PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Histological study of seventeen organs from dugong (Dugong dugon)
items: Estimated projection of oral squamous cell carcinoma annual incidence from twenty years registry data: a retrospective cross-sectional study in Indonesia
items: Development and validation of the dizziness fear-avoidance behaviours and beliefs inventory for patients with vestibular disorders
items: Evaluation of phosphate rock as the only source of phosphorus for the growth of tall and semi-dwarf durum wheat and rye plants using digital phenotyping
items: Antimicrobial resistance and molecular typing of Staphylococcus aureus isolates from raw milk in Hunan Province
items: Genome-wide identification of Apetala2 gene family in Hypericum perforatum L and expression profiles in response to different abiotic and hormonal treatments
items: Low-dose lipopolysaccharide inhibits spinal cord injury-induced neuronal apoptosis by regulating autophagy through the lncRNA MALAT1/Nrf2 axis
items: A retrospective study of consistency between immunohistochemistry and polymerase chain reaction of microsatellite instability in endometrial cancer
items: Impact of dormancy periods on some physiological and biochemical indices of potato tubers
items: First report of ‘Candidatus Phytoplasma asteris’ associated with yellowing, scorching and decline of almond trees in India

Histological study of seventeen organs from dugong (Dugong dugon)
type: item
type: AcademicArticle
description: Background Dugongs are marine mammals with a crescent-shaped tail fluke and a concave trailing margin that belong to the family Dugongidae., They are distributed widely in the warm coastal waters of the Indo-Pacific region. Importantly, the population of dugongs has decreased over the past decades as they have been classified as rare marine mammals. Previous studies have investigated the habitat and genetic diversity of dugongs. However, a comprehensive histological investigation of their tissue has not yet been conducted. This study provides unique insight into the organs of dugongs and compares them with other mammal species. Methods Tissue sections were stained with Harris’s hematoxylin and eosin Y. The histological structure of 17 organ tissues obtained from eight systems was included in this study. Tissue sections were obtained from the urinary system (kidney), muscular system (striated skeletal muscle and smooth muscle), cardiovascular system (cardiac muscle (ventricle), coronary artery, and coronary vein), respiratory system (trachea and lung), gastrointestinal system (esophagus, stomach, small intestine, liver, and pancreas), reproductive system (testis), lymphatic system (spleen and thymus), and endocrine system (pancreas). Results While most structures were similar to those of other mammal species, there were some differences in the tissue sections of dugongs when compared with other mammalian species and manatees. These include the kidneys of dugongs, which were non-lobular and had a smooth, elongated exterior resulting in a long medullary crest, whereas the dugong pyloric epithelium did not have overlying stratified squamous cells and was noticably different from the Florida manatee. Discussion Histological information obtained from various organs of the dugong can serve as an essential foundation of basal data for future microanatomical studies. This information can also be used as high-value data in the diagnosis and pathogenesis of sick dugongs or tho…
format: application/pdf
format: text/html
creator: Patcharaporn Kaewmong
creator: Pathompong Jongjit
creator: Araya Boonkasemsanti
creator: Kongkiat Kittiwattanawong
creator: Piyamat Kongtueng
creator: Pitchaya Matchimakul
creator: Wasan Tangphokhanon
creator: Prapawadee Pirintr
creator: Jaruwan Khonmee
creator: Songphon Buddhasiri
creator: Promporn Piboon
creator: Sonthaya Umsumarng
creator: Raktham Mektrirat
creator: Korakot Nganvongpanit
creator: Wanpitak Pongkan
subject: Conservation Biology
subject: Veterinary Medicine
subject: Zoology
subject: Anatomy and Physiology
subject: Histology
description: doi:10.7717/peerj.15859
publisher: PeerJ Inc.
rights: © 2023 Kaewmong et al.
abstract: Background Dugongs are marine mammals with a crescent-shaped tail fluke and a concave trailing margin that belong to the family Dugongidae., They are distributed widely in the warm coastal waters of the Indo-Pacific region. Importantly, the population of dugongs has decreased over the past decades as they have been classified as rare marine mammals. Previous studies have investigated the habitat and genetic diversity of dugongs. However, a comprehensive histological investigation of their tissue has not yet been conducted. This study provides unique insight into the organs of dugongs and compares them with other mammal species. Methods Tissue sections were stained with Harris’s hematoxylin and eosin Y. The histological structure of 17 organ tissues obtained from eight systems was included in this study. Tissue sections were obtained from the urinary system (kidney), muscular system (striated skeletal muscle and smooth muscle), cardiovascular system (cardiac muscle (ventricle), coronary artery, and coronary vein), respiratory system (trachea and lung), gastrointestinal system (esophagus, stomach, small intestine, liver, and pancreas), reproductive system (testis), lymphatic system (spleen and thymus), and endocrine system (pancreas). Results While most structures were similar to those of other mammal species, there were some differences in the tissue sections of dugongs when compared with other mammalian species and manatees. These include the kidneys of dugongs, which were non-lobular and had a smooth, elongated exterior resulting in a long medullary crest, whereas the dugong pyloric epithelium did not have overlying stratified squamous cells and was noticably different from the Florida manatee. Discussion Histological information obtained from various organs of the dugong can serve as an essential foundation of basal data for future microanatomical studies. This information can also be used as high-value data in the diagnosis and pathogenesis of sick dugongs or tho…
bibliographic citation: Kaewmong et al. (2023) Histological study of seventeen organs from dugong (Dugong dugon). PeerJ 11:e15859 https://doi.org/10.7717/peerj.15859
date submitted: 2023-04-27
date accepted: 2023-07-17
issued: 2023-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kaewmong
  given name: Patcharaporn
author list: Agent
  family name: Jongjit
  given name: Pathompong
author list: Agent
  family name: Boonkasemsanti
  given name: Araya
author list: Agent
  family name: Kittiwattanawong
  given name: Kongkiat
author list: Agent
  family name: Kongtueng
  given name: Piyamat
author list: Agent
  family name: Matchimakul
  given name: Pitchaya
author list: Agent
  family name: Tangphokhanon
  given name: Wasan
author list: Agent
  family name: Pirintr
  given name: Prapawadee
author list: Agent
  family name: Khonmee
  given name: Jaruwan
author list: Agent
  family name: Buddhasiri
  given name: Songphon
author list: Agent
  family name: Piboon
  given name: Promporn
author list: Agent
  family name: Umsumarng
  given name: Sonthaya
author list: Agent
  family name: Mektrirat
  given name: Raktham
author list: Agent
  family name: Nganvongpanit
  given name: Korakot
author list: Agent
  family name: Pongkan
  given name: Wanpitak
doi: 10.7717/peerj.15859
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-29
copyright: © 2023 Kaewmong et al.
attribution name: Kaewmong et al.

Estimated projection of oral squamous cell carcinoma annual incidence from twenty years registry data: a retrospective cross-sectional study in Indonesia
type: item
type: AcademicArticle
description: Background The incidence of oral squamous cell carcinoma (OSCC) has not been well documented in Indonesia. Thus, we aimed to analyze trends and clinicopathological profiles of OSCC cases in Indonesia, focusing on differences between age and sex groups. Methods A cross-sectional study was conducted in Indonesia’s main referral hospital, analyzing 1,093 registered OSCC cases from 2001 to 2020. Trend analysis was performed using Joinpoint regression analysis to determine the annual percentage change (APC) for overall cases and each case group based on age, sex, and anatomical subsites. APC significance was assessed using a Monte Carlo permutation test. The projection of case numbers for the following 5 years (2021–2025) was estimated using linear/non-linear regression analysis and presented as a mathematical function. The significance of the trend slope was measured using an ANOVA test. Demographic and clinicopathological characteristics of OSCC were analyzed according to age and sex, and their comparative analysis was assessed using Chi-square and its alternatives. Results The incidence of OSCC in female patients and in the tongue and buccal mucosa showed a positive trend (APC 2.06%; 3.48%; 8.62%, respectively). Moreover, the incidence of OSCC overall, and in women with OSCC, is projected to increase significantly in the next 5 years following the quadratic model. The mean age of patients was 51.09 ± 14.36 years, with male patients being younger than female patients. The male-to-female ratio was 1.15, and 36.5% of these patients were categorized as young (≤45 years old). The tongue was the predominantly affected site. Prominent pathologic characteristics included well-differentiation, keratinization, and grade I of Bryne’s (1992) cellular differentiation stage. Most patients presented with advanced staging, lymphovascular invasion, and uninvaded margins. Tumor sites and staging varied according to age, while age and tumor sites differed between sexes. Conclusion The r…
format: application/pdf
format: text/html
creator: Nur Rahadiani
creator: Muhammad Habiburrahman
creator: Marini Stephanie
creator: Diah Rini Handjari
creator: Ening Krisnuhoni
subject: Epidemiology
subject: Global Health
subject: Oncology
subject: Pathology
subject: Histology
description: doi:10.7717/peerj.15911
publisher: PeerJ Inc.
rights: © 2023 Rahadiani et al.
abstract: Background The incidence of oral squamous cell carcinoma (OSCC) has not been well documented in Indonesia. Thus, we aimed to analyze trends and clinicopathological profiles of OSCC cases in Indonesia, focusing on differences between age and sex groups. Methods A cross-sectional study was conducted in Indonesia’s main referral hospital, analyzing 1,093 registered OSCC cases from 2001 to 2020. Trend analysis was performed using Joinpoint regression analysis to determine the annual percentage change (APC) for overall cases and each case group based on age, sex, and anatomical subsites. APC significance was assessed using a Monte Carlo permutation test. The projection of case numbers for the following 5 years (2021–2025) was estimated using linear/non-linear regression analysis and presented as a mathematical function. The significance of the trend slope was measured using an ANOVA test. Demographic and clinicopathological characteristics of OSCC were analyzed according to age and sex, and their comparative analysis was assessed using Chi-square and its alternatives. Results The incidence of OSCC in female patients and in the tongue and buccal mucosa showed a positive trend (APC 2.06%; 3.48%; 8.62%, respectively). Moreover, the incidence of OSCC overall, and in women with OSCC, is projected to increase significantly in the next 5 years following the quadratic model. The mean age of patients was 51.09 ± 14.36 years, with male patients being younger than female patients. The male-to-female ratio was 1.15, and 36.5% of these patients were categorized as young (≤45 years old). The tongue was the predominantly affected site. Prominent pathologic characteristics included well-differentiation, keratinization, and grade I of Bryne’s (1992) cellular differentiation stage. Most patients presented with advanced staging, lymphovascular invasion, and uninvaded margins. Tumor sites and staging varied according to age, while age and tumor sites differed between sexes. Conclusion The r…
bibliographic citation: Rahadiani et al. (2023) Estimated projection of oral squamous cell carcinoma annual incidence from twenty years registry data: a retrospective cross-sectional study in Indonesia. PeerJ 11:e15911 https://doi.org/10.7717/peerj.15911
date submitted: 2022-12-22
date accepted: 2023-07-26
issued: 2023-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahadiani
  given name: Nur
author list: Agent
  family name: Habiburrahman
  given name: Muhammad
author list: Agent
  family name: Stephanie
  given name: Marini
author list: Agent
  family name: Handjari
  given name: Diah Rini
author list: Agent
  family name: Krisnuhoni
  given name: Ening
doi: 10.7717/peerj.15911
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-29
copyright: © 2023 Rahadiani et al.
attribution name: Rahadiani et al.

Development and validation of the dizziness fear-avoidance behaviours and beliefs inventory for patients with vestibular disorders
type: item
type: AcademicArticle
description: The purpose of this study is to present the development and analysis of the factorial structure and psychometric properties of a new self-administered questionnaire (Dizziness Fear-Avoidance Behaviours and Beliefs Inventory (D-FABBI)) designed to measure fear-avoidance behaviors and cognitions related to dizziness disability. A mixed-method design combining a qualitative study with an observational and cross-sectional study was employed to develop (content validity) and psychometrically validate (construct validity, reliability, and convergent/discriminant validity) a new instrument. A total of 198 patients with vestibular disorders (acute vestibular syndrome (AVS), 23.2%; chronic vestibular syndrome (CVS), 35.4%; and episodic vestibular syndrome (EVS) 41.4%) were recruited. Sociodemographic characteristics, the Dizziness Handicap Inventory (DHI) and the Hospital Anxiety and Depression Scale (HADS) and D-FABBI were evaluated. The final version of the D-FABBI consists of 17 items distributed across two subscales: activities of daily living fear-avoidance and movement fear-avoidance. The D-FABBI showed high internal consistency (Cronbach α = 0.932; 95% CI [0.91–0.94]) and so did the subscales (Cronbach α > 0.8). The exploratory structural equation model and confirmatory factor analysis provided better fit results, with a comparative fit index and root mean square error of approximation values of 0.907 to 0.081. No floor or ceiling effects were identified. There was a positive, significant, and moderate-strong magnitude correlation with the total DHI (r = 0.62) and low-moderate with respect to the HADS depression (r = 0.35) and HADS anxiety subscales (r = 0.26). The patients with CVS had a higher D-FABBI score than those with AVS or EVS. The D-FABBI appears to be a valid and reliable instrument for measuring the fear-avoidance behaviors and cognition related to dizziness disability of patients with vestibular disorders.
format: application/pdf
format: text/html
creator: Roy La Touche
creator: Rodrigo Castillejos-Carrasco-Muñoz
creator: María Cruz Tapia-Toca
creator: Joaquín Pardo-Montero
creator: Sergio Lerma-Lara
creator: Irene de la Rosa-Díaz
creator: Miguel Ángel Sorrel-Luján
creator: Alba Paris-Alemany
subject: Kinesiology
subject: Neurology
subject: Otorhinolaryngology
subject: Psychiatry and Psychology
subject: Rehabilitation
description: doi:10.7717/peerj.15940
publisher: PeerJ Inc.
rights: © 2023 La Touche et al.
abstract: The purpose of this study is to present the development and analysis of the factorial structure and psychometric properties of a new self-administered questionnaire (Dizziness Fear-Avoidance Behaviours and Beliefs Inventory (D-FABBI)) designed to measure fear-avoidance behaviors and cognitions related to dizziness disability. A mixed-method design combining a qualitative study with an observational and cross-sectional study was employed to develop (content validity) and psychometrically validate (construct validity, reliability, and convergent/discriminant validity) a new instrument. A total of 198 patients with vestibular disorders (acute vestibular syndrome (AVS), 23.2%; chronic vestibular syndrome (CVS), 35.4%; and episodic vestibular syndrome (EVS) 41.4%) were recruited. Sociodemographic characteristics, the Dizziness Handicap Inventory (DHI) and the Hospital Anxiety and Depression Scale (HADS) and D-FABBI were evaluated. The final version of the D-FABBI consists of 17 items distributed across two subscales: activities of daily living fear-avoidance and movement fear-avoidance. The D-FABBI showed high internal consistency (Cronbach α = 0.932; 95% CI [0.91–0.94]) and so did the subscales (Cronbach α > 0.8). The exploratory structural equation model and confirmatory factor analysis provided better fit results, with a comparative fit index and root mean square error of approximation values of 0.907 to 0.081. No floor or ceiling effects were identified. There was a positive, significant, and moderate-strong magnitude correlation with the total DHI (r = 0.62) and low-moderate with respect to the HADS depression (r = 0.35) and HADS anxiety subscales (r = 0.26). The patients with CVS had a higher D-FABBI score than those with AVS or EVS. The D-FABBI appears to be a valid and reliable instrument for measuring the fear-avoidance behaviors and cognition related to dizziness disability of patients with vestibular disorders.
bibliographic citation: La Touche et al. (2023) Development and validation of the dizziness fear-avoidance behaviours and beliefs inventory for patients with vestibular disorders. PeerJ 11:e15940 https://doi.org/10.7717/peerj.15940
date submitted: 2023-03-15
date accepted: 2023-07-31
issued: 2023-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: La Touche
  given name: Roy
author list: Agent
  family name: Castillejos-Carrasco-Muñoz
  given name: Rodrigo
author list: Agent
  family name: Tapia-Toca
  given name: María Cruz
author list: Agent
  family name: Pardo-Montero
  given name: Joaquín
author list: Agent
  family name: Lerma-Lara
  given name: Sergio
author list: Agent
  family name: de la Rosa-Díaz
  given name: Irene
author list: Agent
  family name: Sorrel-Luján
  given name: Miguel Ángel
author list: Agent
  family name: Paris-Alemany
  given name: Alba
doi: 10.7717/peerj.15940
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-29
copyright: © 2023 La Touche et al.
attribution name: La Touche et al.

Evaluation of phosphate rock as the only source of phosphorus for the growth of tall and semi-dwarf durum wheat and rye plants using digital phenotyping
type: item
type: AcademicArticle
description: Background Phosphorus nutrition is important for obtaining high yields of crop plants. However, wheat plants are known to be almost incapable of taking up phosphorus from insoluble phosphate sources, and reduced height genes are supposed to decrease this ability further. Methods We performed a pot experiment using Triticum durum Desf. tall spring variety LD222, its near-isogenic semidwarf line carrying Rht17 (Reduced height 17) gene, and winter rye (Secale cereale L.) variety Chulpan. The individual plants were grown in quartz sand. The phosphorus was provided either as phosphate rock powder mixed with sand, or as monopotassium phosphate solution (normal nutrition control) or was not supplemented at all (no-phosphorus control). Other nutrients were provided in soluble form. During experiment the plants were assessed using the TraitFinder (Phenospex Ltd., Heerlen, Netherlands) digital phenotyping system for a standard set of parameters. Double scan with 90 degrees turns of pots around vertical axis vs. single scan were compared for accuracy of phenotyping. Results The phenotyping showed that at least 20 days of growth after seedling emergence were necessary to get stable differences between genotypes. After this initial period, phenotyping confirmed poor ability of wheat to grow on substrate with phosphate rock as the only source of phosphorus compared to rye; however, Rht17 did not cause an additional reduction in growth parameters other than plant height under this variant of substrate. The agreement between digital phenotyping and conventionally measured traits was at previously reported level for grasses (R2 = 0.85 and 0.88 for digital biomass and 3D leaf area vs. conventionally measured biomass and leaf area, single scan). Among vegetation indices, only the normalized differential vegetation index (NDVI) and the green leaf index (GLI) showed significant correlations with manually measured traits, including the percentage of dead leaves area. The double scan impr…
format: application/pdf
format: text/html
creator: Mikhail Bazhenov
creator: Dmitry Litvinov
creator: Gennady Karlov
creator: Mikhail Divashuk
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.15972
publisher: PeerJ Inc.
rights: © 2023 Bazhenov et al.
abstract: Background Phosphorus nutrition is important for obtaining high yields of crop plants. However, wheat plants are known to be almost incapable of taking up phosphorus from insoluble phosphate sources, and reduced height genes are supposed to decrease this ability further. Methods We performed a pot experiment using Triticum durum Desf. tall spring variety LD222, its near-isogenic semidwarf line carrying Rht17 (Reduced height 17) gene, and winter rye (Secale cereale L.) variety Chulpan. The individual plants were grown in quartz sand. The phosphorus was provided either as phosphate rock powder mixed with sand, or as monopotassium phosphate solution (normal nutrition control) or was not supplemented at all (no-phosphorus control). Other nutrients were provided in soluble form. During experiment the plants were assessed using the TraitFinder (Phenospex Ltd., Heerlen, Netherlands) digital phenotyping system for a standard set of parameters. Double scan with 90 degrees turns of pots around vertical axis vs. single scan were compared for accuracy of phenotyping. Results The phenotyping showed that at least 20 days of growth after seedling emergence were necessary to get stable differences between genotypes. After this initial period, phenotyping confirmed poor ability of wheat to grow on substrate with phosphate rock as the only source of phosphorus compared to rye; however, Rht17 did not cause an additional reduction in growth parameters other than plant height under this variant of substrate. The agreement between digital phenotyping and conventionally measured traits was at previously reported level for grasses (R2 = 0.85 and 0.88 for digital biomass and 3D leaf area vs. conventionally measured biomass and leaf area, single scan). Among vegetation indices, only the normalized differential vegetation index (NDVI) and the green leaf index (GLI) showed significant correlations with manually measured traits, including the percentage of dead leaves area. The double scan impr…
bibliographic citation: Bazhenov et al. (2023) Evaluation of phosphate rock as the only source of phosphorus for the growth of tall and semi-dwarf durum wheat and rye plants using digital phenotyping. PeerJ 11:e15972 https://doi.org/10.7717/peerj.15972
date submitted: 2023-03-03
date accepted: 2023-08-06
issued: 2023-08-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bazhenov
  given name: Mikhail
author list: Agent
  family name: Litvinov
  given name: Dmitry
author list: Agent
  family name: Karlov
  given name: Gennady
author list: Agent
  family name: Divashuk
  given name: Mikhail
doi: 10.7717/peerj.15972
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-29
copyright: © 2023 Bazhenov et al.
attribution name: Bazhenov et al.

Antimicrobial resistance and molecular typing of Staphylococcus aureus isolates from raw milk in Hunan Province
type: item
type: AcademicArticle
description: Background Staphylococcus aureus is one of the most important foodborne pathogens in the world and the main cause of dairy cow mastitis. Few studies have investigated the epidemic pedigree of S. aureus of bovine origin in Hunan, China. Therefore, we aimed to analyze the capsular polysaccharides (CP), molecular typing, and antibiotic resistance characteristics of S. aureus isolated from raw milk of dairy farms in Hunan Province. Methods Between 2018 and 2022, 681 raw milk samples were collected from dairy cows from farms in Changsha, Changde, Shaoyang, Yongzhou, and Chenzhou in Hunan Province. S. aureus was isolated from these samples, and the isolates were subjected to molecular typing, CP typing, and determination of antibiotic resistance through broth dilution and polymerase chain reaction (PCR). Results From 681 raw milk samples, 76 strains of S. aureus were isolated. The pathogenicity of 76 isolates was determined preliminarily by detecting cp5 and cp8 CP genes. Eighteen types of antimicrobial resistance phenotypes of 76 S. aureus strains were detected by the broth dilution method, and 11 kinds of related resistance genes were amplified by PCR. The S. aureus isolates had CP5 (42.10%) and CP8 (57.89%). S. aureus had a multiple antimicrobial resistance rate of 26.75%. The isolated strains had the highest resistance rate to penicillin (82.89%) and showed varying degrees of resistance to other drugs, but no isolate showed resistance to doxycycline. The 76 isolates all carried two or more antibiotic resistance genes, with a maximum of eight antibiotics resistance genes. FemB was detected in all isolates, but none of isolates carried vanA, ermA, or glrA. The 76 isolates were divided into 22 sequence types (ST) and 20 spa types by MLST and spa typing, and the number of t796-ST7 (n = 15) isolates was the highest, which may be the major epidemic strain of multidrug-resistant S. aureus. Conclusion The present findings indicate the need to increase production of the CP8 S.…
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format: text/html
creator: Keming Ning
creator: Rushun Zhou
creator: Manxiang Li
subject: Agricultural Science
subject: Food Science and Technology
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.15847
publisher: PeerJ Inc.
rights: © 2023 Ning et al.
abstract: Background Staphylococcus aureus is one of the most important foodborne pathogens in the world and the main cause of dairy cow mastitis. Few studies have investigated the epidemic pedigree of S. aureus of bovine origin in Hunan, China. Therefore, we aimed to analyze the capsular polysaccharides (CP), molecular typing, and antibiotic resistance characteristics of S. aureus isolated from raw milk of dairy farms in Hunan Province. Methods Between 2018 and 2022, 681 raw milk samples were collected from dairy cows from farms in Changsha, Changde, Shaoyang, Yongzhou, and Chenzhou in Hunan Province. S. aureus was isolated from these samples, and the isolates were subjected to molecular typing, CP typing, and determination of antibiotic resistance through broth dilution and polymerase chain reaction (PCR). Results From 681 raw milk samples, 76 strains of S. aureus were isolated. The pathogenicity of 76 isolates was determined preliminarily by detecting cp5 and cp8 CP genes. Eighteen types of antimicrobial resistance phenotypes of 76 S. aureus strains were detected by the broth dilution method, and 11 kinds of related resistance genes were amplified by PCR. The S. aureus isolates had CP5 (42.10%) and CP8 (57.89%). S. aureus had a multiple antimicrobial resistance rate of 26.75%. The isolated strains had the highest resistance rate to penicillin (82.89%) and showed varying degrees of resistance to other drugs, but no isolate showed resistance to doxycycline. The 76 isolates all carried two or more antibiotic resistance genes, with a maximum of eight antibiotics resistance genes. FemB was detected in all isolates, but none of isolates carried vanA, ermA, or glrA. The 76 isolates were divided into 22 sequence types (ST) and 20 spa types by MLST and spa typing, and the number of t796-ST7 (n = 15) isolates was the highest, which may be the major epidemic strain of multidrug-resistant S. aureus. Conclusion The present findings indicate the need to increase production of the CP8 S.…
bibliographic citation: Ning et al. (2023) Antimicrobial resistance and molecular typing of Staphylococcus aureus isolates from raw milk in Hunan Province. PeerJ 11:e15847 https://doi.org/10.7717/peerj.15847
date submitted: 2023-02-24
date accepted: 2023-07-14
issued: 2023-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ning
  given name: Keming
author list: Agent
  family name: Zhou
  given name: Rushun
author list: Agent
  family name: Li
  given name: Manxiang
doi: 10.7717/peerj.15847
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-28
copyright: ©2023 Ning et al.
attribution name: Ning et al.

Genome-wide identification of Apetala2 gene family in Hypericum perforatum L and expression profiles in response to different abiotic and hormonal treatments
type: item
type: AcademicArticle
description: The Apetala2 (AP2) gene family of transcription factors (TFs) play important functions in plant development, hormonal response, and abiotic stress. To reveal the biological functions and the expression profiles of AP2 genes in Hypericum perforatum, genome-wide identification of HpAP2 family members was conducted. Methods We identified 21 AP2 TFs in H. perforatum using bioinformatic methods; their physical and chemical properties, gene structures, conserved motifs, evolutionary relationships, cis-acting elements, and expression patterns were investigated. Results We found that based on the structural characteristics and evolutionary relationships, the HpAP2 gene family can be divided into three subclasses: euANT, baselANT, and euAP2. A canonical HpAP2 TF shared a conserved protein structure, while a unique motif 6 was found in HpAP2_1, HpAP2_4, and HpAP2_5 from the euANT subgroup, indicating potential biological and regulatory functions of these genes. Furthermore, a total of 59 cis-acting elements were identified, most of which were associated with growth, development, and resistance to stress in plants. Transcriptomics data showed that 57.14% of the genes in the AP2 family were differentially expressed in four organs. For example, HpAP2_18 was specifically expressed in roots and stems, whereas HpAP2_17 and HpAP2_11 were specifically expressed in leaves and flowers, respectively. HpAP2_5, HpAP2_11, and HpAP2_18 showed tissue-specific expression patterns and responded positively to hormones and abiotic stresses. Conclusion These results demonstrated that the HpAP2 family genes are involved in diverse developmental processes and generate responses to abiotic stress conditions in H. perforatum. This article, for the first time, reports the identification and expression profiles of the AP2 family genes in H. perforatum, laying the foundation for future functional studies with these genes.
format: application/pdf
format: text/html
creator: Yonghui Li
creator: Yao Chen
creator: Ruyi Yi
creator: Xueting Yu
creator: Xiangmeng Guo
creator: Fan YiLin
creator: Xiao-Jun Zhou
creator: Huiyuan Ya
creator: Xiangli Yu
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15883
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: The Apetala2 (AP2) gene family of transcription factors (TFs) play important functions in plant development, hormonal response, and abiotic stress. To reveal the biological functions and the expression profiles of AP2 genes in Hypericum perforatum, genome-wide identification of HpAP2 family members was conducted. Methods We identified 21 AP2 TFs in H. perforatum using bioinformatic methods; their physical and chemical properties, gene structures, conserved motifs, evolutionary relationships, cis-acting elements, and expression patterns were investigated. Results We found that based on the structural characteristics and evolutionary relationships, the HpAP2 gene family can be divided into three subclasses: euANT, baselANT, and euAP2. A canonical HpAP2 TF shared a conserved protein structure, while a unique motif 6 was found in HpAP2_1, HpAP2_4, and HpAP2_5 from the euANT subgroup, indicating potential biological and regulatory functions of these genes. Furthermore, a total of 59 cis-acting elements were identified, most of which were associated with growth, development, and resistance to stress in plants. Transcriptomics data showed that 57.14% of the genes in the AP2 family were differentially expressed in four organs. For example, HpAP2_18 was specifically expressed in roots and stems, whereas HpAP2_17 and HpAP2_11 were specifically expressed in leaves and flowers, respectively. HpAP2_5, HpAP2_11, and HpAP2_18 showed tissue-specific expression patterns and responded positively to hormones and abiotic stresses. Conclusion These results demonstrated that the HpAP2 family genes are involved in diverse developmental processes and generate responses to abiotic stress conditions in H. perforatum. This article, for the first time, reports the identification and expression profiles of the AP2 family genes in H. perforatum, laying the foundation for future functional studies with these genes.
bibliographic citation: Li et al. (2023) Genome-wide identification of Apetala2 gene family in Hypericum perforatum L and expression profiles in response to different abiotic and hormonal treatments. PeerJ 11:e15883 https://doi.org/10.7717/peerj.15883
date submitted: 2023-05-17
date accepted: 2023-07-20
issued: 2023-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yonghui
author list: Agent
  family name: Chen
  given name: Yao
author list: Agent
  family name: Yi
  given name: Ruyi
author list: Agent
  family name: Yu
  given name: Xueting
author list: Agent
  family name: Guo
  given name: Xiangmeng
author list: Agent
  family name: YiLin
  given name: Fan
author list: Agent
  family name: Zhou
  given name: Xiao-Jun
author list: Agent
  family name: Ya
  given name: Huiyuan
author list: Agent
  family name: Yu
  given name: Xiangli
doi: 10.7717/peerj.15883
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-28
copyright: © 2023 Li et al.
attribution name: Li et al.

Low-dose lipopolysaccharide inhibits spinal cord injury-induced neuronal apoptosis by regulating autophagy through the lncRNA MALAT1/Nrf2 axis
type: item
type: AcademicArticle
description: Background Spinal cord injury (SCI) is a neurological disease associated with a high disability rate. Low-dose lipopolysaccharide (LPS) has been reported to activate cross-immune tolerance and alleviate the effects of various traumatic stimuli. The present study aimed to explore the effect of LPS on SCI and the potential molecular mechanism. Methods Male Sprague-Dawley (SD) rats were used to established an in vivo SCI model and were intraperitoneally injected with lentivirus particles encoding a MALAT1 small interfering RNA (siRNA) on day 10 prior to SCI and with 0.2 mg/kg LPS 72 h prior to SCI. Basso, Beattie, and Bresnahan (BBB) scoring; HE staining; and TUNEL assay were used to assess neurological function and pathophysiological changes. Western blot and immunohistochemistry (IHC) were used to detect cell autophagy and Nrf2 nuclear translocation. PC12 cells were exposed to oxygen-glucose deprivation/reoxygenation (OGD/R) to establish an in vitro SCI model. In vitro SCI model cells were pretreated with LPS and transfected with siMALAT1 or MALAT1 overexpression plasmid aimed at knocking down MALAT1 or overexpressing MALAT1. The cell counting kit-8 (CCK-8) assay was used to measure the toxicity of LPS towards PC12 cells. Flow cytometry and immunofluorescence analysis were performed to investigate cell apoptosis and Nrf2 nuclear translocation. Results SCI rats preconditioned with low-dose LPS had higher BBB scores, reduced SCI injury, increased MALAT1 expression and activated autophagy and Nrf2 nuclear translocation in the in vivo SCI model. In the in vitro SCI model, low-dose LPS treatment suppressed the apoptotic ratio of PC12 cells, increased MALAT1 expression, activated autophagy, and promoted Nrf2 nuclear translocation. Silencing MALAT1 exacerbated OGD/R injury in vitro and weakened the protective effect of low-dose LPS. Overexpression of MALAT1 inhibits OGD/R-induced apoptosis by inducing autophagy and promoting Nrf2 nuclear translocation. This was also been co…
format: application/pdf
format: text/html
creator: Jianhua Hu
creator: Kun Huang
creator: Feilong Bao
creator: Shixiao Zhong
creator: Qianbo Fan
creator: Weichao Li
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Histology
description: doi:10.7717/peerj.15919
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: Background Spinal cord injury (SCI) is a neurological disease associated with a high disability rate. Low-dose lipopolysaccharide (LPS) has been reported to activate cross-immune tolerance and alleviate the effects of various traumatic stimuli. The present study aimed to explore the effect of LPS on SCI and the potential molecular mechanism. Methods Male Sprague-Dawley (SD) rats were used to established an in vivo SCI model and were intraperitoneally injected with lentivirus particles encoding a MALAT1 small interfering RNA (siRNA) on day 10 prior to SCI and with 0.2 mg/kg LPS 72 h prior to SCI. Basso, Beattie, and Bresnahan (BBB) scoring; HE staining; and TUNEL assay were used to assess neurological function and pathophysiological changes. Western blot and immunohistochemistry (IHC) were used to detect cell autophagy and Nrf2 nuclear translocation. PC12 cells were exposed to oxygen-glucose deprivation/reoxygenation (OGD/R) to establish an in vitro SCI model. In vitro SCI model cells were pretreated with LPS and transfected with siMALAT1 or MALAT1 overexpression plasmid aimed at knocking down MALAT1 or overexpressing MALAT1. The cell counting kit-8 (CCK-8) assay was used to measure the toxicity of LPS towards PC12 cells. Flow cytometry and immunofluorescence analysis were performed to investigate cell apoptosis and Nrf2 nuclear translocation. Results SCI rats preconditioned with low-dose LPS had higher BBB scores, reduced SCI injury, increased MALAT1 expression and activated autophagy and Nrf2 nuclear translocation in the in vivo SCI model. In the in vitro SCI model, low-dose LPS treatment suppressed the apoptotic ratio of PC12 cells, increased MALAT1 expression, activated autophagy, and promoted Nrf2 nuclear translocation. Silencing MALAT1 exacerbated OGD/R injury in vitro and weakened the protective effect of low-dose LPS. Overexpression of MALAT1 inhibits OGD/R-induced apoptosis by inducing autophagy and promoting Nrf2 nuclear translocation. This was also been co…
bibliographic citation: Hu et al. (2023) Low-dose lipopolysaccharide inhibits spinal cord injury-induced neuronal apoptosis by regulating autophagy through the lncRNA MALAT1/Nrf2 axis. PeerJ 11:e15919 https://doi.org/10.7717/peerj.15919
date submitted: 2023-05-05
date accepted: 2023-07-27
issued: 2023-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Jianhua
author list: Agent
  family name: Huang
  given name: Kun
author list: Agent
  family name: Bao
  given name: Feilong
author list: Agent
  family name: Zhong
  given name: Shixiao
author list: Agent
  family name: Fan
  given name: Qianbo
author list: Agent
  family name: Li
  given name: Weichao
doi: 10.7717/peerj.15919
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-28
copyright: ©2023 Hu et al.
attribution name: Hu et al.

A retrospective study of consistency between immunohistochemistry and polymerase chain reaction of microsatellite instability in endometrial cancer
type: item
type: AcademicArticle
description: Objectives Identification of endometrial cancers (EC) with mismatch repair deficiency (dMMR) or microsatellite instability-high (MSI-H) is essential for Lynch syndrome screening and treatment stratification. We aimed to assess the utility of immunohistochemistry (IHC) staining for MMR protein expression and polymerase chain reaction (PCR)-based MSI assays in EC and the correlation between MMR/MSI status and various clinicopathological parameters. Methods We reviewed the clinical and pathological information of 333 patients with EC. MMR protein expression was assessed as retained or lost to determine MMR status by IHC staining, and MSI status was identified by PCR capillary electrophoresis (PCR-CE) testing with a National Cancer Institute (NCI) panel. The correlation of MMR/MSI status with clinicopathological features was determined by statistical analysis. Discrepant results were further analyzed using an alternative PCR-CE MSI (Promega panel) method, MLH1 promoter methylation assays, and next-generation sequencing (NGS). Results Among the EC patients, the overall percentage of dMMR was 25.2%, and the overall percentage of MSI-H was 24%. Among the dMMR patients, 50 (59.5%) showed loss of MLH1 and PMS2 expression, 19 (22.6%) loss of MSH2 and MSH6 expression, and seven (8.3%) and eight (9.5%) loss of PMS2 and MSH6 expression, respectively. The dMMR subgroup was significantly younger than the pMMR subgroup, especially for <60-years-old patients (p = 0.038). In addition, we identified a strong correlation between MMR/MSI status and high-grade endometrioid or nonendometrioid components (p = 0.004 or p = 0.003). IHC staining and PCR-CE assay results showed a high level of overall concordance (98.8%, Cohen’s κ = 0.98). Four patients were found to have dMRR/MSS in both examinations. We reanalyzed them with additional methods. One case showed MLH1 promotor methylation, and the other three cases harbored MSH6 germline pathogenic variations. One of the cases with MSH6 deficien…
format: application/pdf
format: text/html
creator: Cheng Wang
creator: Wei Kuang
creator: Jing Zeng
creator: Yang Ren
creator: Qianqi Liu
creator: Huanxin Sun
creator: Min Feng
creator: Dongni Liang
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Oncology
subject: Pathology
subject: Women’s Health
description: doi:10.7717/peerj.15920
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Objectives Identification of endometrial cancers (EC) with mismatch repair deficiency (dMMR) or microsatellite instability-high (MSI-H) is essential for Lynch syndrome screening and treatment stratification. We aimed to assess the utility of immunohistochemistry (IHC) staining for MMR protein expression and polymerase chain reaction (PCR)-based MSI assays in EC and the correlation between MMR/MSI status and various clinicopathological parameters. Methods We reviewed the clinical and pathological information of 333 patients with EC. MMR protein expression was assessed as retained or lost to determine MMR status by IHC staining, and MSI status was identified by PCR capillary electrophoresis (PCR-CE) testing with a National Cancer Institute (NCI) panel. The correlation of MMR/MSI status with clinicopathological features was determined by statistical analysis. Discrepant results were further analyzed using an alternative PCR-CE MSI (Promega panel) method, MLH1 promoter methylation assays, and next-generation sequencing (NGS). Results Among the EC patients, the overall percentage of dMMR was 25.2%, and the overall percentage of MSI-H was 24%. Among the dMMR patients, 50 (59.5%) showed loss of MLH1 and PMS2 expression, 19 (22.6%) loss of MSH2 and MSH6 expression, and seven (8.3%) and eight (9.5%) loss of PMS2 and MSH6 expression, respectively. The dMMR subgroup was significantly younger than the pMMR subgroup, especially for <60-years-old patients (p = 0.038). In addition, we identified a strong correlation between MMR/MSI status and high-grade endometrioid or nonendometrioid components (p = 0.004 or p = 0.003). IHC staining and PCR-CE assay results showed a high level of overall concordance (98.8%, Cohen’s κ = 0.98). Four patients were found to have dMRR/MSS in both examinations. We reanalyzed them with additional methods. One case showed MLH1 promotor methylation, and the other three cases harbored MSH6 germline pathogenic variations. One of the cases with MSH6 deficien…
bibliographic citation: Wang et al. (2023) A retrospective study of consistency between immunohistochemistry and polymerase chain reaction of microsatellite instability in endometrial cancer. PeerJ 11:e15920 https://doi.org/10.7717/peerj.15920
date submitted: 2023-05-12
date accepted: 2023-07-28
issued: 2023-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Cheng
author list: Agent
  family name: Kuang
  given name: Wei
author list: Agent
  family name: Zeng
  given name: Jing
author list: Agent
  family name: Ren
  given name: Yang
author list: Agent
  family name: Liu
  given name: Qianqi
author list: Agent
  family name: Sun
  given name: Huanxin
author list: Agent
  family name: Feng
  given name: Min
author list: Agent
  family name: Liang
  given name: Dongni
doi: 10.7717/peerj.15920
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-28
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Impact of dormancy periods on some physiological and biochemical indices of potato tubers
type: item
type: AcademicArticle
description: Background Storage of potato tubers is an essential stage of the supply chain, from farm to consumer, to efficiently match supply and demand. However, the quality and yield of potatoes are influenced by physiological changes during storage. Methods This study tested the physiological and biochemical indices in three potato varieties (YunSu 108, YunSu 304 and YunSu 306) during their dormancy periods. Results Three potato varieties with different dormancy periods were used to follow changes in starch, protein and several enzymes during storage. The starch and sugar content of the long-dormant variety (YunSu 108, LDV) were stable, whereas those of the short-dormant variety (YunSu 306, SDV) were variable. Starch synthase activity in the three varieties was initially high, then decreased; the starch content of LDV was relatively stable, that of the medium-dormant variety (YunSu 304, MDV) increased with storage time and peaked at sprouting, and that of SDV was low but variable. The sucrose synthase activity of LDV was significantly higher (p < 0.05) than MDV and SDV in the middle storage period. Two spikes were observed in the invertase activity of SDV, whereas those of MDV and LDV were stable. The reducing sugar content of LDV increased significantly before sprouting, that of MDV slowly decreased and that of SDV dropped sharply. During the whole storage period, pectinase activity in LDV did not change significantly, whereas pectinase in MDV and SDV decreased. The cellulase and protein contents initially increased and then decreased in LDV, and steadily decreased in MDV and SDV. Conclusion The metabolic indices related to starch and sugar in the LDV were relatively stable during storage, whereas those of the SDV varied greatly. SDV showed increased sucrose, reducing sugars and cellulose; LDV PCA plots clustered in the positive quadrant of PC1 and the negative quadrant of PC2, with increased protein, sucrose synthase and starch; MDV had increased soluble starch synthase.
format: application/pdf
format: text/html
creator: Hao Liu
creator: Junhua Li
creator: Duanrong Zhou
creator: Wanhua Cai
creator: Muzammal Rehman
creator: Youhong Feng
creator: Yunxin Kong
creator: Xiaopeng Liu
creator: Shah Fahad
creator: Gang Deng
subject: Agricultural Science
subject: Biochemistry
subject: Ecology
subject: Food Science and Technology
description: doi:10.7717/peerj.15923
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Background Storage of potato tubers is an essential stage of the supply chain, from farm to consumer, to efficiently match supply and demand. However, the quality and yield of potatoes are influenced by physiological changes during storage. Methods This study tested the physiological and biochemical indices in three potato varieties (YunSu 108, YunSu 304 and YunSu 306) during their dormancy periods. Results Three potato varieties with different dormancy periods were used to follow changes in starch, protein and several enzymes during storage. The starch and sugar content of the long-dormant variety (YunSu 108, LDV) were stable, whereas those of the short-dormant variety (YunSu 306, SDV) were variable. Starch synthase activity in the three varieties was initially high, then decreased; the starch content of LDV was relatively stable, that of the medium-dormant variety (YunSu 304, MDV) increased with storage time and peaked at sprouting, and that of SDV was low but variable. The sucrose synthase activity of LDV was significantly higher (p < 0.05) than MDV and SDV in the middle storage period. Two spikes were observed in the invertase activity of SDV, whereas those of MDV and LDV were stable. The reducing sugar content of LDV increased significantly before sprouting, that of MDV slowly decreased and that of SDV dropped sharply. During the whole storage period, pectinase activity in LDV did not change significantly, whereas pectinase in MDV and SDV decreased. The cellulase and protein contents initially increased and then decreased in LDV, and steadily decreased in MDV and SDV. Conclusion The metabolic indices related to starch and sugar in the LDV were relatively stable during storage, whereas those of the SDV varied greatly. SDV showed increased sucrose, reducing sugars and cellulose; LDV PCA plots clustered in the positive quadrant of PC1 and the negative quadrant of PC2, with increased protein, sucrose synthase and starch; MDV had increased soluble starch synthase.
bibliographic citation: Liu et al. (2023) Impact of dormancy periods on some physiological and biochemical indices of potato tubers. PeerJ 11:e15923 https://doi.org/10.7717/peerj.15923
date submitted: 2023-03-03
date accepted: 2023-07-28
issued: 2023-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Hao
author list: Agent
  family name: Li
  given name: Junhua
author list: Agent
  family name: Zhou
  given name: Duanrong
author list: Agent
  family name: Cai
  given name: Wanhua
author list: Agent
  family name: Rehman
  given name: Muzammal
author list: Agent
  family name: Feng
  given name: Youhong
author list: Agent
  family name: Kong
  given name: Yunxin
author list: Agent
  family name: Liu
  given name: Xiaopeng
author list: Agent
  family name: Fahad
  given name: Shah
author list: Agent
  family name: Deng
  given name: Gang
doi: 10.7717/peerj.15923
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-28
copyright: ©2023 Liu et al.
attribution name: Liu et al.

First report of ‘Candidatus Phytoplasma asteris’ associated with yellowing, scorching and decline of almond trees in India
type: item
type: AcademicArticle
description: The almond, a commercially important tree nut crop worldwide, is native to the Mediterranean region. Stone fruit trees are affected by at least 14 ‘Candidatus Phytoplasma’ species globally, among which ‘Candidatus Phytoplasma asteris’ is one of the most widespread phytoplasma infecting Prunus dulcis, causing aster yellows disease. Recently, almond plantations of Nauni region were consistently affected by phytoplasma, as evidenced by visible symptoms, fluorescent microscopic studies and molecular characterization. During several surveys from May to September 2020–2022, almond aster yellows phytoplasma disease showing symptoms such as chlorosis, inward rolling, reddening, scorching and decline with an incidence as high as 40%. Leaf samples were collected from symptomatic almond trees and the presence of phytoplasma was confirmed through fluorescent microscopic studies by employing DAPI (4, 6-diamino-2-phenylindole) that showed distinctive light blue flourescent phytoplasma bodies in phloem sieve tube elements. The presence of phytoplasma in symptomatic almond trees was further confirmed using nested PCR with specific primer pairs followed by amplification of 16S rDNA and 16S-23S rDNA intergenic spacer (IS) fragments. Sequencing and BLAST analysis of expected amplicon of the 16S rDNA gene confirmed that the almond phytoplasma in Himachal Pradesh was identical to the aster yellows group phytoplasma. Phylogenetic analysis of 16S rDNA almond phytoplasma also grouped ‘Prunus dulcis’ aster yellows phytoplasma within 16SrI-B subgroup showed 94% nucleotide identity with ‘Prunus dulcis’ phytoplasma PAEs3 and ‘Prunus dulcis’ phytoplasma PAE28 from Iran. This research presents the first host report of ‘Candidatus Phytoplasma asteris’ infecting almonds in India, expanding the knowledge of the diversity and distribution of phytoplasma strains affecting almond trees globally.
format: application/pdf
format: text/html
creator: Shivani Gupta
creator: Anil Handa
creator: Ajay Brakta
creator: Gulshan Negi
creator: Rahul Kumar Tiwari
creator: Milan Kumar Lal
creator: Ravinder Kumar
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15926
publisher: PeerJ Inc.
rights: © 2023 Gupta et al.
abstract: The almond, a commercially important tree nut crop worldwide, is native to the Mediterranean region. Stone fruit trees are affected by at least 14 ‘Candidatus Phytoplasma’ species globally, among which ‘Candidatus Phytoplasma asteris’ is one of the most widespread phytoplasma infecting Prunus dulcis, causing aster yellows disease. Recently, almond plantations of Nauni region were consistently affected by phytoplasma, as evidenced by visible symptoms, fluorescent microscopic studies and molecular characterization. During several surveys from May to September 2020–2022, almond aster yellows phytoplasma disease showing symptoms such as chlorosis, inward rolling, reddening, scorching and decline with an incidence as high as 40%. Leaf samples were collected from symptomatic almond trees and the presence of phytoplasma was confirmed through fluorescent microscopic studies by employing DAPI (4, 6-diamino-2-phenylindole) that showed distinctive light blue flourescent phytoplasma bodies in phloem sieve tube elements. The presence of phytoplasma in symptomatic almond trees was further confirmed using nested PCR with specific primer pairs followed by amplification of 16S rDNA and 16S-23S rDNA intergenic spacer (IS) fragments. Sequencing and BLAST analysis of expected amplicon of the 16S rDNA gene confirmed that the almond phytoplasma in Himachal Pradesh was identical to the aster yellows group phytoplasma. Phylogenetic analysis of 16S rDNA almond phytoplasma also grouped ‘Prunus dulcis’ aster yellows phytoplasma within 16SrI-B subgroup showed 94% nucleotide identity with ‘Prunus dulcis’ phytoplasma PAEs3 and ‘Prunus dulcis’ phytoplasma PAE28 from Iran. This research presents the first host report of ‘Candidatus Phytoplasma asteris’ infecting almonds in India, expanding the knowledge of the diversity and distribution of phytoplasma strains affecting almond trees globally.
bibliographic citation: Gupta et al. (2023) First report of ‘Candidatus Phytoplasma asteris’ associated with yellowing, scorching and decline of almond trees in India. PeerJ 11:e15926 https://doi.org/10.7717/peerj.15926
date submitted: 2023-06-01
date accepted: 2023-07-30
issued: 2023-08-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gupta
  given name: Shivani
author list: Agent
  family name: Handa
  given name: Anil
author list: Agent
  family name: Brakta
  given name: Ajay
author list: Agent
  family name: Negi
  given name: Gulshan
author list: Agent
  family name: Tiwari
  given name: Rahul Kumar
author list: Agent
  family name: Lal
  given name: Milan Kumar
author list: Agent
  family name: Kumar
  given name: Ravinder
doi: 10.7717/peerj.15926
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-08-28
copyright: ©2023 Gupta et al.
attribution name: Gupta et al.

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