PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Investigation of the relationships between peri-implant diseases, periodontal diseases, and conditions: a cross-sectional study
items: Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders
items: Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke
items: Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol
items: Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae)
items: A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents
items: Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress
items: https://peerj.com/articles/18455
items: PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation
items: The effect of carbonic anhydrase on foraminiferal Mg/Ca

Investigation of the relationships between peri-implant diseases, periodontal diseases, and conditions: a cross-sectional study
type: item
type: AcademicArticle
description: Introduction Peri-implant and periodontal conditions share common underlying factors, including risk factors, microbiology, immunology, and treatment approaches. Aims This study aims to investigate the potential co-occurrence of peri-implant and periodontal conditions. Design One hundred twenty-three implants were divided into three groups: peri-implantitis (41 implants), peri-implant mucositis (41 implants), and peri-implant health (41 implants). Peri-implant and periodontal statuses were assessed using the 2017 AAP/EFP World Workshop on Classification of Periodontal and Peri-implant Diseases and Conditions. All measurements were performed by a single clinician (T.Ş.). One-way analysis of variance was used to compare the study groups according to the data. An assessment was conducted regarding the coexistence of periodontal and peri-implant conditions. Results Patients with peri-implant mucositis predominantly had gingivitis, whereas those with peri-implant health exhibited periodontal health. In contrast, patients with peri-implantitis mostly had gingivitis, with a lower occurrence of periodontitis. A significant difference was observed between the peri-implant and periodontal groups (p = 0.003). Significant differences were observed between peri-implant and periodontal evaluations for plaque indices, gingival indices, probing depth, gingival recession, and clinical attachment level (p = 0.001), (p = 0.006). Conclusions The findings of this study underscore the intricate influence of implant treatment on periodontal health. This observation emphasizes the importance of elucidating the underlying factors to improve clinical management and outcomes in patients with periodontal and peri-implant diseases, highlighting the relevance and potential impact of this research in the field.
format: application/pdf
format: text/html
creator: Tuğba Şahin
subject: Dentistry
description: doi:10.7717/peerj.18663
publisher: PeerJ Inc.
rights: © 2024 Şahin
abstract: Introduction Peri-implant and periodontal conditions share common underlying factors, including risk factors, microbiology, immunology, and treatment approaches. Aims This study aims to investigate the potential co-occurrence of peri-implant and periodontal conditions. Design One hundred twenty-three implants were divided into three groups: peri-implantitis (41 implants), peri-implant mucositis (41 implants), and peri-implant health (41 implants). Peri-implant and periodontal statuses were assessed using the 2017 AAP/EFP World Workshop on Classification of Periodontal and Peri-implant Diseases and Conditions. All measurements were performed by a single clinician (T.Ş.). One-way analysis of variance was used to compare the study groups according to the data. An assessment was conducted regarding the coexistence of periodontal and peri-implant conditions. Results Patients with peri-implant mucositis predominantly had gingivitis, whereas those with peri-implant health exhibited periodontal health. In contrast, patients with peri-implantitis mostly had gingivitis, with a lower occurrence of periodontitis. A significant difference was observed between the peri-implant and periodontal groups (p = 0.003). Significant differences were observed between peri-implant and periodontal evaluations for plaque indices, gingival indices, probing depth, gingival recession, and clinical attachment level (p = 0.001), (p = 0.006). Conclusions The findings of this study underscore the intricate influence of implant treatment on periodontal health. This observation emphasizes the importance of elucidating the underlying factors to improve clinical management and outcomes in patients with periodontal and peri-implant diseases, highlighting the relevance and potential impact of this research in the field.
bibliographic citation: Şahin (2024) Investigation of the relationships between peri-implant diseases, periodontal diseases, and conditions: a cross-sectional study. PeerJ 12:e18663 https://doi.org/10.7717/peerj.18663
date submitted: 2024-09-18
date accepted: 2024-11-18
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Şahin
  given name: Tuğba
doi: 10.7717/peerj.18663
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: © 2024 Şahin
attribution name: Şahin

Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders
type: item
type: AcademicArticle
description: Patients receiving anesthesia and surgery may experience cognitive dysfunction, memory deficits, and mental disturbances, which are referred to as perioperative neurocognitive disorders (PND). The function of the medial prefrontal cortex (mPFC) is disrupted during early phase of PND. To gain insight into the mechanisms of PND, we collected mouse mPFC tissues 6 h post-surgery and performed RNA sequencing analysis. In total, 178 differentially expressed genes (DEGs) were identified, including 105 upregulated and 73 downregulated genes. Bioinformatic analysis highlighted the significant enrichment of these DEGs in several immune-related biological processes and signaling pathways, suggesting that pronounced neuroinflammatory transcriptional programming in the mPFC was evoked during early phase of PND. Interleukin-6 level increased in both serum and mPFC, while the mRNA levels of Il-6, Tnf-α, and Il-1β remained unchanged. Taken together, our findings suggest that a distinct and acute neuroinflammatory response in the mPFC is evoked after peripheral surgery, which might play a key role in the development of PND.
format: application/pdf
format: text/html
creator: Xiaodong Tang
creator: Xuwu Xiang
creator: Yang Yu
creator: Shuyuan Huang
creator: Caifei Pan
creator: Shuyuan Gan
creator: Yongxing Yao
subject: Genomics
subject: Molecular Biology
subject: Neuroscience
subject: Cognitive Disorders
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.18664
publisher: PeerJ Inc.
rights: © 2024 Tang et al.
abstract: Patients receiving anesthesia and surgery may experience cognitive dysfunction, memory deficits, and mental disturbances, which are referred to as perioperative neurocognitive disorders (PND). The function of the medial prefrontal cortex (mPFC) is disrupted during early phase of PND. To gain insight into the mechanisms of PND, we collected mouse mPFC tissues 6 h post-surgery and performed RNA sequencing analysis. In total, 178 differentially expressed genes (DEGs) were identified, including 105 upregulated and 73 downregulated genes. Bioinformatic analysis highlighted the significant enrichment of these DEGs in several immune-related biological processes and signaling pathways, suggesting that pronounced neuroinflammatory transcriptional programming in the mPFC was evoked during early phase of PND. Interleukin-6 level increased in both serum and mPFC, while the mRNA levels of Il-6, Tnf-α, and Il-1β remained unchanged. Taken together, our findings suggest that a distinct and acute neuroinflammatory response in the mPFC is evoked after peripheral surgery, which might play a key role in the development of PND.
bibliographic citation: Tang et al. (2024) Surgery-induced neuroinflammatory transcriptional programs in medial prefrontal cortex of mice during early phase of perioperative neurocognitive disorders. PeerJ 12:e18664 https://doi.org/10.7717/peerj.18664
date submitted: 2024-09-20
date accepted: 2024-11-18
issued: 2024-12-03
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Tang
  given name: Xiaodong
author list: Agent
  family name: Xiang
  given name: Xuwu
author list: Agent
  family name: Yu
  given name: Yang
author list: Agent
  family name: Huang
  given name: Shuyuan
author list: Agent
  family name: Pan
  given name: Caifei
author list: Agent
  family name: Gan
  given name: Shuyuan
author list: Agent
  family name: Yao
  given name: Yongxing
doi: 10.7717/peerj.18664
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-03
copyright: © 2024 Tang et al.
attribution name: Tang et al.

Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke
type: item
type: AcademicArticle
description: Background The Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited. Methods This study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments. Results A total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis-acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix–loop–helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and prov…
format: application/pdf
format: text/html
creator: Hongyan Li
creator: Youhua Yao
creator: Xin Li
creator: Yongmei Cui
creator: Likun An
creator: Baojun Ding
creator: Xiaohua Yao
creator: Kunlun Wu
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.18443
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Background The Myeloblastosis related (MYB) family is one of the most widely distributed transcription factor families in plants and plays a significant role in plant growth and development, hormone signal transduction, and stress response. There are many reports on MYB family species, but the research on Qingke is still limited. Methods This study used comparative genomics methods to analyze gene and protein structure, protein physicochemical properties, chromosome localization, and evolution. A bioinformatics approach was used to systematically analyze the HvMYB gene family. At the milk stage, soft dough stage, and mature stage, White and Blue Qingke grains were selected for RNA sequencing (RNA-seq), among which two proteins interacted (HvMYB and HvMYC). The expression of this gene family was analyzed through RNA-seq, and the expression levels of HvMYB and HvMYC in the grains of two different color varieties were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Finally, the interaction between HvMYB and HvMYC was verified by bimolecular fluorescence complementation (BiFC) experiments. Results A total of 92 Qingke HvMYB genes were identified and analyzed, and 92 HvMYB proteins were classified into five categories. Cis-acting elements associated with abscisic acid response, light response, and methyl jasmonate (MeJA) response were found in the promoter regions of most MYB genes. Using qRT-PCR combined with RNA-seq analysis showed that MYB gene was highly expressed in the soft dough stage and was varietal specific. Subcellular localization indicated that HvMYB was located in the nucleus and cell membrane, HvMYC was located in the nucleus, cell membrane, and cytoplasm. Through BiFC analysis, it has been proven that HvMYB in the MYB family and HvMYC in the basic helix–loop–helix (bHLH) family can interact. This study provides a preliminary theoretical basis for understanding the function and role of the Qingke MYB gene family and prov…
bibliographic citation: Li et al. (2024) Comparative genomics analysis of the MYB gene family in barley: preliminary insights into evolution and biological function in Blue Qingke. PeerJ 12:e18443 https://doi.org/10.7717/peerj.18443
date submitted: 2024-07-11
date accepted: 2024-10-11
issued: 2024-12-02
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Hongyan
author list: Agent
  family name: Yao
  given name: Youhua
author list: Agent
  family name: Li
  given name: Xin
author list: Agent
  family name: Cui
  given name: Yongmei
author list: Agent
  family name: An
  given name: Likun
author list: Agent
  family name: Ding
  given name: Baojun
author list: Agent
  family name: Yao
  given name: Xiaohua
author list: Agent
  family name: Wu
  given name: Kunlun
doi: 10.7717/peerj.18443
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-02
copyright: © 2024 Li et al.
attribution name: Li et al.

Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol
type: item
type: AcademicArticle
description: Background Frequently, the women affected by the genitourinary syndrome of menopause experience genitourinary dysfunctions that profoundly influence their overall health. Even though the symptoms do not jeopardize the women’s lives, the urinary and sexual dysfunctions significantly impact their quality of life. Isolated treatments focused on the main causes of the dysfunctions, such as pelvic floor muscle training (PFMT) and photobiomodulation have shown significant improvements in genitourinary dysfunctions. So, the association of PFMT with photobiomodulation may generate additional effects in the genitourinary area. This study aims to create a PFMT protocol isolated and associated with photobiomodulation therapy in women affected by the genitourinary syndrome of menopause. Methods It is a randomized, controlled, double-blind clinical trial protocol study that will include women experiencing genitourinary symptoms related to menopause, sexually active, never practiced pelvic floor muscle exercise or photobiomodulation treatment, and do not use hormone replacement therapy for at least 3 months. The randomization will allocate the women to three groups: PFMT group, PFMT associated with active intracavitary photobiomodulation group, and PFMT associated with sham intracavitary photobiomodulation group. A total of 16 sessions will be conducted twice a week. The assessments will occur before interventions, after the sixteenth session, and 1 month after the sixteenth session (follow-up). The evaluation will include the pelvic floor muscle vaginal manometry as the primary outcome. Also, the international consultation on incontinence questionnaire—short form, the female sexual function index, the Utian Quality of Life scale, the patient global impression of improvement, the modified Oxford scale, and the vaginal health index will be the secondary outcomes. Discussion Despite there are gold standard treatments such as PFMT, to alleviate genitourinary symptoms, interventions …
format: application/pdf
format: text/html
creator: Lívia Oliveira Bezerra
creator: Maria Letícia Araújo Silva de Carvalho
creator: Edson Silva-Filho
creator: Maria Clara Eugênia de Oliveira
creator: Palloma Rodrigues de Andrade
creator: Maria Thereza Albuquerque Barbosa Cabral Micussi
subject: Clinical Trials
subject: Gynecology and Obstetrics
subject: Urology
subject: Women’s Health
subject: Rehabilitation
description: doi:10.7717/peerj.17848
publisher: PeerJ Inc.
rights: © 2024 Oliveira Bezerra et al.
abstract: Background Frequently, the women affected by the genitourinary syndrome of menopause experience genitourinary dysfunctions that profoundly influence their overall health. Even though the symptoms do not jeopardize the women’s lives, the urinary and sexual dysfunctions significantly impact their quality of life. Isolated treatments focused on the main causes of the dysfunctions, such as pelvic floor muscle training (PFMT) and photobiomodulation have shown significant improvements in genitourinary dysfunctions. So, the association of PFMT with photobiomodulation may generate additional effects in the genitourinary area. This study aims to create a PFMT protocol isolated and associated with photobiomodulation therapy in women affected by the genitourinary syndrome of menopause. Methods It is a randomized, controlled, double-blind clinical trial protocol study that will include women experiencing genitourinary symptoms related to menopause, sexually active, never practiced pelvic floor muscle exercise or photobiomodulation treatment, and do not use hormone replacement therapy for at least 3 months. The randomization will allocate the women to three groups: PFMT group, PFMT associated with active intracavitary photobiomodulation group, and PFMT associated with sham intracavitary photobiomodulation group. A total of 16 sessions will be conducted twice a week. The assessments will occur before interventions, after the sixteenth session, and 1 month after the sixteenth session (follow-up). The evaluation will include the pelvic floor muscle vaginal manometry as the primary outcome. Also, the international consultation on incontinence questionnaire—short form, the female sexual function index, the Utian Quality of Life scale, the patient global impression of improvement, the modified Oxford scale, and the vaginal health index will be the secondary outcomes. Discussion Despite there are gold standard treatments such as PFMT, to alleviate genitourinary symptoms, interventions …
bibliographic citation: Oliveira Bezerra et al. (2024) Pelvic floor muscle training associated with the photobiomodulation therapy for women affected by the genitourinary syndrome of menopause: a study protocol. PeerJ 12:e17848 https://doi.org/10.7717/peerj.17848
date submitted: 2024-01-19
date accepted: 2024-07-10
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oliveira Bezerra
  given name: Lívia
author list: Agent
  family name: de Carvalho
  given name: Maria Letícia Araújo Silva
author list: Agent
  family name: Silva-Filho
  given name: Edson
author list: Agent
  family name: Clara Eugênia de Oliveira
  given name: Maria
author list: Agent
  family name: de Andrade
  given name: Palloma Rodrigues
author list: Agent
  family name: Micussi
  given name: Maria Thereza Albuquerque Barbosa Cabral
doi: 10.7717/peerj.17848
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Oliveira Bezerra et al.
attribution name: Oliveira Bezerra et al.

Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae)
type: item
type: AcademicArticle
description: The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is a serious insect pest of cotton crop. The studies to evaluate the impact of abiotic factors on cotton pests’ biology are limited. The current study was undertaken to determine the impact of abiotic factors (temperature, humidity, photoperiod) and an insecticide (lambda-cyhalothrin) on the biological aspects of P. gossypiella. The results revealed that all the treatments showed a significant impact on different life parameters of P. gossypiella. The temperature exposure at 27 °C revealed a total life span of about 33 days. Maximum mortality for larvae (51.11%), pupae (59.04%) and adults (61.92%) were recorded at 33 °C exposure. Both low and high humidity levels caused negative impacts on life parameters of P. gossypiella. The life span was completed in about 30 days at 60% relative humidity (RH). Maximum mortality for larvae (75.00%) and pupae (49.59%) were recorded at 80% RH level exposure, while adult mortality was maximum (63.09%) at 40% RH level followed by 80% RH level (55.52%). The P. gossypiella exhibited a life span of about 32 days at 14:10 light-dark period. The larval mortality was maximum (14.83%) at 12:12 light-dark period while pupal (47.36%) and adult (48.84%) mortality was maximum at 16:08 light-dark period. Lambdacyhalothrin (LC) showed dose dependent negative impacts on biological aspects of P. gossypiella. The P. gossypiella exhibited a life span of about 26 days at 0.5 ppm LC concentration. The P. gossypiella exposure to highest concentration (LC) revealed maximum mortality of larval (80.22%), pupal (64.63%) and adult (70.74%) stages. Conclusively, the best suited abiotic factor ranges were 27 °C (temperature), 60% (RH) and 14:10 (light-dark) which can be used for successful rearing and bioassay activities of P. gossypiella.
format: application/pdf
format: text/html
creator: Muhammad Jalal Arif
creator: Ahmad Nawaz
creator: Muhammad Sufyan
creator: Muhammad Dildar Gogi
creator: Zain UlAbdin
creator: Muhammad Tayyib
creator: Abid Ali
creator: Waqar Majeed
creator: Manel Ben Ali
creator: Amor Hedfi
subject: Agricultural Science
subject: Entomology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.18399
publisher: PeerJ Inc.
rights: © 2024 Arif et al.
abstract: The pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae) is a serious insect pest of cotton crop. The studies to evaluate the impact of abiotic factors on cotton pests’ biology are limited. The current study was undertaken to determine the impact of abiotic factors (temperature, humidity, photoperiod) and an insecticide (lambda-cyhalothrin) on the biological aspects of P. gossypiella. The results revealed that all the treatments showed a significant impact on different life parameters of P. gossypiella. The temperature exposure at 27 °C revealed a total life span of about 33 days. Maximum mortality for larvae (51.11%), pupae (59.04%) and adults (61.92%) were recorded at 33 °C exposure. Both low and high humidity levels caused negative impacts on life parameters of P. gossypiella. The life span was completed in about 30 days at 60% relative humidity (RH). Maximum mortality for larvae (75.00%) and pupae (49.59%) were recorded at 80% RH level exposure, while adult mortality was maximum (63.09%) at 40% RH level followed by 80% RH level (55.52%). The P. gossypiella exhibited a life span of about 32 days at 14:10 light-dark period. The larval mortality was maximum (14.83%) at 12:12 light-dark period while pupal (47.36%) and adult (48.84%) mortality was maximum at 16:08 light-dark period. Lambdacyhalothrin (LC) showed dose dependent negative impacts on biological aspects of P. gossypiella. The P. gossypiella exhibited a life span of about 26 days at 0.5 ppm LC concentration. The P. gossypiella exposure to highest concentration (LC) revealed maximum mortality of larval (80.22%), pupal (64.63%) and adult (70.74%) stages. Conclusively, the best suited abiotic factor ranges were 27 °C (temperature), 60% (RH) and 14:10 (light-dark) which can be used for successful rearing and bioassay activities of P. gossypiella.
bibliographic citation: Arif et al. (2024) Impacts of abiotic factors and pesticide on the development, phenology, and reproductive biology of pink bollworm, Pectinophora gossypiella (Saunders) (Lepidoptera: Gelechiidae). PeerJ 12:e18399 https://doi.org/10.7717/peerj.18399
date submitted: 2024-06-25
date accepted: 2024-10-04
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Arif
  given name: Muhammad Jalal
author list: Agent
  family name: Nawaz
  given name: Ahmad
author list: Agent
  family name: Sufyan
  given name: Muhammad
author list: Agent
  family name: Gogi
  given name: Muhammad Dildar
author list: Agent
  family name: UlAbdin
  given name: Zain
author list: Agent
  family name: Tayyib
  given name: Muhammad
author list: Agent
  family name: Ali
  given name: Abid
author list: Agent
  family name: Majeed
  given name: Waqar
author list: Agent
  family name: Ali
  given name: Manel Ben
author list: Agent
  family name: Hedfi
  given name: Amor
doi: 10.7717/peerj.18399
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Arif et al.
attribution name: Arif et al.

A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents
type: item
type: AcademicArticle
description: Ecological niche modeling (ENM) is a valuable tool for inferring suitable environmental conditions and estimating species’ geographic distributions. ENM is widely used to assess the potential effects of climate change on species distributions; however, the choice of modeling algorithm introduces substantial uncertainty, especially since future projections cannot be properly validated. In this study, we evaluated the performance of seven popular modeling algorithms—Bioclim, generalized additive models (GAM), generalized linear models (GLM), boosted regression trees (BRT), Maxent, random forest (RF), and support vector machine (SVM)—in transferring ENM across time, using Mexican endemic rodents as a model system. We used a retrospective approach, transferring models from the near past (1950–1979) to more recent conditions (1980–2009) and vice versa, to evaluate their performance in both forecasting and hindcasting. Consistent with previous studies, our results highlight that input data quality and algorithm choice significantly impact model accuracy, but most importantly, we found that algorithm performance varied between forecasting and hindcasting. While no single algorithm outperformed the others in both temporal directions, RF generally showed better performance for forecasting, while Maxent performed better in hindcasting, though it was more sensitive to small sample sizes. Bioclim consistently showed the lowest performance. These findings underscore that not all species or algorithms are suited for temporal projections. Therefore, we strongly recommend conducting a thorough evaluation of the data quality—in terms of quantity and potential biases—of the species of interest. Based on this assessment, appropriate algorithm(s) should be carefully selected and rigorously tested before proceeding with temporal transfers.
format: application/pdf
format: text/html
creator: Claudia N. Moreno-Arzate
creator: Enrique Martínez-Meyer
subject: Biodiversity
subject: Biogeography
subject: Bioinformatics
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.18414
publisher: PeerJ Inc.
rights: © 2024 Moreno-Arzate and Martínez-Meyer
abstract: Ecological niche modeling (ENM) is a valuable tool for inferring suitable environmental conditions and estimating species’ geographic distributions. ENM is widely used to assess the potential effects of climate change on species distributions; however, the choice of modeling algorithm introduces substantial uncertainty, especially since future projections cannot be properly validated. In this study, we evaluated the performance of seven popular modeling algorithms—Bioclim, generalized additive models (GAM), generalized linear models (GLM), boosted regression trees (BRT), Maxent, random forest (RF), and support vector machine (SVM)—in transferring ENM across time, using Mexican endemic rodents as a model system. We used a retrospective approach, transferring models from the near past (1950–1979) to more recent conditions (1980–2009) and vice versa, to evaluate their performance in both forecasting and hindcasting. Consistent with previous studies, our results highlight that input data quality and algorithm choice significantly impact model accuracy, but most importantly, we found that algorithm performance varied between forecasting and hindcasting. While no single algorithm outperformed the others in both temporal directions, RF generally showed better performance for forecasting, while Maxent performed better in hindcasting, though it was more sensitive to small sample sizes. Bioclim consistently showed the lowest performance. These findings underscore that not all species or algorithms are suited for temporal projections. Therefore, we strongly recommend conducting a thorough evaluation of the data quality—in terms of quantity and potential biases—of the species of interest. Based on this assessment, appropriate algorithm(s) should be carefully selected and rigorously tested before proceeding with temporal transfers.
bibliographic citation: Moreno-Arzate et al. (2024) A retrospective approach for evaluating ecological niche modeling transferability over time: the case of Mexican endemic rodents. PeerJ 12:e18414 https://doi.org/10.7717/peerj.18414
date submitted: 2024-04-28
date accepted: 2024-10-07
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno-Arzate
  given name: Claudia N.
author list: Agent
  family name: Martínez-Meyer
  given name: Enrique
doi: 10.7717/peerj.18414
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Moreno-Arzate and Martínez-Meyer
attribution name: Moreno-Arzate and Martínez-Meyer

Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress
type: item
type: AcademicArticle
description: Cinnamyl alcohol dehydrogenase (CAD) is a crucial enzyme in the final stage of lignin monomer biosynthesis. This study focuses on the CAD gene family within Gossypium hirsutum. Through comprehensive genomic analysis, we identified 29 GhiCAD genes within the Gossypium hirsutum genome using a bioinformatics approach. Phylogenetic analysis revealed that the GhiCAD family can be categorized into four subgroups, which are closest to the evolutionary relationship with Arabidopsis thaliana. There are multiple cis-acting elements on the promoters of GhiCAD genes associated with abiotic stress responses. Some GhiCAD genes demonstrated high expression in various tissues like root, leaf, and sepal, as well as in fiber and ovule at different developmental stages (10 days post anthesis (DPA), 15 DPA, 20 DPA, 25 DPA). The transcript levels of GhiCAD23 were notably elevated when exposed to PEG treatment and drought stress (DS). GhiCAD23 is also co-expressed with many known drought response genes, suggesting its involvement in the plant’s reaction to DS. Employing virus-induced gene silencing (VIGS) technology to silence the GhiCAD23 gene, it was found that silencing GhiCAD23 reduced the tolerance of cotton to DS. Under DS, the relative leaf water content, superoxide dismutase (SOD), and catalase (CAT) enzyme activities of the GhiCAD23-silenced cotton plants were decreased by 31.84%, 30.22% and 14.19%, respectively, while malondialdehyde (MDA) was increased by 72.16% compared with the control cohort. Drought promotes the accumulation of lignin, and it was found that silencing the GhiCAD23 reduces lignin accumulation in cotton under DS. The analysis of phenotypic and physiological indicators indicates that GhiCAD23 is vital in cotton’s resistance to DS. This investigation provides an important reference for future comprehensive exploration of the GhiCAD23 gene’s function in cotton’s DS response mechanism.
format: application/pdf
format: text/html
creator: Xin Zhang
creator: Ziyu Wang
creator: Xingyue Zhong
creator: Wanwan Fu
creator: Yuanxin Li
creator: Yunhao Liusui
creator: Yanjun Guo
creator: JingBo Zhang
creator: Bo Li
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18439
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Cinnamyl alcohol dehydrogenase (CAD) is a crucial enzyme in the final stage of lignin monomer biosynthesis. This study focuses on the CAD gene family within Gossypium hirsutum. Through comprehensive genomic analysis, we identified 29 GhiCAD genes within the Gossypium hirsutum genome using a bioinformatics approach. Phylogenetic analysis revealed that the GhiCAD family can be categorized into four subgroups, which are closest to the evolutionary relationship with Arabidopsis thaliana. There are multiple cis-acting elements on the promoters of GhiCAD genes associated with abiotic stress responses. Some GhiCAD genes demonstrated high expression in various tissues like root, leaf, and sepal, as well as in fiber and ovule at different developmental stages (10 days post anthesis (DPA), 15 DPA, 20 DPA, 25 DPA). The transcript levels of GhiCAD23 were notably elevated when exposed to PEG treatment and drought stress (DS). GhiCAD23 is also co-expressed with many known drought response genes, suggesting its involvement in the plant’s reaction to DS. Employing virus-induced gene silencing (VIGS) technology to silence the GhiCAD23 gene, it was found that silencing GhiCAD23 reduced the tolerance of cotton to DS. Under DS, the relative leaf water content, superoxide dismutase (SOD), and catalase (CAT) enzyme activities of the GhiCAD23-silenced cotton plants were decreased by 31.84%, 30.22% and 14.19%, respectively, while malondialdehyde (MDA) was increased by 72.16% compared with the control cohort. Drought promotes the accumulation of lignin, and it was found that silencing the GhiCAD23 reduces lignin accumulation in cotton under DS. The analysis of phenotypic and physiological indicators indicates that GhiCAD23 is vital in cotton’s resistance to DS. This investigation provides an important reference for future comprehensive exploration of the GhiCAD23 gene’s function in cotton’s DS response mechanism.
bibliographic citation: Zhang et al. (2024) Genome-wide identification of the Gossypium hirsutum CAD gene family and functional study of GhiCAD23 under drought stress. PeerJ 12:e18439 https://doi.org/10.7717/peerj.18439
date submitted: 2024-08-20
date accepted: 2024-10-11
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhang
  given name: Xin
author list: Agent
  family name: Wang
  given name: Ziyu
author list: Agent
  family name: Zhong
  given name: Xingyue
author list: Agent
  family name: Fu
  given name: Wanwan
author list: Agent
  family name: Li
  given name: Yuanxin
author list: Agent
  family name: Liusui
  given name: Yunhao
author list: Agent
  family name: Guo
  given name: Yanjun
author list: Agent
  family name: Zhang
  given name: JingBo
author list: Agent
  family name: Li
  given name: Bo
doi: 10.7717/peerj.18439
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

https://peerj.com/articles/18455
type: item
type: AcademicArticle
title: Genome-wide identification and expression analysis of C2H2 zinc finger proteins in Chinese jujube (Ziziphus jujuba Mill.) in different fruit development stages and under different levels of water stress
description: The C2H2 type zinc finger proteins (C2H2-ZFPs) are prevalent motifs found widely across the eukaryotic kingdom, playing crucial roles in various biological processes, including stress responses and plant growth and development. To date, C2H2-ZFPs have been identified in many plant systems, but there have been no reports in Chinese jujube (Ziziphus jujuba Mill.). In this study, a total of 77 ZjC2H2-ZFPs were identified in Chinese jujube and classified into three groups, with set A containing 29 genes, set B containing two genes, and set C containing 46 genes. The set A group genes were further divided into three groups: A1, A2, and A4 (with no member of the A3 subgroup found in jujube). The set C C2H2-ZFPs genes were also further divided into three groups: C1 containing 24 genes, C2 with two genes, and C3 with three genes. These ZjC2H2-ZFPs were distributed on 12 chromosomes and one tandem duplicated pair of ZjC2H2-ZFPs was found on chromosome 4 (ZjC2H2-21 with ZjC2H2-22). Notably, the 77 ZjC2H2-ZFPs identified in this study lacked finger clusters comprising 10 or more repeats. The structure and protein motif analysis of ZjC2H2-ZFPs showed that most C1 subgroup members were enriched with ‘QALGGH’ motif zinc finger helices and the A1a ZjC2H2-ZFPs contained highly conserved ‘SATALLQKAAQMGS’ residues in jujube. A unique finding was the discovery of a conserved non-finger domain (PCYCC motif) in A1 group members, absent in other ZjC2H2-ZFPs and unreported in other species. The enzyme activity of jujube leaves under different water stress treatments were measured, and the results showed that as the degree of water stress increased, the activity of SOD enzymes and H2O2 content also increased. The POD enzyme activity levels of different treatment groups were CK>MS>SS>LS. The levels of malondialdehyde (MDA) content observed under various treatments were notably higher and the proline content was lower in comparison to the control group (CK). Differential expression of ZjC2H2…
format: application/pdf
format: text/html
creator: Xie Zhengwan
creator: Ji Qing
creator: Lihu Wang
creator: Ao Zhang
creator: Shengxing Li
creator: Sunyang Li
creator: Mei Chen
creator: Yang Jiayue
creator: Ruifang Wang
subject: Agricultural Science
subject: Cell Biology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.18455
publisher: PeerJ Inc.
rights: © 2024 Zhengwan et al.
abstract: The C2H2 type zinc finger proteins (C2H2-ZFPs) are prevalent motifs found widely across the eukaryotic kingdom, playing crucial roles in various biological processes, including stress responses and plant growth and development. To date, C2H2-ZFPs have been identified in many plant systems, but there have been no reports in Chinese jujube (Ziziphus jujuba Mill.). In this study, a total of 77 ZjC2H2-ZFPs were identified in Chinese jujube and classified into three groups, with set A containing 29 genes, set B containing two genes, and set C containing 46 genes. The set A group genes were further divided into three groups: A1, A2, and A4 (with no member of the A3 subgroup found in jujube). The set C C2H2-ZFPs genes were also further divided into three groups: C1 containing 24 genes, C2 with two genes, and C3 with three genes. These ZjC2H2-ZFPs were distributed on 12 chromosomes and one tandem duplicated pair of ZjC2H2-ZFPs was found on chromosome 4 (ZjC2H2-21 with ZjC2H2-22). Notably, the 77 ZjC2H2-ZFPs identified in this study lacked finger clusters comprising 10 or more repeats. The structure and protein motif analysis of ZjC2H2-ZFPs showed that most C1 subgroup members were enriched with ‘QALGGH’ motif zinc finger helices and the A1a ZjC2H2-ZFPs contained highly conserved ‘SATALLQKAAQMGS’ residues in jujube. A unique finding was the discovery of a conserved non-finger domain (PCYCC motif) in A1 group members, absent in other ZjC2H2-ZFPs and unreported in other species. The enzyme activity of jujube leaves under different water stress treatments were measured, and the results showed that as the degree of water stress increased, the activity of SOD enzymes and H2O2 content also increased. The POD enzyme activity levels of different treatment groups were CK>MS>SS>LS. The levels of malondialdehyde (MDA) content observed under various treatments were notably higher and the proline content was lower in comparison to the control group (CK). Differential expression of ZjC2H2…
bibliographic citation: Zhengwan et al. (2024) Genome-wide identification and expression analysis of C2H2 zinc finger proteins in Chinese jujube (Ziziphus jujuba Mill.) in different fruit development stages and under different levels of water stress. PeerJ 12:e18455 https://doi.org/10.7717/peerj.18455
date submitted: 2023-09-22
date accepted: 2024-10-14
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhengwan
  given name: Xie
author list: Agent
  family name: Qing
  given name: Ji
author list: Agent
  family name: Wang
  given name: Lihu
author list: Agent
  family name: Zhang
  given name: Ao
author list: Agent
  family name: Li
  given name: Shengxing
author list: Agent
  family name: Li
  given name: Sunyang
author list: Agent
  family name: Chen
  given name: Mei
author list: Agent
  family name: Jiayue
  given name: Yang
author list: Agent
  family name: Wang
  given name: Ruifang
doi: 10.7717/peerj.18455
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: ©2024 Zhengwan et al.
attribution name: Zhengwan et al.

PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation
type: item
type: AcademicArticle
description: Background Presenilin enhancer gamma-secretase subunit (PSENEN), the straight target of metformin, is highly expressed in several cancers. The role of PSENEN in kidney renal clear cell carcinoma (KIRC) has not been reported. Methods PSENEN expression in KIRC specimens was investigated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, as well as by immunohistochemical analysis and qPCR assay. The relationship between PSENEN expression and patient survival was discussed. The biological function of PSENEN in KIRC and its correlation with immune infiltration of KIRC were then investigated, and possible cellular mechanisms were again analyzed. The effects of metformin on KIRC cell proliferation, migration and invasion were discussed in cellular experiments. Results PSENEN was found to be highly expressed in KIRC. The high PSENEN expression was an adverse factor in KIRC. Several immune-related pathways were enriched including immune response, complement and coagulation cascade reactions, and neutrophil extracellular trap formation, as evidenced by enrichment analyses. Immune infiltration analysis revealed that PSENEN expression correlated positively with regulatory T cells. Gene set variation analysis suggested that PSENEN expression correlated positively with oxidative phosphorylation. In addition, a certain concentration of metformin was found to inhibit the proliferation, migration and invasion of KIRC cells, in which PSENEN down-regulation, AMPK up-regulation and mTOR down-regulation were also observed. Conclusions PSENEN may be involved in regulating the immune microenvironment of KIRC, and oxidative phosphorylation may also be a pathway for its involvement in cancer development. PSENEN is a novel prognostic marker for KIRC.
format: application/pdf
format: text/html
creator: Congying Huang
creator: Kaijie Chen
creator: Siyu Zhu
creator: Xin Yang
creator: Jiangang Hou
creator: Xuefeng Gu
subject: Bioinformatics
subject: Nephrology
subject: Oncology
description: doi:10.7717/peerj.18457
publisher: PeerJ Inc.
rights: © 2024 Huang et al.
abstract: Background Presenilin enhancer gamma-secretase subunit (PSENEN), the straight target of metformin, is highly expressed in several cancers. The role of PSENEN in kidney renal clear cell carcinoma (KIRC) has not been reported. Methods PSENEN expression in KIRC specimens was investigated in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, as well as by immunohistochemical analysis and qPCR assay. The relationship between PSENEN expression and patient survival was discussed. The biological function of PSENEN in KIRC and its correlation with immune infiltration of KIRC were then investigated, and possible cellular mechanisms were again analyzed. The effects of metformin on KIRC cell proliferation, migration and invasion were discussed in cellular experiments. Results PSENEN was found to be highly expressed in KIRC. The high PSENEN expression was an adverse factor in KIRC. Several immune-related pathways were enriched including immune response, complement and coagulation cascade reactions, and neutrophil extracellular trap formation, as evidenced by enrichment analyses. Immune infiltration analysis revealed that PSENEN expression correlated positively with regulatory T cells. Gene set variation analysis suggested that PSENEN expression correlated positively with oxidative phosphorylation. In addition, a certain concentration of metformin was found to inhibit the proliferation, migration and invasion of KIRC cells, in which PSENEN down-regulation, AMPK up-regulation and mTOR down-regulation were also observed. Conclusions PSENEN may be involved in regulating the immune microenvironment of KIRC, and oxidative phosphorylation may also be a pathway for its involvement in cancer development. PSENEN is a novel prognostic marker for KIRC.
bibliographic citation: Huang et al. (2024) PSENEN influences the progression of renal clear cell carcinoma by regulating the immune microenvironment and oxidative phosphorylation. PeerJ 12:e18457 https://doi.org/10.7717/peerj.18457
date submitted: 2024-07-23
date accepted: 2024-10-14
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Congying
author list: Agent
  family name: Chen
  given name: Kaijie
author list: Agent
  family name: Zhu
  given name: Siyu
author list: Agent
  family name: Yang
  given name: Xin
author list: Agent
  family name: Hou
  given name: Jiangang
author list: Agent
  family name: Gu
  given name: Xuefeng
doi: 10.7717/peerj.18457
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 Huang et al.
attribution name: Huang et al.

The effect of carbonic anhydrase on foraminiferal Mg/Ca
type: item
type: AcademicArticle
description: Marine biogenic calcium carbonate production plays a role in the exchange of CO2 between ocean and atmosphere. The effect of increased CO2 on calcification and on the resulting chemistry of shells and skeletons, however, is only partly understood. Foraminifera are among the main marine CaCO3 producers and the controls on element partitioning and isotope fractionation is the subject of many recent investigations. The enzyme carbonic anhydrase (CA) was, for example, shown to be vital for CaCO3 deposition in benthic foraminifera and indicates their ability to manipulate their intracellular inorganic carbon chemistry. Here, we tested whether CA affects the partitioning of Na, Mg and Sr in the perforate, large benthic, symbiont-bearing foraminifer Amphistegina lessonii by addition of the inhibitor acetazolamide (AZ). The effect of dissolved CO2 on the effect of CA on element partitioning was also determined using a culturing setup with controlled atmospheric carbon dioxide levels (400–1,600 ppm). Results show that inhibition by AZ reduces calcification greatly and that CO2 has a small, but positive effect on the amount of calcite formed during the incubations. Furthermore, the inhibition of CA activity has a positive effect on element partitioning, most notably Mg. This may be explained by a (n indirect) coupling of inorganic carbon uptake and inward calcium ion pumping.
format: application/pdf
format: text/html
creator: Siham De Goeyse
creator: Chiara Lesuis
creator: Gert-Jan Reichart
creator: Lennart de Nooijer
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.18458
publisher: PeerJ Inc.
rights: © 2024 De Goeyse et al.
abstract: Marine biogenic calcium carbonate production plays a role in the exchange of CO2 between ocean and atmosphere. The effect of increased CO2 on calcification and on the resulting chemistry of shells and skeletons, however, is only partly understood. Foraminifera are among the main marine CaCO3 producers and the controls on element partitioning and isotope fractionation is the subject of many recent investigations. The enzyme carbonic anhydrase (CA) was, for example, shown to be vital for CaCO3 deposition in benthic foraminifera and indicates their ability to manipulate their intracellular inorganic carbon chemistry. Here, we tested whether CA affects the partitioning of Na, Mg and Sr in the perforate, large benthic, symbiont-bearing foraminifer Amphistegina lessonii by addition of the inhibitor acetazolamide (AZ). The effect of dissolved CO2 on the effect of CA on element partitioning was also determined using a culturing setup with controlled atmospheric carbon dioxide levels (400–1,600 ppm). Results show that inhibition by AZ reduces calcification greatly and that CO2 has a small, but positive effect on the amount of calcite formed during the incubations. Furthermore, the inhibition of CA activity has a positive effect on element partitioning, most notably Mg. This may be explained by a (n indirect) coupling of inorganic carbon uptake and inward calcium ion pumping.
bibliographic citation: De Goeyse et al. (2024) The effect of carbonic anhydrase on foraminiferal Mg/Ca. PeerJ 12:e18458 https://doi.org/10.7717/peerj.18458
date submitted: 2023-12-18
date accepted: 2024-10-14
issued: 2024-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Goeyse
  given name: Siham
author list: Agent
  family name: Lesuis
  given name: Chiara
author list: Agent
  family name: Reichart
  given name: Gert-Jan
author list: Agent
  family name: de Nooijer
  given name: Lennart
doi: 10.7717/peerj.18458
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-11-29
copyright: © 2024 De Goeyse et al.
attribution name: De Goeyse et al.

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