PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Clinical characteristics and prognostic analysis of multiple primary malignant neoplasms in female patients with breast cancer or genitalia malignancies
items: Contribution of hippocampal BDNF/CREB signaling pathway and gut microbiota to emotional behavior impairment induced by chronic unpredictable mild stress during pregnancy in rats offspring
items: Genomics enters the deep learning era
items: Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
items: Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress
items: Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells
items: Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area
items: Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)
items: Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche
items: Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease

Clinical characteristics and prognostic analysis of multiple primary malignant neoplasms in female patients with breast cancer or genitalia malignancies
type: item
type: AcademicArticle
description: Background As public awareness of health has increased and diagnostic and treatment options have improved, the survival of patients with malignant tumors has continued to extend, and the population has been aging, the number of multiple primary malignant neoplasms has gradually increased in recent years. There are few reports concerning female patients with multiple primary malignant neoplasms of breast cancer or genitalia malignancies. In this study, we aimed to analyze the clinical characteristics and prognosis of multiple primary malignant neoplasms in female patients with breast cancer or genitalia malignancies, as well as further explore the factors that affect the survival. Methods We collected clinical data on 80 female patients diagnosed with multiple primary malignant neoplasms of the breast or genitalia, described their clinical features. Furthermore, we calculated the survival and prognostic factors for 52 participants. Results In our study, the prevalence rate of multiple primary malignant neoplasms was 0.66% (367/55404). Corresponding to female patients with multiple primary malignant neoplasms of breast cancer or genitalia malignancies, it was 1.4% (80/5707). the median age of diagnosis for the first tumor was 48 years, and the median age of diagnosis for the second tumor was 52 years. Regarding the interval, 67.57% (50/74) of patients were within five years. Most tumors were located in the breast (44.68%), followed by the uterus (20.21%), the ovary (17.02%), and the cervix (15.96%). The overall 12-, 36-and 60-month survival rates of the patients were 86.4%, 74.3%, and 69.8%. For the female patients, the stage (III–IV) (P = 0.046), non-radical surgery (P = 0.002), and types of the last tumor (breast cancer or genitalia malignancies) (P = 0.019) were associated with the poor prognosis. Conclusions Female patients with breast cancer or genital malignancies should pay attention to screening for the second tumor, especially within 4 years after the first t…
format: application/pdf
format: text/html
creator: Li Xiao
creator: Tiantian Cao
creator: Jiali Ou
creator: Weijiang Liang
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.13528
publisher: PeerJ Inc.
rights: © 2022 Xiao et al.
abstract: Background As public awareness of health has increased and diagnostic and treatment options have improved, the survival of patients with malignant tumors has continued to extend, and the population has been aging, the number of multiple primary malignant neoplasms has gradually increased in recent years. There are few reports concerning female patients with multiple primary malignant neoplasms of breast cancer or genitalia malignancies. In this study, we aimed to analyze the clinical characteristics and prognosis of multiple primary malignant neoplasms in female patients with breast cancer or genitalia malignancies, as well as further explore the factors that affect the survival. Methods We collected clinical data on 80 female patients diagnosed with multiple primary malignant neoplasms of the breast or genitalia, described their clinical features. Furthermore, we calculated the survival and prognostic factors for 52 participants. Results In our study, the prevalence rate of multiple primary malignant neoplasms was 0.66% (367/55404). Corresponding to female patients with multiple primary malignant neoplasms of breast cancer or genitalia malignancies, it was 1.4% (80/5707). the median age of diagnosis for the first tumor was 48 years, and the median age of diagnosis for the second tumor was 52 years. Regarding the interval, 67.57% (50/74) of patients were within five years. Most tumors were located in the breast (44.68%), followed by the uterus (20.21%), the ovary (17.02%), and the cervix (15.96%). The overall 12-, 36-and 60-month survival rates of the patients were 86.4%, 74.3%, and 69.8%. For the female patients, the stage (III–IV) (P = 0.046), non-radical surgery (P = 0.002), and types of the last tumor (breast cancer or genitalia malignancies) (P = 0.019) were associated with the poor prognosis. Conclusions Female patients with breast cancer or genital malignancies should pay attention to screening for the second tumor, especially within 4 years after the first t…
bibliographic citation: Xiao et al. (2022) Clinical characteristics and prognostic analysis of multiple primary malignant neoplasms in female patients with breast cancer or genitalia malignancies. PeerJ 10:e13528 https://doi.org/10.7717/peerj.13528
date submitted: 2022-01-10
date accepted: 2022-05-11
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiao
  given name: Li
author list: Agent
  family name: Cao
  given name: Tiantian
author list: Agent
  family name: Ou
  given name: Jiali
author list: Agent
  family name: Liang
  given name: Weijiang
doi: 10.7717/peerj.13528
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: ©2022 Xiao et al.
attribution name: Xiao et al.

Contribution of hippocampal BDNF/CREB signaling pathway and gut microbiota to emotional behavior impairment induced by chronic unpredictable mild stress during pregnancy in rats offspring
type: item
type: AcademicArticle
description: Background Numerous studies have shown that exposure to prenatal maternal stress (PMS) is associated with various psychopathological outcomes of offspring. The accumulating evidence linking bacteria in the gut and neurons in the brain (the microbiota-gut-brain axis) has been aconsensus; however, there is a lack of research on the involvement mechanism of gut microbiota in the regulation of the BDNF/CREB signaling pathway in the hippocampus of prenatally stressed offspring. Methods Pregnant rats were subjected to chronic unpredictable mild stress (CUMS) to establish the prenatal maternal stress model. The body weight was measured and the behavioral changes were recorded. Offspring were tested to determine emotional state using sucrose preference test (SPT), open-field test (OFT) and suspended tail test (STT). Gut microbiota was evaluated by sequencing the microbial 16S rRNA V3–V4 region, and the interactive analysis of bacterial community structure and diversity was carried out. The expression of hippocampal BDNF, TrkB and CREB mRNA and proteins were respectively measured using RT-PCR and Western blotting. Results Prenatal maternal stress increased maternal plasma corticosterone levels, slowed maternal weight gain and caused depression-like behaviors (all P < 0.05). In offspring, prenatal maternal stress increased plasma corticosterone levels (P < 0.05) and emotional behavior changes (depression-like state) were observed (P < 0.05). The species abundance, diversity and composition of the offspring’s gut microbiota changed after the maternal stress during pregnancy (P < 0.05). Compared with the control group’s offspring, the species abundance of Lactobacillaceae was dropped, while the abundance of the Muribaculaceae species abundance was risen. Concurrent, changes in the hippocampal structure of the offspring and decreases in expression of BDNF/CREB signaling were noted (P < 0.05). Conclusions Prenatal maternal stress leads to high corticosterone status and abnormal e…
format: application/pdf
format: text/html
creator: Feng Zhao
creator: Kai Wang
creator: Yujun Wen
creator: Xiaohui Chen
creator: Hongya Liu
creator: Faqiu Qi
creator: Youjuan Fu
creator: Jiashu Zhu
creator: Suzhen Guan
creator: Zhihong Liu
subject: Pediatrics
subject: Public Health
subject: Women’s Health
subject: Mental Health
subject: Environmental Health
description: doi:10.7717/peerj.13605
publisher: PeerJ Inc.
rights: © 2022 Zhao et al.
abstract: Background Numerous studies have shown that exposure to prenatal maternal stress (PMS) is associated with various psychopathological outcomes of offspring. The accumulating evidence linking bacteria in the gut and neurons in the brain (the microbiota-gut-brain axis) has been aconsensus; however, there is a lack of research on the involvement mechanism of gut microbiota in the regulation of the BDNF/CREB signaling pathway in the hippocampus of prenatally stressed offspring. Methods Pregnant rats were subjected to chronic unpredictable mild stress (CUMS) to establish the prenatal maternal stress model. The body weight was measured and the behavioral changes were recorded. Offspring were tested to determine emotional state using sucrose preference test (SPT), open-field test (OFT) and suspended tail test (STT). Gut microbiota was evaluated by sequencing the microbial 16S rRNA V3–V4 region, and the interactive analysis of bacterial community structure and diversity was carried out. The expression of hippocampal BDNF, TrkB and CREB mRNA and proteins were respectively measured using RT-PCR and Western blotting. Results Prenatal maternal stress increased maternal plasma corticosterone levels, slowed maternal weight gain and caused depression-like behaviors (all P < 0.05). In offspring, prenatal maternal stress increased plasma corticosterone levels (P < 0.05) and emotional behavior changes (depression-like state) were observed (P < 0.05). The species abundance, diversity and composition of the offspring’s gut microbiota changed after the maternal stress during pregnancy (P < 0.05). Compared with the control group’s offspring, the species abundance of Lactobacillaceae was dropped, while the abundance of the Muribaculaceae species abundance was risen. Concurrent, changes in the hippocampal structure of the offspring and decreases in expression of BDNF/CREB signaling were noted (P < 0.05). Conclusions Prenatal maternal stress leads to high corticosterone status and abnormal e…
bibliographic citation: Zhao et al. (2022) Contribution of hippocampal BDNF/CREB signaling pathway and gut microbiota to emotional behavior impairment induced by chronic unpredictable mild stress during pregnancy in rats offspring. PeerJ 10:e13605 https://doi.org/10.7717/peerj.13605
date submitted: 2022-03-01
date accepted: 2022-05-26
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Feng
author list: Agent
  family name: Wang
  given name: Kai
author list: Agent
  family name: Wen
  given name: Yujun
author list: Agent
  family name: Chen
  given name: Xiaohui
author list: Agent
  family name: Liu
  given name: Hongya
author list: Agent
  family name: Qi
  given name: Faqiu
author list: Agent
  family name: Fu
  given name: Youjuan
author list: Agent
  family name: Zhu
  given name: Jiashu
author list: Agent
  family name: Guan
  given name: Suzhen
author list: Agent
  family name: Liu
  given name: Zhihong
doi: 10.7717/peerj.13605
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: © 2022 Zhao et al.
attribution name: Zhao et al.

Genomics enters the deep learning era
type: item
type: AcademicArticle
description: The tremendous amount of biological sequence data available, combined with the recent methodological breakthrough in deep learning in domains such as computer vision or natural language processing, is leading today to the transformation of bioinformatics through the emergence of deep genomics, the application of deep learning to genomic sequences. We review here the new applications that the use of deep learning enables in the field, focusing on three aspects: the functional annotation of genomes, the sequence determinants of the genome functions and the possibility to write synthetic genomic sequences.
format: application/pdf
format: text/html
creator: Etienne Routhier
creator: Julien Mozziconacci
subject: Bioinformatics
subject: Genomics
subject: Synthetic Biology
subject: Medical Genetics
subject: Computational Science
description: doi:10.7717/peerj.13613
publisher: PeerJ Inc.
rights: © 2022 Routhier and Mozziconacci
abstract: The tremendous amount of biological sequence data available, combined with the recent methodological breakthrough in deep learning in domains such as computer vision or natural language processing, is leading today to the transformation of bioinformatics through the emergence of deep genomics, the application of deep learning to genomic sequences. We review here the new applications that the use of deep learning enables in the field, focusing on three aspects: the functional annotation of genomes, the sequence determinants of the genome functions and the possibility to write synthetic genomic sequences.
bibliographic citation: Routhier et al. (2022) Genomics enters the deep learning era. PeerJ 10:e13613 https://doi.org/10.7717/peerj.13613
date submitted: 2022-01-24
date accepted: 2022-05-30
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Routhier
  given name: Etienne
author list: Agent
  family name: Mozziconacci
  given name: Julien
doi: 10.7717/peerj.13613
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: © 2022 Routhier and Mozziconacci
attribution name: Routhier and Mozziconacci

Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
type: item
type: AcademicArticle
description: Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalv…
format: application/pdf
format: text/html
creator: Stewart M. Edie
creator: Katie S. Collins
creator: David Jablonski
subject: Evolutionary Studies
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.13617
publisher: PeerJ Inc.
rights: © 2022 Edie et al.
abstract: Background Comparative morphology fundamentally relies on the orientation and alignment of specimens. In the era of geometric morphometrics, point-based homologies are commonly deployed to register specimens and their landmarks in a shared coordinate system. However, the number of point-based homologies commonly diminishes with increasing phylogenetic breadth. These situations invite alternative, often conflicting, approaches to alignment. The bivalve shell (Mollusca: Bivalvia) exemplifies a homologous structure with few universally homologous points—only one can be identified across the Class, the shell ‘beak’. Here, we develop an axis-based framework, grounded in the homology of shell features, to orient shells for landmark-based, comparative morphology. Methods Using 3D scans of species that span the disparity of shell morphology across the Class, multiple modes of scaling, translation, and rotation were applied to test for differences in shell shape. Point-based homologies were used to define body axes, which were then standardized to facilitate specimen alignment via rotation. Resulting alignments were compared using pairwise distances between specimen shapes as defined by surface semilandmarks. Results Analysis of 45 possible alignment schemes finds general conformity among the shape differences of ‘typical’ equilateral shells, but the shape differences among atypical shells can change considerably, particularly those with distinctive modes of growth. Each alignment corresponds to a hypothesis about the ecological, developmental, or evolutionary basis of morphological differences, but we suggest orientation via the hinge line for many analyses of shell shape across the Class, a formalization of the most common approach to morphometrics of shell form. This axis-based approach to aligning specimens facilitates the comparison of approximately continuous differences in shape among phylogenetically broad and morphologically disparate samples, not only within bivalv…
bibliographic citation: Edie et al. (2022) Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia). PeerJ 10:e13617 https://doi.org/10.7717/peerj.13617
date submitted: 2022-03-10
date accepted: 2022-06-01
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Edie
  given name: Stewart M.
author list: Agent
  family name: Collins
  given name: Katie S.
author list: Agent
  family name: Jablonski
  given name: David
doi: 10.7717/peerj.13617
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: © 2022 Edie et al.
attribution name: Edie et al.

Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress
type: item
type: AcademicArticle
description: Hydrangea (Hydrangea macrophylla (Thunb.) Ser.) is a famous ornamental plant species with high resistance to aluminum (Al). The aluminum-activated malate transporter (ALMT) family encodes anion channels, which participate in many physiological processes, such as Al tolerance, pH regulation, stomatal movement, and mineral nutrition. However, systematic studies on the gene family have not been reported in hydrangea. In this study, 11 candidate ALMT family members were identified from the transcriptome data for hydrangea, which could be divided into three clusters according to the phylogenetic tree. The protein physicochemical properties, phylogeny, conserved motifs and protein structure were analyzed. The distribution of base conservative motifs of HmALMTs was consistent with that of other species, with a highly conserved WEP motif. Furthermore, tissue-specific analysis showed that most of the HmALMTs were highly expressed in the stem under Al treatment. In addition, overexpression of HmALMT5, HmALMT9 and HmALMT11 in yeasts enhanced their tolerance to Al stress. Therefore, the above results reveal the functional role of HmALMTs underlying the Al tolerance of hydrangea. The present study provides a reference for further research to elucidate the functional mechanism and expression regulation of the ALMT gene family in hydrangea.
format: application/pdf
format: text/html
creator: Ziyi Qin
creator: Shuangshuang Chen
creator: Jing Feng
creator: Huijie Chen
creator: Xiangyu Qi
creator: Huadi Wang
creator: Yanming Deng
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13620
publisher: PeerJ Inc.
rights: © 2022 Qin et al.
abstract: Hydrangea (Hydrangea macrophylla (Thunb.) Ser.) is a famous ornamental plant species with high resistance to aluminum (Al). The aluminum-activated malate transporter (ALMT) family encodes anion channels, which participate in many physiological processes, such as Al tolerance, pH regulation, stomatal movement, and mineral nutrition. However, systematic studies on the gene family have not been reported in hydrangea. In this study, 11 candidate ALMT family members were identified from the transcriptome data for hydrangea, which could be divided into three clusters according to the phylogenetic tree. The protein physicochemical properties, phylogeny, conserved motifs and protein structure were analyzed. The distribution of base conservative motifs of HmALMTs was consistent with that of other species, with a highly conserved WEP motif. Furthermore, tissue-specific analysis showed that most of the HmALMTs were highly expressed in the stem under Al treatment. In addition, overexpression of HmALMT5, HmALMT9 and HmALMT11 in yeasts enhanced their tolerance to Al stress. Therefore, the above results reveal the functional role of HmALMTs underlying the Al tolerance of hydrangea. The present study provides a reference for further research to elucidate the functional mechanism and expression regulation of the ALMT gene family in hydrangea.
bibliographic citation: Qin et al. (2022) Identification of aluminum-activated malate transporters (ALMT) family genes in hydrangea and functional characterization of HmALMT5/9/11 under aluminum stress. PeerJ 10:e13620 https://doi.org/10.7717/peerj.13620
date submitted: 2022-02-22
date accepted: 2022-06-02
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Ziyi
author list: Agent
  family name: Chen
  given name: Shuangshuang
author list: Agent
  family name: Feng
  given name: Jing
author list: Agent
  family name: Chen
  given name: Huijie
author list: Agent
  family name: Qi
  given name: Xiangyu
author list: Agent
  family name: Wang
  given name: Huadi
author list: Agent
  family name: Deng
  given name: Yanming
doi: 10.7717/peerj.13620
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: © 2022 Qin et al.
attribution name: Qin et al.

Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells
type: item
type: AcademicArticle
description: The widespread two-component system (TCS), QseBC, involves vital virulence regulators in Enterobacteriaceae and Pasteurellaceae. Here we studied the function of QseBC in Glaesserella parasuis. A ΔqseBC mutant was constructed using a Glaesserella parasuis serovar 11 clinical strain SC1401 by natural transformation. Immunofluorescence was used to evaluate cellular adhesion, the levels of inflammation and apoptosis. The ability of ΔqseBC and ΔqseC mutant strains to adhere to PAM and MLE-12 cells was significantly reduced. Additionally, by focusing on the clinical signs, H&E, and IFA for inflammation and apoptosis, we found that the ΔqseBC mutant weakened virulence in the murine models. Together, these findings suggest that QseBC plays an important role in the virulence of Glaesserella parasuis.
format: application/pdf
format: text/html
creator: Xuefeng Yan
creator: Ke Dai
creator: Congwei Gu
creator: Zehui Yu
creator: Manli He
creator: Wudian Xiao
creator: Mingde Zhao
creator: Lvqin He
subject: Biochemistry
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.13648
publisher: PeerJ Inc.
rights: © 2022 Yan et al.
abstract: The widespread two-component system (TCS), QseBC, involves vital virulence regulators in Enterobacteriaceae and Pasteurellaceae. Here we studied the function of QseBC in Glaesserella parasuis. A ΔqseBC mutant was constructed using a Glaesserella parasuis serovar 11 clinical strain SC1401 by natural transformation. Immunofluorescence was used to evaluate cellular adhesion, the levels of inflammation and apoptosis. The ability of ΔqseBC and ΔqseC mutant strains to adhere to PAM and MLE-12 cells was significantly reduced. Additionally, by focusing on the clinical signs, H&E, and IFA for inflammation and apoptosis, we found that the ΔqseBC mutant weakened virulence in the murine models. Together, these findings suggest that QseBC plays an important role in the virulence of Glaesserella parasuis.
bibliographic citation: Yan et al. (2022) Deletion of two-component system QseBC weakened virulence of Glaesserella parasuis in a murine acute infection model and adhesion to host cells. PeerJ 10:e13648 https://doi.org/10.7717/peerj.13648
date submitted: 2022-01-14
date accepted: 2022-06-07
issued: 2022-06-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yan
  given name: Xuefeng
author list: Agent
  family name: Dai
  given name: Ke
author list: Agent
  family name: Gu
  given name: Congwei
author list: Agent
  family name: Yu
  given name: Zehui
author list: Agent
  family name: He
  given name: Manli
author list: Agent
  family name: Xiao
  given name: Wudian
author list: Agent
  family name: Zhao
  given name: Mingde
author list: Agent
  family name: He
  given name: Lvqin
doi: 10.7717/peerj.13648
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-24
copyright: ©2022 Yan et al.
attribution name: Yan et al.

Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area
type: item
type: AcademicArticle
description: Coral reefs in Culebra Bay (North Pacific of Costa Rica) are threatened by multiple anthropogenic disturbances including global warming, overfishing, eutrophication, and invasive species outbreaks. It is possible to assist their recovery by implementing ecological restoration techniques. This study used artificial hexagonal steel structures, called “spiders” to compare growth of Pocillopora spp. coral fragments of different sizes. Three initial fragment class sizes were used: 2, 5 and 8 cm, with each class size having 42 initial fragments. Changes in fragment length, width and area were measured monthly from January to December 2020. Results showed an overall survivorship of 70.21%, and no significant differences in survivorship and linear growth rate were detected between class sizes. The linear growth rates are 4.49 ± 1.19 cm year−1, 5.35 ± 1.48 cm year−1 and 3.25 ± 2.22 cm year−1 for the 2, 5 and 8 cm initial class sizes, respectively. Our results do not show significant differences in growth rates between the different initial fragment sizes. However, since small fragments (2 cm) present higher mortality during the first month, we recommend using larger fragments. In addition, coral fragments grew 48% more during the non-upwelling season, which may suggest that it might be more effective and safer to start the restoration efforts during this period.
format: application/pdf
format: text/html
creator: Lisa Combillet
creator: Sònia Fabregat-Malé
creator: Sebastián Mena
creator: José Andrés Marín-Moraga
creator: Monica Gutierrez
creator: Juan José Alvarado
subject: Conservation Biology
subject: Ecosystem Science
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.13248
publisher: PeerJ Inc.
rights: © 2022 Combillet et al.
abstract: Coral reefs in Culebra Bay (North Pacific of Costa Rica) are threatened by multiple anthropogenic disturbances including global warming, overfishing, eutrophication, and invasive species outbreaks. It is possible to assist their recovery by implementing ecological restoration techniques. This study used artificial hexagonal steel structures, called “spiders” to compare growth of Pocillopora spp. coral fragments of different sizes. Three initial fragment class sizes were used: 2, 5 and 8 cm, with each class size having 42 initial fragments. Changes in fragment length, width and area were measured monthly from January to December 2020. Results showed an overall survivorship of 70.21%, and no significant differences in survivorship and linear growth rate were detected between class sizes. The linear growth rates are 4.49 ± 1.19 cm year−1, 5.35 ± 1.48 cm year−1 and 3.25 ± 2.22 cm year−1 for the 2, 5 and 8 cm initial class sizes, respectively. Our results do not show significant differences in growth rates between the different initial fragment sizes. However, since small fragments (2 cm) present higher mortality during the first month, we recommend using larger fragments. In addition, coral fragments grew 48% more during the non-upwelling season, which may suggest that it might be more effective and safer to start the restoration efforts during this period.
bibliographic citation: Combillet et al. (2022) Pocillopora spp. growth analysis on restoration structures in an Eastern Tropical Pacific upwelling area. PeerJ 10:e13248 https://doi.org/10.7717/peerj.13248
date submitted: 2021-10-01
date accepted: 2022-03-20
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Combillet
  given name: Lisa
author list: Agent
  family name: Fabregat-Malé
  given name: Sònia
author list: Agent
  family name: Mena
  given name: Sebastián
author list: Agent
  family name: Marín-Moraga
  given name: José Andrés
author list: Agent
  family name: Gutierrez
  given name: Monica
author list: Agent
  family name: Alvarado
  given name: Juan José
doi: 10.7717/peerj.13248
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: © 2022 Combillet et al.
attribution name: Combillet et al.

Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC)
type: item
type: AcademicArticle
description: The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC s…
format: application/pdf
format: text/html
creator: Neetu Tyagi
creator: Rahila Sardar
creator: Dinesh Gupta
subject: Bioinformatics
subject: Virology
subject: COVID-19
description: doi:10.7717/peerj.13562
publisher: PeerJ Inc.
rights: © 2022 Tyagi et al.
abstract: The ongoing prevailing COVID-19 pandemic caused by SARS-CoV-2 is becoming one of the major global health concerns worldwide. The SARS-CoV-2 genome encodes spike (S) glycoprotein that plays a very crucial role in viral entry into the host cell via binding of its receptor binding domain (RBD) to the host angiotensin converting enzyme 2 (ACE2) receptor. The continuously evolving SARS-CoV-2 genome results in more severe and transmissible variants characterized by the emergence of novel mutations called ‘variants of concern’ (VOC). The currently designated alpha, beta, gamma, delta and omicron VOC are the focus of this study due to their high transmissibility, increased virulence, and concerns for decreased effectiveness of the available vaccines. In VOC, the spike (S) gene and other non-structural protein mutations may affect the efficacies of the approved COVID-19 vaccines. To understand the diversity of SARS-CoV-2, several studies have been performed on a limited number of sequences. However, only a few studies have focused on codon usage bias (CUBs) pattern analysis of all the VOC strains. Therefore, to evaluate the evolutionary divergence of all VOC S-genes, we performed CUBs analysis on 300,354 sequences to understand the evolutionary relationship with its adaptation in different hosts, i.e., humans, bats, and pangolins. Base composition and RSCU analysis revealed the presence of 20 preferred AU-ended and 10 under-preferred GC-ended codons. In addition, CpG was found to be depleted, which may be attributable to the adaptive response by viruses to escape from the host defense process. Moreover, the ENC values revealed a higher bias in codon usage in the VOC S-gene. Further, the neutrality plot analysis demonstrated that S-genes analyzed in this study are under 83.93% influence of natural selection, suggesting its pivotal role in shaping the CUBs. The CUBs pattern of S-genes was found to be very similar among all the VOC strains. Interestingly, we observed that VOC s…
bibliographic citation: Tyagi et al. (2022) Natural selection plays a significant role in governing the codon usage bias in the novel SARS-CoV-2 variants of concern (VOC). PeerJ 10:e13562 https://doi.org/10.7717/peerj.13562
date submitted: 2022-02-11
date accepted: 2022-05-19
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tyagi
  given name: Neetu
author list: Agent
  family name: Sardar
  given name: Rahila
author list: Agent
  family name: Gupta
  given name: Dinesh
doi: 10.7717/peerj.13562
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: © 2022 Tyagi et al.
attribution name: Tyagi et al.

Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche
type: item
type: AcademicArticle
description: Caddisfly larvae commonly inhabit freshwater ecosystems, where they often create multi-species aggregations. However, while several strategies have been developed to avoid or reduce inter- and intraspecific interactions, most species choose the same time to seek a suitable place for pupation, which can increase competition. The current study assesses the competitive interactions among larvae (5th instar) of three co-existing Hydropsyche species, viz. H. contubernalis, H. pellucidula, and H. modesta, analysing their direct one-on-one interaction and various morphological features, such as size, weight, and mandibles. More than half of the interspecific conflicts ended with a draw, and 80% of intraspecific interactions with a decisive outcome. In fights between species, H. pellucidula was the most successful, and H. modesta the weakest. Our results confirm that among the larvae, competitive interactions were usually decided by body size, especially that of the head capsule. Although wider head capsule and higher weight were advantageous for ~60% of winning larvae, there were no distinct winning species. The chewing mouthpart turned out to be supportive in the fight: regardless of the species, longer and wider mandibles were significant for winning specimens, but not the distance between mandibles. Hence, acquiring a suitable place for pupation is determined by the possession of certain features enhancing the fighting potential of individual larvae, which does not exclude any species from the possibility of closing the life cycle. Future studies on interactions among caddisfly larvae could include experience in fights, volitional features and stridulation (not tested).
format: application/pdf
format: text/html
creator: Mariusz Tszydel
creator: Dagmara Błońska
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.13576
publisher: PeerJ Inc.
rights: © 2022 Tszydel and Błońska
abstract: Caddisfly larvae commonly inhabit freshwater ecosystems, where they often create multi-species aggregations. However, while several strategies have been developed to avoid or reduce inter- and intraspecific interactions, most species choose the same time to seek a suitable place for pupation, which can increase competition. The current study assesses the competitive interactions among larvae (5th instar) of three co-existing Hydropsyche species, viz. H. contubernalis, H. pellucidula, and H. modesta, analysing their direct one-on-one interaction and various morphological features, such as size, weight, and mandibles. More than half of the interspecific conflicts ended with a draw, and 80% of intraspecific interactions with a decisive outcome. In fights between species, H. pellucidula was the most successful, and H. modesta the weakest. Our results confirm that among the larvae, competitive interactions were usually decided by body size, especially that of the head capsule. Although wider head capsule and higher weight were advantageous for ~60% of winning larvae, there were no distinct winning species. The chewing mouthpart turned out to be supportive in the fight: regardless of the species, longer and wider mandibles were significant for winning specimens, but not the distance between mandibles. Hence, acquiring a suitable place for pupation is determined by the possession of certain features enhancing the fighting potential of individual larvae, which does not exclude any species from the possibility of closing the life cycle. Future studies on interactions among caddisfly larvae could include experience in fights, volitional features and stridulation (not tested).
bibliographic citation: Tszydel et al. (2022) Intra- and interspecific competition resulting from spatial coexistence among larvae of closely-related caddisflies from the genus Hydropsyche. PeerJ 10:e13576 https://doi.org/10.7717/peerj.13576
date submitted: 2022-02-09
date accepted: 2022-05-22
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tszydel
  given name: Mariusz
author list: Agent
  family name: Błońska
  given name: Dagmara
doi: 10.7717/peerj.13576
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: © 2022 Tszydel and Błońska
attribution name: Tszydel and Błońska

Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease
type: item
type: AcademicArticle
description: Objective Patients with Parkinson’s disease (PD) have an obvious motor inhibition disorder, which is closely related to their motor symptoms. Although previous studies have shown that exercise can improve their inhibition deficits, the effect of exercise on different types of inhibition (proactive and reactive inhibition) has not been addressed. Methods We used a behavioral paradigm combined with a series of questionnaires to explore the effect of long-term exercise on different types of motor inhibition in 59 patients with PD aged 55–75 years. According to the intensity and frequency of exercise, the participants were divided into regular-exercise and no-exercise groups. To obtain the average reference value for inhibition ability at the same age, we also recruited 30 healthy elderly people as controls. Results The main defect in the motor inhibition of PD is reactive inhibition, while proactive inhibition has no obvious differences compared with healthy controls. Additionally, compared with the non-exercise group, PD in the exercise group showed significantly better reaction speeds and reactive control ability, fewer motor symptoms and negative emotions. Conclusions Taken together, the motor inhibition defects of patients with PD affect only reactive inhibition. In addition, PD with exercise reported fewer negative emotions than that of the non-exercise group, indicating that exercise can relieve negative emotions and improve behavioral symptoms and quality of life in PD to a certain extent. We demonstrate for the first time that exercise has and can improve reactive inhibition in PD patients and has no effect on proactive inhibition.
format: application/pdf
format: text/html
creator: Zhen Wang
creator: Yan-Ling Pi
creator: Yin Wu
creator: Jianing Wei
creator: Yuting Li
creator: Jian Zhang
subject: Cognitive Disorders
subject: Psychiatry and Psychology
subject: Rehabilitation
description: doi:10.7717/peerj.13628
publisher: PeerJ Inc.
rights: © 2022 Wang et al.
abstract: Objective Patients with Parkinson’s disease (PD) have an obvious motor inhibition disorder, which is closely related to their motor symptoms. Although previous studies have shown that exercise can improve their inhibition deficits, the effect of exercise on different types of inhibition (proactive and reactive inhibition) has not been addressed. Methods We used a behavioral paradigm combined with a series of questionnaires to explore the effect of long-term exercise on different types of motor inhibition in 59 patients with PD aged 55–75 years. According to the intensity and frequency of exercise, the participants were divided into regular-exercise and no-exercise groups. To obtain the average reference value for inhibition ability at the same age, we also recruited 30 healthy elderly people as controls. Results The main defect in the motor inhibition of PD is reactive inhibition, while proactive inhibition has no obvious differences compared with healthy controls. Additionally, compared with the non-exercise group, PD in the exercise group showed significantly better reaction speeds and reactive control ability, fewer motor symptoms and negative emotions. Conclusions Taken together, the motor inhibition defects of patients with PD affect only reactive inhibition. In addition, PD with exercise reported fewer negative emotions than that of the non-exercise group, indicating that exercise can relieve negative emotions and improve behavioral symptoms and quality of life in PD to a certain extent. We demonstrate for the first time that exercise has and can improve reactive inhibition in PD patients and has no effect on proactive inhibition.
bibliographic citation: Wang et al. (2022) Selective effects of exercise on reactive and proactive inhibition in Parkinson’s disease. PeerJ 10:e13628 https://doi.org/10.7717/peerj.13628
date submitted: 2022-03-02
date accepted: 2022-06-02
issued: 2022-06-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhen
author list: Agent
  family name: Pi
  given name: Yan-Ling
author list: Agent
  family name: Wu
  given name: Yin
author list: Agent
  family name: Wei
  given name: Jianing
author list: Agent
  family name: Li
  given name: Yuting
author list: Agent
  family name: Zhang
  given name: Jian
author list: Agent
  family name: Wang
  given name: Zhen
doi: 10.7717/peerj.13628
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-06-23
copyright: ©2022 Wang et al.
attribution name: Wang et al.

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