PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genetic characterization of hepatitis B virus genotypes among patients with chronic infection in Sulaimaniyah city, Iraq
items: Surviving on the edge: present and future effects of climate warming on the common frog (Rana temporaria) population in the Montseny massif (NE Iberia)
items: Diagnostic biomarker panels of osteoarthritis: UPLC-QToF/MS-based serum metabolic profiling
items: Occurrence of two myxosporean parasites in the gall bladder of white seabream Diplodus sargus (L.) (Teleostei, Sparidae), with the morphological and molecular description of Ceratomyxa sargus n. sp.
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)

Genetic characterization of hepatitis B virus genotypes among patients with chronic infection in Sulaimaniyah city, Iraq
type: item
type: AcademicArticle
description: Background Hepatitis B virus (HBV) genotypes are distributed unevenly throughout the world’s regions. The researchers’ goal in this study was to find out which HBV genotypes are now prevalent in the blood of chronic HBV patients in Iraq’s Kurdistan Region’s Sulaimaniyah governorate. Methods Genotyping was carried out utilizing Polymerase Chain Reaction (PCR) type-specified primers. Thirty-three chronic HBV patients were included in the HBV genotyping assay. Phylogenic trees of Pre-S1/Pre S2/S genes’ nucleotide sequences were constructed using 36 HBV isolates. Results All the patients had HBV genotype D. Additionally, two samples were further analyzed by sequencing and deposited in GenBank as HBV/Sul-1/2021 accession numbers MZ077051 and HBV/Sul-2/2021 accession numbers MZ077052. Phylogenic analysis indicated that the HBV isolates belong to sub-genotype D1/serotype ayw2. The HBV/Sul-2/2021 had two sequence deletion mutations from G61del-T87del, which accounted for 27 amino acid deletions, and ten other mutations were identified in the carboxylic terminus of the pre-S1 from Q104del-R113del. Accordingly, 37 amino acids were deleted in the S promoter region. Several other substitution mutations were recorded in both HBV isolates. Conclusion Patients with chronic HBV were found to have the HBV sub-genotype D1/subtype ayw2 with no mixed genotypes. HBV/Sul-1/2022, a new strain with a 37-amino acid mutation, was found to be distinct from any previously known HBV isolates.
format: application/pdf
format: text/html
creator: Mardin Othman Abdulqadir
creator: Peshnyar Muhammad Atta Rashid
creator: Ali Hattem Hussain
creator: Heshu Sulaiman Rahman
creator: Shahow Abdulrehman Ezzaddin
subject: Molecular Biology
subject: Virology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.14454
publisher: PeerJ Inc.
rights: © 2023 Abdulqadir et al.
abstract: Background Hepatitis B virus (HBV) genotypes are distributed unevenly throughout the world’s regions. The researchers’ goal in this study was to find out which HBV genotypes are now prevalent in the blood of chronic HBV patients in Iraq’s Kurdistan Region’s Sulaimaniyah governorate. Methods Genotyping was carried out utilizing Polymerase Chain Reaction (PCR) type-specified primers. Thirty-three chronic HBV patients were included in the HBV genotyping assay. Phylogenic trees of Pre-S1/Pre S2/S genes’ nucleotide sequences were constructed using 36 HBV isolates. Results All the patients had HBV genotype D. Additionally, two samples were further analyzed by sequencing and deposited in GenBank as HBV/Sul-1/2021 accession numbers MZ077051 and HBV/Sul-2/2021 accession numbers MZ077052. Phylogenic analysis indicated that the HBV isolates belong to sub-genotype D1/serotype ayw2. The HBV/Sul-2/2021 had two sequence deletion mutations from G61del-T87del, which accounted for 27 amino acid deletions, and ten other mutations were identified in the carboxylic terminus of the pre-S1 from Q104del-R113del. Accordingly, 37 amino acids were deleted in the S promoter region. Several other substitution mutations were recorded in both HBV isolates. Conclusion Patients with chronic HBV were found to have the HBV sub-genotype D1/subtype ayw2 with no mixed genotypes. HBV/Sul-1/2022, a new strain with a 37-amino acid mutation, was found to be distinct from any previously known HBV isolates.
bibliographic citation: Abdulqadir et al. (2023) Genetic characterization of hepatitis B virus genotypes among patients with chronic infection in Sulaimaniyah city, Iraq. PeerJ 11:e14454 https://doi.org/10.7717/peerj.14454
date submitted: 2022-05-09
date accepted: 2022-11-02
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdulqadir
  given name: Mardin Othman
author list: Agent
  family name: Rashid
  given name: Peshnyar Muhammad Atta
author list: Agent
  family name: Hussain
  given name: Ali Hattem
author list: Agent
  family name: Rahman
  given name: Heshu Sulaiman
author list: Agent
  family name: Ezzaddin
  given name: Shahow Abdulrehman
doi: 10.7717/peerj.14454
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: ©2023 Abdulqadir et al.
attribution name: Abdulqadir et al.

Surviving on the edge: present and future effects of climate warming on the common frog (Rana temporaria) population in the Montseny massif (NE Iberia)
type: item
type: AcademicArticle
description: The Montseny massif shelters the southernmost western populations of common frogs (Rana temporaria) that live in a Mediterranean climate, one which poses a challenge for the species’ persistence in a scenario of rising temperatures. We evaluated the effect of climate change at three levels. First, we analysed if there has been an advancement in the onset of spawning period due to the increase in temperatures. Second, we analysed the impact of climatic variables on the onset of the spawning period and, third, how the distribution of this species could vary according to the predictions with regard to rising temperatures for the end of this century. From 2009 to 2021, we found there had been an increase in temperatures of 0.439 °C/decade, more than the 0.1 °C indicated by estimates for the second half of the previous century. We found an advancement in the onset of the reproduction process of 26 days/decade for the period 2009–2022, a change that has been even more marked during the last eight years, when data were annually recorded. Minimum temperatures and the absence of frost days in the week prior to the onset of the spawning period determine the start of reproduction. Predictions on habitat availability for spawning provided by climatic niche analysis for the period 2021–2100 show a potential contraction of the species range in the Montseny and, remarkably, much isolation from the neighbouring populations.
format: application/pdf
format: text/html
creator: Albert Montori
creator: Fèlix Amat
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Climate Change Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.14527
publisher: PeerJ Inc.
rights: © 2023 Montori and Amat
abstract: The Montseny massif shelters the southernmost western populations of common frogs (Rana temporaria) that live in a Mediterranean climate, one which poses a challenge for the species’ persistence in a scenario of rising temperatures. We evaluated the effect of climate change at three levels. First, we analysed if there has been an advancement in the onset of spawning period due to the increase in temperatures. Second, we analysed the impact of climatic variables on the onset of the spawning period and, third, how the distribution of this species could vary according to the predictions with regard to rising temperatures for the end of this century. From 2009 to 2021, we found there had been an increase in temperatures of 0.439 °C/decade, more than the 0.1 °C indicated by estimates for the second half of the previous century. We found an advancement in the onset of the reproduction process of 26 days/decade for the period 2009–2022, a change that has been even more marked during the last eight years, when data were annually recorded. Minimum temperatures and the absence of frost days in the week prior to the onset of the spawning period determine the start of reproduction. Predictions on habitat availability for spawning provided by climatic niche analysis for the period 2021–2100 show a potential contraction of the species range in the Montseny and, remarkably, much isolation from the neighbouring populations.
bibliographic citation: Montori et al. (2023) Surviving on the edge: present and future effects of climate warming on the common frog (Rana temporaria) population in the Montseny massif (NE Iberia). PeerJ 11:e14527 https://doi.org/10.7717/peerj.14527
date submitted: 2022-07-20
date accepted: 2022-11-15
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montori
  given name: Albert
author list: Agent
  family name: Amat
  given name: Fèlix
doi: 10.7717/peerj.14527
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Montori and Amat
attribution name: Montori and Amat

Diagnostic biomarker panels of osteoarthritis: UPLC-QToF/MS-based serum metabolic profiling
type: item
type: AcademicArticle
description: Osteoarthritis (OA) is the most common joint disease in the world, characterized by pain and loss of joint function, which has led to a serious reduction in the quality of patients’ lives. In this work, ultrahigh performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-QToF/MS) in conjunction with multivariate pattern recognition methods and an univariate statistical analysis scheme were applied to explore the serum metabolic signatures within OA group (n = 31), HC (healthy controls) group (n = 57) and non-OA group (n = 19) for early diagnosis and differential diagnosis of OA. Based on logistic regression analysis and receiver operating characteristic (ROC) curve analysis, seven metabolites, including phosphatidylcholine (18:0/22:6), p-cresol sulfate and so on, were identified as critical metabolites for the diagnosis of OA and HC and yielded an area under the curve (AUC) of 0.978. The other panel of unknown m/z 239.091, phosphatidylcholine (18:0/18:0) and phenylalanine were found to distinguish OA from non-OA and achieved an AUC of 0.888. These potential biomarkers are mainly involved in lipid metabolism, glucose metabolism and amino acid metabolism. It is expected to reveal new insight into OA pathogenesis from changed metabolic pathways.
format: application/pdf
format: text/html
creator: Xinxin Lin
creator: Shiqi He
creator: Suyu Wu
creator: Tianwen Zhang
creator: Sisi Gong
creator: Tang Minjie
creator: Yao Gao
subject: Biochemistry
subject: Surgery and Surgical Specialties
subject: Metabolic Sciences
description: doi:10.7717/peerj.14563
publisher: PeerJ Inc.
rights: © 2023 Lin et al.
abstract: Osteoarthritis (OA) is the most common joint disease in the world, characterized by pain and loss of joint function, which has led to a serious reduction in the quality of patients’ lives. In this work, ultrahigh performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-QToF/MS) in conjunction with multivariate pattern recognition methods and an univariate statistical analysis scheme were applied to explore the serum metabolic signatures within OA group (n = 31), HC (healthy controls) group (n = 57) and non-OA group (n = 19) for early diagnosis and differential diagnosis of OA. Based on logistic regression analysis and receiver operating characteristic (ROC) curve analysis, seven metabolites, including phosphatidylcholine (18:0/22:6), p-cresol sulfate and so on, were identified as critical metabolites for the diagnosis of OA and HC and yielded an area under the curve (AUC) of 0.978. The other panel of unknown m/z 239.091, phosphatidylcholine (18:0/18:0) and phenylalanine were found to distinguish OA from non-OA and achieved an AUC of 0.888. These potential biomarkers are mainly involved in lipid metabolism, glucose metabolism and amino acid metabolism. It is expected to reveal new insight into OA pathogenesis from changed metabolic pathways.
bibliographic citation: Lin et al. (2023) Diagnostic biomarker panels of osteoarthritis: UPLC-QToF/MS-based serum metabolic profiling. PeerJ 11:e14563 https://doi.org/10.7717/peerj.14563
date submitted: 2022-03-16
date accepted: 2022-11-22
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Xinxin
author list: Agent
  family name: He
  given name: Shiqi
author list: Agent
  family name: Wu
  given name: Suyu
author list: Agent
  family name: Zhang
  given name: Tianwen
author list: Agent
  family name: Gong
  given name: Sisi
author list: Agent
  family name: Minjie
  given name: Tang
author list: Agent
  family name: Gao
  given name: Yao
doi: 10.7717/peerj.14563
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Lin et al.
attribution name: Lin et al.

Occurrence of two myxosporean parasites in the gall bladder of white seabream Diplodus sargus (L.) (Teleostei, Sparidae), with the morphological and molecular description of Ceratomyxa sargus n. sp.
type: item
type: AcademicArticle
description: Myxosporeans are widespread cnidarian parasites that usually parasitize fish as part of their complex life cycle, thus constituting a potential threat for the aquaculture industry. White seabream Diplodus sargus (L.) is a commercially valuable sparid fish reared in Southern European aquacultures. Nonetheless, knowledge on myxosporean infections potentially harming the sustainable production of this fish is extremely limited. In this study, a myxosporean survey was conducted on D. sargus specimens reared in two Southern Portuguese fish farms. Two coelozoic myxosporeans were detected infecting the gall bladder, and are herein reported based on microscopic and molecular procedures: Ceratomyxa sargus n. sp. and Zschokkella auratis Rocha et al., 2013, previously described from reared stocks of gilthead seabream Sparus aurata in the same geographic locality. Ceratomyxa sargus n. sp. is the 12th species of the genus to be reported from Southern European sparids, reinforcing a substantial radiation of Ceratomyxa within this fish family and geographic region. SSU rRNA-based Bayesian inference and maximum likelihood analyses revealed C. sargus n. sp. positioned separately from other sparid-infecting Ceratomyxa spp. reported from Southern European countries, demonstrating that this species does not share a more immediate common ancestor with its closest relatives based on host affinity and geography. The recognition of a novel sparid-infecting lineage within the Ceratomyxa clade strengthens the contention that this genus entered sparid fish multiple times, namely in the Southern European region. The identification of Zschokkella auratis infections in D. sargus demonstrates that host shift has occurred among sparids reared in the Southern Portuguese coast. This agrees with the broad host specificity that is usually attributed to this genus, and that may be suggested to be the outcome of the capacity of the Zschokkella morphotype to undergo host shift/switch based on our finding…
format: application/pdf
format: text/html
creator: Sónia Rocha
creator: Luís Filipe Rangel
creator: Graça Casal
creator: Ricardo Severino
creator: Florbela Soares
creator: Pedro Rodrigues
creator: Maria João Santos
subject: Marine Biology
subject: Parasitology
subject: Taxonomy
description: doi:10.7717/peerj.14599
publisher: PeerJ Inc.
rights: © 2023 Rocha et al.
abstract: Myxosporeans are widespread cnidarian parasites that usually parasitize fish as part of their complex life cycle, thus constituting a potential threat for the aquaculture industry. White seabream Diplodus sargus (L.) is a commercially valuable sparid fish reared in Southern European aquacultures. Nonetheless, knowledge on myxosporean infections potentially harming the sustainable production of this fish is extremely limited. In this study, a myxosporean survey was conducted on D. sargus specimens reared in two Southern Portuguese fish farms. Two coelozoic myxosporeans were detected infecting the gall bladder, and are herein reported based on microscopic and molecular procedures: Ceratomyxa sargus n. sp. and Zschokkella auratis Rocha et al., 2013, previously described from reared stocks of gilthead seabream Sparus aurata in the same geographic locality. Ceratomyxa sargus n. sp. is the 12th species of the genus to be reported from Southern European sparids, reinforcing a substantial radiation of Ceratomyxa within this fish family and geographic region. SSU rRNA-based Bayesian inference and maximum likelihood analyses revealed C. sargus n. sp. positioned separately from other sparid-infecting Ceratomyxa spp. reported from Southern European countries, demonstrating that this species does not share a more immediate common ancestor with its closest relatives based on host affinity and geography. The recognition of a novel sparid-infecting lineage within the Ceratomyxa clade strengthens the contention that this genus entered sparid fish multiple times, namely in the Southern European region. The identification of Zschokkella auratis infections in D. sargus demonstrates that host shift has occurred among sparids reared in the Southern Portuguese coast. This agrees with the broad host specificity that is usually attributed to this genus, and that may be suggested to be the outcome of the capacity of the Zschokkella morphotype to undergo host shift/switch based on our finding…
bibliographic citation: Rocha et al. (2023) Occurrence of two myxosporean parasites in the gall bladder of white seabream Diplodus sargus (L.) (Teleostei, Sparidae), with the morphological and molecular description of Ceratomyxa sargus n. sp.. PeerJ 11:e14599 https://doi.org/10.7717/peerj.14599
date submitted: 2022-04-08
date accepted: 2022-11-29
issued: 2023-01-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rocha
  given name: Sónia
author list: Agent
  family name: Filipe Rangel
  given name: Luís
author list: Agent
  family name: Casal
  given name: Graça
author list: Agent
  family name: Severino
  given name: Ricardo
author list: Agent
  family name: Soares
  given name: Florbela
author list: Agent
  family name: Rodrigues
  given name: Pedro
author list: Agent
  family name: Santos
  given name: Maria João
doi: 10.7717/peerj.14599
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-13
copyright: © 2023 Rocha et al.
attribution name: Rocha et al.

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.

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