PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Telomere-to-telomere genome assembly of Phaeodactylum tricornutum
items: Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity
items: Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2
items: The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents
items: Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
items: Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area
items: Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
items: Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations
items: Sea urchins: an update on their pharmacological properties
items: The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species

Telomere-to-telomere genome assembly of Phaeodactylum tricornutum
type: item
type: AcademicArticle
description: Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.
format: application/pdf
format: text/html
creator: Daniel J. Giguere
creator: Alexander T. Bahcheli
creator: Samuel S. Slattery
creator: Rushali R. Patel
creator: Tyler S. Browne
creator: Martin Flatley
creator: Bogumil J. Karas
creator: David R. Edgell
creator: Gregory B. Gloor
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Plant Science
subject: Synthetic Biology
description: doi:10.7717/peerj.13607
publisher: PeerJ Inc.
rights: © 2022 Giguere et al.
abstract: Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.
bibliographic citation: Giguere et al. (2022) Telomere-to-telomere genome assembly of Phaeodactylum tricornutum. PeerJ 10:e13607 https://doi.org/10.7717/peerj.13607
date submitted: 2021-05-11
date accepted: 2022-05-27
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Giguere
  given name: Daniel J.
author list: Agent
  family name: Bahcheli
  given name: Alexander T.
author list: Agent
  family name: Slattery
  given name: Samuel S.
author list: Agent
  family name: Patel
  given name: Rushali R.
author list: Agent
  family name: Browne
  given name: Tyler S.
author list: Agent
  family name: Flatley
  given name: Martin
author list: Agent
  family name: Karas
  given name: Bogumil J.
author list: Agent
  family name: Edgell
  given name: David R.
author list: Agent
  family name: Gloor
  given name: Gregory B.
doi: 10.7717/peerj.13607
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Giguere et al.
attribution name: Giguere et al.

Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity
type: item
type: AcademicArticle
description: Background Interleukin-18 (IL-18) is prone to form multimers resulting in inactive aggregates, making this cytokine unstable for clinical use. Therefore, mutations have been introduced into recombinant IL-18 to overcome this issue. Methods To prevent the formation of disulfide bonds between the IL-18 molecules, multiple mutations targeting surface cysteines (C38, C68, C76, and C127) were introduced into our previously modified human IL-18 double mutant E6K+T63A (IL-18 DM) by direct gene synthesis. The open reading frames of IL-18 wild-type (WT), IL-18 DM, and IL-18 multiple mutant E6K+T63A+C38S+C68S+C76S+C127S (IL-18 DM1234) were inserted in the pET28a expression vector and transformed into Escherichia coli Rosetta2 (DE3) pLysS cells for protein production. The inclusion bodies of WT and mutated IL-18 were extracted by sonication and refolded by stepwise dialysis using 8 M urea as the starting concentration. The refolded IL-18 proteins were tested for aggregation using the ProteoStat protein aggregation assay. Their activity was also investigated by treating NK-92MI cells with each IL-18 at concentrations of 75, 150, and 300 ng/ml with 0.5 ng/ml of human IL-12 and interferon-gamma (IFN-γ) levels in the supernatant were evaluated using ELISA. The structure of modified IL-18 was visualized using molecular dynamics (MD) simulations. Results IL-18 DM1234 exhibited the lowest aggregation signal, approximately 1.79- and 1.63-fold less than that of the WT and IL-18 DM proteins. Additionally, the IFN-γ inducing activity of IL-18 DM1234 was about 10 and 2.8 times higher than that of the WT and IL-18 DM, respectively. MD simulations revealed that binding site I of IL-18 DM1234 was altered mainly due to surface cysteine replacement with serine (C-to-S substitution). This is the first report showing that C-to-S substitutions in IL-18 improved its activity and stability, suggesting the use of this modified IL-18 for medical purposes in the future.
format: application/pdf
format: text/html
creator: Jirakrit Saetang
creator: Niran Roongsawang
creator: Surasak Sangkhathat
creator: Supayang Piyawan Voravuthikunchai
creator: Natnaree Sangkaew
creator: Napat Prompat
creator: Teerapol Srichana
creator: Varomyalin Tipmanee
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
subject: Translational Medicine
description: doi:10.7717/peerj.13626
publisher: PeerJ Inc.
rights: © 2022 Saetang et al.
abstract: Background Interleukin-18 (IL-18) is prone to form multimers resulting in inactive aggregates, making this cytokine unstable for clinical use. Therefore, mutations have been introduced into recombinant IL-18 to overcome this issue. Methods To prevent the formation of disulfide bonds between the IL-18 molecules, multiple mutations targeting surface cysteines (C38, C68, C76, and C127) were introduced into our previously modified human IL-18 double mutant E6K+T63A (IL-18 DM) by direct gene synthesis. The open reading frames of IL-18 wild-type (WT), IL-18 DM, and IL-18 multiple mutant E6K+T63A+C38S+C68S+C76S+C127S (IL-18 DM1234) were inserted in the pET28a expression vector and transformed into Escherichia coli Rosetta2 (DE3) pLysS cells for protein production. The inclusion bodies of WT and mutated IL-18 were extracted by sonication and refolded by stepwise dialysis using 8 M urea as the starting concentration. The refolded IL-18 proteins were tested for aggregation using the ProteoStat protein aggregation assay. Their activity was also investigated by treating NK-92MI cells with each IL-18 at concentrations of 75, 150, and 300 ng/ml with 0.5 ng/ml of human IL-12 and interferon-gamma (IFN-γ) levels in the supernatant were evaluated using ELISA. The structure of modified IL-18 was visualized using molecular dynamics (MD) simulations. Results IL-18 DM1234 exhibited the lowest aggregation signal, approximately 1.79- and 1.63-fold less than that of the WT and IL-18 DM proteins. Additionally, the IFN-γ inducing activity of IL-18 DM1234 was about 10 and 2.8 times higher than that of the WT and IL-18 DM, respectively. MD simulations revealed that binding site I of IL-18 DM1234 was altered mainly due to surface cysteine replacement with serine (C-to-S substitution). This is the first report showing that C-to-S substitutions in IL-18 improved its activity and stability, suggesting the use of this modified IL-18 for medical purposes in the future.
bibliographic citation: Saetang et al. (2022) Surface cysteine to serine substitutions in IL-18 reduce aggregation and enhance activity. PeerJ 10:e13626 https://doi.org/10.7717/peerj.13626
date submitted: 2022-03-15
date accepted: 2022-06-02
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Saetang
  given name: Jirakrit
author list: Agent
  family name: Roongsawang
  given name: Niran
author list: Agent
  family name: Sangkhathat
  given name: Surasak
author list: Agent
  family name: Voravuthikunchai
  given name: Supayang Piyawan
author list: Agent
  family name: Sangkaew
  given name: Natnaree
author list: Agent
  family name: Prompat
  given name: Napat
author list: Agent
  family name: Srichana
  given name: Teerapol
author list: Agent
  family name: Tipmanee
  given name: Varomyalin
doi: 10.7717/peerj.13626
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Saetang et al.
attribution name: Saetang et al.

Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2
type: item
type: AcademicArticle
description: Background The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions. Methods To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant. Results Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2’s N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.
format: application/pdf
format: text/html
creator: Priya Antony
creator: Amie Jobe
creator: Ranjit Vijayan
subject: Bioinformatics
subject: Computational Biology
subject: COVID-19
description: doi:10.7717/peerj.13680
publisher: PeerJ Inc.
rights: © 2022 Antony et al.
abstract: Background The COVID-19 pandemic is still a global public health issue. Omicron, a SARS-CoV-2 B.1.1.529 variant, has raised concerns about transmission and vaccine effectiveness. Omicron currently has the greatest number of variantions. Methods To gain a better understanding of the significance of these variations and the dynamics of the interaction between the Omicron spike (S) protein and its human host factor angiotensin-converting enzyme 2 (ACE2), triplicate 500 ns molecular dynamics simulations were run using the structure of the S protein’s receptor-binding domain (RBD) in complex with ACE2. The interaction and binding energy, determined using the molecular mechanics—generalized Born surface area approach, were compared to the original SARS-CoV-2 and the B.1.617 variant. Results Though mutations K417N and G496S in the S protein RBD disrupt interactions found in the original SARS-CoV-2 complex, mutations Q493R and N501Y introduce interactions not found in the original complex. Interaction at a key viral hotspot and hydrophobic contacts at ACE2’s N-terminus were preserved, but intermolecular hydrogen bonds and polar contacts in the S-ACE2 interface were lower than in the original SARS-CoV-2 interface.
bibliographic citation: Antony et al. (2022) Dynamics of the interaction between the receptor-binding domain of SARS-CoV-2 Omicron (B.1.1.529) variant and human angiotensin-converting enzyme 2. PeerJ 10:e13680 https://doi.org/10.7717/peerj.13680
date submitted: 2022-03-28
date accepted: 2022-06-14
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antony
  given name: Priya
author list: Agent
  family name: Jobe
  given name: Amie
author list: Agent
  family name: Vijayan
  given name: Ranjit
doi: 10.7717/peerj.13680
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Antony et al.
attribution name: Antony et al.

The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents
type: item
type: AcademicArticle
description: Background Extensive literature revealed the relations of depression with behavioral inhibition system (BIS) and behavioral activation system (BAS) as vulnerability and with resilience separately. Besides, the concept of resilience is still broad and ambiguous. Thus, this study aimed to reveal the mediation of two aspects of resilience: trait and process, in the relations of BIS and BAS to depression among adolescents. Methods The data set used in this study was a cross-sectional survey among 965 adolescents. The obtained data from the self-reported questionnaires used in this study were as below: Depression Serf-Rating Scale for Children (DSRS-C), Behavioral Inhibition and Behavioral Activation System Scale (BIS/BASS), and Bidimensional Resilience Scale (BRS). Structural equation modeling (SEM) was conducted to verify the hypothesized relations among BIS/BAS, trait and behavior resilience, and depressive symptoms. Results The obtained indices of fit from SEM were good or sufficient (χ2 = 562.911, df = 96, p < 0.001; CFI = 0.925; NFI = 0.913; RMSEA = 0.073, 90% CI [0.067, 0.079]; SRMR = 0.066). And the modeling showed that both BIS/BAS directly and indirectly influenced to depression. The indirect effects of BIS/BAS were mediated only trait resilience except the indirect effect of BIS via behavioral resilience. Discussion Our results suggested that trait resilience played a significant mediation role in the relationships between BIS/BAS and depression. Trait but not process resilience could be considered suitable as an intervention target in line with decreasing depression.
format: application/pdf
format: text/html
creator: Akihiro Masuyama
creator: Takahiro Kubo
creator: Hiroki Shinkawa
creator: Daichi Sugawara
subject: Pediatrics
subject: Psychiatry and Psychology
subject: Mental Health
description: doi:10.7717/peerj.13687
publisher: PeerJ Inc.
rights: © 2022 Masuyama et al.
abstract: Background Extensive literature revealed the relations of depression with behavioral inhibition system (BIS) and behavioral activation system (BAS) as vulnerability and with resilience separately. Besides, the concept of resilience is still broad and ambiguous. Thus, this study aimed to reveal the mediation of two aspects of resilience: trait and process, in the relations of BIS and BAS to depression among adolescents. Methods The data set used in this study was a cross-sectional survey among 965 adolescents. The obtained data from the self-reported questionnaires used in this study were as below: Depression Serf-Rating Scale for Children (DSRS-C), Behavioral Inhibition and Behavioral Activation System Scale (BIS/BASS), and Bidimensional Resilience Scale (BRS). Structural equation modeling (SEM) was conducted to verify the hypothesized relations among BIS/BAS, trait and behavior resilience, and depressive symptoms. Results The obtained indices of fit from SEM were good or sufficient (χ2 = 562.911, df = 96, p < 0.001; CFI = 0.925; NFI = 0.913; RMSEA = 0.073, 90% CI [0.067, 0.079]; SRMR = 0.066). And the modeling showed that both BIS/BAS directly and indirectly influenced to depression. The indirect effects of BIS/BAS were mediated only trait resilience except the indirect effect of BIS via behavioral resilience. Discussion Our results suggested that trait resilience played a significant mediation role in the relationships between BIS/BAS and depression. Trait but not process resilience could be considered suitable as an intervention target in line with decreasing depression.
bibliographic citation: Masuyama et al. (2022) The roles of trait and process resilience in relation of BIS/BAS and depressive symptoms among adolescents. PeerJ 10:e13687 https://doi.org/10.7717/peerj.13687
date submitted: 2022-03-25
date accepted: 2022-06-15
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Masuyama
  given name: Akihiro
author list: Agent
  family name: Kubo
  given name: Takahiro
author list: Agent
  family name: Shinkawa
  given name: Hiroki
author list: Agent
  family name: Sugawara
  given name: Daichi
doi: 10.7717/peerj.13687
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Masuyama et al.
attribution name: Masuyama et al.

Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus
type: item
type: AcademicArticle
description: Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
format: application/pdf
format: text/html
creator: Zhaokui Du
creator: Weida Lin
creator: Jinxing Zhu
creator: Junmin Li
subject: Agricultural Science
subject: Biochemistry
subject: Bioinformatics
subject: Plant Science
description: doi:10.7717/peerj.13689
publisher: PeerJ Inc.
rights: © 2022 Du et al.
abstract: Background Cyclocarya paliurus is a tree well known for its edible and medicinal leaves. Amino acids are essential nutritional components that are present in foods and closely related to the flavor and quality of tea. However, the abundance of amino acids and the regulation of amino acid biosynthesis in the leaves of C. paliurus have not been investigated across different developmental stages. Methods A combined metabolomic and transcriptomic analysis was employed to investigate the changes in the amino acid profile over several developmental stages (S1, the smallest fully expanded leaf; S3, full leaf enlargement and full leaf thickness; and S2, an intermediate developmental stage between S1 and S3) and the molecular mechanism was elucidated. Results The results showed that leaves at the S1 stage had the highest content, while those at the S3 stage had the lowest content of amino acids; fourteen differentially expressed genes were involved in the glycolysis pathway, the tricarboxylic acid cycle and the pentose phosphate pathway, which indicated that the reduced abundance of amino acids in the leaves of C. paliurus (mature leaves) may be attributable to reduced gene expression related to carbohydrate metabolism. Four basic leucine zipper transcription factors might play important roles in the regulation of the biosynthesis of amino acids in the leaves of C. paliurus. Conclusions Leaves at the S1 stage are recommended for high quality tea production because of their high content of amino acids, while leaves at the S2 stage are recommended for generous tea production because of their high levels of sweet flavor amino acids (alanine) and essential amino acids (methionine, phenylalanine, threonine, and tryptophan).
bibliographic citation: Du et al. (2022) Amino acids profiling and transcriptomic data integration demonstrates the dynamic regulation of amino acids synthesis in the leaves of Cyclocarya paliurus. PeerJ 10:e13689 https://doi.org/10.7717/peerj.13689
date submitted: 2021-08-31
date accepted: 2022-06-16
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Du
  given name: Zhaokui
author list: Agent
  family name: Lin
  given name: Weida
author list: Agent
  family name: Zhu
  given name: Jinxing
author list: Agent
  family name: Li
  given name: Junmin
doi: 10.7717/peerj.13689
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: © 2022 Du et al.
attribution name: Du et al.

Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area
type: item
type: AcademicArticle
description: We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could b…
format: application/pdf
format: text/html
creator: Mauricio Heredia-Pech
creator: Mariana Chávez-Pesqueira
creator: Matilde M. Ortiz-García
creator: Rubén Humberto Andueza-Noh
creator: María Isabel Chacón-Sánchez
creator: Jaime Martínez-Castillo
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13690
publisher: PeerJ Inc.
rights: © 2022 Heredia-Pech et al.
abstract: We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found HE values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., HE = 0.27 and HE = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could b…
bibliographic citation: Heredia-Pech et al. (2022) Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area. PeerJ 10:e13690 https://doi.org/10.7717/peerj.13690
date submitted: 2022-01-28
date accepted: 2022-06-16
issued: 2022-07-05
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Heredia-Pech
  given name: Mauricio
author list: Agent
  family name: Chávez-Pesqueira
  given name: Mariana
author list: Agent
  family name: Ortiz-García
  given name: Matilde M.
author list: Agent
  family name: Andueza-Noh
  given name: Rubén Humberto
author list: Agent
  family name: Chacón-Sánchez
  given name: María Isabel
author list: Agent
  family name: Martínez-Castillo
  given name: Jaime
doi: 10.7717/peerj.13690
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-05
copyright: ©2022 Heredia-Pech et al.
attribution name: Heredia-Pech et al.

Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis)
type: item
type: AcademicArticle
description: Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
format: application/pdf
format: text/html
creator: Zhenfan Yu
creator: Dongdong Zhang
creator: Bin Zeng
creator: Xingyue Liu
creator: Jiahui Yang
creator: Wenwen Gao
creator: Xintong Ma
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.13491
publisher: PeerJ Inc.
rights: © 2022 Yu et al.
abstract: Background WRKY (WRKY DNA-binding domain) transcription factors an important gene family that widely regulates plant resistance to biological and abiotic stresses, such as drought, salt and ion stresses. However, research on the WRKY family in almond has not yet been reported. Almond is an economically important fruit tree in Xinjiang that have strong resistance to various stresses. Results A total of 62 PdWRKY genes were identified (including six pairs of homologous genes), and the phylogenetic tree was divided into three groups according to the WRKY domain and zinc finger motifs. The members of each group had a significant number of conserved motifs and exons/introns distributed unevenly across eight chromosomes, as well as 24 pairs of fragment duplicates and nine pairs of tandem duplicates. Moreover, the synteny and Ka/Ks analyses of the WRKY genes among almond and distinct species provided more detailed evidence for PdWRKY genes evolution. The examination of different tissue expression patterns showed that PdWRKY genes have tissue-specific expression characteristics. The qRT–PCR results showed that PdWRKY genes participate in the resistance of almond to the effects of low-temperature, drought and salt stress and that the expression levels of these genes change over time, exhibiting spatiotemporal expression characteristics. It is worth noting that many genes play a significant role in low-temperature stress resistance. In addition, based on the conserved WRKY motif, 321 candidate target genes were identified as having functions in multiple pathways. Conclusions We conducted systematic bioinformatics analysis and abiotic stress research on the WRKY gene family in almond, laying the foundation for future PdWRKY genes research and improvements to almond production and breeding.
bibliographic citation: Yu et al. (2022) Characterization of the WRKY gene family reveals its contribution to the adaptability of almond (Prunus dulcis). PeerJ 10:e13491 https://doi.org/10.7717/peerj.13491
date submitted: 2022-01-31
date accepted: 2022-05-03
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yu
  given name: Zhenfan
author list: Agent
  family name: Zhang
  given name: Dongdong
author list: Agent
  family name: Zeng
  given name: Bin
author list: Agent
  family name: Liu
  given name: Xingyue
author list: Agent
  family name: Yang
  given name: Jiahui
author list: Agent
  family name: Gao
  given name: Wenwen
author list: Agent
  family name: Ma
  given name: Xintong
doi: 10.7717/peerj.13491
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Yu et al.
attribution name: Yu et al.

Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations
type: item
type: AcademicArticle
description: Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
format: application/pdf
format: text/html
creator: Fidji Berio
creator: Yann Bayle
creator: Daniel Baum
creator: Nicolas Goudemand
creator: Mélanie Debiais-Thibaud
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.13575
publisher: PeerJ Inc.
rights: © 2022 Berio et al.
abstract: Shark populations that are distributed alongside a latitudinal gradient often display body size differences at sexual maturity and vicariance patterns related to their number of tooth files. Previous works have demonstrated that Scyliorhinus canicula populations differ between the northeastern Atlantic Ocean and the Mediterranean Sea based on biological features and genetic analysis. In this study, we sample more than 3,000 teeth from 56 S. canicula specimens caught incidentally off Roscoff and Banyuls-sur-Mer. We investigate population differences based on tooth shape and form by using two approaches. Classification results show that the classical geometric morphometric framework is outperformed by an original Random Forests-based framework. Visually, both S. canicula populations share similar ontogenetic trends and timing of gynandric heterodonty emergence but the Atlantic population has bigger, blunter teeth, and less numerous accessory cusps than the Mediterranean population. According to the models, the populations are best differentiated based on their lateral tooth edges, which bear accessory cusps, and the tooth centroid sizes significantly improve classification performances. The differences observed are discussed in light of dietary and behavioural habits of the populations considered. The method proposed in this study could be further adapted to complement DNA analyses to identify shark species or populations based on tooth morphologies. This process would be of particular interest for fisheries management and identification of shark fossils.
bibliographic citation: Berio et al. (2022) Hide and seek shark teeth in Random Forests: machine learning applied to Scyliorhinus canicula populations. PeerJ 10:e13575 https://doi.org/10.7717/peerj.13575
date submitted: 2022-01-18
date accepted: 2022-05-22
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Berio
  given name: Fidji
author list: Agent
  family name: Bayle
  given name: Yann
author list: Agent
  family name: Baum
  given name: Daniel
author list: Agent
  family name: Goudemand
  given name: Nicolas
author list: Agent
  family name: Debiais-Thibaud
  given name: Mélanie
doi: 10.7717/peerj.13575
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Berio et al.
attribution name: Berio et al.

Sea urchins: an update on their pharmacological properties
type: item
type: AcademicArticle
description: Sea urchins are a group of benthic invertebrates characterized by having rigid globose bodies, covered in spines, and have an innate immune system that has allowed them to survive in the environment and defend against many pathogens that affect them. They are consumed for their unique flavor, but also for possessing a rich source of bioactive compounds which make them a source for a wide array of medicinal properties. Thus, these may be used to discover and develop new drugs such as anti-bacterials, anti-carcinogenics and anti-virals. Precisely for those reasons, this revision is centered on the known biological activities in various sea urchin species. Recently, the potential pharmacological benefits of nine sea urchin species [Diadema antillarum (Philippi 1845), Echinometra mathaei (de Blainville), Evechinus chloroticus (Valenciennes), Mesocentrotus nudus (Agassiz, 1863), Paracentrotus lividus (Lamarck, 1816), Scaphechinus mirabilis (Agazzis, 1863), Stomopneustes variolaris (Lamarck, 1816), Tripneustes depressus (Agassiz, 1863), and Tripneustes ventricosus (Lamarck, 1816)] have been evaluated. Our work includes a comprehensive review of the anti-fungal, anti-parasitic, anti-inflammatory, hepatoprotective, anti-viral, anti-diabetic, anti-lipidemic, gastro-protective and anti-cardiotoxic effects. Furthermore, we revised the compounds responsible of these pharmacological effects. This work was intended for a broad readership in the fields of pharmacology, drugs and devices, marine biology and aquaculture, fisheries and fish science. Our results suggest that organic extracts, as well as pure compounds obtained from several parts of sea urchin bodies are effective in vitro and in vivo pharmacological models. As such, these properties manifest the potential use of sea urchins to develop emergent active ingredients.
format: application/pdf
format: text/html
creator: Dulce María Moreno-García
creator: Monica Salas-Rojas
creator: Eduardo Fernández-Martínez
creator: Ma del Rocío López-Cuellar
creator: Carolina G. Sosa-Gutierrez
creator: Armando Peláez-Acero
creator: Nallely Rivero-Perez
creator: Adrian Zaragoza-Bastida
creator: Deyanira Ojeda-Ramírez
subject: Marine Biology
subject: Drugs and Devices
subject: Pharmacology
description: doi:10.7717/peerj.13606
publisher: PeerJ Inc.
rights: © 2022 Moreno-García et al.
abstract: Sea urchins are a group of benthic invertebrates characterized by having rigid globose bodies, covered in spines, and have an innate immune system that has allowed them to survive in the environment and defend against many pathogens that affect them. They are consumed for their unique flavor, but also for possessing a rich source of bioactive compounds which make them a source for a wide array of medicinal properties. Thus, these may be used to discover and develop new drugs such as anti-bacterials, anti-carcinogenics and anti-virals. Precisely for those reasons, this revision is centered on the known biological activities in various sea urchin species. Recently, the potential pharmacological benefits of nine sea urchin species [Diadema antillarum (Philippi 1845), Echinometra mathaei (de Blainville), Evechinus chloroticus (Valenciennes), Mesocentrotus nudus (Agassiz, 1863), Paracentrotus lividus (Lamarck, 1816), Scaphechinus mirabilis (Agazzis, 1863), Stomopneustes variolaris (Lamarck, 1816), Tripneustes depressus (Agassiz, 1863), and Tripneustes ventricosus (Lamarck, 1816)] have been evaluated. Our work includes a comprehensive review of the anti-fungal, anti-parasitic, anti-inflammatory, hepatoprotective, anti-viral, anti-diabetic, anti-lipidemic, gastro-protective and anti-cardiotoxic effects. Furthermore, we revised the compounds responsible of these pharmacological effects. This work was intended for a broad readership in the fields of pharmacology, drugs and devices, marine biology and aquaculture, fisheries and fish science. Our results suggest that organic extracts, as well as pure compounds obtained from several parts of sea urchin bodies are effective in vitro and in vivo pharmacological models. As such, these properties manifest the potential use of sea urchins to develop emergent active ingredients.
bibliographic citation: Moreno-García et al. (2022) Sea urchins: an update on their pharmacological properties. PeerJ 10:e13606 https://doi.org/10.7717/peerj.13606
date submitted: 2021-12-06
date accepted: 2022-05-26
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Moreno-García
  given name: Dulce María
author list: Agent
  family name: Salas-Rojas
  given name: Monica
author list: Agent
  family name: Fernández-Martínez
  given name: Eduardo
author list: Agent
  family name: López-Cuellar
  given name: Ma del Rocío
author list: Agent
  family name: Sosa-Gutierrez
  given name: Carolina G.
author list: Agent
  family name: Peláez-Acero
  given name: Armando
author list: Agent
  family name: Rivero-Perez
  given name: Nallely
author list: Agent
  family name: Zaragoza-Bastida
  given name: Adrian
author list: Agent
  family name: Ojeda-Ramírez
  given name: Deyanira
doi: 10.7717/peerj.13606
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Moreno-García et al.
attribution name: Moreno-García et al.

The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species
type: item
type: AcademicArticle
description: Background Ice-free areas in the Antarctic region are strongly limited. The presence of marine mammals and birds in those areas influence soil properties and vegetation composition. Studies on the terrestrial diatom flora in soils influenced by sea birds in the Maritime Antarctic region are scarce. Methods Samples were collected from two transects on the western shore of the Admiralty Bay region. Light and scanning electron microscopic observations and statistical analyses were conducted to consider the impact of penguin rookeries on soil diatom assemblages. Results The disturbance associated with the presence of penguin rookeries clearly influences the soil diatom diversity. Assemblages from areas with the highest nutrient input were characterized by a much lower diversity with only few species dominating the flora. One of recorded taxa could not be assigned to any of the known species. Therefore, based on the combination of morphological features analyzed using light and scanning electron microscopes and comparison with similar taxa in the Antarctic region and worldwide, the species is described hereby as new to science–Luticola kaweckae sp.nov. The new species is characteristic for soil habitats with strong penguin influence.
format: application/pdf
format: text/html
creator: Natalia Kochman-Kędziora
creator: Teresa Noga
creator: Maria Olech
creator: Bart Van de Vijver
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Taxonomy
description: doi:10.7717/peerj.13624
publisher: PeerJ Inc.
rights: © 2022 Kochman-Kędziora et al.
abstract: Background Ice-free areas in the Antarctic region are strongly limited. The presence of marine mammals and birds in those areas influence soil properties and vegetation composition. Studies on the terrestrial diatom flora in soils influenced by sea birds in the Maritime Antarctic region are scarce. Methods Samples were collected from two transects on the western shore of the Admiralty Bay region. Light and scanning electron microscopic observations and statistical analyses were conducted to consider the impact of penguin rookeries on soil diatom assemblages. Results The disturbance associated with the presence of penguin rookeries clearly influences the soil diatom diversity. Assemblages from areas with the highest nutrient input were characterized by a much lower diversity with only few species dominating the flora. One of recorded taxa could not be assigned to any of the known species. Therefore, based on the combination of morphological features analyzed using light and scanning electron microscopes and comparison with similar taxa in the Antarctic region and worldwide, the species is described hereby as new to science–Luticola kaweckae sp.nov. The new species is characteristic for soil habitats with strong penguin influence.
bibliographic citation: Kochman-Kędziora et al. (2022) The influence of penguin activity on soil diatom assemblages on King George Island, Antarctica with the description of a new Luticola species. PeerJ 10:e13624 https://doi.org/10.7717/peerj.13624
date submitted: 2022-01-21
date accepted: 2022-06-02
issued: 2022-07-04
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kochman-Kędziora
  given name: Natalia
author list: Agent
  family name: Noga
  given name: Teresa
author list: Agent
  family name: Olech
  given name: Maria
author list: Agent
  family name: Van de Vijver
  given name: Bart
doi: 10.7717/peerj.13624
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-07-04
copyright: © 2022 Kochman-Kędziora et al.
attribution name: Kochman-Kędziora et al.

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