PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Transcriptome analysis of ovary culture-induced embryogenesis in cucumber (Cucumis sativus L.)
items: The posttraumatic stress interview for children (KID-PIN): development and validation of a semi-structured interview of PTSD symptoms among displaced children in the Middle East
items: Sex-specific covariance between metabolic rate, behaviour and morphology in the ground beetle Carabus hortensis
items: Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting
items: Marine soundscape and fish biophony of a Mediterranean marine protected area
items: ANXA9 as a novel prognostic biomarker associated with immune infiltrates in gastric cancer
items: The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection
items: Morpho-physiological effects of environmental stress on yield and quality of sweet corn varieties (Zea mays L.)
items: Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears
items: Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes

Transcriptome analysis of ovary culture-induced embryogenesis in cucumber (Cucumis sativus L.)
type: item
type: AcademicArticle
description: Background. Ovary culture is a useful technique used to generate double haploid (DH) cucumber (Cucumis sativus L.) plants. However, cucumber ovary culture have a low rate of embryo induction and plant regeneration. Moreover, the cucumber embryogenesis mechanism remains unclear. In this study, we explored the molecular basis of cucumber embryogenesis in order to establish a foundation for a more efficient ovary culture method. Using transcriptome sequencing, we also investigated the differential expression of genes during the embryogenesis process. Methods. Cytological and morphological observations have divided cucumber ovary culture into three stages: early embryo development (T0), embryo morphogenesis (T1, T2, T3 and T4), and shoot formation (T5). We selected six key time points for transcriptome sequencing and analysis: T0 (the ovules were cultured for 0 d), T1 (the ovules were cultured for 2 d), T2 (the embryos were cultured for 10 d), T3 (the embryos were cultured for 20 d), T4 (the embryos were cultured for 30 d), and T5 (the shoots after 60 d culture). Results. We used cytology and morphology to observe the characteristics of the cucumber’s developmental transformation during embryogenesis and plant regeneration. The differentially expressed genes(DEGs) at developmental transition points were analyzed using transcriptome sequencing. In the early embryogenesis stage, the cells expanded, which was the signal for gametophytes to switch to the sporophyte development pathway. RNA-seq revealed that when compared to the fresh unpollinated ovaries, there were 3,468 up-regulated genes in the embryos, including hormone signal transduction genes, hormone response genes, and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. In the embryo morphogenesis stage (from cell division to cotyledon-embryo formation), 480 genes that functioned in protein complex binding, microtubule binding, tetrapyrro…
format: application/pdf
format: text/html
creator: Ying Deng
creator: Wenyuan Fu
creator: Bing Tang
creator: Lian Tao
creator: Lu Zhang
creator: Xia Zhou
creator: Qingqing Wang
creator: Ji Li
creator: Jinfeng Chen
subject: Agricultural Science
subject: Developmental Biology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12145
publisher: PeerJ Inc.
rights: © 2021 Deng et al.
abstract: Background. Ovary culture is a useful technique used to generate double haploid (DH) cucumber (Cucumis sativus L.) plants. However, cucumber ovary culture have a low rate of embryo induction and plant regeneration. Moreover, the cucumber embryogenesis mechanism remains unclear. In this study, we explored the molecular basis of cucumber embryogenesis in order to establish a foundation for a more efficient ovary culture method. Using transcriptome sequencing, we also investigated the differential expression of genes during the embryogenesis process. Methods. Cytological and morphological observations have divided cucumber ovary culture into three stages: early embryo development (T0), embryo morphogenesis (T1, T2, T3 and T4), and shoot formation (T5). We selected six key time points for transcriptome sequencing and analysis: T0 (the ovules were cultured for 0 d), T1 (the ovules were cultured for 2 d), T2 (the embryos were cultured for 10 d), T3 (the embryos were cultured for 20 d), T4 (the embryos were cultured for 30 d), and T5 (the shoots after 60 d culture). Results. We used cytology and morphology to observe the characteristics of the cucumber’s developmental transformation during embryogenesis and plant regeneration. The differentially expressed genes(DEGs) at developmental transition points were analyzed using transcriptome sequencing. In the early embryogenesis stage, the cells expanded, which was the signal for gametophytes to switch to the sporophyte development pathway. RNA-seq revealed that when compared to the fresh unpollinated ovaries, there were 3,468 up-regulated genes in the embryos, including hormone signal transduction genes, hormone response genes, and stress-induced genes. The reported embryogenesis-related genes BBM, HSP90 and AGL were also actively expressed during this stage. In the embryo morphogenesis stage (from cell division to cotyledon-embryo formation), 480 genes that functioned in protein complex binding, microtubule binding, tetrapyrro…
bibliographic citation: Deng et al. (2021) Transcriptome analysis of ovary culture-induced embryogenesis in cucumber (Cucumis sativus L.). PeerJ 9:e12145 https://doi.org/10.7717/peerj.12145
date submitted: 2020-03-31
date accepted: 2021-08-19
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Deng
  given name: Ying
author list: Agent
  family name: Fu
  given name: Wenyuan
author list: Agent
  family name: Tang
  given name: Bing
author list: Agent
  family name: Tao
  given name: Lian
author list: Agent
  family name: Zhang
  given name: Lu
author list: Agent
  family name: Zhou
  given name: Xia
author list: Agent
  family name: Wang
  given name: Qingqing
author list: Agent
  family name: Li
  given name: Ji
author list: Agent
  family name: Chen
  given name: Jinfeng
doi: 10.7717/peerj.12145
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Deng et al.
attribution name: Deng et al.

The posttraumatic stress interview for children (KID-PIN): development and validation of a semi-structured interview of PTSD symptoms among displaced children in the Middle East
type: item
type: AcademicArticle
description: Background In populations affected by mass disaster such as armed conflict and displacement, children are at risk of developing mental ill-health, in particular post-traumatic stress disorder (PTSD). Valid and reliable screening instruments are needed to assess the severity of PTSD symptoms among children and to identify individuals in need of treatment. Method In the context of an ongoing war in the Middle East, we developed the KID-PIN as a semi-structured interview for PTSD symptoms that can be administered by trained paraprofessionals. To achieve a culturally and contextually appropriate instrument, the development was based on open-ended interviews with affected children and involved both local and international experts. Using the KID-PIN and instruments for constructs associated with PTSD, 332 Iraqi and Syrian displaced children were interviewed. A subset of the sample (n = 86) participated in validation interviews based on experts applying the Clinician-Administered PTSD Scale for DSM-5—Child/Adolescent Version (CAPS-CA-5). Results The KID-PIN demonstrated excellent internal consistency (Cronbach’s alpha = 0.94) with good convergent validity. Confirmatory factor analyses of the KID-PIN showed an acceptable fit with the DSM-5 and other common models; the best fit was reached with the Hybrid model. Receiver operating characteristic analyses indicated that the cut-off score of 28 or higher on the KID-PIN is the optimum cut-off for a probable PTSD diagnosis. Conclusion The utility of the newly developed KID-PIN as a screening instrument for PTSD in children is supported by the measure’s high internal consistency and good convergent and structural validity, as well as its diagnostic accuracy.
format: application/pdf
format: text/html
creator: Hawkar Ibrahim
creator: Claudia Catani
creator: Frank Neuner
subject: Global Health
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Public Health
subject: Mental Health
description: doi:10.7717/peerj.12403
publisher: PeerJ Inc.
rights: © 2021 Ibrahim et al.
abstract: Background In populations affected by mass disaster such as armed conflict and displacement, children are at risk of developing mental ill-health, in particular post-traumatic stress disorder (PTSD). Valid and reliable screening instruments are needed to assess the severity of PTSD symptoms among children and to identify individuals in need of treatment. Method In the context of an ongoing war in the Middle East, we developed the KID-PIN as a semi-structured interview for PTSD symptoms that can be administered by trained paraprofessionals. To achieve a culturally and contextually appropriate instrument, the development was based on open-ended interviews with affected children and involved both local and international experts. Using the KID-PIN and instruments for constructs associated with PTSD, 332 Iraqi and Syrian displaced children were interviewed. A subset of the sample (n = 86) participated in validation interviews based on experts applying the Clinician-Administered PTSD Scale for DSM-5—Child/Adolescent Version (CAPS-CA-5). Results The KID-PIN demonstrated excellent internal consistency (Cronbach’s alpha = 0.94) with good convergent validity. Confirmatory factor analyses of the KID-PIN showed an acceptable fit with the DSM-5 and other common models; the best fit was reached with the Hybrid model. Receiver operating characteristic analyses indicated that the cut-off score of 28 or higher on the KID-PIN is the optimum cut-off for a probable PTSD diagnosis. Conclusion The utility of the newly developed KID-PIN as a screening instrument for PTSD in children is supported by the measure’s high internal consistency and good convergent and structural validity, as well as its diagnostic accuracy.
bibliographic citation: Ibrahim et al. (2021) The posttraumatic stress interview for children (KID-PIN): development and validation of a semi-structured interview of PTSD symptoms among displaced children in the Middle East. PeerJ 9:e12403 https://doi.org/10.7717/peerj.12403
date submitted: 2020-11-23
date accepted: 2021-10-07
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ibrahim
  given name: Hawkar
author list: Agent
  family name: Catani
  given name: Claudia
author list: Agent
  family name: Neuner
  given name: Frank
doi: 10.7717/peerj.12403
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Ibrahim et al.
attribution name: Ibrahim et al.

Sex-specific covariance between metabolic rate, behaviour and morphology in the ground beetle Carabus hortensis
type: item
type: AcademicArticle
description: Background Individuals within the same species often differ in their metabolic rates, which may covary with behavioural traits (such as exploration), that are consistent across time and/or contexts, and morphological traits. Yet, despite the frequent occurrence of sexual dimorphisms in morphology and behaviour, few studies have assessed whether and how sexes differ in metabolic trait covariances. Methods We investigated sex-specific relationships among resting or active metabolic rate (RMR and AMR, respectively) with exploratory behaviour, measured independently of metabolic rate in a novel environment, body size and body mass, in Carabus hortensis ground beetles. Results RMR, AMR and exploratory behaviour were repeatable among individuals across time, except for male RMR which was unrepeatable. Female RMR neither correlated with exploratory behaviour nor body size/body mass. In contrast, AMR was correlated with both body size and exploratory behaviour. Males with larger body sizes had higher AMR, whereas females with larger body sizes had lower AMR. Both male and female AMR were significantly related to exploratory behaviour, though the relationships between AMR and exploration were body mass-dependent in males and temperature-dependent in females. Discussion Differences between sexes exist in the covariances between metabolic rate, body size and exploratory behaviour. This suggests that selection acts differently on males and females to produce these trait covariances with potentially important consequences for individual fitness.
format: application/pdf
format: text/html
creator: Elisabeth Yarwood
creator: Claudia Drees
creator: Jeremy E. Niven
creator: Wiebke Schuett
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.12455
publisher: PeerJ Inc.
rights: © 2021 Yarwood et al.
abstract: Background Individuals within the same species often differ in their metabolic rates, which may covary with behavioural traits (such as exploration), that are consistent across time and/or contexts, and morphological traits. Yet, despite the frequent occurrence of sexual dimorphisms in morphology and behaviour, few studies have assessed whether and how sexes differ in metabolic trait covariances. Methods We investigated sex-specific relationships among resting or active metabolic rate (RMR and AMR, respectively) with exploratory behaviour, measured independently of metabolic rate in a novel environment, body size and body mass, in Carabus hortensis ground beetles. Results RMR, AMR and exploratory behaviour were repeatable among individuals across time, except for male RMR which was unrepeatable. Female RMR neither correlated with exploratory behaviour nor body size/body mass. In contrast, AMR was correlated with both body size and exploratory behaviour. Males with larger body sizes had higher AMR, whereas females with larger body sizes had lower AMR. Both male and female AMR were significantly related to exploratory behaviour, though the relationships between AMR and exploration were body mass-dependent in males and temperature-dependent in females. Discussion Differences between sexes exist in the covariances between metabolic rate, body size and exploratory behaviour. This suggests that selection acts differently on males and females to produce these trait covariances with potentially important consequences for individual fitness.
bibliographic citation: Yarwood et al. (2021) Sex-specific covariance between metabolic rate, behaviour and morphology in the ground beetle Carabus hortensis. PeerJ 9:e12455 https://doi.org/10.7717/peerj.12455
date submitted: 2021-04-28
date accepted: 2021-10-18
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yarwood
  given name: Elisabeth
author list: Agent
  family name: Drees
  given name: Claudia
author list: Agent
  family name: Niven
  given name: Jeremy E.
author list: Agent
  family name: Schuett
  given name: Wiebke
doi: 10.7717/peerj.12455
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Yarwood et al.
attribution name: Yarwood et al.

Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting
type: item
type: AcademicArticle
description: Background Plesiosaurs, diapsid crown-group Sauropterygia, inhabited the oceans from the Late Triassic to the Late Cretaceous. Their most exceptional characteristic are four hydrofoil-like flippers. The question whether plesiosaurs employed their four flippers in underwater flight, rowing flight, or rowing has not been settled yet. Plesiosaur locomotory muscles have been reconstructed in the past, but neither the pelvic muscles nor the distal fore- and hindflipper musculature have been reconstructed entirely. Methods All plesiosaur locomotory muscles were reconstructed in order to find out whether it is possible to identify muscles that are necessary for underwater flight including those that enable flipper rotation and twisting. Flipper twisting has been proven by hydrodynamic studies to be necessary for efficient underwater flight. So, Cryptoclidus eurymerus fore- and hindflipper muscles and ligaments were reconstructed using the extant phylogenetic bracket (Testudines, Crocodylia, and Lepidosauria) and correlated with osteological features and checked for their functionality. Muscle functions were geometrically derived in relation to the glenoid and acetabulum position. Additionally, myology of functionally analogous Chelonioidea, Spheniscidae, Otariinae, and Cetacea is used to extract general myological adaptations of secondary aquatic tetrapods to inform the phylogenetically inferred muscle reconstructions. Results A total of 52 plesiosaur fore- and hindflipper muscles were reconstructed. Amongst these are flipper depressors, elevators, retractors, protractors, and rotators. These muscles enable a fore- and hindflipper downstroke and upstroke, the two sequences that represent an underwater flight flipper beat cycle. Additionally, other muscles were capable of twisting fore- and hindflippers along their length axis during down- and upstroke accordingly. A combination of these muscles that actively aid in flipper twisting and intermetacarpal/intermetatarsal and m…
format: application/pdf
format: text/html
creator: Anna Krahl
creator: Ulrich Witzel
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.12537
publisher: PeerJ Inc.
rights: © 2021 Krahl and Witzel
abstract: Background Plesiosaurs, diapsid crown-group Sauropterygia, inhabited the oceans from the Late Triassic to the Late Cretaceous. Their most exceptional characteristic are four hydrofoil-like flippers. The question whether plesiosaurs employed their four flippers in underwater flight, rowing flight, or rowing has not been settled yet. Plesiosaur locomotory muscles have been reconstructed in the past, but neither the pelvic muscles nor the distal fore- and hindflipper musculature have been reconstructed entirely. Methods All plesiosaur locomotory muscles were reconstructed in order to find out whether it is possible to identify muscles that are necessary for underwater flight including those that enable flipper rotation and twisting. Flipper twisting has been proven by hydrodynamic studies to be necessary for efficient underwater flight. So, Cryptoclidus eurymerus fore- and hindflipper muscles and ligaments were reconstructed using the extant phylogenetic bracket (Testudines, Crocodylia, and Lepidosauria) and correlated with osteological features and checked for their functionality. Muscle functions were geometrically derived in relation to the glenoid and acetabulum position. Additionally, myology of functionally analogous Chelonioidea, Spheniscidae, Otariinae, and Cetacea is used to extract general myological adaptations of secondary aquatic tetrapods to inform the phylogenetically inferred muscle reconstructions. Results A total of 52 plesiosaur fore- and hindflipper muscles were reconstructed. Amongst these are flipper depressors, elevators, retractors, protractors, and rotators. These muscles enable a fore- and hindflipper downstroke and upstroke, the two sequences that represent an underwater flight flipper beat cycle. Additionally, other muscles were capable of twisting fore- and hindflippers along their length axis during down- and upstroke accordingly. A combination of these muscles that actively aid in flipper twisting and intermetacarpal/intermetatarsal and m…
bibliographic citation: Krahl et al. (2021) Foreflipper and hindflipper muscle reconstructions of Cryptoclidus eurymerus in comparison to functional analogues: introduction of a myological mechanism for flipper twisting. PeerJ 9:e12537 https://doi.org/10.7717/peerj.12537
date submitted: 2021-01-21
date accepted: 2021-11-03
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Krahl
  given name: Anna
author list: Agent
  family name: Witzel
  given name: Ulrich
doi: 10.7717/peerj.12537
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Krahl and Witzel
attribution name: Krahl and Witzel

Marine soundscape and fish biophony of a Mediterranean marine protected area
type: item
type: AcademicArticle
description: Background Marine soundscape is the aggregation of sound sources known as geophony, biophony, and anthrophony. The soundscape analysis, in terms of collection and analysis of acoustic signals, has been proposed as a tool to evaluate the specific features of ecological assemblages and to estimate their acoustic variability over space and time. This study aimed to characterise the Capo Caccia-Isola Piana Marine Protected Area (Italy, Western Mediterranean Sea) soundscape over short temporal (few days) and spatial scales (few km) and to quantify the main anthropogenic and biological components, with a focus on fish biophonies. Methods Within the MPA, three sites were chosen each in a different protection zone (A for the integral protection, B as the partial protection, and C as the general protection). In each site, two underwater autonomous acoustic recorders were deployed in July 2020 at a depth of about 10 m on rocky bottoms. To characterise the contribution of both biophonies and anthrophonies, sea ambient noise (SAN) levels were measured as sound pressure level (SPL dB re: 1 μ Pa-rms) at eight 1/3 octave bands, centred from 125 Hz to 16 kHz, and biological and anthropogenic sounds were noted. Fish sounds were classified and counted following a catalogue of known fish sounds from the Mediterranean Sea based on the acoustic characteristic of sound types. A contemporary fish visual census had been carried out at the test sites. Results SPL were different by site, time (day vs. night), and hour. SPLs bands centred at 125, 250, and 500 Hz were significantly higher in the daytime, due to the high number of boats per minute whose noise dominated the soundscapes. The loudest man-made noise was found in the A zone, followed by the B and the C zone, confirming that MPA current regulations do not provide protection from acoustic pollution. The dominant biological components of the MPA soundscape were the impulsive sounds generated by some invertebrates, snapping shrimps and …
format: application/pdf
format: text/html
creator: Gabriella La Manna
creator: Marta Picciulin
creator: Alessia Crobu
creator: Francesco Perretti
creator: Fabio Ronchetti
creator: Michele Manghi
creator: Alberto Ruiu
creator: Giulia Ceccherelli
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.12551
publisher: PeerJ Inc.
rights: © 2021 La Manna et al.
abstract: Background Marine soundscape is the aggregation of sound sources known as geophony, biophony, and anthrophony. The soundscape analysis, in terms of collection and analysis of acoustic signals, has been proposed as a tool to evaluate the specific features of ecological assemblages and to estimate their acoustic variability over space and time. This study aimed to characterise the Capo Caccia-Isola Piana Marine Protected Area (Italy, Western Mediterranean Sea) soundscape over short temporal (few days) and spatial scales (few km) and to quantify the main anthropogenic and biological components, with a focus on fish biophonies. Methods Within the MPA, three sites were chosen each in a different protection zone (A for the integral protection, B as the partial protection, and C as the general protection). In each site, two underwater autonomous acoustic recorders were deployed in July 2020 at a depth of about 10 m on rocky bottoms. To characterise the contribution of both biophonies and anthrophonies, sea ambient noise (SAN) levels were measured as sound pressure level (SPL dB re: 1 μ Pa-rms) at eight 1/3 octave bands, centred from 125 Hz to 16 kHz, and biological and anthropogenic sounds were noted. Fish sounds were classified and counted following a catalogue of known fish sounds from the Mediterranean Sea based on the acoustic characteristic of sound types. A contemporary fish visual census had been carried out at the test sites. Results SPL were different by site, time (day vs. night), and hour. SPLs bands centred at 125, 250, and 500 Hz were significantly higher in the daytime, due to the high number of boats per minute whose noise dominated the soundscapes. The loudest man-made noise was found in the A zone, followed by the B and the C zone, confirming that MPA current regulations do not provide protection from acoustic pollution. The dominant biological components of the MPA soundscape were the impulsive sounds generated by some invertebrates, snapping shrimps and …
bibliographic citation: La Manna et al. (2021) Marine soundscape and fish biophony of a Mediterranean marine protected area. PeerJ 9:e12551 https://doi.org/10.7717/peerj.12551
date submitted: 2021-05-13
date accepted: 2021-11-04
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: La Manna
  given name: Gabriella
author list: Agent
  family name: Picciulin
  given name: Marta
author list: Agent
  family name: Crobu
  given name: Alessia
author list: Agent
  family name: Perretti
  given name: Francesco
author list: Agent
  family name: Ronchetti
  given name: Fabio
author list: Agent
  family name: Manghi
  given name: Michele
author list: Agent
  family name: Ruiu
  given name: Alberto
author list: Agent
  family name: Ceccherelli
  given name: Giulia
doi: 10.7717/peerj.12551
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 La Manna et al.
attribution name: La Manna et al.

ANXA9 as a novel prognostic biomarker associated with immune infiltrates in gastric cancer
type: item
type: AcademicArticle
description: Background Gastric cancer (GC) is the most prevalent malignancy among the digestive system tumors. Increasing evidence has revealed that lower mRNA expression of ANXA9 is associated with a poor prognosis in colorectal cancer. However, the role of ANXA9 in GC remains largely unknown. Material and Methods The Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas databases were used to investigate the expression of ANXA9 in GC, which was then validated in the four Gene Expression Omnibus (GEO) datasets. The diagnostic value of ANXA9 for GC patients was demonstrated using a receiver operating characteristic (ROC) curve. The correlation between ANXA9 expression and clinicopathological parameters was analyzed in The Cancer Genome Atlas (TCGA) and UALCAN databases. The Kaplan-Meier (K-M) survival curve was used to elucidate the relationship between ANXA9 expression and the survival time of GC patients. We then performed a gene set enrichment analysis (GSEA) to explore the biological functions of ANXA9. The relationship of ANXA9 expression and cancer immune infiltrates was analyzed using the Tumor Immune Estimation Resource (TIMER). In addition, the potential mechanism of ANXA9 in GC was investigated by analyzing its related genes. Results ANXA9 was significantly up-regulated in GC tissues and showed obvious diagnostic value. The expression of ANXA9 was related to the age, gender, grade, TP53 mutation, and histological subtype of GC patients. We also found that ANXA9 expression was associated with immune-related biological function. ANXA9 expression was also correlated with the infiltration level of CD8+ T cells, neutrophils, and dendritic cells in GC. Additionally, copy number variation (VNV) of ANXA9 occurred in GC patients. Function enrichment analyses revealed that ANXA9 plays a role in the GC progression by interacting with its related genes. Conclusions Our results provide strong evidence of ANXA9 expression as a prognostic indicator related t…
format: application/pdf
format: text/html
creator: Tongtong Zhang
creator: Suyang Yu
creator: Shipeng Zhao
subject: Bioinformatics
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.12605
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Background Gastric cancer (GC) is the most prevalent malignancy among the digestive system tumors. Increasing evidence has revealed that lower mRNA expression of ANXA9 is associated with a poor prognosis in colorectal cancer. However, the role of ANXA9 in GC remains largely unknown. Material and Methods The Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas databases were used to investigate the expression of ANXA9 in GC, which was then validated in the four Gene Expression Omnibus (GEO) datasets. The diagnostic value of ANXA9 for GC patients was demonstrated using a receiver operating characteristic (ROC) curve. The correlation between ANXA9 expression and clinicopathological parameters was analyzed in The Cancer Genome Atlas (TCGA) and UALCAN databases. The Kaplan-Meier (K-M) survival curve was used to elucidate the relationship between ANXA9 expression and the survival time of GC patients. We then performed a gene set enrichment analysis (GSEA) to explore the biological functions of ANXA9. The relationship of ANXA9 expression and cancer immune infiltrates was analyzed using the Tumor Immune Estimation Resource (TIMER). In addition, the potential mechanism of ANXA9 in GC was investigated by analyzing its related genes. Results ANXA9 was significantly up-regulated in GC tissues and showed obvious diagnostic value. The expression of ANXA9 was related to the age, gender, grade, TP53 mutation, and histological subtype of GC patients. We also found that ANXA9 expression was associated with immune-related biological function. ANXA9 expression was also correlated with the infiltration level of CD8+ T cells, neutrophils, and dendritic cells in GC. Additionally, copy number variation (VNV) of ANXA9 occurred in GC patients. Function enrichment analyses revealed that ANXA9 plays a role in the GC progression by interacting with its related genes. Conclusions Our results provide strong evidence of ANXA9 expression as a prognostic indicator related t…
bibliographic citation: Zhang et al. (2021) ANXA9 as a novel prognostic biomarker associated with immune infiltrates in gastric cancer. PeerJ 9:e12605 https://doi.org/10.7717/peerj.12605
date submitted: 2021-06-08
date accepted: 2021-11-16
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Tongtong
author list: Agent
  family name: Yu
  given name: Suyang
author list: Agent
  family name: Zhao
  given name: Shipeng
doi: 10.7717/peerj.12605
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Zhang et al.
attribution name: Zhang et al.

The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection
type: item
type: AcademicArticle
description: Background Cnidarians are the most ancient venomous organisms. They store a cocktail of venom proteins inside unique stinging organelles called nematocysts. When a cnidarian encounters chemical and physical cues from a potential threat or prey animal, the nematocyst is triggered and fires a harpoon-like tubule to penetrate and inject venom into the prey. Nematocysts are present in all Cnidaria, including the morphologically simple Myxozoa, which are a speciose group of microscopic, spore-forming, obligate parasites of fish and invertebrates. Rather than predation or defense, myxozoans use nematocysts for adhesion to hosts, but the involvement of venom in this process is poorly understood. Recent work shows some myxozoans have a reduced repertoire of venom-like compounds (VLCs) relative to free-living cnidarians, however the function of these proteins is not known. Methods We searched for VLCs in the nematocyst proteome and a time-series infection transcriptome of Ceratonova shasta, a myxozoan parasite of salmonid fish. We used four parallel approaches to detect VLCs: BLAST and HMMER searches to preexisting cnidarian venom datasets, the machine learning tool ToxClassifier, and structural modeling of nematocyst proteomes. Sequences that scored positive by at least three methods were considered VLCs. We then mapped their time-series expressions in the fish host and analyzed their phylogenetic relatedness to sequences from other venomous animals. Results We identified eight VLCs, all of which have closely related sequences in other myxozoan datasets, suggesting a conserved venom profile across Myxozoa, and an overall reduction in venom diversity relative to free-living cnidarians. Expression of the VLCs over the 3-week fish infection varied considerably: three sequences were most expressed at one day post-exposure in the fish’s gills; whereas expression of the other five VLCs peaked at 21 days post-exposure in the intestines, coinciding with the formation of mature para…
format: application/pdf
format: text/html
creator: Benjamin Americus
creator: Nicole Hams
creator: Anna M. L. Klompen
creator: Gema Alama-Bermejo
creator: Tamar Lotan
creator: Jerri L. Bartholomew
creator: Stephen D. Atkinson
subject: Bioinformatics
subject: Molecular Biology
subject: Parasitology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.12606
publisher: PeerJ Inc.
rights: © 2021 Americus et al.
abstract: Background Cnidarians are the most ancient venomous organisms. They store a cocktail of venom proteins inside unique stinging organelles called nematocysts. When a cnidarian encounters chemical and physical cues from a potential threat or prey animal, the nematocyst is triggered and fires a harpoon-like tubule to penetrate and inject venom into the prey. Nematocysts are present in all Cnidaria, including the morphologically simple Myxozoa, which are a speciose group of microscopic, spore-forming, obligate parasites of fish and invertebrates. Rather than predation or defense, myxozoans use nematocysts for adhesion to hosts, but the involvement of venom in this process is poorly understood. Recent work shows some myxozoans have a reduced repertoire of venom-like compounds (VLCs) relative to free-living cnidarians, however the function of these proteins is not known. Methods We searched for VLCs in the nematocyst proteome and a time-series infection transcriptome of Ceratonova shasta, a myxozoan parasite of salmonid fish. We used four parallel approaches to detect VLCs: BLAST and HMMER searches to preexisting cnidarian venom datasets, the machine learning tool ToxClassifier, and structural modeling of nematocyst proteomes. Sequences that scored positive by at least three methods were considered VLCs. We then mapped their time-series expressions in the fish host and analyzed their phylogenetic relatedness to sequences from other venomous animals. Results We identified eight VLCs, all of which have closely related sequences in other myxozoan datasets, suggesting a conserved venom profile across Myxozoa, and an overall reduction in venom diversity relative to free-living cnidarians. Expression of the VLCs over the 3-week fish infection varied considerably: three sequences were most expressed at one day post-exposure in the fish’s gills; whereas expression of the other five VLCs peaked at 21 days post-exposure in the intestines, coinciding with the formation of mature para…
bibliographic citation: Americus et al. (2021) The cnidarian parasite Ceratonova shasta utilizes inherited and recruited venom-like compounds during infection. PeerJ 9:e12606 https://doi.org/10.7717/peerj.12606
date submitted: 2021-07-02
date accepted: 2021-11-16
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Americus
  given name: Benjamin
author list: Agent
  family name: Hams
  given name: Nicole
author list: Agent
  family name: Klompen
  given name: Anna M. L.
author list: Agent
  family name: Alama-Bermejo
  given name: Gema
author list: Agent
  family name: Lotan
  given name: Tamar
author list: Agent
  family name: Bartholomew
  given name: Jerri L.
author list: Agent
  family name: Atkinson
  given name: Stephen D.
doi: 10.7717/peerj.12606
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Americus et al.
attribution name: Americus et al.

Morpho-physiological effects of environmental stress on yield and quality of sweet corn varieties (Zea mays L.)
type: item
type: AcademicArticle
description: Sweet corn is cultivated in different climatic regions of the world, and consumed either fresh or processed. Morpho-physiological effects of environmental stress on yield, yield components and quality of some sweet corn varieties were investigated in field experiments conducted at Southeastern Anatolia Region of Turkey during 2019 and 2020 growing seasons. The experimental lay out was randomized blocks with three replicates. Eight candidates and two control sweet corn varieties classified as moderate maturity (FAO 650–700) were used in field experiment. Mean values of pollen fertility rate (PFR, %), total soluble solids (TSS, °Brix), abscisic acid (ABA, nmol/g DW), ear length (EL, cm), plant height (PH, cm), number of grains per cob (CGN, grain) and fresh cob yield (FCY, t ha−1) were significantly different between years and sweet corn varieties. The PFR, TSS, ABA, EL, PH, CGN and FCY ranged from 40.29–67.65%, 13.24–20.09 °brix, 7.74–21.04 nmol/g DW, 9.69–15.98 cm, 97.80–171.34 cm, 289.15–420.33 grain and 4.15–10.23 t ha−1 respectively. The FCY, yield components and PFR values in the second year that had a higher temperature and lower relative humidity were lower compared to the first year, while ABA and TSS values were higher in the second year. Statistically significant correlations were recorded between the parameters investigated except FCY and TSS. The FCY and other parameters of sweet corn varieties, which produced high ABA phytohormone, were high, and the ABA hormone significantly contributed to plant growth under stress conditions. The results revealed that the PFR physiological parameter and ABA hormone in the plants provide important information about stress level and stress tolerance level of the cultivars, respectively. Despite adverse environmental stress conditions, the FCY of ŞADA-18.7 variety, one of the candidate varieties, was higher than that of the control and the mean value of the experiment.
format: application/pdf
format: text/html
creator: Timucin Tas
creator: Arzu Mutlu
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.12613
publisher: PeerJ Inc.
rights: © 2021 Tas and Mutlu
abstract: Sweet corn is cultivated in different climatic regions of the world, and consumed either fresh or processed. Morpho-physiological effects of environmental stress on yield, yield components and quality of some sweet corn varieties were investigated in field experiments conducted at Southeastern Anatolia Region of Turkey during 2019 and 2020 growing seasons. The experimental lay out was randomized blocks with three replicates. Eight candidates and two control sweet corn varieties classified as moderate maturity (FAO 650–700) were used in field experiment. Mean values of pollen fertility rate (PFR, %), total soluble solids (TSS, °Brix), abscisic acid (ABA, nmol/g DW), ear length (EL, cm), plant height (PH, cm), number of grains per cob (CGN, grain) and fresh cob yield (FCY, t ha−1) were significantly different between years and sweet corn varieties. The PFR, TSS, ABA, EL, PH, CGN and FCY ranged from 40.29–67.65%, 13.24–20.09 °brix, 7.74–21.04 nmol/g DW, 9.69–15.98 cm, 97.80–171.34 cm, 289.15–420.33 grain and 4.15–10.23 t ha−1 respectively. The FCY, yield components and PFR values in the second year that had a higher temperature and lower relative humidity were lower compared to the first year, while ABA and TSS values were higher in the second year. Statistically significant correlations were recorded between the parameters investigated except FCY and TSS. The FCY and other parameters of sweet corn varieties, which produced high ABA phytohormone, were high, and the ABA hormone significantly contributed to plant growth under stress conditions. The results revealed that the PFR physiological parameter and ABA hormone in the plants provide important information about stress level and stress tolerance level of the cultivars, respectively. Despite adverse environmental stress conditions, the FCY of ŞADA-18.7 variety, one of the candidate varieties, was higher than that of the control and the mean value of the experiment.
bibliographic citation: Tas et al. (2021) Morpho-physiological effects of environmental stress on yield and quality of sweet corn varieties (Zea mays L.). PeerJ 9:e12613 https://doi.org/10.7717/peerj.12613
date submitted: 2021-06-08
date accepted: 2021-11-18
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tas
  given name: Timucin
author list: Agent
  family name: Mutlu
  given name: Arzu
doi: 10.7717/peerj.12613
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Tas and Mutlu
attribution name: Tas and Mutlu

Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears
type: item
type: AcademicArticle
description: The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.
format: application/pdf
format: text/html
creator: Yarui Wei
creator: Shuliang Zhao
creator: Na Liu
creator: Yuxing Zhang
subject: Agricultural Science
subject: Bioinformatics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12617
publisher: PeerJ Inc.
rights: © 2021 Wei et al.
abstract: The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) plays a master regulatory role in the salicylic acid (SA) signal transduction pathway and plant systemic acquired resistance (SAR). Members of the NPR1-like gene family have been reported to the associated with biotic/abiotic stress in many plants, however the genome-wide characterization of NPR1-like genes has not been carried out in Chinese pear (Pyrus bretschneideri Reld). In this study, a systematic analysis was conducted on the characteristics of the NPR1-like genes in P. bretschneideri Reld at the whole-genome level. A total nine NPR1-like genes were detected which eight genes were located on six chromosomes and one gene was mapped to scaffold. Based on the phylogenetic analysis, the nine PbrNPR1-like proteins were divided into three clades (Clades I–III) had similar gene structure, domain and conserved motifs. We sorted the cis-acting elements into three clades, including plant growth and development, stress responses, and hormone responses in the promoter regions of PbrNPR1-like genes. The result of qPCR analysis showed that expression diversity of PbrNPR1-like genes in various tissues. All the genes were up-regulated after SA treatment in leaves except for Pbrgene8896. PbrNPR1-like genes showed circadian rhythm and significantly different expression levels after inoculation with Alternaria alternata. These findings provide a solid insight for understanding the functions and evolution of PbrNPR1-like genes in Chinese pear.
bibliographic citation: Wei et al. (2021) Genome-wide identification, evolution, and expression analysis of the NPR1-like gene family in pears. PeerJ 9:e12617 https://doi.org/10.7717/peerj.12617
date submitted: 2021-04-07
date accepted: 2021-11-18
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Yarui
author list: Agent
  family name: Zhao
  given name: Shuliang
author list: Agent
  family name: Liu
  given name: Na
author list: Agent
  family name: Zhang
  given name: Yuxing
doi: 10.7717/peerj.12617
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: © 2021 Wei et al.
attribution name: Wei et al.

Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes
type: item
type: AcademicArticle
description: Background Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific. Methods We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22–39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations. Results In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these difference…
format: application/pdf
format: text/html
creator: Hsiu-Chin Lin
creator: Chia-Jung Tsai
creator: Hui-Yu Wang
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Marine Biology
description: doi:10.7717/peerj.12639
publisher: PeerJ Inc.
rights: © 2021 Lin et al.
abstract: Background Species-specific information on distribution and demographic patterns provides important implications for conservation and fisheries management. However, such information is often lacking for morphologically-similar species, which may lead to biases in the assessments of these species and even decrease effort towards sustainable management. Here, we aimed to uncover the distribution range, population structure and demographic history for four exploited Trichiurus cutlassfishes using genetics. These cutlassfishes contribute substantial global fisheries catch, with a high proportion of catch harvested from the NW Pacific. Methods We chose the widely available mitochondrial 16S ribosomal RNA (16S) as the genetic marker for cutlassfishes. We compiled the 16S sequence data from both the GenBank and a survey of trawler catch samples along the NW Pacific coasts 22–39°N. Genealogical relationships within each species was visualized with haplotype networks and potential population differentiations were further evaluated with AMOVA. Demographic histories were estimated using neutrality test, mismatch analysis, and the Bayesian skyline plot. The reconstructed phylogenetic trees were used to delimit and estimate the divergence time of species and included populations. Results In each of two cosmopolitan species, T. lepturus and T. nanhaiensis, we observed distinct populations along the coasts of warm oceans; such population differentiation might result from historical geographic barriers in the Pleistocene. In the NW Pacific, four Trichiurus species vary in their distribution habitats, which reflect differential ecological niches among these species. The small-sized T. brevis are primarily found in nearshore habitats; the warm-affiliated T. nanhaiensis are present along the path of the Kuroshio Current; the cold-affiliated T. japonicus spatially diverged from the widely-distributed T. lepturus, with the latter mainly occupy in warmer regions. Despite these difference…
bibliographic citation: Lin et al. (2021) Variation in global distribution, population structures, and demographic history for four Trichiurus cutlassfishes. PeerJ 9:e12639 https://doi.org/10.7717/peerj.12639
date submitted: 2021-06-17
date accepted: 2021-11-24
issued: 2021-12-15
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Hsiu-Chin
author list: Agent
  family name: Tsai
  given name: Chia-Jung
author list: Agent
  family name: Wang
  given name: Hui-Yu
doi: 10.7717/peerj.12639
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-12-15
copyright: ©2021 Lin et al.
attribution name: Lin et al.

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