PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus
items: Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae)
items: Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization
items: Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance
items: Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem
items: Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus (Nelumbo nucifera)
items: Integrating microRNA expression, miRNA-mRNA regulation network and signal pathway: a novel strategy for lung cancer biomarker discovery
items: Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanxi, China
items: Association between IL-1B (-511)/IL-1RN (VNTR) polymorphisms and type 2 diabetes: a systematic review and meta-analysis
items: Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey)

Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus
type: item
type: AcademicArticle
description: Background Infection with Mycobacterium abscessus is usually chronic and is associated with clarithromycin resistance. Increasing drug resistance is a major public-health problem and has led to the search for new antimycobacterial agents. We evaluated the antimycobacterial activity, toxicity, and synergistic effects of several plant secondary metabolites against M. abscessus. Methods Twenty-three compounds were evaluated for antimycobacterial activity against thirty M. abscessus clinical isolates by broth microdilution to determine their minimum inhibitory concentration (MIC) values. Toxicity was evaluated using red and white blood cells (RBCs and WBCs). The compounds were used in combination with clarithromycin to investigate the possibility of synergistic activity. Results Five out of twenty-three compounds (RL008, RL009, RL011, RL012 and RL013) exhibited interesting antimycobacterial activity against M. abscessus, with MIC values ranging from <1 to >128 μg/mL. These extracts did not induce hemolytic effect on RBCs and displayed low toxicity against WBCs. The five least-toxic compounds were tested for synergism with clarithromycin against seven isolates with inducible clarithromycin resistance and seven with acquired clarithromycin resistance. The best synergistic results against these isolates were observed for RL008 and RL009 (8/14 isolates; 57%). Conclusions This study demonstrated antimycobacterial and synergistic activities of pure compounds extracted from medicinal plants against clarithromycin-resistant M. abscessus. This synergistic action, together with clarithromycin, may be effective for treating infections and should be further studied for the development of novel antimicrobial agents.
format: application/pdf
format: text/html
creator: Auttawit Sirichoat
creator: Irin Kham-ngam
creator: Orawee Kaewprasert
creator: Pimjai Ananta
creator: Awat Wisetsai
creator: Ratsami Lekphrom
creator: Kiatichai Faksri
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.12391
publisher: PeerJ Inc.
rights: © 2021 Sirichoat et al.
abstract: Background Infection with Mycobacterium abscessus is usually chronic and is associated with clarithromycin resistance. Increasing drug resistance is a major public-health problem and has led to the search for new antimycobacterial agents. We evaluated the antimycobacterial activity, toxicity, and synergistic effects of several plant secondary metabolites against M. abscessus. Methods Twenty-three compounds were evaluated for antimycobacterial activity against thirty M. abscessus clinical isolates by broth microdilution to determine their minimum inhibitory concentration (MIC) values. Toxicity was evaluated using red and white blood cells (RBCs and WBCs). The compounds were used in combination with clarithromycin to investigate the possibility of synergistic activity. Results Five out of twenty-three compounds (RL008, RL009, RL011, RL012 and RL013) exhibited interesting antimycobacterial activity against M. abscessus, with MIC values ranging from <1 to >128 μg/mL. These extracts did not induce hemolytic effect on RBCs and displayed low toxicity against WBCs. The five least-toxic compounds were tested for synergism with clarithromycin against seven isolates with inducible clarithromycin resistance and seven with acquired clarithromycin resistance. The best synergistic results against these isolates were observed for RL008 and RL009 (8/14 isolates; 57%). Conclusions This study demonstrated antimycobacterial and synergistic activities of pure compounds extracted from medicinal plants against clarithromycin-resistant M. abscessus. This synergistic action, together with clarithromycin, may be effective for treating infections and should be further studied for the development of novel antimicrobial agents.
bibliographic citation: Sirichoat et al. (2021) Assessment of antimycobacterial activities of pure compounds extracted from Thai medicinal plants against clarithromycin-resistant Mycobacterium abscessus. PeerJ 9:e12391 https://doi.org/10.7717/peerj.12391
date submitted: 2021-07-19
date accepted: 2021-10-05
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sirichoat
  given name: Auttawit
author list: Agent
  family name: Kham-ngam
  given name: Irin
author list: Agent
  family name: Kaewprasert
  given name: Orawee
author list: Agent
  family name: Ananta
  given name: Pimjai
author list: Agent
  family name: Wisetsai
  given name: Awat
author list: Agent
  family name: Lekphrom
  given name: Ratsami
author list: Agent
  family name: Faksri
  given name: Kiatichai
doi: 10.7717/peerj.12391
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: © 2021 Sirichoat et al.
attribution name: Sirichoat et al.

Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae)
type: item
type: AcademicArticle
description: Hematological characteristics reflect the health status of animals and their physiological adaptation to the environment. However, few studies focused on the species of Diploderma. In this study, the blood cells and the hematological parameters of Diploderma micangshanensis, a species endemic to China, were examined based on 48 healthy adult (32 males and 16 females). The blood cells and hematological parameters of D. micangshanensis were similar to those of other lizard species. Although the values of erythrocyte morphometric characters and hematological parameters varied between males and females, the differences were only significant in the case of the hematocrit and erythrocyte size, which may allow for higher oxygen availability in males. Hemoglobin, mean corpuscular hemoglobin concentration, and mean corpuscle volume were strongly affected by the snout-vent length and/or body mass, which reflect the physiological adaptation to the oxygen requirement of different individuals. This is the first report of hematological data from a species of Diploderma, and the results will provide data for research on the adaptive evolution and health assessment in this species and other congeners.
format: application/pdf
format: text/html
creator: Yinlong Bai
creator: Guanglu Li
creator: Shuaichao Lin
creator: Jianli Xiong
subject: Biochemistry
subject: Veterinary Medicine
subject: Zoology
subject: Hematology
description: doi:10.7717/peerj.12397
publisher: PeerJ Inc.
rights: © 2021 Bai et al.
abstract: Hematological characteristics reflect the health status of animals and their physiological adaptation to the environment. However, few studies focused on the species of Diploderma. In this study, the blood cells and the hematological parameters of Diploderma micangshanensis, a species endemic to China, were examined based on 48 healthy adult (32 males and 16 females). The blood cells and hematological parameters of D. micangshanensis were similar to those of other lizard species. Although the values of erythrocyte morphometric characters and hematological parameters varied between males and females, the differences were only significant in the case of the hematocrit and erythrocyte size, which may allow for higher oxygen availability in males. Hemoglobin, mean corpuscular hemoglobin concentration, and mean corpuscle volume were strongly affected by the snout-vent length and/or body mass, which reflect the physiological adaptation to the oxygen requirement of different individuals. This is the first report of hematological data from a species of Diploderma, and the results will provide data for research on the adaptive evolution and health assessment in this species and other congeners.
bibliographic citation: Bai et al. (2021) Blood cells and hematological parameters of the mountain dragon, Diploderma micangshanensis (Squamata: Lacertilia: Agamidae). PeerJ 9:e12397 https://doi.org/10.7717/peerj.12397
date submitted: 2021-06-14
date accepted: 2021-10-06
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Yinlong
author list: Agent
  family name: Li
  given name: Guanglu
author list: Agent
  family name: Lin
  given name: Shuaichao
author list: Agent
  family name: Xiong
  given name: Jianli
doi: 10.7717/peerj.12397
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Bai et al.
attribution name: Bai et al.

Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization
type: item
type: AcademicArticle
description: Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridiz…
format: application/pdf
format: text/html
creator: Aaron Liston
creator: Kevin A. Weitemier
creator: Lucas Letelier
creator: János Podani
creator: Yu Zong
creator: Lang Liu
creator: Timothy A. Dickinson
subject: Genomics
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.12418
publisher: PeerJ Inc.
rights: © 2021 Liston et al.
abstract: Background Hawthorn species (Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these groups are subject to disagreement. Gametophytic apomixis and polyploidy are prevalent in the genus, and disagreement concerns whether and how apomictic genotypes should be recognized taxonomically. Recent studies suggest that many polyploids arise from hybridization between members of different infrageneric groups. Methods We used target capture and high throughput sequencing to obtain nucleotide sequences for 257 nuclear loci and nearly complete chloroplast genomes from a sample of hawthorns representing all five currently recognized subgenera. Our sample is structured to include two examples of intersubgeneric hybrids and their putative diploid and tetraploid parents. We queried the alignment of nuclear loci directly for evidence of hybridization, and compared individual gene trees with each other, and with both the maximum likelihood plastome tree and the nuclear concatenated and multilocus coalescent-based trees. Tree comparisons provided a promising, if challenging (because of the number of comparisons involved) method for visualizing variation in tree topology. We found it useful to deploy comparisons based not only on tree-tree distances but also on a metric of tree-tree concordance that uses extrinsic information about the relatedness of the terminals in comparing tree topologies. Results We obtained well-supported phylogenies from plastome sequences and from a minimum of 244 low copy-number nuclear loci. These are consistent with a previous morphology-based subgeneric classification of the genus. Despite the high heterogeneity of individual gene trees, we corroborate earlier evidence for the importance of hybridiz…
bibliographic citation: Liston et al. (2021) Phylogeny of Crataegus (Rosaceae) based on 257 nuclear loci and chloroplast genomes: evaluating the impact of hybridization. PeerJ 9:e12418 https://doi.org/10.7717/peerj.12418
date submitted: 2021-01-04
date accepted: 2021-10-10
issued: 2021-10-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liston
  given name: Aaron
author list: Agent
  family name: Weitemier
  given name: Kevin A.
author list: Agent
  family name: Letelier
  given name: Lucas
author list: Agent
  family name: Podani
  given name: János
author list: Agent
  family name: Zong
  given name: Yu
author list: Agent
  family name: Liu
  given name: Lang
author list: Agent
  family name: Dickinson
  given name: Timothy A.
doi: 10.7717/peerj.12418
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-26
copyright: ©2021 Liston et al.
attribution name: Liston et al.

Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance
type: item
type: AcademicArticle
description: Background Reduced tactile acuity has been observed in several chronic pain conditions and has been proposed as a clinical indicator of somatosensory impairments related to the condition. As some interventions targeting these impairments have resulted in pain reduction, assessing tactile acuity may have significant clinical potential. While two-point discrimination threshold (TPDT) is a popular method of assessing tactile acuity, large measurement error has been observed (impeding responsiveness) and its validity has been questioned. The recently developed semi-automated ‘imprint Tactile Acuity Device’ (iTAD) may improve tactile acuity assessment, but clinimetric properties of its scores (accuracy score, response time and rate correct score) need further examination. Aims Experiment 1: To determine inter-rater reliability and measurement error of TPDT and iTAD assessments. Experiment 2: To determine internal consistencies and floor or ceiling effects of iTAD scores, and investigate effects of age, sex, and anthropometry on performance. Methods Experiment 1: To assess inter-rater reliability (ICC(2,1)) and measurement error (coefficient of variation (CoV)), three assessors each performed TPDT and iTAD assessments at the neck in forty healthy participants. Experiment 2: To assess internal consistency (ICC(2,k)) and floor or ceiling effects (skewness z-scores), one hundred healthy participants performed the iTAD’s localisation and orientation tests. Balanced for sex, participants were equally divided over five age brackets (18–30, 31–40, 41–50, 51–60 and 61–70). Age, sex, body mass index (BMI) and neck surface area were assessed to examine their direct (using multiple linear regression analysis) and indirect (using sequential mediation analysis) relationship with iTAD scores. Results Mean ICC(2,1) was moderate for TPDT (0.70) and moderate-to-good for the various iTAD scores (0.65–0.86). The CoV was 25.3% for TPDT and ranged from 6.1% to 16.5% for iTAD scores. Internal …
format: application/pdf
format: text/html
creator: Nick A. Olthof
creator: Michel W. Coppieters
creator: G Lorimer Moseley
creator: Michele Sterling
creator: Dylan J. Chippindall
creator: Daniel S. Harvie
subject: Anesthesiology and Pain Management
subject: Drugs and Devices
subject: Neurology
description: doi:10.7717/peerj.12192
publisher: PeerJ Inc.
rights: © 2021 Olthof et al.
abstract: Background Reduced tactile acuity has been observed in several chronic pain conditions and has been proposed as a clinical indicator of somatosensory impairments related to the condition. As some interventions targeting these impairments have resulted in pain reduction, assessing tactile acuity may have significant clinical potential. While two-point discrimination threshold (TPDT) is a popular method of assessing tactile acuity, large measurement error has been observed (impeding responsiveness) and its validity has been questioned. The recently developed semi-automated ‘imprint Tactile Acuity Device’ (iTAD) may improve tactile acuity assessment, but clinimetric properties of its scores (accuracy score, response time and rate correct score) need further examination. Aims Experiment 1: To determine inter-rater reliability and measurement error of TPDT and iTAD assessments. Experiment 2: To determine internal consistencies and floor or ceiling effects of iTAD scores, and investigate effects of age, sex, and anthropometry on performance. Methods Experiment 1: To assess inter-rater reliability (ICC(2,1)) and measurement error (coefficient of variation (CoV)), three assessors each performed TPDT and iTAD assessments at the neck in forty healthy participants. Experiment 2: To assess internal consistency (ICC(2,k)) and floor or ceiling effects (skewness z-scores), one hundred healthy participants performed the iTAD’s localisation and orientation tests. Balanced for sex, participants were equally divided over five age brackets (18–30, 31–40, 41–50, 51–60 and 61–70). Age, sex, body mass index (BMI) and neck surface area were assessed to examine their direct (using multiple linear regression analysis) and indirect (using sequential mediation analysis) relationship with iTAD scores. Results Mean ICC(2,1) was moderate for TPDT (0.70) and moderate-to-good for the various iTAD scores (0.65–0.86). The CoV was 25.3% for TPDT and ranged from 6.1% to 16.5% for iTAD scores. Internal …
bibliographic citation: Olthof et al. (2021) Modernising tactile acuity assessment; clinimetrics of semi-automated tests and effects of age, sex and anthropometry on performance. PeerJ 9:e12192 https://doi.org/10.7717/peerj.12192
date submitted: 2021-05-06
date accepted: 2021-08-31
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olthof
  given name: Nick A.
author list: Agent
  family name: Coppieters
  given name: Michel W.
author list: Agent
  family name: Moseley
  given name: G Lorimer
author list: Agent
  family name: Sterling
  given name: Michele
author list: Agent
  family name: Chippindall
  given name: Dylan J.
author list: Agent
  family name: Harvie
  given name: Daniel S.
doi: 10.7717/peerj.12192
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: ©2021 Olthof et al.
attribution name: Olthof et al.

Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem
type: item
type: AcademicArticle
description: This study was carried out during January 2020–December 2020 in a semi-desert ecosystem in southern Sonora, Mexico, to determine the annual and daily variations in water potential and the normalized difference vegetation index (NDVI) of Bursera fagaroides Engl., Monogr. Phan., Parkinsonia aculeata L., Sp. Pl.; Prosopis laevigata (Humb. & Bonpl. ex Willd.), and Atriplex canescens (Pursh) Nutt. Soil electrical conductivity, cation content, and physical characteristics were determined at two depths, and water potential (ψ) was measured in roots, stems, and leaves. The daily leaf ψ was measured every 15 days each month to determine the duration of stress (hours) and the stress intensity (SI). The electrical conductivity determinations classified the soil in the experimental area as strongly saline. A significant difference was noted in electrical conductivity between soil depths. The four studied species showed significant gradients of ψ in their organs. In this soil, all four species remained in a stressed condition for approximately 11 h per day. The mean SI was 27%, and B. fagaroides Engl., Monogr. Phan. showed the lowest value. The four species showed increased NDVI values during the rainy months, with P. laevigata (Humb. & Bonpl. ex Willd.) and Parkinsonia aculeata L., Sp. Pl. showing the highest values. The capacity for ψ decrease under saline conditions identified A. canescens (Pursh) Nutt., B. fagaroides Engl., Monogr. Phan. and P. aculeata L., Sp. Pl. as practical and feasible alternatives for establishment in saline soils in southern Sonora for purposes of soil recovery and reforestation.
format: application/pdf
format: text/html
creator: Hebert Hernán Soto Gonzáles
creator: Ofelda Peñuelas-Rubio
creator: Leandris Argentel-Martínez
creator: Aurelio Leyva Ponce
creator: María Hermelinda Herrera Andrade
creator: Mirza Hasanuzzaman
creator: Jorge González Aguilera
creator: Paulo Eduardo Teodoro
subject: Biodiversity
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.12297
publisher: PeerJ Inc.
rights: © 2021 Soto Gonzáles et al.
abstract: This study was carried out during January 2020–December 2020 in a semi-desert ecosystem in southern Sonora, Mexico, to determine the annual and daily variations in water potential and the normalized difference vegetation index (NDVI) of Bursera fagaroides Engl., Monogr. Phan., Parkinsonia aculeata L., Sp. Pl.; Prosopis laevigata (Humb. & Bonpl. ex Willd.), and Atriplex canescens (Pursh) Nutt. Soil electrical conductivity, cation content, and physical characteristics were determined at two depths, and water potential (ψ) was measured in roots, stems, and leaves. The daily leaf ψ was measured every 15 days each month to determine the duration of stress (hours) and the stress intensity (SI). The electrical conductivity determinations classified the soil in the experimental area as strongly saline. A significant difference was noted in electrical conductivity between soil depths. The four studied species showed significant gradients of ψ in their organs. In this soil, all four species remained in a stressed condition for approximately 11 h per day. The mean SI was 27%, and B. fagaroides Engl., Monogr. Phan. showed the lowest value. The four species showed increased NDVI values during the rainy months, with P. laevigata (Humb. & Bonpl. ex Willd.) and Parkinsonia aculeata L., Sp. Pl. showing the highest values. The capacity for ψ decrease under saline conditions identified A. canescens (Pursh) Nutt., B. fagaroides Engl., Monogr. Phan. and P. aculeata L., Sp. Pl. as practical and feasible alternatives for establishment in saline soils in southern Sonora for purposes of soil recovery and reforestation.
bibliographic citation: Soto Gonzáles et al. (2021) Salinity effects on water potential and the normalized difference vegetation index in four species of a saline semi-arid ecosystem. PeerJ 9:e12297 https://doi.org/10.7717/peerj.12297
date submitted: 2021-04-09
date accepted: 2021-09-21
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Soto Gonzáles
  given name: Hebert Hernán
author list: Agent
  family name: Peñuelas-Rubio
  given name: Ofelda
author list: Agent
  family name: Argentel-Martínez
  given name: Leandris
author list: Agent
  family name: Leyva Ponce
  given name: Aurelio
author list: Agent
  family name: Herrera Andrade
  given name: María Hermelinda
author list: Agent
  family name: Hasanuzzaman
  given name: Mirza
author list: Agent
  family name: González Aguilera
  given name: Jorge
author list: Agent
  family name: Eduardo Teodoro
  given name: Paulo
doi: 10.7717/peerj.12297
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: © 2021 Soto Gonzáles et al.
attribution name: Soto Gonzáles et al.

Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus (Nelumbo nucifera)
type: item
type: AcademicArticle
description: Lotus (Nelumbo nucifera) is a highly recognized flower with high ornamental value. Flower color and flower morphology are two main factors for flower lotus breeding. Petaloidy is a universal phenomenon in lotus flowers. However, the genetic regulation of floral organ petaloidy in lotus remains elusive. In this study, the transcriptomic analysis was performed among three organs, including petal, carpel petaloidy, and carpel in lotus. A total of 1,568 DEGs related to carpel petaloidy were identified. Our study identified one floral homeotic gene encoded by the MADS-box transcription factor, AGAMOUS (AG) as the candidate gene for petaloid in lotus. Meanwhile, a predicted labile boundary in floral organs of N. nucifera was hypothesized. In summary, our results explored the candidate genes related to carpel petaloidy, setting a theoretical basis for the molecular regulation of petaloid phenotype.
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format: text/html
creator: Zhongyuan Lin
creator: Dingding Cao
creator: Rebecca Njeri Damaris
creator: Pingfang Yang
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12322
publisher: PeerJ Inc.
rights: © 2021 Lin et al.
abstract: Lotus (Nelumbo nucifera) is a highly recognized flower with high ornamental value. Flower color and flower morphology are two main factors for flower lotus breeding. Petaloidy is a universal phenomenon in lotus flowers. However, the genetic regulation of floral organ petaloidy in lotus remains elusive. In this study, the transcriptomic analysis was performed among three organs, including petal, carpel petaloidy, and carpel in lotus. A total of 1,568 DEGs related to carpel petaloidy were identified. Our study identified one floral homeotic gene encoded by the MADS-box transcription factor, AGAMOUS (AG) as the candidate gene for petaloid in lotus. Meanwhile, a predicted labile boundary in floral organs of N. nucifera was hypothesized. In summary, our results explored the candidate genes related to carpel petaloidy, setting a theoretical basis for the molecular regulation of petaloid phenotype.
bibliographic citation: Lin et al. (2021) Comparative transcriptomic analysis provides insight into carpel petaloidy in lotus (Nelumbo nucifera). PeerJ 9:e12322 https://doi.org/10.7717/peerj.12322
date submitted: 2021-05-06
date accepted: 2021-09-25
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Zhongyuan
author list: Agent
  family name: Cao
  given name: Dingding
author list: Agent
  family name: Damaris
  given name: Rebecca Njeri
author list: Agent
  family name: Yang
  given name: Pingfang
doi: 10.7717/peerj.12322
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: ©2021 Lin et al.
attribution name: Lin et al.

Integrating microRNA expression, miRNA-mRNA regulation network and signal pathway: a novel strategy for lung cancer biomarker discovery
type: item
type: AcademicArticle
description: Background Since there are inextricably connections among molecules in the biological networks, it would be a more efficient and accurate research strategy to screen microRNA (miRNA) markers combining with miRNA-mRNA regulatory networks. The independent regulation mode is more “fragile” and “influential” than the co-regulation mode. miRNAs can be used as biomarkers if they can independently regulate hub genes with important roles in the PPI network, simultaneously the expression products of the regulated hub genes play important roles in the signaling pathways of related tissue diseases. Methods We collected miRNA expression of non-small cell lung cancer (NSCLC) from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Volcano plot and signal-to-noise ratio (SNR) methods were used to obtain significant differentially expressed (SDE) miRNAs from the TCGA database and GEO database, respectively. A human miRNA-mRNA regulatory network was constructed and the number of genes uniquely targeted (NOG) by a certain miRNA was calculated. The area under the curve (AUC) values were used to screen for clinical sensitivity and specificity. The candidate markers were obtained using the criteria of the top five maximum AUC values and NOG ≥ 3. The protein–protein interaction (PPI) network was constructed and independently regulated hub genes were obtained. Gene Ontology (GO) analysis and KEGG pathway analysis were used to identify genes involved in cancer-related pathways. Finally, the miRNA which can independently regulate a hub gene and the hub gene can participate in an important cancer-related pathway was considered as a biomarker. The AUC values and gene expression profile analysis from two external GEO datasets as well as literature validation were used to verify the screening capability and reliability of this marker. Results Fifteen SDE miRNAs in lung cancer were obtained from the intersection of volcano plot and SNR based on the GEO databa…
format: application/pdf
format: text/html
creator: Renqing Nie
creator: Wenling Niu
creator: Tang Tang
creator: Jin Zhang
creator: Xiaoyi Zhang
subject: Bioinformatics
subject: Molecular Biology
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.12369
publisher: PeerJ Inc.
rights: © 2021 Nie et al.
abstract: Background Since there are inextricably connections among molecules in the biological networks, it would be a more efficient and accurate research strategy to screen microRNA (miRNA) markers combining with miRNA-mRNA regulatory networks. The independent regulation mode is more “fragile” and “influential” than the co-regulation mode. miRNAs can be used as biomarkers if they can independently regulate hub genes with important roles in the PPI network, simultaneously the expression products of the regulated hub genes play important roles in the signaling pathways of related tissue diseases. Methods We collected miRNA expression of non-small cell lung cancer (NSCLC) from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. Volcano plot and signal-to-noise ratio (SNR) methods were used to obtain significant differentially expressed (SDE) miRNAs from the TCGA database and GEO database, respectively. A human miRNA-mRNA regulatory network was constructed and the number of genes uniquely targeted (NOG) by a certain miRNA was calculated. The area under the curve (AUC) values were used to screen for clinical sensitivity and specificity. The candidate markers were obtained using the criteria of the top five maximum AUC values and NOG ≥ 3. The protein–protein interaction (PPI) network was constructed and independently regulated hub genes were obtained. Gene Ontology (GO) analysis and KEGG pathway analysis were used to identify genes involved in cancer-related pathways. Finally, the miRNA which can independently regulate a hub gene and the hub gene can participate in an important cancer-related pathway was considered as a biomarker. The AUC values and gene expression profile analysis from two external GEO datasets as well as literature validation were used to verify the screening capability and reliability of this marker. Results Fifteen SDE miRNAs in lung cancer were obtained from the intersection of volcano plot and SNR based on the GEO databa…
bibliographic citation: Nie et al. (2021) Integrating microRNA expression, miRNA-mRNA regulation network and signal pathway: a novel strategy for lung cancer biomarker discovery. PeerJ 9:e12369 https://doi.org/10.7717/peerj.12369
date submitted: 2021-06-25
date accepted: 2021-10-01
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nie
  given name: Renqing
author list: Agent
  family name: Niu
  given name: Wenling
author list: Agent
  family name: Tang
  given name: Tang
author list: Agent
  family name: Zhang
  given name: Jin
author list: Agent
  family name: Zhang
  given name: Xiaoyi
doi: 10.7717/peerj.12369
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: © 2021 Nie et al.
attribution name: Nie et al.

Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanxi, China
type: item
type: AcademicArticle
description: Objectives We carried out a retrospective study to investigate the drug susceptibility and genetic relationship of clinical Escherichia coli isolates from patients with BSIs in Shanxi, China. Methods E. coli isolates causing BSIs were consecutively collected from June 2019 to March 2020. Antimicrobial susceptibility testing was performed by broth microdilution method. PCR was used to detect antimicrobial resistance genes coding for extended-spectrum β-lactamases (ESBLs), phylogenetic groups and seven housekeeping genes of E. coli. Results A total of 76 E. coli were collected. Antimicrobial susceptibility testing revealed that the top six E. coli resistant antibiotics were ampicillin (90.7%), ciprofloxacin (69.7%), cefazolin (65.7%), levofloxacin (63.1%), ceftriaxone and cefotaxime (56.5%). Among the 76 isolates, 43 produced ESBLs. Molecular analysis showed that CTX-M-14 was the most common ESBLs, followed by CTX-M-15 and CTX-M-55. Phylogenetic group D (42.2%) predominated, followed by group B2 (34.2%), group A (18.4%) and group B1 (5.2%). The most prevalent sequence types (STs) were ST131 (15/76), ST69 (12/76) and ST38 (6/76). Conclusions This study is the first to report the phenotypic and molecular characteristics of E. coli isolated from BSIs in Shanxi, China. Our results indicated a high prevalence of MDR in E. coli strains isolated from BSIs and a serious spread of ESBL genes in Shanxi, especially the epidemiological blaCTX-M. Phylogenetic analysis indicated genetic diversity among E. coli BSIs isolates.
format: application/pdf
format: text/html
creator: Yanjun Zhang
creator: Hairu Wang
creator: Yanfang Li
creator: Yabin Hou
creator: Chonghua Hao
subject: Microbiology
subject: Epidemiology
subject: Hematology
subject: Infectious Diseases
description: doi:10.7717/peerj.12371
publisher: PeerJ Inc.
rights: © 2021 Zhang et al.
abstract: Objectives We carried out a retrospective study to investigate the drug susceptibility and genetic relationship of clinical Escherichia coli isolates from patients with BSIs in Shanxi, China. Methods E. coli isolates causing BSIs were consecutively collected from June 2019 to March 2020. Antimicrobial susceptibility testing was performed by broth microdilution method. PCR was used to detect antimicrobial resistance genes coding for extended-spectrum β-lactamases (ESBLs), phylogenetic groups and seven housekeeping genes of E. coli. Results A total of 76 E. coli were collected. Antimicrobial susceptibility testing revealed that the top six E. coli resistant antibiotics were ampicillin (90.7%), ciprofloxacin (69.7%), cefazolin (65.7%), levofloxacin (63.1%), ceftriaxone and cefotaxime (56.5%). Among the 76 isolates, 43 produced ESBLs. Molecular analysis showed that CTX-M-14 was the most common ESBLs, followed by CTX-M-15 and CTX-M-55. Phylogenetic group D (42.2%) predominated, followed by group B2 (34.2%), group A (18.4%) and group B1 (5.2%). The most prevalent sequence types (STs) were ST131 (15/76), ST69 (12/76) and ST38 (6/76). Conclusions This study is the first to report the phenotypic and molecular characteristics of E. coli isolated from BSIs in Shanxi, China. Our results indicated a high prevalence of MDR in E. coli strains isolated from BSIs and a serious spread of ESBL genes in Shanxi, especially the epidemiological blaCTX-M. Phylogenetic analysis indicated genetic diversity among E. coli BSIs isolates.
bibliographic citation: Zhang et al. (2021) Drug susceptibility and molecular epidemiology of Escherichia coli in bloodstream infections in Shanxi, China. PeerJ 9:e12371 https://doi.org/10.7717/peerj.12371
date submitted: 2021-06-15
date accepted: 2021-10-01
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yanjun
author list: Agent
  family name: Wang
  given name: Hairu
author list: Agent
  family name: Li
  given name: Yanfang
author list: Agent
  family name: Hou
  given name: Yabin
author list: Agent
  family name: Hao
  given name: Chonghua
doi: 10.7717/peerj.12371
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: ©2021 Zhang et al.
attribution name: Zhang et al.

Association between IL-1B (-511)/IL-1RN (VNTR) polymorphisms and type 2 diabetes: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Interleukin-1 (IL-1) plays an essential role in the immune pro-inflammatory process, which is regarded as one of many factors in the development of type 2 diabetes mellitus (T2DM). Several case-control studies have illustrated the association of the IL-1B (-511) (rs16944, Chr 2:112,837,290, C/T Intragenic, Transition Substitution) and IL-1RN (VNTR) (gene for IL-1 receptor antagonist, IL-1RA, 86 bp tandem repeats in intron 2) polymorphisms with T2DM risk. However, the results were inconsistent and inconclusive. We performed a meta-analysis (registry number: CRD42021268494) to assess the association of the IL-1B (-511) and IL-1RN (VNTR) polymorphisms with T2DM risk. Random-effects models were applied to calculate the pooled ORs (odds ratios) and 95% CIs (confidence intervals) to test the strength of the association in the overall group and subgroups stratified by ethnicity, respectively. Between-study heterogeneity and publication bias were evaluated by the Q-test, I2 statistic, Harbord test, and Peters test accordingly. Sensitivity analyses were also performed. A total of 12 publications evaluating the association of IL-1B (-511) and IL-1RN (VNTR) polymorphisms with the risk of T2DM development were included. The meta-analysis showed that IL-1RN (VNTR) was related to the increasing development of T2DM risk in the recessive model (OR = 1.62, 95% CI [1.09–2.42], Phet = 0.377, Pz = 0.018) and in the homozygous model (OR = 2.02, 95% CI [1.07–3.83], Phet = 0.085, Pz = 0.031), and the IL-1RN 2* allele was found a significant association with evaluated T2DM risk in all ethnicities (OR = 2.08, 95% CI [1.43–3.02], Phet < 0.001, Pz < 0.001) and in EA (OR = 2.01, 95% CI [1.53–2.66], Phet = 0.541, Pz < 0.001). Moreover, stratification by ethnicity revealed that IL-1B (-511) was associated with a decreased risk of T2DM in the dominant model (OR=0.76, 95% CI [0.59–0.97], Phet = 0.218, Pz = 0.027) and codominant model (OR = 0.73, 95% CI [0.54–0.99], Phet = 0.141, Pz = 0.040) in the…
format: application/pdf
format: text/html
creator: Juan Jiao
creator: Zhaoping Wang
creator: Yanfei Guo
creator: Jie Liu
creator: Xiuqing Huang
creator: Xiaolin Ni
creator: Danni Gao
creator: Liang Sun
creator: Xiaoquan Zhu
creator: Qi Zhou
creator: Ze Yang
creator: Huiping Yuan
subject: Diabetes and Endocrinology
subject: Epidemiology
subject: Medical Genetics
description: doi:10.7717/peerj.12384
publisher: PeerJ Inc.
rights: © 2021 Jiao et al.
abstract: Interleukin-1 (IL-1) plays an essential role in the immune pro-inflammatory process, which is regarded as one of many factors in the development of type 2 diabetes mellitus (T2DM). Several case-control studies have illustrated the association of the IL-1B (-511) (rs16944, Chr 2:112,837,290, C/T Intragenic, Transition Substitution) and IL-1RN (VNTR) (gene for IL-1 receptor antagonist, IL-1RA, 86 bp tandem repeats in intron 2) polymorphisms with T2DM risk. However, the results were inconsistent and inconclusive. We performed a meta-analysis (registry number: CRD42021268494) to assess the association of the IL-1B (-511) and IL-1RN (VNTR) polymorphisms with T2DM risk. Random-effects models were applied to calculate the pooled ORs (odds ratios) and 95% CIs (confidence intervals) to test the strength of the association in the overall group and subgroups stratified by ethnicity, respectively. Between-study heterogeneity and publication bias were evaluated by the Q-test, I2 statistic, Harbord test, and Peters test accordingly. Sensitivity analyses were also performed. A total of 12 publications evaluating the association of IL-1B (-511) and IL-1RN (VNTR) polymorphisms with the risk of T2DM development were included. The meta-analysis showed that IL-1RN (VNTR) was related to the increasing development of T2DM risk in the recessive model (OR = 1.62, 95% CI [1.09–2.42], Phet = 0.377, Pz = 0.018) and in the homozygous model (OR = 2.02, 95% CI [1.07–3.83], Phet = 0.085, Pz = 0.031), and the IL-1RN 2* allele was found a significant association with evaluated T2DM risk in all ethnicities (OR = 2.08, 95% CI [1.43–3.02], Phet < 0.001, Pz < 0.001) and in EA (OR = 2.01, 95% CI [1.53–2.66], Phet = 0.541, Pz < 0.001). Moreover, stratification by ethnicity revealed that IL-1B (-511) was associated with a decreased risk of T2DM in the dominant model (OR=0.76, 95% CI [0.59–0.97], Phet = 0.218, Pz = 0.027) and codominant model (OR = 0.73, 95% CI [0.54–0.99], Phet = 0.141, Pz = 0.040) in the…
bibliographic citation: Jiao et al. (2021) Association between IL-1B (-511)/IL-1RN (VNTR) polymorphisms and type 2 diabetes: a systematic review and meta-analysis. PeerJ 9:e12384 https://doi.org/10.7717/peerj.12384
date submitted: 2021-07-27
date accepted: 2021-10-04
issued: 2021-10-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiao
  given name: Juan
author list: Agent
  family name: Wang
  given name: Zhaoping
author list: Agent
  family name: Guo
  given name: Yanfei
author list: Agent
  family name: Liu
  given name: Jie
author list: Agent
  family name: Huang
  given name: Xiuqing
author list: Agent
  family name: Ni
  given name: Xiaolin
author list: Agent
  family name: Gao
  given name: Danni
author list: Agent
  family name: Sun
  given name: Liang
author list: Agent
  family name: Zhu
  given name: Xiaoquan
author list: Agent
  family name: Zhou
  given name: Qi
author list: Agent
  family name: Yang
  given name: Ze
author list: Agent
  family name: Yuan
  given name: Huiping
doi: 10.7717/peerj.12384
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-25
copyright: ©2021 Jiao et al.
attribution name: Jiao et al.

Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey)
type: item
type: AcademicArticle
description: In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to Nitzschia aurariae but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that N. anatoliensis may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as Nitzschia communis. It also revealed the very close genetic proximity between N. anatoliensis and the endosymbiont of the dinotom Kryptoperidinium foliaceum, providing additional clues on what might have been the original species of diatoms to enter symbiosis.
format: application/pdf
format: text/html
creator: Cüneyt Nadir Solak
creator: Romain Gastineau
creator: Claude Lemieux
creator: Monique Turmel
creator: Ewa Gorecka
creator: Rosa Trobajo
creator: Mateusz Rybak
creator: Elif Yılmaz
creator: Andrzej Witkowski
subject: Biodiversity
subject: Genomics
subject: Taxonomy
subject: Freshwater Biology
description: doi:10.7717/peerj.12220
publisher: PeerJ Inc.
rights: © 2021 Solak et al.
abstract: In this article we describe Nitzschia anatoliensis Górecka, Gastineau & Solak sp. nov., an example of a diatom species inhabiting extreme habitats. The new species has been isolated and successfully grown from the highly alkaline Van Lake in East Turkey. The description is based on morphology (light and scanning electron microscopy), the sequencing of its organellar genomes and several molecular phylogenies. This species could easily be overlooked because of its extreme similarity to Nitzschia aurariae but molecular phylogenies indicate that they are only distantly related. Furthermore, molecular data suggest that N. anatoliensis may occur in several alkaline lakes of Asia Minor and Siberia, but was previously misidentified as Nitzschia communis. It also revealed the very close genetic proximity between N. anatoliensis and the endosymbiont of the dinotom Kryptoperidinium foliaceum, providing additional clues on what might have been the original species of diatoms to enter symbiosis.
bibliographic citation: Solak et al. (2021) Nitzschia anatoliensis sp. nov., a cryptic diatom species from the highly alkaline Van Lake (Turkey). PeerJ 9:e12220 https://doi.org/10.7717/peerj.12220
date submitted: 2020-08-04
date accepted: 2021-09-06
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Solak
  given name: Cüneyt Nadir
author list: Agent
  family name: Gastineau
  given name: Romain
author list: Agent
  family name: Lemieux
  given name: Claude
author list: Agent
  family name: Turmel
  given name: Monique
author list: Agent
  family name: Gorecka
  given name: Ewa
author list: Agent
  family name: Trobajo
  given name: Rosa
author list: Agent
  family name: Rybak
  given name: Mateusz
author list: Agent
  family name: Yılmaz
  given name: Elif
author list: Agent
  family name: Witkowski
  given name: Andrzej
doi: 10.7717/peerj.12220
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: © 2021 Solak et al.
attribution name: Solak et al.

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