PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest
items: PFI-3 induces vasorelaxation with potency to reduce extracellular calcium influx in rat mesenteric artery
items: Identifying C1QB, ITGAM, and ITGB2 as potential diagnostic candidate genes for diabetic nephropathy using bioinformatics analysis
items: A low-tech method for monitoring survival and growth of coral transplants at a boutique restoration site
items: minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data
items: Supplementation of PUFA extracted from microalgae for the development of chicken patties
items: Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau
items: Spatio-temporal evolution and prediction of carbon storage in Kunming based on PLUS and InVEST models
items: Transcriptome analysis reveals genes associated with wool fineness in merinos
items: Morphometric analysis of odontoid process among Arab population: a retrospective cone beam CT study

Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest
type: item
type: AcademicArticle
description: Background The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex. Methods We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations. Results Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.
format: application/pdf
format: text/html
creator: Caroline Batistim Oswald
creator: Rafael Félix de Magalhães
creator: Paulo C.A. Garcia
creator: Fabrício R. Santos
creator: Selvino Neckel-Oliveira
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.15393
publisher: PeerJ Inc.
rights: © 2023 Oswald et al.
abstract: Background The delimitation of cryptic species is a challenge for biodiversity conservation. Anurans show high cryptic diversity levels, and molecular species delimitation methods could help identify putative new species. Additionally, species delimitation approaches can provide important results for cryptic species conservation, with integrative methods adding robustness to results. Ischnocnema manezinho was described from Santa Catarina Island (SCI), southern Brazil. More recently, some inventories indicated continental populations supposedly similar in morphology to it. If these records are confirmed as I. manezinho, it would likely change its endangered status on National Red List, removing the species from conservation agendas. We investigated the threatened frog Ischnocnema manezinho, to evaluate if the continental populations belong to this species or if they form an undescribed species complex. Methods We used coalescent, distance, and allele-sharing-based species delimitation methods and integrative analyses of morphometric and bioacoustics traits to test evolutionary independence between I. manezinho from SCI, Arvoredo Island, and continental populations. Results Ischnocnema manezinho is restricted to Santa Catarina Island, while the five remaining lineages should be further investigated through a taxonomic review. Our results point to a small geographic range of Ischnocnema manezinho. Additionally, the species occurs in isolated fragments of forest in SCI surrounded by expanding urban areas, confirming its status as Endangered. Thus, the protection and monitoring of I. manezinho and the taxonomic description of the continental and Arvoredo Island candidate species should be priorities.
bibliographic citation: Oswald et al. (2023) Integrative species delimitation helps to find the hidden diversity of the leaf-litter frog Ischnocnema manezinho (Garcia, 1996) (Anura, Brachycephalidae), endemic to the southern Atlantic Forest. PeerJ 11:e15393 https://doi.org/10.7717/peerj.15393
date submitted: 2022-08-30
date accepted: 2023-04-20
issued: 2023-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Oswald
  given name: Caroline Batistim
author list: Agent
  family name: Magalhães
  given name: Rafael Félix de
author list: Agent
  family name: Garcia
  given name: Paulo C.A.
author list: Agent
  family name: Santos
  given name: Fabrício R.
author list: Agent
  family name: Neckel-Oliveira
  given name: Selvino
doi: 10.7717/peerj.15393
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-25
copyright: ©2023 Oswald et al.
attribution name: Oswald et al.

PFI-3 induces vasorelaxation with potency to reduce extracellular calcium influx in rat mesenteric artery
type: item
type: AcademicArticle
description: Background PFI-3 is a small-molecule inhibitor that targets the bromodomains (BRDs) of Brahma-related gene 1 (BRG1). This monomeric compound, which has high selectivity and potent cellular effects, has recently been developed. Although PFI-3 has been reported as a potential therapeutic agent targeting thrombomodulin, its role in the regulation of vascular function remains unknown. Therefore, we aimed to investigate the impact of PFI-3 on arterial vessel tone. Methods A microvascular tension measurement device (DMT) was utilized to identify alterations in vascular tension within the mesenteric artery. To detect variations in cytosolic [Ca2+]i, a Fluo-3/AM fluorescent probe and fluorescence microscope were employed. Additionally, whole-cell patch clamp techniques were utilized to evaluate the activity of L-type voltage-dependent calcium channels (VDCCs) in cultured arterial smooth muscle cells (A10 cells). Results PFI-3 exerted a dose-dependent relaxation effect on rat mesenteric arteries with both intact and denuded endothelium after phenylephrine (PE)- and high-K+-induced constriction. PFI-3-induced vasorelaxation was not affected by the presence of L-NAME/ODQ or K+ channel blockers (Gli/TEA). PFI-3 abolished Ca2+-induced contraction on endothelium-denuded mesenteric arteries preincubated by PE in Ca2+-free solution. Incubation with TG had no impact on PFI-3-induced vasorelaxation pre-contracted by PE. PFI-3 reduced Ca2+-induced contraction on endothelium-denuded mesenteric arteries pre-incubated by KCl (60 mM) in Ca2+-free solution. PFI-3 declined extracellular calcium influx in A10 cells detected by Fluo-3/AM fluorescent probe and fluorescence microscope. Furthermore, we observed that PFI-3 decreased the current densities of L-type VDCC by whole-cell patch clamp techniques. Conclusions PFI-3 blunted PE and high K+-induced vasoconstriction independent of endothelium on rat mesenteric artery. The vasodilatory effect of PFI-3 may be attributed to its inhibition of VD…
format: application/pdf
format: text/html
creator: Jing Li
creator: Xue-Qi Liang
creator: Yun-Feng Cui
creator: Yu-Yang Fu
creator: Zi-Yue Ma
creator: Ying-Tao Cui
creator: Xian-Hui Dong
creator: Hai-Jun Huang
creator: Ting-Ting Tong
creator: Ya-Mei Zhu
creator: Ya-Dong Xue
creator: Yong-Zhen Wang
creator: Tao Ban
creator: Rong Huo
subject: Cell Biology
subject: Pharmacology
description: doi:10.7717/peerj.15407
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background PFI-3 is a small-molecule inhibitor that targets the bromodomains (BRDs) of Brahma-related gene 1 (BRG1). This monomeric compound, which has high selectivity and potent cellular effects, has recently been developed. Although PFI-3 has been reported as a potential therapeutic agent targeting thrombomodulin, its role in the regulation of vascular function remains unknown. Therefore, we aimed to investigate the impact of PFI-3 on arterial vessel tone. Methods A microvascular tension measurement device (DMT) was utilized to identify alterations in vascular tension within the mesenteric artery. To detect variations in cytosolic [Ca2+]i, a Fluo-3/AM fluorescent probe and fluorescence microscope were employed. Additionally, whole-cell patch clamp techniques were utilized to evaluate the activity of L-type voltage-dependent calcium channels (VDCCs) in cultured arterial smooth muscle cells (A10 cells). Results PFI-3 exerted a dose-dependent relaxation effect on rat mesenteric arteries with both intact and denuded endothelium after phenylephrine (PE)- and high-K+-induced constriction. PFI-3-induced vasorelaxation was not affected by the presence of L-NAME/ODQ or K+ channel blockers (Gli/TEA). PFI-3 abolished Ca2+-induced contraction on endothelium-denuded mesenteric arteries preincubated by PE in Ca2+-free solution. Incubation with TG had no impact on PFI-3-induced vasorelaxation pre-contracted by PE. PFI-3 reduced Ca2+-induced contraction on endothelium-denuded mesenteric arteries pre-incubated by KCl (60 mM) in Ca2+-free solution. PFI-3 declined extracellular calcium influx in A10 cells detected by Fluo-3/AM fluorescent probe and fluorescence microscope. Furthermore, we observed that PFI-3 decreased the current densities of L-type VDCC by whole-cell patch clamp techniques. Conclusions PFI-3 blunted PE and high K+-induced vasoconstriction independent of endothelium on rat mesenteric artery. The vasodilatory effect of PFI-3 may be attributed to its inhibition of VD…
bibliographic citation: Li et al. (2023) PFI-3 induces vasorelaxation with potency to reduce extracellular calcium influx in rat mesenteric artery. PeerJ 11:e15407 https://doi.org/10.7717/peerj.15407
date submitted: 2022-11-15
date accepted: 2023-04-21
issued: 2023-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: Jing
author list: Agent
  family name: Liang
  given name: Xue-Qi
author list: Agent
  family name: Cui
  given name: Yun-Feng
author list: Agent
  family name: Fu
  given name: Yu-Yang
author list: Agent
  family name: Ma
  given name: Zi-Yue
author list: Agent
  family name: Cui
  given name: Ying-Tao
author list: Agent
  family name: Dong
  given name: Xian-Hui
author list: Agent
  family name: Huang
  given name: Hai-Jun
author list: Agent
  family name: Tong
  given name: Ting-Ting
author list: Agent
  family name: Zhu
  given name: Ya-Mei
author list: Agent
  family name: Xue
  given name: Ya-Dong
author list: Agent
  family name: Wang
  given name: Yong-Zhen
author list: Agent
  family name: Ban
  given name: Tao
author list: Agent
  family name: Huo
  given name: Rong
doi: 10.7717/peerj.15407
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-25
copyright: ©2023 Li et al.
attribution name: Li et al.

Identifying C1QB, ITGAM, and ITGB2 as potential diagnostic candidate genes for diabetic nephropathy using bioinformatics analysis
type: item
type: AcademicArticle
description: Background Diabetic nephropathy (DN), the most intractable complication in diabetes patients, can lead to proteinuria and progressive reduction of glomerular filtration rate (GFR), which seriously affects the quality of life of patients and is associated with high mortality. However, the lack of accurate key candidate genes makes diagnosis of DN very difficult. This study aimed to identify new potential candidate genes for DN using bioinformatics, and elucidated the mechanism of DN at the cellular transcriptional level. Methods The microarray dataset GSE30529 was downloaded from the Gene Expression Omnibus Database (GEO), and the differentially expressed genes (DEGs) were screened by R software. We used Gene Ontology (GO), gene set enrichment analysis (GSEA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to identify the signal pathways and genes. Protein-protein interaction (PPI) networks were constructed using the STRING database. The GSE30122 dataset was selected as the validation set. Receiver operating characteristic (ROC) curves were applied to evaluate the predictive value of genes. An area under curve (AUC) greater than 0.85 was considered to be of high diagnostic value. Several online databases were used to predict miRNAs and transcription factors (TFs) capable of binding hub genes. Cytoscape was used for constructing a miRNA-mRNA-TF network. The online database ‘nephroseq’ predicted the correlation between genes and kidney function. The serum level of creatinine, BUN, and albumin, and the urinary protein/creatinine ratio of the DN rat model were detected. The expression of hub genes was further verified through qPCR. Data were analyzed statistically using Student’s t-test by the ‘ggpubr’ package. Results A total of 463 DEGs were identified from GSE30529. According to enrichment analysis, DEGs were mainly enriched in the immune response, coagulation cascades, and cytokine signaling pathways. Twenty hub genes with the highest …
format: application/pdf
format: text/html
creator: Yongzheng Hu
creator: Yani Yu
creator: Hui Dong
creator: Wei Jiang
subject: Bioinformatics
subject: Genomics
subject: Nephrology
subject: Medical Genetics
description: doi:10.7717/peerj.15437
publisher: PeerJ Inc.
rights: © 2023 Hu et al.
abstract: Background Diabetic nephropathy (DN), the most intractable complication in diabetes patients, can lead to proteinuria and progressive reduction of glomerular filtration rate (GFR), which seriously affects the quality of life of patients and is associated with high mortality. However, the lack of accurate key candidate genes makes diagnosis of DN very difficult. This study aimed to identify new potential candidate genes for DN using bioinformatics, and elucidated the mechanism of DN at the cellular transcriptional level. Methods The microarray dataset GSE30529 was downloaded from the Gene Expression Omnibus Database (GEO), and the differentially expressed genes (DEGs) were screened by R software. We used Gene Ontology (GO), gene set enrichment analysis (GSEA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to identify the signal pathways and genes. Protein-protein interaction (PPI) networks were constructed using the STRING database. The GSE30122 dataset was selected as the validation set. Receiver operating characteristic (ROC) curves were applied to evaluate the predictive value of genes. An area under curve (AUC) greater than 0.85 was considered to be of high diagnostic value. Several online databases were used to predict miRNAs and transcription factors (TFs) capable of binding hub genes. Cytoscape was used for constructing a miRNA-mRNA-TF network. The online database ‘nephroseq’ predicted the correlation between genes and kidney function. The serum level of creatinine, BUN, and albumin, and the urinary protein/creatinine ratio of the DN rat model were detected. The expression of hub genes was further verified through qPCR. Data were analyzed statistically using Student’s t-test by the ‘ggpubr’ package. Results A total of 463 DEGs were identified from GSE30529. According to enrichment analysis, DEGs were mainly enriched in the immune response, coagulation cascades, and cytokine signaling pathways. Twenty hub genes with the highest …
bibliographic citation: Hu et al. (2023) Identifying C1QB, ITGAM, and ITGB2 as potential diagnostic candidate genes for diabetic nephropathy using bioinformatics analysis. PeerJ 11:e15437 https://doi.org/10.7717/peerj.15437
date submitted: 2022-12-15
date accepted: 2023-04-27
issued: 2023-05-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Yongzheng
author list: Agent
  family name: Yu
  given name: Yani
author list: Agent
  family name: Dong
  given name: Hui
author list: Agent
  family name: Jiang
  given name: Wei
doi: 10.7717/peerj.15437
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-25
copyright: ©2023 Hu et al.
attribution name: Hu et al.

A low-tech method for monitoring survival and growth of coral transplants at a boutique restoration site
type: item
type: AcademicArticle
description: Background Coral reef restoration projects are becoming a popular corporate environmental responsibility activity at hotel resorts. Such involvement of private businesses offers the potential to expand restoration into a new socioeconomic sector. However, the scarcity of user-friendly monitoring methods for hotel staff, but robust enough to detect changes over time, hinders the ability to quantify the success or failure of the restoration activity. Here, we present a monitoring method of easy application by hotel staff, without scientific training, using the standard resources available at a hotel resort. Methods Survival and growth of coral transplants were evaluated over 1 year at a boutique coral reef restoration site. The restoration was tailored to the needs of a hotel resort in Seychelles, Indian Ocean. A total of 2,015 nursery-grown corals of branching (four genera, 15 species), massive (16 genera, 23 species), and encrusting (seven genera, seven species) growth types were transplanted to a 1–3 m deep degraded patch reef. A unique cement mix was used to transplant corals onto the hard substrate. On the north side of each coral selected for monitoring, we attached an 8.2 cm × 8.2 cm reflective tile. We used reflective tiles instead of numbered tags due to the expected amount of biofouling growing on the tag surface. Every coral was recorded with top view photography (perpendicular to the plane of coral attachment), with the reflective square in the field of view. We drafted a map of the site to facilitate navigation and re-sighting of the monitored colonies. Then, we developed a simple monitoring protocol for hotel staff. Using the map, and the reflective tiles, the divers located the coral colonies, recorded status (alive, dead, bleaching), and took a photograph. We measured the two-dimensional coral planar area and the change in colony size over time using contour tissue measurements of photographs. Results The monitoring method was robust enough to detect t…
format: application/pdf
format: text/html
creator: Sarah Frias-Torres
creator: Claude Reveret
creator: Kerstin Henri
creator: Nirmal Shah
creator: Phanor Hernando Montoya Maya
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.15062
publisher: PeerJ Inc.
rights: © 2023 Frias-Torres et al.
abstract: Background Coral reef restoration projects are becoming a popular corporate environmental responsibility activity at hotel resorts. Such involvement of private businesses offers the potential to expand restoration into a new socioeconomic sector. However, the scarcity of user-friendly monitoring methods for hotel staff, but robust enough to detect changes over time, hinders the ability to quantify the success or failure of the restoration activity. Here, we present a monitoring method of easy application by hotel staff, without scientific training, using the standard resources available at a hotel resort. Methods Survival and growth of coral transplants were evaluated over 1 year at a boutique coral reef restoration site. The restoration was tailored to the needs of a hotel resort in Seychelles, Indian Ocean. A total of 2,015 nursery-grown corals of branching (four genera, 15 species), massive (16 genera, 23 species), and encrusting (seven genera, seven species) growth types were transplanted to a 1–3 m deep degraded patch reef. A unique cement mix was used to transplant corals onto the hard substrate. On the north side of each coral selected for monitoring, we attached an 8.2 cm × 8.2 cm reflective tile. We used reflective tiles instead of numbered tags due to the expected amount of biofouling growing on the tag surface. Every coral was recorded with top view photography (perpendicular to the plane of coral attachment), with the reflective square in the field of view. We drafted a map of the site to facilitate navigation and re-sighting of the monitored colonies. Then, we developed a simple monitoring protocol for hotel staff. Using the map, and the reflective tiles, the divers located the coral colonies, recorded status (alive, dead, bleaching), and took a photograph. We measured the two-dimensional coral planar area and the change in colony size over time using contour tissue measurements of photographs. Results The monitoring method was robust enough to detect t…
bibliographic citation: Frias-Torres et al. (2023) A low-tech method for monitoring survival and growth of coral transplants at a boutique restoration site. PeerJ 11:e15062 https://doi.org/10.7717/peerj.15062
date submitted: 2021-11-08
date accepted: 2023-02-22
issued: 2023-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Frias-Torres
  given name: Sarah
author list: Agent
  family name: Reveret
  given name: Claude
author list: Agent
  family name: Henri
  given name: Kerstin
author list: Agent
  family name: Shah
  given name: Nirmal
author list: Agent
  family name: Montoya Maya
  given name: Phanor Hernando
doi: 10.7717/peerj.15062
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-24
copyright: ©2023 Frias-Torres et al.
attribution name: Frias-Torres et al.

minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data
type: item
type: AcademicArticle
description: Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs’ running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets.
format: application/pdf
format: text/html
creator: Kian Soon Hoon
creator: Deborah C. Holt
creator: Sarah Auburn
creator: Peter Shaw
creator: Philip M. Giffard
subject: Bioinformatics
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.15339
publisher: PeerJ Inc.
rights: © 2023 Hoon et al.
abstract: Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs’ running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets.
bibliographic citation: Hoon et al. (2023) minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data. PeerJ 11:e15339 https://doi.org/10.7717/peerj.15339
date submitted: 2022-09-21
date accepted: 2023-04-12
issued: 2023-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoon
  given name: Kian Soon
author list: Agent
  family name: Holt
  given name: Deborah C.
author list: Agent
  family name: Auburn
  given name: Sarah
author list: Agent
  family name: Shaw
  given name: Peter
author list: Agent
  family name: Giffard
  given name: Philip M.
doi: 10.7717/peerj.15339
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-24
copyright: ©2023 Hoon et al.
attribution name: Hoon et al.

Supplementation of PUFA extracted from microalgae for the development of chicken patties
type: item
type: AcademicArticle
description: In recent years, there has been a growing interest in development of a diverse range of foods that are enriched with omega-3 fatty acids. It is widely recognized that through dietary interventions, the lipid fraction of food can be modified to enhance its nutritional content. This study is aimed to develop chicken patties enriched with poly unstaurated fatty acids (PUFAs) extracted from microalgae aurintricarboxylic acid (ATA) concentration of 0% (T0), 1% (T1), 2% (T2), and 3% (T3). All treatments were stored at −18 °C for one month and analysed at an interval of 0, 10, 20, and 30 days to assess the effect of PUFAs supplementation on physicochemical, oxidative, microbiological and organoleptic properties of chicken patties. The results revealed that moisture content was significantly increased during the storage; the maximum moisture was observed in T0 (67.25% ± 0.03) on day 0, while the minimun was found in T3 (64.69% ± 0.04) on day 30. Supplemenatation of PUFAs in chicken patties significantly enhanced the fat content of the product the highest fat content was observed for T3 (9.7% ± 0.06. An increase in PUFAs concentration led to a significant increase in thiobarbituric acid reactive substances (TBARS). TBARS were increased from 1.22 ± 0.43 at 0 days to 1.48 ± 0.39 at 30 days of storage. The PUFAs incorporation negatively effected sensory acceptance of the product ranging from (8.41 ± 0.17 to 7.28 ± 0.12). However, the sensory scores were in acceptable range for supplemented patties as compared to control sample. Treatment T3 depicted the highest nutritional content. The sensory and physiochemical analysis of supplemented patties suggested that PUFAs extracted from microalgae can be used as a functional ingredient in the preparation various meat products particularly chicken meta patties. However, antioxidants should be added to to prevent lipid oxidation in the product.
format: application/pdf
format: text/html
creator: Sidra Dr
creator: Muhammad Muneeb Zaman
creator: Zunaira Farooq
creator: Amina Hafeez
creator: Muhammad Wasim Sajid
creator: Muhammad Rizwan Tariq
creator: Shinawar Waseem Ali
creator: Sajid Ali
creator: Muhammad Shafiq
creator: Madiha Iftikhar
creator: Waseem Safdar
creator: Umair Ali
creator: Maria Kanwal
creator: Zujaja Umer
creator: Zunaira Basharat
subject: Agricultural Science
subject: Biochemistry
subject: Biotechnology
subject: Food Science and Technology
description: doi:10.7717/peerj.15355
publisher: PeerJ Inc.
rights: © 2023 Dr et al.
abstract: In recent years, there has been a growing interest in development of a diverse range of foods that are enriched with omega-3 fatty acids. It is widely recognized that through dietary interventions, the lipid fraction of food can be modified to enhance its nutritional content. This study is aimed to develop chicken patties enriched with poly unstaurated fatty acids (PUFAs) extracted from microalgae aurintricarboxylic acid (ATA) concentration of 0% (T0), 1% (T1), 2% (T2), and 3% (T3). All treatments were stored at −18 °C for one month and analysed at an interval of 0, 10, 20, and 30 days to assess the effect of PUFAs supplementation on physicochemical, oxidative, microbiological and organoleptic properties of chicken patties. The results revealed that moisture content was significantly increased during the storage; the maximum moisture was observed in T0 (67.25% ± 0.03) on day 0, while the minimun was found in T3 (64.69% ± 0.04) on day 30. Supplemenatation of PUFAs in chicken patties significantly enhanced the fat content of the product the highest fat content was observed for T3 (9.7% ± 0.06. An increase in PUFAs concentration led to a significant increase in thiobarbituric acid reactive substances (TBARS). TBARS were increased from 1.22 ± 0.43 at 0 days to 1.48 ± 0.39 at 30 days of storage. The PUFAs incorporation negatively effected sensory acceptance of the product ranging from (8.41 ± 0.17 to 7.28 ± 0.12). However, the sensory scores were in acceptable range for supplemented patties as compared to control sample. Treatment T3 depicted the highest nutritional content. The sensory and physiochemical analysis of supplemented patties suggested that PUFAs extracted from microalgae can be used as a functional ingredient in the preparation various meat products particularly chicken meta patties. However, antioxidants should be added to to prevent lipid oxidation in the product.
bibliographic citation: Dr et al. (2023) Supplementation of PUFA extracted from microalgae for the development of chicken patties. PeerJ 11:e15355 https://doi.org/10.7717/peerj.15355
date submitted: 2023-01-24
date accepted: 2023-04-14
issued: 2023-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dr
  given name: Sidra
author list: Agent
  family name: Zaman
  given name: Muhammad Muneeb
author list: Agent
  family name: Farooq
  given name: Zunaira
author list: Agent
  family name: Hafeez
  given name: Amina
author list: Agent
  family name: Sajid
  given name: Muhammad Wasim
author list: Agent
  family name: Tariq
  given name: Muhammad Rizwan
author list: Agent
  family name: Ali
  given name: Shinawar Waseem
author list: Agent
  family name: Ali
  given name: Sajid
author list: Agent
  family name: Shafiq
  given name: Muhammad
author list: Agent
  family name: Iftikhar
  given name: Madiha
author list: Agent
  family name: Safdar
  given name: Waseem
author list: Agent
  family name: Ali
  given name: Umair
author list: Agent
  family name: Kanwal
  given name: Maria
author list: Agent
  family name: Umer
  given name: Zujaja
author list: Agent
  family name: Basharat
  given name: Zunaira
doi: 10.7717/peerj.15355
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-24
copyright: ©2023 Dr et al.
attribution name: Dr et al.

Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau
type: item
type: AcademicArticle
description: In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.
format: application/pdf
format: text/html
creator: Shuting Chen
creator: Pengxi Cao
creator: Ting Li
creator: Yuyan Wang
creator: Xing Liu
subject: Microbiology
subject: Molecular Biology
subject: Mycology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15361
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: In the extreme alpine climate of the Qinghai-Tibet Plateau (QTP), plant growth and reproduction are limited by extremely cold temperatures, low soil moisture, and scarce nutrient availability. The root-associated microbiome indirectly promotes plant growth and plays a role in the fitness of plants on the QTP, particularly in Tibetan medicinal plants. Despite the importance of the root-associated microbiome, little is known about the root zone. This study used high-throughput sequencing to investigate two medicinal Meconopsis plants, M. horridula and M. integrifolia, to determine whether habitat or plant identity had a more significant impact on the microbial composition of the roots. The fungal sequences were obtained using ITS-1 and ITS-2, and bacterial sequences were obtained using 16S rRNA. Different microbial patterns were observed in the microbial compositions of fungi and bacteria in the root zones of two Meconopsis plants. In contrast to bacteria, which were not significantly impacted by plant identity or habitat, the fungi in the root zone were significantly impacted by plant identity, but not habitat. In addition, the synergistic effect was more significant than the antagonistic effect in the correlation between fungi and bacteria in the root zone soil. The fungal structure was influenced by total nitrogen and pH, whereas the structure of bacterial communities was influenced by soil moisture and organic matter. Plant identity had a greater influence on fungal structure than habitat in two Meconopsis plants. The dissimilarity of fungal communities suggests that more attention should be paid to fungi-plant interactions.
bibliographic citation: Chen et al. (2023) Microbial diversity patterns in the root zone of two Meconopsis plants on the Qinghai-Tibet Plateau. PeerJ 11:e15361 https://doi.org/10.7717/peerj.15361
date submitted: 2022-10-10
date accepted: 2023-04-16
issued: 2023-05-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Shuting
author list: Agent
  family name: Cao
  given name: Pengxi
author list: Agent
  family name: Li
  given name: Ting
author list: Agent
  family name: Wang
  given name: Yuyan
author list: Agent
  family name: Liu
  given name: Xing
doi: 10.7717/peerj.15361
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-24
copyright: © 2023 Chen et al.
attribution name: Chen et al.

Spatio-temporal evolution and prediction of carbon storage in Kunming based on PLUS and InVEST models
type: item
type: AcademicArticle
description: Carbon storage is a critical ecosystem service provided by terrestrial environmental systems that can effectively reduce regional carbon emissions and is critical for achieving carbon neutrality and carbon peak. We conducted a study in Kunming and analyzed the land utilization data for 2000, 2010, and 2020. We assessed the features of land utilization conversion and forecasted land utilization under three development patterns in 2030 on the basis of the Patch-generating Land Use Simulation (PLUS) model. We used the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model to estimate changes in carbon storage trends under three development scenarios in 2000, 2010, 2020, and 2030 and the impact of socioeconomic and natural factors on carbon storage. The results of the study indicated that (1) carbon storage is intimately associated with land utilization practices. Carbon storage in Kunming in 2000, 2010, and 2020 was 1.146 × 108 t, 1.139 × 108 t, and 1.120 × 108 t, respectively. During the 20 years, forest land decreased by 142.28 km2, and the decrease in forest land area caused a loss of carbon storage. (2) Carbon storage in 2030 was predicted to be 1.102 × 108 t, 1.136 × 108 t, and 1.105 × 108 t, respectively, under the trend continuation scenario, eco-friendly scenario, and comprehensive development scenario, indicating that implementing ecological protection and cultivated land protection measures can facilitate regional ecosystem carbon storage restoration. (3) Impervious surfaces and vegetation have the greatest influence on carbon storage for the study area. A spatial global and local negative correlation was found between impervious surface coverage and ecosystem carbon storage. A spatial global and local positive correlation was found between NDVI and ecosystem carbon storage. Therefore, ecological and farmland protection policies need to be strengthened, the expansion of impervious surfaces should be strictly controlled, and vegetation covera…
format: application/pdf
format: text/html
creator: Yimin Li
creator: Xue Yang
creator: Bowen Wu
creator: Juanzhen Zhao
creator: Wenxue Jiang
creator: Xianjie Feng
creator: Yuanting Li
subject: Ecosystem Science
subject: Natural Resource Management
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.15285
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Carbon storage is a critical ecosystem service provided by terrestrial environmental systems that can effectively reduce regional carbon emissions and is critical for achieving carbon neutrality and carbon peak. We conducted a study in Kunming and analyzed the land utilization data for 2000, 2010, and 2020. We assessed the features of land utilization conversion and forecasted land utilization under three development patterns in 2030 on the basis of the Patch-generating Land Use Simulation (PLUS) model. We used the Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) model to estimate changes in carbon storage trends under three development scenarios in 2000, 2010, 2020, and 2030 and the impact of socioeconomic and natural factors on carbon storage. The results of the study indicated that (1) carbon storage is intimately associated with land utilization practices. Carbon storage in Kunming in 2000, 2010, and 2020 was 1.146 × 108 t, 1.139 × 108 t, and 1.120 × 108 t, respectively. During the 20 years, forest land decreased by 142.28 km2, and the decrease in forest land area caused a loss of carbon storage. (2) Carbon storage in 2030 was predicted to be 1.102 × 108 t, 1.136 × 108 t, and 1.105 × 108 t, respectively, under the trend continuation scenario, eco-friendly scenario, and comprehensive development scenario, indicating that implementing ecological protection and cultivated land protection measures can facilitate regional ecosystem carbon storage restoration. (3) Impervious surfaces and vegetation have the greatest influence on carbon storage for the study area. A spatial global and local negative correlation was found between impervious surface coverage and ecosystem carbon storage. A spatial global and local positive correlation was found between NDVI and ecosystem carbon storage. Therefore, ecological and farmland protection policies need to be strengthened, the expansion of impervious surfaces should be strictly controlled, and vegetation covera…
bibliographic citation: Li et al. (2023) Spatio-temporal evolution and prediction of carbon storage in Kunming based on PLUS and InVEST models. PeerJ 11:e15285 https://doi.org/10.7717/peerj.15285
date submitted: 2023-01-03
date accepted: 2023-04-03
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yimin
author list: Agent
  family name: Yang
  given name: Xue
author list: Agent
  family name: Wu
  given name: Bowen
author list: Agent
  family name: Zhao
  given name: Juanzhen
author list: Agent
  family name: Jiang
  given name: Wenxue
author list: Agent
  family name: Feng
  given name: Xianjie
author list: Agent
  family name: Li
  given name: Yuanting
doi: 10.7717/peerj.15285
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: © 2023 Li et al.
attribution name: Li et al.

Transcriptome analysis reveals genes associated with wool fineness in merinos
type: item
type: AcademicArticle
description: Hair/wool usually plays an important role in maintaining animal physiological activities, and the economic value of wool cannot be ignored. At present, people set higher demands on wool fineness. Hence, improving wool fineness is the concern of fine wool sheep breeding. Using RNA-Seq to screen the potential candidate genes that associate with wool fineness can provide theoretical references for fine-wool sheep breeding, and also provide us new ideas for further understand the molecular regulation mechanism of hair growth. In this study, we compared the expression pattern difference of genome-wide genes between the skin transcriptomes of Subo and Chinese Merinos. The results showed that, 16 candidate differentially expressed genes (DEGs) (Included: CACNA1S, GP5, LOC101102392, HSF5, SLITRK2, LOC101104661, CREB3L4, COL1A1, PTPRR, SFRP4, LOC443220, COL6A6, COL6A5, LAMA1, LOC114115342 and LOC101116863 genes) that may associate with wool fineness were screened, and these genes were located in signaling pathways that regulate hair follicle development, cycle or hair growth. It is worth noting that, among the 16 DEGs, COL1A1 gene has the highest expression level in Merino skins, and the fold change of LOC101116863 gene is the highest, and the structures of these two genes are both highly conserved in different species. In conclusion, we speculate that these two genes may play a key role in regulating wool fineness and respectively have similar and conserved functions in different species.
format: application/pdf
format: text/html
creator: Shengchao Ma
creator: Li Long
creator: Xixia Huang
creator: Kechuan Tian
creator: Yuezhen Tian
creator: Cuiling Wu
creator: Zhiwen Zhao
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Data Science
description: doi:10.7717/peerj.15327
publisher: PeerJ Inc.
rights: © 2023 Ma et al.
abstract: Hair/wool usually plays an important role in maintaining animal physiological activities, and the economic value of wool cannot be ignored. At present, people set higher demands on wool fineness. Hence, improving wool fineness is the concern of fine wool sheep breeding. Using RNA-Seq to screen the potential candidate genes that associate with wool fineness can provide theoretical references for fine-wool sheep breeding, and also provide us new ideas for further understand the molecular regulation mechanism of hair growth. In this study, we compared the expression pattern difference of genome-wide genes between the skin transcriptomes of Subo and Chinese Merinos. The results showed that, 16 candidate differentially expressed genes (DEGs) (Included: CACNA1S, GP5, LOC101102392, HSF5, SLITRK2, LOC101104661, CREB3L4, COL1A1, PTPRR, SFRP4, LOC443220, COL6A6, COL6A5, LAMA1, LOC114115342 and LOC101116863 genes) that may associate with wool fineness were screened, and these genes were located in signaling pathways that regulate hair follicle development, cycle or hair growth. It is worth noting that, among the 16 DEGs, COL1A1 gene has the highest expression level in Merino skins, and the fold change of LOC101116863 gene is the highest, and the structures of these two genes are both highly conserved in different species. In conclusion, we speculate that these two genes may play a key role in regulating wool fineness and respectively have similar and conserved functions in different species.
bibliographic citation: Ma et al. (2023) Transcriptome analysis reveals genes associated with wool fineness in merinos. PeerJ 11:e15327 https://doi.org/10.7717/peerj.15327
date submitted: 2022-10-11
date accepted: 2023-04-10
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Shengchao
author list: Agent
  family name: Long
  given name: Li
author list: Agent
  family name: Huang
  given name: Xixia
author list: Agent
  family name: Tian
  given name: Kechuan
author list: Agent
  family name: Tian
  given name: Yuezhen
author list: Agent
  family name: Wu
  given name: Cuiling
author list: Agent
  family name: Zhao
  given name: Zhiwen
doi: 10.7717/peerj.15327
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: ©2023 Ma et al.
attribution name: Ma et al.

Morphometric analysis of odontoid process among Arab population: a retrospective cone beam CT study
type: item
type: AcademicArticle
description: Objective This study aims to evaluate the feasibility of using cone beam computed tomography (CBCT) scans to assess the odontoid process diameter in the Arab population and to determine whether one or two cortical screws can be used for treating odontoid fractures. Methods The odontoid process of 142 individuals aged 12–75 years, including 72 males (mean age: 35.5) and 70 females (mean age: 36.2), were analyzed using CBCT scans. The sagittal and coronal CBCT views were used to evaluate the antero-posterior (AP) and transverse diameters of the odontoid process. Results Males had substantially bigger transverse and AP diameters of the odontoid process than females (p < 0.05 & P < 0.01 respectively). Among the sample, 97 individuals (67.4%) had external transverse diameter (METD) of less than 9 mm which is slightly bigger than that of Indians and 48 individuals (31.83%) had enough room for two 3.5 mm or two 2.7 mm screws as their METD was more than 9 mm like that of Greek and Turkish. Age had no significant impact on the morphometric measurements of the odontoid process. Conclusion More than sixty percent of the sample had METDs of less than 9 millimeters, indicating that a single 4.5-mm Herbert screw may be suggested for fixing fractured odontoid processes in the Arab population.
format: application/pdf
format: text/html
creator: Asmaa Uthman
creator: Basheer Salman
creator: Hawraa Shams Aldeen
creator: Hesham Marei
creator: Sura F. Al-Bayati
creator: Natheer H. Al-Rawi
subject: Anthropology
subject: Anatomy and Physiology
subject: Dentistry
subject: Radiology and Medical Imaging
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.15411
publisher: PeerJ Inc.
rights: © 2023 Uthman et al.
abstract: Objective This study aims to evaluate the feasibility of using cone beam computed tomography (CBCT) scans to assess the odontoid process diameter in the Arab population and to determine whether one or two cortical screws can be used for treating odontoid fractures. Methods The odontoid process of 142 individuals aged 12–75 years, including 72 males (mean age: 35.5) and 70 females (mean age: 36.2), were analyzed using CBCT scans. The sagittal and coronal CBCT views were used to evaluate the antero-posterior (AP) and transverse diameters of the odontoid process. Results Males had substantially bigger transverse and AP diameters of the odontoid process than females (p < 0.05 & P < 0.01 respectively). Among the sample, 97 individuals (67.4%) had external transverse diameter (METD) of less than 9 mm which is slightly bigger than that of Indians and 48 individuals (31.83%) had enough room for two 3.5 mm or two 2.7 mm screws as their METD was more than 9 mm like that of Greek and Turkish. Age had no significant impact on the morphometric measurements of the odontoid process. Conclusion More than sixty percent of the sample had METDs of less than 9 millimeters, indicating that a single 4.5-mm Herbert screw may be suggested for fixing fractured odontoid processes in the Arab population.
bibliographic citation: Uthman et al. (2023) Morphometric analysis of odontoid process among Arab population: a retrospective cone beam CT study. PeerJ 11:e15411 https://doi.org/10.7717/peerj.15411
date submitted: 2023-01-11
date accepted: 2023-04-23
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Uthman
  given name: Asmaa
author list: Agent
  family name: Salman
  given name: Basheer
author list: Agent
  family name: Shams Aldeen
  given name: Hawraa
author list: Agent
  family name: Marei
  given name: Hesham
author list: Agent
  family name: Al-Bayati
  given name: Sura F.
author list: Agent
  family name: Al-Rawi
  given name: Natheer H.
doi: 10.7717/peerj.15411
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: ©2023 Uthman et al.
attribution name: Uthman et al.

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