Jae Hak Sohn
creator: Jin-Soo Kim
creator: Jae-Suk Choi
subject: Biochemistry
subject: Biotechnology
subject: Food Science and Technology
subject: Evidence Based Medicine
description: doi:10.7717/peerj.6181
publisher: PeerJ Inc.
rights: © 2018 Bashir et al.
abstract: Pacific chub mackerel (Scomber japonicus) is an important fish throughout the world, especially in East Asian countries, including Korea, China, and Japan. Protein hydrolysates from marine sources are commonly used as nutritional supplements, functional ingredients, and flavor enhancers in the food, beverage, and pharmaceutical industries. Antioxidants isolated from fish are relatively easy to prepare, are cost effective, and have no reported side effects. Hence, the present study aimed to investigate the in vivo antioxidant activities of mackerel muscle protein hydrolysate (MMPH) prepared using Protamex. The in vivo bioactivities of MMPH were investigated in alcoholic fatty liver mice (C57BL/6). Serum alanine aminotransferase and aspartate aminotransferase levels were comparable in test and control mice, whereas serum triglyceride and lipid peroxidation levels significantly (p < 0.05; p < 0.001) decreased after administration of MMPH (100–500 mg kg−1), especially at a concentration of 100 mg kg−1. A significant (p < 0.05) reduction in xanthine oxidase activity was observed in all groups treated with MMPH (100–500 mg kg−1), as compared with the control group. Significantly (p < 0.05) higher superoxide dismutase (SOD) activity/protein expression and regulated catalase (CAT) activity/protein expression levels were observed in groups administered MMPH (100–500 mg kg−1), especially at a concentration of 100 mg kg−1. These results show that the abundant amino acids of S. japonicus play an important role in the cytosol of the liver cells by directly participating in the expression of xanthine oxidase and the detoxifying SOD and CAT proteins, thereby enhancing antioxidant ability and ultimately, inhibiting lipid peroxidation. This study demonstrated that muscle protein hydrolysate from S. japonicus has strong antioxidant activities.
bibliographic citation: Bashir et al. (2018) In vivo antioxidant activity of mackerel (Scomber japonicus) muscle protein hydrolysate. PeerJ 6:e6181 https://doi.org/10.7717/peerj.6181
date submitted: 2018-09-19
date accepted: 2018-11-28
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bashir
  given name: Khawaja Muhammad Imran
author list: Agent
  family name: Mohibbullah
  given name: Md.
author list: Agent
  family name: An
  given name: Jeong Hyeon
author list: Agent
  family name: Choi
  given name: Ji-Yeon
author list: Agent
  family name: Hong
  given name: Yong-Ki
author list: Agent
  family name: Sohn
  given name: Jae Hak
author list: Agent
  family name: Kim
  given name: Jin-Soo
author list: Agent
  family name: Choi
  given name: Jae-Suk
doi: 10.7717/peerj.6181
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: ©2018 Bashir et al.
attribution name: Bashir et al.

Modulation of corticomotor excitability in response to distal focal cooling
type: item
type: AcademicArticle
description: Background Thermal stimulation has been proposed as a modality to facilitate motor recovery in neurological populations, such as stroke. Recently (Ansari, Remaud & Tremblay, 2018), we showed that application of cold or warm stimuli distally to a single digit produced a variable and short lasting modulation in corticomotor excitability. Here, our goal was to extend these observations to determine whether an increase in stimulation area could elicit more consistent modulation. Methods Participants (n = 22) consisted of a subset who participated in our initial study. Participants were asked to come for a second testing session where the thermal protocol was repeated but with extending the stimulation area from single-digit (SD) to multi-digits (MD, four fingers, no thumb). As in the first session, skin temperature and motor evoked potentials (MEPs) elicited with transcranial magnetic stimulation were measured at baseline (BL, neutral gel pack at 22 °C), at 1 min during the cooling application (pre-cooled 10 °C gel pack) and 5 and 10 min post-cooling (PC5 and PC10). The analysis combined the data obtained previously with single-SD cooling (Ansari, Remaud & Tremblay, 2018) with those obtained here for MD cooling. Results At BL, participants exhibited comparable measures of resting corticomotor excitability between testing sessions. MD cooling induced similar reductions in skin temperature as those recorded with SD cooling with a peak decline at C1 of respectively, −11.0 and −10.3 °C. For MEPs, the primary analysis revealed no main effect attributable to the stimulation area. A secondary analysis of individual responses to MD cooling revealed that half of the participants exhibited delayed MEP facilitation (11/22), while the other half showed delayed inhibition (10/22); which was sustained in the post-cooling phase. More importantly, a correlation between variations in MEP amplitude recorded during the SD cooling session with those recorded in the second session with MD c…
format: application/pdf
format: text/html
creator: Yekta Ansari
creator: Anthony Remaud
creator: François Tremblay
subject: Neuroscience
subject: Kinesiology
subject: Neurology
description: doi:10.7717/peerj.6163
publisher: PeerJ Inc.
rights: © 2018 Ansari et al.
abstract: Background Thermal stimulation has been proposed as a modality to facilitate motor recovery in neurological populations, such as stroke. Recently (Ansari, Remaud & Tremblay, 2018), we showed that application of cold or warm stimuli distally to a single digit produced a variable and short lasting modulation in corticomotor excitability. Here, our goal was to extend these observations to determine whether an increase in stimulation area could elicit more consistent modulation. Methods Participants (n = 22) consisted of a subset who participated in our initial study. Participants were asked to come for a second testing session where the thermal protocol was repeated but with extending the stimulation area from single-digit (SD) to multi-digits (MD, four fingers, no thumb). As in the first session, skin temperature and motor evoked potentials (MEPs) elicited with transcranial magnetic stimulation were measured at baseline (BL, neutral gel pack at 22 °C), at 1 min during the cooling application (pre-cooled 10 °C gel pack) and 5 and 10 min post-cooling (PC5 and PC10). The analysis combined the data obtained previously with single-SD cooling (Ansari, Remaud & Tremblay, 2018) with those obtained here for MD cooling. Results At BL, participants exhibited comparable measures of resting corticomotor excitability between testing sessions. MD cooling induced similar reductions in skin temperature as those recorded with SD cooling with a peak decline at C1 of respectively, −11.0 and −10.3 °C. For MEPs, the primary analysis revealed no main effect attributable to the stimulation area. A secondary analysis of individual responses to MD cooling revealed that half of the participants exhibited delayed MEP facilitation (11/22), while the other half showed delayed inhibition (10/22); which was sustained in the post-cooling phase. More importantly, a correlation between variations in MEP amplitude recorded during the SD cooling session with those recorded in the second session with MD c…
bibliographic citation: Ansari et al. (2018) Modulation of corticomotor excitability in response to distal focal cooling. PeerJ 6:e6163 https://doi.org/10.7717/peerj.6163
date submitted: 2018-10-03
date accepted: 2018-11-27
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ansari
  given name: Yekta
author list: Agent
  family name: Remaud
  given name: Anthony
author list: Agent
  family name: Tremblay
  given name: François
doi: 10.7717/peerj.6163
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: © 2018 Ansari et al.
attribution name: Ansari et al.

Species turnover in plants does not predict turnover in flower-visiting insects
type: item
type: AcademicArticle
description: Congruence between plant and insect diversity is considered possibly useful in conservation planning, as the better known plants could be surrogates for the lesser known insects. There has been little quantification of congruence across space, especially in biodiversity rich areas. We compare here species richness, and turnover relationships between plants and flower-visiting insects across space (0.5–80 km) in natural areas of a biodiversity hotspot, the Greater Cape Floristic Region, South Africa. A total of 22,352 anthophile individuals in 198 species and 348 plant species were sampled. A comparison between the plants and anthophiles suggest significant concordance between the two assemblages. However, turnover was weaker in plants than in anthophiles. Plant turnover decreased with greater geographical distance between plot pairs. In contrast, insect turnover remained high with increasing geographical distance between plot pairs. These findings suggest that while patterns of plant diversity and distribution shape flower-visiting insect assemblages, they are not reliable surrogates. The conservation significance of these results is that specialist mutualisms are at greatest risk, and that set-asides on farms would help improve the functional connectivity leading to the maintenance of the full range of mutualisms.
format: application/pdf
format: text/html
creator: John P. Simaika
creator: Michael Samways
creator: Sven M. Vrdoljak
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.6139
publisher: PeerJ Inc.
rights: © 2018 Simaika et al.
abstract: Congruence between plant and insect diversity is considered possibly useful in conservation planning, as the better known plants could be surrogates for the lesser known insects. There has been little quantification of congruence across space, especially in biodiversity rich areas. We compare here species richness, and turnover relationships between plants and flower-visiting insects across space (0.5–80 km) in natural areas of a biodiversity hotspot, the Greater Cape Floristic Region, South Africa. A total of 22,352 anthophile individuals in 198 species and 348 plant species were sampled. A comparison between the plants and anthophiles suggest significant concordance between the two assemblages. However, turnover was weaker in plants than in anthophiles. Plant turnover decreased with greater geographical distance between plot pairs. In contrast, insect turnover remained high with increasing geographical distance between plot pairs. These findings suggest that while patterns of plant diversity and distribution shape flower-visiting insect assemblages, they are not reliable surrogates. The conservation significance of these results is that specialist mutualisms are at greatest risk, and that set-asides on farms would help improve the functional connectivity leading to the maintenance of the full range of mutualisms.
bibliographic citation: Simaika et al. (2018) Species turnover in plants does not predict turnover in flower-visiting insects. PeerJ 6:e6139 https://doi.org/10.7717/peerj.6139
date submitted: 2018-05-15
date accepted: 2018-11-20
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simaika
  given name: John P.
author list: Agent
  family name: Samways
  given name: Michael
author list: Agent
  family name: Vrdoljak
  given name: Sven M.
doi: 10.7717/peerj.6139
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: © 2018 Simaika et al.
attribution name: Simaika et al.

Application of insect-proof nets in pesticide-free rice creates an altered microclimate and differential agronomic performance
type: item
type: AcademicArticle
description: Background Insect-proof nets are commonly used in crop production and scientific research because of their environmental, economic, and agronomic benefits. However, insect-proof nets can unintentionally alter the microclimate inside the screenhouse and therefore greatly affect plant growth and yield. To examine the microclimate and agronomic performance of pesticide-free rice under insect-proof nets, two-year field experiments were carried out in 2011 and 2012. Methods In the present study, the experiment was conducted by using a split-plot design considering the cultivation environment (open field cultivation (OFC) and insect-proof nets cultivation (IPNC)) as the main plot and the varieties as the subplot (Suxiangjing3 and Nanjing44). Results IPNC significantly reduced the air speed and solar radiation, and slightly increased the daytime soil temperature, daytime air temperature, and nighttime relative humidity. By contrast, the nighttime soil temperature, nighttime air temperature, and daytime relative humidity were relatively unaffected. The grain yield of both rice cultivars decreased significantly under IPNC, which was largely attributed to the reduced panicle number. The reduced panicle number was largely associated with the decreased maximum tiller number, which was positively correlated with the tillering rate, time of tillering onset, and tillering cessation for both rice cultivars under IPNC. In addition, dry matter accumulation significantly decreased for both rice cultivars under IPNC, which was mainly caused by the decreased leaf area duration resulting from the reduced leaf area index. By contrast, the mean net assimilation rate was relatively unaffected by IPNC. Discussion Insect-proof nets altered the microclimate in comparison with OFC by reducing the air speed and changing the radiation regime, which significantly affected dry matter production and yield of both japonica rice cultivars. Our results indicated that cultivation measures that could inc…
format: application/pdf
format: text/html
creator: Guoying Yang
creator: Zhi Guo
creator: Hongting Ji
creator: Jing Sheng
creator: Liugen Chen
creator: Yanwen Zhao
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.6135
publisher: PeerJ Inc.
rights: © 2018 Yang et al.
abstract: Background Insect-proof nets are commonly used in crop production and scientific research because of their environmental, economic, and agronomic benefits. However, insect-proof nets can unintentionally alter the microclimate inside the screenhouse and therefore greatly affect plant growth and yield. To examine the microclimate and agronomic performance of pesticide-free rice under insect-proof nets, two-year field experiments were carried out in 2011 and 2012. Methods In the present study, the experiment was conducted by using a split-plot design considering the cultivation environment (open field cultivation (OFC) and insect-proof nets cultivation (IPNC)) as the main plot and the varieties as the subplot (Suxiangjing3 and Nanjing44). Results IPNC significantly reduced the air speed and solar radiation, and slightly increased the daytime soil temperature, daytime air temperature, and nighttime relative humidity. By contrast, the nighttime soil temperature, nighttime air temperature, and daytime relative humidity were relatively unaffected. The grain yield of both rice cultivars decreased significantly under IPNC, which was largely attributed to the reduced panicle number. The reduced panicle number was largely associated with the decreased maximum tiller number, which was positively correlated with the tillering rate, time of tillering onset, and tillering cessation for both rice cultivars under IPNC. In addition, dry matter accumulation significantly decreased for both rice cultivars under IPNC, which was mainly caused by the decreased leaf area duration resulting from the reduced leaf area index. By contrast, the mean net assimilation rate was relatively unaffected by IPNC. Discussion Insect-proof nets altered the microclimate in comparison with OFC by reducing the air speed and changing the radiation regime, which significantly affected dry matter production and yield of both japonica rice cultivars. Our results indicated that cultivation measures that could inc…
bibliographic citation: Yang et al. (2018) Application of insect-proof nets in pesticide-free rice creates an altered microclimate and differential agronomic performance. PeerJ 6:e6135 https://doi.org/10.7717/peerj.6135
date submitted: 2018-08-06
date accepted: 2018-11-18
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Guoying
author list: Agent
  family name: Guo
  given name: Zhi
author list: Agent
  family name: Ji
  given name: Hongting
author list: Agent
  family name: Sheng
  given name: Jing
author list: Agent
  family name: Chen
  given name: Liugen
author list: Agent
  family name: Zhao
  given name: Yanwen
doi: 10.7717/peerj.6135
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: ©2018 Yang et al.
attribution name: Yang et al.

Shell variability in the stem turtles Proterochersis spp.
type: item
type: AcademicArticle
description: Background Turtle shells tend to exhibit frequent and substantial variability, both in bone and scute layout. Aside from secondary changes, caused by diseases, parasites, and trauma, this variability appears to be inherent and result from stochastic or externally induced flaws of developmental programs. It is, thus, expected to be present in fossil turtle species at least as prominently, as in modern populations. Descriptions of variability and ontogeny are, however, rare for fossil turtles, mainly due to rarity, incompleteness, damage, and post-mortem deformation of their remains. This paper is an attempt at description and interpretation of external shell variability in representatives of the oldest true turtles, Proterochersis robusta and Proterochersis porebensis (Proterochersidae, the sister group to all other known testudinatans) from the Late Triassic (Norian) of Germany and Poland. Methods All the available shell remains of Proterochersis robusta (13 specimens) and Proterochersis porebensis (275 specimens) were studied morphologically in order to identify any ontogenetic changes, intraspecific variability, sexual dimorphism, and shell abnormalities. To test the inferred sexual dimorphism, shape analyses were performed for two regions (gular and anal) of the plastron. Results Proterochersis spp. exhibits large shell variability, and at least some of the observed changes seem to be correlated with ontogeny (growth of gulars, extragulars, caudals, and marginals, disappearance of middorsal keel on the carapace). Several specimens show abnormal layout of scute sulci, several others unusual morphologies of vertebral scute areas, one has an additional pair of plastral scutes, and one extraordinarily pronounced, likely pathological, growth rings on the carapace. Both species are represented in a wide spectrum of sizes, from hatchlings to old, mature individuals. The largest fragmentary specimens of Proterochersis porebensis allow estimation of its maximal carapace l…
format: application/pdf
format: text/html
creator: Tomasz Szczygielski
creator: Justyna Słowiak
creator: Dawid Dróżdż
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.6134
publisher: PeerJ Inc.
rights: © 2018 Szczygielski et al.
abstract: Background Turtle shells tend to exhibit frequent and substantial variability, both in bone and scute layout. Aside from secondary changes, caused by diseases, parasites, and trauma, this variability appears to be inherent and result from stochastic or externally induced flaws of developmental programs. It is, thus, expected to be present in fossil turtle species at least as prominently, as in modern populations. Descriptions of variability and ontogeny are, however, rare for fossil turtles, mainly due to rarity, incompleteness, damage, and post-mortem deformation of their remains. This paper is an attempt at description and interpretation of external shell variability in representatives of the oldest true turtles, Proterochersis robusta and Proterochersis porebensis (Proterochersidae, the sister group to all other known testudinatans) from the Late Triassic (Norian) of Germany and Poland. Methods All the available shell remains of Proterochersis robusta (13 specimens) and Proterochersis porebensis (275 specimens) were studied morphologically in order to identify any ontogenetic changes, intraspecific variability, sexual dimorphism, and shell abnormalities. To test the inferred sexual dimorphism, shape analyses were performed for two regions (gular and anal) of the plastron. Results Proterochersis spp. exhibits large shell variability, and at least some of the observed changes seem to be correlated with ontogeny (growth of gulars, extragulars, caudals, and marginals, disappearance of middorsal keel on the carapace). Several specimens show abnormal layout of scute sulci, several others unusual morphologies of vertebral scute areas, one has an additional pair of plastral scutes, and one extraordinarily pronounced, likely pathological, growth rings on the carapace. Both species are represented in a wide spectrum of sizes, from hatchlings to old, mature individuals. The largest fragmentary specimens of Proterochersis porebensis allow estimation of its maximal carapace l…
bibliographic citation: Szczygielski et al. (2018) Shell variability in the stem turtles Proterochersis spp.. PeerJ 6:e6134 https://doi.org/10.7717/peerj.6134
date submitted: 2018-06-27
date accepted: 2018-11-19
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Szczygielski
  given name: Tomasz
author list: Agent
  family name: Słowiak
  given name: Justyna
author list: Agent
  family name: Dróżdż
  given name: Dawid
doi: 10.7717/peerj.6134
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: © 2018 Szczygielski et al.
attribution name: Szczygielski et al.

Non-invasive monitoring of glucocorticoid metabolite concentrations in urine and faeces of the Sungazer (Smaug giganteus)
type: item
type: AcademicArticle
description: Developing non-invasive techniques for monitoring physiological stress responses has been conducted in a number of mammal and bird species, revolutionizing field-based endocrinology and conservation practices. However, studies validating and monitoring glucocorticoid concentrations in reptiles are still limited. The aim of the study was to validate a method for monitoring glucocorticoid metabolite concentrations in urine (uGCM) and faeces (fGCM) of the cordylid lizard, the Sungazer (Smaug giganteus). An adrenocorticotropic hormone (ACTH) challenge was conducted on one male and two females with both urine and faecal material being collected during baseline and post-injection periods. Steroid extracts were analysed with four enzyme immunoassays (EIAs)namely: 11-oxoaetiocholanolone, 5α-pregnane-3β-11β-21-triol-20-one, tetrahydrocorticosterone, and corticosterone. A considerable response in fGCM and uGCM concentrations following ACTH administration was observed in all subjects, with the 5α-pregnane-3β-11β-21-triol-20-one and tetrahydrocorticosterone EIAs appearing to be the most suited for monitoring alterations in glucocorticoid metabolite concentrations in S. giganteus using faeces or urine as hormone matrix. Both EIAs showed a significantly higher concentration of glucocorticoid metabolites in faeces compared to urine for both sexes. Collectively, the findings of this study confirmed that both urine and faeces can be used to non-invasively assess adrenocortical function in S. giganteus.
format: application/pdf
format: text/html
creator: Juan Scheun
creator: Dominique Greeff
creator: Andre Ganswindt
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.6132
publisher: PeerJ Inc.
rights: © 2018 Scheun et al.
abstract: Developing non-invasive techniques for monitoring physiological stress responses has been conducted in a number of mammal and bird species, revolutionizing field-based endocrinology and conservation practices. However, studies validating and monitoring glucocorticoid concentrations in reptiles are still limited. The aim of the study was to validate a method for monitoring glucocorticoid metabolite concentrations in urine (uGCM) and faeces (fGCM) of the cordylid lizard, the Sungazer (Smaug giganteus). An adrenocorticotropic hormone (ACTH) challenge was conducted on one male and two females with both urine and faecal material being collected during baseline and post-injection periods. Steroid extracts were analysed with four enzyme immunoassays (EIAs)namely: 11-oxoaetiocholanolone, 5α-pregnane-3β-11β-21-triol-20-one, tetrahydrocorticosterone, and corticosterone. A considerable response in fGCM and uGCM concentrations following ACTH administration was observed in all subjects, with the 5α-pregnane-3β-11β-21-triol-20-one and tetrahydrocorticosterone EIAs appearing to be the most suited for monitoring alterations in glucocorticoid metabolite concentrations in S. giganteus using faeces or urine as hormone matrix. Both EIAs showed a significantly higher concentration of glucocorticoid metabolites in faeces compared to urine for both sexes. Collectively, the findings of this study confirmed that both urine and faeces can be used to non-invasively assess adrenocortical function in S. giganteus.
bibliographic citation: Scheun et al. (2018) Non-invasive monitoring of glucocorticoid metabolite concentrations in urine and faeces of the Sungazer (Smaug giganteus). PeerJ 6:e6132 https://doi.org/10.7717/peerj.6132
date submitted: 2018-09-18
date accepted: 2018-11-19
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scheun
  given name: Juan
author list: Agent
  family name: Greeff
  given name: Dominique
author list: Agent
  family name: Ganswindt
  given name: Andre
doi: 10.7717/peerj.6132
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: ©2018 Scheun et al.
attribution name: Scheun et al.

Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae)
type: item
type: AcademicArticle
description: We describe Arge bella Wei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome of A. bella has a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in the A. bella mitochondrial genome as compared to the ancestral type in insects: trnM and trnQ are shuffled, while trnW is translocated from the trnW-trnC-trnY cluster to a location downstream of trnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except for trnS1. H821 of rrnS and H976 of rrnL are redundant. A phylogenetic analysis based on mitochondrial genome sequences of A. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea.
format: application/pdf
format: text/html
creator: Shiyu Du
creator: Gengyun Niu
creator: Tommi Nyman
creator: Meicai Wei
subject: Entomology
subject: Genomics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6131
publisher: PeerJ Inc.
rights: © 2018 Du et al.
abstract: We describe Arge bella Wei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome of A. bella has a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in the A. bella mitochondrial genome as compared to the ancestral type in insects: trnM and trnQ are shuffled, while trnW is translocated from the trnW-trnC-trnY cluster to a location downstream of trnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except for trnS1. H821 of rrnS and H976 of rrnL are redundant. A phylogenetic analysis based on mitochondrial genome sequences of A. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea.
bibliographic citation: Du et al. (2018) Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae). PeerJ 6:e6131 https://doi.org/10.7717/peerj.6131
date submitted: 2018-10-02
date accepted: 2018-11-17
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Shiyu
author list: Agent
  family name: Niu
  given name: Gengyun
author list: Agent
  family name: Nyman
  given name: Tommi
author list: Agent
  family name: Wei
  given name: Meicai
doi: 10.7717/peerj.6131
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: ©2018 Du et al.
attribution name: Du et al.

Biochemical and growth responses of silver maple (Acer saccharinum L.) to sodium chloride and calcium chloride
type: item
type: AcademicArticle
description: The present research investigated the response of silver maple (Acer saccharinum L.) to salt treatment. The short- and long-term effects of NaCl and CaCl2 treatments on plant fitness characteristics (growth parameters, leaf chlorophyll content) and biochemical stress-coping mechanisms (proline accumulation as well as enzymatic activities) were examined. We found that the silver maple response to salt stress strictly depended on salt type and dose—calcium chloride was less toxic than sodium chloride, but high concentrations of both salts negatively influenced plant growth. The accumulation of proline, slight changes in the activity of superoxide dismutase and marked changes in catalase and peroxidase activities in the roots and leaves indicated complexity of the plant response. It was also shown that after one year, enzymatic parameters were restabilized, which indicates plant recovery, but the reduced mass of seedlings suggests that one year is not enough to cope with the prolonged cyclic salt stress, both resulting from NaCl and CaCl2 application. Therefore, seedlings of silver maple should be considered as moderately susceptible to salinity. Hence, it is recommended to use silver maple on non-de-iced urban areas, while planting on often de-iced roads should be avoided.
format: application/pdf
format: text/html
creator: Jacek Patykowski
creator: Jeremi Kołodziejek
creator: Mateusz Wala
subject: Plant Science
subject: Biosphere Interactions
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.5958
publisher: PeerJ Inc.
rights: © 2018 Patykowski et al.
abstract: The present research investigated the response of silver maple (Acer saccharinum L.) to salt treatment. The short- and long-term effects of NaCl and CaCl2 treatments on plant fitness characteristics (growth parameters, leaf chlorophyll content) and biochemical stress-coping mechanisms (proline accumulation as well as enzymatic activities) were examined. We found that the silver maple response to salt stress strictly depended on salt type and dose—calcium chloride was less toxic than sodium chloride, but high concentrations of both salts negatively influenced plant growth. The accumulation of proline, slight changes in the activity of superoxide dismutase and marked changes in catalase and peroxidase activities in the roots and leaves indicated complexity of the plant response. It was also shown that after one year, enzymatic parameters were restabilized, which indicates plant recovery, but the reduced mass of seedlings suggests that one year is not enough to cope with the prolonged cyclic salt stress, both resulting from NaCl and CaCl2 application. Therefore, seedlings of silver maple should be considered as moderately susceptible to salinity. Hence, it is recommended to use silver maple on non-de-iced urban areas, while planting on often de-iced roads should be avoided.
bibliographic citation: Patykowski et al. (2018) Biochemical and growth responses of silver maple (Acer saccharinum L.) to sodium chloride and calcium chloride. PeerJ 6:e5958 https://doi.org/10.7717/peerj.5958
date submitted: 2018-05-08
date accepted: 2018-10-18
issued: 2018-12-21
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Patykowski
  given name: Jacek
author list: Agent
  family name: Kołodziejek
  given name: Jeremi
author list: Agent
  family name: Wala
  given name: Mateusz
doi: 10.7717/peerj.5958
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-12-21
copyright: ©2018 Patykowski et al.
attribution name: Patykowski et al.

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