PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest
items: Minimizing the variables of voiding spot assay for comparison between laboratories
items: Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer
items: Determination of the affinity constants for phage display albumin-binding peptides

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.

Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest
type: item
type: AcademicArticle
description: Background Soil microenvironmental variables showed an important key in α and β-tree diversity in Neotropical montane oak forest. Thus, understanding the microenvironment fluctuation at small-fragment effects on tree diversity is crucial in maintaining the montane oak ecosystems. In this study, we hypothesized that within a relatively small-fragment (151.63 ha), tree α and β-diversity fluctuate and specific soil microenvironmental factors could influence tree species diversity to answer three questions: Do tree α and β-diversity differ among transects, even in a short-distance between them? Do microenvironmental variables influence tree diversity composition that occurs within a relict Neotropical montane oak forest? Is there a particular microenvironmental variable influencing tree species-specific? Methods We established four permanent transects during a year in a relict Neotropical montane oak forest, we assessed tree diversity and specific microenvironmental variables (soil moisture, soil temperature, pH, depth litterfall and light incidence). This allowed us to evaluate how microenvironmental variables at small-fragment influence α and β-tree diversity and tree species-specific. Results Our results showed that α-diversity was not different among transects; however, β-diversity of tree species was mostly explained by turnover and soil moisture, soil temperature, and light incidence were the microenvironmental variables that triggered the replacement (i.e., one species by another). Those variables also had effect on tree species-specific: Mexican beech (Fagus mexicana), Quebracho (Quercus delgadoana), Pezma (Cyathea fulva), Aguacatillo (Beilschmiedia mexicana), Pezma (Dicksonia sellowiana var. arachneosa), and Mountain magnolia (Magnolia schiedeana). Discussion Our results confirm our hypothesis related to β-diversity but not with α-diversity; however, the tree community structure of the diversity was similar among transects. Our study represents the first effort…
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format: text/html
creator: Luis F. López-Calvillo
creator: Pilar Carbó-Ramírez
creator: Ernesto C. Rodríguez-Ramírez
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.15415
publisher: PeerJ Inc.
rights: © 2023 López-Calvillo et al.
abstract: Background Soil microenvironmental variables showed an important key in α and β-tree diversity in Neotropical montane oak forest. Thus, understanding the microenvironment fluctuation at small-fragment effects on tree diversity is crucial in maintaining the montane oak ecosystems. In this study, we hypothesized that within a relatively small-fragment (151.63 ha), tree α and β-diversity fluctuate and specific soil microenvironmental factors could influence tree species diversity to answer three questions: Do tree α and β-diversity differ among transects, even in a short-distance between them? Do microenvironmental variables influence tree diversity composition that occurs within a relict Neotropical montane oak forest? Is there a particular microenvironmental variable influencing tree species-specific? Methods We established four permanent transects during a year in a relict Neotropical montane oak forest, we assessed tree diversity and specific microenvironmental variables (soil moisture, soil temperature, pH, depth litterfall and light incidence). This allowed us to evaluate how microenvironmental variables at small-fragment influence α and β-tree diversity and tree species-specific. Results Our results showed that α-diversity was not different among transects; however, β-diversity of tree species was mostly explained by turnover and soil moisture, soil temperature, and light incidence were the microenvironmental variables that triggered the replacement (i.e., one species by another). Those variables also had effect on tree species-specific: Mexican beech (Fagus mexicana), Quebracho (Quercus delgadoana), Pezma (Cyathea fulva), Aguacatillo (Beilschmiedia mexicana), Pezma (Dicksonia sellowiana var. arachneosa), and Mountain magnolia (Magnolia schiedeana). Discussion Our results confirm our hypothesis related to β-diversity but not with α-diversity; however, the tree community structure of the diversity was similar among transects. Our study represents the first effort…
bibliographic citation: López-Calvillo et al. (2023) Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest. PeerJ 11:e15415 https://doi.org/10.7717/peerj.15415
date submitted: 2022-12-30
date accepted: 2023-04-24
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: López-Calvillo
  given name: Luis F.
author list: Agent
  family name: Carbó-Ramírez
  given name: Pilar
author list: Agent
  family name: Rodríguez-Ramírez
  given name: Ernesto C.
doi: 10.7717/peerj.15415
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: ©2023 López-Calvillo et al.
attribution name: López-Calvillo et al.

Minimizing the variables of voiding spot assay for comparison between laboratories
type: item
type: AcademicArticle
description: The voiding spot assay (VSA) is increasingly being adopted as a standard method for assessing mouse urinary function. However, VSA outcomes are highly sensitive to housing environment and procedural parameters. Many variables exist among laboratories, including analytical software, type of daily housing cage, transportation, and the time of the day. Some of these variables, such as the time of VSA and analytical software, have been shown to result in inconsistency and incomparability of data. In this study, we evaluated whether the results of VSA can be compared across laboratories by minimizing these variables. We found that analytical tools between Fiji and MATLAB are in good agreement in the quantification of VSA parameters, especially primary voiding spot (PVS) parameters. Unexpectedly, we found that mice housed in different daily home cages did not alter voiding patterns in a standard VSA cage. Nonetheless, we still recommend acclimation when performing VSA in unfamiliar cages. Notably, mice are highly sensitive to transportation and the time in the morning versus afternoon, which can induce significant changes in voiding patterns. Therefore, a standardized period among laboratories and allowing 2–3 days of rest for mice acclimation after transportation are necessary for VSA. Finally, we performed VSA using identical procedural parameters in two laboratories from two geographical locations to compare the results of VSA and concluded that it is possible to generate limited comparable VSA data, such as PVS volume.
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creator: Chuang Luo
creator: Juan Liu
creator: Jiali Yang
creator: Xiang Xie
creator: Weiqun Yu
creator: Huan Chen
subject: Animal Behavior
subject: Biochemistry
subject: Zoology
description: doi:10.7717/peerj.15420
publisher: PeerJ Inc.
rights: © 2023 Luo et al.
abstract: The voiding spot assay (VSA) is increasingly being adopted as a standard method for assessing mouse urinary function. However, VSA outcomes are highly sensitive to housing environment and procedural parameters. Many variables exist among laboratories, including analytical software, type of daily housing cage, transportation, and the time of the day. Some of these variables, such as the time of VSA and analytical software, have been shown to result in inconsistency and incomparability of data. In this study, we evaluated whether the results of VSA can be compared across laboratories by minimizing these variables. We found that analytical tools between Fiji and MATLAB are in good agreement in the quantification of VSA parameters, especially primary voiding spot (PVS) parameters. Unexpectedly, we found that mice housed in different daily home cages did not alter voiding patterns in a standard VSA cage. Nonetheless, we still recommend acclimation when performing VSA in unfamiliar cages. Notably, mice are highly sensitive to transportation and the time in the morning versus afternoon, which can induce significant changes in voiding patterns. Therefore, a standardized period among laboratories and allowing 2–3 days of rest for mice acclimation after transportation are necessary for VSA. Finally, we performed VSA using identical procedural parameters in two laboratories from two geographical locations to compare the results of VSA and concluded that it is possible to generate limited comparable VSA data, such as PVS volume.
bibliographic citation: Luo et al. (2023) Minimizing the variables of voiding spot assay for comparison between laboratories. PeerJ 11:e15420 https://doi.org/10.7717/peerj.15420
date submitted: 2023-01-10
date accepted: 2023-04-25
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Chuang
author list: Agent
  family name: Liu
  given name: Juan
author list: Agent
  family name: Yang
  given name: Jiali
author list: Agent
  family name: Xie
  given name: Xiang
author list: Agent
  family name: Yu
  given name: Weiqun
author list: Agent
  family name: Chen
  given name: Huan
doi: 10.7717/peerj.15420
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: ©2023 Luo et al.
attribution name: Luo et al.

Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer
type: item
type: AcademicArticle
description: Among the Arctic seas, the largest volume of river runoff (~45% of the total river-water inflow into the Arctic Ocean) enters the Siberian Kara Sea. The viral communities of the Kara Sea are important for the functioning of the marine ecosystem. Studies of virus–prokaryote interactions on the Kara Sea shelf have been conducted only in spring and autumn. Here, we investigated the abundance of free viruses, viruses attached to prokaryotes, and pico-sized detrital particles; the morphology (shape and size) of the viruses, viral infection and virus-mediated mortality of prokaryotes in early summer, i.e., during a seasonal ice melting period and maximum inflow of river-water volumes with high concentrations of dissolved and suspended organic carbon. Seawater samples for microbial analyses were collected across the Kara Sea shelf zone on board the Norilskiy Nickel as a research platform from June 29 to July 15, 2018. Abundances of prokaryotes (range (0.6–25.3) × 105 cells mL−1) and free viruses (range (10–117) × 105 viruses mL−1) were correlated (r = 0.63, p = 0.005) with an average virus: prokaryote ratio of 23.9 ± 5.3. The abundance of free viruses and viral-mediated mortality of prokaryotes were significantly higher in early summer than in early spring and autumn. Free viruses with a capsid diameter of 16–304 nm were recorded in the examined water samples. Waters in the Kara Sea shelf contained high concentrations of suspended organic particles 0.25–4.0 µm in size (range (0.6–25.3) × 105 particles mL−1). The proportions of free viruses, viruses attached to prokaryotes, and viruses attached to pico-sized detrital particles were 89.8 ± 6.0%, 2.2 ± 0.6% and 8.0 ± 1.3%, respectively, of the total virioplankton abundance (on average (61.5 ± 6.2) × 105 viruses mL−1). Viruses smaller than 60 nm clearly dominated at all studied sites. The majority of free viruses were not tailed. We estimated that an average of 1.4% (range 0.4–3.5%) of the prokaryote community was visibly infe…
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creator: Alexander Ivanovich Kopylov
creator: Elena Anatoliyevna Zabotkina
creator: Andrey Fiodorovich Sazhin
creator: Nadezda Romanova
creator: Nikolay Belyaev
creator: Anastasia Drozdova
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.15457
publisher: PeerJ Inc.
rights: © 2023 Kopylov et al.
abstract: Among the Arctic seas, the largest volume of river runoff (~45% of the total river-water inflow into the Arctic Ocean) enters the Siberian Kara Sea. The viral communities of the Kara Sea are important for the functioning of the marine ecosystem. Studies of virus–prokaryote interactions on the Kara Sea shelf have been conducted only in spring and autumn. Here, we investigated the abundance of free viruses, viruses attached to prokaryotes, and pico-sized detrital particles; the morphology (shape and size) of the viruses, viral infection and virus-mediated mortality of prokaryotes in early summer, i.e., during a seasonal ice melting period and maximum inflow of river-water volumes with high concentrations of dissolved and suspended organic carbon. Seawater samples for microbial analyses were collected across the Kara Sea shelf zone on board the Norilskiy Nickel as a research platform from June 29 to July 15, 2018. Abundances of prokaryotes (range (0.6–25.3) × 105 cells mL−1) and free viruses (range (10–117) × 105 viruses mL−1) were correlated (r = 0.63, p = 0.005) with an average virus: prokaryote ratio of 23.9 ± 5.3. The abundance of free viruses and viral-mediated mortality of prokaryotes were significantly higher in early summer than in early spring and autumn. Free viruses with a capsid diameter of 16–304 nm were recorded in the examined water samples. Waters in the Kara Sea shelf contained high concentrations of suspended organic particles 0.25–4.0 µm in size (range (0.6–25.3) × 105 particles mL−1). The proportions of free viruses, viruses attached to prokaryotes, and viruses attached to pico-sized detrital particles were 89.8 ± 6.0%, 2.2 ± 0.6% and 8.0 ± 1.3%, respectively, of the total virioplankton abundance (on average (61.5 ± 6.2) × 105 viruses mL−1). Viruses smaller than 60 nm clearly dominated at all studied sites. The majority of free viruses were not tailed. We estimated that an average of 1.4% (range 0.4–3.5%) of the prokaryote community was visibly infe…
bibliographic citation: Kopylov et al. (2023) Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer. PeerJ 11:e15457 https://doi.org/10.7717/peerj.15457
date submitted: 2022-11-04
date accepted: 2023-05-03
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kopylov
  given name: Alexander Ivanovich
author list: Agent
  family name: Zabotkina
  given name: Elena Anatoliyevna
author list: Agent
  family name: Sazhin
  given name: Andrey Fiodorovich
author list: Agent
  family name: Romanova
  given name: Nadezda
author list: Agent
  family name: Belyaev
  given name: Nikolay
author list: Agent
  family name: Drozdova
  given name: Anastasia
doi: 10.7717/peerj.15457
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: © 2023 Kopylov et al.
attribution name: Kopylov et al.

Determination of the affinity constants for phage display albumin-binding peptides
type: item
type: AcademicArticle
description: Background Phage display technology has been established as a powerful screening approach to select ligands or peptides for binding to proteins. Despite rapid growth in the field, there has been a relative dearth of quantitative criteria to measure the effectiveness of the process of phage display screening. Since human serum albumin (HSA) has been extensively studied as a drug carrier to extend the plasma half-life of protein therapeutics, the use of phage display technology is required for identifying albumin-binding peptides as the very promising strategy of albumin-binding against albumin fusion. The construction of albumin-binding drug requires the assessment of a large quantity of HSA-binding peptide (HSA binder) candidates for conjugation with therapeutic proteins. The use of the linear epitope mapping method has allowed researchers to discover many HSA-binding peptides. However, it may be inefficient to select these peptides based on sequence identity via randomly sequencing individual phage clones from enrichment pools. Method Here, a simple assessment method to facilitate phage display selection of HSA-binding peptides was recommended. With experimentally determined phage titer, one can calculate the specificity ratios, the recovery yields and the relative dissociation constants, which are defined as quantitative criteria for panning and characterization of the binding phage fused peptides. Results Consequently, this approach may not only enable more rapid and low-cost phage display screening, but also efficiently reduce pseudo-positive phages selected as HSA binders for conjugation with therapeutic proteins.
format: application/pdf
format: text/html
creator: Yi-Feng Shi
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
subject: Synthetic Biology
description: doi:10.7717/peerj.15078
publisher: PeerJ Inc.
rights: © 2023 Shi
abstract: Background Phage display technology has been established as a powerful screening approach to select ligands or peptides for binding to proteins. Despite rapid growth in the field, there has been a relative dearth of quantitative criteria to measure the effectiveness of the process of phage display screening. Since human serum albumin (HSA) has been extensively studied as a drug carrier to extend the plasma half-life of protein therapeutics, the use of phage display technology is required for identifying albumin-binding peptides as the very promising strategy of albumin-binding against albumin fusion. The construction of albumin-binding drug requires the assessment of a large quantity of HSA-binding peptide (HSA binder) candidates for conjugation with therapeutic proteins. The use of the linear epitope mapping method has allowed researchers to discover many HSA-binding peptides. However, it may be inefficient to select these peptides based on sequence identity via randomly sequencing individual phage clones from enrichment pools. Method Here, a simple assessment method to facilitate phage display selection of HSA-binding peptides was recommended. With experimentally determined phage titer, one can calculate the specificity ratios, the recovery yields and the relative dissociation constants, which are defined as quantitative criteria for panning and characterization of the binding phage fused peptides. Results Consequently, this approach may not only enable more rapid and low-cost phage display screening, but also efficiently reduce pseudo-positive phages selected as HSA binders for conjugation with therapeutic proteins.
bibliographic citation: Shi (2023) Determination of the affinity constants for phage display albumin-binding peptides. PeerJ 11:e15078 https://doi.org/10.7717/peerj.15078
date submitted: 2020-12-21
date accepted: 2023-02-24
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Yi-Feng
doi: 10.7717/peerj.15078
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: ©2023 Shi
attribution name: Shi

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