PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis
items: Higher bee abundance, but not pest abundance, in landscapes with more agriculture on a late-flowering legume crop in tropical smallholder farms
items: Retinoic Acid Induced Protein 14 (Rai14) is dispensable for mouse spermatogenesis
items: Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration
items: Metasychis varicollaris sp. nov. and report of Metasychis gotoi (Maldanidae, Annelida) from the China Seas
items: QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan
items: Effects of training frequency on muscular strength for trained men under volume matched conditions
items: Estimation of parameters for a humidity-dependent compartmental model of the COVID-19 outbreak
items: Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula
items: Pseudocnidae of ribbon worms (Nemertea): ultrastructure, maturation, and functional morphology

Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis
type: item
type: AcademicArticle
description: Background Pueraria lobata (Willd.) Ohwi is a valuable herb used in traditional Chinese medicine. Isoflavonoids are the major bioactive compounds in P. lobata, namely puerarin, daidzin, glycitin, genistin, daidzein, and glycitein, which have pharmacological properties of anti-cardiovascular, anti-hypertension, anti-inflammatory, and anti-arrhythmic. Methods To characterize the corresponding genes of the compounds in the isoflavonoid pathway, RNA sequencing (RNA-Seq) analyses of roots, stems, and leaves of P. lobata were carried out on the BGISEQ-500 sequencing platform. Results We identified 140,905 unigenes in total, of which 109,687 were annotated in public databases, after assembling the transcripts from all three tissues. Multiple genes encoding key enzymes, such as IF7GT and transcription factors, associated with isoflavonoid biosynthesis were identified and then further analyzed. Quantitative real-time PCR (qRT-PCR) results of some genes encoding key enzymes were consistent with our RNA-Seq analysis. Differentially expressed genes (DEGs) were determined by analyzing the expression profiles of roots compared with other tissues (leaves and stems). This analysis revealed numerous DEGs that were either uniquely expressed or up-regulated in the roots. Finally, quantitative analyses of isoflavonoid metabolites occurring in the three P. lobata tissue types were done via high-performance liquid-chromatography and tandem mass spectrometry methodology (HPLC-MS/MS). Our comprehensive transcriptome investigation substantially expands the genomic resources of P. lobata and provides valuable knowledge on both gene expression regulation and promising candidate genes that are involved in plant isoflavonoid pathways.
format: application/pdf
format: text/html
creator: Chenkai Wang
creator: Nenggui Xu
creator: Shuai Cui
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
subject: Pharmacology
description: doi:10.7717/peerj.10885
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Background Pueraria lobata (Willd.) Ohwi is a valuable herb used in traditional Chinese medicine. Isoflavonoids are the major bioactive compounds in P. lobata, namely puerarin, daidzin, glycitin, genistin, daidzein, and glycitein, which have pharmacological properties of anti-cardiovascular, anti-hypertension, anti-inflammatory, and anti-arrhythmic. Methods To characterize the corresponding genes of the compounds in the isoflavonoid pathway, RNA sequencing (RNA-Seq) analyses of roots, stems, and leaves of P. lobata were carried out on the BGISEQ-500 sequencing platform. Results We identified 140,905 unigenes in total, of which 109,687 were annotated in public databases, after assembling the transcripts from all three tissues. Multiple genes encoding key enzymes, such as IF7GT and transcription factors, associated with isoflavonoid biosynthesis were identified and then further analyzed. Quantitative real-time PCR (qRT-PCR) results of some genes encoding key enzymes were consistent with our RNA-Seq analysis. Differentially expressed genes (DEGs) were determined by analyzing the expression profiles of roots compared with other tissues (leaves and stems). This analysis revealed numerous DEGs that were either uniquely expressed or up-regulated in the roots. Finally, quantitative analyses of isoflavonoid metabolites occurring in the three P. lobata tissue types were done via high-performance liquid-chromatography and tandem mass spectrometry methodology (HPLC-MS/MS). Our comprehensive transcriptome investigation substantially expands the genomic resources of P. lobata and provides valuable knowledge on both gene expression regulation and promising candidate genes that are involved in plant isoflavonoid pathways.
bibliographic citation: Wang et al. (2021) Comparative transcriptome analysis of roots, stems, and leaves of Pueraria lobata (Willd.) Ohwi: identification of genes involved in isoflavonoid biosynthesis. PeerJ 9:e10885 https://doi.org/10.7717/peerj.10885
date submitted: 2020-07-31
date accepted: 2021-01-12
issued: 2021-02-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Chenkai
author list: Agent
  family name: Xu
  given name: Nenggui
author list: Agent
  family name: Cui
  given name: Shuai
doi: 10.7717/peerj.10885
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-22
copyright: ©2021 Wang et al.
attribution name: Wang et al.

Higher bee abundance, but not pest abundance, in landscapes with more agriculture on a late-flowering legume crop in tropical smallholder farms
type: item
type: AcademicArticle
description: Background Landscape composition is known to affect both beneficial insect and pest communities on crop fields. Landscape composition therefore can impact ecosystem (dis)services provided by insects to crops. Though landscape effects on ecosystem service providers have been studied in large-scale agriculture in temperate regions, there is a lack of representation of tropical smallholder agriculture within this field of study, especially in sub-Sahara Africa. Legume crops can provide important food security and soil improvement benefits to vulnerable agriculturalists. However, legumes are dependent on pollinating insects, particularly bees (Hymenoptera: Apiformes) for production and are vulnerable to pests. We selected 10 pigeon pea (Fabaceae: Cajunus cajan (L.)) fields in Malawi with varying proportions of semi-natural habitat and agricultural area within a 1 km radius to study: (1) how the proportion of semi-natural habitat and agricultural area affects the abundance and richness of bees and abundance of florivorous blister beetles (Coleoptera: Melloidae), (2) if the proportion of flowers damaged and fruit set difference between open and bagged flowers are correlated with the proportion of semi-natural habitat or agricultural area and (3) if pigeon pea fruit set difference between open and bagged flowers in these landscapes was constrained by pest damage or improved by bee visitation. Methods We performed three, ten-minute, 15 m, transects per field to assess blister beetle abundance and bee abundance and richness. Bees were captured and identified to (morpho)species. We assessed the proportion of flowers damaged by beetles during the flowering period. We performed a pollinator and pest exclusion experiment on 15 plants per field to assess whether fruit set was pollinator limited or constrained by pests. Results In our study, bee abundance was higher in areas with proportionally more agricultural area surrounding the fields. This effect was mostly driven by an incr…
format: application/pdf
format: text/html
creator: Cassandra Vogel
creator: Timothy L. Chunga
creator: Xiaoxuan Sun
creator: Katja Poveda
creator: Ingolf Steffan-Dewenter
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.10732
publisher: PeerJ Inc.
rights: © 2021 Vogel et al.
abstract: Background Landscape composition is known to affect both beneficial insect and pest communities on crop fields. Landscape composition therefore can impact ecosystem (dis)services provided by insects to crops. Though landscape effects on ecosystem service providers have been studied in large-scale agriculture in temperate regions, there is a lack of representation of tropical smallholder agriculture within this field of study, especially in sub-Sahara Africa. Legume crops can provide important food security and soil improvement benefits to vulnerable agriculturalists. However, legumes are dependent on pollinating insects, particularly bees (Hymenoptera: Apiformes) for production and are vulnerable to pests. We selected 10 pigeon pea (Fabaceae: Cajunus cajan (L.)) fields in Malawi with varying proportions of semi-natural habitat and agricultural area within a 1 km radius to study: (1) how the proportion of semi-natural habitat and agricultural area affects the abundance and richness of bees and abundance of florivorous blister beetles (Coleoptera: Melloidae), (2) if the proportion of flowers damaged and fruit set difference between open and bagged flowers are correlated with the proportion of semi-natural habitat or agricultural area and (3) if pigeon pea fruit set difference between open and bagged flowers in these landscapes was constrained by pest damage or improved by bee visitation. Methods We performed three, ten-minute, 15 m, transects per field to assess blister beetle abundance and bee abundance and richness. Bees were captured and identified to (morpho)species. We assessed the proportion of flowers damaged by beetles during the flowering period. We performed a pollinator and pest exclusion experiment on 15 plants per field to assess whether fruit set was pollinator limited or constrained by pests. Results In our study, bee abundance was higher in areas with proportionally more agricultural area surrounding the fields. This effect was mostly driven by an incr…
bibliographic citation: Vogel et al. (2021) Higher bee abundance, but not pest abundance, in landscapes with more agriculture on a late-flowering legume crop in tropical smallholder farms. PeerJ 9:e10732 https://doi.org/10.7717/peerj.10732
date submitted: 2020-09-07
date accepted: 2020-12-17
issued: 2021-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vogel
  given name: Cassandra
author list: Agent
  family name: Chunga
  given name: Timothy L.
author list: Agent
  family name: Sun
  given name: Xiaoxuan
author list: Agent
  family name: Poveda
  given name: Katja
author list: Agent
  family name: Steffan-Dewenter
  given name: Ingolf
doi: 10.7717/peerj.10732
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-19
copyright: ©2021 Vogel et al.
attribution name: Vogel et al.

Retinoic Acid Induced Protein 14 (Rai14) is dispensable for mouse spermatogenesis
type: item
type: AcademicArticle
description: Background Retinoic Acid Induced Protein 14 (Rai14) is an evolutionarily conserved gene that is highly expressed in the testis. Previous experiments have reported that small interfering RNA (siRNA)-mediated gene knockdown (KD) of Rai14 in rat testis disrupted spermatid polarity and transport. Of note, a gene knockout (KO) model is considered the “gold standard” for in vivo assessment of crucial gene functions. Herein, we used CRISPR/Cas9-based gene editing to investigate the in vivo role of Rai14 in mouse testis. Methods Sperm concentration and motility were assayed using a computer-assisted sperm analysis (CASA) system. Histological and immunofluorescence (IF) staining and transmission electron microscopy (TEM) were used to visualize the effects of Rai14 KO in the testes and epididymides. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) was used to determine apoptotic cells. Gene transcript levels were calculated by real-time quantitative PCR. Results Rai14 KO in mice depicted normal fertility and complete spermatogenesis, which is in sharp contrast with the results reported previously in a Rai14 KD rat model. Sperm parameters and cellular apoptosis did not appear to differ between wild-type (WT) and KO group. Mechanistically, in contrast to the well-known role of Rai14 in modulating the dynamics of F-actin at the ectoplasmic specialization (ES) junction in the testis, morphological changes of ES junction exhibited no differences between Rai14 KO and WT testes. Moreover, the F-actin surrounded at the ES junction was also comparable between the two groups. Conclusion In summary, our study demonstrates that Rai14 is dispensable for mouse spermatogenesis and fertility. Although the results of this study were negative, the phenotypic information obtained herein provide an enhanced understanding of the role of Rai14 in the testis, and researchers may refer to these results to avoid conducting redundant experiments.
format: application/pdf
format: text/html
creator: Yangyang Wu
creator: Ting Wang
creator: Zigao Zhao
creator: Siyu Liu
creator: Cong Shen
creator: Hong Li
creator: Mingxi Liu
creator: Bo Zheng
creator: Jun Yu
creator: Xiaoyan Huang
subject: Cell Biology
subject: Developmental Biology
subject: Andrology
subject: Histology
description: doi:10.7717/peerj.10847
publisher: PeerJ Inc.
rights: © 2021 Wu et al.
abstract: Background Retinoic Acid Induced Protein 14 (Rai14) is an evolutionarily conserved gene that is highly expressed in the testis. Previous experiments have reported that small interfering RNA (siRNA)-mediated gene knockdown (KD) of Rai14 in rat testis disrupted spermatid polarity and transport. Of note, a gene knockout (KO) model is considered the “gold standard” for in vivo assessment of crucial gene functions. Herein, we used CRISPR/Cas9-based gene editing to investigate the in vivo role of Rai14 in mouse testis. Methods Sperm concentration and motility were assayed using a computer-assisted sperm analysis (CASA) system. Histological and immunofluorescence (IF) staining and transmission electron microscopy (TEM) were used to visualize the effects of Rai14 KO in the testes and epididymides. Terminal deoxynucleotidyl transferase-dUTP nick-end labeling (TUNEL) was used to determine apoptotic cells. Gene transcript levels were calculated by real-time quantitative PCR. Results Rai14 KO in mice depicted normal fertility and complete spermatogenesis, which is in sharp contrast with the results reported previously in a Rai14 KD rat model. Sperm parameters and cellular apoptosis did not appear to differ between wild-type (WT) and KO group. Mechanistically, in contrast to the well-known role of Rai14 in modulating the dynamics of F-actin at the ectoplasmic specialization (ES) junction in the testis, morphological changes of ES junction exhibited no differences between Rai14 KO and WT testes. Moreover, the F-actin surrounded at the ES junction was also comparable between the two groups. Conclusion In summary, our study demonstrates that Rai14 is dispensable for mouse spermatogenesis and fertility. Although the results of this study were negative, the phenotypic information obtained herein provide an enhanced understanding of the role of Rai14 in the testis, and researchers may refer to these results to avoid conducting redundant experiments.
bibliographic citation: Wu et al. (2021) Retinoic Acid Induced Protein 14 (Rai14) is dispensable for mouse spermatogenesis. PeerJ 9:e10847 https://doi.org/10.7717/peerj.10847
date submitted: 2020-10-01
date accepted: 2021-01-06
issued: 2021-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Yangyang
author list: Agent
  family name: Wang
  given name: Ting
author list: Agent
  family name: Zhao
  given name: Zigao
author list: Agent
  family name: Liu
  given name: Siyu
author list: Agent
  family name: Shen
  given name: Cong
author list: Agent
  family name: Li
  given name: Hong
author list: Agent
  family name: Liu
  given name: Mingxi
author list: Agent
  family name: Zheng
  given name: Bo
author list: Agent
  family name: Yu
  given name: Jun
author list: Agent
  family name: Huang
  given name: Xiaoyan
doi: 10.7717/peerj.10847
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-19
copyright: ©2021 Wu et al.
attribution name: Wu et al.

Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration
type: item
type: AcademicArticle
description: Background Sex steroids administration in meat producing animals is forbidden within the EU to preserve consumers’ safety, but continuous monitoring to identify resurgence of their misuse is needed. Among biomarkers related to sex steroids abuse in veal calves the regucalcin (RGN) mRNA perturbations in testis have been described in RNAlater samples. To setup novel diagnostic method, to update current tests available in National Residue Control Plans (NRCPs) and in legal dispute when illicit practices on farm animals are suspected, the reliability of RGN profiling was assessed by histological and molecular techniques. Methods Formalin fixed paraffin embedded (FFPE) testis samples, chosen being the most effective preservation strategy adopted by histological NRCPs and allowing easier retrospective analysis if required by legal disputes, were analyzed from veal calves treated with nandrolone, 17β-estradiol and a cocktail of the two hormones. RGN levels were determined by quantitative Real Time PCR and Immunohistochemistry assays. Test performances were assessed and compared by multiple ROC curves. Results Both tests resulted sensitive and specific, allowing to enrich, in future field investigation, novel integrated diagnostic protocols needed to unveil sex steroid abuse. Discussion Developed RT-qPCR and IHC methods confirmed RGN as a useful and robust biomarker to detect illegal administration of sex steroid hormones in veal calves. The developed methods, successfully applied to ten years old FFPE blocks, could allow both retrospective analysis, when supplementary investigations are requested by authorities, and future implementation of current NRCPs.
format: application/pdf
format: text/html
creator: Alessandro Benedetto
creator: Elena Biasibetti
creator: Chiara Beltramo
creator: Valentina Audino
creator: Simone Peletto
creator: Elena Maria Bozzetta
creator: Marzia Pezzolato
subject: Agricultural Science
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
subject: Histology
description: doi:10.7717/peerj.10894
publisher: PeerJ Inc.
rights: © 2021 Benedetto et al.
abstract: Background Sex steroids administration in meat producing animals is forbidden within the EU to preserve consumers’ safety, but continuous monitoring to identify resurgence of their misuse is needed. Among biomarkers related to sex steroids abuse in veal calves the regucalcin (RGN) mRNA perturbations in testis have been described in RNAlater samples. To setup novel diagnostic method, to update current tests available in National Residue Control Plans (NRCPs) and in legal dispute when illicit practices on farm animals are suspected, the reliability of RGN profiling was assessed by histological and molecular techniques. Methods Formalin fixed paraffin embedded (FFPE) testis samples, chosen being the most effective preservation strategy adopted by histological NRCPs and allowing easier retrospective analysis if required by legal disputes, were analyzed from veal calves treated with nandrolone, 17β-estradiol and a cocktail of the two hormones. RGN levels were determined by quantitative Real Time PCR and Immunohistochemistry assays. Test performances were assessed and compared by multiple ROC curves. Results Both tests resulted sensitive and specific, allowing to enrich, in future field investigation, novel integrated diagnostic protocols needed to unveil sex steroid abuse. Discussion Developed RT-qPCR and IHC methods confirmed RGN as a useful and robust biomarker to detect illegal administration of sex steroid hormones in veal calves. The developed methods, successfully applied to ten years old FFPE blocks, could allow both retrospective analysis, when supplementary investigations are requested by authorities, and future implementation of current NRCPs.
bibliographic citation: Benedetto et al. (2021) Regucalcin expression profiles in veal calf testis: validation of histological and molecular tests to detect sex steroids illicit administration. PeerJ 9:e10894 https://doi.org/10.7717/peerj.10894
date submitted: 2020-05-27
date accepted: 2021-01-13
issued: 2021-02-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Benedetto
  given name: Alessandro
author list: Agent
  family name: Biasibetti
  given name: Elena
author list: Agent
  family name: Beltramo
  given name: Chiara
author list: Agent
  family name: Audino
  given name: Valentina
author list: Agent
  family name: Peletto
  given name: Simone
author list: Agent
  family name: Bozzetta
  given name: Elena Maria
author list: Agent
  family name: Pezzolato
  given name: Marzia
doi: 10.7717/peerj.10894
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-19
copyright: ©2021 Benedetto et al.
attribution name: Benedetto et al.

Metasychis varicollaris sp. nov. and report of Metasychis gotoi (Maldanidae, Annelida) from the China Seas
type: item
type: AcademicArticle
description: Polychaete species are widely distributed throughout Indo-Pacific and European waters. We collected Metasychis specimens from the China Seas to report on Metasychis varicollaris sp. n. and Metasychis gotoi (Izuka, 1902) in greater detail. Geographic analysis of the potential distribution areas of M. gotoi indicates that it may be found in most coastal areas of China. The newly discovered species, M. varicollaris and M. gotoi, have an overlapping distribution in the northern South China Sea. Metasychis varicollaris sp. n. is characterized by a crenulated cephalic rim, complete collar on chaetiger 1, a packet-shaped anal funnel, and a spirally-fringed notochaetae with spiral pectinate bands imbricated over the main shaft. Our study provides a taxonomic key to all species of Metasychis.
format: application/pdf
format: text/html
creator: Yueyun Wang
creator: Xinzheng Li
creator: Chunsheng Wang
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10608
publisher: PeerJ Inc.
rights: © 2021 Wang et al.
abstract: Polychaete species are widely distributed throughout Indo-Pacific and European waters. We collected Metasychis specimens from the China Seas to report on Metasychis varicollaris sp. n. and Metasychis gotoi (Izuka, 1902) in greater detail. Geographic analysis of the potential distribution areas of M. gotoi indicates that it may be found in most coastal areas of China. The newly discovered species, M. varicollaris and M. gotoi, have an overlapping distribution in the northern South China Sea. Metasychis varicollaris sp. n. is characterized by a crenulated cephalic rim, complete collar on chaetiger 1, a packet-shaped anal funnel, and a spirally-fringed notochaetae with spiral pectinate bands imbricated over the main shaft. Our study provides a taxonomic key to all species of Metasychis.
bibliographic citation: Wang et al. (2021) Metasychis varicollaris sp. nov. and report of Metasychis gotoi (Maldanidae, Annelida) from the China Seas. PeerJ 9:e10608 https://doi.org/10.7717/peerj.10608
date submitted: 2020-07-03
date accepted: 2020-11-29
issued: 2021-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yueyun
author list: Agent
  family name: Li
  given name: Xinzheng
author list: Agent
  family name: Wang
  given name: Chunsheng
doi: 10.7717/peerj.10608
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-18
copyright: © 2021 Wang et al.
attribution name: Wang et al.

QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan
type: item
type: AcademicArticle
description: Background The success of wheat production is largely dependent on local breeding projects that focus on the development of high-yielding cultivars with the use of novel molecular tools. One strategy for improving wheat productivity involves the deployment of diverse germplasms with a high potential yield. An important factor for achieving success involves the dissection of quantitative trait loci (QTLs) for complex agronomic traits, such as grain yield components, in targeted environments for wheat growth. Methods In this study, we tested the United Kingdom (UK) spring set of the doubled haploid (DH) reference population derived from the cross between two British cultivars, Avalon (winter wheat) and Cadenza (spring wheat), in the Northern, Central, and Southern regions (Karabalyk, Karaganda, Kyzylorda) of Kazakhstan over three years (2013–2015). The DH population has previously been genotyped by UK scientists using 3647 polymorphic DNA markers. The list of tested traits includes the heading time, seed maturation time, plant height, spike length, productive tillering, number of kernels per spike, number of kernels per meter, thousand kernel weight, and yield per square meter. Windows QTL Cartographer was applied for QTL mapping using the composite interval mapping method. Results In total, 83 out of 232 QTLs were identified as stable QTLs from at least two environments. A literature survey suggests that 40 QTLs had previously been reported elsewhere, indicating that this study identified 43 QTLs that are presumably novel marker-trait associations (MTA) for these environments. Hence, the phenotyping of the DH population in new environments led to the discovery of novel MTAs. The identified SNP markers associated with agronomic traits in the DH population could be successfully used in local Kazakh breeding projects for the improvement of wheat productivity.
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format: text/html
creator: Akerke Amalova
creator: Saule Abugalieva
creator: Vladimir Chudinov
creator: Grigoriy Sereda
creator: Laura Tokhetova
creator: Alima Abdikhalyk
creator: Yerlan Turuspekov
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10733
publisher: PeerJ Inc.
rights: © 2021 Amalova et al.
abstract: Background The success of wheat production is largely dependent on local breeding projects that focus on the development of high-yielding cultivars with the use of novel molecular tools. One strategy for improving wheat productivity involves the deployment of diverse germplasms with a high potential yield. An important factor for achieving success involves the dissection of quantitative trait loci (QTLs) for complex agronomic traits, such as grain yield components, in targeted environments for wheat growth. Methods In this study, we tested the United Kingdom (UK) spring set of the doubled haploid (DH) reference population derived from the cross between two British cultivars, Avalon (winter wheat) and Cadenza (spring wheat), in the Northern, Central, and Southern regions (Karabalyk, Karaganda, Kyzylorda) of Kazakhstan over three years (2013–2015). The DH population has previously been genotyped by UK scientists using 3647 polymorphic DNA markers. The list of tested traits includes the heading time, seed maturation time, plant height, spike length, productive tillering, number of kernels per spike, number of kernels per meter, thousand kernel weight, and yield per square meter. Windows QTL Cartographer was applied for QTL mapping using the composite interval mapping method. Results In total, 83 out of 232 QTLs were identified as stable QTLs from at least two environments. A literature survey suggests that 40 QTLs had previously been reported elsewhere, indicating that this study identified 43 QTLs that are presumably novel marker-trait associations (MTA) for these environments. Hence, the phenotyping of the DH population in new environments led to the discovery of novel MTAs. The identified SNP markers associated with agronomic traits in the DH population could be successfully used in local Kazakh breeding projects for the improvement of wheat productivity.
bibliographic citation: Amalova et al. (2021) QTL mapping of agronomic traits in wheat using the UK Avalon × Cadenza reference mapping population grown in Kazakhstan. PeerJ 9:e10733 https://doi.org/10.7717/peerj.10733
date submitted: 2020-09-11
date accepted: 2020-12-17
issued: 2021-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amalova
  given name: Akerke
author list: Agent
  family name: Abugalieva
  given name: Saule
author list: Agent
  family name: Chudinov
  given name: Vladimir
author list: Agent
  family name: Sereda
  given name: Grigoriy
author list: Agent
  family name: Tokhetova
  given name: Laura
author list: Agent
  family name: Abdikhalyk
  given name: Alima
author list: Agent
  family name: Turuspekov
  given name: Yerlan
doi: 10.7717/peerj.10733
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-18
copyright: ©2021 Amalova et al.
attribution name: Amalova et al.

Effects of training frequency on muscular strength for trained men under volume matched conditions
type: item
type: AcademicArticle
description: Background In resistance training, the role of training frequency to increase maximal strength is often debated. However, the limited data available does not allow for clear training frequency “optimization” recommendations. The purpose of this study was to investigate the effects of training frequency on maximal muscular strength and rate of perceived exertion (RPE). The total weekly training volume was equally distributed between two and four sessions per muscle group. Methods Twenty-one experienced resistance-trained male subjects (height: 1.85 ± 0.06 m, body mass: 85.3 ± 12.3 kg, age: 27.6 ± 7.6 years) were tested prior to and after an 8-week training period in one-repetition maximum (1RM) barbell back squat and bench press. Subjects were randomly assigned to a SPLIT group (n = 10), in which there were two training sessions of squats and lower-body exercises and two training sessions of bench press and upper-body exercises, or a FULLBODY group (n = 11), in which four sessions with squats, bench press and supplementary exercises were conducted every session. In each session, the subjects rated their RPE after barbell back squat, bench press, and the full session. Results Both groups significantly increased 1RM strength in barbell back squat (SPLIT group: +13.25 kg; FULLBODY group: +14.31 kg) and bench press (SPLIT group: +7.75 kg; FULLBODY group: +8.86 kg) but training frequency did not affect this increase for squat (p = 0.640) or bench press (p = 0.431). Both groups showed a significant effect for time on RPE on all three measurements. The analyses showed only an interaction effect between groups on time for the RPE after the squat exercise (p = 0.002). Conclusion We conclude that there are no additional benefits of increasing the training frequency from two to four sessions under volume-equated conditions, but it could be favorable to spread the total training volume into several training bouts through the week to avoid potential increases in RPE, especially a…
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format: text/html
creator: Emil Johnsen
creator: Roland van den Tillaar
subject: Kinesiology
subject: Public Health
description: doi:10.7717/peerj.10781
publisher: PeerJ Inc.
rights: © 2021 Johnsen and van den Tillaar
abstract: Background In resistance training, the role of training frequency to increase maximal strength is often debated. However, the limited data available does not allow for clear training frequency “optimization” recommendations. The purpose of this study was to investigate the effects of training frequency on maximal muscular strength and rate of perceived exertion (RPE). The total weekly training volume was equally distributed between two and four sessions per muscle group. Methods Twenty-one experienced resistance-trained male subjects (height: 1.85 ± 0.06 m, body mass: 85.3 ± 12.3 kg, age: 27.6 ± 7.6 years) were tested prior to and after an 8-week training period in one-repetition maximum (1RM) barbell back squat and bench press. Subjects were randomly assigned to a SPLIT group (n = 10), in which there were two training sessions of squats and lower-body exercises and two training sessions of bench press and upper-body exercises, or a FULLBODY group (n = 11), in which four sessions with squats, bench press and supplementary exercises were conducted every session. In each session, the subjects rated their RPE after barbell back squat, bench press, and the full session. Results Both groups significantly increased 1RM strength in barbell back squat (SPLIT group: +13.25 kg; FULLBODY group: +14.31 kg) and bench press (SPLIT group: +7.75 kg; FULLBODY group: +8.86 kg) but training frequency did not affect this increase for squat (p = 0.640) or bench press (p = 0.431). Both groups showed a significant effect for time on RPE on all three measurements. The analyses showed only an interaction effect between groups on time for the RPE after the squat exercise (p = 0.002). Conclusion We conclude that there are no additional benefits of increasing the training frequency from two to four sessions under volume-equated conditions, but it could be favorable to spread the total training volume into several training bouts through the week to avoid potential increases in RPE, especially a…
bibliographic citation: Johnsen et al. (2021) Effects of training frequency on muscular strength for trained men under volume matched conditions. PeerJ 9:e10781 https://doi.org/10.7717/peerj.10781
date submitted: 2020-08-12
date accepted: 2020-12-23
issued: 2021-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johnsen
  given name: Emil
author list: Agent
  family name: van den Tillaar
  given name: Roland
doi: 10.7717/peerj.10781
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-18
copyright: © 2021 Johnsen and van den Tillaar
attribution name: Johnsen and van den Tillaar

Estimation of parameters for a humidity-dependent compartmental model of the COVID-19 outbreak
type: item
type: AcademicArticle
description: Building an effective and highly usable epidemiology model presents two main challenges: finding the appropriate, realistic enough model that takes into account complex biological, social and environmental parameters and efficiently estimating the parameter values with which the model can accurately match the available outbreak data, provide useful projections. The reproduction number of the novel coronavirus (SARS-CoV-2) has been found to vary over time, potentially being influenced by a multitude of factors such as varying control strategies, changes in public awareness and reaction or, as a recent study suggests, sensitivity to temperature or humidity changes. To take into consideration these constantly evolving factors, the paper introduces a time dynamic, humidity-dependent SEIR-type extended epidemiological model with range-defined parameters. Using primarily the historical data of the outbreak from Northern and Southern Italy and with the help of stochastic global optimization algorithms, we are able to determine a model parameter estimation that provides a high-quality fit to the data. The time-dependent contact rate showed a quick drop to a value slightly below 2. Applying the model for the COVID-19 outbreak in the northern region of Italy, we obtained parameters that suggest a slower shrinkage of the contact rate to a value slightly above 4. These findings indicate that model fitting and validation, even on a limited amount of available data, can provide useful insights and projections, uncover aspects that upon improvement might help mitigate the disease spreading.
format: application/pdf
format: text/html
creator: Csaba Farkas
creator: David Iclanzan
creator: Boróka Olteán-Péter
creator: Géza Vekov
subject: Computational Biology
subject: Mathematical Biology
subject: Epidemiology
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.10790
publisher: PeerJ Inc.
rights: © 2021 Farkas et al.
abstract: Building an effective and highly usable epidemiology model presents two main challenges: finding the appropriate, realistic enough model that takes into account complex biological, social and environmental parameters and efficiently estimating the parameter values with which the model can accurately match the available outbreak data, provide useful projections. The reproduction number of the novel coronavirus (SARS-CoV-2) has been found to vary over time, potentially being influenced by a multitude of factors such as varying control strategies, changes in public awareness and reaction or, as a recent study suggests, sensitivity to temperature or humidity changes. To take into consideration these constantly evolving factors, the paper introduces a time dynamic, humidity-dependent SEIR-type extended epidemiological model with range-defined parameters. Using primarily the historical data of the outbreak from Northern and Southern Italy and with the help of stochastic global optimization algorithms, we are able to determine a model parameter estimation that provides a high-quality fit to the data. The time-dependent contact rate showed a quick drop to a value slightly below 2. Applying the model for the COVID-19 outbreak in the northern region of Italy, we obtained parameters that suggest a slower shrinkage of the contact rate to a value slightly above 4. These findings indicate that model fitting and validation, even on a limited amount of available data, can provide useful insights and projections, uncover aspects that upon improvement might help mitigate the disease spreading.
bibliographic citation: Farkas et al. (2021) Estimation of parameters for a humidity-dependent compartmental model of the COVID-19 outbreak. PeerJ 9:e10790 https://doi.org/10.7717/peerj.10790
date submitted: 2020-04-02
date accepted: 2020-12-26
issued: 2021-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Farkas
  given name: Csaba
author list: Agent
  family name: Iclanzan
  given name: David
author list: Agent
  family name: Olteán-Péter
  given name: Boróka
author list: Agent
  family name: Vekov
  given name: Géza
doi: 10.7717/peerj.10790
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-18
copyright: © 2021 Farkas et al.
attribution name: Farkas et al.

Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula
type: item
type: AcademicArticle
description: Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benc…
format: application/pdf
format: text/html
creator: Anastasiia K. Kimeklis
creator: Grigory V. Gladkov
creator: Aleksei O. Zverev
creator: Arina A. Kichko
creator: Evgeny E. Andronov
creator: Elena I. Ergina
creator: Igor V. Kostenko
creator: Evgeny V. Abakumov
subject: Bioinformatics
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.10871
publisher: PeerJ Inc.
rights: © 2021 Kimeklis et al.
abstract: Rendzic Leptosols are intrazonal soils formed on limestone bedrock. The specialty of these soils is that parent rock material is more influential in shaping soil characteristics than zonal factors such as climate, especially during soil formation. Unlike fast evolving Podzols due to their leaching regime, Leptosols do not undergo rapid development due to the nature of the limestone. Little is known how microbiome reflects this process, so we assessed microbiome composition of Rendzic Leptosols of different ages, arising from disruption and subsequent reclamation. The mountains and foothills that cover much of the Crimean Peninsula are ideal for this type of study, as the soils were formed on limestone and have been subjected to anthropogenic impacts through much of human history. Microbiomes of four soil sites forming a chronosequence, including different soil horizons, were studied using sequencing of 16S rRNA gene libraries and quantitative PCR. Dominant phyla for all soil sites were Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Thaumarchaeota, Planctomycetes, Verrucomicrobia and Firmicutes. Alpha diversity was similar across sites and tended to be higher in topsoil. Beta diversity showed that microbiomes diverged according to the soil site and the soil horizon. The oldest and the youngest soils had the most similar microbiomes, which could have been caused by their geographic proximity. Oligotrophic bacteria from Chitinophagaceae, Blastocatellaceae and Rubrobacteriaceae dominated the microbiome of these soils. The microbiome of 700-year old soil was the most diverse. This soil was from the only study location with topsoil formed by plant litter, which provided additional nutrients and could have been the driving force of this differentiation. Consistent with this assumption, this soil was abundant in copiotrophic bacteria from Proteobacteria and Actinobacteria phyla. The microbiome of 50-year old Leptosol was more similar to the microbiome of benc…
bibliographic citation: Kimeklis et al. (2021) Microbiomes of different ages in Rendzic Leptosols in the Crimean Peninsula. PeerJ 9:e10871 https://doi.org/10.7717/peerj.10871
date submitted: 2020-07-21
date accepted: 2021-01-10
issued: 2021-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kimeklis
  given name: Anastasiia K.
author list: Agent
  family name: Gladkov
  given name: Grigory V.
author list: Agent
  family name: Zverev
  given name: Aleksei O.
author list: Agent
  family name: Kichko
  given name: Arina A.
author list: Agent
  family name: Andronov
  given name: Evgeny E.
author list: Agent
  family name: Ergina
  given name: Elena I.
author list: Agent
  family name: Kostenko
  given name: Igor V.
author list: Agent
  family name: Abakumov
  given name: Evgeny V.
doi: 10.7717/peerj.10871
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-18
copyright: ©2021 Kimeklis et al.
attribution name: Kimeklis et al.

Pseudocnidae of ribbon worms (Nemertea): ultrastructure, maturation, and functional morphology
type: item
type: AcademicArticle
description: The fine structure of mature pseudocnidae of 32 species of nemerteans, representatives of 20 genera, six families, and two classes was investigated with scanning and transmission electron microscopy. Pseudocnidae are composed of four layers (cortex, medulla, precore layer, and core) in most species investigated, but the degree of development and position of each layer can vary between different species. The secretion products comprising immature pseudocnidae segregate into separate layers: a thin envelope, which subsequently separates into the cortex and medulla and an extensive internal layer. We distinguish two pseudocnida types: type I is characterized by a two-layered core and type II by a three-layered core. Type I pseudocnidae are present in archinemertean species, Carinoma mutabilis, and in all pilidiophoran species, except Heteronemertea sp. 5DS; type II pseudocnidae occur in all studied species of Tubulanidae and the basal Heteronemertea sp. 5DS. Based on the structure of the discharged pseudocnidae observed in eleven species of palaeonemerteans and in eight species of pilidiophorans, we distinguish three different mechanisms (1–3) of core extrusion/discharge with the following characteristics and distribution: (1) the outer core layer is everted simultaneously with the tube-like layer and occurs in type I pseudocnidae of most species; (2) the extruded core is formed by both eversion of the outer core layer and medullar layer, and occurs in type I pseudocnidae of Micrura cf. bella; (3) the eversion of the outer core layer begins together with the core rod and core rod lamina and occurs in type II pseudocnidae. Morpho-functional comparison with other extrusomes (cnidae, sagittocysts, rhabdtites, and paracnids) confirm that pseudocnidae are homologous structures that are unique to nemerteans.
format: application/pdf
format: text/html
creator: Timur Yu Magarlamov
creator: James M. Turbeville
creator: Alexei V. Chernyshev
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.10912
publisher: PeerJ Inc.
rights: © 2021 Magarlamov et al.
abstract: The fine structure of mature pseudocnidae of 32 species of nemerteans, representatives of 20 genera, six families, and two classes was investigated with scanning and transmission electron microscopy. Pseudocnidae are composed of four layers (cortex, medulla, precore layer, and core) in most species investigated, but the degree of development and position of each layer can vary between different species. The secretion products comprising immature pseudocnidae segregate into separate layers: a thin envelope, which subsequently separates into the cortex and medulla and an extensive internal layer. We distinguish two pseudocnida types: type I is characterized by a two-layered core and type II by a three-layered core. Type I pseudocnidae are present in archinemertean species, Carinoma mutabilis, and in all pilidiophoran species, except Heteronemertea sp. 5DS; type II pseudocnidae occur in all studied species of Tubulanidae and the basal Heteronemertea sp. 5DS. Based on the structure of the discharged pseudocnidae observed in eleven species of palaeonemerteans and in eight species of pilidiophorans, we distinguish three different mechanisms (1–3) of core extrusion/discharge with the following characteristics and distribution: (1) the outer core layer is everted simultaneously with the tube-like layer and occurs in type I pseudocnidae of most species; (2) the extruded core is formed by both eversion of the outer core layer and medullar layer, and occurs in type I pseudocnidae of Micrura cf. bella; (3) the eversion of the outer core layer begins together with the core rod and core rod lamina and occurs in type II pseudocnidae. Morpho-functional comparison with other extrusomes (cnidae, sagittocysts, rhabdtites, and paracnids) confirm that pseudocnidae are homologous structures that are unique to nemerteans.
bibliographic citation: Magarlamov et al. (2021) Pseudocnidae of ribbon worms (Nemertea): ultrastructure, maturation, and functional morphology. PeerJ 9:e10912 https://doi.org/10.7717/peerj.10912
date submitted: 2020-08-31
date accepted: 2021-01-16
issued: 2021-02-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Magarlamov
  given name: Timur Yu
author list: Agent
  family name: Turbeville
  given name: James M.
author list: Agent
  family name: Chernyshev
  given name: Alexei V.
doi: 10.7717/peerj.10912
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-18
copyright: © 2021 Magarlamov et al.
attribution name: Magarlamov et al.

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