PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Both landscape heterogeneity and configuration determine Woodlarks (Lullula arborea) breeding territories
items: Toxicity of clothianidin to common Eastern North American fireflies
items: Real-world experience of switching from tenofovir disoproxil fumarate to tenofovir alafenamide in patients with chronic hepatitis B: a retrospective study
items: UBE2E3 regulates cellular senescence and osteogenic differentiation of BMSCs during aging
items: Misinformation effects in an online sample: results of an experimental study with a five day retention interval
items: De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
items: Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish
items: Childhood parasitic infections and gastrointestinal illness in indigenous communities at Lake Atitlán, Guatemala
items: Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts
items: Estimating the differences in critical thermal maximum and metabolic rate of Helicoverpa punctigera (Wallengren) (Lepidoptera: Noctuidae) across life stages

Both landscape heterogeneity and configuration determine Woodlarks (Lullula arborea) breeding territories
type: item
type: AcademicArticle
description: Farmland birds have declined in the last decades mostly due to agriculture intensification. The Woodlark Lullula arborea, a farmland species of conservation concern and protected by the European Bird Directive, occurs in a variety of habitats across its geographic range. Although habitat heterogeneity has been recognized as a key feature, the preference or avoidance of particular habitat attributes might differ across its range because different localities may have distinct conditions. Such variation would challenge conservation efforts at the local level. Our aim was to assess habitat associations of Woodlarks and determine whether the habitat attributes identified as important in other locations across its range could be generalised and applied to Austrian populations. In addition, habitat associations can be influenced by land-use change. We examined changes in land use from 2007 to 2016 in 15 municipalities surrounding areas occupied by Woodlarks. We quantified the composition and configuration of the local landscape surrounding 18 singing males’ territories and 16 non-territory sites. We found that the probability of Woodlarks territories increased with landscape heterogeneity between 50% and 70%, increased with dispersed bare soil patches, decreased with overall patch density and were away from dirt roads. Contrary to our expectation, there was no indication of land-use change. In contrast to previous studies, vegetation height, the presence and proximity to woodland were not identified as important habitat characteristics. Thus, some conservation recommendations can be derived from other localities, for example, maintaining or enhancing landscape heterogeneity. However, others should be adapted to local conditions. In Austria, conservation efforts should focus on including dispersed patches of bare soil and limiting the development of dirt roads nearby Woodlark territories, in addition to promoting a heterogeneous landscape.
format: application/pdf
format: text/html
creator: Marlies Resch
creator: Marcela Suarez-Rubio
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.12476
publisher: PeerJ Inc.
rights: © 2021 Resch and Suarez-Rubio
abstract: Farmland birds have declined in the last decades mostly due to agriculture intensification. The Woodlark Lullula arborea, a farmland species of conservation concern and protected by the European Bird Directive, occurs in a variety of habitats across its geographic range. Although habitat heterogeneity has been recognized as a key feature, the preference or avoidance of particular habitat attributes might differ across its range because different localities may have distinct conditions. Such variation would challenge conservation efforts at the local level. Our aim was to assess habitat associations of Woodlarks and determine whether the habitat attributes identified as important in other locations across its range could be generalised and applied to Austrian populations. In addition, habitat associations can be influenced by land-use change. We examined changes in land use from 2007 to 2016 in 15 municipalities surrounding areas occupied by Woodlarks. We quantified the composition and configuration of the local landscape surrounding 18 singing males’ territories and 16 non-territory sites. We found that the probability of Woodlarks territories increased with landscape heterogeneity between 50% and 70%, increased with dispersed bare soil patches, decreased with overall patch density and were away from dirt roads. Contrary to our expectation, there was no indication of land-use change. In contrast to previous studies, vegetation height, the presence and proximity to woodland were not identified as important habitat characteristics. Thus, some conservation recommendations can be derived from other localities, for example, maintaining or enhancing landscape heterogeneity. However, others should be adapted to local conditions. In Austria, conservation efforts should focus on including dispersed patches of bare soil and limiting the development of dirt roads nearby Woodlark territories, in addition to promoting a heterogeneous landscape.
bibliographic citation: Resch et al. (2021) Both landscape heterogeneity and configuration determine Woodlarks (Lullula arborea) breeding territories. PeerJ 9:e12476 https://doi.org/10.7717/peerj.12476
date submitted: 2021-06-16
date accepted: 2021-10-20
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Resch
  given name: Marlies
author list: Agent
  family name: Suarez-Rubio
  given name: Marcela
doi: 10.7717/peerj.12476
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: © 2021 Resch and Suarez-Rubio
attribution name: Resch and Suarez-Rubio

Toxicity of clothianidin to common Eastern North American fireflies
type: item
type: AcademicArticle
description: Background Previous research suggests that fireflies (Coleoptera: Lampyridae) are susceptible to commonly used insecticides. In the United States, there has been a rapid and widespread adoption of neonicotinoid insecticides, predominantly used as seed coatings on large-acreage crops like corn, soy, and cotton. Neonicotinoid insecticides are persistent in soil yet mobile in water, so they have potential to contaminate firefly habitats both in and adjacent to application sites. As a result, fireflies may be at high risk of exposure to neonicotinoids, possibly jeopardizing this already at-risk group of charismatic insects. Methods To assess the sensitivity of fireflies to neonicotinoids, we exposed larvae of Photuris versicolor complex and Photinus pyralis to multiple levels of clothianidin-treated soil and monitored feeding behavior, protective soil chamber formation, intoxication, and mortality. Results Pt. versicolor and Pn. pyralis larvae exhibited long-term intoxication and mortality at concentrations above 1,000 ng g−1 soil (1 ppm). Under sub-lethal clothianidin exposure, firefly larvae fed less and spent less time in protective soil chambers, two behavioral changes that could decrease larval survival in the wild. Discussion Both firefly species demonstrated sub-lethal responses in the lab to clothianidin exposure at field-realistic concentrations, although Pt. versicolor and Pn. pyralis appeared to tolerate higher clothianidin exposure relative to other soil invertebrates and beetle species. While these two firefly species, which are relatively widespread in North America, appear somewhat tolerant of neonicotinoid exposure in a laboratory setting, further work is needed to extend this conclusion to wild populations, especially in rare or declining taxa.
format: application/pdf
format: text/html
creator: Kirsten Ann Pearsons
creator: Sarah E. Lower
creator: John F. Tooker
subject: Entomology
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.12495
publisher: PeerJ Inc.
rights: © 2021 Pearsons et al.
abstract: Background Previous research suggests that fireflies (Coleoptera: Lampyridae) are susceptible to commonly used insecticides. In the United States, there has been a rapid and widespread adoption of neonicotinoid insecticides, predominantly used as seed coatings on large-acreage crops like corn, soy, and cotton. Neonicotinoid insecticides are persistent in soil yet mobile in water, so they have potential to contaminate firefly habitats both in and adjacent to application sites. As a result, fireflies may be at high risk of exposure to neonicotinoids, possibly jeopardizing this already at-risk group of charismatic insects. Methods To assess the sensitivity of fireflies to neonicotinoids, we exposed larvae of Photuris versicolor complex and Photinus pyralis to multiple levels of clothianidin-treated soil and monitored feeding behavior, protective soil chamber formation, intoxication, and mortality. Results Pt. versicolor and Pn. pyralis larvae exhibited long-term intoxication and mortality at concentrations above 1,000 ng g−1 soil (1 ppm). Under sub-lethal clothianidin exposure, firefly larvae fed less and spent less time in protective soil chambers, two behavioral changes that could decrease larval survival in the wild. Discussion Both firefly species demonstrated sub-lethal responses in the lab to clothianidin exposure at field-realistic concentrations, although Pt. versicolor and Pn. pyralis appeared to tolerate higher clothianidin exposure relative to other soil invertebrates and beetle species. While these two firefly species, which are relatively widespread in North America, appear somewhat tolerant of neonicotinoid exposure in a laboratory setting, further work is needed to extend this conclusion to wild populations, especially in rare or declining taxa.
bibliographic citation: Pearsons et al. (2021) Toxicity of clothianidin to common Eastern North American fireflies. PeerJ 9:e12495 https://doi.org/10.7717/peerj.12495
date submitted: 2021-09-16
date accepted: 2021-10-25
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pearsons
  given name: Kirsten Ann
author list: Agent
  family name: Lower
  given name: Sarah E.
author list: Agent
  family name: Tooker
  given name: John F.
doi: 10.7717/peerj.12495
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: ©2021 Pearsons et al.
attribution name: Pearsons et al.

Real-world experience of switching from tenofovir disoproxil fumarate to tenofovir alafenamide in patients with chronic hepatitis B: a retrospective study
type: item
type: AcademicArticle
description: Background Tenofovir alafenamide (TAF) has good viral suppression efficacy and less adverse effect than tenofovir disoproxil fumarate (TDF). Real-world studies on the antiviral efficacy and safety of switching from TDF to TAF in patients with chronic hepatitis B (CHB) are limited. Methods This retrospective study included 167 nucleos(t)ide analogue (NA)-naive patients with CHB. All the patients received TDF at least 12 months before switching and TAF at least 12 months after switching at a single medical center. The Friedman test with Dunn–Bonferroni post hoc tests and repeated-measures analysis of variance was used to analyze the effect of complete viral suppression, alanine aminotransferase (ALT) level normalization, renal function changes, body weight, and body mass index in the periods before and after switching. Results The mean age and TDF treatment duration were 52 ± 11 years and 2.8 years (interquartile range, 1.51–5.15 years), respectively. The complete viral suppression rate was similar between the time of switching and 48 weeks after switching to TAF (77.8% vs 76%, P = 1.000). The percentage of alanine aminotransferase (ALT) normalization increased from 26.3% at TDF start to 81.4% (P < 0.001) at time of switching and 89.2% at 48 weeks after switching to TAF (P = 0.428). The median estimated glomerular filtration rate decreased from 100.09 mL/min/1.73 m² at TDF start to 91.97 mL/min/1.73 m² (P < 0.001) at the time of switching and stabilized at 48 weeks after switching to TAF (93.47 mL/min/1.73m², P = 1.000). The body weight decreased from 69.2 ± 12.2 kg at TDF start to 67.4 ± 12.1 kg (P < 0.001) at the time of switching to TAF and returned to 68.7 ± 12.7 kg (P < 0.001) 48 weeks thereafter. The body mass index (BMI) decreased from 25 ± 3.3 kg/m² at TDF start to 24.5 ± 3.3 kg/m² (P = 0.002) at the time of switching to TAF and returned to 25.1 ± 3.6 kg/m² (P < 0.001) 48 weeks thereafter. Conclusions Our study showed that switching to TAF from TDF had good an…
format: application/pdf
format: text/html
creator: Pei-Yuan Su
creator: Wei-Wen Su
creator: Yu-Chun Hsu
creator: Siou-Ping Huang
creator: Hsu-Heng Yen
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
subject: Infectious Diseases
description: doi:10.7717/peerj.12527
publisher: PeerJ Inc.
rights: © 2021 Su et al.
abstract: Background Tenofovir alafenamide (TAF) has good viral suppression efficacy and less adverse effect than tenofovir disoproxil fumarate (TDF). Real-world studies on the antiviral efficacy and safety of switching from TDF to TAF in patients with chronic hepatitis B (CHB) are limited. Methods This retrospective study included 167 nucleos(t)ide analogue (NA)-naive patients with CHB. All the patients received TDF at least 12 months before switching and TAF at least 12 months after switching at a single medical center. The Friedman test with Dunn–Bonferroni post hoc tests and repeated-measures analysis of variance was used to analyze the effect of complete viral suppression, alanine aminotransferase (ALT) level normalization, renal function changes, body weight, and body mass index in the periods before and after switching. Results The mean age and TDF treatment duration were 52 ± 11 years and 2.8 years (interquartile range, 1.51–5.15 years), respectively. The complete viral suppression rate was similar between the time of switching and 48 weeks after switching to TAF (77.8% vs 76%, P = 1.000). The percentage of alanine aminotransferase (ALT) normalization increased from 26.3% at TDF start to 81.4% (P < 0.001) at time of switching and 89.2% at 48 weeks after switching to TAF (P = 0.428). The median estimated glomerular filtration rate decreased from 100.09 mL/min/1.73 m² at TDF start to 91.97 mL/min/1.73 m² (P < 0.001) at the time of switching and stabilized at 48 weeks after switching to TAF (93.47 mL/min/1.73m², P = 1.000). The body weight decreased from 69.2 ± 12.2 kg at TDF start to 67.4 ± 12.1 kg (P < 0.001) at the time of switching to TAF and returned to 68.7 ± 12.7 kg (P < 0.001) 48 weeks thereafter. The body mass index (BMI) decreased from 25 ± 3.3 kg/m² at TDF start to 24.5 ± 3.3 kg/m² (P = 0.002) at the time of switching to TAF and returned to 25.1 ± 3.6 kg/m² (P < 0.001) 48 weeks thereafter. Conclusions Our study showed that switching to TAF from TDF had good an…
bibliographic citation: Su et al. (2021) Real-world experience of switching from tenofovir disoproxil fumarate to tenofovir alafenamide in patients with chronic hepatitis B: a retrospective study. PeerJ 9:e12527 https://doi.org/10.7717/peerj.12527
date submitted: 2021-08-18
date accepted: 2021-11-01
issued: 2021-11-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Pei-Yuan
author list: Agent
  family name: Su
  given name: Wei-Wen
author list: Agent
  family name: Hsu
  given name: Yu-Chun
author list: Agent
  family name: Huang
  given name: Siou-Ping
author list: Agent
  family name: Yen
  given name: Hsu-Heng
doi: 10.7717/peerj.12527
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-19
copyright: © 2021 Su et al.
attribution name: Su et al.

UBE2E3 regulates cellular senescence and osteogenic differentiation of BMSCs during aging
type: item
type: AcademicArticle
description: Background Osteoporosis has gradually become a public health problem in the world. However, the exact molecular mechanism of osteoporosis still remains unclear. Senescence and osteogenic differentiation inhibition of bone marrow mesenchymal stem cells (BMSCs ) are supposed to play an important part in osteoporosis. Methods We used two gene expression profiles (GSE35956 and GSE35958) associated with osteoporosis and selected the promising gene Ubiquitin-conjugating enzyme E2 E3 (UBE2E3). We then verified its function and mechanism by in vitro experiments. Results UBE2E3 was highly expressed in the bone marrow and positively associated with osteogenesis related genes. Besides, UBE2E3 expression reduced in old BMSCs compared with that in young BMSCs. In in vitro experiments, knockdown of UBE2E3 accelerated cellular senescence and inhibited osteogenic differentiation of young BMSCs. On the other hand, overexpression of UBE2E3 attenuated cellular senescence as well as enhanced osteogenic differentiation of old BMSCs. Mechanistically, UBE2E3 might regulate the nuclear factor erythroid 2-related factor (Nrf2) and control its function, thus affecting the senescence and osteogenic differentiation of BMSCs. Conclusion UBE2E3 may be potentially involved in the pathogenesis of osteoporosis by regulating cellular senescence and osteogenic differentiation of BMSCs.
format: application/pdf
format: text/html
creator: Yalin Liu
creator: Guangping Cai
creator: Peng Chen
creator: Tiejian Jiang
creator: Zhuying Xia
subject: Geriatrics
subject: Orthopedics
subject: Metabolic Sciences
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.12253
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background Osteoporosis has gradually become a public health problem in the world. However, the exact molecular mechanism of osteoporosis still remains unclear. Senescence and osteogenic differentiation inhibition of bone marrow mesenchymal stem cells (BMSCs ) are supposed to play an important part in osteoporosis. Methods We used two gene expression profiles (GSE35956 and GSE35958) associated with osteoporosis and selected the promising gene Ubiquitin-conjugating enzyme E2 E3 (UBE2E3). We then verified its function and mechanism by in vitro experiments. Results UBE2E3 was highly expressed in the bone marrow and positively associated with osteogenesis related genes. Besides, UBE2E3 expression reduced in old BMSCs compared with that in young BMSCs. In in vitro experiments, knockdown of UBE2E3 accelerated cellular senescence and inhibited osteogenic differentiation of young BMSCs. On the other hand, overexpression of UBE2E3 attenuated cellular senescence as well as enhanced osteogenic differentiation of old BMSCs. Mechanistically, UBE2E3 might regulate the nuclear factor erythroid 2-related factor (Nrf2) and control its function, thus affecting the senescence and osteogenic differentiation of BMSCs. Conclusion UBE2E3 may be potentially involved in the pathogenesis of osteoporosis by regulating cellular senescence and osteogenic differentiation of BMSCs.
bibliographic citation: Liu et al. (2021) UBE2E3 regulates cellular senescence and osteogenic differentiation of BMSCs during aging. PeerJ 9:e12253 https://doi.org/10.7717/peerj.12253
date submitted: 2021-06-27
date accepted: 2021-09-14
issued: 2021-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Yalin
author list: Agent
  family name: Cai
  given name: Guangping
author list: Agent
  family name: Chen
  given name: Peng
author list: Agent
  family name: Jiang
  given name: Tiejian
author list: Agent
  family name: Xia
  given name: Zhuying
doi: 10.7717/peerj.12253
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-18
copyright: ©2021 Liu et al.
attribution name: Liu et al.

Misinformation effects in an online sample: results of an experimental study with a five day retention interval
type: item
type: AcademicArticle
description: Traditional face-to-face laboratory studies have contributed greatly to our understanding of how misinformation effects develop. However, an area of emerging concern that has been relatively under-researched is the impact of misinformation following exposure to traumatic events that are viewed online. Here we describe a novel method for investigating misinformation effects in an online context. Participants (N = 99) completed the study online. They first watched a 10-min video of a fictional school shooting. Between 5 and 10 days later, they were randomly assigned to receive misinformation or no misinformation about the video before completing a recognition test. Misinformed participants were less accurate at discriminating between misinformation and true statements than control participants. This effect was most strongly supported by ROC analyses (Cohen’s d = 0.59, BF10 = 8.34). Misinformation effects can be established in an online experiment using candid violent viral-style video stimuli.
format: application/pdf
format: text/html
creator: Olivia Sievwright
creator: Michael Philipp
creator: Aaron Drummond
creator: Katie Knapp
creator: Kirsty Ross
subject: Psychiatry and Psychology
subject: Legal Issues
description: doi:10.7717/peerj.12299
publisher: PeerJ Inc.
rights: © 2021 Sievwright et al.
abstract: Traditional face-to-face laboratory studies have contributed greatly to our understanding of how misinformation effects develop. However, an area of emerging concern that has been relatively under-researched is the impact of misinformation following exposure to traumatic events that are viewed online. Here we describe a novel method for investigating misinformation effects in an online context. Participants (N = 99) completed the study online. They first watched a 10-min video of a fictional school shooting. Between 5 and 10 days later, they were randomly assigned to receive misinformation or no misinformation about the video before completing a recognition test. Misinformed participants were less accurate at discriminating between misinformation and true statements than control participants. This effect was most strongly supported by ROC analyses (Cohen’s d = 0.59, BF10 = 8.34). Misinformation effects can be established in an online experiment using candid violent viral-style video stimuli.
bibliographic citation: Sievwright et al. (2021) Misinformation effects in an online sample: results of an experimental study with a five day retention interval. PeerJ 9:e12299 https://doi.org/10.7717/peerj.12299
date submitted: 2021-03-16
date accepted: 2021-09-21
issued: 2021-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sievwright
  given name: Olivia
author list: Agent
  family name: Philipp
  given name: Michael
author list: Agent
  family name: Drummond
  given name: Aaron
author list: Agent
  family name: Knapp
  given name: Katie
author list: Agent
  family name: Ross
  given name: Kirsty
doi: 10.7717/peerj.12299
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-18
copyright: © 2021 Sievwright et al.
attribution name: Sievwright et al.

De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
type: item
type: AcademicArticle
description: The aim of this study was to generate and analyze the atlas of the loggerhead turtle blood transcriptome by RNA-seq, as well as identify and characterize thioredoxin (Tnxs) and peroxiredoxin (Prdxs) antioxidant enzymes of the greatest interest in the control of peroxide levels and other biological functions. The transcriptome of loggerhead turtle was sequenced using the Illumina Hiseq 2000 platform and de novo assembly was performed using the Trinity pipeline. The assembly comprised 515,597 contigs with an N50 of 2,631 bp. Contigs were analyzed with CD-Hit obtaining 374,545 unigenes, of which 165,676 had ORFs encoding putative proteins longer than 100 amino acids. A total of 52,147 (31.5%) of these transcripts had significant homology matches in at least one of the five databases used. From the enrichment of GO terms, 180 proteins with antioxidant activity were identified, among these 28 Prdxs and 50 putative Tnxs. The putative proteins of loggerhead turtles encoded by the genes Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip were predicted and characterized in silico. When comparing Prdxs and Txns of loggerhead turtle with homologous human proteins, they showed 18 (9%), 52 (18%) 94 (43%), 36 (16%), 35 (33%) and 74 (19%) amino acid mutations respectively. However, they showed high conservation in active sites and structural motifs (98%), with few specific modifications. Of these, Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip presented 0, 25, 18, three, six and two deleterious changes. This study provides a high quality blood transcriptome and functional annotation of loggerhead sea turtles.
format: application/pdf
format: text/html
creator: Javier Hernández-Fernández
creator: Andrés Mauricio Pinzón Velasco
creator: Ellie Anne López Barrera
creator: María Del Pilar Rodríguez Becerra
creator: José Luis Villanueva-Cañas
creator: M. Mar Alba
creator: Leonardo Mariño Ramírez
subject: Bioinformatics
subject: Genomics
subject: Marine Biology
subject: Molecular Biology
subject: Ecotoxicology
description: doi:10.7717/peerj.12395
publisher: PeerJ Inc.
rights: © 2021 Hernández-Fernández et al.
abstract: The aim of this study was to generate and analyze the atlas of the loggerhead turtle blood transcriptome by RNA-seq, as well as identify and characterize thioredoxin (Tnxs) and peroxiredoxin (Prdxs) antioxidant enzymes of the greatest interest in the control of peroxide levels and other biological functions. The transcriptome of loggerhead turtle was sequenced using the Illumina Hiseq 2000 platform and de novo assembly was performed using the Trinity pipeline. The assembly comprised 515,597 contigs with an N50 of 2,631 bp. Contigs were analyzed with CD-Hit obtaining 374,545 unigenes, of which 165,676 had ORFs encoding putative proteins longer than 100 amino acids. A total of 52,147 (31.5%) of these transcripts had significant homology matches in at least one of the five databases used. From the enrichment of GO terms, 180 proteins with antioxidant activity were identified, among these 28 Prdxs and 50 putative Tnxs. The putative proteins of loggerhead turtles encoded by the genes Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip were predicted and characterized in silico. When comparing Prdxs and Txns of loggerhead turtle with homologous human proteins, they showed 18 (9%), 52 (18%) 94 (43%), 36 (16%), 35 (33%) and 74 (19%) amino acid mutations respectively. However, they showed high conservation in active sites and structural motifs (98%), with few specific modifications. Of these, Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip presented 0, 25, 18, three, six and two deleterious changes. This study provides a high quality blood transcriptome and functional annotation of loggerhead sea turtles.
bibliographic citation: Hernández-Fernández et al. (2021) De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins. PeerJ 9:e12395 https://doi.org/10.7717/peerj.12395
date submitted: 2021-01-14
date accepted: 2021-10-06
issued: 2021-11-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hernández-Fernández
  given name: Javier
author list: Agent
  family name: Pinzón Velasco
  given name: Andrés Mauricio
author list: Agent
  family name: López Barrera
  given name: Ellie Anne
author list: Agent
  family name: Rodríguez Becerra
  given name: María Del Pilar
author list: Agent
  family name: Villanueva-Cañas
  given name: José Luis
author list: Agent
  family name: Alba
  given name: M. Mar
author list: Agent
  family name: Mariño Ramírez
  given name: Leonardo
doi: 10.7717/peerj.12395
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-18
copyright: ©2021 Hernández-Fernández et al.
attribution name: Hernández-Fernández et al.

Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish
type: item
type: AcademicArticle
description: Background The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. Methods Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. Results Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such …
format: application/pdf
format: text/html
creator: Wilson Xieu
creator: Levi S. Lewis
creator: Feng Zhao
creator: Rachel A. Fichman
creator: Malte Willmes
creator: Tien-Chieh Hung
creator: Luke Ellison
creator: Troy Stevenson
creator: Galen Tigan
creator: Andrew A. Schultz
creator: James A. Hobbs
subject: Aquaculture, Fisheries and Fish Science
subject: Developmental Biology
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.12280
publisher: PeerJ Inc.
rights: © 2021 Xieu et al.
abstract: Background The application of otolith-based tools to inform the management and conservation of fishes first requires taxon- and stage-specific validation. The Delta Smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the upper San Francisco Estuary (SFE), California, United States, serves as a key indicator species in the SFE; thus, understanding this species’ vital rates and population dynamics is valuable for assessing the overall health of the estuary. Otolith-based tools have been developed and applied across multiple life stages of Delta Smelt to reconstruct age structure, growth, phenology, and migration. However, key methodological assumptions have yet to be validated, thus limiting confidence in otolith-derived metrics that are important for informing major water management decisions in the SFE. Methods Using known-age cultured Delta Smelt and multiple independent otolith analysts, we examined otolith formation, otolith-somatic proportionality, aging accuracy and precision, left-right symmetry, and the effects of image magnification for larval, juvenile, and adult Delta Smelt. Results Overall, otolith size varied linearly with fish size (from 10–60 mm), explaining 99% of the variation in fish length, despite a unique slope for larvae < 10 mm. Otolith-somatic proportionality was similar among wild and cultured specimens. Aging precision among independent analysts was 98% and aging accuracy relative to known ages was 96%, with age estimates exhibiting negligible differences among left and right otoliths. Though error generally increased with age, percent error decreased from 0–30 days-post-hatch, with precision remaining relatively high (≥ 95%) thereafter. Increased magnification (400×) further improved aging accuracy for the oldest, slowest-growing individuals. Together, these results indicate that otolith-based techniques provide reliable age and growth reconstructions for larval, juvenile, and adult Delta Smelt. Such …
bibliographic citation: Xieu et al. (2021) Experimental validation of otolith-based age and growth reconstructions across multiple life stages of a critically endangered estuarine fish. PeerJ 9:e12280 https://doi.org/10.7717/peerj.12280
date submitted: 2021-02-24
date accepted: 2021-09-20
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xieu
  given name: Wilson
author list: Agent
  family name: Lewis
  given name: Levi S.
author list: Agent
  family name: Zhao
  given name: Feng
author list: Agent
  family name: Fichman
  given name: Rachel A.
author list: Agent
  family name: Willmes
  given name: Malte
author list: Agent
  family name: Hung
  given name: Tien-Chieh
author list: Agent
  family name: Ellison
  given name: Luke
author list: Agent
  family name: Stevenson
  given name: Troy
author list: Agent
  family name: Tigan
  given name: Galen
author list: Agent
  family name: Schultz
  given name: Andrew A.
author list: Agent
  family name: Hobbs
  given name: James A.
doi: 10.7717/peerj.12280
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: ©2021 Xieu et al.
attribution name: Xieu et al.

Childhood parasitic infections and gastrointestinal illness in indigenous communities at Lake Atitlán, Guatemala
type: item
type: AcademicArticle
description: Lake Atitlán has experienced a decline in water quality resulting from cultural eutrophication. Indigenous Mayans who already face disproportionate health challenges rely directly on the lake water. Our objectives were to: (1) estimate prevalence of shedding of water-borne fecal parasites among children 5 years of age and younger, (2) assess household-reported incidence of gastrointestinal illness in children, and (3) characterize water sources, treatment, and sanitation conditions in households. We hypothesized that household use of untreated lake water results in increased risk of shedding of parasites and gastrointestinal symptoms. A cross-sectional fecal sampling and physical exam of 401 children were conducted along with WASH surveys in partnership with healthcare providers in seven communities. Fecal samples were screened for Giardia lamblia and Cryptosporidium parvum, using a rapid ELISA, with a portion examined by microscope. The prevalence of parasite shedding was 12.2% (9.7% for Giardia; 2.5% for Cryptosporidium). Risk factors for Giardia shedding included age 3 years or older (3.4 odds ratio, z-stat = 2.781 p = 0.0054), low height-for-age z-score (2.3 odds ratio, z-stat = 2.225, p = 0.0216), lack of any household water treatment (2.5 odds ratio, z-stat = 2.492, p < 0.0012), and open access to household latrine (2.04 odds ratio, z-stat = 1.992, p = 0.0464). The majority (77.3%) of households reported water treatment, boiling and gravity fed filters as the most widespread practices. The vast majority of households (92%) reported usage of a latrine, while 40% reported open and shared access beyond their household. An overwhelming majority of households reported diarrhea and fever several times per year or greater, with approximately half reporting vomiting at that frequency. Lake water use was identified as a risk factor for households reporting frequent gastrointestinal symptoms (odds ratio of 2.5, 4.4, and 2.6; z-stat of 3.10, 3.65, and 3.0; p-values of 0.…
format: application/pdf
format: text/html
creator: Amber Roegner
creator: Mónica N. Orozco
creator: Claudia Jarquin
creator: William Boegel
creator: Clara Secaira
creator: Marlin E. Caballeros
creator: Lujain Al-Saleh
creator: Eliška Rejmánková
subject: Parasitology
subject: Gastroenterology and Hepatology
subject: Global Health
subject: Pediatrics
subject: Public Health
description: doi:10.7717/peerj.12331
publisher: PeerJ Inc.
rights: © 2021 Roegner et al.
abstract: Lake Atitlán has experienced a decline in water quality resulting from cultural eutrophication. Indigenous Mayans who already face disproportionate health challenges rely directly on the lake water. Our objectives were to: (1) estimate prevalence of shedding of water-borne fecal parasites among children 5 years of age and younger, (2) assess household-reported incidence of gastrointestinal illness in children, and (3) characterize water sources, treatment, and sanitation conditions in households. We hypothesized that household use of untreated lake water results in increased risk of shedding of parasites and gastrointestinal symptoms. A cross-sectional fecal sampling and physical exam of 401 children were conducted along with WASH surveys in partnership with healthcare providers in seven communities. Fecal samples were screened for Giardia lamblia and Cryptosporidium parvum, using a rapid ELISA, with a portion examined by microscope. The prevalence of parasite shedding was 12.2% (9.7% for Giardia; 2.5% for Cryptosporidium). Risk factors for Giardia shedding included age 3 years or older (3.4 odds ratio, z-stat = 2.781 p = 0.0054), low height-for-age z-score (2.3 odds ratio, z-stat = 2.225, p = 0.0216), lack of any household water treatment (2.5 odds ratio, z-stat = 2.492, p < 0.0012), and open access to household latrine (2.04 odds ratio, z-stat = 1.992, p = 0.0464). The majority (77.3%) of households reported water treatment, boiling and gravity fed filters as the most widespread practices. The vast majority of households (92%) reported usage of a latrine, while 40% reported open and shared access beyond their household. An overwhelming majority of households reported diarrhea and fever several times per year or greater, with approximately half reporting vomiting at that frequency. Lake water use was identified as a risk factor for households reporting frequent gastrointestinal symptoms (odds ratio of 2.5, 4.4, and 2.6; z-stat of 3.10, 3.65, and 3.0; p-values of 0.…
bibliographic citation: Roegner et al. (2021) Childhood parasitic infections and gastrointestinal illness in indigenous communities at Lake Atitlán, Guatemala. PeerJ 9:e12331 https://doi.org/10.7717/peerj.12331
date submitted: 2021-01-14
date accepted: 2021-09-27
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roegner
  given name: Amber
author list: Agent
  family name: Orozco
  given name: Mónica N.
author list: Agent
  family name: Jarquin
  given name: Claudia
author list: Agent
  family name: Boegel
  given name: William
author list: Agent
  family name: Secaira
  given name: Clara
author list: Agent
  family name: Caballeros
  given name: Marlin E.
author list: Agent
  family name: Al-Saleh
  given name: Lujain
author list: Agent
  family name: Rejmánková
  given name: Eliška
doi: 10.7717/peerj.12331
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: ©2021 Roegner et al.
attribution name: Roegner et al.

Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts
type: item
type: AcademicArticle
description: Rumen bacteria make the greatest contribution to rumen fermentation that enables the host animal to utilize the ingested feeds. Agro-industrial byproducts (AIP) such as olive cake (OC) and date palm byproducts (discarded dates (DD), and date palm fronds (DPF)) represent a practical solution to the deficiency in common feed resources. In this study, thirty-six growing Barki lambs were divided into three groups to evaluate the effect of untraditional diets including the AIP on the growth performance. Subsequently, nine adult Barki rams were used to evaluate the effect of experimental diets on rumen fermentation and rumen bacteria. Three rations were used: common concentrate mixture (S1), common untraditional concentrate mixture including OC and DD (S2), and the same concentrate mixture in S2 supplemented with roughage as DPF enriched with 15% molasses (S3). The animals in S2 group showed higher dry matter intake (DMI) and lower relative growth rate (RGR) as compared to the animals in S1 group. However, the animals in S3 group were the lowest in DMI but achieved RGR by about 87.6% of that in the S1 group. Rumen pH, acetic and butyric acids were more prevalent in animals of S3 group and rumen ammonia (NH3-N), total volatile fatty acids (TVFA), propionic acid were higher in S1. Rumen enzymes activities were higher in S1 group followed by S3 and S2. The bacterial population was more prevalent in S1 and microbial diversity was higher in the S3 group. Principal coordinate analysis revealed clusters associated with diet type and the relative abundance of bacteria varied between sheep groups. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes; whereas, Prevotella, Ruminococcus, and Butyrivibrio were the dominant genera. Results indicate that diet S3 supplemented by OC, DD, and DPF could replace the conventional feed mixture.
format: application/pdf
format: text/html
creator: Alaa Emara Rabee
creator: Khalid Z. Kewan
creator: Ebrahim A. Sabra
creator: Hassan M. El Shaer
creator: Mebarek Lamara
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.12447
publisher: PeerJ Inc.
rights: © 2021 Rabee et al.
abstract: Rumen bacteria make the greatest contribution to rumen fermentation that enables the host animal to utilize the ingested feeds. Agro-industrial byproducts (AIP) such as olive cake (OC) and date palm byproducts (discarded dates (DD), and date palm fronds (DPF)) represent a practical solution to the deficiency in common feed resources. In this study, thirty-six growing Barki lambs were divided into three groups to evaluate the effect of untraditional diets including the AIP on the growth performance. Subsequently, nine adult Barki rams were used to evaluate the effect of experimental diets on rumen fermentation and rumen bacteria. Three rations were used: common concentrate mixture (S1), common untraditional concentrate mixture including OC and DD (S2), and the same concentrate mixture in S2 supplemented with roughage as DPF enriched with 15% molasses (S3). The animals in S2 group showed higher dry matter intake (DMI) and lower relative growth rate (RGR) as compared to the animals in S1 group. However, the animals in S3 group were the lowest in DMI but achieved RGR by about 87.6% of that in the S1 group. Rumen pH, acetic and butyric acids were more prevalent in animals of S3 group and rumen ammonia (NH3-N), total volatile fatty acids (TVFA), propionic acid were higher in S1. Rumen enzymes activities were higher in S1 group followed by S3 and S2. The bacterial population was more prevalent in S1 and microbial diversity was higher in the S3 group. Principal coordinate analysis revealed clusters associated with diet type and the relative abundance of bacteria varied between sheep groups. The bacterial community was dominated by phylum Bacteroidetes and Firmicutes; whereas, Prevotella, Ruminococcus, and Butyrivibrio were the dominant genera. Results indicate that diet S3 supplemented by OC, DD, and DPF could replace the conventional feed mixture.
bibliographic citation: Rabee et al. (2021) Rumen bacterial community profile and fermentation in Barki sheep fed olive cake and date palm byproducts. PeerJ 9:e12447 https://doi.org/10.7717/peerj.12447
date submitted: 2021-09-02
date accepted: 2021-10-18
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rabee
  given name: Alaa Emara
author list: Agent
  family name: Kewan
  given name: Khalid Z.
author list: Agent
  family name: Sabra
  given name: Ebrahim A.
author list: Agent
  family name: El Shaer
  given name: Hassan M.
author list: Agent
  family name: Lamara
  given name: Mebarek
doi: 10.7717/peerj.12447
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: © 2021 Rabee et al.
attribution name: Rabee et al.

Estimating the differences in critical thermal maximum and metabolic rate of Helicoverpa punctigera (Wallengren) (Lepidoptera: Noctuidae) across life stages
type: item
type: AcademicArticle
description: Temperature is a crucial driver of insect activity and physiological processes throughout their life-history, and heat stress may impact life stages (larvae, pupae and adult) in different ways. Using thermolimit respirometry, we assessed the critical thermal maxima (CTmax-temperature at which an organism loses neuromuscular control), CO2 emission rate (V́CO2) and Q10 (a measure of V́CO2 temperature sensitivity) of three different life stages of Helicoverpa punctigera (Wallengren) by increasing their temperature exposure from 25 °C to 55 °C at a rate of 0.25 °C min−1. We found that the CTmax of larvae (49.1 °C ± 0.3 °C) was higher than pupae (47.4 °C ± 0.2 °C) and adults (46.9 °C ± 0.2 °C). The mean mass-specific CO2 emission rate (ml V́CO2 h−1) of larvae (0.26 ± 0.03 ml V́CO2 h−1) was also higher than adults (0.24 ± 0.04 ml V́CO2 h−1) and pupae (0.06 ± 0.02 ml V́CO2 h−1). The Q10: 25–35 °C for adults (2.01 ± 0.22) was significantly higher compared to larvae (1.40 ± 0.06) and Q10: 35–45 °C for adults (3.42 ± 0.24) was significantly higher compared to larvae (1.95 ± 0.08) and pupae (1.42 ± 0.98) respectively. We have established the upper thermal tolerance of H. punctigera, which will lead to a better understanding of the thermal physiology of this species both in its native range, and as a pest species in agricultural systems.
format: application/pdf
format: text/html
creator: Samuel A. Bawa
creator: Peter C. Gregg
creator: Alice P. Del Soccoro
creator: Cara Miller
creator: Nigel R. Andrew
subject: Agricultural Science
subject: Entomology
subject: Zoology
subject: Climate Change Biology
description: doi:10.7717/peerj.12479
publisher: PeerJ Inc.
rights: © 2021 Bawa et al.
abstract: Temperature is a crucial driver of insect activity and physiological processes throughout their life-history, and heat stress may impact life stages (larvae, pupae and adult) in different ways. Using thermolimit respirometry, we assessed the critical thermal maxima (CTmax-temperature at which an organism loses neuromuscular control), CO2 emission rate (V́CO2) and Q10 (a measure of V́CO2 temperature sensitivity) of three different life stages of Helicoverpa punctigera (Wallengren) by increasing their temperature exposure from 25 °C to 55 °C at a rate of 0.25 °C min−1. We found that the CTmax of larvae (49.1 °C ± 0.3 °C) was higher than pupae (47.4 °C ± 0.2 °C) and adults (46.9 °C ± 0.2 °C). The mean mass-specific CO2 emission rate (ml V́CO2 h−1) of larvae (0.26 ± 0.03 ml V́CO2 h−1) was also higher than adults (0.24 ± 0.04 ml V́CO2 h−1) and pupae (0.06 ± 0.02 ml V́CO2 h−1). The Q10: 25–35 °C for adults (2.01 ± 0.22) was significantly higher compared to larvae (1.40 ± 0.06) and Q10: 35–45 °C for adults (3.42 ± 0.24) was significantly higher compared to larvae (1.95 ± 0.08) and pupae (1.42 ± 0.98) respectively. We have established the upper thermal tolerance of H. punctigera, which will lead to a better understanding of the thermal physiology of this species both in its native range, and as a pest species in agricultural systems.
bibliographic citation: Bawa et al. (2021) Estimating the differences in critical thermal maximum and metabolic rate of Helicoverpa punctigera (Wallengren) (Lepidoptera: Noctuidae) across life stages. PeerJ 9:e12479 https://doi.org/10.7717/peerj.12479
date submitted: 2021-03-17
date accepted: 2021-10-21
issued: 2021-11-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bawa
  given name: Samuel A.
author list: Agent
  family name: Gregg
  given name: Peter C.
author list: Agent
  family name: Del Soccoro
  given name: Alice P.
author list: Agent
  family name: Miller
  given name: Cara
author list: Agent
  family name: Andrew
  given name: Nigel R.
doi: 10.7717/peerj.12479
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-11-17
copyright: © 2021 Bawa et al.
attribution name: Bawa et al.

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