PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Membrane potential (Vmem) measurements during mesenchymal stem cell (MSC) proliferation and osteogenic differentiation
items: Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4
items: Positive association between epiphytes and competitiveness of the brown algal genus Lobophora against corals
items: Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean
items: Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies
items: Synthesis of silver nanoparticles using a modified Tollens’ method in conjunction with phytochemicals and assessment of their antimicrobial activity
items: Predictors of foot care behaviours in patients with diabetes in Turkey
items: The detailed distribution of T cell subpopulations in immune-stable renal allograft recipients: a single center study
items: Molecular evidence for sex reversal in wild populations of green frogs (Rana clamitans)
items: Tamilokus mabinia, a new, anatomically divergent genus and species of wood-boring bivalve from the Philippines

Membrane potential (Vmem) measurements during mesenchymal stem cell (MSC) proliferation and osteogenic differentiation
type: item
type: AcademicArticle
description: Background Electrochemical signals play an important role in cell communication and behavior. Electrically charged ions transported across cell membranes maintain an electrochemical imbalance that gives rise to bioelectric signaling, called membrane potential or Vmem. Vmem plays a key role in numerous inter- and intracellular functions that regulate cell behaviors like proliferation, differentiation and migration, all playing a critical role in embryonic development, healing, and regeneration. Methods With the goal of analyzing the changes in Vmem during cell proliferation and differentiation, here we used direct current electrical stimulation (EStim) to promote cell proliferation and differentiation and simultaneously tracked the corresponding changes in Vmem in adipose derived mesenchymal stem cells (AT-MSC). Results We found that EStim caused increased AT-MSC proliferation that corresponded to Vmem depolarization and increased osteogenic differentiation that corresponded to Vmem hyperpolarization. Taken together, this shows that Vmem changes associated with EStim induced cell proliferation and differentiation can be accurately tracked during these important cell functions. Using this tool to monitor Vmem changes associated with these important cell behaviors we hope to learn more about how these electrochemical cues regulate cell function with the ultimate goal of developing new EStim based treatments capable of controlling healing and regeneration.
format: application/pdf
format: text/html
creator: Mit Balvantray Bhavsar
creator: Gloria Cato
creator: Alexander Hauschild
creator: Liudmila Leppik
creator: Karla Mychellyne Costa Oliveira
creator: Maria José Eischen-Loges
creator: John Howard Barker
subject: Bioengineering
subject: Cell Biology
subject: Statistics
description: doi:10.7717/peerj.6341
publisher: PeerJ Inc.
rights: © 2019 Bhavsar et al.
abstract: Background Electrochemical signals play an important role in cell communication and behavior. Electrically charged ions transported across cell membranes maintain an electrochemical imbalance that gives rise to bioelectric signaling, called membrane potential or Vmem. Vmem plays a key role in numerous inter- and intracellular functions that regulate cell behaviors like proliferation, differentiation and migration, all playing a critical role in embryonic development, healing, and regeneration. Methods With the goal of analyzing the changes in Vmem during cell proliferation and differentiation, here we used direct current electrical stimulation (EStim) to promote cell proliferation and differentiation and simultaneously tracked the corresponding changes in Vmem in adipose derived mesenchymal stem cells (AT-MSC). Results We found that EStim caused increased AT-MSC proliferation that corresponded to Vmem depolarization and increased osteogenic differentiation that corresponded to Vmem hyperpolarization. Taken together, this shows that Vmem changes associated with EStim induced cell proliferation and differentiation can be accurately tracked during these important cell functions. Using this tool to monitor Vmem changes associated with these important cell behaviors we hope to learn more about how these electrochemical cues regulate cell function with the ultimate goal of developing new EStim based treatments capable of controlling healing and regeneration.
bibliographic citation: Bhavsar et al. (2019) Membrane potential (Vmem) measurements during mesenchymal stem cell (MSC) proliferation and osteogenic differentiation. PeerJ 7:e6341 https://doi.org/10.7717/peerj.6341
date submitted: 2018-10-24
date accepted: 2018-12-22
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bhavsar
  given name: Mit Balvantray
author list: Agent
  family name: Cato
  given name: Gloria
author list: Agent
  family name: Hauschild
  given name: Alexander
author list: Agent
  family name: Leppik
  given name: Liudmila
author list: Agent
  family name: Costa Oliveira
  given name: Karla Mychellyne
author list: Agent
  family name: Eischen-Loges
  given name: Maria José
author list: Agent
  family name: Barker
  given name: John Howard
doi: 10.7717/peerj.6341
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Bhavsar et al.
attribution name: Bhavsar et al.

Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4
type: item
type: AcademicArticle
description: The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
format: application/pdf
format: text/html
creator: Han Ming Gan
creator: Melvin V.L. Lee
creator: Michael A. Savka
subject: Agricultural Science
subject: Genomics
subject: Microbiology
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6366
publisher: PeerJ Inc.
rights: © 2019 Gan et al.
abstract: The reported Agrobacterium radiobacter DSM 30174T genome is highly fragmented, hindering robust comparative genomics and genome-based taxonomic analysis. We re-sequenced the Agrobacterium radiobacter type strain, generating a dramatically improved genome with high contiguity. In addition, we sequenced the genome of Agrobacterium tumefaciens B6T, enabling for the first time, a proper comparative genomics of these contentious Agrobacterium species. We provide concrete evidence that the previously reported Agrobacterium radiobacter type strain genome (Accession Number: ASXY01) is contaminated which explains its abnormally large genome size and fragmented assembly. We propose that Agrobacterium tumefaciens be reclassified as Agrobacterium radiobacter subsp. tumefaciens and that Agrobacterium radiobacter retains it species status with the proposed name of Agrobacterium radiobacter subsp. radiobacter. This proposal is based, first on the high pairwise genome-scale average nucleotide identity supporting the amalgamation of both Agrobacterium radiobacter and Agrobacterium tumefaciens into a single species. Second, maximum likelihood tree construction based on the concatenated alignment of shared genes (core genes) among related strains indicates that Agrobacterium radiobacter NCPPB3001 is sufficiently divergent from Agrobacterium tumefaciens to propose two independent sub-clades. Third, Agrobacterium tumefaciens demonstrates the genomic potential to synthesize the L configuration of fucose in its lipid polysaccharide, fostering its ability to colonize plant cells more effectively than Agrobacterium radiobacter.
bibliographic citation: Gan et al. (2019) Improved genome of Agrobacterium radiobacter type strain provides new taxonomic insight into Agrobacterium genomospecies 4. PeerJ 7:e6366 https://doi.org/10.7717/peerj.6366
date submitted: 2018-10-23
date accepted: 2018-12-20
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Han Ming
author list: Agent
  family name: Lee
  given name: Melvin V.L.
author list: Agent
  family name: Savka
  given name: Michael A.
doi: 10.7717/peerj.6366
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Gan et al.
attribution name: Gan et al.

Positive association between epiphytes and competitiveness of the brown algal genus Lobophora against corals
type: item
type: AcademicArticle
description: Observations of coral–algal competition can provide valuable information about the state of coral reef ecosystems. Here, we report contact rates and apparent competition states for six shallow lagoonal reefs in Fiji. A total of 81.4% of examined coral perimeters were found to be in contact with algae, with turf algae (54.7%) and macroalgae of the genus Lobophora (16.8%) representing the most frequently observed contacts. Turf algae competitiveness was low, with 21.8% of coral–turf contacts being won by the algae (i.e. overgrowth or bleaching of coral tissue). In contrast, Lobophora competitiveness against corals was high, with 62.5% of contacts being won by the alga. The presence of epiphytic algae on Lobophora was associated with significantly greater algal competitiveness against corals, with 75.8% and 21.1% of interactions recorded as algal wins in the presence and absence of epiphytes, respectively. Sedimentation rate, herbivorous fish biomass, and coral colony size did not have a significant effect on Lobophora–coral interactions. This research indicates a novel and important role of epiphytes in driving the outcome of coral–algal contacts.
format: application/pdf
format: text/html
creator: Andreas Eich
creator: Amanda K. Ford
creator: Maggy M. Nugues
creator: Ryan S. McAndrews
creator: Christian Wild
creator: Sebastian C.A. Ferse
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6380
publisher: PeerJ Inc.
rights: © 2019 Eich et al.
abstract: Observations of coral–algal competition can provide valuable information about the state of coral reef ecosystems. Here, we report contact rates and apparent competition states for six shallow lagoonal reefs in Fiji. A total of 81.4% of examined coral perimeters were found to be in contact with algae, with turf algae (54.7%) and macroalgae of the genus Lobophora (16.8%) representing the most frequently observed contacts. Turf algae competitiveness was low, with 21.8% of coral–turf contacts being won by the algae (i.e. overgrowth or bleaching of coral tissue). In contrast, Lobophora competitiveness against corals was high, with 62.5% of contacts being won by the alga. The presence of epiphytic algae on Lobophora was associated with significantly greater algal competitiveness against corals, with 75.8% and 21.1% of interactions recorded as algal wins in the presence and absence of epiphytes, respectively. Sedimentation rate, herbivorous fish biomass, and coral colony size did not have a significant effect on Lobophora–coral interactions. This research indicates a novel and important role of epiphytes in driving the outcome of coral–algal contacts.
bibliographic citation: Eich et al. (2019) Positive association between epiphytes and competitiveness of the brown algal genus Lobophora against corals. PeerJ 7:e6380 https://doi.org/10.7717/peerj.6380
date submitted: 2018-06-15
date accepted: 2018-12-28
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Eich
  given name: Andreas
author list: Agent
  family name: Ford
  given name: Amanda K.
author list: Agent
  family name: Nugues
  given name: Maggy M.
author list: Agent
  family name: McAndrews
  given name: Ryan S.
author list: Agent
  family name: Wild
  given name: Christian
author list: Agent
  family name: Ferse
  given name: Sebastian C.A.
doi: 10.7717/peerj.6380
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Eich et al.
attribution name: Eich et al.

Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean
type: item
type: AcademicArticle
description: Background Understanding the role of communities of arbuscular mycorrhizal fungi (AMF) in agricultural systems is imperative for enhancing crop production. The key variables influencing change in AMF communities are the type of cover crop species or the type of subsequent host crop species. However, how maize and soybean performance is related to the diversity of AMF communities in cover cropping systems remains unclear. We therefore investigated which cover cropping or host identity is the most important factor in shaping AMF community structure in subsequent crop roots using an Illumina Miseq platform amplicon sequencing. Methods In this study, we established three cover crop systems (Italian ryegrass, hairy vetch, and brown mustard) or bare fallow prior to planting maize and soybean as cash crops. After cover cropping, we divided the cover crop experimental plots into two subsequent crop plots (maize and soybean) to understand which cover cropping or host crop identity is an important factor for determining the AMF communities and diversity both in maize and soybeans. Results We found that most of the operational taxonomic units (OTUs) in root samples were common in both maize and soybean, and the proportion of common generalists in this experiment for maize and soybean roots was 79.5% according to the multinomial species classification method (CLAM test). The proportion of OTUs specifically detected in only maize and soybean was 9.6% and 10.8%, respectively. Additionally, the cover cropping noticeably altered the AMF community structure in the maize and soybean roots. However, the differentiation of AMF communities between maize and soybean was not significantly different. Discussion Our results suggest cover cropping prior to planting maize and soybean may be a strong factor for shaping AMF community structure in subsequent maize and soybean roots rather than two host crop identities. Additionally, we could not determine the suitable rotational combination for …
format: application/pdf
format: text/html
creator: Masao Higo
creator: Yuya Tatewaki
creator: Kento Gunji
creator: Akari Kaseda
creator: Katsunori Isobe
subject: Agricultural Science
subject: Ecology
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.6403
publisher: PeerJ Inc.
rights: © 2019 Higo et al.
abstract: Background Understanding the role of communities of arbuscular mycorrhizal fungi (AMF) in agricultural systems is imperative for enhancing crop production. The key variables influencing change in AMF communities are the type of cover crop species or the type of subsequent host crop species. However, how maize and soybean performance is related to the diversity of AMF communities in cover cropping systems remains unclear. We therefore investigated which cover cropping or host identity is the most important factor in shaping AMF community structure in subsequent crop roots using an Illumina Miseq platform amplicon sequencing. Methods In this study, we established three cover crop systems (Italian ryegrass, hairy vetch, and brown mustard) or bare fallow prior to planting maize and soybean as cash crops. After cover cropping, we divided the cover crop experimental plots into two subsequent crop plots (maize and soybean) to understand which cover cropping or host crop identity is an important factor for determining the AMF communities and diversity both in maize and soybeans. Results We found that most of the operational taxonomic units (OTUs) in root samples were common in both maize and soybean, and the proportion of common generalists in this experiment for maize and soybean roots was 79.5% according to the multinomial species classification method (CLAM test). The proportion of OTUs specifically detected in only maize and soybean was 9.6% and 10.8%, respectively. Additionally, the cover cropping noticeably altered the AMF community structure in the maize and soybean roots. However, the differentiation of AMF communities between maize and soybean was not significantly different. Discussion Our results suggest cover cropping prior to planting maize and soybean may be a strong factor for shaping AMF community structure in subsequent maize and soybean roots rather than two host crop identities. Additionally, we could not determine the suitable rotational combination for …
bibliographic citation: Higo et al. (2019) Cover cropping can be a stronger determinant than host crop identity for arbuscular mycorrhizal fungal communities colonizing maize and soybean. PeerJ 7:e6403 https://doi.org/10.7717/peerj.6403
date submitted: 2018-08-24
date accepted: 2019-01-07
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Higo
  given name: Masao
author list: Agent
  family name: Tatewaki
  given name: Yuya
author list: Agent
  family name: Gunji
  given name: Kento
author list: Agent
  family name: Kaseda
  given name: Akari
author list: Agent
  family name: Isobe
  given name: Katsunori
doi: 10.7717/peerj.6403
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Higo et al.
attribution name: Higo et al.

Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies
type: item
type: AcademicArticle
description: Sugarcane-soybean intercropping has been widely used to control disease and improve nutrition in the field. However, the response of the soil microbial community diversity and structure to intercropping is not well understood. Since microbial diversity corresponds to soil quality and plant health, a pot experiment was conducted with sugarcane intercropped with soybean. Rhizosphere soil was collected 40 days after sowing, and MiSeq sequencing was utilized to analyze the soil microbial community diversity and composition. Soil columns were used to assess the influence of intercropping on soil microbial activity (soil respiration and carbon-use efficiency: nitrogen-use efficiency ratio). PICRUSt and FUNGuild analysis were conducted to predict microbial functional profiling. Our results showed that intercropping decreased pH by approximately 8.9% and enhanced the soil organic carbon, dissolved organic carbon, and available nitrogen (N) by 5.5%, 13.4%, and 10.0%, respectively. These changes in physicochemical properties corresponded to increased microbial diversity and shifts in soil microbial communities. Microbial community correlated significantly (p < 0.05) with soil respiration rates and nutrient use efficiency. Furthermore, intercropping influenced microbial functions, such as carbon fixation pathways in prokaryotes, citrate cycle (TCA cycle) of bacteria and wood saprotrophs of fungi. These overrepresented functions might accelerate nutrient conversion and control phytopathogens in soil.
format: application/pdf
format: text/html
creator: Tengxiang Lian
creator: Yinghui Mu
creator: Jian Jin
creator: Qibin Ma
creator: Yanbo Cheng
creator: Zhandong Cai
creator: Hai Nian
subject: Agricultural Science
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.6412
publisher: PeerJ Inc.
rights: © 2019 Lian et al.
abstract: Sugarcane-soybean intercropping has been widely used to control disease and improve nutrition in the field. However, the response of the soil microbial community diversity and structure to intercropping is not well understood. Since microbial diversity corresponds to soil quality and plant health, a pot experiment was conducted with sugarcane intercropped with soybean. Rhizosphere soil was collected 40 days after sowing, and MiSeq sequencing was utilized to analyze the soil microbial community diversity and composition. Soil columns were used to assess the influence of intercropping on soil microbial activity (soil respiration and carbon-use efficiency: nitrogen-use efficiency ratio). PICRUSt and FUNGuild analysis were conducted to predict microbial functional profiling. Our results showed that intercropping decreased pH by approximately 8.9% and enhanced the soil organic carbon, dissolved organic carbon, and available nitrogen (N) by 5.5%, 13.4%, and 10.0%, respectively. These changes in physicochemical properties corresponded to increased microbial diversity and shifts in soil microbial communities. Microbial community correlated significantly (p < 0.05) with soil respiration rates and nutrient use efficiency. Furthermore, intercropping influenced microbial functions, such as carbon fixation pathways in prokaryotes, citrate cycle (TCA cycle) of bacteria and wood saprotrophs of fungi. These overrepresented functions might accelerate nutrient conversion and control phytopathogens in soil.
bibliographic citation: Lian et al. (2019) Impact of intercropping on the coupling between soil microbial community structure, activity, and nutrient-use efficiencies. PeerJ 7:e6412 https://doi.org/10.7717/peerj.6412
date submitted: 2018-08-02
date accepted: 2018-12-31
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lian
  given name: Tengxiang
author list: Agent
  family name: Mu
  given name: Yinghui
author list: Agent
  family name: Jin
  given name: Jian
author list: Agent
  family name: Ma
  given name: Qibin
author list: Agent
  family name: Cheng
  given name: Yanbo
author list: Agent
  family name: Cai
  given name: Zhandong
author list: Agent
  family name: Nian
  given name: Hai
doi: 10.7717/peerj.6412
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Lian et al.
attribution name: Lian et al.

Synthesis of silver nanoparticles using a modified Tollens’ method in conjunction with phytochemicals and assessment of their antimicrobial activity
type: item
type: AcademicArticle
description: Background Silver nanoparticles (AgNPs) have attracted great attention due to their outstanding electrical, optical, magnetic, catalytic, and antimicrobial properties. However, there is a need for alternative production methods that use less toxic precursors and reduce their undesirable by-products. Phyto-extracts from the leaves of olive and rosemary plants can be used as reducing agents and (in conjunction with Tollens’ reagent) can even enhance AgNP antimicrobial activity. Methods Conditions for the proposed hybrid synthesis method were optimized for olive leaf extracts (OLEs) and rosemary leaf extracts (RLEs). The resultant AgNPs were characterized using UV–visible spectroscopy, an environmental scanning electron microscope, and Dynamic Light Scattering analysis. An atomic absorption spectrophotometer was used to measure AgNP concentration. Fourier transform infrared spectroscopy (FTIR) was used to determine the specific functional groups responsible for the reduction of both silver nitrate and capping agents in the leaf extract. Additionally, the antimicrobial properties of the synthesized AgNPs were assessed against Gram-negative bacteria (Escherichia coli and Salmonella enterica) and Gram-positive bacteria (Staphylococcus aureus), by using both the Kirby–Bauer and broth microdilution methods on Mueller–Hinton (MH) agar plates. Results and Discussion A simple, feasible, and rapid method has been successfully developed for silver nanoparticle synthesis by reducing Tollens’ reagent using leaf extracts from olive and rosemary plants (widely available in Jordan). Scanning electron microscopy images showed that the method produces AgNPs with a spherical shape and average core sizes of 45 ± 2 and 38 ± 3 nm for OLE and RLE, respectively. A negative zeta potential (ζ) of −43.15 ± 3.65 mV for OLE-AgNPs and −33.65 ± 2.88mV for RLE-AgNPs proved the stability of silver nanoparticles. FTIR spectra for AgNPs and leaf extracts indicated that the compounds present in the leaf…
format: application/pdf
format: text/html
creator: Muna A. AbuDalo
creator: Ismaeel R. Al-Mheidat
creator: Alham W. Al-Shurafat
creator: Colleen Grinham
creator: Vinka Oyanedel-Craver
subject: Microbiology
subject: Green Chemistry
description: doi:10.7717/peerj.6413
publisher: PeerJ Inc.
rights: © 2019 AbuDalo et al.
abstract: Background Silver nanoparticles (AgNPs) have attracted great attention due to their outstanding electrical, optical, magnetic, catalytic, and antimicrobial properties. However, there is a need for alternative production methods that use less toxic precursors and reduce their undesirable by-products. Phyto-extracts from the leaves of olive and rosemary plants can be used as reducing agents and (in conjunction with Tollens’ reagent) can even enhance AgNP antimicrobial activity. Methods Conditions for the proposed hybrid synthesis method were optimized for olive leaf extracts (OLEs) and rosemary leaf extracts (RLEs). The resultant AgNPs were characterized using UV–visible spectroscopy, an environmental scanning electron microscope, and Dynamic Light Scattering analysis. An atomic absorption spectrophotometer was used to measure AgNP concentration. Fourier transform infrared spectroscopy (FTIR) was used to determine the specific functional groups responsible for the reduction of both silver nitrate and capping agents in the leaf extract. Additionally, the antimicrobial properties of the synthesized AgNPs were assessed against Gram-negative bacteria (Escherichia coli and Salmonella enterica) and Gram-positive bacteria (Staphylococcus aureus), by using both the Kirby–Bauer and broth microdilution methods on Mueller–Hinton (MH) agar plates. Results and Discussion A simple, feasible, and rapid method has been successfully developed for silver nanoparticle synthesis by reducing Tollens’ reagent using leaf extracts from olive and rosemary plants (widely available in Jordan). Scanning electron microscopy images showed that the method produces AgNPs with a spherical shape and average core sizes of 45 ± 2 and 38 ± 3 nm for OLE and RLE, respectively. A negative zeta potential (ζ) of −43.15 ± 3.65 mV for OLE-AgNPs and −33.65 ± 2.88mV for RLE-AgNPs proved the stability of silver nanoparticles. FTIR spectra for AgNPs and leaf extracts indicated that the compounds present in the leaf…
bibliographic citation: AbuDalo et al. (2019) Synthesis of silver nanoparticles using a modified Tollens’ method in conjunction with phytochemicals and assessment of their antimicrobial activity. PeerJ 7:e6413 https://doi.org/10.7717/peerj.6413
date submitted: 2017-12-24
date accepted: 2018-12-30
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: AbuDalo
  given name: Muna A.
author list: Agent
  family name: Al-Mheidat
  given name: Ismaeel R.
author list: Agent
  family name: Al-Shurafat
  given name: Alham W.
author list: Agent
  family name: Grinham
  given name: Colleen
author list: Agent
  family name: Oyanedel-Craver
  given name: Vinka
doi: 10.7717/peerj.6413
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 AbuDalo et al.
attribution name: AbuDalo et al.

Predictors of foot care behaviours in patients with diabetes in Turkey
type: item
type: AcademicArticle
description: Background The management of diabetic foot complications is challenging, time-consuming and costly. Such complications frequently recur, and the feet of individuals with diabetes can be easily infected. The variables that predict foot care behaviours must be identified to improve foot care attitudes and behaviours. Thus, this study aimed to evaluate the predictors of foot care behaviours in individuals with diabetes and the role of these variables. Methods This descriptive and analytic study was carried out between July 2015 and July 2016, and 368 outpatients with diabetes from a public hospital in Turkey were included. The participants had no communication, psychiatric or neurological problems and had been diagnosed with diabetes for at least 1 year. Foot care behaviour was the dependent variable and was evaluated with the foot care behaviour questionnaire. The relationship among foot care behaviours and sociodemographic characteristics, diabetes-related attitudes, disease perception, health beliefs and perceived social support was evaluated. Factors that independently predicted effective foot care behaviours were estimated via a linear regression analysis. Results The foot care behaviour score of the participants was above average (54.8 ± 5.0). Gender (t = −2.38, p = 0.018), history of a foot wound (t = −2.74, p = 0.006), nephropathy (t = 3.13, p = 0.002), duration subscale of the illness perception scores (t = 2.26, p = 0.024) and personal control subscale of the health belief scores (t = −2.07, p = 0.038) were significant predictors of foot care behaviours. These variables, which provided model compatibility, accounted for approximately 22.0% of the total variance of the foot care behaviour score (R = 0.47, R2 = 0.22, F = 5.48, p ≤ 0.001). Discussion Our results show factors that may affect diabetic foot care behaviours. Several of these factors prevent individuals from practising these behaviours. Further studies on the roles of barriers as predictors of foot c…
format: application/pdf
format: text/html
creator: Yasemin Yıldırım Usta
creator: Yurdanur Dikmen
creator: Songül Yorgun
creator: İkbal Berdo
subject: Diabetes and Endocrinology
subject: Nursing
description: doi:10.7717/peerj.6416
publisher: PeerJ Inc.
rights: © 2019 Yıldırım Usta et al.
abstract: Background The management of diabetic foot complications is challenging, time-consuming and costly. Such complications frequently recur, and the feet of individuals with diabetes can be easily infected. The variables that predict foot care behaviours must be identified to improve foot care attitudes and behaviours. Thus, this study aimed to evaluate the predictors of foot care behaviours in individuals with diabetes and the role of these variables. Methods This descriptive and analytic study was carried out between July 2015 and July 2016, and 368 outpatients with diabetes from a public hospital in Turkey were included. The participants had no communication, psychiatric or neurological problems and had been diagnosed with diabetes for at least 1 year. Foot care behaviour was the dependent variable and was evaluated with the foot care behaviour questionnaire. The relationship among foot care behaviours and sociodemographic characteristics, diabetes-related attitudes, disease perception, health beliefs and perceived social support was evaluated. Factors that independently predicted effective foot care behaviours were estimated via a linear regression analysis. Results The foot care behaviour score of the participants was above average (54.8 ± 5.0). Gender (t = −2.38, p = 0.018), history of a foot wound (t = −2.74, p = 0.006), nephropathy (t = 3.13, p = 0.002), duration subscale of the illness perception scores (t = 2.26, p = 0.024) and personal control subscale of the health belief scores (t = −2.07, p = 0.038) were significant predictors of foot care behaviours. These variables, which provided model compatibility, accounted for approximately 22.0% of the total variance of the foot care behaviour score (R = 0.47, R2 = 0.22, F = 5.48, p ≤ 0.001). Discussion Our results show factors that may affect diabetic foot care behaviours. Several of these factors prevent individuals from practising these behaviours. Further studies on the roles of barriers as predictors of foot c…
bibliographic citation: Yıldırım Usta et al. (2019) Predictors of foot care behaviours in patients with diabetes in Turkey. PeerJ 7:e6416 https://doi.org/10.7717/peerj.6416
date submitted: 2018-09-10
date accepted: 2019-01-09
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yıldırım Usta
  given name: Yasemin
author list: Agent
  family name: Dikmen
  given name: Yurdanur
author list: Agent
  family name: Yorgun
  given name: Songül
author list: Agent
  family name: Berdo
  given name: İkbal
doi: 10.7717/peerj.6416
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Yıldırım Usta et al.
attribution name: Yıldırım Usta et al.

The detailed distribution of T cell subpopulations in immune-stable renal allograft recipients: a single center study
type: item
type: AcademicArticle
description: Background Most renal allograft recipients reach a stable immune state (neither rejection nor infection) after transplantation. However, the detailed distribution of overall T lymphocyte subsets in the peripheral blood of these immune-stable renal transplant recipients remains unclear. We aim to identify differences between this stable immune state and a healthy immune state. Methods In total, 103 recipients underwent renal transplantation from 2012 to 2016 and received regular follow-up in our clinic. A total of 88 of these 103 recipients were enrolled in our study according to the inclusion and exclusion criteria. A total of 47 patients were 1 year post-transplantation, and 41 were 5 years post-transplantation. In addition, 41 healthy volunteers were recruited from our physical examination clinic. Detailed T cell subpopulations from the peripheral blood were assessed via flow cytometry. The parental frequency of each subset was calculated and compared among the diverse groups. Results The demographics and baseline characteristics of every group were analyzed. The frequency of total T cells (CD3+) was decreased in the renal allograft recipients. No difference in the variation of the CD4+, CD8+, and activated (HLA-DR+) T cell subsets was noted among the diverse groups. Regarding T cell receptor (TCR) markers, significant reductions were found in the proportion of γδ T cells and their Vδ2 subset in the renal allograft recipients. The proportions of both CD4+ and CD8+ programmed cell death protein (PD) 1+ T cell subsets were increased in the renal allograft recipients. The CD27+CD28+ T cell proportions in both the CD4+ and CD8+ populations were significantly decreased in the allograft recipients, but the opposite results were found for both CD4+ and CD8+ CD27-CD28- T cells. An increased percentage of CD4+ effector memory T cells and a declined fraction of CD8+ central memory T cells were found in the renal allograft recipients. Conclusion Limited differences in genera…
format: application/pdf
format: text/html
creator: Quan Zhuang
creator: Bo Peng
creator: Wei Wei
creator: Hang Gong
creator: Meng Yu
creator: Min Yang
creator: Lian Liu
creator: Yingzi Ming
subject: Immunology
subject: Urology
description: doi:10.7717/peerj.6417
publisher: PeerJ Inc.
rights: © 2019 Zhuang et al.
abstract: Background Most renal allograft recipients reach a stable immune state (neither rejection nor infection) after transplantation. However, the detailed distribution of overall T lymphocyte subsets in the peripheral blood of these immune-stable renal transplant recipients remains unclear. We aim to identify differences between this stable immune state and a healthy immune state. Methods In total, 103 recipients underwent renal transplantation from 2012 to 2016 and received regular follow-up in our clinic. A total of 88 of these 103 recipients were enrolled in our study according to the inclusion and exclusion criteria. A total of 47 patients were 1 year post-transplantation, and 41 were 5 years post-transplantation. In addition, 41 healthy volunteers were recruited from our physical examination clinic. Detailed T cell subpopulations from the peripheral blood were assessed via flow cytometry. The parental frequency of each subset was calculated and compared among the diverse groups. Results The demographics and baseline characteristics of every group were analyzed. The frequency of total T cells (CD3+) was decreased in the renal allograft recipients. No difference in the variation of the CD4+, CD8+, and activated (HLA-DR+) T cell subsets was noted among the diverse groups. Regarding T cell receptor (TCR) markers, significant reductions were found in the proportion of γδ T cells and their Vδ2 subset in the renal allograft recipients. The proportions of both CD4+ and CD8+ programmed cell death protein (PD) 1+ T cell subsets were increased in the renal allograft recipients. The CD27+CD28+ T cell proportions in both the CD4+ and CD8+ populations were significantly decreased in the allograft recipients, but the opposite results were found for both CD4+ and CD8+ CD27-CD28- T cells. An increased percentage of CD4+ effector memory T cells and a declined fraction of CD8+ central memory T cells were found in the renal allograft recipients. Conclusion Limited differences in genera…
bibliographic citation: Zhuang et al. (2019) The detailed distribution of T cell subpopulations in immune-stable renal allograft recipients: a single center study. PeerJ 7:e6417 https://doi.org/10.7717/peerj.6417
date submitted: 2018-08-22
date accepted: 2019-01-09
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhuang
  given name: Quan
author list: Agent
  family name: Peng
  given name: Bo
author list: Agent
  family name: Wei
  given name: Wei
author list: Agent
  family name: Gong
  given name: Hang
author list: Agent
  family name: Yu
  given name: Meng
author list: Agent
  family name: Yang
  given name: Min
author list: Agent
  family name: Liu
  given name: Lian
author list: Agent
  family name: Ming
  given name: Yingzi
doi: 10.7717/peerj.6417
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Zhuang et al.
attribution name: Zhuang et al.

Molecular evidence for sex reversal in wild populations of green frogs (Rana clamitans)
type: item
type: AcademicArticle
description: In vertebrates, sex determination occurs along a continuum from strictly genotypic (GSD), where sex is entirely guided by genes, to strictly environmental (ESD), where rearing conditions, like temperature, determine phenotypic sex. Along this continuum are taxa which have combined genetic and environmental contributions to sex determination (GSD + EE), where some individuals experience environmental effects which cause them to sex reverse and develop their phenotypic sex opposite their genotypic sex. Amphibians are often assumed to be strictly GSD with sex reversal typically considered abnormal. Despite calls to understand the relative natural and anthropogenic causes of amphibian sex reversal, sex reversal has not been closely studied across populations of any wild amphibian, particularly in contrasting environmental conditions. Here, we use sex-linked molecular markers to discover sex reversal in wild populations of green frogs (Rana clamitans) inhabiting ponds in either undeveloped, forested landscapes or in suburban neighborhoods. Our work here begins to suggest that sex reversal may be common within and across green frog populations, occurring in 12 of 16 populations and with frequencies of 2–16% of individuals sampled within populations. Additionally, our results also suggest that intersex phenotypic males and sex reversal are not correlated with each other and are also not correlated with suburban land use. While sex reversal and intersex are often considered aberrant responses to human activities and associated pollution, we found no such associations here. Our data perhaps begin to suggest that, relative to what is often suggested, sex reversal may be a relatively natural process in amphibians. Future research should focus on assessing interactions between genes and the environment to understand the molecular and exogenous basis of sex determination in green frogs and in other amphibians.
format: application/pdf
format: text/html
creator: Max R. Lambert
creator: Tien Tran
creator: Andrzej Kilian
creator: Tariq Ezaz
creator: David K. Skelly
subject: Conservation Biology
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
subject: Ecotoxicology
description: doi:10.7717/peerj.6449
publisher: PeerJ Inc.
rights: © 2019 Lambert et al.
abstract: In vertebrates, sex determination occurs along a continuum from strictly genotypic (GSD), where sex is entirely guided by genes, to strictly environmental (ESD), where rearing conditions, like temperature, determine phenotypic sex. Along this continuum are taxa which have combined genetic and environmental contributions to sex determination (GSD + EE), where some individuals experience environmental effects which cause them to sex reverse and develop their phenotypic sex opposite their genotypic sex. Amphibians are often assumed to be strictly GSD with sex reversal typically considered abnormal. Despite calls to understand the relative natural and anthropogenic causes of amphibian sex reversal, sex reversal has not been closely studied across populations of any wild amphibian, particularly in contrasting environmental conditions. Here, we use sex-linked molecular markers to discover sex reversal in wild populations of green frogs (Rana clamitans) inhabiting ponds in either undeveloped, forested landscapes or in suburban neighborhoods. Our work here begins to suggest that sex reversal may be common within and across green frog populations, occurring in 12 of 16 populations and with frequencies of 2–16% of individuals sampled within populations. Additionally, our results also suggest that intersex phenotypic males and sex reversal are not correlated with each other and are also not correlated with suburban land use. While sex reversal and intersex are often considered aberrant responses to human activities and associated pollution, we found no such associations here. Our data perhaps begin to suggest that, relative to what is often suggested, sex reversal may be a relatively natural process in amphibians. Future research should focus on assessing interactions between genes and the environment to understand the molecular and exogenous basis of sex determination in green frogs and in other amphibians.
bibliographic citation: Lambert et al. (2019) Molecular evidence for sex reversal in wild populations of green frogs (Rana clamitans). PeerJ 7:e6449 https://doi.org/10.7717/peerj.6449
date submitted: 2018-08-28
date accepted: 2019-01-15
issued: 2019-02-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lambert
  given name: Max R.
author list: Agent
  family name: Tran
  given name: Tien
author list: Agent
  family name: Kilian
  given name: Andrzej
author list: Agent
  family name: Ezaz
  given name: Tariq
author list: Agent
  family name: Skelly
  given name: David K.
doi: 10.7717/peerj.6449
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-08
copyright: © 2019 Lambert et al.
attribution name: Lambert et al.

Tamilokus mabinia, a new, anatomically divergent genus and species of wood-boring bivalve from the Philippines
type: item
type: AcademicArticle
description: Here we describe an anatomically divergent wood-boring bivalve belonging to the family Teredinidae. Specimens were collected off the coast of Mabini, Batangas, Philippines, in February 2018, from sunken driftwood at a depth of less than 2 m. A combination of characteristics differentiates these specimens from members of previously named teredinid genera and species. Most notable among these include: an enlarged cephalic hood which extends across the posterior slope of the shell valves and integrates into the posterior adductor muscle; a unique structure, which we term the ‘cephalic collar’, formed by protruding folds of the mantle immediately ventral to the foot and extending past the posterior margin of the valves; a large globular stomach located entirely posterior to the posterior adductor muscle and extending substantially beyond the posterior gape of the valves; an elongate crystalline style and style sac extending from the base of the foot, past the posterior adductor muscle, to the posteriorly located stomach; calcareous pallets distinct from those of described genera; a prominently flared mantle collar which extends midway along the stalk of the pallets; and, separated siphons that bear a pigmented pinstripe pattern with highly elaborate compound papillae on the incurrent siphon aperture. We used Micro-Computed Tomography (Micro-CT) to build a virtual 3D anatomical model of this organism, confirming the spatial arrangement of the structures described above. Phylogenetic analysis of the small (18S) and large (28S) nuclear rRNA gene sequences, place this bivalve within the Teredindae on a branch well differentiated from previously named genera and species. We propose the new genus and species Tamilokus mabinia to accommodate these organisms, raising the total number of genera in this economically and environmentally important family to 17. This study demonstrates the efficacy of Micro-CT for anatomical description of a systematically challenging group of bival…
format: application/pdf
format: text/html
creator: J. Reuben Shipway
creator: Marvin A. Altamia
creator: Gary Rosenberg
creator: Gisela P. Concepcion
creator: Margo G. Haygood
creator: Daniel L. Distel
subject: Biodiversity
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6256
publisher: PeerJ Inc.
rights: © 2019 Shipway et al.
abstract: Here we describe an anatomically divergent wood-boring bivalve belonging to the family Teredinidae. Specimens were collected off the coast of Mabini, Batangas, Philippines, in February 2018, from sunken driftwood at a depth of less than 2 m. A combination of characteristics differentiates these specimens from members of previously named teredinid genera and species. Most notable among these include: an enlarged cephalic hood which extends across the posterior slope of the shell valves and integrates into the posterior adductor muscle; a unique structure, which we term the ‘cephalic collar’, formed by protruding folds of the mantle immediately ventral to the foot and extending past the posterior margin of the valves; a large globular stomach located entirely posterior to the posterior adductor muscle and extending substantially beyond the posterior gape of the valves; an elongate crystalline style and style sac extending from the base of the foot, past the posterior adductor muscle, to the posteriorly located stomach; calcareous pallets distinct from those of described genera; a prominently flared mantle collar which extends midway along the stalk of the pallets; and, separated siphons that bear a pigmented pinstripe pattern with highly elaborate compound papillae on the incurrent siphon aperture. We used Micro-Computed Tomography (Micro-CT) to build a virtual 3D anatomical model of this organism, confirming the spatial arrangement of the structures described above. Phylogenetic analysis of the small (18S) and large (28S) nuclear rRNA gene sequences, place this bivalve within the Teredindae on a branch well differentiated from previously named genera and species. We propose the new genus and species Tamilokus mabinia to accommodate these organisms, raising the total number of genera in this economically and environmentally important family to 17. This study demonstrates the efficacy of Micro-CT for anatomical description of a systematically challenging group of bival…
bibliographic citation: Shipway et al. (2019) Tamilokus mabinia, a new, anatomically divergent genus and species of wood-boring bivalve from the Philippines. PeerJ 7:e6256 https://doi.org/10.7717/peerj.6256
date submitted: 2018-08-15
date accepted: 2018-12-10
issued: 2019-02-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shipway
  given name: J. Reuben
author list: Agent
  family name: Altamia
  given name: Marvin A.
author list: Agent
  family name: Rosenberg
  given name: Gary
author list: Agent
  family name: Concepcion
  given name: Gisela P.
author list: Agent
  family name: Haygood
  given name: Margo G.
author list: Agent
  family name: Distel
  given name: Daniel L.
doi: 10.7717/peerj.6256
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-02-07
copyright: ©2019 Shipway et al.
attribution name: Shipway et al.

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