PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Evaluating the reliability of media reports for gathering information about illegal wildlife trade seizures
items: Identification and charactering of APX genes provide new insights in abiotic stresses response in Brassica napus
items: A new juvenile Yamaceratops (Dinosauria, Ceratopsia) from the Javkhlant Formation (Upper Cretaceous) of Mongolia
items: Validation of a dual-task exercise program to improve balance and gait speed in older people (DualPro): a Delphi study
items: Influence of biological maturation status on selected anthropometric and physical fitness variables in adolescent male volleyball players
items: Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis
items: Geochemical characteristics of strontium isotopes in a coastal watershed: implications for anthropogenic influenced chemical weathering and export flux
items: Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds in alkaline grasslands
items: Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept
items: Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata)

Evaluating the reliability of media reports for gathering information about illegal wildlife trade seizures
type: item
type: AcademicArticle
description: Illegal wildlife trade (IWT) is threatening many species across the world. It is important to better understand the scale and characteristics of IWT to inform conservation priorities and actions. However, IWT usually takes place covertly, meaning that the data on species, trade routes and volumes is limited. This means that conservationists often have to rely on publicly available law enforcement reports of seizures as potential indicators of the magnitude and characteristics of IWT. Still, even these data may be difficult to access, leading conservationists to use media reports of seizures instead. This is the case in countries like Nepal, which have limited capacity in data keeping and reporting, and no centralized data management system. Yet reliance on media reports risks introducing further biases, which are rarely acknowledged or discussed. Here we characterize IWT in Nepal by comparing data from three sources of information on IWT between January 2005 and July 2017: seizure reports from three Nepali national daily newspapers, official seizure records for Kathmandu district, and data on additional enforcement efforts against IWT in Nepal. We found a strong positive correlation between the number of official and media-reported seizures over time, but media under-reported seizure numbers, with 78% of seizures going unreported. Seizures of charismatic, protected species were reported more often and seizure reports involving tigers were most likely to be reported (57%). Media reports appeared to be a good indicator of trends and the species being seized but not overall seizure number, with the media largely underestimating total seizure numbers. Therefore, media reports cannot be solely relied upon when it comes to informing conservation decision-making. We recommend that conservationists triangulate different data sources when using seizure data reported in the media to more rigorously characterise IWT.
format: application/pdf
format: text/html
creator: Kumar Paudel
creator: Amy Hinsley
creator: Diogo Veríssimo
creator: Ej Milner-Gulland
subject: Biodiversity
subject: Conservation Biology
description: doi:10.7717/peerj.13156
publisher: PeerJ Inc.
rights: © 2022 Paudel et al.
abstract: Illegal wildlife trade (IWT) is threatening many species across the world. It is important to better understand the scale and characteristics of IWT to inform conservation priorities and actions. However, IWT usually takes place covertly, meaning that the data on species, trade routes and volumes is limited. This means that conservationists often have to rely on publicly available law enforcement reports of seizures as potential indicators of the magnitude and characteristics of IWT. Still, even these data may be difficult to access, leading conservationists to use media reports of seizures instead. This is the case in countries like Nepal, which have limited capacity in data keeping and reporting, and no centralized data management system. Yet reliance on media reports risks introducing further biases, which are rarely acknowledged or discussed. Here we characterize IWT in Nepal by comparing data from three sources of information on IWT between January 2005 and July 2017: seizure reports from three Nepali national daily newspapers, official seizure records for Kathmandu district, and data on additional enforcement efforts against IWT in Nepal. We found a strong positive correlation between the number of official and media-reported seizures over time, but media under-reported seizure numbers, with 78% of seizures going unreported. Seizures of charismatic, protected species were reported more often and seizure reports involving tigers were most likely to be reported (57%). Media reports appeared to be a good indicator of trends and the species being seized but not overall seizure number, with the media largely underestimating total seizure numbers. Therefore, media reports cannot be solely relied upon when it comes to informing conservation decision-making. We recommend that conservationists triangulate different data sources when using seizure data reported in the media to more rigorously characterise IWT.
bibliographic citation: Paudel et al. (2022) Evaluating the reliability of media reports for gathering information about illegal wildlife trade seizures. PeerJ 10:e13156 https://doi.org/10.7717/peerj.13156
date submitted: 2021-12-14
date accepted: 2022-03-02
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Paudel
  given name: Kumar
author list: Agent
  family name: Hinsley
  given name: Amy
author list: Agent
  family name: Veríssimo
  given name: Diogo
author list: Agent
  family name: Milner-Gulland
  given name: Ej
doi: 10.7717/peerj.13156
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Paudel et al.
attribution name: Paudel et al.

Identification and charactering of APX genes provide new insights in abiotic stresses response in Brassica napus
type: item
type: AcademicArticle
description: Ascorbate peroxidase (APX) plays an important role in scavenging H2O2 and balancing ROS content in plant cells, which is of great significance for the growth and development of life and resistance to external stress. However, up to now, APXs in Brassica napus (B. napus) have not been systematically characterized. In this study, a total of 26 BnaAPX genes were identified, which were distributed on 13 chromosomes and divided into five phylogenetic branches. Gene structure analysis showed that they had a wide varied number of exons while BnaAPXs proteins contained more similar motifs in the same phylogenetic branches. qRT-PCR analysis of 26 BnaAPX gene expression patterns showed that three putative cytosol BnaAPX genes BnaAPX1, BnaAPX2, BnaAPX9, two putatice microsomal genes BnaAPX18 and BnaAPX25 were up-regulated rapidly and robustly under high salt, water shortage and high temperature stresses. In addition, the above three abiotic stresses led to a significant increase in APX activity. The results provide basic and comprehensive information for further functional characterization of APX gene family in B. napus.
format: application/pdf
format: text/html
creator: Jiao Pan
creator: Lei Zhang
creator: Min Chen
creator: Yuxuan Ruan
creator: Peifang Li
creator: Zhihui Guo
creator: Boyu Liu
creator: Ying Ruan
creator: Mu Xiao
creator: Yong Huang
subject: Agricultural Science
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.13166
publisher: PeerJ Inc.
rights: © 2022 Pan et al.
abstract: Ascorbate peroxidase (APX) plays an important role in scavenging H2O2 and balancing ROS content in plant cells, which is of great significance for the growth and development of life and resistance to external stress. However, up to now, APXs in Brassica napus (B. napus) have not been systematically characterized. In this study, a total of 26 BnaAPX genes were identified, which were distributed on 13 chromosomes and divided into five phylogenetic branches. Gene structure analysis showed that they had a wide varied number of exons while BnaAPXs proteins contained more similar motifs in the same phylogenetic branches. qRT-PCR analysis of 26 BnaAPX gene expression patterns showed that three putative cytosol BnaAPX genes BnaAPX1, BnaAPX2, BnaAPX9, two putatice microsomal genes BnaAPX18 and BnaAPX25 were up-regulated rapidly and robustly under high salt, water shortage and high temperature stresses. In addition, the above three abiotic stresses led to a significant increase in APX activity. The results provide basic and comprehensive information for further functional characterization of APX gene family in B. napus.
bibliographic citation: Pan et al. (2022) Identification and charactering of APX genes provide new insights in abiotic stresses response in Brassica napus. PeerJ 10:e13166 https://doi.org/10.7717/peerj.13166
date submitted: 2021-09-23
date accepted: 2022-03-04
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pan
  given name: Jiao
author list: Agent
  family name: Zhang
  given name: Lei
author list: Agent
  family name: Chen
  given name: Min
author list: Agent
  family name: Ruan
  given name: Yuxuan
author list: Agent
  family name: Li
  given name: Peifang
author list: Agent
  family name: Guo
  given name: Zhihui
author list: Agent
  family name: Liu
  given name: Boyu
author list: Agent
  family name: Ruan
  given name: Ying
author list: Agent
  family name: Xiao
  given name: Mu
author list: Agent
  family name: Huang
  given name: Yong
doi: 10.7717/peerj.13166
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Pan et al.
attribution name: Pan et al.

A new juvenile Yamaceratops (Dinosauria, Ceratopsia) from the Javkhlant Formation (Upper Cretaceous) of Mongolia
type: item
type: AcademicArticle
description: Here we report a new articulated skeleton of Yamaceratops dorngobiensis (MPC-D 100/553) from the Khugenetjavkhlant locality at the Shine Us Khudag (Javkhlant Formation, ?Santonian-Campanian) of the eastern Gobi Desert, Mongolia, which represents the first substantially complete skeleton and the first juvenile individual of this taxon. The specimen includes a nearly complete cranium and large portions of the vertebral column and appendicular skeleton. Its skull is about 2/3 the size of the holotype specimen, based on mandibular length. Its juvenile ontogenetic stage is confirmed by multiple indicators of skeletal and morphological immaturity known in ceratopsians, such as the long-grained surface texture on the long bones, the smooth external surface on the postorbital, open neurocentral sutures of all caudal vertebrae, a large orbit relative to the postorbital and jugal, the low angle of the lacrimal ventral ramus relative to the maxillary teeth row, narrow frontal, and straight ventral edge of the dentary. Osteohistological analysis of MPC-D 100/553 recovered three lines of arrested growth, implying around 3 years of age when it died, and verified this specimen’s immature ontogenetic stage. The specimen adds a new autapomorphy of Yamaceratops, the anteroventral margin of the fungiform dorsal end of the lacrimal being excluded from the antorbital fossa. Furthermore, it shows a unique combination of diagnostic features of some other basal neoceratopsians: the ventrally hooked rostral bone as in Aquilops americanus and very tall middle caudal neural spines about or more than four times as high as the centrum as in Koreaceratops hwaseongensis, Montanoceratops cerorhynchus, and Protoceratops andrewsi. The jugal with the subtemporal ramus deeper than the suborbital ramus as in the holotype specimen is also shared with A. americanus, Liaoceratops yanzigouensis, and juvenile P. andrewsi. Adding 38 new scorings into the recent comprehensive data matrix of basal Neoceratopsi…
format: application/pdf
format: text/html
creator: Minyoung Son
creator: Yuong-Nam Lee
creator: Badamkhatan Zorigt
creator: Yoshitsugu Kobayashi
creator: Jin-Young Park
creator: Sungjin Lee
creator: Su-Hwan Kim
creator: Kang Young Lee
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.13176
publisher: PeerJ Inc.
rights: © 2022 Son et al.
abstract: Here we report a new articulated skeleton of Yamaceratops dorngobiensis (MPC-D 100/553) from the Khugenetjavkhlant locality at the Shine Us Khudag (Javkhlant Formation, ?Santonian-Campanian) of the eastern Gobi Desert, Mongolia, which represents the first substantially complete skeleton and the first juvenile individual of this taxon. The specimen includes a nearly complete cranium and large portions of the vertebral column and appendicular skeleton. Its skull is about 2/3 the size of the holotype specimen, based on mandibular length. Its juvenile ontogenetic stage is confirmed by multiple indicators of skeletal and morphological immaturity known in ceratopsians, such as the long-grained surface texture on the long bones, the smooth external surface on the postorbital, open neurocentral sutures of all caudal vertebrae, a large orbit relative to the postorbital and jugal, the low angle of the lacrimal ventral ramus relative to the maxillary teeth row, narrow frontal, and straight ventral edge of the dentary. Osteohistological analysis of MPC-D 100/553 recovered three lines of arrested growth, implying around 3 years of age when it died, and verified this specimen’s immature ontogenetic stage. The specimen adds a new autapomorphy of Yamaceratops, the anteroventral margin of the fungiform dorsal end of the lacrimal being excluded from the antorbital fossa. Furthermore, it shows a unique combination of diagnostic features of some other basal neoceratopsians: the ventrally hooked rostral bone as in Aquilops americanus and very tall middle caudal neural spines about or more than four times as high as the centrum as in Koreaceratops hwaseongensis, Montanoceratops cerorhynchus, and Protoceratops andrewsi. The jugal with the subtemporal ramus deeper than the suborbital ramus as in the holotype specimen is also shared with A. americanus, Liaoceratops yanzigouensis, and juvenile P. andrewsi. Adding 38 new scorings into the recent comprehensive data matrix of basal Neoceratopsi…
bibliographic citation: Son et al. (2022) A new juvenile Yamaceratops (Dinosauria, Ceratopsia) from the Javkhlant Formation (Upper Cretaceous) of Mongolia. PeerJ 10:e13176 https://doi.org/10.7717/peerj.13176
date submitted: 2021-07-08
date accepted: 2022-03-06
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Son
  given name: Minyoung
author list: Agent
  family name: Lee
  given name: Yuong-Nam
author list: Agent
  family name: Zorigt
  given name: Badamkhatan
author list: Agent
  family name: Kobayashi
  given name: Yoshitsugu
author list: Agent
  family name: Park
  given name: Jin-Young
author list: Agent
  family name: Lee
  given name: Sungjin
author list: Agent
  family name: Kim
  given name: Su-Hwan
author list: Agent
  family name: Lee
  given name: Kang Young
doi: 10.7717/peerj.13176
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Son et al.
attribution name: Son et al.

Validation of a dual-task exercise program to improve balance and gait speed in older people (DualPro): a Delphi study
type: item
type: AcademicArticle
description: Background Most physical exercise programs for older people work the physical component in isolation, excluding cognitive aspects. Previous studies reported that both components (physical and cognitive) are necessary for correct functioning of older people in the society. Purpose To create and validate a dual-task exercise program (DualPro) to improve balance and gait speed in older people. Methods Expert consensus or the Delphi Method was used for validation. A group of 17 experts in neurorehabilitation and geriatrics was recruited to assess the proposed exercise program. They were selected taking into account their experience in clinical practice as well as their knowledge of the subject through the use of the expert competence coefficient (K). Online questionnaires were sent with a total of 11 exercises, which had to be rated using a “Likert” scale from 1 to 7. Results Two rounds were conducted to achieve 100% consensus in all exercises. The interquartile range of each exercise in both rounds was stable. During the second round, the relative interquartile range was less than 15% in all the questions, thus demonstrating consensus among the experts. Conclusion Experts in neurorehabilitation and geriatrics have concluded the validity of the progressive and systematized program of dual-task exercises focused on improving balance and gait speed for older people. This exercise program can help in the homogenization of the use of dual-task exercises in future studies and in professional practice.
format: application/pdf
format: text/html
creator: Luz Adriana Varela-Vásquez
creator: Montserrat Girabent-Farrés
creator: Almudena Medina-Rincón
creator: Sandra Rierola-Fochs
creator: Javier Jerez-Roig
creator: Eduard Minobes-Molina
subject: Geriatrics
subject: Kinesiology
subject: Rehabilitation
description: doi:10.7717/peerj.13204
publisher: PeerJ Inc.
rights: © 2022 Varela-Vásquez et al.
abstract: Background Most physical exercise programs for older people work the physical component in isolation, excluding cognitive aspects. Previous studies reported that both components (physical and cognitive) are necessary for correct functioning of older people in the society. Purpose To create and validate a dual-task exercise program (DualPro) to improve balance and gait speed in older people. Methods Expert consensus or the Delphi Method was used for validation. A group of 17 experts in neurorehabilitation and geriatrics was recruited to assess the proposed exercise program. They were selected taking into account their experience in clinical practice as well as their knowledge of the subject through the use of the expert competence coefficient (K). Online questionnaires were sent with a total of 11 exercises, which had to be rated using a “Likert” scale from 1 to 7. Results Two rounds were conducted to achieve 100% consensus in all exercises. The interquartile range of each exercise in both rounds was stable. During the second round, the relative interquartile range was less than 15% in all the questions, thus demonstrating consensus among the experts. Conclusion Experts in neurorehabilitation and geriatrics have concluded the validity of the progressive and systematized program of dual-task exercises focused on improving balance and gait speed for older people. This exercise program can help in the homogenization of the use of dual-task exercises in future studies and in professional practice.
bibliographic citation: Varela-Vásquez et al. (2022) Validation of a dual-task exercise program to improve balance and gait speed in older people (DualPro): a Delphi study. PeerJ 10:e13204 https://doi.org/10.7717/peerj.13204
date submitted: 2021-09-16
date accepted: 2022-03-10
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Varela-Vásquez
  given name: Luz Adriana
author list: Agent
  family name: Girabent-Farrés
  given name: Montserrat
author list: Agent
  family name: Medina-Rincón
  given name: Almudena
author list: Agent
  family name: Rierola-Fochs
  given name: Sandra
author list: Agent
  family name: Jerez-Roig
  given name: Javier
author list: Agent
  family name: Minobes-Molina
  given name: Eduard
doi: 10.7717/peerj.13204
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Varela-Vásquez et al.
attribution name: Varela-Vásquez et al.

Influence of biological maturation status on selected anthropometric and physical fitness variables in adolescent male volleyball players
type: item
type: AcademicArticle
description: Background The identification of sport talent among adolescent athletes is a topic that in recent years has been a major focus of interest for both the scientific community and sport managers. Both anthropometry and physical performance through fitness tests have demonstrated to be key elements. Biological maturation, due to its influence on anthropometric variables and physical fitness, has also been studied in relation to sport talent identification. Objective To analyse differences according to biological maturation status in anthropometric characteristics and performance in physical fitness tests, and to determine which variables predict better performance in physical fitness tests in adolescent volleyball players. Methods A cross-sectional design was followed to collect the data. A total of 48 male sub-elite volleyball players (14.17 ± 0.73 years) completed a socio-demographic and sports ad hoc questionnaire. Anthropometric variables were measured following the guidelines of the International Society for the Advancement in Kinanthropometry (ISAK) including four basic measurements (body mass, height, sitting height and arm span); eight skinfolds (triceps, biceps, subscapular, iliac crest, supraspinale, abdominal, thigh and calf); four girths (arm relaxed, flexed and tensed arm, middle thigh and calf); five breadths (biacromial, biileocrestal, humerus, femur and bi-styloid); three lengths (acromiale-radiale, radiale-stylion and stylion-medio dactilion); and a height (ilioespinale). Physical fitness was assessed, including the sit-and-reach, back scratch, long jump, medicine ball throw, counter movement jump (CMJ), 20 meters sprint, and agility tests. Furthermore, maturity offset and age at peak height velocity (APHV) was calculated. Results Significant differences were found in the body mass (Mean Difference, MD = 20.86–30.75), height (MD = 11.72–19.09), sitting height (MD = 4.27–10.27), arm span (MD = 12.91–20.78), body mass index (MD = 3.72–5.63), upper limb le…
format: application/pdf
format: text/html
creator: Mario Albaladejo-Saura
creator: Raquel Vaquero-Cristóbal
creator: Juan A. García-Roca
creator: Francisco Esparza-Ros
subject: Anatomy and Physiology
subject: Kinesiology
subject: Pediatrics
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.13216
publisher: PeerJ Inc.
rights: © 2022 Albaladejo-Saura et al.
abstract: Background The identification of sport talent among adolescent athletes is a topic that in recent years has been a major focus of interest for both the scientific community and sport managers. Both anthropometry and physical performance through fitness tests have demonstrated to be key elements. Biological maturation, due to its influence on anthropometric variables and physical fitness, has also been studied in relation to sport talent identification. Objective To analyse differences according to biological maturation status in anthropometric characteristics and performance in physical fitness tests, and to determine which variables predict better performance in physical fitness tests in adolescent volleyball players. Methods A cross-sectional design was followed to collect the data. A total of 48 male sub-elite volleyball players (14.17 ± 0.73 years) completed a socio-demographic and sports ad hoc questionnaire. Anthropometric variables were measured following the guidelines of the International Society for the Advancement in Kinanthropometry (ISAK) including four basic measurements (body mass, height, sitting height and arm span); eight skinfolds (triceps, biceps, subscapular, iliac crest, supraspinale, abdominal, thigh and calf); four girths (arm relaxed, flexed and tensed arm, middle thigh and calf); five breadths (biacromial, biileocrestal, humerus, femur and bi-styloid); three lengths (acromiale-radiale, radiale-stylion and stylion-medio dactilion); and a height (ilioespinale). Physical fitness was assessed, including the sit-and-reach, back scratch, long jump, medicine ball throw, counter movement jump (CMJ), 20 meters sprint, and agility tests. Furthermore, maturity offset and age at peak height velocity (APHV) was calculated. Results Significant differences were found in the body mass (Mean Difference, MD = 20.86–30.75), height (MD = 11.72–19.09), sitting height (MD = 4.27–10.27), arm span (MD = 12.91–20.78), body mass index (MD = 3.72–5.63), upper limb le…
bibliographic citation: Albaladejo-Saura et al. (2022) Influence of biological maturation status on selected anthropometric and physical fitness variables in adolescent male volleyball players. PeerJ 10:e13216 https://doi.org/10.7717/peerj.13216
date submitted: 2022-01-20
date accepted: 2022-03-14
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Albaladejo-Saura
  given name: Mario
author list: Agent
  family name: Vaquero-Cristóbal
  given name: Raquel
author list: Agent
  family name: García-Roca
  given name: Juan A.
author list: Agent
  family name: Esparza-Ros
  given name: Francisco
doi: 10.7717/peerj.13216
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Albaladejo-Saura et al.
attribution name: Albaladejo-Saura et al.

Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis
type: item
type: AcademicArticle
description: Background Dendrobium catenatum is a valuable traditional medicinal herb with high commercial value. D. catenatum stems contain abundant polysaccharides which are one of the main bioactive components. However, although some genes related to the synthesis of the polysaccharides have been reported, more key genes need to be further elucidated. Results In this study, the contents of polysaccharides and mannose in D. catenatum stems at four developmental stages were compared, and the stems’ transcriptomes were analyzed to explore the synthesis mechanism of the polysaccharides. Many genes involved in starch and sucrose metabolisms were identified by KEGG pathway analysis. Further analysis found that sucrose synthase (SUS; EC 2.4.1.13) gene maybe participated in the polysaccharide synthesis. Hence, we further investigated the genomic characteristics and evolution relationships of the SUS family in plants. The result suggested that the SUS gene of D. catenatum (DcSUS) had undergone the expansion characterized by tandem duplication which might be related to the enrichment of the polysaccharides in D. catenatum stems. Moreover, expression analyses of the DcSUS displayed significant divergent patterns in different tissues and could be divided into two main groups in the stems with four developmental stages. Conclusion In general, our results revealed that DcSUS is likely involved in the metabolic process of the stem polysaccharides, providing crucial clues for exploiting the key genes associated with the polysaccharide synthesis.
format: application/pdf
format: text/html
creator: Min Jiang
creator: Shangyun Li
creator: Changling Zhao
creator: Mingfu Zhao
creator: Shaozhong Xu
creator: Guosong Wen
subject: Agricultural Science
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.13222
publisher: PeerJ Inc.
rights: © 2022 Jiang et al.
abstract: Background Dendrobium catenatum is a valuable traditional medicinal herb with high commercial value. D. catenatum stems contain abundant polysaccharides which are one of the main bioactive components. However, although some genes related to the synthesis of the polysaccharides have been reported, more key genes need to be further elucidated. Results In this study, the contents of polysaccharides and mannose in D. catenatum stems at four developmental stages were compared, and the stems’ transcriptomes were analyzed to explore the synthesis mechanism of the polysaccharides. Many genes involved in starch and sucrose metabolisms were identified by KEGG pathway analysis. Further analysis found that sucrose synthase (SUS; EC 2.4.1.13) gene maybe participated in the polysaccharide synthesis. Hence, we further investigated the genomic characteristics and evolution relationships of the SUS family in plants. The result suggested that the SUS gene of D. catenatum (DcSUS) had undergone the expansion characterized by tandem duplication which might be related to the enrichment of the polysaccharides in D. catenatum stems. Moreover, expression analyses of the DcSUS displayed significant divergent patterns in different tissues and could be divided into two main groups in the stems with four developmental stages. Conclusion In general, our results revealed that DcSUS is likely involved in the metabolic process of the stem polysaccharides, providing crucial clues for exploiting the key genes associated with the polysaccharide synthesis.
bibliographic citation: Jiang et al. (2022) Identification and analysis of sucrose synthase gene family associated with polysaccharide biosynthesis in Dendrobium catenatum by transcriptomic analysis. PeerJ 10:e13222 https://doi.org/10.7717/peerj.13222
date submitted: 2021-12-28
date accepted: 2022-03-14
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Min
author list: Agent
  family name: Li
  given name: Shangyun
author list: Agent
  family name: Zhao
  given name: Changling
author list: Agent
  family name: Zhao
  given name: Mingfu
author list: Agent
  family name: Xu
  given name: Shaozhong
author list: Agent
  family name: Wen
  given name: Guosong
doi: 10.7717/peerj.13222
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Jiang et al.
attribution name: Jiang et al.

Geochemical characteristics of strontium isotopes in a coastal watershed: implications for anthropogenic influenced chemical weathering and export flux
type: item
type: AcademicArticle
description: Coastal watershed are essential in transporting dissolved loads from terrestrial biogeochemical process of surface environment to the adjacent oceans. The solute chemistry of coastal river water contains significant information about environmental processes under the impact of both natural lithology and anthropogenic pressure. In this study, strontium (Sr) isotopes and water chemistry data of the Jiulongjiang (JLJ) river water were analyzed in detail to trace the contribution of bedrock weathering, and quantify Sr flux to the East China Sea (ECS). The dissolved Sr contents ranged 0.07–0.90 μmol L−1 and greatly fluctuated where tributaries encountered, and 87Sr/86Sr values relatively fluctuated between 0.7140 and 0.7514. Silicate weathering was identified to be the predominant contribution of riverine dissolved loads. Strontium flux to the ocean in dry season was estimated to be 689.2 tons per year, implying an essential influence on oceanic strontium evolution. In accordance with forward model, the silicate weathering rate and CO2 consumption rate were 55.7 tons km−2 per year and 16.9 × 105 mol km−2 per year, respectively, slightly higher than world average. Considering anthropogenic impacts alongside the river, the integrated effect of lower runoff and longer retention time of river water in dry season may aggravate weathering processes. Although CO2 sink by silicate weathering in JLJ seems less than the sink in world’s central reservoirs, it should still be taken into consideration for coastal carbon budget. These findings highlight the use of geochemical characteristics of strontium and its isotopes in identifying weathering process and output flux to the ocean, which provides basic data for sustainable coastal water resource management.
format: application/pdf
format: text/html
creator: Shitong Zhang
creator: Guilin Han
creator: Jie Zeng
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.13223
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Coastal watershed are essential in transporting dissolved loads from terrestrial biogeochemical process of surface environment to the adjacent oceans. The solute chemistry of coastal river water contains significant information about environmental processes under the impact of both natural lithology and anthropogenic pressure. In this study, strontium (Sr) isotopes and water chemistry data of the Jiulongjiang (JLJ) river water were analyzed in detail to trace the contribution of bedrock weathering, and quantify Sr flux to the East China Sea (ECS). The dissolved Sr contents ranged 0.07–0.90 μmol L−1 and greatly fluctuated where tributaries encountered, and 87Sr/86Sr values relatively fluctuated between 0.7140 and 0.7514. Silicate weathering was identified to be the predominant contribution of riverine dissolved loads. Strontium flux to the ocean in dry season was estimated to be 689.2 tons per year, implying an essential influence on oceanic strontium evolution. In accordance with forward model, the silicate weathering rate and CO2 consumption rate were 55.7 tons km−2 per year and 16.9 × 105 mol km−2 per year, respectively, slightly higher than world average. Considering anthropogenic impacts alongside the river, the integrated effect of lower runoff and longer retention time of river water in dry season may aggravate weathering processes. Although CO2 sink by silicate weathering in JLJ seems less than the sink in world’s central reservoirs, it should still be taken into consideration for coastal carbon budget. These findings highlight the use of geochemical characteristics of strontium and its isotopes in identifying weathering process and output flux to the ocean, which provides basic data for sustainable coastal water resource management.
bibliographic citation: Zhang et al. (2022) Geochemical characteristics of strontium isotopes in a coastal watershed: implications for anthropogenic influenced chemical weathering and export flux. PeerJ 10:e13223 https://doi.org/10.7717/peerj.13223
date submitted: 2021-12-03
date accepted: 2022-03-14
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Shitong
author list: Agent
  family name: Han
  given name: Guilin
author list: Agent
  family name: Zeng
  given name: Jie
doi: 10.7717/peerj.13223
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds in alkaline grasslands
type: item
type: AcademicArticle
description: Background Soil seed banks play a central role in vegetation dynamics and may be an important source of ecological restoration. However, the vast majority of seed bank studies examined only the uppermost soil layers (0–10 cm); hence, our knowledge on the depth distribution of seed bank and the ecological significance of deeply buried seeds is limited. The aim of our study was to examine the fine-scale vertical distribution of soil seed bank to a depth of 80 cm, which is one of the largest studied depth gradients so far. Our model systems were alkaline grasslands in East-Hungary, characterised by harsh environmental conditions, due to Solonetz soil reference group with Vertic horizon. We asked the following questions: (1) How do the seedling density and species richness of soil seed bank change along a vertical gradient and to what depth can germinable seeds be detected? (2) What is the relationship between the depth distribution of the germinable seeds and the species traits? Methods In each of the five study sites, four soil cores (4 cm diameter) of 80 cm depth were collected with an auger for soil seed bank analysis. Each sample was divided into sixteen 5-cm segments by depth (320 segments in total). Samples were concentrated by washing over sieves and then germinated in an unheated greenhouse. Soil penetration resistance was measured in situ next to each core location (0–80 cm depth, 1-cm resolution). We tested the number and species richness of seedlings observed in the soil segments (N = 320), using negative binomial generalized linear regression models, in which sampling layer and penetration resistance were the predictor variables. We ran the models for morphological groups (graminoids/forbs), ecological groups (grassland species/weeds) and life-form categories (short-lived/perennial). We also tested whether seed shape index, seed mass, water requirement or salt tolerance of the species influence the vertical distribution of their seed bank. Results Germinabl…
format: application/pdf
format: text/html
creator: Ágnes Tóth
creator: Balázs Deák
creator: Katalin Tóth
creator: Réka Kiss
creator: Katalin Lukács
creator: Zoltán Rádai
creator: Laura Godó
creator: Sándor Borza
creator: András Kelemen
creator: Tamás Miglécz
creator: Zoltán Bátori
creator: Tibor József Novák
creator: Orsolya Valkó
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.13226
publisher: PeerJ Inc.
rights: © 2022 Tóth et al.
abstract: Background Soil seed banks play a central role in vegetation dynamics and may be an important source of ecological restoration. However, the vast majority of seed bank studies examined only the uppermost soil layers (0–10 cm); hence, our knowledge on the depth distribution of seed bank and the ecological significance of deeply buried seeds is limited. The aim of our study was to examine the fine-scale vertical distribution of soil seed bank to a depth of 80 cm, which is one of the largest studied depth gradients so far. Our model systems were alkaline grasslands in East-Hungary, characterised by harsh environmental conditions, due to Solonetz soil reference group with Vertic horizon. We asked the following questions: (1) How do the seedling density and species richness of soil seed bank change along a vertical gradient and to what depth can germinable seeds be detected? (2) What is the relationship between the depth distribution of the germinable seeds and the species traits? Methods In each of the five study sites, four soil cores (4 cm diameter) of 80 cm depth were collected with an auger for soil seed bank analysis. Each sample was divided into sixteen 5-cm segments by depth (320 segments in total). Samples were concentrated by washing over sieves and then germinated in an unheated greenhouse. Soil penetration resistance was measured in situ next to each core location (0–80 cm depth, 1-cm resolution). We tested the number and species richness of seedlings observed in the soil segments (N = 320), using negative binomial generalized linear regression models, in which sampling layer and penetration resistance were the predictor variables. We ran the models for morphological groups (graminoids/forbs), ecological groups (grassland species/weeds) and life-form categories (short-lived/perennial). We also tested whether seed shape index, seed mass, water requirement or salt tolerance of the species influence the vertical distribution of their seed bank. Results Germinabl…
bibliographic citation: Tóth et al. (2022) Vertical distribution of soil seed bank and the ecological importance of deeply buried seeds in alkaline grasslands. PeerJ 10:e13226 https://doi.org/10.7717/peerj.13226
date submitted: 2021-11-24
date accepted: 2022-03-15
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tóth
  given name: Ágnes
author list: Agent
  family name: Deák
  given name: Balázs
author list: Agent
  family name: Tóth
  given name: Katalin
author list: Agent
  family name: Kiss
  given name: Réka
author list: Agent
  family name: Lukács
  given name: Katalin
author list: Agent
  family name: Rádai
  given name: Zoltán
author list: Agent
  family name: Godó
  given name: Laura
author list: Agent
  family name: Borza
  given name: Sándor
author list: Agent
  family name: Kelemen
  given name: András
author list: Agent
  family name: Miglécz
  given name: Tamás
author list: Agent
  family name: Bátori
  given name: Zoltán
author list: Agent
  family name: Novák
  given name: Tibor József
author list: Agent
  family name: Valkó
  given name: Orsolya
doi: 10.7717/peerj.13226
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Tóth et al.
attribution name: Tóth et al.

Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept
type: item
type: AcademicArticle
description: The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krąpiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as “marshes” (marshland surface), “shrubs” (shrub surface), and “forests” (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequ…
format: application/pdf
format: text/html
creator: Joanna Pakulnicka
creator: Paweł Buczyński
creator: Edyta Buczyńska
creator: Edyta Stępień
creator: Agnieszka Szlauer-Łukaszewska
creator: Robert Stryjecki
creator: Aleksandra Bańkowska
creator: Vladimir Pešić
creator: Ewa Filip
creator: Andrzej Zawal
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13232
publisher: PeerJ Inc.
rights: © 2022 Pakulnicka et al.
abstract: The main goal of the study was to recognize the mechanisms underlying assemblage structuring of aquatic beetle fauna inhabiting a medium-sized, lowland river exposed to anthropogenic pressures. An attempt was made to identify the impact of numerous abiotic factors on how beetle communities are formed, with particular emphasis on geomorphological and landscape-related factors, which tend to be omitted from many studies of aquatic organisms. Our intention was to refer the results of our study to the general assumptions of the River Continuum Concept. Field studies were conducted in 2010, at 13 sites located along the Krąpiel River (north-western Poland). In total, 3,269 beetles were captured, representing 120 species and five ecological groups: crenophiles, rheophiles, rheobionts, stagnobionts a and stagnobionts b, which differ in environmental preferences. The core of the identified fauna was composed of stagnobionts, while rheophiles and rheobionts accounted for only 20% of the entire collected material. The formation of beetle assemblages was affected both by local factors, with an impact on aquatic environments, and by geomorphological factors, influencing a larger catchment. This was reflected in the high degree of conformity between dendrograms presenting similarities in the fauna at the studied sites, including the clustering of sites based on the abiotic factors that differentiated these sites. The presence of buffer zones, surfaces of patches denoted as “marshes” (marshland surface), “shrubs” (shrub surface), and “forests” (forest surface), and the distance to those patches seem to be the most important landscape factors affecting beetle communities. Of the factors influencing the aquatic environment, the following exerted the strongest effect: insolation, vegetation cover, presence of organic matter and BOD5, and anthropogenic pressure. The changes in assemblages of beetles determined in our study in the particular sections of the river course were a consequ…
bibliographic citation: Pakulnicka et al. (2022) Sequentiality of beetle communities in the longitudinal gradient of a lowland river in the context of the river continuum concept. PeerJ 10:e13232 https://doi.org/10.7717/peerj.13232
date submitted: 2021-10-04
date accepted: 2022-03-16
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pakulnicka
  given name: Joanna
author list: Agent
  family name: Buczyński
  given name: Paweł
author list: Agent
  family name: Buczyńska
  given name: Edyta
author list: Agent
  family name: Stępień
  given name: Edyta
author list: Agent
  family name: Szlauer-Łukaszewska
  given name: Agnieszka
author list: Agent
  family name: Stryjecki
  given name: Robert
author list: Agent
  family name: Bańkowska
  given name: Aleksandra
author list: Agent
  family name: Pešić
  given name: Vladimir
author list: Agent
  family name: Filip
  given name: Ewa
author list: Agent
  family name: Zawal
  given name: Andrzej
doi: 10.7717/peerj.13232
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: © 2022 Pakulnicka et al.
attribution name: Pakulnicka et al.

Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata)
type: item
type: AcademicArticle
description: Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3–V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
format: application/pdf
format: text/html
creator: Zihao Zhou
creator: Hongying Wu
creator: Dinghong Li
creator: Wenlong Zeng
creator: Jinlong Huang
creator: Zhengjun Wu
subject: Ecology
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.13245
publisher: PeerJ Inc.
rights: © 2022 Zhou et al.
abstract: Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3–V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
bibliographic citation: Zhou et al. (2022) Comparison of gut microbiome in the Chinese mud snail (Cipangopaludina chinensis) and the invasive golden apple snail (Pomacea canaliculata). PeerJ 10:e13245 https://doi.org/10.7717/peerj.13245
date submitted: 2021-12-10
date accepted: 2022-03-18
issued: 2022-04-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Zihao
author list: Agent
  family name: Wu
  given name: Hongying
author list: Agent
  family name: Li
  given name: Dinghong
author list: Agent
  family name: Zeng
  given name: Wenlong
author list: Agent
  family name: Huang
  given name: Jinlong
author list: Agent
  family name: Wu
  given name: Zhengjun
doi: 10.7717/peerj.13245
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-04-05
copyright: ©2022 Zhou et al.
attribution name: Zhou et al.

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