PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A new approach for increasing graduate students’ science communication capacity and confidence
items: Modeling the effects of water temperature on the population dynamics of Galba viatrix and infection by Fasciola hepatica: a two-year survey in Andean Patagonia, Argentina
items: Quorum sensing signals of the grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: use of inducible expression and polymeric resin to sequester acyl-homoserine lactones
items: Exploring the potential role of ENPP2 in polycystic ovary syndrome and endometrial cancer through bioinformatic analysis
items: Antimicrobial resistance pattern of Escherichia coli isolated from imported frozen shrimp in Saudi Arabia
items: Construction and clinical application of a risk model based on N6-methyladenosine regulators for colorectal cancer
items: Vegetation–soil–microbiota dynamics across a 50-year reconstructed grassland chronosequence on the Loess Plateau of China
items: Effect of seedling size on post-planting growth and survival of five Mexican Pinus species and their hybrids
items: The movement and distribution of pregnant spotted ragged-tooth sharks, Carcharias taurus, in the iSimangaliso Wetland Park, South Africa
items: Visual codon: a user-friendly Python program for viewing and optimizing gene GC content

A new approach for increasing graduate students’ science communication capacity and confidence
type: item
type: AcademicArticle
description: There is an increasing demand for emerging scientists to improve their ability to communicate with public audiences, yet little research investigates the effectiveness of science communication training for graduate students. We responded to this need by developing SciWrite@URI—an interdisciplinary model for science graduate students designed around three learning outcomes based on tenets from the field of writing and rhetoric—habitual writing, multiple genres, and frequent review. SciWrite students completed courses and a science communication internship, attended writing workshops, and became tutors at a newly established Graduate Writing Center. After 2 years of training, students more frequently wrote multiple drafts and engaged in peer review, increased their confidence as writers, and decreased their apprehension about writing. We conclude the tenets of the SciWrite program helped students improve as science communicators, and we make suggestions for effective ways graduate departments and training programs might implement and build on our model.
format: application/pdf
format: text/html
creator: Erin R. Harrington
creator: Scott R. McWilliams
creator: Nancy E. Karraker
creator: Caroline Gottschalk Druschke
creator: Jenna Morton-Aiken
creator: Elaine Finan
creator: Ingrid E. Lofgren
subject: Science and Medical Education
description: doi:10.7717/peerj.18594
publisher: PeerJ Inc.
rights: © 2024 Harrington et al.
abstract: There is an increasing demand for emerging scientists to improve their ability to communicate with public audiences, yet little research investigates the effectiveness of science communication training for graduate students. We responded to this need by developing SciWrite@URI—an interdisciplinary model for science graduate students designed around three learning outcomes based on tenets from the field of writing and rhetoric—habitual writing, multiple genres, and frequent review. SciWrite students completed courses and a science communication internship, attended writing workshops, and became tutors at a newly established Graduate Writing Center. After 2 years of training, students more frequently wrote multiple drafts and engaged in peer review, increased their confidence as writers, and decreased their apprehension about writing. We conclude the tenets of the SciWrite program helped students improve as science communicators, and we make suggestions for effective ways graduate departments and training programs might implement and build on our model.
bibliographic citation: Harrington et al. (2024) A new approach for increasing graduate students’ science communication capacity and confidence. PeerJ 12:e18594 https://doi.org/10.7717/peerj.18594
date submitted: 2023-08-14
date accepted: 2024-11-05
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harrington
  given name: Erin R.
author list: Agent
  family name: McWilliams
  given name: Scott R.
author list: Agent
  family name: Karraker
  given name: Nancy E.
author list: Agent
  family name: Gottschalk Druschke
  given name: Caroline
author list: Agent
  family name: Morton-Aiken
  given name: Jenna
author list: Agent
  family name: Finan
  given name: Elaine
author list: Agent
  family name: Lofgren
  given name: Ingrid E.
doi: 10.7717/peerj.18594
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Harrington et al.
attribution name: Harrington et al.

Modeling the effects of water temperature on the population dynamics of Galba viatrix and infection by Fasciola hepatica: a two-year survey in Andean Patagonia, Argentina
type: item
type: AcademicArticle
description: Background The trematode parasite Fasciola hepatica (liver fluke) can infect livestock, wild mammals, and humans, generating serious economic losses worldwide. Aquatic or amphibious snails of the Lymnaeidae family are the intermediate host of this parasite. Both snail population dynamics and parasite development are closely associated with temperature, although most field studies have recorded air temperature rather than water temperature. Our aim was to statistically model the population dynamics of lymnaeid snails and their infection by F. hepatica under natural environmental conditions in Northwest Andean Patagonia. Methods For two years, we sampled snails monthly in four bodies of water, while registering water and air temperature hourly, and assessing F. hepatica infection in snails. Hierarchical Bayesian modeling allowed us to estimate the functional relationship between water temperature and population growth, the probability of detecting snails, and infection by F. hepatica. Results A total of 1,411 Galba viatrix snails were collected, identified, and analyzed for F. hepatica infection. All sites showed seasonal variation in the number of snails collected and in water temperature as well as sharp variations in snail counts between surveys adjacent in time. The hierarchical model revealed that water temperature acts, at least, at two different time scales: water temperature at the time of sampling determines snail detection probability, whereas the average water temperature between sampling dates affects lymnaeid population growth. We found maximum F. hepatica prevalences in snails of 40% (2/5 and 4/10), followed by 33% (65/197). These are the highest prevalences recorded in G. viatrix populations in Argentina to date. Our modeling evidenced that the positive effects of water temperature on infection probability increases with snail size and prevalence on the previous survey, while previous prevalence strongly enhances the effects of snail size. Conclusions O…
format: application/pdf
format: text/html
creator: Paula Soler
creator: Juan Manuel Gurevitz
creator: Juan Manuel Morales
creator: Marcela Larroza
subject: Ecology
subject: Parasitology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.18648
publisher: PeerJ Inc.
rights: © 2024 Soler et al.
abstract: Background The trematode parasite Fasciola hepatica (liver fluke) can infect livestock, wild mammals, and humans, generating serious economic losses worldwide. Aquatic or amphibious snails of the Lymnaeidae family are the intermediate host of this parasite. Both snail population dynamics and parasite development are closely associated with temperature, although most field studies have recorded air temperature rather than water temperature. Our aim was to statistically model the population dynamics of lymnaeid snails and their infection by F. hepatica under natural environmental conditions in Northwest Andean Patagonia. Methods For two years, we sampled snails monthly in four bodies of water, while registering water and air temperature hourly, and assessing F. hepatica infection in snails. Hierarchical Bayesian modeling allowed us to estimate the functional relationship between water temperature and population growth, the probability of detecting snails, and infection by F. hepatica. Results A total of 1,411 Galba viatrix snails were collected, identified, and analyzed for F. hepatica infection. All sites showed seasonal variation in the number of snails collected and in water temperature as well as sharp variations in snail counts between surveys adjacent in time. The hierarchical model revealed that water temperature acts, at least, at two different time scales: water temperature at the time of sampling determines snail detection probability, whereas the average water temperature between sampling dates affects lymnaeid population growth. We found maximum F. hepatica prevalences in snails of 40% (2/5 and 4/10), followed by 33% (65/197). These are the highest prevalences recorded in G. viatrix populations in Argentina to date. Our modeling evidenced that the positive effects of water temperature on infection probability increases with snail size and prevalence on the previous survey, while previous prevalence strongly enhances the effects of snail size. Conclusions O…
bibliographic citation: Soler et al. (2024) Modeling the effects of water temperature on the population dynamics of Galba viatrix and infection by Fasciola hepatica: a two-year survey in Andean Patagonia, Argentina. PeerJ 12:e18648 https://doi.org/10.7717/peerj.18648
date submitted: 2024-08-06
date accepted: 2024-11-14
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soler
  given name: Paula
author list: Agent
  family name: Gurevitz
  given name: Juan Manuel
author list: Agent
  family name: Morales
  given name: Juan Manuel
author list: Agent
  family name: Larroza
  given name: Marcela
doi: 10.7717/peerj.18648
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Soler et al.
attribution name: Soler et al.

Quorum sensing signals of the grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: use of inducible expression and polymeric resin to sequester acyl-homoserine lactones
type: item
type: AcademicArticle
description: Background A grapevine crown gall tumor strain, Novosphingobium sp. strain Rr2-17 was previously reported to accumulate copious amounts of diverse quorum sensing signals during growth. Genome sequencing identified a single luxI homolog in strain Rr2-17, suggesting that it may encode for a AHL synthase with broad substrate range, pending functional validation. The exact identity of the complete suite of AHLs formed by novIspR1 is largely unknown. Methods This study validates the function of novIspR1 through inducible expression in Escherichia coli and in the wild-type parental strain Rr2-17. We further enhanced the capture of acyl homoserine lactone (AHL) signals produced by novIspR1 using polymeric resin XAD-16 and separated the AHLs by one- and two-dimensional thin layer chromatography followed by detection using AHL-dependent whole cell biosensor strains. Lastly, the complete number of AHLs produced by novIspR1 in our system was identified by LC-MS/MS analyses. Results The single LuxI homolog of N. sp. Rr2-17, NovIspR1, is able to produce up to eleven different AHL signals, including AHLs: C8-, C10-, C12-, C14-homoserine lactone (HSL) as well as AHLs with OH substitutions at the third carbon and includes 3-OH-C6-, 3-OH-C8-, 3-OH-C10-, 3-OH-C12- and 3-OH-C14-HSL. The most abundant AHL produced was identified as 3-OH-C8-HSL and isopropyl-D-1-thiogalactopyranoside (IPTG) induction of novIspR1 expression in wild type parental Rr2-17 strain increased its concentration by 6.8-fold when compared to the same strain with the vector only control plasmid. Similar increases were identified with the next two most abundant AHLs, 3-OH-C10- and unsubstituted C8-HSL. The presence of 2% w/v of XAD-16 resin in the growth culture bound 99.3 percent of the major AHL (3-OH-C8-HSL) produced by IPTG-induced overexpression of novIspR1 in Rr2-17 strain. This study significantly adds to our understanding of the AHL class of quorum sensing system in a grapevine crown gall tumor associated No…
format: application/pdf
format: text/html
creator: Han Ming Gan
creator: Lucas Dailey
creator: Peter Wengert
creator: Nigel Halliday
creator: Paul Williams
creator: André O. Hudson
creator: Michael A. Savka
subject: Biotechnology
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.18657
publisher: PeerJ Inc.
rights: © 2024 Gan et al.
abstract: Background A grapevine crown gall tumor strain, Novosphingobium sp. strain Rr2-17 was previously reported to accumulate copious amounts of diverse quorum sensing signals during growth. Genome sequencing identified a single luxI homolog in strain Rr2-17, suggesting that it may encode for a AHL synthase with broad substrate range, pending functional validation. The exact identity of the complete suite of AHLs formed by novIspR1 is largely unknown. Methods This study validates the function of novIspR1 through inducible expression in Escherichia coli and in the wild-type parental strain Rr2-17. We further enhanced the capture of acyl homoserine lactone (AHL) signals produced by novIspR1 using polymeric resin XAD-16 and separated the AHLs by one- and two-dimensional thin layer chromatography followed by detection using AHL-dependent whole cell biosensor strains. Lastly, the complete number of AHLs produced by novIspR1 in our system was identified by LC-MS/MS analyses. Results The single LuxI homolog of N. sp. Rr2-17, NovIspR1, is able to produce up to eleven different AHL signals, including AHLs: C8-, C10-, C12-, C14-homoserine lactone (HSL) as well as AHLs with OH substitutions at the third carbon and includes 3-OH-C6-, 3-OH-C8-, 3-OH-C10-, 3-OH-C12- and 3-OH-C14-HSL. The most abundant AHL produced was identified as 3-OH-C8-HSL and isopropyl-D-1-thiogalactopyranoside (IPTG) induction of novIspR1 expression in wild type parental Rr2-17 strain increased its concentration by 6.8-fold when compared to the same strain with the vector only control plasmid. Similar increases were identified with the next two most abundant AHLs, 3-OH-C10- and unsubstituted C8-HSL. The presence of 2% w/v of XAD-16 resin in the growth culture bound 99.3 percent of the major AHL (3-OH-C8-HSL) produced by IPTG-induced overexpression of novIspR1 in Rr2-17 strain. This study significantly adds to our understanding of the AHL class of quorum sensing system in a grapevine crown gall tumor associated No…
bibliographic citation: Gan et al. (2024) Quorum sensing signals of the grapevine crown gall bacterium, Novosphingobium sp. Rr2-17: use of inducible expression and polymeric resin to sequester acyl-homoserine lactones. PeerJ 12:e18657 https://doi.org/10.7717/peerj.18657
date submitted: 2024-06-17
date accepted: 2024-11-17
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Han Ming
author list: Agent
  family name: Dailey
  given name: Lucas
author list: Agent
  family name: Wengert
  given name: Peter
author list: Agent
  family name: Halliday
  given name: Nigel
author list: Agent
  family name: Williams
  given name: Paul
author list: Agent
  family name: Hudson
  given name: André O.
author list: Agent
  family name: Savka
  given name: Michael A.
doi: 10.7717/peerj.18657
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Gan et al.
attribution name: Gan et al.

Exploring the potential role of ENPP2 in polycystic ovary syndrome and endometrial cancer through bioinformatic analysis
type: item
type: AcademicArticle
description: Background Growing evidence indicates a significant correlation between polycystic ovary syndrome (PCOS) and endometrial carcinoma (EC); nevertheless, the fundamental molecular mechanisms involved continue to be unclear. Methods Initially, differential analysis, the least absolute shrinkage and selection operator (LASSO) regression, and support vector machine-recursive feature elimination (SVM-RFE) algorithms were employed to identify candidate genes associated with ferroptosis in PCOS. Subsequently, the TCGA-UCEC data were utilized to pinpoint the core gene. Then, the expression of ENPP2 in granulosa cells and endometrium of PCOS was validated using real-time PCR (RT-qPCR). Additionally, we investigated the role of ENPP2 in the progression from PCOS to EC through western blotting (WB), colony formation assay, cell scratch assay, transwell assay, and immunofluorescence (IF). Subsequently, ENPP2 gene set enrichment analysis (GSEA) analyses were conducted to identify common pathways involved in PCOS and EC, which were then verified by RT-qPCR. Finally, immune infiltration and the tumor microenvironment (TME) were explored to examine the involvement of ENPP2 in EC progression. Results The datasets TCGA-UCEC (pertaining to EC), GSE34526, GSE137684, and GSE6798 (related to PCOS) were procured and subjected to analysis. The gene ENPP2 has been recognized as the shared element connecting PCOS and EC. Next, we observed a significant downregulation of ENPP2 expression in the granulosa cells in PCOS compared to the normal patients, while an upregulation of ENPP2 expression was observed in the endometrium of hyperandrogenic PCOS patients relative to the normal. In vitro, the WB revealed that 5-dihydrotestosterone (DHT) upregulated ENPP2 expression in Ishikawa and HEC-1-A cells. Additionally, we found that ENPP2 promoted the proliferation, migration, and invasion of Ishikawa and HEC-1-A cells. Subsequently, we discovered that overexpressed ENPP2 may lead to an increase in CYP19…
format: application/pdf
format: text/html
creator: Xumin Zhang
creator: Jianrong Liu
creator: Chunmei Bai
creator: Yang Li
creator: Yanxin Fan
subject: Bioinformatics
subject: Cell Biology
subject: Gynecology and Obstetrics
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.18666
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background Growing evidence indicates a significant correlation between polycystic ovary syndrome (PCOS) and endometrial carcinoma (EC); nevertheless, the fundamental molecular mechanisms involved continue to be unclear. Methods Initially, differential analysis, the least absolute shrinkage and selection operator (LASSO) regression, and support vector machine-recursive feature elimination (SVM-RFE) algorithms were employed to identify candidate genes associated with ferroptosis in PCOS. Subsequently, the TCGA-UCEC data were utilized to pinpoint the core gene. Then, the expression of ENPP2 in granulosa cells and endometrium of PCOS was validated using real-time PCR (RT-qPCR). Additionally, we investigated the role of ENPP2 in the progression from PCOS to EC through western blotting (WB), colony formation assay, cell scratch assay, transwell assay, and immunofluorescence (IF). Subsequently, ENPP2 gene set enrichment analysis (GSEA) analyses were conducted to identify common pathways involved in PCOS and EC, which were then verified by RT-qPCR. Finally, immune infiltration and the tumor microenvironment (TME) were explored to examine the involvement of ENPP2 in EC progression. Results The datasets TCGA-UCEC (pertaining to EC), GSE34526, GSE137684, and GSE6798 (related to PCOS) were procured and subjected to analysis. The gene ENPP2 has been recognized as the shared element connecting PCOS and EC. Next, we observed a significant downregulation of ENPP2 expression in the granulosa cells in PCOS compared to the normal patients, while an upregulation of ENPP2 expression was observed in the endometrium of hyperandrogenic PCOS patients relative to the normal. In vitro, the WB revealed that 5-dihydrotestosterone (DHT) upregulated ENPP2 expression in Ishikawa and HEC-1-A cells. Additionally, we found that ENPP2 promoted the proliferation, migration, and invasion of Ishikawa and HEC-1-A cells. Subsequently, we discovered that overexpressed ENPP2 may lead to an increase in CYP19…
bibliographic citation: Zhang et al. (2024) Exploring the potential role of ENPP2 in polycystic ovary syndrome and endometrial cancer through bioinformatic analysis. PeerJ 12:e18666 https://doi.org/10.7717/peerj.18666
date submitted: 2024-07-24
date accepted: 2024-11-18
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xumin
author list: Agent
  family name: Liu
  given name: Jianrong
author list: Agent
  family name: Bai
  given name: Chunmei
author list: Agent
  family name: Li
  given name: Yang
author list: Agent
  family name: Fan
  given name: Yanxin
doi: 10.7717/peerj.18666
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Antimicrobial resistance pattern of Escherichia coli isolated from imported frozen shrimp in Saudi Arabia
type: item
type: AcademicArticle
description: Contamination of seafood products with multi-drug-resistant (MDR) bacteria is considered to be a potential source for the spread of MDR bacteria in communities. However, little is known about the extent of the contamination of seafood, in particular shrimp, with MDR bacteria in Saudi Arabia. In this study, imported frozen shrimp in retail markets were examined for the antimicrobial susceptibility patterns of Escherichia coli. Escherichia coli was isolated from 40 frozen shrimp samples; a total of 25 and 15 shrimp samples were imported from China and Vietnam, respectively. Of the 40 examined frozen shrimp samples, 30 tested positive for E. coli, resulting in an overall isolation rate of 75%, with a total of 180 isolates being identified. The largest number of positive samples for E. coli isolates (n = 140) were found in 22 out of 25 samples from frozen shrimp imported from China. Additionally, eight out of 15 samples from frozen shrimp imported from Vietnam were positive for E. coli, leading to the recovery of 40 isolates. Overall, the susceptibilities among E. coli isolates were observed against 99.4% for amikacin, augmentin and kanamycin, 95% for cefoxitin and 92.7% for ceftazidime and nitrofurantoin. High percentage of the isolates exhibited resistance to cephalothin (174/180, 96.6%), ampicillin (167/180, 92.7%), Cephalexin (163/180. 90.5%), piperacillin (156/180, 86.6%), ceftriaxone (123/180, 68.3%), nalidixic acid (95/180, 52.7%), trimethoprim sulphamethoxazole (90/180, 50%), and tetracycline (88/180, 48.8%). Additionally, the MDR (resistant to ≥3 different class of antimicrobials) rate among E. coli isolates was 94.4% (170/180). A relatively high intermediate resistance of 60% (108/180) was exhibited for aztreonam. Notably, E. coli showed 71 different antibiotic resistance patterns with the multiple antibiotic resistant (MAR) index ranging from 0.04 to 0.66 and 89.4% of E. coli isolates recorded very significant MAR indexes above the range of 0.2. In this study…
format: application/pdf
format: text/html
creator: Ibrahim Alhabib
creator: Nasreldin Elhadi
subject: Aquaculture, Fisheries and Fish Science
subject: Food Science and Technology
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.18689
publisher: PeerJ Inc.
rights: © 2024 Alhabib and Elhadi
abstract: Contamination of seafood products with multi-drug-resistant (MDR) bacteria is considered to be a potential source for the spread of MDR bacteria in communities. However, little is known about the extent of the contamination of seafood, in particular shrimp, with MDR bacteria in Saudi Arabia. In this study, imported frozen shrimp in retail markets were examined for the antimicrobial susceptibility patterns of Escherichia coli. Escherichia coli was isolated from 40 frozen shrimp samples; a total of 25 and 15 shrimp samples were imported from China and Vietnam, respectively. Of the 40 examined frozen shrimp samples, 30 tested positive for E. coli, resulting in an overall isolation rate of 75%, with a total of 180 isolates being identified. The largest number of positive samples for E. coli isolates (n = 140) were found in 22 out of 25 samples from frozen shrimp imported from China. Additionally, eight out of 15 samples from frozen shrimp imported from Vietnam were positive for E. coli, leading to the recovery of 40 isolates. Overall, the susceptibilities among E. coli isolates were observed against 99.4% for amikacin, augmentin and kanamycin, 95% for cefoxitin and 92.7% for ceftazidime and nitrofurantoin. High percentage of the isolates exhibited resistance to cephalothin (174/180, 96.6%), ampicillin (167/180, 92.7%), Cephalexin (163/180. 90.5%), piperacillin (156/180, 86.6%), ceftriaxone (123/180, 68.3%), nalidixic acid (95/180, 52.7%), trimethoprim sulphamethoxazole (90/180, 50%), and tetracycline (88/180, 48.8%). Additionally, the MDR (resistant to ≥3 different class of antimicrobials) rate among E. coli isolates was 94.4% (170/180). A relatively high intermediate resistance of 60% (108/180) was exhibited for aztreonam. Notably, E. coli showed 71 different antibiotic resistance patterns with the multiple antibiotic resistant (MAR) index ranging from 0.04 to 0.66 and 89.4% of E. coli isolates recorded very significant MAR indexes above the range of 0.2. In this study…
bibliographic citation: Alhabib et al. (2024) Antimicrobial resistance pattern of Escherichia coli isolated from imported frozen shrimp in Saudi Arabia. PeerJ 12:e18689 https://doi.org/10.7717/peerj.18689
date submitted: 2024-08-29
date accepted: 2024-11-20
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alhabib
  given name: Ibrahim
author list: Agent
  family name: Elhadi
  given name: Nasreldin
doi: 10.7717/peerj.18689
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Alhabib and Elhadi
attribution name: Alhabib and Elhadi

Construction and clinical application of a risk model based on N6-methyladenosine regulators for colorectal cancer
type: item
type: AcademicArticle
description: Background Colorectal cancer (CRC) shows a high incidence in developed countries. This study established a prognosis signature based on N6-methyladenosine (m6A) regulators involved in CRC progression. Method The bulk RNA-seq data from the Atlas and Compass of Immune-Colon cancer-Microbiome interactions (AC-ICAM) and GSE33113 CRC datasets were obtained from the cBioportal and GEO databases, and a total of 21 m6A regulators genes were collected from a previous study. The scRNA-seq analysis of the GSE146771 cohort was conducted applying the Seurat and harmony R packages. Consensus clustering based on the expressions of m6A regulators was performed with the ConsensusClusterPlus package. The ggGSEA package was used for the Gene Set Enrichment Analysis (GSEA). The un/multivariate and LASSO Cox analysis were performed applying the “survival” and “glmnet” packages for developing a risk model. The pRRophetic and GSVA packages were utilized to analyze potential drugs for CRC and immune infiltration in different risk groups, followed by the Kaplan–Meier (KM) survival and ROC analysis with the “survival” and “timeROC” packages. In vitro assays included the quantitative polymerase chain reaction (qPCR), wound healing and transwell were performed. Results CRC patients in the AC-ICAM cohort were assigned into three molecular subtypes (S1, 2 and 3) based on nine m6A regulator genes. Specifically, the prognostic outcome of the S3 was the most favorable, while that of the S1 was the worst and this subtype was associated with the activation of NF-kB, TNF-α and hypoxia pathways. Three key genes, namely, methyltransferase-like 3 (METTL3), insulinolike Growth Factor2 mRNA-Binding Protein 3 (IGF2BP3) and YTH domain-containing protein 2 (YTHDC2), selected from the 9 m6A regulator genes were combined into a RiskScore, which showed a high classification effectiveness in dividing the patients into high- and low-risk groups. Inhibition of the expression of METTL3A or that of IGF2BP3 suppressed…
format: application/pdf
format: text/html
creator: Hanhan Zhu
creator: Yu Yang
creator: Zhenfeng Zhou
subject: Bioinformatics
subject: Cell Biology
subject: Immunology
subject: Oncology
description: doi:10.7717/peerj.18719
publisher: PeerJ Inc.
rights: © 2024 Zhu et al.
abstract: Background Colorectal cancer (CRC) shows a high incidence in developed countries. This study established a prognosis signature based on N6-methyladenosine (m6A) regulators involved in CRC progression. Method The bulk RNA-seq data from the Atlas and Compass of Immune-Colon cancer-Microbiome interactions (AC-ICAM) and GSE33113 CRC datasets were obtained from the cBioportal and GEO databases, and a total of 21 m6A regulators genes were collected from a previous study. The scRNA-seq analysis of the GSE146771 cohort was conducted applying the Seurat and harmony R packages. Consensus clustering based on the expressions of m6A regulators was performed with the ConsensusClusterPlus package. The ggGSEA package was used for the Gene Set Enrichment Analysis (GSEA). The un/multivariate and LASSO Cox analysis were performed applying the “survival” and “glmnet” packages for developing a risk model. The pRRophetic and GSVA packages were utilized to analyze potential drugs for CRC and immune infiltration in different risk groups, followed by the Kaplan–Meier (KM) survival and ROC analysis with the “survival” and “timeROC” packages. In vitro assays included the quantitative polymerase chain reaction (qPCR), wound healing and transwell were performed. Results CRC patients in the AC-ICAM cohort were assigned into three molecular subtypes (S1, 2 and 3) based on nine m6A regulator genes. Specifically, the prognostic outcome of the S3 was the most favorable, while that of the S1 was the worst and this subtype was associated with the activation of NF-kB, TNF-α and hypoxia pathways. Three key genes, namely, methyltransferase-like 3 (METTL3), insulinolike Growth Factor2 mRNA-Binding Protein 3 (IGF2BP3) and YTH domain-containing protein 2 (YTHDC2), selected from the 9 m6A regulator genes were combined into a RiskScore, which showed a high classification effectiveness in dividing the patients into high- and low-risk groups. Inhibition of the expression of METTL3A or that of IGF2BP3 suppressed…
bibliographic citation: Zhu et al. (2024) Construction and clinical application of a risk model based on N6-methyladenosine regulators for colorectal cancer. PeerJ 12:e18719 https://doi.org/10.7717/peerj.18719
date submitted: 2024-09-19
date accepted: 2024-11-26
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Hanhan
author list: Agent
  family name: Yang
  given name: Yu
author list: Agent
  family name: Zhou
  given name: Zhenfeng
doi: 10.7717/peerj.18719
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Zhu et al.
attribution name: Zhu et al.

Vegetation–soil–microbiota dynamics across a 50-year reconstructed grassland chronosequence on the Loess Plateau of China
type: item
type: AcademicArticle
description: Alfalfa (Medicago sativa L.) establishment is an effective strategy for grassland reconstruction in degraded ecosystems. However, the mechanisms underlying vegetation succession in reconstructed grasslands following alfalfa establishment remain elusive. In this study, we investigated vegetation community, soil quality and rhizosphere microbiota dynamics across a reconstructed grassland chronosequence in the loess region of Northwest China. A space-for-time substitution method was used to evaluate grassland vegetation coverage and alfalfa production performance in nine stands of different ages (1–50 years old). High-throughput sequencing was conducted to characterise rhizosphere microbial communities associated with alfalfa. The plant heights, yields and stem-to-leaf ratios of alfalfa all peaked in the 7-year-old stand and then decreased in older stands, with Stipa bungeana replacing alfalfa as the dominant species in the 50-year-old stand. Soil bulk density and major nutrient contents were highest in the artificial grassland (1–10 years). Soil enzyme activities (e.g., urease and sucrase) were enhanced in the transitional grassland (10–30 years), accompanied by enrichment of potentially beneficial microbial taxa (e.g., Actinobacteria and Mortierella) and functional fungi (e.g., saprotrophs and symbiotrophs) in the rhizosphere. Soil water content, total porosity and rhizosphere microbial diversity reached their maximum levels in the natural grassland (>30 years). The results indicate that alfalfa establishment alters soil structure and nutrient status in the short term, creating an optimal rhizosphere micro-environment. The improved soil conditions and rhizosphere microbiota are favourable for subsequent establishment of native grass species, leading to the formation of a stable semi-natural grasslands.
format: application/pdf
format: text/html
creator: Yuanyuan Ma
creator: Yan Shen
creator: Ling Jin
creator: Yu Tian
creator: Hongbin Ma
creator: Jian Lan
creator: Bingzhe Fu
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
description: doi:10.7717/peerj.18723
publisher: PeerJ Inc.
rights: © 2024 Ma et al.
abstract: Alfalfa (Medicago sativa L.) establishment is an effective strategy for grassland reconstruction in degraded ecosystems. However, the mechanisms underlying vegetation succession in reconstructed grasslands following alfalfa establishment remain elusive. In this study, we investigated vegetation community, soil quality and rhizosphere microbiota dynamics across a reconstructed grassland chronosequence in the loess region of Northwest China. A space-for-time substitution method was used to evaluate grassland vegetation coverage and alfalfa production performance in nine stands of different ages (1–50 years old). High-throughput sequencing was conducted to characterise rhizosphere microbial communities associated with alfalfa. The plant heights, yields and stem-to-leaf ratios of alfalfa all peaked in the 7-year-old stand and then decreased in older stands, with Stipa bungeana replacing alfalfa as the dominant species in the 50-year-old stand. Soil bulk density and major nutrient contents were highest in the artificial grassland (1–10 years). Soil enzyme activities (e.g., urease and sucrase) were enhanced in the transitional grassland (10–30 years), accompanied by enrichment of potentially beneficial microbial taxa (e.g., Actinobacteria and Mortierella) and functional fungi (e.g., saprotrophs and symbiotrophs) in the rhizosphere. Soil water content, total porosity and rhizosphere microbial diversity reached their maximum levels in the natural grassland (>30 years). The results indicate that alfalfa establishment alters soil structure and nutrient status in the short term, creating an optimal rhizosphere micro-environment. The improved soil conditions and rhizosphere microbiota are favourable for subsequent establishment of native grass species, leading to the formation of a stable semi-natural grasslands.
bibliographic citation: Ma et al. (2024) Vegetation–soil–microbiota dynamics across a 50-year reconstructed grassland chronosequence on the Loess Plateau of China. PeerJ 12:e18723 https://doi.org/10.7717/peerj.18723
date submitted: 2024-04-30
date accepted: 2024-11-26
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Yuanyuan
author list: Agent
  family name: Shen
  given name: Yan
author list: Agent
  family name: Jin
  given name: Ling
author list: Agent
  family name: Tian
  given name: Yu
author list: Agent
  family name: Ma
  given name: Hongbin
author list: Agent
  family name: Lan
  given name: Jian
author list: Agent
  family name: Fu
  given name: Bingzhe
doi: 10.7717/peerj.18723
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Ma et al.
attribution name: Ma et al.

Effect of seedling size on post-planting growth and survival of five Mexican Pinus species and their hybrids
type: item
type: AcademicArticle
description: Background Seedling growth and survival depend on seedling quality. However, there is no experimental evidence showing that the seedling dimensions of the abundant, economically important and widely distributed tree species Pinus arizonica, P. durangensis, P. engelmannii, P. leiophylla, and P. teocote and their hybrids effectively improve survival and growth in reforestations and plantations in Mexico. Therefore, the aim was to evaluate the influence of initial morphological parameters of 2,007 nursery seedlings of these species and their hybrids on their growth and survival 44 months after planting in the Sierra Madre Occidental, Mexico. Methods Spearman’s coefficient (rs) and the unbiased conditional pseudo coefficient of determination (R2c) between each specific predictor and each response variable and their 95% confidence interval (CI95%) were determined using Random Forest, generalized linear model, and bootstrapping. By bootstrapping, the potential environmental heterogeneity inside the trial fields and its impact on the results were also quantified. Results Among the studied species and their hybrids moderate correlations were observed between the nursery seedling dimensions and the plant dimensions 44 months after planting. However, only weak significant correlations were found between survival rate (SR) and height (H) (rs = 0.10) and between SR and robustness index (HRCD) both before planting (rs = 0.06). Also, weak significant R2c values of the seedlings RCD, H and HRCD were detected with respect to the corresponding RCD, H and SR 44 months after planting, respectively. Furthermore, the predictor variable “seed provenance” (with 23 provenances) significantly explained the variation in the post-planting RCD, H and SR of the seedlings, with R2c values ranging from 0.10 to 0.15. The low width of the CI95% shows that the environmental conditions in the trial fields were quite homogeneous. Discussion The results also show that the inclusion of “confounding” var…
format: application/pdf
format: text/html
creator: José Alberto Ponce-Figueroa
creator: Pablo Antúnez
creator: José Ciro Hernández-Díaz
creator: José Ángel Prieto-Ruíz
creator: Artemio Carrillo-Parra
creator: Pablito Marcelo López-Serrano
creator: Christian Wehenkel
subject: Plant Science
subject: Natural Resource Management
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.18725
publisher: PeerJ Inc.
rights: © 2024 Ponce-Figueroa et al.
abstract: Background Seedling growth and survival depend on seedling quality. However, there is no experimental evidence showing that the seedling dimensions of the abundant, economically important and widely distributed tree species Pinus arizonica, P. durangensis, P. engelmannii, P. leiophylla, and P. teocote and their hybrids effectively improve survival and growth in reforestations and plantations in Mexico. Therefore, the aim was to evaluate the influence of initial morphological parameters of 2,007 nursery seedlings of these species and their hybrids on their growth and survival 44 months after planting in the Sierra Madre Occidental, Mexico. Methods Spearman’s coefficient (rs) and the unbiased conditional pseudo coefficient of determination (R2c) between each specific predictor and each response variable and their 95% confidence interval (CI95%) were determined using Random Forest, generalized linear model, and bootstrapping. By bootstrapping, the potential environmental heterogeneity inside the trial fields and its impact on the results were also quantified. Results Among the studied species and their hybrids moderate correlations were observed between the nursery seedling dimensions and the plant dimensions 44 months after planting. However, only weak significant correlations were found between survival rate (SR) and height (H) (rs = 0.10) and between SR and robustness index (HRCD) both before planting (rs = 0.06). Also, weak significant R2c values of the seedlings RCD, H and HRCD were detected with respect to the corresponding RCD, H and SR 44 months after planting, respectively. Furthermore, the predictor variable “seed provenance” (with 23 provenances) significantly explained the variation in the post-planting RCD, H and SR of the seedlings, with R2c values ranging from 0.10 to 0.15. The low width of the CI95% shows that the environmental conditions in the trial fields were quite homogeneous. Discussion The results also show that the inclusion of “confounding” var…
bibliographic citation: Ponce-Figueroa et al. (2024) Effect of seedling size on post-planting growth and survival of five Mexican Pinus species and their hybrids. PeerJ 12:e18725 https://doi.org/10.7717/peerj.18725
date submitted: 2024-09-05
date accepted: 2024-11-26
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ponce-Figueroa
  given name: José Alberto
author list: Agent
  family name: Antúnez
  given name: Pablo
author list: Agent
  family name: Hernández-Díaz
  given name: José Ciro
author list: Agent
  family name: Prieto-Ruíz
  given name: José Ángel
author list: Agent
  family name: Carrillo-Parra
  given name: Artemio
author list: Agent
  family name: López-Serrano
  given name: Pablito Marcelo
author list: Agent
  family name: Wehenkel
  given name: Christian
doi: 10.7717/peerj.18725
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Ponce-Figueroa et al.
attribution name: Ponce-Figueroa et al.

The movement and distribution of pregnant spotted ragged-tooth sharks, Carcharias taurus, in the iSimangaliso Wetland Park, South Africa
type: item
type: AcademicArticle
description: The spotted ragged-tooth shark, Carcharias taurus, is widely distributed in subtropical continental coastal seas. In South Africa, it is commonly found along the entire south and east coasts, including the iSimangaliso Wetland Park (IWP) in the far north, which is the largest Marine Protected Area on the South African coast. Pregnant females occur there for much of the year, with the largest aggregations in summer. It is here we used remote underwater photography (RUP), supplemented with in-situ surveys to photo-identify individuals, using unique spot patterns. Three known aggregation sites (Raggie Reef, Quarter-Mile Reef and Mushroom Rocks) were monitored over a 5-year period between 2018 and 2023. We photo-identified 574 individuals (569 females and five males) and registered 1,200 sightings, using images of the right flank. The identification of new individuals persisted throughout the study, with the discovery curve showing no signs of reaching an asymptote. A total of 97% (n = 550) of females observed were noticeably pregnant. Individuals were consistently identified across all sample years and at all three reefs, exhibiting movements among the three monitored sites. The reproductive cycle is generally regarded as 2 years, but some females appeared to have a 2-year rest between pregnancies. Raggie Reef, which lies in the sanctuary zone, emerged as the reef with the highest index of popularity, as individuals were present almost constantly (90% of the sampling days). The findings of this study confirm the crucial role that the IWP plays in the conservation of a species that is globally Critically Endangered.
format: application/pdf
format: text/html
creator: Sara C. Cerqueira
creator: Jennifer Margaret Olbers
creator: Grant Smith
creator: Michelle Carpenter
creator: Mário J. Pereira
creator: Geremy Cliff
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.18736
publisher: PeerJ Inc.
rights: © 2024 Cerqueira et al.
abstract: The spotted ragged-tooth shark, Carcharias taurus, is widely distributed in subtropical continental coastal seas. In South Africa, it is commonly found along the entire south and east coasts, including the iSimangaliso Wetland Park (IWP) in the far north, which is the largest Marine Protected Area on the South African coast. Pregnant females occur there for much of the year, with the largest aggregations in summer. It is here we used remote underwater photography (RUP), supplemented with in-situ surveys to photo-identify individuals, using unique spot patterns. Three known aggregation sites (Raggie Reef, Quarter-Mile Reef and Mushroom Rocks) were monitored over a 5-year period between 2018 and 2023. We photo-identified 574 individuals (569 females and five males) and registered 1,200 sightings, using images of the right flank. The identification of new individuals persisted throughout the study, with the discovery curve showing no signs of reaching an asymptote. A total of 97% (n = 550) of females observed were noticeably pregnant. Individuals were consistently identified across all sample years and at all three reefs, exhibiting movements among the three monitored sites. The reproductive cycle is generally regarded as 2 years, but some females appeared to have a 2-year rest between pregnancies. Raggie Reef, which lies in the sanctuary zone, emerged as the reef with the highest index of popularity, as individuals were present almost constantly (90% of the sampling days). The findings of this study confirm the crucial role that the IWP plays in the conservation of a species that is globally Critically Endangered.
bibliographic citation: Cerqueira et al. (2024) The movement and distribution of pregnant spotted ragged-tooth sharks, Carcharias taurus, in the iSimangaliso Wetland Park, South Africa. PeerJ 12:e18736 https://doi.org/10.7717/peerj.18736
date submitted: 2024-09-25
date accepted: 2024-11-28
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cerqueira
  given name: Sara C.
author list: Agent
  family name: Olbers
  given name: Jennifer Margaret
author list: Agent
  family name: Smith
  given name: Grant
author list: Agent
  family name: Carpenter
  given name: Michelle
author list: Agent
  family name: Pereira
  given name: Mário J.
author list: Agent
  family name: Cliff
  given name: Geremy
doi: 10.7717/peerj.18736
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Cerqueira et al.
attribution name: Cerqueira et al.

Visual codon: a user-friendly Python program for viewing and optimizing gene GC content
type: item
type: AcademicArticle
description: Due to the codon bias of different species, codon optimization is usually carried out in the process of heterologous protein expression. At present, there are a variety of codon optimization tools. However, the optimized sequences may still have high or low points of local guanine and cytosine (GC) content, which is not conducive to the primer design of gene subcloning, and also makes it difficult to perform the experiment of synthesizing the whole gene with DNA fragments by polymerase chain reaction (PCR) reaction. In this study, we present a stand-alone software written in Python, with which users can manually check and adjust the GC content of sequence-optimized genes. The software takes the codon frequency of Escherichia coli as default and can work with other species as well. It provides a Graphical User Interface (GUI) interface, which allows users to change codons and intuitively see the effect of codon changes on local GC content. Our program brings convenience for the optimization of gene GC content and the subsequent gene cloning experiments.
format: application/pdf
format: text/html
creator: Shiming Lin
creator: Fei Xu
creator: Bifang Huang
creator: Li-li Zhao
creator: Danni Pan
creator: Shiqiang Lin
subject: Biochemistry
subject: Bioinformatics
subject: Biotechnology
subject: Molecular Biology
subject: Synthetic Biology
description: doi:10.7717/peerj.18755
publisher: PeerJ Inc.
rights: © 2024 Lin et al.
abstract: Due to the codon bias of different species, codon optimization is usually carried out in the process of heterologous protein expression. At present, there are a variety of codon optimization tools. However, the optimized sequences may still have high or low points of local guanine and cytosine (GC) content, which is not conducive to the primer design of gene subcloning, and also makes it difficult to perform the experiment of synthesizing the whole gene with DNA fragments by polymerase chain reaction (PCR) reaction. In this study, we present a stand-alone software written in Python, with which users can manually check and adjust the GC content of sequence-optimized genes. The software takes the codon frequency of Escherichia coli as default and can work with other species as well. It provides a Graphical User Interface (GUI) interface, which allows users to change codons and intuitively see the effect of codon changes on local GC content. Our program brings convenience for the optimization of gene GC content and the subsequent gene cloning experiments.
bibliographic citation: Lin et al. (2024) Visual codon: a user-friendly Python program for viewing and optimizing gene GC content. PeerJ 12:e18755 https://doi.org/10.7717/peerj.18755
date submitted: 2024-10-04
date accepted: 2024-12-03
issued: 2024-12-20
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Shiming
author list: Agent
  family name: Xu
  given name: Fei
author list: Agent
  family name: Huang
  given name: Bifang
author list: Agent
  family name: Zhao
  given name: Li-li
author list: Agent
  family name: Pan
  given name: Danni
author list: Agent
  family name: Lin
  given name: Shiqiang
doi: 10.7717/peerj.18755
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-12-20
copyright: © 2024 Lin et al.
attribution name: Lin et al.

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