PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Seasonal patterns in nest survival of a subtropical wading bird, the Hawaiian Stilt (Himantopus mexicanus knudseni)
items: Effect of ultra-processed foods consumption on glycemic control and gestational weight gain in pregnant with pregestational diabetes mellitus using carbohydrate counting
items: Night of the hunter: using cameras to quantify nocturnal activity in desert spiders
items: TLR4 promoter rs1927914 variant contributes to the susceptibility of esophageal squamous cell carcinoma in the Chinese population
items: Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere
items: Brown bear communication hubs: patterns and correlates of tree rubbing and pedal marking at a long-term marking site
items: Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study
items: Transcriptome analysis reveals liver metabolism programming in kids from nutritional restricted goats during mid-gestation
items: ATR-FTIR, EDS and SEM evaluations of enamel structure after treatment with hydrogen peroxide bleaching agents loaded with nano-hydroxyapatite particles
items: Dynamics of locomotion in the seed harvesting ant Messor barbarus: effect of individual body mass and transported load mass

Seasonal patterns in nest survival of a subtropical wading bird, the Hawaiian Stilt (Himantopus mexicanus knudseni)
type: item
type: AcademicArticle
description: Nest survival is influenced by where and when birds decide to breed. For ground-nesting species, nest-site characteristics, such as vegetation height and proximity to water, may impact the likelihood of nest flooding or depredation. Further, habitat characteristics, and thus nest survival, may fluctuate across the breeding season. The Hawaiian Stilt (‘Ae‘o; Himantopus mexicanus knudseni) is an endangered Hawaiian waterbird that nests in wetlands across the Hawaiian Islands. In this study, we used observational surveys and nest cameras to examine the impact of nest-site characteristics and day of nesting season on nest survival of the Hawaiian Stilt. Early nests had a higher chance of survival than late nests. For most of the nesting season, taller vegetation was correlated with increased nest survival, while shorter vegetation was correlated with increased nest survival late in the nesting season. Seasonal patterns in nest survival may be due to changes in parental behavior or predator activity. Nest depredation was responsible for 55% of confirmed nest failures and introduced mammals were the primary nest predators. Our study is the first to examine seasonality in nest survival of Hawaiian Stilts and suggests that, despite longer nesting seasons and year-round occupation of wetlands, late nesters in subtropical regions may have lower nest survival than early nesters, similar to trends observed in temperate regions.
format: application/pdf
format: text/html
creator: Kristen C. Harmon
creator: Nathaniel H. Wehr
creator: Melissa R. Price
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.10399
publisher: PeerJ Inc.
rights: © 2021 Harmon et al.
abstract: Nest survival is influenced by where and when birds decide to breed. For ground-nesting species, nest-site characteristics, such as vegetation height and proximity to water, may impact the likelihood of nest flooding or depredation. Further, habitat characteristics, and thus nest survival, may fluctuate across the breeding season. The Hawaiian Stilt (‘Ae‘o; Himantopus mexicanus knudseni) is an endangered Hawaiian waterbird that nests in wetlands across the Hawaiian Islands. In this study, we used observational surveys and nest cameras to examine the impact of nest-site characteristics and day of nesting season on nest survival of the Hawaiian Stilt. Early nests had a higher chance of survival than late nests. For most of the nesting season, taller vegetation was correlated with increased nest survival, while shorter vegetation was correlated with increased nest survival late in the nesting season. Seasonal patterns in nest survival may be due to changes in parental behavior or predator activity. Nest depredation was responsible for 55% of confirmed nest failures and introduced mammals were the primary nest predators. Our study is the first to examine seasonality in nest survival of Hawaiian Stilts and suggests that, despite longer nesting seasons and year-round occupation of wetlands, late nesters in subtropical regions may have lower nest survival than early nesters, similar to trends observed in temperate regions.
bibliographic citation: Harmon et al. (2021) Seasonal patterns in nest survival of a subtropical wading bird, the Hawaiian Stilt (Himantopus mexicanus knudseni). PeerJ 9:e10399 https://doi.org/10.7717/peerj.10399
date submitted: 2020-04-30
date accepted: 2020-10-29
issued: 2021-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Harmon
  given name: Kristen C.
author list: Agent
  family name: Wehr
  given name: Nathaniel H.
author list: Agent
  family name: Price
  given name: Melissa R.
doi: 10.7717/peerj.10399
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-01
copyright: © 2021 Harmon et al.
attribution name: Harmon et al.

Effect of ultra-processed foods consumption on glycemic control and gestational weight gain in pregnant with pregestational diabetes mellitus using carbohydrate counting
type: item
type: AcademicArticle
description: Aims The aims were to evaluate the consumption of ultra-processed foods by pregnant women with pre-existing diabetes mellitus (DM) using the carbohydrate counting method, in addition to investigating the association with total gestational weight gain and glycemic control. Methods A cohort study of adult Brazilian pregnant women with pre-existing DM. Dietary intake was evaluated adopting the NOVA classification to identify the reported consumption of ultra-processed foods. Weight was measured at all consultations and laboratory tests were evaluated at each gestational trimester. Multivariate linear regression was used in the analysis. Results Pregnant women (n = 42) presented mean total gestational weight gain of 12.02 ± 4.8 kg, 65.8% of them with inadequate weight gain. Daily consumption of ultra-processed foods was 272.37 ± 170.55 kcal. The increase of every 1 kcal in the calorie intake from ultra-processed foods in the third trimester increased glycated hemoglobin by 0.007% (β = 0.007, p = 0.025), raised 1-h postprandial glucose by 0.14 mg/dL (β = 0.143, p = 0.011), and added 0.11 kg to total gestational weight gain (β = 0.11, p = 0.006). Conclusion Ultra-processed food consumption influenced glycemic control and total gestational weight gain in pregnant women with DM.
format: application/pdf
format: text/html
creator: Carolina F. M. Silva
creator: Claudia Saunders
creator: Wilza Peres
creator: Bárbara Folino
creator: Taiana Kamel
creator: Mayara Silva dos Santos
creator: Patrícia Padilha
subject: Diabetes and Endocrinology
subject: Gynecology and Obstetrics
subject: Nutrition
subject: Women’s Health
description: doi:10.7717/peerj.10514
publisher: PeerJ Inc.
rights: © 2021 Silva et al.
abstract: Aims The aims were to evaluate the consumption of ultra-processed foods by pregnant women with pre-existing diabetes mellitus (DM) using the carbohydrate counting method, in addition to investigating the association with total gestational weight gain and glycemic control. Methods A cohort study of adult Brazilian pregnant women with pre-existing DM. Dietary intake was evaluated adopting the NOVA classification to identify the reported consumption of ultra-processed foods. Weight was measured at all consultations and laboratory tests were evaluated at each gestational trimester. Multivariate linear regression was used in the analysis. Results Pregnant women (n = 42) presented mean total gestational weight gain of 12.02 ± 4.8 kg, 65.8% of them with inadequate weight gain. Daily consumption of ultra-processed foods was 272.37 ± 170.55 kcal. The increase of every 1 kcal in the calorie intake from ultra-processed foods in the third trimester increased glycated hemoglobin by 0.007% (β = 0.007, p = 0.025), raised 1-h postprandial glucose by 0.14 mg/dL (β = 0.143, p = 0.011), and added 0.11 kg to total gestational weight gain (β = 0.11, p = 0.006). Conclusion Ultra-processed food consumption influenced glycemic control and total gestational weight gain in pregnant women with DM.
bibliographic citation: Silva et al. (2021) Effect of ultra-processed foods consumption on glycemic control and gestational weight gain in pregnant with pregestational diabetes mellitus using carbohydrate counting. PeerJ 9:e10514 https://doi.org/10.7717/peerj.10514
date submitted: 2020-04-17
date accepted: 2020-11-17
issued: 2021-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Carolina F. M.
author list: Agent
  family name: Saunders
  given name: Claudia
author list: Agent
  family name: Peres
  given name: Wilza
author list: Agent
  family name: Folino
  given name: Bárbara
author list: Agent
  family name: Kamel
  given name: Taiana
author list: Agent
  family name: dos Santos
  given name: Mayara Silva
author list: Agent
  family name: Padilha
  given name: Patrícia
doi: 10.7717/peerj.10514
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-01
copyright: © 2021 Silva et al.
attribution name: Silva et al.

Night of the hunter: using cameras to quantify nocturnal activity in desert spiders
type: item
type: AcademicArticle
description: Invertebrates dominate the animal world in terms of abundance, diversity and biomass, and play critical roles in maintaining ecosystem function. Despite their obvious importance, disproportionate research attention remains focused on vertebrates, with knowledge and understanding of invertebrate ecology still lacking. Due to their inherent advantages, usage of camera traps in ecology has risen dramatically over the last three decades, especially for research on mammals. However, few studies have used cameras to reliably detect fauna such as invertebrates or used cameras to examine specific aspects of invertebrate ecology. Previous research investigating the interaction between wolf spiders (Lycosidae: Lycosa spp.) and the lesser hairy-footed dunnart (Sminthopsis youngsoni) found that camera traps provide a viable method for examining temporal activity patterns and interactions between these species. Here, we re-examine lycosid activity to determine whether these patterns vary with different environmental conditions, specifically between burned and unburned habitats and the crests and bases of sand dunes, and whether cameras are able to detect other invertebrate fauna. Twenty-four cameras were deployed over a 3-month period in an arid region in central Australia, capturing 2,356 confirmed images of seven invertebrate taxa, including 155 time-lapse images of lycosids. Overall, there was no clear difference in temporal activity with respect to dune position or fire history, but twice as many lycosids were detected in unburned compared to burned areas. Despite some limitations, camera traps appear to have considerable utility as a tool for determining the diel activity patterns and habitat use of larger arthropods such as wolf spiders, and we recommend greater uptake in their usage in future.
format: application/pdf
format: text/html
creator: Tamara I. Potter
creator: Aaron C. Greenville
creator: Christopher R. Dickman
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.10684
publisher: PeerJ Inc.
rights: © 2021 Potter et al.
abstract: Invertebrates dominate the animal world in terms of abundance, diversity and biomass, and play critical roles in maintaining ecosystem function. Despite their obvious importance, disproportionate research attention remains focused on vertebrates, with knowledge and understanding of invertebrate ecology still lacking. Due to their inherent advantages, usage of camera traps in ecology has risen dramatically over the last three decades, especially for research on mammals. However, few studies have used cameras to reliably detect fauna such as invertebrates or used cameras to examine specific aspects of invertebrate ecology. Previous research investigating the interaction between wolf spiders (Lycosidae: Lycosa spp.) and the lesser hairy-footed dunnart (Sminthopsis youngsoni) found that camera traps provide a viable method for examining temporal activity patterns and interactions between these species. Here, we re-examine lycosid activity to determine whether these patterns vary with different environmental conditions, specifically between burned and unburned habitats and the crests and bases of sand dunes, and whether cameras are able to detect other invertebrate fauna. Twenty-four cameras were deployed over a 3-month period in an arid region in central Australia, capturing 2,356 confirmed images of seven invertebrate taxa, including 155 time-lapse images of lycosids. Overall, there was no clear difference in temporal activity with respect to dune position or fire history, but twice as many lycosids were detected in unburned compared to burned areas. Despite some limitations, camera traps appear to have considerable utility as a tool for determining the diel activity patterns and habitat use of larger arthropods such as wolf spiders, and we recommend greater uptake in their usage in future.
bibliographic citation: Potter et al. (2021) Night of the hunter: using cameras to quantify nocturnal activity in desert spiders. PeerJ 9:e10684 https://doi.org/10.7717/peerj.10684
date submitted: 2020-07-03
date accepted: 2020-12-10
issued: 2021-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Potter
  given name: Tamara I.
author list: Agent
  family name: Greenville
  given name: Aaron C.
author list: Agent
  family name: Dickman
  given name: Christopher R.
doi: 10.7717/peerj.10684
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-01
copyright: ©2021 Potter et al.
attribution name: Potter et al.

TLR4 promoter rs1927914 variant contributes to the susceptibility of esophageal squamous cell carcinoma in the Chinese population
type: item
type: AcademicArticle
description: Background Toll-like receptor 4 (TLR4), as a key regulator of both innate and acquired immunity, has been linked with the development of various cancers, including esophageal cancer. This study aims to analyze the association of potential functional genetic polymorphisms in TLR4 with the risk of esophageal cancer. Methods This case-control study involved in 480 ESCC patients and 480 health controls. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to genotype TLR4 rs1927914 polymorphism. Taqman probe method was used to determine the genotypes of TLR4 rs11536891 and rs7873784 variants. The relationship between TLR4 genetic variation and ESCC risk was analyzed by Logistic regression model by calculating the odds ratio (OR) and 95% confidence interval (95% CI). Results Compared with TLR4 rs1927914 AA genotype carriers, GG carriers had a lower ESCC risk (OR = 0.59, 95% CI [0.38–0.93], P = 0.023). Stratification analysis by age showed that TLR4 rs1927914 GG could affect the risk of ESCC in elderly people (OR = 0.59, 95% CI [0.36–0.97]). Smoking stratification analysis indicated that rs1927914 GG carriers were related to ESCC susceptibility among non-smokers (OR = 0.36, 95% CI [0.18–0.73]). Dual luciferase reporter assay suggested that rs1927914 G-containing TLR4 promoter displayed a 1.76-fold higher luciferase activity than rs1927914 A-containing counterpart in KYSE30 cells. Electrophoretic mobility shift assay (EMSA) showed the KYSE30 cell nuclear extract was able to bind the probe with rs1927914 G allele and this DNA-protein interaction could be eliminated by competition assays with unlabeled rs1927914 G probe, which indicating that the binding is sequence-specific. Our results also showed that TLR4 rs7873784 (G>C) and rs11536891 (T>C) conformed to complete genetic linkage. The genotype distributions of TLR4 rs11536891 variant among ESCC patients and normal controls have no statistical significance. Conclusion The TLR4 rs1927914 va…
format: application/pdf
format: text/html
creator: Jiaying Li
creator: Hongjiao Wu
creator: Hui Gao
creator: Ruihuan Kou
creator: Yuning Xie
creator: Zhi Zhang
creator: Xuemei Zhang
subject: Genetics
subject: Molecular Biology
subject: Epidemiology
subject: Oncology
description: doi:10.7717/peerj.10754
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Toll-like receptor 4 (TLR4), as a key regulator of both innate and acquired immunity, has been linked with the development of various cancers, including esophageal cancer. This study aims to analyze the association of potential functional genetic polymorphisms in TLR4 with the risk of esophageal cancer. Methods This case-control study involved in 480 ESCC patients and 480 health controls. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to genotype TLR4 rs1927914 polymorphism. Taqman probe method was used to determine the genotypes of TLR4 rs11536891 and rs7873784 variants. The relationship between TLR4 genetic variation and ESCC risk was analyzed by Logistic regression model by calculating the odds ratio (OR) and 95% confidence interval (95% CI). Results Compared with TLR4 rs1927914 AA genotype carriers, GG carriers had a lower ESCC risk (OR = 0.59, 95% CI [0.38–0.93], P = 0.023). Stratification analysis by age showed that TLR4 rs1927914 GG could affect the risk of ESCC in elderly people (OR = 0.59, 95% CI [0.36–0.97]). Smoking stratification analysis indicated that rs1927914 GG carriers were related to ESCC susceptibility among non-smokers (OR = 0.36, 95% CI [0.18–0.73]). Dual luciferase reporter assay suggested that rs1927914 G-containing TLR4 promoter displayed a 1.76-fold higher luciferase activity than rs1927914 A-containing counterpart in KYSE30 cells. Electrophoretic mobility shift assay (EMSA) showed the KYSE30 cell nuclear extract was able to bind the probe with rs1927914 G allele and this DNA-protein interaction could be eliminated by competition assays with unlabeled rs1927914 G probe, which indicating that the binding is sequence-specific. Our results also showed that TLR4 rs7873784 (G>C) and rs11536891 (T>C) conformed to complete genetic linkage. The genotype distributions of TLR4 rs11536891 variant among ESCC patients and normal controls have no statistical significance. Conclusion The TLR4 rs1927914 va…
bibliographic citation: Li et al. (2021) TLR4 promoter rs1927914 variant contributes to the susceptibility of esophageal squamous cell carcinoma in the Chinese population. PeerJ 9:e10754 https://doi.org/10.7717/peerj.10754
date submitted: 2020-08-18
date accepted: 2020-12-21
issued: 2021-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiaying
author list: Agent
  family name: Wu
  given name: Hongjiao
author list: Agent
  family name: Gao
  given name: Hui
author list: Agent
  family name: Kou
  given name: Ruihuan
author list: Agent
  family name: Xie
  given name: Yuning
author list: Agent
  family name: Zhang
  given name: Zhi
author list: Agent
  family name: Zhang
  given name: Xuemei
doi: 10.7717/peerj.10754
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-01
copyright: ©2021 Li et al.
attribution name: Li et al.

Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere
type: item
type: AcademicArticle
description: Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.
format: application/pdf
format: text/html
creator: Anna N. Neretina
creator: Dmitry P. Karabanov
creator: Veronika Sacherova
creator: Alexey A. Kotov
subject: Biogeography
subject: Genetics
subject: Molecular Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.10804
publisher: PeerJ Inc.
rights: © 2021 Neretina et al.
abstract: Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.
bibliographic citation: Neretina et al. (2021) Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere. PeerJ 9:e10804 https://doi.org/10.7717/peerj.10804
date submitted: 2020-09-11
date accepted: 2020-12-30
issued: 2021-02-01
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Neretina
  given name: Anna N.
author list: Agent
  family name: Karabanov
  given name: Dmitry P.
author list: Agent
  family name: Sacherova
  given name: Veronika
author list: Agent
  family name: Kotov
  given name: Alexey A.
doi: 10.7717/peerj.10804
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-02-01
copyright: ©2021 Neretina et al.
attribution name: Neretina et al.

Brown bear communication hubs: patterns and correlates of tree rubbing and pedal marking at a long-term marking site
type: item
type: AcademicArticle
description: Chemical communication is important for many species of mammals. Male brown bears, Ursus arctos, mark trees with a secretion from glands located on their back. The recent discovery of pedal glands and pedal-marking at a site used for tree-rubbing led us to hypothesize that both types of marking form part of a more complex communication system. We describe the patterns of chemical communication used by different age and sex classes, including differences in the roles of these classes as information providers or receivers over four years at a long-term marking site. Using video recordings from a camera trap, we registered a total of 285 bear-visits and 419 behavioral events associated with chemical communication. Bears visited the site more frequently during the mating season, during which communication behaviors were more frequent. A typical visit by male bears consisted of sniffing the depressions where animals pedal mark, performing pedal-marking, sniffing the tree, and, finally, rubbing against the trunk of the tree. Adult males performed most pedal- and tree-marking (95% and 66% of the cases, respectively). Males pedal-marked and tree-rubbed in 81% and 48% of their visits and sniffed the pedal marks and the tree in 23% and 59% of visits, respectively. Adult females never pedal marked, and juveniles did so at very low frequencies. Females rubbed against the tree in just 9% of their visits; they sniffed the tree and the pedal marks in 51% and 21% of their visits, respectively. All sex and age classes performed pedal- and tree-sniffing. There were significant associations between behaviors indicating that different behaviors tended to occur during the same visit and were more likely if another individual had recently visited. These associations leading to repeated marking of the site can promote the establishment of long-term marking sites. Marking sites defined by trees and the trails leading to them seem to act as communication hubs that brown bears use to share a…
format: application/pdf
format: text/html
creator: Eloy Revilla
creator: Damián Ramos Fernández
creator: Alberto Fernández-Gil
creator: Agnieszka Sergiel
creator: Nuria Selva
creator: Javier Naves
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.10447
publisher: PeerJ Inc.
rights: © 2021 Revilla et al.
abstract: Chemical communication is important for many species of mammals. Male brown bears, Ursus arctos, mark trees with a secretion from glands located on their back. The recent discovery of pedal glands and pedal-marking at a site used for tree-rubbing led us to hypothesize that both types of marking form part of a more complex communication system. We describe the patterns of chemical communication used by different age and sex classes, including differences in the roles of these classes as information providers or receivers over four years at a long-term marking site. Using video recordings from a camera trap, we registered a total of 285 bear-visits and 419 behavioral events associated with chemical communication. Bears visited the site more frequently during the mating season, during which communication behaviors were more frequent. A typical visit by male bears consisted of sniffing the depressions where animals pedal mark, performing pedal-marking, sniffing the tree, and, finally, rubbing against the trunk of the tree. Adult males performed most pedal- and tree-marking (95% and 66% of the cases, respectively). Males pedal-marked and tree-rubbed in 81% and 48% of their visits and sniffed the pedal marks and the tree in 23% and 59% of visits, respectively. Adult females never pedal marked, and juveniles did so at very low frequencies. Females rubbed against the tree in just 9% of their visits; they sniffed the tree and the pedal marks in 51% and 21% of their visits, respectively. All sex and age classes performed pedal- and tree-sniffing. There were significant associations between behaviors indicating that different behaviors tended to occur during the same visit and were more likely if another individual had recently visited. These associations leading to repeated marking of the site can promote the establishment of long-term marking sites. Marking sites defined by trees and the trails leading to them seem to act as communication hubs that brown bears use to share a…
bibliographic citation: Revilla et al. (2021) Brown bear communication hubs: patterns and correlates of tree rubbing and pedal marking at a long-term marking site. PeerJ 9:e10447 https://doi.org/10.7717/peerj.10447
date submitted: 2018-11-14
date accepted: 2020-11-07
issued: 2021-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Revilla
  given name: Eloy
author list: Agent
  family name: Ramos Fernández
  given name: Damián
author list: Agent
  family name: Fernández-Gil
  given name: Alberto
author list: Agent
  family name: Sergiel
  given name: Agnieszka
author list: Agent
  family name: Selva
  given name: Nuria
author list: Agent
  family name: Naves
  given name: Javier
doi: 10.7717/peerj.10447
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-29
copyright: ©2021 Revilla et al.
attribution name: Revilla et al.

Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study
type: item
type: AcademicArticle
description: Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.
format: application/pdf
format: text/html
creator: Alicia N. Massa
creator: Marina Bressano
creator: Juan H. Soave
creator: Mario I. Buteler
creator: Guillermo Seijo
creator: Victor S. Sobolev
creator: Valerie A. Orner
creator: Claudio Oddino
creator: Sara J. Soave
creator: Paola C. Faustinelli
creator: Francisco J. de Blas
creator: Marshall C. Lamb
creator: Renee S. Arias
subject: Agricultural Science
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10581
publisher: PeerJ Inc.
rights: © 2021
abstract: Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.
bibliographic citation: Massa et al. (2021) Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study. PeerJ 9:e10581 https://doi.org/10.7717/peerj.10581
date submitted: 2020-06-27
date accepted: 2020-11-24
issued: 2021-01-29
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Massa
  given name: Alicia N.
author list: Agent
  family name: Bressano
  given name: Marina
author list: Agent
  family name: Soave
  given name: Juan H.
author list: Agent
  family name: Buteler
  given name: Mario I.
author list: Agent
  family name: Seijo
  given name: Guillermo
author list: Agent
  family name: Sobolev
  given name: Victor S.
author list: Agent
  family name: Orner
  given name: Valerie A.
author list: Agent
  family name: Oddino
  given name: Claudio
author list: Agent
  family name: Soave
  given name: Sara J.
author list: Agent
  family name: Faustinelli
  given name: Paola C.
author list: Agent
  family name: de Blas
  given name: Francisco J.
author list: Agent
  family name: Lamb
  given name: Marshall C.
author list: Agent
  family name: Arias
  given name: Renee S.
doi: 10.7717/peerj.10581
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-29

Transcriptome analysis reveals liver metabolism programming in kids from nutritional restricted goats during mid-gestation
type: item
type: AcademicArticle
description: Background Maternal nutrient restriction during pregnancy causes a metabolic disorder that threatens the offspring’s health in humans and animals. However, the molecular mechanism of how undernutrition affecting hepatic metabolism of fetal or postnatal offspring is still unclear. We aimed to investigate transcriptomic changes of fetal livers in response to maternal malnutrition in goats during mid-gestation and to explore whether these changes would disappear when the nutrition was recovered to normal level during mid-gestation using goats (Capra hircus) as the experimental animals. Methods Fifty-three pregnant goats were subjected to a control (100% of the maintenance requirements, CON) or a restricted (60% of the maintenance requirements on day 45 to day 100 of gestation and then realimentation, RES) diet. A total of 16 liver samples were collected from fetal goats on day 100 of gestation and goat kids of postnatal day 90 to obtain hepatic transcriptional profiles using RNA-Seq. Results Principal component analysis of the hepatic transcriptomes presented a clear separation by growth phase (fetus and kid) rather than treatment. Maternal undernutrition up-regulated 86 genes and down-regulated 76 genes in the fetal liver of the FR group as compared to the FC group. KEGG pathway analysis showed the DEGs mainly enriched in protein digestion and absorption, steroid biosynthesis, carbohydrate digestion and absorption and bile secretion. A total of 118 significant DEGs (fold change > 1.2 and FDR < 0.1) within KR vs. KC comparison was identified with 79 up-regulated genes and down-regulated 39 genes, and these DEGs mainly enriched in the biosynthesis of amino acids, citrate cycle, valine, leucine and isoleucine biosynthesis and carbon metabolism. Conclusion Hepatic transcriptome analysis showed that maternal undernutrition promoted protein digestion and absorption in the fetal livers, while which restrained carbohydrate metabolism and citric acid cycle in the livers of kid…
format: application/pdf
format: text/html
creator: Chao Yang
creator: Xiaoling Zhou
creator: Hong Yang
creator: Kefyalew Gebeyew
creator: Qiongxian Yan
creator: Chuanshe Zhou
creator: Zhixiong He
creator: Zhiliang Tan
subject: Agricultural Science
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.10593
publisher: PeerJ Inc.
rights: © 2021 Yang et al.
abstract: Background Maternal nutrient restriction during pregnancy causes a metabolic disorder that threatens the offspring’s health in humans and animals. However, the molecular mechanism of how undernutrition affecting hepatic metabolism of fetal or postnatal offspring is still unclear. We aimed to investigate transcriptomic changes of fetal livers in response to maternal malnutrition in goats during mid-gestation and to explore whether these changes would disappear when the nutrition was recovered to normal level during mid-gestation using goats (Capra hircus) as the experimental animals. Methods Fifty-three pregnant goats were subjected to a control (100% of the maintenance requirements, CON) or a restricted (60% of the maintenance requirements on day 45 to day 100 of gestation and then realimentation, RES) diet. A total of 16 liver samples were collected from fetal goats on day 100 of gestation and goat kids of postnatal day 90 to obtain hepatic transcriptional profiles using RNA-Seq. Results Principal component analysis of the hepatic transcriptomes presented a clear separation by growth phase (fetus and kid) rather than treatment. Maternal undernutrition up-regulated 86 genes and down-regulated 76 genes in the fetal liver of the FR group as compared to the FC group. KEGG pathway analysis showed the DEGs mainly enriched in protein digestion and absorption, steroid biosynthesis, carbohydrate digestion and absorption and bile secretion. A total of 118 significant DEGs (fold change > 1.2 and FDR < 0.1) within KR vs. KC comparison was identified with 79 up-regulated genes and down-regulated 39 genes, and these DEGs mainly enriched in the biosynthesis of amino acids, citrate cycle, valine, leucine and isoleucine biosynthesis and carbon metabolism. Conclusion Hepatic transcriptome analysis showed that maternal undernutrition promoted protein digestion and absorption in the fetal livers, while which restrained carbohydrate metabolism and citric acid cycle in the livers of kid…
bibliographic citation: Yang et al. (2021) Transcriptome analysis reveals liver metabolism programming in kids from nutritional restricted goats during mid-gestation. PeerJ 9:e10593 https://doi.org/10.7717/peerj.10593
date submitted: 2020-07-07
date accepted: 2020-11-26
issued: 2021-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Chao
author list: Agent
  family name: Zhou
  given name: Xiaoling
author list: Agent
  family name: Yang
  given name: Hong
author list: Agent
  family name: Gebeyew
  given name: Kefyalew
author list: Agent
  family name: Yan
  given name: Qiongxian
author list: Agent
  family name: Zhou
  given name: Chuanshe
author list: Agent
  family name: He
  given name: Zhixiong
author list: Agent
  family name: Tan
  given name: Zhiliang
doi: 10.7717/peerj.10593
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-29
copyright: ©2021 Yang et al.
attribution name: Yang et al.

ATR-FTIR, EDS and SEM evaluations of enamel structure after treatment with hydrogen peroxide bleaching agents loaded with nano-hydroxyapatite particles
type: item
type: AcademicArticle
description: Background Tooth whitening is one of the most requested dental treatments, but it still presents some side effects. Indeed, the bleaching agent can generate patients’ discomfort and dental hard tissue damages, not achieving an efficient and long-lasting treatment with optimum whitening effect. To overcome these limitations, the bleaching agents containing nano-hydroxyapatite can represent a reliable solution to avoid these detrimental effects. Methods In this study, human third molars were treated with commercial bleaching agents, containing nano-hydroxyapatite (nHA) and 6% (at-home treatment), 12% and 18% (in-office treatments) of hydrogen peroxide (HP), named respectively G1, G2 and G3. The results were evaluated descriptively and analytically using Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR), Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray spectroscopy (EDS), comparing the treated groups with a commercial gel containing 10% carbamide peroxide (CONV) and with a non-treated control group (CTRL). Results ATR-FTIR analysis revealed a similar composition in carbonates and phosphates for CTRL, G1 and G2 groups, which showed no significant differences in their spectral profiles; an increased amount of organic matter was found in G3, while CONV displayed an intermediate behavior. SEM analysis did not highlight significant changes in the enamel microstructure of G1 and CONV when compared to CTRL; the pattern observed in G2 presented a slight increase of enamel irregularities, while G3 displayed a partial removal of the aprismatic layer and microporosities. No evident effects due to nHA were observed in the structure of the hydroxyapatite component of G1, G2 and CONV, if compared to CTRL, while G3 showed a slight loss of crystallinity. In all groups, EDS identified slight changes in the concentration of chemical elements O and Ca, while the Ca/P ratio was similar when compared to CTRL. Conclusion The obtained results sugge…
format: application/pdf
format: text/html
creator: Giulia Orilisi
creator: Vincenzo Tosco
creator: Riccardo Monterubbianesi
creator: Valentina Notarstefano
creator: Mutlu Özcan
creator: Angelo Putignano
creator: Giovanna Orsini
subject: Biochemistry
subject: Biotechnology
subject: Anatomy and Physiology
subject: Dentistry
subject: Drugs and Devices
description: doi:10.7717/peerj.10606
publisher: PeerJ Inc.
rights: © 2021 Orilisi et al.
abstract: Background Tooth whitening is one of the most requested dental treatments, but it still presents some side effects. Indeed, the bleaching agent can generate patients’ discomfort and dental hard tissue damages, not achieving an efficient and long-lasting treatment with optimum whitening effect. To overcome these limitations, the bleaching agents containing nano-hydroxyapatite can represent a reliable solution to avoid these detrimental effects. Methods In this study, human third molars were treated with commercial bleaching agents, containing nano-hydroxyapatite (nHA) and 6% (at-home treatment), 12% and 18% (in-office treatments) of hydrogen peroxide (HP), named respectively G1, G2 and G3. The results were evaluated descriptively and analytically using Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy (ATR-FTIR), Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray spectroscopy (EDS), comparing the treated groups with a commercial gel containing 10% carbamide peroxide (CONV) and with a non-treated control group (CTRL). Results ATR-FTIR analysis revealed a similar composition in carbonates and phosphates for CTRL, G1 and G2 groups, which showed no significant differences in their spectral profiles; an increased amount of organic matter was found in G3, while CONV displayed an intermediate behavior. SEM analysis did not highlight significant changes in the enamel microstructure of G1 and CONV when compared to CTRL; the pattern observed in G2 presented a slight increase of enamel irregularities, while G3 displayed a partial removal of the aprismatic layer and microporosities. No evident effects due to nHA were observed in the structure of the hydroxyapatite component of G1, G2 and CONV, if compared to CTRL, while G3 showed a slight loss of crystallinity. In all groups, EDS identified slight changes in the concentration of chemical elements O and Ca, while the Ca/P ratio was similar when compared to CTRL. Conclusion The obtained results sugge…
bibliographic citation: Orilisi et al. (2021) ATR-FTIR, EDS and SEM evaluations of enamel structure after treatment with hydrogen peroxide bleaching agents loaded with nano-hydroxyapatite particles. PeerJ 9:e10606 https://doi.org/10.7717/peerj.10606
date submitted: 2020-07-16
date accepted: 2020-11-28
issued: 2021-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Orilisi
  given name: Giulia
author list: Agent
  family name: Tosco
  given name: Vincenzo
author list: Agent
  family name: Monterubbianesi
  given name: Riccardo
author list: Agent
  family name: Notarstefano
  given name: Valentina
author list: Agent
  family name: Özcan
  given name: Mutlu
author list: Agent
  family name: Putignano
  given name: Angelo
author list: Agent
  family name: Orsini
  given name: Giovanna
doi: 10.7717/peerj.10606
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-29
copyright: © 2021 Orilisi et al.
attribution name: Orilisi et al.

Dynamics of locomotion in the seed harvesting ant Messor barbarus: effect of individual body mass and transported load mass
type: item
type: AcademicArticle
description: Ants are well-known for their amazing load carriage performances. Yet, the biomechanics of locomotion during load transport in these insects has so far been poorly investigated. Here, we present a study of the biomechanics of unloaded and loaded locomotion in the polymorphic seed-harvesting ant Messor barbarus (Linnaeus, 1767). This species is characterized by a strong intra-colonial size polymorphism with allometric relationships between the different body parts of the workers. In particular, big ants have much larger heads relative to their size than small ants. Their center of mass is thus shifted forward and even more so when they are carrying a load in their mandibles. We investigated the dynamics of the ant center of mass during unloaded and loaded locomotion. We found that during both unloaded and loaded locomotion, the kinetic energy and gravitational potential energy of the ant center of mass are in phase, which is in agreement with what has been described by other authors as a grounded-running gait. During unloaded locomotion, small and big ants do not display the same posture. However, they expend the same amount of mechanical energy to raise and accelerate their center of mass per unit of distance and per unit of body mass. While carrying a load, compared to the unloaded situation, ants seem to modify their locomotion gradually with increasing load mass. Therefore, loaded and unloaded locomotion do not involve discrete types of gait. Moreover, small ants carrying small loads expend less mechanical energy per unit of distance and per unit of body mass and their locomotion thus seem more mechanically efficient.
format: application/pdf
format: text/html
creator: Hugo Merienne
creator: Gérard Latil
creator: Pierre Moretto
creator: Vincent Fourcassié
subject: Animal Behavior
subject: Entomology
subject: Zoology
description: doi:10.7717/peerj.10664
publisher: PeerJ Inc.
rights: © 2021 Merienne et al.
abstract: Ants are well-known for their amazing load carriage performances. Yet, the biomechanics of locomotion during load transport in these insects has so far been poorly investigated. Here, we present a study of the biomechanics of unloaded and loaded locomotion in the polymorphic seed-harvesting ant Messor barbarus (Linnaeus, 1767). This species is characterized by a strong intra-colonial size polymorphism with allometric relationships between the different body parts of the workers. In particular, big ants have much larger heads relative to their size than small ants. Their center of mass is thus shifted forward and even more so when they are carrying a load in their mandibles. We investigated the dynamics of the ant center of mass during unloaded and loaded locomotion. We found that during both unloaded and loaded locomotion, the kinetic energy and gravitational potential energy of the ant center of mass are in phase, which is in agreement with what has been described by other authors as a grounded-running gait. During unloaded locomotion, small and big ants do not display the same posture. However, they expend the same amount of mechanical energy to raise and accelerate their center of mass per unit of distance and per unit of body mass. While carrying a load, compared to the unloaded situation, ants seem to modify their locomotion gradually with increasing load mass. Therefore, loaded and unloaded locomotion do not involve discrete types of gait. Moreover, small ants carrying small loads expend less mechanical energy per unit of distance and per unit of body mass and their locomotion thus seem more mechanically efficient.
bibliographic citation: Merienne et al. (2021) Dynamics of locomotion in the seed harvesting ant Messor barbarus: effect of individual body mass and transported load mass. PeerJ 9:e10664 https://doi.org/10.7717/peerj.10664
date submitted: 2020-08-25
date accepted: 2020-12-07
issued: 2021-01-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Merienne
  given name: Hugo
author list: Agent
  family name: Latil
  given name: Gérard
author list: Agent
  family name: Moretto
  given name: Pierre
author list: Agent
  family name: Fourcassié
  given name: Vincent
doi: 10.7717/peerj.10664
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-01-29
copyright: ©2021 Merienne et al.
attribution name: Merienne et al.

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