PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex
items: Relationships between parents’ academic backgrounds and incomes and building students’ healthy eating habits
items: Stinging wasps (Hymenoptera: Aculeata), which species have the longest sting?
items: Influence and reliability of lower-limb arterial occlusion pressure at different body positions
items: From in silico to in vitro: a trip to reveal flavonoid binding on the Rattus norvegicus Kir6.1 ATP-sensitive inward rectifier potassium channel
items: From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes
items: Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient
items: Is the future already here? The impact of climate change on the distribution of the eastern coral snake (Micrurus fulvius)
items: Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study
items: Improved quality of life and joint functions in patients with knee rheumatoid arthritis who underwent five portal arthroscopic synovectomy

Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex
type: item
type: AcademicArticle
description: Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S FST = 0.13; SEQ-N FST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentiall…
format: application/pdf
format: text/html
creator: Md Rakeb-Ul Islam
creator: Daniel J. Schmidt
creator: David A. Crook
creator: Jane M. Hughes
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Zoology
description: doi:10.7717/peerj.4654
publisher: PeerJ Inc.
rights: © 2018 Islam et al.
abstract: Freshwater fishes often exhibit high genetic population structure due to the prevalence of dispersal barriers (e.g., waterfalls) whereas population structure in diadromous fishes tends to be weaker and driven by natal homing behaviour and/or isolation by distance. The Australian smelt (Retropinnidae: Retropinna semoni) is a native fish with a broad distribution spanning inland and coastal drainages of south-eastern Australia. Previous studies have demonstrated variability in population genetic structure and movement behaviour (potamodromy, facultative diadromy, estuarine residence) across the southern part of its geographic range. Some of this variability may be explained by the existence of multiple cryptic species. Here, we examined genetic structure of populations towards the northern extent of the species’ distribution, using ten microsatellite loci and sequences of the mitochondrial cyt b gene. We tested the hypothesis that genetic connectivity among rivers should be low due to a lack of dispersal via the marine environment, but high within rivers due to dispersal. We investigated populations corresponding with two putative cryptic species, SEQ-North (SEQ-N), and SEQ-South (SEQ-S) lineages occurring in south east Queensland drainages. These two groups formed monophyletic clades in the mtDNA gene tree and among river phylogeographic structure was also evident within each clade. In agreement with our hypothesis, highly significant overall FST values suggested that both groups exhibit very low dispersal among rivers (SEQ-S FST = 0.13; SEQ-N FST= 0.27). Microsatellite data indicated that connectivity among sites within rivers was also limited, suggesting dispersal may not homogenise populations at the within-river scale. Northern groups in the Australian smelt cryptic species complex exhibit comparatively higher among-river population structure and smaller geographic ranges than southern groups. These properties make northern Australian smelt populations potentiall…
bibliographic citation: Islam et al. (2018) Patterns of genetic structuring at the northern limits of the Australian smelt (Retropinna semoni) cryptic species complex. PeerJ 6:e4654 https://doi.org/10.7717/peerj.4654
date submitted: 2017-09-25
date accepted: 2018-03-31
issued: 2018-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Islam
  given name: Md Rakeb-Ul
author list: Agent
  family name: Schmidt
  given name: Daniel J.
author list: Agent
  family name: Crook
  given name: David A.
author list: Agent
  family name: Hughes
  given name: Jane M.
doi: 10.7717/peerj.4654
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-03
copyright: ©2018 Islam et al.
attribution name: Islam et al.

Relationships between parents’ academic backgrounds and incomes and building students’ healthy eating habits
type: item
type: AcademicArticle
description: Background Building healthy eating habit is essential for all people. School and family are the prime institutions to instill this habit during early age. This study is aimed at understanding the impact of family such as parents’ educations and incomes on building students’ healthy eating habits. Methods A survey on building students’ eating habits was conducted among primary school students of grade 4 (11 years) and 5 (12 years) from Kulim district, Malaysia. Data from 318 respondents were analysed. Descriptive statistics were used to find the present scenario of their knowledge, attitude and practices towards their eating habits while one-way ANOVA and independent sample t-test were used to find the differences between their practices based on students’ gender, parents’ educations and incomes. Results The study finds that the students have a good knowledge of types of healthy food but yet their preferences are towards the unhealthy food. Though the students’ gender and parents’ educations are not found significantly related to students’ knowledge, attitude and practices towards healthy eating habits, parents’ incomes have significant influence on promoting the healthy eating habit. Discussion Findings of this study can be useful to guide parents in healthy food choices and suggest them to be models to their children in building healthy eating habits.
format: application/pdf
format: text/html
creator: Kazi Enamul Hoque
creator: Kazi Fardinul Hoque
creator: Revethy A/P Thanabalan
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.4563
publisher: PeerJ Inc.
rights: © 2018 Hoque et al.
abstract: Background Building healthy eating habit is essential for all people. School and family are the prime institutions to instill this habit during early age. This study is aimed at understanding the impact of family such as parents’ educations and incomes on building students’ healthy eating habits. Methods A survey on building students’ eating habits was conducted among primary school students of grade 4 (11 years) and 5 (12 years) from Kulim district, Malaysia. Data from 318 respondents were analysed. Descriptive statistics were used to find the present scenario of their knowledge, attitude and practices towards their eating habits while one-way ANOVA and independent sample t-test were used to find the differences between their practices based on students’ gender, parents’ educations and incomes. Results The study finds that the students have a good knowledge of types of healthy food but yet their preferences are towards the unhealthy food. Though the students’ gender and parents’ educations are not found significantly related to students’ knowledge, attitude and practices towards healthy eating habits, parents’ incomes have significant influence on promoting the healthy eating habit. Discussion Findings of this study can be useful to guide parents in healthy food choices and suggest them to be models to their children in building healthy eating habits.
bibliographic citation: Hoque et al. (2018) Relationships between parents’ academic backgrounds and incomes and building students’ healthy eating habits. PeerJ 6:e4563 https://doi.org/10.7717/peerj.4563
date submitted: 2017-08-01
date accepted: 2018-03-12
issued: 2018-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hoque
  given name: Kazi Enamul
author list: Agent
  family name: Hoque
  given name: Kazi Fardinul
author list: Agent
  family name: A/P Thanabalan
  given name: Revethy
doi: 10.7717/peerj.4563
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-03
copyright: © 2018 Hoque et al.
attribution name: Hoque et al.

Stinging wasps (Hymenoptera: Aculeata), which species have the longest sting?
type: item
type: AcademicArticle
description: The stings of bees, wasps, and ants are something that catches the attention of anyone that experiences them. While many recent studies have focused on the pain inflicted by the stings of various stinging wasps, bees, or ants (Hymenoptera: Aculeata), little is known about how the length of the sting itself varies between species. Here, we investigate the sting length of a variety of aculeate wasps, and compare that to reported pain and toxicity values. We find that velvet ants (Hymenoptera: Mutillidae) have the longest sting compared to their body size out of any bee, wasp, or ant species. We also find that there is no link between relative sting length and pain; however, we did find an inverse relationship between relative sting length and toxicity with taxa having shorter relative stings being more toxic. While we found a significant relationship between host use and relative sting length, we suggest that the long sting length of the velvet ants is also related to their suite of defenses to avoid predation.
format: application/pdf
format: text/html
creator: Emily A. Sadler
creator: James P. Pitts
creator: Joseph S. Wilson
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.4743
publisher: PeerJ Inc.
rights: © 2018 Sadler et al.
abstract: The stings of bees, wasps, and ants are something that catches the attention of anyone that experiences them. While many recent studies have focused on the pain inflicted by the stings of various stinging wasps, bees, or ants (Hymenoptera: Aculeata), little is known about how the length of the sting itself varies between species. Here, we investigate the sting length of a variety of aculeate wasps, and compare that to reported pain and toxicity values. We find that velvet ants (Hymenoptera: Mutillidae) have the longest sting compared to their body size out of any bee, wasp, or ant species. We also find that there is no link between relative sting length and pain; however, we did find an inverse relationship between relative sting length and toxicity with taxa having shorter relative stings being more toxic. While we found a significant relationship between host use and relative sting length, we suggest that the long sting length of the velvet ants is also related to their suite of defenses to avoid predation.
bibliographic citation: Sadler et al. (2018) Stinging wasps (Hymenoptera: Aculeata), which species have the longest sting?. PeerJ 6:e4743 https://doi.org/10.7717/peerj.4743
date submitted: 2018-03-08
date accepted: 2018-04-19
issued: 2018-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sadler
  given name: Emily A.
author list: Agent
  family name: Pitts
  given name: James P.
author list: Agent
  family name: Wilson
  given name: Joseph S.
doi: 10.7717/peerj.4743
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-02
copyright: © 2018 Sadler et al.
attribution name: Sadler et al.

Influence and reliability of lower-limb arterial occlusion pressure at different body positions
type: item
type: AcademicArticle
description: Background Total arterial occlusive pressure (AOP) is used to prescribe pressures for surgery, blood flow restriction exercise (BFRE) and ischemic preconditioning (IPC). AOP is often measured in a supine position; however, the influence of body position on AOP measurement is unknown and may influence level of occlusion in different positions during BFR and IPC. The aim of this study was therefore to investigate the influence of body position on AOP. Methods Fifty healthy individuals (age = 29 ± 6 y) underwent AOP measurements on the dominant lower-limb in supine, seated and standing positions in a randomised order. AOP was measured automatically using the Delfi Personalised Tourniquet System device, with each measurement separated by 5 min of rest. Results Arterial occlusive pressure was significantly lower in the supine position compared to the seated position (187.00 ± 32.5 vs 204.00 ± 28.5 mmHg, p < 0.001) and standing position (187.00 ± 32.5 vs 241.50 ± 49.3 mmHg, p < 0.001). AOP was significantly higher in the standing position compared to the seated position (241.50 ± 49.3 vs 204.00 ± 28.5 mmHg, p < 0.001). Discussion Arterial occlusive pressure measurement is body position dependent, thus for accurate prescription of occlusion pressure during surgery, BFR and IPC, AOP should be measured in the position intended for subsequent application of occlusion.
format: application/pdf
format: text/html
creator: Luke Hughes
creator: Owen Jeffries
creator: Mark Waldron
creator: Ben Rosenblatt
creator: Conor Gissane
creator: Bruce Paton
creator: Stephen D. Patterson
subject: Anatomy and Physiology
subject: Kinesiology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.4697
publisher: PeerJ Inc.
rights: © 2018 Hughes et al.
abstract: Background Total arterial occlusive pressure (AOP) is used to prescribe pressures for surgery, blood flow restriction exercise (BFRE) and ischemic preconditioning (IPC). AOP is often measured in a supine position; however, the influence of body position on AOP measurement is unknown and may influence level of occlusion in different positions during BFR and IPC. The aim of this study was therefore to investigate the influence of body position on AOP. Methods Fifty healthy individuals (age = 29 ± 6 y) underwent AOP measurements on the dominant lower-limb in supine, seated and standing positions in a randomised order. AOP was measured automatically using the Delfi Personalised Tourniquet System device, with each measurement separated by 5 min of rest. Results Arterial occlusive pressure was significantly lower in the supine position compared to the seated position (187.00 ± 32.5 vs 204.00 ± 28.5 mmHg, p < 0.001) and standing position (187.00 ± 32.5 vs 241.50 ± 49.3 mmHg, p < 0.001). AOP was significantly higher in the standing position compared to the seated position (241.50 ± 49.3 vs 204.00 ± 28.5 mmHg, p < 0.001). Discussion Arterial occlusive pressure measurement is body position dependent, thus for accurate prescription of occlusion pressure during surgery, BFR and IPC, AOP should be measured in the position intended for subsequent application of occlusion.
bibliographic citation: Hughes et al. (2018) Influence and reliability of lower-limb arterial occlusion pressure at different body positions. PeerJ 6:e4697 https://doi.org/10.7717/peerj.4697
date submitted: 2018-02-14
date accepted: 2018-04-12
issued: 2018-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hughes
  given name: Luke
author list: Agent
  family name: Jeffries
  given name: Owen
author list: Agent
  family name: Waldron
  given name: Mark
author list: Agent
  family name: Rosenblatt
  given name: Ben
author list: Agent
  family name: Gissane
  given name: Conor
author list: Agent
  family name: Paton
  given name: Bruce
author list: Agent
  family name: Patterson
  given name: Stephen D.
doi: 10.7717/peerj.4697
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-02
copyright: © 2018 Hughes et al.
attribution name: Hughes et al.

From in silico to in vitro: a trip to reveal flavonoid binding on the Rattus norvegicus Kir6.1 ATP-sensitive inward rectifier potassium channel
type: item
type: AcademicArticle
description: Background ATP-sensitive inward rectifier potassium channels (Kir), are a potassium channel family involved in many physiological processes. KATP dysfunctions are observed in several diseases such as hypoglycaemia, hyperinsulinemia, Prinzmetal angina–like symptoms, cardiovascular diseases. Methods A broader view of the KATP mechanism is needed in order to operate on their regulation, and in this work we clarify the structure of the Rattus norvegicus ATP-sensitive inward rectifier potassium channel 8 (Kir6.1), which has been obtained through a homology modelling procedure. Due to the medical use of flavonoids, a considerable increase in studies on their influence on human health has recently been observed, therefore our aim is to study, through computational methods, the three-dimensional (3D) conformation together with mechanism of action of Kir6.1 with three flavonoids. Results Computational analysis by performing molecular dynamics (MD) and docking simulation on rat 3D modelled structure have been completed, in its closed and open conformation state and in complex with Quercetin, 5-Hydroxyflavone and Rutin flavonoids. Our study showed that only Quercetin and 5-Hydroxyflavone were responsible for a significant down-regulation of the Kir6.1 activity, stabilising it in a closed conformation. This hypothesis was supported by in vitro experiments demonstrating that Quercetin and 5-Hydroxyflavone were capable to inhibit KATP currents of rat tail main artery myocytes recorded by the patch-clamp technique. Conclusion Combined methodological approaches, such as molecular modelling, docking and MD simulations of Kir6.1 channel, used to elucidate flavonoids intrinsic mechanism of action, are introduced, revealing a new potential druggable protein site.
format: application/pdf
format: text/html
creator: Alfonso Trezza
creator: Vittoria Cicaloni
creator: Piera Porciatti
creator: Andrea Langella
creator: Fabio Fusi
creator: Simona Saponara
creator: Ottavia Spiga
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.4680
publisher: PeerJ Inc.
rights: © 2018 Trezza et al.
abstract: Background ATP-sensitive inward rectifier potassium channels (Kir), are a potassium channel family involved in many physiological processes. KATP dysfunctions are observed in several diseases such as hypoglycaemia, hyperinsulinemia, Prinzmetal angina–like symptoms, cardiovascular diseases. Methods A broader view of the KATP mechanism is needed in order to operate on their regulation, and in this work we clarify the structure of the Rattus norvegicus ATP-sensitive inward rectifier potassium channel 8 (Kir6.1), which has been obtained through a homology modelling procedure. Due to the medical use of flavonoids, a considerable increase in studies on their influence on human health has recently been observed, therefore our aim is to study, through computational methods, the three-dimensional (3D) conformation together with mechanism of action of Kir6.1 with three flavonoids. Results Computational analysis by performing molecular dynamics (MD) and docking simulation on rat 3D modelled structure have been completed, in its closed and open conformation state and in complex with Quercetin, 5-Hydroxyflavone and Rutin flavonoids. Our study showed that only Quercetin and 5-Hydroxyflavone were responsible for a significant down-regulation of the Kir6.1 activity, stabilising it in a closed conformation. This hypothesis was supported by in vitro experiments demonstrating that Quercetin and 5-Hydroxyflavone were capable to inhibit KATP currents of rat tail main artery myocytes recorded by the patch-clamp technique. Conclusion Combined methodological approaches, such as molecular modelling, docking and MD simulations of Kir6.1 channel, used to elucidate flavonoids intrinsic mechanism of action, are introduced, revealing a new potential druggable protein site.
bibliographic citation: Trezza et al. (2018) From in silico to in vitro: a trip to reveal flavonoid binding on the Rattus norvegicus Kir6.1 ATP-sensitive inward rectifier potassium channel. PeerJ 6:e4680 https://doi.org/10.7717/peerj.4680
date submitted: 2017-09-21
date accepted: 2018-04-09
issued: 2018-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Trezza
  given name: Alfonso
author list: Agent
  family name: Cicaloni
  given name: Vittoria
author list: Agent
  family name: Porciatti
  given name: Piera
author list: Agent
  family name: Langella
  given name: Andrea
author list: Agent
  family name: Fusi
  given name: Fabio
author list: Agent
  family name: Saponara
  given name: Simona
author list: Agent
  family name: Spiga
  given name: Ottavia
doi: 10.7717/peerj.4680
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-02
copyright: © 2018 Trezza et al.
attribution name: Trezza et al.

From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes
type: item
type: AcademicArticle
description: With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library f…
format: application/pdf
format: text/html
creator: Nadine Havemann
creator: Martin M. Gossner
creator: Lars Hendrich
creator: Jèrôme Morinière
creator: Rolf Niedringhaus
creator: Peter Schäfer
creator: Michael J. Raupach
subject: Biodiversity
subject: Entomology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.4577
publisher: PeerJ Inc.
rights: © 2018 Havemann et al.
abstract: With about 5,000 species worldwide, the Heteroptera or true bugs are the most diverse taxon among the hemimetabolous insects in aquatic and semi-aquatic ecosystems. Species may be found in almost every freshwater environment and have very specific habitat requirements, making them excellent bioindicator organisms for water quality. However, a correct determination by morphology is challenging in many species groups due to high morphological variability and polymorphisms within, but low variability between species. Furthermore, it is very difficult or even impossible to identify the immature life stages or females of some species, e.g., of the corixid genus Sigara. In this study we tested the effectiveness of a DNA barcode library to discriminate species of the Gerromorpha and Nepomorpha of Germany. We analyzed about 700 specimens of 67 species, with 63 species sampled in Germany, covering more than 90% of all recorded species. Our library included various morphological similar taxa, e.g., species within the genera Sigara and Notonecta as well as water striders of the genus Gerris. Fifty-five species (82%) were unambiguously assigned to a single Barcode Index Number (BIN) by their barcode sequences, whereas BIN sharing was observed for 10 species. Furthermore, we found monophyletic lineages for 52 analyzed species. Our data revealed interspecific K2P distances with below 2.2% for 18 species. Intraspecific distances above 2.2% were shown for 11 species. We found evidence for hybridization between various corixid species (Sigara, Callicorixa), but our molecular data also revealed exceptionally high intraspecific distances as a consequence of distinct mitochondrial lineages for Cymatia coleoptrata and the pygmy backswimmer Plea minutissima. Our study clearly demonstrates the usefulness of DNA barcodes for the identification of the aquatic Heteroptera of Germany and adjacent regions. In this context, our data set represents an essential baseline for a reference library f…
bibliographic citation: Havemann et al. (2018) From water striders to water bugs: the molecular diversity of aquatic Heteroptera (Gerromorpha, Nepomorpha) of Germany based on DNA barcodes. PeerJ 6:e4577 https://doi.org/10.7717/peerj.4577
date submitted: 2017-12-07
date accepted: 2018-03-14
issued: 2018-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Havemann
  given name: Nadine
author list: Agent
  family name: Gossner
  given name: Martin M.
author list: Agent
  family name: Hendrich
  given name: Lars
author list: Agent
  family name: Morinière
  given name: Jèrôme
author list: Agent
  family name: Niedringhaus
  given name: Rolf
author list: Agent
  family name: Schäfer
  given name: Peter
author list: Agent
  family name: Raupach
  given name: Michael J.
doi: 10.7717/peerj.4577
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-02
copyright: © 2018 Havemann et al.
attribution name: Havemann et al.

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient
type: item
type: AcademicArticle
description: Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex inter…
format: application/pdf
format: text/html
creator: Angus Angermeyer
creator: Sarah C. Crosby
creator: Julie A. Huber
subject: Ecosystem Science
subject: Microbiology
subject: Biosphere Interactions
subject: Biogeochemistry
description: doi:10.7717/peerj.4735
publisher: PeerJ Inc.
rights: © 2018 Angermeyer et al.
abstract: Dispersal and environmental selection are two of the most important factors that govern the distributions of microbial communities in nature. While dispersal rates are often inferred by measuring the degree to which community similarity diminishes with increasing geographic distance, determining the extent to which environmental selection impacts the distribution of microbes is more complex. To address this knowledge gap, we performed a large reciprocal transplant experiment to simulate the dispersal of US East Coast salt marsh Spartina alterniflora rhizome-associated microbial sediment communities across a latitudinal gradient and determined if any shifts in microbial community composition occurred as a result of the transplantation. Using bacterial 16S rRNA gene sequencing, we did not observe large-scale changes in community composition over a five-month S. alterniflora summer growing season and found that transplanted communities more closely resembled their origin sites than their destination sites. Furthermore, transplanted communities grouped predominantly by region, with two sites from the north and three sites to the south hosting distinct bacterial taxa, suggesting that sediment communities transplanted from north to south tended to retain their northern microbial distributions, and south to north maintained a southern distribution. A small number of potential indicator 16S rRNA gene sequences had distributions that were strongly correlated to both temperature and nitrogen, indicating that some organisms are more sensitive to environmental factors than others. These results provide new insight into the microbial biogeography of salt marsh sediments and suggest that established bacterial communities in frequently-inundated environments may be both highly resistant to invasion and resilient to some environmental shifts. However, the extent to which environmental selection impacts these communities is taxon specific and variable, highlighting the complex inter…
bibliographic citation: Angermeyer et al. (2018) Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient. PeerJ 6:e4735 https://doi.org/10.7717/peerj.4735
date submitted: 2018-02-01
date accepted: 2018-04-19
issued: 2018-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Angermeyer
  given name: Angus
author list: Agent
  family name: Crosby
  given name: Sarah C.
author list: Agent
  family name: Huber
  given name: Julie A.
doi: 10.7717/peerj.4735
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-01
copyright: © 2018 Angermeyer et al.
attribution name: Angermeyer et al.

Is the future already here? The impact of climate change on the distribution of the eastern coral snake (Micrurus fulvius)
type: item
type: AcademicArticle
description: Anthropogenic climate change is a significant global driver of species distribution change. Although many species have undergone range expansion at their poleward limits, data on several taxonomic groups are still lacking. A common method for studying range shifts is using species distribution models to evaluate current, and predict future, distributions. Notably, many sources of ‘current’ climate data used in species distribution modeling use the years 1950–2000 to calculate climatic averages. However, this does not account for recent (post 2000) climate change. This study examines the influence of climate change on the eastern coral snake (Micrurus fulvius). Specifically, we: (1) identified the current range and suitable environment of M. fulvius in the Southeastern United States, (2) investigated the potential impacts of climate change on the distribution of M. fulvius, and (3) evaluated the utility of future models in predicting recent (2001–2015) records. We used the species distribution modeling program Maxent and compared both current (1950–2000) and future (2050) climate conditions. Future climate models showed a shift in the distribution of suitable habitat across a significant portion of the range; however, results also suggest that much of the Southeastern United States will be outside the range of current conditions, suggesting that there may be no-analog environments in the future. Most strikingly, future models were more effective than the current models at predicting recent records, suggesting that range shifts may already be occurring. These results have implications for both M. fulvius and its Batesian mimics. More broadly, we recommend future Maxent studies consider using future climate data along with current data to better estimate the current distribution.
format: application/pdf
format: text/html
creator: Jennifer N. Archis
creator: Christopher Akcali
creator: Bryan L. Stuart
creator: David Kikuchi
creator: Amanda J. Chunco
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Climate Change Biology
description: doi:10.7717/peerj.4647
publisher: PeerJ Inc.
rights: © 2018 Archis et al.
abstract: Anthropogenic climate change is a significant global driver of species distribution change. Although many species have undergone range expansion at their poleward limits, data on several taxonomic groups are still lacking. A common method for studying range shifts is using species distribution models to evaluate current, and predict future, distributions. Notably, many sources of ‘current’ climate data used in species distribution modeling use the years 1950–2000 to calculate climatic averages. However, this does not account for recent (post 2000) climate change. This study examines the influence of climate change on the eastern coral snake (Micrurus fulvius). Specifically, we: (1) identified the current range and suitable environment of M. fulvius in the Southeastern United States, (2) investigated the potential impacts of climate change on the distribution of M. fulvius, and (3) evaluated the utility of future models in predicting recent (2001–2015) records. We used the species distribution modeling program Maxent and compared both current (1950–2000) and future (2050) climate conditions. Future climate models showed a shift in the distribution of suitable habitat across a significant portion of the range; however, results also suggest that much of the Southeastern United States will be outside the range of current conditions, suggesting that there may be no-analog environments in the future. Most strikingly, future models were more effective than the current models at predicting recent records, suggesting that range shifts may already be occurring. These results have implications for both M. fulvius and its Batesian mimics. More broadly, we recommend future Maxent studies consider using future climate data along with current data to better estimate the current distribution.
bibliographic citation: Archis et al. (2018) Is the future already here? The impact of climate change on the distribution of the eastern coral snake (Micrurus fulvius). PeerJ 6:e4647 https://doi.org/10.7717/peerj.4647
date submitted: 2017-06-29
date accepted: 2018-03-30
issued: 2018-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Archis
  given name: Jennifer N.
author list: Agent
  family name: Akcali
  given name: Christopher
author list: Agent
  family name: Stuart
  given name: Bryan L.
author list: Agent
  family name: Kikuchi
  given name: David
author list: Agent
  family name: Chunco
  given name: Amanda J.
doi: 10.7717/peerj.4647
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-01
copyright: ©2018 Archis et al.
attribution name: Archis et al.

Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study
type: item
type: AcademicArticle
description: Background The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking are associated with differences in the oral and gut microbiota, in comparison to non-smoking controls. Methods We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing. Results Tobacco smokers had significantly different bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with a higher relative abundance of Prevotella (P = 0.006) and lowered Bacteroides (P = 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls. Discussion The current pilot data demonstrate that tobacco smoking is associated with signicant differences in the oral and gut microbiome in humans. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted.
format: application/pdf
format: text/html
creator: Christopher J. Stewart
creator: Thomas A. Auchtung
creator: Nadim J. Ajami
creator: Kenia Velasquez
creator: Daniel P. Smith
creator: Richard De La Garza
creator: Ramiro Salas
creator: Joseph F. Petrosino
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.4693
publisher: PeerJ Inc.
rights: © 2018 Stewart et al.
abstract: Background The use of electronic cigarettes (ECs) has increased drastically over the past five years, primarily as an alternative to smoking tobacco cigarettes. However, the adverse effects of acute and long-term use of ECs on the microbiota have not been explored. In this pilot study, we sought to determine if ECs or tobacco smoking are associated with differences in the oral and gut microbiota, in comparison to non-smoking controls. Methods We examined a human cohort consisting of 30 individuals: 10 EC users, 10 tobacco smokers, and 10 controls. We collected cross-sectional fecal, buccal swabs, and saliva samples from each participant. All samples underwent V4 16S rRNA gene sequencing. Results Tobacco smokers had significantly different bacterial profiles in all sample types when compared to controls, and in feces and buccal swabs when compared to EC users. The most significant associations were found in the gut, with a higher relative abundance of Prevotella (P = 0.006) and lowered Bacteroides (P = 0.036) in tobacco smokers. The Shannon diversity was also significantly reduced (P = 0.009) in fecal samples collected from tobacco smokers compared to controls. No significant difference was found in the alpha diversity, beta-diversity or taxonomic relative abundances between EC users and controls. Discussion The current pilot data demonstrate that tobacco smoking is associated with signicant differences in the oral and gut microbiome in humans. However, validation in larger cohorts and greater understanding of the short and long-term impact of EC use on microbiota composition and function is warranted.
bibliographic citation: Stewart et al. (2018) Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study. PeerJ 6:e4693 https://doi.org/10.7717/peerj.4693
date submitted: 2018-03-02
date accepted: 2018-04-10
issued: 2018-04-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Stewart
  given name: Christopher J.
author list: Agent
  family name: Auchtung
  given name: Thomas A.
author list: Agent
  family name: Ajami
  given name: Nadim J.
author list: Agent
  family name: Velasquez
  given name: Kenia
author list: Agent
  family name: Smith
  given name: Daniel P.
author list: Agent
  family name: De La Garza
  given name: Richard
author list: Agent
  family name: Salas
  given name: Ramiro
author list: Agent
  family name: Petrosino
  given name: Joseph F.
doi: 10.7717/peerj.4693
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-04-30
copyright: © 2018 Stewart et al.
attribution name: Stewart et al.

Improved quality of life and joint functions in patients with knee rheumatoid arthritis who underwent five portal arthroscopic synovectomy
type: item
type: AcademicArticle
description: Objectives To evaluate the outcomes of patients with rheumatoid arthritis (RA) of the knee who underwent five portal arthroscopic synovectomy, with or without post-operative negative pressure drainage (NPD). Material and Methods A prospective clinical trial was performed. Patients with class I, II, and III RA of the knee were enrolled. They underwent five portal arthroscopic synovectomy. Post-operatively, they received either NPD (group A) or non-NPD (group B). Health assessment questionnaire (HAQ), disease activity score 28 (DAS 28), and Lysholm knee joint score were evaluated before the operations, and at six weeks, three months, and one year after the operations. Results A total of 36 patients were enrolled into the study, with 63.9% (23) female patients and mean age of 47.2 years old. All of the patients had clinical symptoms (joint swelling, pain, and dysfunction) for at least six months with poor responses to the traditional pharmaceutical therapy. There were 12, 16, and eight patients in class I, II, and III RA groups, respectively (six IA, six IB, eight IIA, eight IIB, four IIIA, and four IIIB). One year after the operation, patients had statistically significant improvements on HAQ, DAS 28, and Lysholm knee joint scores. More improvements were observed in patients with class I diseases. There were no statistically significant differences between group A and B. Conclusion Five portal arthroscopic synovectomy could increase the quality of life, decrease disease activities, and improve joint functions in patients with RA. More benefits were observed in patients with early disease developments. Patients in the NPD group did not show more improvements compared to the patients in the non-NPD group.
format: application/pdf
format: text/html
creator: Wen-Xin Liu
creator: Yao Jiang
creator: Qing-Xiang Hu
creator: Xie-Bo You
subject: Clinical Trials
subject: Immunology
subject: Orthopedics
subject: Rheumatology
description: doi:10.7717/peerj.4727
publisher: PeerJ Inc.
rights: © 2018 Liu et al.
abstract: Objectives To evaluate the outcomes of patients with rheumatoid arthritis (RA) of the knee who underwent five portal arthroscopic synovectomy, with or without post-operative negative pressure drainage (NPD). Material and Methods A prospective clinical trial was performed. Patients with class I, II, and III RA of the knee were enrolled. They underwent five portal arthroscopic synovectomy. Post-operatively, they received either NPD (group A) or non-NPD (group B). Health assessment questionnaire (HAQ), disease activity score 28 (DAS 28), and Lysholm knee joint score were evaluated before the operations, and at six weeks, three months, and one year after the operations. Results A total of 36 patients were enrolled into the study, with 63.9% (23) female patients and mean age of 47.2 years old. All of the patients had clinical symptoms (joint swelling, pain, and dysfunction) for at least six months with poor responses to the traditional pharmaceutical therapy. There were 12, 16, and eight patients in class I, II, and III RA groups, respectively (six IA, six IB, eight IIA, eight IIB, four IIIA, and four IIIB). One year after the operation, patients had statistically significant improvements on HAQ, DAS 28, and Lysholm knee joint scores. More improvements were observed in patients with class I diseases. There were no statistically significant differences between group A and B. Conclusion Five portal arthroscopic synovectomy could increase the quality of life, decrease disease activities, and improve joint functions in patients with RA. More benefits were observed in patients with early disease developments. Patients in the NPD group did not show more improvements compared to the patients in the non-NPD group.
bibliographic citation: Liu et al. (2018) Improved quality of life and joint functions in patients with knee rheumatoid arthritis who underwent five portal arthroscopic synovectomy. PeerJ 6:e4727 https://doi.org/10.7717/peerj.4727
date submitted: 2018-02-14
date accepted: 2018-04-17
issued: 2018-04-30
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Wen-Xin
author list: Agent
  family name: Jiang
  given name: Yao
author list: Agent
  family name: Hu
  given name: Qing-Xiang
author list: Agent
  family name: You
  given name: Xie-Bo
doi: 10.7717/peerj.4727
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-04-30
copyright: © 2018 Liu et al.
attribution name: Liu et al.

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