PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls
items: Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV
items: Lowland tapir distribution and habitat loss in South America
items: An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus)
items: Regional drivers of clutch loss reveal important trade-offs for beach-nesting birds
items: Canopy position has a profound effect on soybean seed composition
items: Tissue and serum samples of patients with papillary thyroid cancer with and without benign background demonstrate different altered expression of proteins
items: Genetic signatures of ecological diversity along an urbanization gradient
items: Comparative cephalopod shell strength and the role of septum morphology on stress distribution
items: Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7

Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls
type: item
type: AcademicArticle
description: Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.
format: application/pdf
format: text/html
creator: Daniel Belstrøm
creator: Rosa R. Jersie-Christensen
creator: David Lyon
creator: Christian Damgaard
creator: Lars J. Jensen
creator: Palle Holmstrup
creator: Jesper V. Olsen
subject: Microbiology
subject: Dentistry
subject: Immunology
description: doi:10.7717/peerj.2433
publisher: PeerJ Inc.
rights: © 2016 Belstrøm et al.
abstract: Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.
bibliographic citation: Belstrøm et al. (2016) Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls. PeerJ 4:e2433 https://doi.org/10.7717/peerj.2433
date submitted: 2016-06-29
date accepted: 2016-08-12
issued: 2016-09-14
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Belstrøm
  given name: Daniel
author list: Agent
  family name: Jersie-Christensen
  given name: Rosa R.
author list: Agent
  family name: Lyon
  given name: David
author list: Agent
  family name: Damgaard
  given name: Christian
author list: Agent
  family name: Jensen
  given name: Lars J.
author list: Agent
  family name: Holmstrup
  given name: Palle
author list: Agent
  family name: Olsen
  given name: Jesper V.
doi: 10.7717/peerj.2433
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-14
copyright: © 2016 Belstrøm et al.
attribution name: Belstrøm et al.

Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV
type: item
type: AcademicArticle
description: Pain burden is high in people living with HIV (PLWH), but the effect of this pain on functionality is equivocal. Resilience, the ability to cope with adversity, may promote adaptation to pain, so we hypothesised that higher resilience would correlate with less pain-related impairment of activity. We recruited 197 black South African PLWH, 99 with chronic pain (CP) and 98 patients without. We measured pain intensity and interference using the Brief Pain Inventory, and resilience using the Resilience Scale. Participants were generally highly resilient. Greater resilience correlated with better health-related quality of life, but not with pain intensity or interference. We also measured physical activity objectively, by actigraphy, in a subset of patients (37 with chronic pain and 31 without chronic pain), who wore accelerometers for two weeks. There was no difference in duration or intensity of activity between those with and without pain, and activity was not associated with resilience. In this sample, pain was not associated with altered physical activity. Resilience did not explain differences in pain intensity or pain interference but was associated with improved quality of life. Financial stresses and the fear of HIV stigma may have driven patients to conceal pain and to suppress its expected impairment of activity.
format: application/pdf
format: text/html
creator: Antonia L. Wadley
creator: Duncan Mitchell
creator: Peter R. Kamerman
subject: Anesthesiology and Pain Management
subject: HIV
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.2464
publisher: PeerJ Inc.
rights: © 2016 Wadley et al.
abstract: Pain burden is high in people living with HIV (PLWH), but the effect of this pain on functionality is equivocal. Resilience, the ability to cope with adversity, may promote adaptation to pain, so we hypothesised that higher resilience would correlate with less pain-related impairment of activity. We recruited 197 black South African PLWH, 99 with chronic pain (CP) and 98 patients without. We measured pain intensity and interference using the Brief Pain Inventory, and resilience using the Resilience Scale. Participants were generally highly resilient. Greater resilience correlated with better health-related quality of life, but not with pain intensity or interference. We also measured physical activity objectively, by actigraphy, in a subset of patients (37 with chronic pain and 31 without chronic pain), who wore accelerometers for two weeks. There was no difference in duration or intensity of activity between those with and without pain, and activity was not associated with resilience. In this sample, pain was not associated with altered physical activity. Resilience did not explain differences in pain intensity or pain interference but was associated with improved quality of life. Financial stresses and the fear of HIV stigma may have driven patients to conceal pain and to suppress its expected impairment of activity.
bibliographic citation: Wadley et al. (2016) Resilience does not explain the dissociation between chronic pain and physical activity in South Africans living with HIV. PeerJ 4:e2464 https://doi.org/10.7717/peerj.2464
date submitted: 2016-05-06
date accepted: 2016-08-19
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wadley
  given name: Antonia L.
author list: Agent
  family name: Mitchell
  given name: Duncan
author list: Agent
  family name: Kamerman
  given name: Peter R.
doi: 10.7717/peerj.2464
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: © 2016 Wadley et al.
attribution name: Wadley et al.

Lowland tapir distribution and habitat loss in South America
type: item
type: AcademicArticle
description: The development of species distribution models (SDMs) can help conservation efforts by generating potential distributions and identifying areas of high environmental suitability for protection. Our study presents a distribution and habitat map for lowland tapir in South America. We also describe the potential habitat suitability of various geographical regions and habitat loss, inside and outside of protected areas network. Two different SDM approaches, MAXENT and ENFA, produced relative different Habitat Suitability Maps for the lowland tapir. While MAXENT was efficient at identifying areas as suitable or unsuitable, it was less efficient (when compared to the results by ENFA) at identifying the gradient of habitat suitability. MAXENT is a more multifaceted technique that establishes more complex relationships between dependent and independent variables. Our results demonstrate that for at least one species, the lowland tapir, the use of a simple consensual approach (average of ENFA and MAXENT models outputs) better reflected its current distribution patterns. The Brazilian ecoregions have the highest habitat loss for the tapir. Cerrado and Atlantic Forest account for nearly half (48.19%) of the total area lost. The Amazon region contains the largest area under protection, and the most extensive remaining habitat for the tapir, but also showed high levels of habitat loss outside protected areas, which increases the importance of support for proper management.
format: application/pdf
format: text/html
creator: Jose Luis Passos Cordeiro
creator: José M.V. Fragoso
creator: Danielle Crawshaw
creator: Luiz Flamarion B. Oliveira
subject: Biodiversity
subject: Biogeography
subject: Conservation Biology
subject: Ecology
description: doi:10.7717/peerj.2456
publisher: PeerJ Inc.
rights: © 2016 Cordeiro et al.
abstract: The development of species distribution models (SDMs) can help conservation efforts by generating potential distributions and identifying areas of high environmental suitability for protection. Our study presents a distribution and habitat map for lowland tapir in South America. We also describe the potential habitat suitability of various geographical regions and habitat loss, inside and outside of protected areas network. Two different SDM approaches, MAXENT and ENFA, produced relative different Habitat Suitability Maps for the lowland tapir. While MAXENT was efficient at identifying areas as suitable or unsuitable, it was less efficient (when compared to the results by ENFA) at identifying the gradient of habitat suitability. MAXENT is a more multifaceted technique that establishes more complex relationships between dependent and independent variables. Our results demonstrate that for at least one species, the lowland tapir, the use of a simple consensual approach (average of ENFA and MAXENT models outputs) better reflected its current distribution patterns. The Brazilian ecoregions have the highest habitat loss for the tapir. Cerrado and Atlantic Forest account for nearly half (48.19%) of the total area lost. The Amazon region contains the largest area under protection, and the most extensive remaining habitat for the tapir, but also showed high levels of habitat loss outside protected areas, which increases the importance of support for proper management.
bibliographic citation: Cordeiro et al. (2016) Lowland tapir distribution and habitat loss in South America. PeerJ 4:e2456 https://doi.org/10.7717/peerj.2456
date submitted: 2015-12-09
date accepted: 2016-08-17
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cordeiro
  given name: Jose Luis Passos
author list: Agent
  family name: Fragoso
  given name: José M.V.
author list: Agent
  family name: Crawshaw
  given name: Danielle
author list: Agent
  family name: Oliveira
  given name: Luiz Flamarion B.
doi: 10.7717/peerj.2456
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Cordeiro et al.
attribution name: Cordeiro et al.

An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus)
type: item
type: AcademicArticle
description: Background African grey parrots (Psittacus erithacus) are kept as pets and are frequently hand-reared. It has been observed that hand-reared African grey parrots may develop behavioral disorders such as feather damaging behavior (FDB). It is well known that chronic stress is involved in behavioral disorders in captive parrots. The main glucocorticoid in birds is corticosterone; its quantification provides information about adrenocortical activity and is considered to be a reliable indicator of stress levels in birds. We analyzed the differences in the excretion of corticosterone metabolites (CM) in the droppings of African grey parrots characterized by: 1. different rearing histories (parent rearing vs. hand rearing); and 2. the presence or absence of FDB in hand-reared parrots. Methods A total of 82 African grey parrots that were kept in captivity were considered. According to breeding methods, three groups of birds were defined: 1. The parent-reared (PR) parrots included birds kept in pairs (n = 30 pairs) with a conspecific partner of the opposite sex. All of these birds were healthy and never showed FDB signs; 2. The healthy hand-reared parrots (H-HR) included pet parrots individually kept, that were hand-reared and did not display any sign of FDB (n = 11, 7 males and 4 females); 3. The FDB hand-reared parrot (FDB-HR) included pet parrots individually kept, that were hand-reared and displayed FDB (n = 11, 7 males and 4 females). Droppings were collected in the morning over three alternating days in autumn 2014 and spring 2015. The CM were determined using a multi-species corticosterone enzyme immunoassay kit. Split-plot repeated-measure ANOVA was used to examine any differences using group, season and group × season as the main factors. Results Different quantities of CM in droppings were found for the three groups. The mean CM value was 587 ng/g in the PR parrots, 494 ng/g in the H-HR parrots and 1,744 ng/g in the FDB-HR parrots, irrespective of the season. The …
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creator: Pierluca Costa
creator: Elisabetta Macchi
creator: Emanuela Valle
creator: Michele De Marco
creator: Daniele M. Nucera
creator: Laura Gasco
creator: Achille Schiavone
subject: Animal Behavior
subject: Veterinary Medicine
description: doi:10.7717/peerj.2462
publisher: PeerJ Inc.
rights: © 2016 Costa et al.
abstract: Background African grey parrots (Psittacus erithacus) are kept as pets and are frequently hand-reared. It has been observed that hand-reared African grey parrots may develop behavioral disorders such as feather damaging behavior (FDB). It is well known that chronic stress is involved in behavioral disorders in captive parrots. The main glucocorticoid in birds is corticosterone; its quantification provides information about adrenocortical activity and is considered to be a reliable indicator of stress levels in birds. We analyzed the differences in the excretion of corticosterone metabolites (CM) in the droppings of African grey parrots characterized by: 1. different rearing histories (parent rearing vs. hand rearing); and 2. the presence or absence of FDB in hand-reared parrots. Methods A total of 82 African grey parrots that were kept in captivity were considered. According to breeding methods, three groups of birds were defined: 1. The parent-reared (PR) parrots included birds kept in pairs (n = 30 pairs) with a conspecific partner of the opposite sex. All of these birds were healthy and never showed FDB signs; 2. The healthy hand-reared parrots (H-HR) included pet parrots individually kept, that were hand-reared and did not display any sign of FDB (n = 11, 7 males and 4 females); 3. The FDB hand-reared parrot (FDB-HR) included pet parrots individually kept, that were hand-reared and displayed FDB (n = 11, 7 males and 4 females). Droppings were collected in the morning over three alternating days in autumn 2014 and spring 2015. The CM were determined using a multi-species corticosterone enzyme immunoassay kit. Split-plot repeated-measure ANOVA was used to examine any differences using group, season and group × season as the main factors. Results Different quantities of CM in droppings were found for the three groups. The mean CM value was 587 ng/g in the PR parrots, 494 ng/g in the H-HR parrots and 1,744 ng/g in the FDB-HR parrots, irrespective of the season. The …
bibliographic citation: Costa et al. (2016) An association between feather damaging behavior and corticosterone metabolite excretion in captive African grey parrots (Psittacus erithacus). PeerJ 4:e2462 https://doi.org/10.7717/peerj.2462
date submitted: 2016-04-20
date accepted: 2016-08-18
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Costa
  given name: Pierluca
author list: Agent
  family name: Macchi
  given name: Elisabetta
author list: Agent
  family name: Valle
  given name: Emanuela
author list: Agent
  family name: De Marco
  given name: Michele
author list: Agent
  family name: Nucera
  given name: Daniele M.
author list: Agent
  family name: Gasco
  given name: Laura
author list: Agent
  family name: Schiavone
  given name: Achille
doi: 10.7717/peerj.2462
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Costa et al.
attribution name: Costa et al.

Regional drivers of clutch loss reveal important trade-offs for beach-nesting birds
type: item
type: AcademicArticle
description: Coastal birds are critical ecosystem constituents on sandy shores, yet are threatened by depressed reproductive success resulting from direct and indirect anthropogenic and natural pressures. Few studies examine clutch fate across the wide range of environments experienced by birds; instead, most focus at the small site scale. We examine survival of model shorebird clutches as an index of true clutch survival at a regional scale (∼200 km), encompassing a variety of geomorphologies, predator communities, and human use regimes in southeast Queensland, Australia. Of the 132 model nests deployed and monitored with cameras, 45 (34%) survived the experimental exposure period. Thirty-five (27%) were lost to flooding, 32 (24%) were depredated, nine (7%) buried by sand, seven (5%) destroyed by people, three (2%) failed by unknown causes, and one (1%) was destroyed by a dog. Clutch fate differed substantially among regions, particularly with respect to losses from flooding and predation. ‘Topographic’ exposure was the main driver of mortality of nests placed close to the drift line near the base of dunes, which were lost to waves (particularly during storms) and to a lesser extent depredation. Predators determined the fate of clutches not lost to waves, with the depredation probability largely influenced by region. Depredation probability declined as nests were backed by higher dunes and were placed closer to vegetation. This study emphasizes the scale at which clutch fate and survival varies within a regional context, the prominence of corvids as egg predators, the significant role of flooding as a source of nest loss, and the multiple trade-offs faced by beach-nesting birds and those that manage them.
format: application/pdf
format: text/html
creator: Brooke Maslo
creator: Thomas A. Schlacher
creator: Michael A. Weston
creator: Chantal M. Huijbers
creator: Chris Anderson
creator: Ben L. Gilby
creator: Andrew D. Olds
creator: Rod M. Connolly
creator: David S. Schoeman
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.2460
publisher: PeerJ Inc.
rights: © 2016 Maslo et al.
abstract: Coastal birds are critical ecosystem constituents on sandy shores, yet are threatened by depressed reproductive success resulting from direct and indirect anthropogenic and natural pressures. Few studies examine clutch fate across the wide range of environments experienced by birds; instead, most focus at the small site scale. We examine survival of model shorebird clutches as an index of true clutch survival at a regional scale (∼200 km), encompassing a variety of geomorphologies, predator communities, and human use regimes in southeast Queensland, Australia. Of the 132 model nests deployed and monitored with cameras, 45 (34%) survived the experimental exposure period. Thirty-five (27%) were lost to flooding, 32 (24%) were depredated, nine (7%) buried by sand, seven (5%) destroyed by people, three (2%) failed by unknown causes, and one (1%) was destroyed by a dog. Clutch fate differed substantially among regions, particularly with respect to losses from flooding and predation. ‘Topographic’ exposure was the main driver of mortality of nests placed close to the drift line near the base of dunes, which were lost to waves (particularly during storms) and to a lesser extent depredation. Predators determined the fate of clutches not lost to waves, with the depredation probability largely influenced by region. Depredation probability declined as nests were backed by higher dunes and were placed closer to vegetation. This study emphasizes the scale at which clutch fate and survival varies within a regional context, the prominence of corvids as egg predators, the significant role of flooding as a source of nest loss, and the multiple trade-offs faced by beach-nesting birds and those that manage them.
bibliographic citation: Maslo et al. (2016) Regional drivers of clutch loss reveal important trade-offs for beach-nesting birds. PeerJ 4:e2460 https://doi.org/10.7717/peerj.2460
date submitted: 2016-05-11
date accepted: 2016-08-18
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Maslo
  given name: Brooke
author list: Agent
  family name: Schlacher
  given name: Thomas A.
author list: Agent
  family name: Weston
  given name: Michael A.
author list: Agent
  family name: Huijbers
  given name: Chantal M.
author list: Agent
  family name: Anderson
  given name: Chris
author list: Agent
  family name: Gilby
  given name: Ben L.
author list: Agent
  family name: Olds
  given name: Andrew D.
author list: Agent
  family name: Connolly
  given name: Rod M.
author list: Agent
  family name: Schoeman
  given name: David S.
doi: 10.7717/peerj.2460
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Maslo et al.
attribution name: Maslo et al.

Canopy position has a profound effect on soybean seed composition
type: item
type: AcademicArticle
description: Although soybean seeds appear homogeneous, their composition (protein, oil and mineral concentrations) can vary significantly with the canopy position where they were produced. In studies with 10 cultivars grown over a 3-yr period, we found that seeds produced at the top of the canopy have higher concentrations of protein but less oil and lower concentrations of minerals such as Mg, Fe, and Cu compared to seeds produced at the bottom of the canopy. Among cultivars, mean protein concentration (average of different positions) correlated positively with mean concentrations of S, Zn and Fe, but not other minerals. Therefore, on a whole plant basis, the uptake and allocation of S, Zn and Fe to seeds correlated with the production and allocation of reduced N to seed protein; however, the reduced N and correlated minerals (S, Zn and Fe) showed different patterns of allocation among node positions. For example, while mean concentrations of protein and Fe correlated positively, the two parameters correlated negatively in terms of variation with canopy position. Altering the microenvironment within the soybean canopy by removing neighboring plants at flowering increased protein concentration in particular at lower node positions and thus altered the node-position gradient in protein (and oil) without altering the distribution of Mg, Fe and Cu, suggesting different underlying control mechanisms. Metabolomic analysis of developing seeds at different positions in the canopy suggests that availability of free asparagine may be a positive determinant of storage protein accumulation in seeds and may explain the increased protein accumulation in seeds produced at the top of the canopy. Our results establish node-position variation in seed constituents and provide a new experimental system to identify genes controlling key aspects of seed composition. In addition, our results provide an unexpected and simple approach to link agronomic practices to improve human nutrition and health i…
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creator: Steven C. Huber
creator: Kunzhi Li
creator: Randall Nelson
creator: Alexander Ulanov
creator: Catherine M. DeMuro
creator: Ivan Baxter
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.2452
publisher: PeerJ Inc.
rights: © 2016 Huber et al.
abstract: Although soybean seeds appear homogeneous, their composition (protein, oil and mineral concentrations) can vary significantly with the canopy position where they were produced. In studies with 10 cultivars grown over a 3-yr period, we found that seeds produced at the top of the canopy have higher concentrations of protein but less oil and lower concentrations of minerals such as Mg, Fe, and Cu compared to seeds produced at the bottom of the canopy. Among cultivars, mean protein concentration (average of different positions) correlated positively with mean concentrations of S, Zn and Fe, but not other minerals. Therefore, on a whole plant basis, the uptake and allocation of S, Zn and Fe to seeds correlated with the production and allocation of reduced N to seed protein; however, the reduced N and correlated minerals (S, Zn and Fe) showed different patterns of allocation among node positions. For example, while mean concentrations of protein and Fe correlated positively, the two parameters correlated negatively in terms of variation with canopy position. Altering the microenvironment within the soybean canopy by removing neighboring plants at flowering increased protein concentration in particular at lower node positions and thus altered the node-position gradient in protein (and oil) without altering the distribution of Mg, Fe and Cu, suggesting different underlying control mechanisms. Metabolomic analysis of developing seeds at different positions in the canopy suggests that availability of free asparagine may be a positive determinant of storage protein accumulation in seeds and may explain the increased protein accumulation in seeds produced at the top of the canopy. Our results establish node-position variation in seed constituents and provide a new experimental system to identify genes controlling key aspects of seed composition. In addition, our results provide an unexpected and simple approach to link agronomic practices to improve human nutrition and health i…
bibliographic citation: Huber et al. (2016) Canopy position has a profound effect on soybean seed composition. PeerJ 4:e2452 https://doi.org/10.7717/peerj.2452
date submitted: 2016-03-30
date accepted: 2016-08-16
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huber
  given name: Steven C.
author list: Agent
  family name: Li
  given name: Kunzhi
author list: Agent
  family name: Nelson
  given name: Randall
author list: Agent
  family name: Ulanov
  given name: Alexander
author list: Agent
  family name: DeMuro
  given name: Catherine M.
author list: Agent
  family name: Baxter
  given name: Ivan
doi: 10.7717/peerj.2452
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Huber et al.
attribution name: Huber et al.

Tissue and serum samples of patients with papillary thyroid cancer with and without benign background demonstrate different altered expression of proteins
type: item
type: AcademicArticle
description: Background Papillary thyroid cancer (PTC) is mainly diagnosed using fine-needle aspiration biopsy. This most common form of well-differentiated thyroid cancer occurs with or without a background of benign thyroid goiter (BTG). Methods In the present study, a gel-based proteomics analysis was performed to analyse the expression of proteins in tissue and serum samples of PTC patients with (PTCb; n = 6) and without a history of BTG (PTCa; n = 8) relative to patients with BTG (n = 20). This was followed by confirmation of the levels of proteins which showed significant altered abundances of more than two-fold difference (p < 0.01) in the tissue and serum samples of the same subjects using ELISA. Results The data of our study showed that PTCa and PTCb distinguish themselves from BTG in the types of tissue and serum proteins of altered abundance. While higher levels of alpha-1 antitrypsin (A1AT) and heat shock 70 kDa protein were associated with PTCa, lower levels of A1AT, protein disulfide isomerase and ubiquitin-conjugating enzyme E2 N seemed apparent in the PTCb. In case of the serum proteins, higher abundances of A1AT and alpha 1-beta glycoprotein were detected in PTCa, while PTCb was associated with enhanced apolipoprotein A-IV and alpha 2-HS glycoprotein (AHSG). The different altered expression of tissue and serum A1AT as well as serum AHSG between PTCa and PTCb patients were also validated by ELISA. Discussion The distinctive altered abundances of the tissue and serum proteins form preliminary indications that PTCa and PTCb are two distinct cancers of the thyroid that are etiologically and mechanistically different although it is currently not possible to rule out that they may also be due other reasons such as the different stages of the malignant disease. These proteins stand to have a potential use as tissue or serum biomarkers to discriminate the three different thyroid neoplasms although this requires further validation in clinically representative populations…
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format: text/html
creator: Mardiaty Iryani Abdullah
creator: Ching Chin Lee
creator: Sarni Mat Junit
creator: Khoon Leong Ng
creator: Onn Haji Hashim
subject: Biochemistry
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.2450
publisher: PeerJ Inc.
rights: © 2016 Abdullah et al.
abstract: Background Papillary thyroid cancer (PTC) is mainly diagnosed using fine-needle aspiration biopsy. This most common form of well-differentiated thyroid cancer occurs with or without a background of benign thyroid goiter (BTG). Methods In the present study, a gel-based proteomics analysis was performed to analyse the expression of proteins in tissue and serum samples of PTC patients with (PTCb; n = 6) and without a history of BTG (PTCa; n = 8) relative to patients with BTG (n = 20). This was followed by confirmation of the levels of proteins which showed significant altered abundances of more than two-fold difference (p < 0.01) in the tissue and serum samples of the same subjects using ELISA. Results The data of our study showed that PTCa and PTCb distinguish themselves from BTG in the types of tissue and serum proteins of altered abundance. While higher levels of alpha-1 antitrypsin (A1AT) and heat shock 70 kDa protein were associated with PTCa, lower levels of A1AT, protein disulfide isomerase and ubiquitin-conjugating enzyme E2 N seemed apparent in the PTCb. In case of the serum proteins, higher abundances of A1AT and alpha 1-beta glycoprotein were detected in PTCa, while PTCb was associated with enhanced apolipoprotein A-IV and alpha 2-HS glycoprotein (AHSG). The different altered expression of tissue and serum A1AT as well as serum AHSG between PTCa and PTCb patients were also validated by ELISA. Discussion The distinctive altered abundances of the tissue and serum proteins form preliminary indications that PTCa and PTCb are two distinct cancers of the thyroid that are etiologically and mechanistically different although it is currently not possible to rule out that they may also be due other reasons such as the different stages of the malignant disease. These proteins stand to have a potential use as tissue or serum biomarkers to discriminate the three different thyroid neoplasms although this requires further validation in clinically representative populations…
bibliographic citation: Abdullah et al. (2016) Tissue and serum samples of patients with papillary thyroid cancer with and without benign background demonstrate different altered expression of proteins. PeerJ 4:e2450 https://doi.org/10.7717/peerj.2450
date submitted: 2016-03-18
date accepted: 2016-08-16
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abdullah
  given name: Mardiaty Iryani
author list: Agent
  family name: Lee
  given name: Ching Chin
author list: Agent
  family name: Mat Junit
  given name: Sarni
author list: Agent
  family name: Ng
  given name: Khoon Leong
author list: Agent
  family name: Hashim
  given name: Onn Haji
doi: 10.7717/peerj.2450
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: © 2016 Abdullah et al.
attribution name: Abdullah et al.

Genetic signatures of ecological diversity along an urbanization gradient
type: item
type: AcademicArticle
description: Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.
format: application/pdf
format: text/html
creator: Ryan P. Kelly
creator: James L. O’Donnell
creator: Natalie C. Lowell
creator: Andrew O. Shelton
creator: Jameal F. Samhouri
creator: Shannon M. Hennessey
creator: Blake E. Feist
creator: Gregory D. Williams
subject: Biodiversity
subject: Biosphere Interactions
subject: Ecology
subject: Environmental Sciences
description: doi:10.7717/peerj.2444
publisher: PeerJ Inc.
rights: © 2016
abstract: Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore marine eelgrass communities and assess the relationship between these ecological communities and the degree of urbanization in the surrounding watershed. Counter to conventional wisdom, we find strongly increasing richness and decreasing beta diversity with greater urbanization, and similar trends in the diversity of life histories with urbanization. We also find evidence that urbanization influences nearshore communities at local (hundreds of meters) rather than regional (tens of km) scales. Given that different survey methods sample different components of an ecosystem, we then discuss the advantages of eDNA—which we use here to detect hundreds of taxa simultaneously—as a complement to traditional ecological sampling, particularly in the context of broad ecological assessments where exhaustive manual sampling is impractical. Genetic data are a powerful means of uncovering human-ecosystem interactions that might otherwise remain hidden; nevertheless, no sampling method reveals the whole of a biological community.
bibliographic citation: Kelly et al. (2016) Genetic signatures of ecological diversity along an urbanization gradient. PeerJ 4:e2444 https://doi.org/10.7717/peerj.2444
date submitted: 2016-07-12
date accepted: 2016-08-13
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Kelly
  given name: Ryan P.
author list: Agent
  family name: O’Donnell
  given name: James L.
author list: Agent
  family name: Lowell
  given name: Natalie C.
author list: Agent
  family name: Shelton
  given name: Andrew O.
author list: Agent
  family name: Samhouri
  given name: Jameal F.
author list: Agent
  family name: Hennessey
  given name: Shannon M.
author list: Agent
  family name: Feist
  given name: Blake E.
author list: Agent
  family name: Williams
  given name: Gregory D.
doi: 10.7717/peerj.2444
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13

Comparative cephalopod shell strength and the role of septum morphology on stress distribution
type: item
type: AcademicArticle
description: The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio u…
format: application/pdf
format: text/html
creator: Robert Lemanis
creator: Stefan Zachow
creator: René Hoffmann
subject: Computational Biology
subject: Marine Biology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.2434
publisher: PeerJ Inc.
rights: © 2016 Lemanis et al.
abstract: The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio u…
bibliographic citation: Lemanis et al. (2016) Comparative cephalopod shell strength and the role of septum morphology on stress distribution. PeerJ 4:e2434 https://doi.org/10.7717/peerj.2434
date submitted: 2016-04-07
date accepted: 2016-08-12
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lemanis
  given name: Robert
author list: Agent
  family name: Zachow
  given name: Stefan
author list: Agent
  family name: Hoffmann
  given name: René
doi: 10.7717/peerj.2434
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: ©2016 Lemanis et al.
attribution name: Lemanis et al.

Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7
type: item
type: AcademicArticle
description: Background Shiga toxin-producing Escherichia coli (STEC) is one of the most common and widely distributed foodborne pathogens that has been frequently implicated in gastrointestinal and urinary tract infections. Moreover, high rates of multiple antibiotic-resistant E. coli strains have been reported worldwide. Due to the emergence of antibiotic-resistant strains, bacteriophages are considered an attractive alternative to biocontrol pathogenic bacteria. Characterization is a preliminary step towards designing a phage for biocontrol. Methods In this study, we describe the characterization of a bacteriophage designated phiC119, which can infect and lyse several multidrug-resistant STEC strains and some Salmonella strains. The phage genome was screened to detect the stx-genes using PCR, morphological analysis, host range was determined, and genome sequencing were carried out, as well as an analysis of the cohesive ends and identification of the type of genetic material through enzymatic digestion of the genome. Results Analysis of the bacteriophage particles by transmission electron microscopy showed that it had an icosahedral head and a long tail, characteristic of the family Siphoviridae. The phage exhibits broad host range against multidrug-resistant and highly virulent E. coli isolates. One-step growth experiments revealed that the phiC119 phage presented a large burst size (210 PFU/cell) and a latent period of 20 min. Based on genomic analysis, the phage contains a linear double-stranded DNA genome with a size of 47,319 bp. The phage encodes 75 putative proteins, but lysogeny and virulence genes were not found in the phiC119 genome. Conclusion These results suggest that phage phiC119 may be a good biological control agent. However, further studies are required to ensure its control of STEC and to confirm the safety of phage use.
format: application/pdf
format: text/html
creator: Luis Amarillas
creator: Cristóbal Chaidez
creator: Arturo González-Robles
creator: Yadira Lugo-Melchor
creator: Josefina León-Félix
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.2423
publisher: PeerJ Inc.
rights: © 2016 Amarillas et al.
abstract: Background Shiga toxin-producing Escherichia coli (STEC) is one of the most common and widely distributed foodborne pathogens that has been frequently implicated in gastrointestinal and urinary tract infections. Moreover, high rates of multiple antibiotic-resistant E. coli strains have been reported worldwide. Due to the emergence of antibiotic-resistant strains, bacteriophages are considered an attractive alternative to biocontrol pathogenic bacteria. Characterization is a preliminary step towards designing a phage for biocontrol. Methods In this study, we describe the characterization of a bacteriophage designated phiC119, which can infect and lyse several multidrug-resistant STEC strains and some Salmonella strains. The phage genome was screened to detect the stx-genes using PCR, morphological analysis, host range was determined, and genome sequencing were carried out, as well as an analysis of the cohesive ends and identification of the type of genetic material through enzymatic digestion of the genome. Results Analysis of the bacteriophage particles by transmission electron microscopy showed that it had an icosahedral head and a long tail, characteristic of the family Siphoviridae. The phage exhibits broad host range against multidrug-resistant and highly virulent E. coli isolates. One-step growth experiments revealed that the phiC119 phage presented a large burst size (210 PFU/cell) and a latent period of 20 min. Based on genomic analysis, the phage contains a linear double-stranded DNA genome with a size of 47,319 bp. The phage encodes 75 putative proteins, but lysogeny and virulence genes were not found in the phiC119 genome. Conclusion These results suggest that phage phiC119 may be a good biological control agent. However, further studies are required to ensure its control of STEC and to confirm the safety of phage use.
bibliographic citation: Amarillas et al. (2016) Characterization of novel bacteriophage phiC119 capable of lysing multidrug-resistant Shiga toxin-producing Escherichia coli O157:H7. PeerJ 4:e2423 https://doi.org/10.7717/peerj.2423
date submitted: 2016-04-15
date accepted: 2016-08-09
issued: 2016-09-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amarillas
  given name: Luis
author list: Agent
  family name: Chaidez
  given name: Cristóbal
author list: Agent
  family name: González-Robles
  given name: Arturo
author list: Agent
  family name: Lugo-Melchor
  given name: Yadira
author list: Agent
  family name: León-Félix
  given name: Josefina
doi: 10.7717/peerj.2423
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-09-13
copyright: © 2016 Amarillas et al.
attribution name: Amarillas et al.

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