PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: The quality of the fossil record across higher taxa: compositional fidelity of phyla and classes in benthic marine associations
items: Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover
items: Antibiotic resistance profile of Helicobacter pylori to 14 antibiotics: a multicenter study in Fujian, China
items: A novel immunogenic cell death signature for the prediction of prognosis and therapies in glioma
items: Diet and physical activity and metabolic disorders in patients with schizophrenia and bipolar affective disorder in the Polish population
items: Ecological indicators reveal historical regime shifts in the Black Sea ecosystem
items: Vet the journal before you submit: turnaround times of journals publishing in zoological medicine and related fields
items: A retrospective study on expression and clinical significance of PHH3, Ki67 and P53 in bladder exophytic papillary urothelial neoplasms
items: In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants
items: Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China

The quality of the fossil record across higher taxa: compositional fidelity of phyla and classes in benthic marine associations
type: item
type: AcademicArticle
description: Although the fossil record preserves a wealth of historical data about past ecosystems, the current paradigm, which postulates that fossils provide faithful archives of ecological information, stems from research primarily focused on a single group of organisms known for their high fossilization potential: molluscs. Here, we quantify the fidelity of higher taxa (six phyla and 11 classes) by comparing live communities and sympatric dead remains (death assemblages) using comprehensive surveys of benthic marine invertebrates from coastal habitats in North Carolina (U.S.A). We found that although community composition differed between the two assemblages across phyla and classes, these differences were predictable with an overabundance of robust and more preservable groups. In addition, dead molluscs appear to be an excellent proxy for all taxa when tracking spatio-temporal patterns and shifts in community structure using a variety of ecological metrics, including measures of α, γ, and β diversity/evenness. This suggests that despite filters imposed by differential preservation of taxa and time-averaging, the fossil record is likely to be reliable with respect to relative comparisons of composition and diversity in shallow benthic marine paleocommunities. This is consistent with previous work indicating that shallow marine death assemblages can yield robust ecological estimates adequate for assessing the variability of ecosystems that existed under natural, pre-anthropogenic conditions.
format: application/pdf
format: text/html
creator: Carrie Tyler
creator: Michał Kowalewski
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.15574
publisher: PeerJ Inc.
rights: © 2023 Tyler and Kowalewski
abstract: Although the fossil record preserves a wealth of historical data about past ecosystems, the current paradigm, which postulates that fossils provide faithful archives of ecological information, stems from research primarily focused on a single group of organisms known for their high fossilization potential: molluscs. Here, we quantify the fidelity of higher taxa (six phyla and 11 classes) by comparing live communities and sympatric dead remains (death assemblages) using comprehensive surveys of benthic marine invertebrates from coastal habitats in North Carolina (U.S.A). We found that although community composition differed between the two assemblages across phyla and classes, these differences were predictable with an overabundance of robust and more preservable groups. In addition, dead molluscs appear to be an excellent proxy for all taxa when tracking spatio-temporal patterns and shifts in community structure using a variety of ecological metrics, including measures of α, γ, and β diversity/evenness. This suggests that despite filters imposed by differential preservation of taxa and time-averaging, the fossil record is likely to be reliable with respect to relative comparisons of composition and diversity in shallow benthic marine paleocommunities. This is consistent with previous work indicating that shallow marine death assemblages can yield robust ecological estimates adequate for assessing the variability of ecosystems that existed under natural, pre-anthropogenic conditions.
bibliographic citation: Tyler et al. (2023) The quality of the fossil record across higher taxa: compositional fidelity of phyla and classes in benthic marine associations. PeerJ 11:e15574 https://doi.org/10.7717/peerj.15574
date submitted: 2023-02-02
date accepted: 2023-05-25
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tyler
  given name: Carrie
author list: Agent
  family name: Kowalewski
  given name: Michał
doi: 10.7717/peerj.15574
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: ©2023 Tyler and Kowalewski
attribution name: Tyler and Kowalewski

Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover
type: item
type: AcademicArticle
description: Background White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover. Methods and Results In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress. Conclusion The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold s…
format: application/pdf
format: text/html
creator: Manman Li
creator: Xueqi Zhang
creator: Tianxiang Zhang
creator: Yan Bai
creator: Chao Chen
creator: Donglin Guo
creator: Changhong Guo
creator: Yongjun Shu
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.15610
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover. Methods and Results In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress. Conclusion The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold s…
bibliographic citation: Li et al. (2023) Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover. PeerJ 11:e15610 https://doi.org/10.7717/peerj.15610
date submitted: 2023-03-13
date accepted: 2023-05-31
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Manman
author list: Agent
  family name: Zhang
  given name: Xueqi
author list: Agent
  family name: Zhang
  given name: Tianxiang
author list: Agent
  family name: Bai
  given name: Yan
author list: Agent
  family name: Chen
  given name: Chao
author list: Agent
  family name: Guo
  given name: Donglin
author list: Agent
  family name: Guo
  given name: Changhong
author list: Agent
  family name: Shu
  given name: Yongjun
doi: 10.7717/peerj.15610
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Li et al.
attribution name: Li et al.

Antibiotic resistance profile of Helicobacter pylori to 14 antibiotics: a multicenter study in Fujian, China
type: item
type: AcademicArticle
description: Background and aim Efficacy of Helicobacter pylori (H. pylori) eradication is related to the local antimicrobial resistance epidemiology. We aimed to investigate the antibiotic resistance of H. pylori in Fujian, China. Methods H. pylori-infected patients in four centers were enrolled in the study from Oct 2019 to Jan 2022. The bacteria were isolated, cultured and identified from the biopsy of patients’ gastric mucosa samples. Antimicrobial susceptibility testing was performed by a modified broth microdilution method for H. pylori to seven guideline-recommended antibiotics and seven potential choices for H. pylori eradication. Results A total of 205 H. pylori strains were isolated. The resistance rates of amoxicillin (AMX), amoxicillin and clavulanate potassium (AMC), cefixime (CFM), gentamicin (GEN), tetracycline (TET), doxycycline (DOX), azithromycin (AZM), clarithromycin (CLR), levofloxacin (LVFX), sparfloxacin (SPFX), metronidazole (MTZ), tinidazole (TID), rifampicin (RFP) and furazolidone (FZD) were 11.22%, 12.20%, 7.32%, 12.20%, 4.88%, 4.39%, 44.39%, 43.90%, 30.24%, 21.46%, 40.98%, 45.85%, 5.37% and 10.24%, respectively. The rates of pan-sensitivity, single, double, triple and multiple resistance for seven guideline-recommended antibiotics were 32.68%, 30.24%, 13.17%, 7.76%, and 14.15%, respectively. The main double-resistance patterns were CLR+MTZ (10/205, 5%) and CLR+LVFX (9/205, 4%). The main triple-resistance pattern was CLR+MTZ+ LVFX (15/205, 7%). Conclusions In Fujian, the prevalence of H. pylori resistance to AZM, CLR, LVFX, SPFX, MTZ, and TID was high, whereas that to AMX, AMC, GEN, CFM, TET, DOX, RFP and FZD was relatively low. CFM and DOX are promising new choices for H. pylori eradication.
format: application/pdf
format: text/html
creator: Xueping Huang
creator: Baihe Wu
creator: Qiuzhao Chen
creator: Yushan Chen
creator: Xinhua Ji
creator: Xiang Zhou
creator: Biao Suo
creator: Zhihui Lin
creator: Xiaoling Zheng
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.15611
publisher: PeerJ Inc.
rights: © 2023 Huang et al.
abstract: Background and aim Efficacy of Helicobacter pylori (H. pylori) eradication is related to the local antimicrobial resistance epidemiology. We aimed to investigate the antibiotic resistance of H. pylori in Fujian, China. Methods H. pylori-infected patients in four centers were enrolled in the study from Oct 2019 to Jan 2022. The bacteria were isolated, cultured and identified from the biopsy of patients’ gastric mucosa samples. Antimicrobial susceptibility testing was performed by a modified broth microdilution method for H. pylori to seven guideline-recommended antibiotics and seven potential choices for H. pylori eradication. Results A total of 205 H. pylori strains were isolated. The resistance rates of amoxicillin (AMX), amoxicillin and clavulanate potassium (AMC), cefixime (CFM), gentamicin (GEN), tetracycline (TET), doxycycline (DOX), azithromycin (AZM), clarithromycin (CLR), levofloxacin (LVFX), sparfloxacin (SPFX), metronidazole (MTZ), tinidazole (TID), rifampicin (RFP) and furazolidone (FZD) were 11.22%, 12.20%, 7.32%, 12.20%, 4.88%, 4.39%, 44.39%, 43.90%, 30.24%, 21.46%, 40.98%, 45.85%, 5.37% and 10.24%, respectively. The rates of pan-sensitivity, single, double, triple and multiple resistance for seven guideline-recommended antibiotics were 32.68%, 30.24%, 13.17%, 7.76%, and 14.15%, respectively. The main double-resistance patterns were CLR+MTZ (10/205, 5%) and CLR+LVFX (9/205, 4%). The main triple-resistance pattern was CLR+MTZ+ LVFX (15/205, 7%). Conclusions In Fujian, the prevalence of H. pylori resistance to AZM, CLR, LVFX, SPFX, MTZ, and TID was high, whereas that to AMX, AMC, GEN, CFM, TET, DOX, RFP and FZD was relatively low. CFM and DOX are promising new choices for H. pylori eradication.
bibliographic citation: Huang et al. (2023) Antibiotic resistance profile of Helicobacter pylori to 14 antibiotics: a multicenter study in Fujian, China. PeerJ 11:e15611 https://doi.org/10.7717/peerj.15611
date submitted: 2023-03-03
date accepted: 2023-05-31
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Xueping
author list: Agent
  family name: Wu
  given name: Baihe
author list: Agent
  family name: Chen
  given name: Qiuzhao
author list: Agent
  family name: Chen
  given name: Yushan
author list: Agent
  family name: Ji
  given name: Xinhua
author list: Agent
  family name: Zhou
  given name: Xiang
author list: Agent
  family name: Suo
  given name: Biao
author list: Agent
  family name: Lin
  given name: Zhihui
author list: Agent
  family name: Zheng
  given name: Xiaoling
doi: 10.7717/peerj.15611
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Huang et al.
attribution name: Huang et al.

A novel immunogenic cell death signature for the prediction of prognosis and therapies in glioma
type: item
type: AcademicArticle
description: Glioma is a primary cranial malignancy with high recurrence rate, poor prognosis and high mortality. However, the roles of immunogenic cell death (ICD) in glioma remain unclear. Twenty ICD genes were analyzed to be differentially expressed between glioma tissues and non-tumor tissues in 371 glioma patients from The Cancer Genome Atlas (TCGA). Patients were classified into three subgroups via unsupervised clustering. Interestingly, the features of cell-infiltrating from three clusters were matched with three immune phenotypes. An applied scoring system was built depending on the expression of hub ICD-related genes. Notably, the ICD-related score was linked with immune checkpoints and the prognosis of glioma patients. In addition, the applied risk model could be used for the prediction of the effect of chemotherapy and immunotherapy for glioma patients. Furthermore, MYD88 was identified to play key roles in the risk model for glioma patients. MYD88 was specifically expressed in malignant cells and validated to correlate with cell proliferation and invasion. Ligand–receptor pairs are determined as novel communications indicating between immunocytes and malignant cells. Therefore, our research established an ICD-related score to investigate the potential effect to chemotherapy and immunotherapy for glioma patients and indicated that MYD88 was a key role in this risk model.
format: application/pdf
format: text/html
creator: Jianhua Zhang
creator: Jin Du
creator: Zhihai Jin
creator: Jiang Qian
creator: Jinfa Xu
subject: Bioinformatics
subject: Cell Biology
subject: Neuroscience
subject: Neurology
subject: Oncology
description: doi:10.7717/peerj.15615
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Glioma is a primary cranial malignancy with high recurrence rate, poor prognosis and high mortality. However, the roles of immunogenic cell death (ICD) in glioma remain unclear. Twenty ICD genes were analyzed to be differentially expressed between glioma tissues and non-tumor tissues in 371 glioma patients from The Cancer Genome Atlas (TCGA). Patients were classified into three subgroups via unsupervised clustering. Interestingly, the features of cell-infiltrating from three clusters were matched with three immune phenotypes. An applied scoring system was built depending on the expression of hub ICD-related genes. Notably, the ICD-related score was linked with immune checkpoints and the prognosis of glioma patients. In addition, the applied risk model could be used for the prediction of the effect of chemotherapy and immunotherapy for glioma patients. Furthermore, MYD88 was identified to play key roles in the risk model for glioma patients. MYD88 was specifically expressed in malignant cells and validated to correlate with cell proliferation and invasion. Ligand–receptor pairs are determined as novel communications indicating between immunocytes and malignant cells. Therefore, our research established an ICD-related score to investigate the potential effect to chemotherapy and immunotherapy for glioma patients and indicated that MYD88 was a key role in this risk model.
bibliographic citation: Zhang et al. (2023) A novel immunogenic cell death signature for the prediction of prognosis and therapies in glioma. PeerJ 11:e15615 https://doi.org/10.7717/peerj.15615
date submitted: 2023-04-26
date accepted: 2023-06-01
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Jianhua
author list: Agent
  family name: Du
  given name: Jin
author list: Agent
  family name: Jin
  given name: Zhihai
author list: Agent
  family name: Qian
  given name: Jiang
author list: Agent
  family name: Xu
  given name: Jinfa
doi: 10.7717/peerj.15615
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Zhang et al.
attribution name: Zhang et al.

Diet and physical activity and metabolic disorders in patients with schizophrenia and bipolar affective disorder in the Polish population
type: item
type: AcademicArticle
description: Introduction There are numerous reports of a higher prevalence of metabolic disorders in patients with schizophrenia and bipolar disorder (BD), yet its connections to diet and physical activity remain not fully explained. This article aimed to evaluate diet, physical activity and selected biochemical and anthropometric parameters associated with metabolism in patients with schizophrenia and BD and to analyse the relationships between these variables in the subjects. Materials and Methods A total of 126 adults participated in the study: 47 patients with schizophrenia, 54 patients with BD and 25 patients in mental illness remission (reference group). Data were collected on the underlying illness and concomitant illnesses, and the severity of symptoms of the current episode was assessed using the following scales: PANSS, MADRS and YMRS. An assessment of the subjects’ diet (KomPAN questionnaire) and their physical activity (International Physical Activity Questionnaire) was carried out. Anthropometric and blood pressure measurements were taken and BMI and WHR were calculated. Serum concentrations of fasting glucose, TSH, total cholesterol, LDL and HDL fractions, triglycerides and leptin, ghrelin and resistin were determined. For statistical analysis, the significance level was set at 0.05. For multiple comparisons one way ANOVA or Kruskal Wallis were used with post hoc Tukey and Dunn tests, respectively. To determine correlation of variables, Pearson’s linear correlation coefficient or Spearman’s rank correlation coefficient were used. Results A total of 50.8% of the subjects had at least one metabolic disorder—most commonly excessive body weight (66.7%) and abdominal obesity (64.3%). Patients did not differ significantly in terms of physical activity, but they did differ in mean time spent sitting—with this being significantly longer for all groups than in the general population. The subjects differed in diet: patients with BD consumed less unhealthy foods than patient…
format: application/pdf
format: text/html
creator: Magdalena Głodek
creator: Maria Skibinska
creator: Aleksandra Suwalska
subject: Neurology
subject: Nutrition
subject: Psychiatry and Psychology
subject: Metabolic Sciences
subject: Obesity
description: doi:10.7717/peerj.15617
publisher: PeerJ Inc.
rights: © 2023 Głodek et al.
abstract: Introduction There are numerous reports of a higher prevalence of metabolic disorders in patients with schizophrenia and bipolar disorder (BD), yet its connections to diet and physical activity remain not fully explained. This article aimed to evaluate diet, physical activity and selected biochemical and anthropometric parameters associated with metabolism in patients with schizophrenia and BD and to analyse the relationships between these variables in the subjects. Materials and Methods A total of 126 adults participated in the study: 47 patients with schizophrenia, 54 patients with BD and 25 patients in mental illness remission (reference group). Data were collected on the underlying illness and concomitant illnesses, and the severity of symptoms of the current episode was assessed using the following scales: PANSS, MADRS and YMRS. An assessment of the subjects’ diet (KomPAN questionnaire) and their physical activity (International Physical Activity Questionnaire) was carried out. Anthropometric and blood pressure measurements were taken and BMI and WHR were calculated. Serum concentrations of fasting glucose, TSH, total cholesterol, LDL and HDL fractions, triglycerides and leptin, ghrelin and resistin were determined. For statistical analysis, the significance level was set at 0.05. For multiple comparisons one way ANOVA or Kruskal Wallis were used with post hoc Tukey and Dunn tests, respectively. To determine correlation of variables, Pearson’s linear correlation coefficient or Spearman’s rank correlation coefficient were used. Results A total of 50.8% of the subjects had at least one metabolic disorder—most commonly excessive body weight (66.7%) and abdominal obesity (64.3%). Patients did not differ significantly in terms of physical activity, but they did differ in mean time spent sitting—with this being significantly longer for all groups than in the general population. The subjects differed in diet: patients with BD consumed less unhealthy foods than patient…
bibliographic citation: Głodek et al. (2023) Diet and physical activity and metabolic disorders in patients with schizophrenia and bipolar affective disorder in the Polish population. PeerJ 11:e15617 https://doi.org/10.7717/peerj.15617
date submitted: 2023-04-26
date accepted: 2023-06-01
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Głodek
  given name: Magdalena
author list: Agent
  family name: Skibinska
  given name: Maria
author list: Agent
  family name: Suwalska
  given name: Aleksandra
doi: 10.7717/peerj.15617
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Głodek et al.
attribution name: Głodek et al.

Ecological indicators reveal historical regime shifts in the Black Sea ecosystem
type: item
type: AcademicArticle
description: Background The Black Sea is one of the most anthropogenically disturbed marine ecosystems in the world because of introduced species, fisheries overexploitation, nutrient enrichment via pollution through river discharge, and the impacts of climate change. It has undergone significant ecosystem transformations since the 1960s. The infamous anchovy and alien warty comb jelly Mnemiopsis leidyi shift that occurred in 1989 is the most well-known example of the drastic extent of anthropogenic disturbance in the Black Sea. Although a vast body of literature exists on the Black Sea ecosystem, a holistic look at the multidecadal changes in the Black Sea ecosystem using an ecosystem- and ecology-based approach is still lacking. Hence, this work is dedicated to filling this gap. Methods First, a dynamic food web model of the Black Sea extending from 1960 to 1999 was established and validated against time-series data. Next, an ecological network analysis was performed to calculate the time series of synthetic ecological indicators, and a regime shift analysis was performed on the time series of indicators. Results The model successfully replicated the regime shifts observed in the Black Sea. The results showed that the Black Sea ecosystem experienced four regime shifts and was reorganized due to effects instigated by overfishing in the 1960s, eutrophication and establishment of trophic dead-end organisms in the 1970s, and overfishing and intensifying interspecies trophic competition by the overpopulation of some r-selected organisms (i.e., jellyfish species) in the 1980s. Overall, these changes acted concomitantly to erode the structure and function of the ecosystem by manipulating the food web to reorganize itself through the introduction and selective removal of organisms and eutrophication. Basin-wide, cross-national management efforts, especially with regard to pollution and fisheries, could have prevented the undesirable changes observed in the Black Sea ecosystem and shou…
format: application/pdf
format: text/html
creator: Ekin Akoglu
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Environmental Impacts
subject: Biological Oceanography
description: doi:10.7717/peerj.15649
publisher: PeerJ Inc.
rights: © 2023 Akoglu
abstract: Background The Black Sea is one of the most anthropogenically disturbed marine ecosystems in the world because of introduced species, fisheries overexploitation, nutrient enrichment via pollution through river discharge, and the impacts of climate change. It has undergone significant ecosystem transformations since the 1960s. The infamous anchovy and alien warty comb jelly Mnemiopsis leidyi shift that occurred in 1989 is the most well-known example of the drastic extent of anthropogenic disturbance in the Black Sea. Although a vast body of literature exists on the Black Sea ecosystem, a holistic look at the multidecadal changes in the Black Sea ecosystem using an ecosystem- and ecology-based approach is still lacking. Hence, this work is dedicated to filling this gap. Methods First, a dynamic food web model of the Black Sea extending from 1960 to 1999 was established and validated against time-series data. Next, an ecological network analysis was performed to calculate the time series of synthetic ecological indicators, and a regime shift analysis was performed on the time series of indicators. Results The model successfully replicated the regime shifts observed in the Black Sea. The results showed that the Black Sea ecosystem experienced four regime shifts and was reorganized due to effects instigated by overfishing in the 1960s, eutrophication and establishment of trophic dead-end organisms in the 1970s, and overfishing and intensifying interspecies trophic competition by the overpopulation of some r-selected organisms (i.e., jellyfish species) in the 1980s. Overall, these changes acted concomitantly to erode the structure and function of the ecosystem by manipulating the food web to reorganize itself through the introduction and selective removal of organisms and eutrophication. Basin-wide, cross-national management efforts, especially with regard to pollution and fisheries, could have prevented the undesirable changes observed in the Black Sea ecosystem and shou…
bibliographic citation: Akoglu (2023) Ecological indicators reveal historical regime shifts in the Black Sea ecosystem. PeerJ 11:e15649 https://doi.org/10.7717/peerj.15649
date submitted: 2023-03-21
date accepted: 2023-06-06
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Akoglu
  given name: Ekin
doi: 10.7717/peerj.15649
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: © 2023 Akoglu
attribution name: Akoglu

Vet the journal before you submit: turnaround times of journals publishing in zoological medicine and related fields
type: item
type: AcademicArticle
description: Many factors influence selection of a target journal for publishing scientific papers, including “fit” within the journal’s scope, acceptance rate, readership, open access options, submission and publication costs, journal quality, and timeliness of publication. Timeliness of publication can be a critical factor affecting career development, but many journals are not transparent about turnaround times. Here we evaluated 49 journals publishing papers in zoological medicine and related fields between 2017 and 2022, and aggregated and examined distributions of turnaround time of journals that publicly provided the requisite data, in order to aid authors in selecting target journals that best meet their needs. Of 49 journals evaluated, 39 provided necessary dates for reconstructing turnaround times. Of these, median times to acceptance ranged from 37 to 338 days, and median times to publication ranged from 41 to 403.5 days. The percentage of papers published in greater than 1 year (“slow”) ranged from 0 to 57.1%, while the percentage of papers published in under 6 months (“timely”) ranged from 0.8 to 99.8%. Acceptance rates and times to first decision were available for only 22% and 20%, respectively, of journals evaluated. Results may prove useful for authors deciding where to submit their works, depending on how they prioritize the many factors involved.
format: application/pdf
format: text/html
creator: Brendan Runde
creator: Craig Harms
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.15656
publisher: PeerJ Inc.
rights: © 2023 Runde and Harms
abstract: Many factors influence selection of a target journal for publishing scientific papers, including “fit” within the journal’s scope, acceptance rate, readership, open access options, submission and publication costs, journal quality, and timeliness of publication. Timeliness of publication can be a critical factor affecting career development, but many journals are not transparent about turnaround times. Here we evaluated 49 journals publishing papers in zoological medicine and related fields between 2017 and 2022, and aggregated and examined distributions of turnaround time of journals that publicly provided the requisite data, in order to aid authors in selecting target journals that best meet their needs. Of 49 journals evaluated, 39 provided necessary dates for reconstructing turnaround times. Of these, median times to acceptance ranged from 37 to 338 days, and median times to publication ranged from 41 to 403.5 days. The percentage of papers published in greater than 1 year (“slow”) ranged from 0 to 57.1%, while the percentage of papers published in under 6 months (“timely”) ranged from 0.8 to 99.8%. Acceptance rates and times to first decision were available for only 22% and 20%, respectively, of journals evaluated. Results may prove useful for authors deciding where to submit their works, depending on how they prioritize the many factors involved.
bibliographic citation: Runde et al. (2023) Vet the journal before you submit: turnaround times of journals publishing in zoological medicine and related fields. PeerJ 11:e15656 https://doi.org/10.7717/peerj.15656
date submitted: 2023-01-25
date accepted: 2023-06-07
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Runde
  given name: Brendan
author list: Agent
  family name: Harms
  given name: Craig
doi: 10.7717/peerj.15656
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: ©2023 Runde and Harms
attribution name: Runde and Harms

A retrospective study on expression and clinical significance of PHH3, Ki67 and P53 in bladder exophytic papillary urothelial neoplasms
type: item
type: AcademicArticle
description: Background Exophytic papillary urothelial neoplasms (EPUN) are difficult to diagnose pathologically and are well-known for their heterogeneous prognoses. Thus, searching for an objective and accurate diagnostic marker is of great clinical value in improving the outcomes of EPUN patients. PHH3 was reported to be expressed explicitly in the mitotic phase of the cell cycle, and recent studies have shown that PHH3 expression was associated with the differential diagnosis and prognosis of many tumors. However, its significance in EPUN remains unclear. This study aimed to determine the expression of PHH3 in different EPUN, compare its expression with cell-cycle related proteins Ki67 and P53, and analyze its significance in the differential diagnosis and prognostic value for high-grade papillary urothelial carcinoma (HGPUC), low-grade papillary urothelial carcinoma (LGPUC), papillary urothelial neoplasm of low malignant potential (PUNLMP) and urothelial papilloma (UP). Methods We retrospectively analyzed the pathological diagnosis and clinical features of 26 HGPUC cases, 43 LGPUC cases, 21 PUNLMP cases and 11 UP cases. PHH3, Ki67 and P53 were detected by immunohistochemistry in 101 EPUN cases samples. The cut-off values of PHH3 mitosis count (PHMC), HE mitosis count (HEMC), Ki67 and P53 in the different EPUN were determined using the ROC curve. The distribution of counts in each group and its relationship with clinical parameters and prognosis of EPUN patients were also analyzed. Results The determination coefficient (R2 = 0.9980) of PHMC were more potent than those of HEMC (R2 = 0.9734) in the EPUN mitotic counts microscopically by both pathologists. Of the 101 EPUN cases investigated, significant positive linear correlations were found between PHMC and HEMC, PHMC and Ki67, and HEMC and Ki67 (P < 0.0001). In HGPUC, LGPUC, PUNLMP and UP, a decreasing trend was observed in the median and range of PHMC/10HPFs, HEMC/10HPFs, Ki67 (%) and P53 (%). PHMC, HEMC, Ki67 and P53 were …
format: application/pdf
format: text/html
creator: Gaoxiu Qi
creator: Jinmeng Liu
creator: Shuqi Tao
creator: Wenyuan Fan
creator: Haoning Zheng
creator: Meihong Wang
creator: Hanchao Yang
creator: Yongting Liu
creator: Huancai Liu
creator: Fenghua Zhou
subject: Oncology
subject: Pathology
subject: Urology
subject: Histology
description: doi:10.7717/peerj.15675
publisher: PeerJ Inc.
rights: © 2023 Qi et al.
abstract: Background Exophytic papillary urothelial neoplasms (EPUN) are difficult to diagnose pathologically and are well-known for their heterogeneous prognoses. Thus, searching for an objective and accurate diagnostic marker is of great clinical value in improving the outcomes of EPUN patients. PHH3 was reported to be expressed explicitly in the mitotic phase of the cell cycle, and recent studies have shown that PHH3 expression was associated with the differential diagnosis and prognosis of many tumors. However, its significance in EPUN remains unclear. This study aimed to determine the expression of PHH3 in different EPUN, compare its expression with cell-cycle related proteins Ki67 and P53, and analyze its significance in the differential diagnosis and prognostic value for high-grade papillary urothelial carcinoma (HGPUC), low-grade papillary urothelial carcinoma (LGPUC), papillary urothelial neoplasm of low malignant potential (PUNLMP) and urothelial papilloma (UP). Methods We retrospectively analyzed the pathological diagnosis and clinical features of 26 HGPUC cases, 43 LGPUC cases, 21 PUNLMP cases and 11 UP cases. PHH3, Ki67 and P53 were detected by immunohistochemistry in 101 EPUN cases samples. The cut-off values of PHH3 mitosis count (PHMC), HE mitosis count (HEMC), Ki67 and P53 in the different EPUN were determined using the ROC curve. The distribution of counts in each group and its relationship with clinical parameters and prognosis of EPUN patients were also analyzed. Results The determination coefficient (R2 = 0.9980) of PHMC were more potent than those of HEMC (R2 = 0.9734) in the EPUN mitotic counts microscopically by both pathologists. Of the 101 EPUN cases investigated, significant positive linear correlations were found between PHMC and HEMC, PHMC and Ki67, and HEMC and Ki67 (P < 0.0001). In HGPUC, LGPUC, PUNLMP and UP, a decreasing trend was observed in the median and range of PHMC/10HPFs, HEMC/10HPFs, Ki67 (%) and P53 (%). PHMC, HEMC, Ki67 and P53 were …
bibliographic citation: Qi et al. (2023) A retrospective study on expression and clinical significance of PHH3, Ki67 and P53 in bladder exophytic papillary urothelial neoplasms. PeerJ 11:e15675 https://doi.org/10.7717/peerj.15675
date submitted: 2023-02-22
date accepted: 2023-06-11
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Gaoxiu
author list: Agent
  family name: Liu
  given name: Jinmeng
author list: Agent
  family name: Tao
  given name: Shuqi
author list: Agent
  family name: Fan
  given name: Wenyuan
author list: Agent
  family name: Zheng
  given name: Haoning
author list: Agent
  family name: Wang
  given name: Meihong
author list: Agent
  family name: Yang
  given name: Hanchao
author list: Agent
  family name: Liu
  given name: Yongting
author list: Agent
  family name: Liu
  given name: Huancai
author list: Agent
  family name: Zhou
  given name: Fenghua
doi: 10.7717/peerj.15675
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: ©2023 Qi et al.
attribution name: Qi et al.

In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants
type: item
type: AcademicArticle
description: Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in compa…
format: application/pdf
format: text/html
creator: So Youn Won
creator: Prabhakaran Soundararajan
creator: Vadivelmurugan Irulappan
creator: Jung Sun Kim
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.15696
publisher: PeerJ Inc.
rights: © 2023 Won et al.
abstract: Single-cell C4 (SCC4) plants with bienertioid anatomy carry out photosynthesis in a single cell. Chloroplast movement is the underlying phenomenon, where chloroplast unusual positioning 1 (CHUP1) plays a key role. This study aimed to characterize CHUP1 and CHUP1-like proteins in an SCC4 photosynthetic plant, Bienertia sinuspersici. Also, a comparative analysis of SCC4 CHUP1 was made with C3, C4, and CAM model plants including an extant basal angiosperm, Amborella. The CHUP1 gene exists as a single copy from the basal angiosperms to SCC4 plants. Our analysis identified that Chenopodium quinoa, a recently duplicated allotetraploid, has two copies of CHUP1. In addition, the numbers of CHUP1-like and its associated proteins such as CHUP1-like_a, CHUP1-like_b, HPR, TPR, and ABP varied between the species. Hidden Markov Model analysis showed that the gene size of CHUP1-like_a and CHUP1-like_b of SCC4 species, Bienertia, and Suaeda were enlarged than other plants. Also, we identified that CHUP1-like_a and CHUP1-like_b are absent in Arabidopsis and Amborella, respectively. Motif analysis identified several conserved and variable motifs based on the orders (monocot and dicot) as well as photosynthetic pathways. For instance, CAM plants such as pineapple and cactus shared certain motifs of CHUP1-like_a irrespective of their distant phylogenetic relationship. The free ratio model showed that CHUP1 maintained purifying selection, whereas CHUP1-like_a and CHUP1-like_b have adaptive functions between SCC4 plants and quinoa. Similarly, rice and maize branches displayed functional diversification on CHUP1-like_b. Relative gene expression data showed that during the subcellular compartmentalization process of Bienertia, CHUP1 and actin-binding proteins (ABP) genes showed a similar pattern of expression. Altogether, the results of this study provide insight into the evolutionary and functional details of CHUP1 and its associated proteins in the development of the SCC4 system in compa…
bibliographic citation: Won et al. (2023) In-silico, evolutionary, and functional analysis of CHUP1 and its related proteins in Bienertia sinuspersici—a comparative study across C3, C4, CAM, and SCC4 model plants. PeerJ 11:e15696 https://doi.org/10.7717/peerj.15696
date submitted: 2022-09-08
date accepted: 2023-06-14
issued: 2023-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Won
  given name: So Youn
author list: Agent
  family name: Soundararajan
  given name: Prabhakaran
author list: Agent
  family name: Irulappan
  given name: Vadivelmurugan
author list: Agent
  family name: Kim
  given name: Jung Sun
doi: 10.7717/peerj.15696
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-11
copyright: ©2023 Won et al.
attribution name: Won et al.

Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China
type: item
type: AcademicArticle
description: The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, a…
format: application/pdf
format: text/html
creator: Yaru Zhao
creator: Dulan Bao
creator: Ying Sun
creator: Yajie Meng
creator: Ziteng Li
creator: Rui Liu
creator: Jiwei Lang
creator: Li Liu
creator: Li Gao
subject: Microbiology
subject: Zoology
description: doi:10.7717/peerj.15462
publisher: PeerJ Inc.
rights: © 2023 Zhao et al.
abstract: The gut microbiota promotes host health by maintaining homeostasis and enhancing digestive efficiency. The gut microflora in wild birds affects host physiological characteristics, nutritional status, and stress response. The relict gull (Larus Relictus, a Chinese national first-class protected species) and the black-necked grebe (Podiceps Nigricollis, a secondary protected species) bred in the Ordos Relic Gull National Nature Reserve share similar feeding habits and living environments but are distantly related genetically. To explore the composition and differences in the gut microbiota of these two key protected avian species in Erdos Relic Gull National Nature Reserve and provide a basis for their protection, 16S rRNA gene high-throughput sequencing was performed and the gut microbial diversity and composition of the relict gull (L. Relictus) and black-necked grebe (P. Nigricollis) was characterized. In total, 445 OTUs (operational taxonomic units) were identified and classified into 15 phyla, 22 classes, 64 orders, 126 families, and 249 genera. Alpha diversity analysis indicates that the gut microbial richness of the relict gull is significantly lower than that of the black-necked grebe. Gut microbe composition differs significantly between the two species. The most abundant bacterial phyla in these samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes. The prominent phylum in the relict gull was Proteobacteria, whereas the prominent phylum in the black-necked grebe was Firmicutes. The average relative abundance of the 17 genera identified was greater than 1%. The dominant genus in the relict gull was Escherichia-Shigella, whereas Halomonas was dominant in the black-necked grebe. Microbial functional analyses indicate that environmental factors exert a greater impact on relict gulls than on black-necked grebes. Compared with the relict gull, the black-necked grebe was able to use food more efficiently to accumulate its nutrient requirements, a…
bibliographic citation: Zhao et al. (2023) Comparative analysis of the gut bacteria of the relict gull (Larus Relictus) and black-necked grebe (Podiceps Nigricollis) in Erdos Relic Gull National Nature Reserve in Inner Mongolia, China. PeerJ 11:e15462 https://doi.org/10.7717/peerj.15462
date submitted: 2023-01-26
date accepted: 2023-05-04
issued: 2023-07-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Yaru
author list: Agent
  family name: Bao
  given name: Dulan
author list: Agent
  family name: Sun
  given name: Ying
author list: Agent
  family name: Meng
  given name: Yajie
author list: Agent
  family name: Li
  given name: Ziteng
author list: Agent
  family name: Liu
  given name: Rui
author list: Agent
  family name: Lang
  given name: Jiwei
author list: Agent
  family name: Liu
  given name: Li
author list: Agent
  family name: Gao
  given name: Li
doi: 10.7717/peerj.15462
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-07-10
copyright: ©2023 Zhao et al.
attribution name: Zhao et al.

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