PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East
items: Chinese striped-neck turtles vocalize underwater and show differences in peak frequency among different age and sex groups
items: Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber
items: Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies
items: Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil
items: Systematic identification of smORFs in domestic silkworm (Bombyx mori)
items: A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain)
items: A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology
items: Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study
items: Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems

Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East
type: item
type: AcademicArticle
description: The taxonomic concept of the genus Stenocaris Sars, 1909 is uncertain because none of the synapomorphies for the species of Stenocaris are defined. Detailed comparison of previous records of Stenocaris minor (T. Scott, 1892) from different localities reveals that this species represents a species complex composed of two species, S. minor s. str. and S. minor sensu Cottarelli & Venanzetti, 1989. Because the latter species has fundamental differences in the nature of the fifth leg in females and the sexual dimorphism of the second leg in males, we propose a new species for S. minor sensu Cottarelli & Venanzetti, 1989, S. figaroloensis sp. nov. We also suggest that S. minor sensu Apostolov, 1971, S. minor sensu Marinov, 1971, and S. minor sensu Apostolov & Marinov, 1988 from the Black Sea and S. minor sensu Wilson, 1932 from North America should be relegated to species inquirenda in the genus. Taxonomic review of the morphology of all Stenocaris species indicated that the generic concept must be restricted to accommodate S. minor s. str., S. gracilis Sars, 1909, S. intermedia Itô, 1972, S. figaroloensis sp. nov., and the South Korean new species, S. marcida sp. nov., based on the synapomorphic condition of the confluent fifth leg in males. As a result of our analysis, two Stenocaris species, S. baltica Arlt, 1983 and S. pygmaea Noodt, 1955, are transferred to the genus Vermicaris Kornev & Chertoprud, 2008 as V. baltica (Arlt, 1983) comb. nov. and V. pygmaea (Noodt, 1955) comb. nov. based on the synapomorphic characters of a reduced condition of the second and fifth legs. Additionally, S. arenicola Wilson, 1932 and S. kliei (Kunz, 1938) are allocated to a new genus, Huysicaris gen. nov., mainly characterized by obvious caudal rami with a recurved dorsal spinous process and convex inner margins, as H. arenicola (Wilson, 1932) comb. nov. and H. kliei (Kunz, 1938) comb. nov. A marine interstitial harpacticoid collected from the subtidal substrate off Dok-do Island in the E…
format: application/pdf
format: text/html
creator: Jong Guk Kim
creator: Kyuhee Cho
creator: Seong Myeong Yoon
creator: Jimin Lee
subject: Biodiversity
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14623
publisher: PeerJ Inc.
rights: © 2023 Kim et al.
abstract: The taxonomic concept of the genus Stenocaris Sars, 1909 is uncertain because none of the synapomorphies for the species of Stenocaris are defined. Detailed comparison of previous records of Stenocaris minor (T. Scott, 1892) from different localities reveals that this species represents a species complex composed of two species, S. minor s. str. and S. minor sensu Cottarelli & Venanzetti, 1989. Because the latter species has fundamental differences in the nature of the fifth leg in females and the sexual dimorphism of the second leg in males, we propose a new species for S. minor sensu Cottarelli & Venanzetti, 1989, S. figaroloensis sp. nov. We also suggest that S. minor sensu Apostolov, 1971, S. minor sensu Marinov, 1971, and S. minor sensu Apostolov & Marinov, 1988 from the Black Sea and S. minor sensu Wilson, 1932 from North America should be relegated to species inquirenda in the genus. Taxonomic review of the morphology of all Stenocaris species indicated that the generic concept must be restricted to accommodate S. minor s. str., S. gracilis Sars, 1909, S. intermedia Itô, 1972, S. figaroloensis sp. nov., and the South Korean new species, S. marcida sp. nov., based on the synapomorphic condition of the confluent fifth leg in males. As a result of our analysis, two Stenocaris species, S. baltica Arlt, 1983 and S. pygmaea Noodt, 1955, are transferred to the genus Vermicaris Kornev & Chertoprud, 2008 as V. baltica (Arlt, 1983) comb. nov. and V. pygmaea (Noodt, 1955) comb. nov. based on the synapomorphic characters of a reduced condition of the second and fifth legs. Additionally, S. arenicola Wilson, 1932 and S. kliei (Kunz, 1938) are allocated to a new genus, Huysicaris gen. nov., mainly characterized by obvious caudal rami with a recurved dorsal spinous process and convex inner margins, as H. arenicola (Wilson, 1932) comb. nov. and H. kliei (Kunz, 1938) comb. nov. A marine interstitial harpacticoid collected from the subtidal substrate off Dok-do Island in the E…
bibliographic citation: Kim et al. (2023) Taxonomic review of the genus Stenocaris Sars (Copepoda, Harpacticoida, Cylindropsyllidae), with (re)descriptions of two Stenocaris species from the Far East. PeerJ 11:e14623 https://doi.org/10.7717/peerj.14623
date submitted: 2022-07-27
date accepted: 2022-12-02
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kim
  given name: Jong Guk
author list: Agent
  family name: Cho
  given name: Kyuhee
author list: Agent
  family name: Yoon
  given name: Seong Myeong
author list: Agent
  family name: Lee
  given name: Jimin
doi: 10.7717/peerj.14623
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Kim et al.
attribution name: Kim et al.

Chinese striped-neck turtles vocalize underwater and show differences in peak frequency among different age and sex groups
type: item
type: AcademicArticle
description: Background Turtle vocalizations play an important role throughout their lives by expressing individual information (position, emotion, or physiological status), reflecting mating preferences, and synchronizing incubation. The Chinese striped-neck turtle (Mauremys sinensis) is one of the most widely distributed freshwater turtles in China, whose wild population is critically endangered. However, its vocalization has not been studied, which can be the basis for behavioral and ecological studies. Methods Five different sex–age groups of turtles were recorded underwater in a soundproof room. Cluster analysis and principal component analysis for classification of Chinese striped-neck turtle calls were unreasonable. The turtle calls were manually sought using visual and aural inspection of the recordings in Raven Pro 1.5 software and classified according to differences perceived through auditory inspection and the morphological characteristics of the spectrograms. The results of similarity analysis verified the reliability of manual classification. We compared the peak frequency of the calls among different age and sex groups. Results We identified ten M. sinensis call types, displayed their spectra and waveforms, and described their auditory characteristics. Most calls produced by the turtles were low-frequency. Some high-frequency call types, that are common in other turtle species were also produced. Similar to other turtles, the Chinese striped-neck turtle generates harmonic vocalizations. Courtship behaviors were observed when one of the call types occurred in the mixed-sex group. Adult females produced more high-frequency call types, and subadult males had higher vocalizations than other groups. These results provide a basis for future research on the function of vocalizations, field monitoring, and conservation of this species.
format: application/pdf
format: text/html
creator: Lu Zhou
creator: Jinhong Lei
creator: Xiaofei Zhai
creator: Haitao Shi
creator: Jichao Wang
subject: Animal Behavior
subject: Ecology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14628
publisher: PeerJ Inc.
rights: © 2023 Zhou et al.
abstract: Background Turtle vocalizations play an important role throughout their lives by expressing individual information (position, emotion, or physiological status), reflecting mating preferences, and synchronizing incubation. The Chinese striped-neck turtle (Mauremys sinensis) is one of the most widely distributed freshwater turtles in China, whose wild population is critically endangered. However, its vocalization has not been studied, which can be the basis for behavioral and ecological studies. Methods Five different sex–age groups of turtles were recorded underwater in a soundproof room. Cluster analysis and principal component analysis for classification of Chinese striped-neck turtle calls were unreasonable. The turtle calls were manually sought using visual and aural inspection of the recordings in Raven Pro 1.5 software and classified according to differences perceived through auditory inspection and the morphological characteristics of the spectrograms. The results of similarity analysis verified the reliability of manual classification. We compared the peak frequency of the calls among different age and sex groups. Results We identified ten M. sinensis call types, displayed their spectra and waveforms, and described their auditory characteristics. Most calls produced by the turtles were low-frequency. Some high-frequency call types, that are common in other turtle species were also produced. Similar to other turtles, the Chinese striped-neck turtle generates harmonic vocalizations. Courtship behaviors were observed when one of the call types occurred in the mixed-sex group. Adult females produced more high-frequency call types, and subadult males had higher vocalizations than other groups. These results provide a basis for future research on the function of vocalizations, field monitoring, and conservation of this species.
bibliographic citation: Zhou et al. (2023) Chinese striped-neck turtles vocalize underwater and show differences in peak frequency among different age and sex groups. PeerJ 11:e14628 https://doi.org/10.7717/peerj.14628
date submitted: 2022-02-16
date accepted: 2022-12-02
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhou
  given name: Lu
author list: Agent
  family name: Lei
  given name: Jinhong
author list: Agent
  family name: Zhai
  given name: Xiaofei
author list: Agent
  family name: Shi
  given name: Haitao
author list: Agent
  family name: Wang
  given name: Jichao
doi: 10.7717/peerj.14628
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: ©2023 Zhou et al.
attribution name: Zhou et al.

Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber
type: item
type: AcademicArticle
description: Background The calmodulin-like (CML) protein is a crucial Ca2+-binding protein that can sense and conduct the Ca2+ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable. Methods In this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR). Results Forty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development-related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs.
format: application/pdf
format: text/html
creator: Yunfen Liu
creator: Feilong Yin
creator: Lingyan Liao
creator: Liang Shuai
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14637
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Background The calmodulin-like (CML) protein is a crucial Ca2+-binding protein that can sense and conduct the Ca2+ signal in response to extracellular stimuli. The CML protein families have been identified and characterized in many species. Nevertheless, scarce information on cucumber CML is retrievable. Methods In this study, bioinformatic analyses, including gene structure, conserved domain, phylogenetic relationship, chromosome distribution, and gene synteny, were comprehensively performed to identify and characterize CsCML gene members. Spatiotemporal expression analysis in different organs and environment conditions were assayed with real-time quantitative polymerase chain reaction (qRT-PCR). Results Forty-four CsCMLs family members were well characterized, and the results showed that the 44 CsCML proteins contained one to four EF-hand domains without other functional domains. Most of the CsCML proteins were intron-less and unevenly distributed on seven chromosomes; two tandemly duplicated gene pairs and three segmentally duplicated gene pairs were identified in the cucumber genome. Cis-acting element analysis showed that the hormone, stress, and plant growth and development-related elements were in the promotor regions. In addition, spatiotemporal expression analysis revealed distinctive expression patterns for CsCML genes in different tissues and environmental conditions, and a putative protein interaction network also confirmed their potential role in responding to various stimuli. These results provide a foundation for understanding CsCMLs and provide a theoretical basis for further study of the physiological functions of CsCMLs.
bibliographic citation: Liu et al. (2023) Genome-wide identification and expression analysis of calmodulin-like proteins in cucumber. PeerJ 11:e14637 https://doi.org/10.7717/peerj.14637
date submitted: 2022-09-13
date accepted: 2022-12-05
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yunfen
author list: Agent
  family name: Yin
  given name: Feilong
author list: Agent
  family name: Liao
  given name: Lingyan
author list: Agent
  family name: Shuai
  given name: Liang
doi: 10.7717/peerj.14637
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies
type: item
type: AcademicArticle
description: The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms’ shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundanc…
format: application/pdf
format: text/html
creator: Joyce Dutra
creator: Rosimeire Gomes
creator: Glen Jasper Yupanqui García
creator: Danitza Xiomara Romero-Cale
creator: Mariana Santos Cardoso
creator: Vinicius Waldow
creator: Claudia Groposo
creator: Rubens N. Akamine
creator: Maira Sousa
creator: Henrique Figueiredo
creator: Vasco Azevedo
creator: Aristóteles Góes-Neto
subject: Bioinformatics
subject: Microbiology
description: doi:10.7717/peerj.14642
publisher: PeerJ Inc.
rights: © 2023 Dutra et al.
abstract: The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms’ shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundanc…
bibliographic citation: Dutra et al. (2023) Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies. PeerJ 11:e14642 https://doi.org/10.7717/peerj.14642
date submitted: 2022-08-03
date accepted: 2022-12-05
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dutra
  given name: Joyce
author list: Agent
  family name: Gomes
  given name: Rosimeire
author list: Agent
  family name: Yupanqui García
  given name: Glen Jasper
author list: Agent
  family name: Romero-Cale
  given name: Danitza Xiomara
author list: Agent
  family name: Santos Cardoso
  given name: Mariana
author list: Agent
  family name: Waldow
  given name: Vinicius
author list: Agent
  family name: Groposo
  given name: Claudia
author list: Agent
  family name: Akamine
  given name: Rubens N.
author list: Agent
  family name: Sousa
  given name: Maira
author list: Agent
  family name: Figueiredo
  given name: Henrique
author list: Agent
  family name: Azevedo
  given name: Vasco
author list: Agent
  family name: Góes-Neto
  given name: Aristóteles
doi: 10.7717/peerj.14642
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Dutra et al.
attribution name: Dutra et al.

Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil
type: item
type: AcademicArticle
description: The construction of high-speed roads has resulted in large amounts of steep and exposed cut slopes, posing more potential hazards in areas with mountains and hills. Vegetation restoration is an effective and environmentally-friendly way to restore exposed slopes using outside soil spray seeding, though it is difficult to establish a vegetation cover. Spraying artificial soil on high and steep slopes is a challenging task as it is difficult to keep the fluid mixture on sloped surfaces. Because of these challenges, this study applied different combinations of cement and soil aggregates in artificial soil, measuring final soil properties after one growing season. Experimental results showed that there were substantial differences in all basic soil parameters and in the soil quality index after different treatments. In particular, adding 5–10% cement content could improve the adhesion of artificial soil without remarkably reducing soil quality; adding 0.09% of soil aggregate was also beneficial to soil nutrient availability. These findings indicate that the combination of cement and soil aggregates could be applied in artificial soils for the ecological restoration of steep slope vegetation. Adding cement to the soil increased the alkaline levels of the soil, so it is important to reduce artificial soil pH in the future. The application of a cement and soil aggregate should be considered in the field for the ecological restoration of slope vegetation, and the impact of this addition on slope stability and vegetation growth should be explored with further research.
format: application/pdf
format: text/html
creator: Zhuxin Mao
creator: Qian Li
creator: Yuchao Wang
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.14657
publisher: PeerJ Inc.
rights: © 2023 Mao et al.
abstract: The construction of high-speed roads has resulted in large amounts of steep and exposed cut slopes, posing more potential hazards in areas with mountains and hills. Vegetation restoration is an effective and environmentally-friendly way to restore exposed slopes using outside soil spray seeding, though it is difficult to establish a vegetation cover. Spraying artificial soil on high and steep slopes is a challenging task as it is difficult to keep the fluid mixture on sloped surfaces. Because of these challenges, this study applied different combinations of cement and soil aggregates in artificial soil, measuring final soil properties after one growing season. Experimental results showed that there were substantial differences in all basic soil parameters and in the soil quality index after different treatments. In particular, adding 5–10% cement content could improve the adhesion of artificial soil without remarkably reducing soil quality; adding 0.09% of soil aggregate was also beneficial to soil nutrient availability. These findings indicate that the combination of cement and soil aggregates could be applied in artificial soils for the ecological restoration of steep slope vegetation. Adding cement to the soil increased the alkaline levels of the soil, so it is important to reduce artificial soil pH in the future. The application of a cement and soil aggregate should be considered in the field for the ecological restoration of slope vegetation, and the impact of this addition on slope stability and vegetation growth should be explored with further research.
bibliographic citation: Mao et al. (2023) Research on the application of a cement and soil aggregate for the ecological restoration of vegetation in artificial soil. PeerJ 11:e14657 https://doi.org/10.7717/peerj.14657
date submitted: 2022-04-21
date accepted: 2022-12-08
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mao
  given name: Zhuxin
author list: Agent
  family name: Li
  given name: Qian
author list: Agent
  family name: Wang
  given name: Yuchao
doi: 10.7717/peerj.14657
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: ©2023 Mao et al.
attribution name: Mao et al.

Systematic identification of smORFs in domestic silkworm (Bombyx mori)
type: item
type: AcademicArticle
description: The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species.
format: application/pdf
format: text/html
creator: Linrong Wan
creator: Wenfu Xiao
creator: Ziyan Huang
creator: Anlian Zhou
creator: Yaming Jiang
creator: Bangxing Zou
creator: Binbin Liu
creator: Cao Deng
creator: Youhong Zhang
subject: Agricultural Science
subject: Bioinformatics
subject: Entomology
subject: Genomics
subject: Zoology
description: doi:10.7717/peerj.14682
publisher: PeerJ Inc.
rights: © 2022 Wan et al.
abstract: The silkworm (Bombyx mori) is not only an excellent model species, but also an important agricultural economic insect. Taking it as the research object, its advantages of low maintenance cost and no biohazard risks are considered. Small open reading frames (smORFs) are an important class of genomic elements that can produce bioactive peptides. However, the smORFs in silkworm had been poorly identified and studied. To further study the smORFs in silkworm, systematic genome-wide identification is essential. Here, we identified and analyzed smORFs in the silkworm using comprehensive methods. Our results showed that at least 738 highly reliable smORFs were found in B. mori and that 34,401 possible smORFs were partially supported. We also identified some differentially expressed and tissue-specific-expressed smORFs, which may be closely related to the characteristics and functions of the tissues. This article provides a basis for subsequent research on smORFs in silkworm, and also hopes to provide a reference point for future research methods for smORFs in other species.
bibliographic citation: Wan et al. (2023) Systematic identification of smORFs in domestic silkworm (Bombyx mori). PeerJ 11:e14682 https://doi.org/10.7717/peerj.14682
date submitted: 2022-10-12
date accepted: 2022-12-13
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wan
  given name: Linrong
author list: Agent
  family name: Xiao
  given name: Wenfu
author list: Agent
  family name: Huang
  given name: Ziyan
author list: Agent
  family name: Zhou
  given name: Anlian
author list: Agent
  family name: Jiang
  given name: Yaming
author list: Agent
  family name: Zou
  given name: Bangxing
author list: Agent
  family name: Liu
  given name: Binbin
author list: Agent
  family name: Deng
  given name: Cao
author list: Agent
  family name: Zhang
  given name: Youhong
doi: 10.7717/peerj.14682
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: ©2022 Wan et al.
attribution name: Wan et al.

A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain)
type: item
type: AcademicArticle
description: Hybotidae fly species, also known as dance flies, in Cretaceous ambers have been described from Lebanon, France, Myanmar, Russia, and Canada. Here we describe Grimaldipeza coelica gen. et sp. n., and recognize another two un-named species, in Spanish amber from the middle Albian El Soplao and lower Cenomanian La Hoya outcrops. The fore tibial gland is present in the new genus, which is characteristic of the family Hybotidae. We compare Grimaldipeza coelica gen. et sp. n. with the holotypes of Trichinites cretaceus Hennig, 1970 and Ecommocydromia difficilis Schlüter, 1978, and clarify some morphological details present in the latter two species. Further taxonomic placement beyond family of the here described new genus was not possible and remains incertae sedis within Hybotidae until extant subfamilies are better defined. We provide new paleoecological data of the hybotids, together with paleogeographical and life paleoenvironmental notes. A table with the known Cretaceous Hybotidae is provided. Furthermore, the La Hoya amber-bearing outcrop is described in detail, filling the information gap for this deposit.
format: application/pdf
format: text/html
creator: Mónica M. Solórzano-Kraemer
creator: Bradley J. Sinclair
creator: Antonio Arillo
creator: Sergio Álvarez-Parra
subject: Biodiversity
subject: Entomology
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.14692
publisher: PeerJ Inc.
rights: © 2023 Solórzano-Kraemer et al.
abstract: Hybotidae fly species, also known as dance flies, in Cretaceous ambers have been described from Lebanon, France, Myanmar, Russia, and Canada. Here we describe Grimaldipeza coelica gen. et sp. n., and recognize another two un-named species, in Spanish amber from the middle Albian El Soplao and lower Cenomanian La Hoya outcrops. The fore tibial gland is present in the new genus, which is characteristic of the family Hybotidae. We compare Grimaldipeza coelica gen. et sp. n. with the holotypes of Trichinites cretaceus Hennig, 1970 and Ecommocydromia difficilis Schlüter, 1978, and clarify some morphological details present in the latter two species. Further taxonomic placement beyond family of the here described new genus was not possible and remains incertae sedis within Hybotidae until extant subfamilies are better defined. We provide new paleoecological data of the hybotids, together with paleogeographical and life paleoenvironmental notes. A table with the known Cretaceous Hybotidae is provided. Furthermore, the La Hoya amber-bearing outcrop is described in detail, filling the information gap for this deposit.
bibliographic citation: Solórzano-Kraemer et al. (2023) A new genus of dance fly (Diptera: Empidoidea: Hybotidae) from Cretaceous Spanish ambers and introduction to the fossiliferous amber outcrop of La Hoya (Castellón Province, Spain). PeerJ 11:e14692 https://doi.org/10.7717/peerj.14692
date submitted: 2022-09-23
date accepted: 2022-12-14
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solórzano-Kraemer
  given name: Mónica M.
author list: Agent
  family name: J. Sinclair
  given name: Bradley
author list: Agent
  family name: Arillo
  given name: Antonio
author list: Agent
  family name: Álvarez-Parra
  given name: Sergio
doi: 10.7717/peerj.14692
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Solórzano-Kraemer et al.
attribution name: Solórzano-Kraemer et al.

A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology
type: item
type: AcademicArticle
description: After its original description, the Middle Miocene gekkotan Palaeogekko risgoviensis remained an enigma for palaeontologists due to a rather poor knowledge of its osteology and relationships. Coming from a single locality in southern Germany, this gecko lived in central Europe during a period when a single gekkotan lineage (i.e., euleptine sphaerodactylids) is confidently reported to have inhabited the continent. However, it is unclear whether P. risgoviensis may represent a member of this same lineage or a second clade of Gekkota. In order to shed light on this issue, the type material of P. risgoviensis is here redescribed, refigured and extensively compared with extinct and extant geckos from Europe. A phylogenetic analysis is also conducted in order to investigate its relationships. The new observations confirm the validity of the German species as a distinct taxon, and exclude the previously-suggested chimeric status of the type material of this gecko (with the exception of a single dentary included in the type series, which clearly belong to a different lizard). Phylogenetic relationships of Palaeogekko are still unclear, though, with different positions within the gekkotan tree recovered for the taxon. Nevertheless, it is confidently supported as a non-eublepharid gekkonoid, in agreement with hypothesys presented by other scholars.
format: application/pdf
format: text/html
creator: Andrea Villa
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14717
publisher: PeerJ Inc.
rights: © 2023 Villa
abstract: After its original description, the Middle Miocene gekkotan Palaeogekko risgoviensis remained an enigma for palaeontologists due to a rather poor knowledge of its osteology and relationships. Coming from a single locality in southern Germany, this gecko lived in central Europe during a period when a single gekkotan lineage (i.e., euleptine sphaerodactylids) is confidently reported to have inhabited the continent. However, it is unclear whether P. risgoviensis may represent a member of this same lineage or a second clade of Gekkota. In order to shed light on this issue, the type material of P. risgoviensis is here redescribed, refigured and extensively compared with extinct and extant geckos from Europe. A phylogenetic analysis is also conducted in order to investigate its relationships. The new observations confirm the validity of the German species as a distinct taxon, and exclude the previously-suggested chimeric status of the type material of this gecko (with the exception of a single dentary included in the type series, which clearly belong to a different lizard). Phylogenetic relationships of Palaeogekko are still unclear, though, with different positions within the gekkotan tree recovered for the taxon. Nevertheless, it is confidently supported as a non-eublepharid gekkonoid, in agreement with hypothesys presented by other scholars.
bibliographic citation: Villa (2023) A redescription of Palaeogekko risgoviensis (Squamata, Gekkota) from the Middle Miocene of Germany, with new data on its morphology. PeerJ 11:e14717 https://doi.org/10.7717/peerj.14717
date submitted: 2022-10-26
date accepted: 2022-12-19
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Villa
  given name: Andrea
doi: 10.7717/peerj.14717
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Villa
attribution name: Villa

Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study
type: item
type: AcademicArticle
description: Background Tensiomyography (TMG) is a non-invasive instrument for measuring mechanical muscle contraction characteristics and measuring the maximum displacement of the muscle belly in the radial direction with respect to the muscle and the time needed to achieve this from electrical stimulation. There have been only been a reports of TMG in healthy adults. A systematic review of TMG reported a low proportion of female participants, with a small sample size. Therefore, it is unclear whether there is a difference in TMG parameters according to sex and between dominant and non-dominant feet. Furthermore, the relationship between TMG parameters and evaluations commonly used in clinical practice has not been clarified. This study aimed to clarify the characteristics of muscle contraction of the rectus femoris using TMG according to sex among healthy college students and its relationship with muscle function evaluation, such as lower limb muscle mass and muscle strength. Methods This cross-sectional study included 91 healthy university students (18–24 years). Five tools were used: TMG, lower-limb muscle mass, rectus femoris thickness, isometric knee joint extension torque, and thigh circumference. Each parameter was compared by the generalized linear mixed model (GLMM) and Bonferroni’s multiple comparison test, with sex as the without-subject factor and dominant/non-dominant foot as the within-subject factor. The correlation between the TMG parameters and other parameters was examined using Pearson’s correlation coefficient for both males and females. Results The results of the GLMM, in terms of the TMG parameters, an interaction was observed for maximum displacement (Dm); in the results of the multiple comparison test, Dm for the non-dominant leg was significantly lower in females than in males. A main effect and interaction were not observed for delay time (Td) and contraction time (Tc) by sex, dominant foot, or non-dominant foot. There was a main effect of sex on muscl…
format: application/pdf
format: text/html
creator: Yasuaki Kusumoto
creator: Hayato Goto
creator: Kohei Chiba
creator: Sakiko Oonishi
creator: Junko Tsuchiya
subject: Kinesiology
subject: Orthopedics
subject: Rehabilitation
subject: Sports Medicine
description: doi:10.7717/peerj.14732
publisher: PeerJ Inc.
rights: © 2023 Kusumoto et al.
abstract: Background Tensiomyography (TMG) is a non-invasive instrument for measuring mechanical muscle contraction characteristics and measuring the maximum displacement of the muscle belly in the radial direction with respect to the muscle and the time needed to achieve this from electrical stimulation. There have been only been a reports of TMG in healthy adults. A systematic review of TMG reported a low proportion of female participants, with a small sample size. Therefore, it is unclear whether there is a difference in TMG parameters according to sex and between dominant and non-dominant feet. Furthermore, the relationship between TMG parameters and evaluations commonly used in clinical practice has not been clarified. This study aimed to clarify the characteristics of muscle contraction of the rectus femoris using TMG according to sex among healthy college students and its relationship with muscle function evaluation, such as lower limb muscle mass and muscle strength. Methods This cross-sectional study included 91 healthy university students (18–24 years). Five tools were used: TMG, lower-limb muscle mass, rectus femoris thickness, isometric knee joint extension torque, and thigh circumference. Each parameter was compared by the generalized linear mixed model (GLMM) and Bonferroni’s multiple comparison test, with sex as the without-subject factor and dominant/non-dominant foot as the within-subject factor. The correlation between the TMG parameters and other parameters was examined using Pearson’s correlation coefficient for both males and females. Results The results of the GLMM, in terms of the TMG parameters, an interaction was observed for maximum displacement (Dm); in the results of the multiple comparison test, Dm for the non-dominant leg was significantly lower in females than in males. A main effect and interaction were not observed for delay time (Td) and contraction time (Tc) by sex, dominant foot, or non-dominant foot. There was a main effect of sex on muscl…
bibliographic citation: Kusumoto et al. (2023) Characteristics of muscle contraction of the rectus femoris using tensiomyography by sex in healthy college students: a cross-sectional study. PeerJ 11:e14732 https://doi.org/10.7717/peerj.14732
date submitted: 2022-05-16
date accepted: 2022-12-20
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kusumoto
  given name: Yasuaki
author list: Agent
  family name: Goto
  given name: Hayato
author list: Agent
  family name: Chiba
  given name: Kohei
author list: Agent
  family name: Oonishi
  given name: Sakiko
author list: Agent
  family name: Tsuchiya
  given name: Junko
doi: 10.7717/peerj.14732
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Kusumoto et al.
attribution name: Kusumoto et al.

Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems
type: item
type: AcademicArticle
description: The Costa Rican Paramo is a unique ecosystem with high levels of endemism that is geographically isolated from the Andean Paramos. Paramo ecosystems occur above Montane Forests, below the permanent snow level, and their vegetation differs notably from that of adjacent Montane Forests. We compared the composition and beta diversity of blooming plant species using phenological data from functional plant groups (i.e., insect-visited, bird-visited and insect + bird-visited plants) between a Paramo and a Montane Forest site in Costa Rica and analyzed seasonal changes in blooming plant diversity between the rainy and dry seasons. Species richness was higher in the Montane Forest for all plant categories, except for insect-visited plants, which was higher in the Paramo. Beta diversity and blooming plant composition differed between both ecosystems and seasons. Differences in species richness and beta diversity between Paramo and the adjacent Montane Forest are likely the result of dispersal events that occurred during the last glacial period and subsequent isolation, as climate turned to tropical conditions after the Pleistocene, and to stressful abiotic conditions in the Paramo ecosystem that limit species establishment. Differences in blooming plant composition between both ecosystems and seasons are likely attributed to differential effects of climatic cues triggering the flowering events in each ecosystem, but phylogenetic conservatism cannot be discarded. Analyses of species composition and richness based on flowering phenology data are useful to evaluate potential floral resources for floral visitors (insects and birds) and how these resources change spatially and temporarily in endangered ecosystems such as the Paramo.
format: application/pdf
format: text/html
creator: E. Jacob Cristóbal-Pérez
creator: Gilbert Barrantes
creator: Alfredo Cascante-Marín
creator: Ruth Madrigal-Brenes
creator: Paul Hanson
creator: Eric J. Fuchs
subject: Biodiversity
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.14445
publisher: PeerJ Inc.
rights: © 2023 Cristóbal-Pérez et al.
abstract: The Costa Rican Paramo is a unique ecosystem with high levels of endemism that is geographically isolated from the Andean Paramos. Paramo ecosystems occur above Montane Forests, below the permanent snow level, and their vegetation differs notably from that of adjacent Montane Forests. We compared the composition and beta diversity of blooming plant species using phenological data from functional plant groups (i.e., insect-visited, bird-visited and insect + bird-visited plants) between a Paramo and a Montane Forest site in Costa Rica and analyzed seasonal changes in blooming plant diversity between the rainy and dry seasons. Species richness was higher in the Montane Forest for all plant categories, except for insect-visited plants, which was higher in the Paramo. Beta diversity and blooming plant composition differed between both ecosystems and seasons. Differences in species richness and beta diversity between Paramo and the adjacent Montane Forest are likely the result of dispersal events that occurred during the last glacial period and subsequent isolation, as climate turned to tropical conditions after the Pleistocene, and to stressful abiotic conditions in the Paramo ecosystem that limit species establishment. Differences in blooming plant composition between both ecosystems and seasons are likely attributed to differential effects of climatic cues triggering the flowering events in each ecosystem, but phylogenetic conservatism cannot be discarded. Analyses of species composition and richness based on flowering phenology data are useful to evaluate potential floral resources for floral visitors (insects and birds) and how these resources change spatially and temporarily in endangered ecosystems such as the Paramo.
bibliographic citation: Cristóbal-Pérez et al. (2023) Blooming plant species diversity patterns in two adjacent Costa Rican highland ecosystems. PeerJ 11:e14445 https://doi.org/10.7717/peerj.14445
date submitted: 2022-09-03
date accepted: 2022-11-01
issued: 2023-01-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cristóbal-Pérez
  given name: E. Jacob
author list: Agent
  family name: Barrantes
  given name: Gilbert
author list: Agent
  family name: Cascante-Marín
  given name: Alfredo
author list: Agent
  family name: Madrigal-Brenes
  given name: Ruth
author list: Agent
  family name: Hanson
  given name: Paul
author list: Agent
  family name: Fuchs
  given name: Eric J.
doi: 10.7717/peerj.14445
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-12
copyright: ©2023 Cristóbal-Pérez et al.
attribution name: Cristóbal-Pérez et al.

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