PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Allocation pattern and accumulation potential of carbon stock in natural spruce forests in northwest China
items: Effect of Sofosbuvir plus Ribavirin therapy on hepatitis C patients in Pakistan: a retrospective study
items: Physical fitness predicts technical-tactical and time-motion profile in simulated Judo and Brazilian Jiu-Jitsu matches
items: A survey on sleep assessment methods
items: The global burden of HIV-1 drug resistance in the past 20 years
items: Rapid evolution of the Helicobacter pylori AlpA adhesin in a high gastric cancer risk region from Colombia
items: Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs
items: Shelters can negatively affect growth and welfare in lumpfish if feed is delivered continuously
items: Fingerprinting snakes: paleontological and paleoecological implications of zygantral growth rings in Serpentes
items: Feeding behavior and trophic interaction of three shark species in the Galapagos Marine Reserve

Allocation pattern and accumulation potential of carbon stock in natural spruce forests in northwest China
type: item
type: AcademicArticle
description: Background The spruce forests are dominant communities in northwest China, and play a key role in national carbon budgets. However, the patterns of carbon stock distribution and accumulation potential across stand ages are poorly documented. Methods We investigated the carbon stocks in biomass and soil in the natural spruce forests in the region by surveys on 39 plots. Biomass of tree components were estimated using allometric equations previously established based on tree height and diameter at breast height, while biomass in understory (shrub and herb) and forest floor were determined by total harvesting method. Fine root biomass was estimated by soil coring technique. Carbon stocks in various biomass components and soil (0–100 cm) were estimated by analyzing the carbon content of each component. Results The results showed that carbon stock in these forest ecosystems can be as high as 510.1 t ha−1, with an average of 449.4 t ha−1. Carbon stock ranged from 28.1 to 93.9 t ha−1 and from 0.6 to 8.7 t ha−1 with stand ages in trees and deadwoods, respectively. The proportion of shrubs, herbs, fine roots, litter and deadwoods ranged from 0.1% to 1% of the total ecosystem carbon, and was age-independent. Fine roots and deadwood which contribute to about 2% of the biomass carbon should be attached considerable weight in the investigation of natural forests. Soil carbon stock did not show a changing trend with stand age, ranging from 254.2 to 420.0 t ha−1 with an average of 358.7 t ha−1. The average value of carbon sequestration potential for these forests was estimated as 29.4 t ha−1, with the lower aged ones being the dominant contributor. The maximum carbon sequestration rate was 2.47 t ha−1 year−1 appearing in the growth stage of 37–56 years. Conclusion The carbon stock in biomass was the major contributor to the increment of carbon stock in ecosystems. Stand age is not a good predictor of soil carbon stocks and accurate evaluation of the soil carbon dynamics thus requi…
format: application/pdf
format: text/html
creator: Jun-Wei Yue
creator: Jin-Hong Guan
creator: Lei Deng
creator: Jian-Guo Zhang
creator: Guoqing Li
creator: Sheng Du
subject: Ecosystem Science
subject: Environmental Impacts
subject: Forestry
description: doi:10.7717/peerj.4859
publisher: PeerJ Inc.
rights: © 2018 Yue et al.
abstract: Background The spruce forests are dominant communities in northwest China, and play a key role in national carbon budgets. However, the patterns of carbon stock distribution and accumulation potential across stand ages are poorly documented. Methods We investigated the carbon stocks in biomass and soil in the natural spruce forests in the region by surveys on 39 plots. Biomass of tree components were estimated using allometric equations previously established based on tree height and diameter at breast height, while biomass in understory (shrub and herb) and forest floor were determined by total harvesting method. Fine root biomass was estimated by soil coring technique. Carbon stocks in various biomass components and soil (0–100 cm) were estimated by analyzing the carbon content of each component. Results The results showed that carbon stock in these forest ecosystems can be as high as 510.1 t ha−1, with an average of 449.4 t ha−1. Carbon stock ranged from 28.1 to 93.9 t ha−1 and from 0.6 to 8.7 t ha−1 with stand ages in trees and deadwoods, respectively. The proportion of shrubs, herbs, fine roots, litter and deadwoods ranged from 0.1% to 1% of the total ecosystem carbon, and was age-independent. Fine roots and deadwood which contribute to about 2% of the biomass carbon should be attached considerable weight in the investigation of natural forests. Soil carbon stock did not show a changing trend with stand age, ranging from 254.2 to 420.0 t ha−1 with an average of 358.7 t ha−1. The average value of carbon sequestration potential for these forests was estimated as 29.4 t ha−1, with the lower aged ones being the dominant contributor. The maximum carbon sequestration rate was 2.47 t ha−1 year−1 appearing in the growth stage of 37–56 years. Conclusion The carbon stock in biomass was the major contributor to the increment of carbon stock in ecosystems. Stand age is not a good predictor of soil carbon stocks and accurate evaluation of the soil carbon dynamics thus requi…
bibliographic citation: Yue et al. (2018) Allocation pattern and accumulation potential of carbon stock in natural spruce forests in northwest China. PeerJ 6:e4859 https://doi.org/10.7717/peerj.4859
date submitted: 2018-01-30
date accepted: 2018-05-08
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yue
  given name: Jun-Wei
author list: Agent
  family name: Guan
  given name: Jin-Hong
author list: Agent
  family name: Deng
  given name: Lei
author list: Agent
  family name: Zhang
  given name: Jian-Guo
author list: Agent
  family name: Li
  given name: Guoqing
author list: Agent
  family name: Du
  given name: Sheng
doi: 10.7717/peerj.4859
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: © 2018 Yue et al.
attribution name: Yue et al.

Effect of Sofosbuvir plus Ribavirin therapy on hepatitis C patients in Pakistan: a retrospective study
type: item
type: AcademicArticle
description: Background The annual global deaths from viral hepatitis is 1.4 million. Pakistan has the second highest burden of hepatitis C in the world. There is dire need to evaluate the response of new direct acting antivirals for the treatment of hepatitis C patients in Pakistan. World Health Organization has developed a strategy to treat 80% of HCV patients by 2030. In Pakistan, HCV treatment rate is 1%. The aim of the study was to analyze the effect of Sofosbuvir plus Ribavirin therapy on HCV patients in Pakistan. Methods An observational study was conducted at Fauji Foundation Hospital Rawalpindi from November-2016 to July-2017. All the drugs were administered according to the guidelines of Asia Pacific Association for the Study of Liver (APASL) for the treatment of HCV patients. A total 327 chronic HCV patients were enrolled in the study and 304 completed the treatment. Patients belonged to three different groups including treatment: Naïve patients (n = 107), Non-Responder patients (n = 126) and patients who relapsed to Interferon therapy (n = 71). All the patients were given Sofosbuvir plus Ribavirin therapy for 24 weeks and the early virological response (EVR) and end treatment response (ETR) was calculated. Different parameters including patient age, viral load, viral genotype, blood picture, ultrasound findings and liver function tests were also studied. Results Out of 304 patients, 301 (99%) achieved EVR and 300 achieved ETR (98.7%). End treatment response was 95.6% in HCV genotype 1 and 98.9% in HCV genotype 3 patients. ETR was 99.06% in treatment Naïve, 99.20% in non-responders and 97.18% in previously relapsed patients. We did not find the association of any host and viral factor in the determination of EVR and ETR. Conclusion The Sofosbuvir plus Ribavirin treatment is highly effective, safe and cost-effective for the treatment of hepatitis C patients in Pakistan.
format: application/pdf
format: text/html
creator: Zubia Jamil
creator: Yasir Waheed
creator: Maryam Malik
creator: Asghar A. Durrani
subject: Virology
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.4853
publisher: PeerJ Inc.
rights: © 2018 Jamil et al.
abstract: Background The annual global deaths from viral hepatitis is 1.4 million. Pakistan has the second highest burden of hepatitis C in the world. There is dire need to evaluate the response of new direct acting antivirals for the treatment of hepatitis C patients in Pakistan. World Health Organization has developed a strategy to treat 80% of HCV patients by 2030. In Pakistan, HCV treatment rate is 1%. The aim of the study was to analyze the effect of Sofosbuvir plus Ribavirin therapy on HCV patients in Pakistan. Methods An observational study was conducted at Fauji Foundation Hospital Rawalpindi from November-2016 to July-2017. All the drugs were administered according to the guidelines of Asia Pacific Association for the Study of Liver (APASL) for the treatment of HCV patients. A total 327 chronic HCV patients were enrolled in the study and 304 completed the treatment. Patients belonged to three different groups including treatment: Naïve patients (n = 107), Non-Responder patients (n = 126) and patients who relapsed to Interferon therapy (n = 71). All the patients were given Sofosbuvir plus Ribavirin therapy for 24 weeks and the early virological response (EVR) and end treatment response (ETR) was calculated. Different parameters including patient age, viral load, viral genotype, blood picture, ultrasound findings and liver function tests were also studied. Results Out of 304 patients, 301 (99%) achieved EVR and 300 achieved ETR (98.7%). End treatment response was 95.6% in HCV genotype 1 and 98.9% in HCV genotype 3 patients. ETR was 99.06% in treatment Naïve, 99.20% in non-responders and 97.18% in previously relapsed patients. We did not find the association of any host and viral factor in the determination of EVR and ETR. Conclusion The Sofosbuvir plus Ribavirin treatment is highly effective, safe and cost-effective for the treatment of hepatitis C patients in Pakistan.
bibliographic citation: Jamil et al. (2018) Effect of Sofosbuvir plus Ribavirin therapy on hepatitis C patients in Pakistan: a retrospective study. PeerJ 6:e4853 https://doi.org/10.7717/peerj.4853
date submitted: 2018-02-13
date accepted: 2018-05-04
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jamil
  given name: Zubia
author list: Agent
  family name: Waheed
  given name: Yasir
author list: Agent
  family name: Malik
  given name: Maryam
author list: Agent
  family name: Durrani
  given name: Asghar A.
doi: 10.7717/peerj.4853
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Jamil et al.
attribution name: Jamil et al.

Physical fitness predicts technical-tactical and time-motion profile in simulated Judo and Brazilian Jiu-Jitsu matches
type: item
type: AcademicArticle
description: Background Among combat sports, Judo and Brazilian Jiu-Jitsu (BJJ) present elevated physical fitness demands from the high-intensity intermittent efforts. However, information regarding how metabolic and neuromuscular physical fitness is associated with technical-tactical performance in Judo and BJJ fights is not available. This study aimed to relate indicators of physical fitness with combat performance variables in Judo and BJJ. Methods The sample consisted of Judo (n = 16) and BJJ (n = 24) male athletes. At the first meeting, the physical tests were applied and, in the second, simulated fights were performed for later notational analysis. Results The main findings indicate: (i) high reproducibility of the proposed instrument and protocol used for notational analysis in a mobile device; (ii) differences in the technical-tactical and time-motion patterns between modalities; (iii) performance-related variables are different in Judo and BJJ; and (iv) regression models based on metabolic fitness variables may account for up to 53% of the variances in technical-tactical and/or time-motion variables in Judo and up to 31% in BJJ, whereas neuromuscular fitness models can reach values up to 44 and 73% of prediction in Judo and BJJ, respectively. When all components are combined, they can explain up to 90% of high intensity actions in Judo. Discussion In conclusion, performance prediction models in simulated combat indicate that anaerobic, aerobic and neuromuscular fitness variables contribute to explain time-motion variables associated with high intensity and technical-tactical variables in Judo and BJJ fights.
format: application/pdf
format: text/html
creator: Victor S. Coswig
creator: Paulo Gentil
creator: João C.A. Bueno
creator: Bruno Follmer
creator: Vitor A. Marques
creator: Fabrício B. Del Vecchio
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.4851
publisher: PeerJ Inc.
rights: © 2018 Coswig et al.
abstract: Background Among combat sports, Judo and Brazilian Jiu-Jitsu (BJJ) present elevated physical fitness demands from the high-intensity intermittent efforts. However, information regarding how metabolic and neuromuscular physical fitness is associated with technical-tactical performance in Judo and BJJ fights is not available. This study aimed to relate indicators of physical fitness with combat performance variables in Judo and BJJ. Methods The sample consisted of Judo (n = 16) and BJJ (n = 24) male athletes. At the first meeting, the physical tests were applied and, in the second, simulated fights were performed for later notational analysis. Results The main findings indicate: (i) high reproducibility of the proposed instrument and protocol used for notational analysis in a mobile device; (ii) differences in the technical-tactical and time-motion patterns between modalities; (iii) performance-related variables are different in Judo and BJJ; and (iv) regression models based on metabolic fitness variables may account for up to 53% of the variances in technical-tactical and/or time-motion variables in Judo and up to 31% in BJJ, whereas neuromuscular fitness models can reach values up to 44 and 73% of prediction in Judo and BJJ, respectively. When all components are combined, they can explain up to 90% of high intensity actions in Judo. Discussion In conclusion, performance prediction models in simulated combat indicate that anaerobic, aerobic and neuromuscular fitness variables contribute to explain time-motion variables associated with high intensity and technical-tactical variables in Judo and BJJ fights.
bibliographic citation: Coswig et al. (2018) Physical fitness predicts technical-tactical and time-motion profile in simulated Judo and Brazilian Jiu-Jitsu matches. PeerJ 6:e4851 https://doi.org/10.7717/peerj.4851
date submitted: 2018-03-08
date accepted: 2018-05-06
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coswig
  given name: Victor S.
author list: Agent
  family name: Gentil
  given name: Paulo
author list: Agent
  family name: Bueno
  given name: João C.A.
author list: Agent
  family name: Follmer
  given name: Bruno
author list: Agent
  family name: Marques
  given name: Vitor A.
author list: Agent
  family name: Del Vecchio
  given name: Fabrício B.
doi: 10.7717/peerj.4851
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Coswig et al.
attribution name: Coswig et al.

A survey on sleep assessment methods
type: item
type: AcademicArticle
description: Purpose A literature review is presented that aims to summarize and compare current methods to evaluate sleep. Methods Current sleep assessment methods have been classified according to different criteria; e.g., objective (polysomnography, actigraphy…) vs. subjective (sleep questionnaires, diaries…), contact vs. contactless devices, and need for medical assistance vs. self-assessment. A comparison of validation studies is carried out for each method, identifying their sensitivity and specificity reported in the literature. Finally, the state of the market has also been reviewed with respect to customers’ opinions about current sleep apps. Results A taxonomy that classifies the sleep detection methods. A description of each method that includes the tendencies of their underlying technologies analyzed in accordance with the literature. A comparison in terms of precision of existing validation studies and reports. Discussion In order of accuracy, sleep detection methods may be arranged as follows: Questionnaire < Sleep diary < Contactless devices < Contact devices < Polysomnography A literature review suggests that current subjective methods present a sensitivity between 73% and 97.7%, while their specificity ranges in the interval 50%–96%. Objective methods such as actigraphy present a sensibility higher than 90%. However, their specificity is low compared to their sensitivity, being one of the limitations of such technology. Moreover, there are other factors, such as the patient’s perception of her or his sleep, that can be provided only by subjective methods. Therefore, sleep detection methods should be combined to produce a synergy between objective and subjective methods. The review of the market indicates the most valued sleep apps, but it also identifies problems and gaps, e.g., many hardware devices have not been validated and (especially software apps) should be studied before their clinical use.
format: application/pdf
format: text/html
creator: Vanessa Ibáñez
creator: Josep Silva
creator: Omar Cauli
subject: Global Health
subject: Neurology
description: doi:10.7717/peerj.4849
publisher: PeerJ Inc.
rights: © 2018 Ibáñez et al.
abstract: Purpose A literature review is presented that aims to summarize and compare current methods to evaluate sleep. Methods Current sleep assessment methods have been classified according to different criteria; e.g., objective (polysomnography, actigraphy…) vs. subjective (sleep questionnaires, diaries…), contact vs. contactless devices, and need for medical assistance vs. self-assessment. A comparison of validation studies is carried out for each method, identifying their sensitivity and specificity reported in the literature. Finally, the state of the market has also been reviewed with respect to customers’ opinions about current sleep apps. Results A taxonomy that classifies the sleep detection methods. A description of each method that includes the tendencies of their underlying technologies analyzed in accordance with the literature. A comparison in terms of precision of existing validation studies and reports. Discussion In order of accuracy, sleep detection methods may be arranged as follows: Questionnaire < Sleep diary < Contactless devices < Contact devices < Polysomnography A literature review suggests that current subjective methods present a sensitivity between 73% and 97.7%, while their specificity ranges in the interval 50%–96%. Objective methods such as actigraphy present a sensibility higher than 90%. However, their specificity is low compared to their sensitivity, being one of the limitations of such technology. Moreover, there are other factors, such as the patient’s perception of her or his sleep, that can be provided only by subjective methods. Therefore, sleep detection methods should be combined to produce a synergy between objective and subjective methods. The review of the market indicates the most valued sleep apps, but it also identifies problems and gaps, e.g., many hardware devices have not been validated and (especially software apps) should be studied before their clinical use.
bibliographic citation: Ibáñez et al. (2018) A survey on sleep assessment methods. PeerJ 6:e4849 https://doi.org/10.7717/peerj.4849
date submitted: 2018-02-17
date accepted: 2018-05-07
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ibáñez
  given name: Vanessa
author list: Agent
  family name: Silva
  given name: Josep
author list: Agent
  family name: Cauli
  given name: Omar
doi: 10.7717/peerj.4849
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Ibáñez et al.
attribution name: Ibáñez et al.

The global burden of HIV-1 drug resistance in the past 20 years
type: item
type: AcademicArticle
description: Genotypic drug resistance testing has been an integral part of the clinical management of HIV patients for almost 20 years, not only assisting treatment choices but also informing drug development. Accurate estimations on the worldwide circulation of drug resistance are difficult to obtain, particularly in low/middle-income countries. In this work, we queried two of the largest public HIV sequence repositories in the world—Los Alamos and Stanford HIVdb—to derive global prevalence, time trends and geodemographic predictors of HIV drug resistance. Different genotypic interpretation systems were used to ascertain resistance to reverse transcriptase and protease inhibitors. Continental, subtype-specific (including circulating recombinant forms) stratification as well as analysis on drug-naïve isolates were performed. Geographic information system analysis correlated country-specific drug resistance to sociodemographic and health indicators obtained from the World Bank. By looking at over 33,000 sequences worldwide between 1996 and 2016, increasing drug resistance trends with non-B subtypes and recombinants were found; transmitted drug resistance appeared to remain stable in the last decade. While an increase in drug resistance is expected with antiretroviral therapy rollout in resource-constrained areas, the plateau effect in areas covered by the most modern drug regimens warns against the downgrading of the resistance issue.
format: application/pdf
format: text/html
creator: Maurizio Zazzi
creator: Hui Hu
creator: Mattia Prosperi
subject: Virology
subject: Epidemiology
subject: Global Health
subject: HIV
subject: Statistics
description: doi:10.7717/peerj.4848
publisher: PeerJ Inc.
rights: © 2018 Zazzi et al.
abstract: Genotypic drug resistance testing has been an integral part of the clinical management of HIV patients for almost 20 years, not only assisting treatment choices but also informing drug development. Accurate estimations on the worldwide circulation of drug resistance are difficult to obtain, particularly in low/middle-income countries. In this work, we queried two of the largest public HIV sequence repositories in the world—Los Alamos and Stanford HIVdb—to derive global prevalence, time trends and geodemographic predictors of HIV drug resistance. Different genotypic interpretation systems were used to ascertain resistance to reverse transcriptase and protease inhibitors. Continental, subtype-specific (including circulating recombinant forms) stratification as well as analysis on drug-naïve isolates were performed. Geographic information system analysis correlated country-specific drug resistance to sociodemographic and health indicators obtained from the World Bank. By looking at over 33,000 sequences worldwide between 1996 and 2016, increasing drug resistance trends with non-B subtypes and recombinants were found; transmitted drug resistance appeared to remain stable in the last decade. While an increase in drug resistance is expected with antiretroviral therapy rollout in resource-constrained areas, the plateau effect in areas covered by the most modern drug regimens warns against the downgrading of the resistance issue.
bibliographic citation: Zazzi et al. (2018) The global burden of HIV-1 drug resistance in the past 20 years. PeerJ 6:e4848 https://doi.org/10.7717/peerj.4848
date submitted: 2018-02-19
date accepted: 2018-05-07
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zazzi
  given name: Maurizio
author list: Agent
  family name: Hu
  given name: Hui
author list: Agent
  family name: Prosperi
  given name: Mattia
doi: 10.7717/peerj.4848
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Zazzi et al.
attribution name: Zazzi et al.

Rapid evolution of the Helicobacter pylori AlpA adhesin in a high gastric cancer risk region from Colombia
type: item
type: AcademicArticle
description: To be able to survive, Helicobacter pylori must adhere to the gastric epithelial cells of its human host. For this purpose, the bacterium employs an array of adhesins, for example, AlpA. The adhesin AlpA has been proposed as a major adhesin because of its critical role in human stomach colonization. Therefore, understanding how AlpA evolved could be important for the development of new diagnostic strategies. However, the genetic variation and microevolutionary patterns of alpA have not been described in Colombia. The study aim was to describe the variation patterns and microevolutionary process of alpA in Colombian clinical isolates of H. pylori. The existing polymorphisms, which are deviations from the neutral model of molecular evolution, and the genetic differentiation of the alpA gene from Colombian clinical isolates of H. pylori were determined. The analysis shows that gene conversion and purifying selection have shaped the evolution of three different variants of alpA in Colombia.
format: application/pdf
format: text/html
creator: Andrés Julián Gutiérrez-Escobar
creator: Gina Méndez-Callejas
creator: Orlando Acevedo
creator: Maria Mercedes Bravo
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genetics
subject: Microbiology
description: doi:10.7717/peerj.4846
publisher: PeerJ Inc.
rights: © 2018 Gutiérrez-Escobar et al.
abstract: To be able to survive, Helicobacter pylori must adhere to the gastric epithelial cells of its human host. For this purpose, the bacterium employs an array of adhesins, for example, AlpA. The adhesin AlpA has been proposed as a major adhesin because of its critical role in human stomach colonization. Therefore, understanding how AlpA evolved could be important for the development of new diagnostic strategies. However, the genetic variation and microevolutionary patterns of alpA have not been described in Colombia. The study aim was to describe the variation patterns and microevolutionary process of alpA in Colombian clinical isolates of H. pylori. The existing polymorphisms, which are deviations from the neutral model of molecular evolution, and the genetic differentiation of the alpA gene from Colombian clinical isolates of H. pylori were determined. The analysis shows that gene conversion and purifying selection have shaped the evolution of three different variants of alpA in Colombia.
bibliographic citation: Gutiérrez-Escobar et al. (2018) Rapid evolution of the Helicobacter pylori AlpA adhesin in a high gastric cancer risk region from Colombia. PeerJ 6:e4846 https://doi.org/10.7717/peerj.4846
date submitted: 2018-03-02
date accepted: 2018-05-06
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gutiérrez-Escobar
  given name: Andrés Julián
author list: Agent
  family name: Méndez-Callejas
  given name: Gina
author list: Agent
  family name: Acevedo
  given name: Orlando
author list: Agent
  family name: Bravo
  given name: Maria Mercedes
doi: 10.7717/peerj.4846
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Gutiérrez-Escobar et al.
attribution name: Gutiérrez-Escobar et al.

Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs
type: item
type: AcademicArticle
description: Toll-like receptors (TLRs) are an important component of innate immunity, the first line of pathogen defence. One of the major roles of TLRs includes recognition of pathogen-associated molecular patterns. Amphibians are currently facing population declines and even extinction due to chytridiomycosis caused by the Batrachochytrium dendrobatidis (Bd) fungus. Evidence from other vertebrates shows that TLR2 and TLR4 are involved in innate immunity against various fungi. Such genes therefore may play a functional role in amphibian-chytridiomycosis dynamics. Frogs from East Asia appear to be tolerant to Bd, so we examined the genetic diversity that underlies TLR2 and TLR4 from three Japanese Ranidae frog species, Rana japonica, R. ornativentris and R. tagoi tagoi (n = 5 per species). We isolated 27 TLR2 and 20 TLR4 alleles and found that these genes are evolutionarily conserved, with overall evidence supporting purifying selection. In contrast, site-by-site analysis of selection identified several specific codon sites under positive selection, some of which were located in the variable leucine rich repeat domains. In addition, preliminary expression levels of TLR2 and TLR4 from transcriptome data showed overall low expression. Although it remains unclear whether infectious pathogens are a selective force acting on TLRs of Japanese frogs, our results support that certain sites in TLRs of these species may have experienced pathogen-mediated selection.
format: application/pdf
format: text/html
creator: Quintin Lau
creator: Takeshi Igawa
creator: Tiffany A. Kosch
creator: Yoko Satta
subject: Evolutionary Studies
subject: Molecular Biology
description: doi:10.7717/peerj.4842
publisher: PeerJ Inc.
rights: © 2018 Lau et al.
abstract: Toll-like receptors (TLRs) are an important component of innate immunity, the first line of pathogen defence. One of the major roles of TLRs includes recognition of pathogen-associated molecular patterns. Amphibians are currently facing population declines and even extinction due to chytridiomycosis caused by the Batrachochytrium dendrobatidis (Bd) fungus. Evidence from other vertebrates shows that TLR2 and TLR4 are involved in innate immunity against various fungi. Such genes therefore may play a functional role in amphibian-chytridiomycosis dynamics. Frogs from East Asia appear to be tolerant to Bd, so we examined the genetic diversity that underlies TLR2 and TLR4 from three Japanese Ranidae frog species, Rana japonica, R. ornativentris and R. tagoi tagoi (n = 5 per species). We isolated 27 TLR2 and 20 TLR4 alleles and found that these genes are evolutionarily conserved, with overall evidence supporting purifying selection. In contrast, site-by-site analysis of selection identified several specific codon sites under positive selection, some of which were located in the variable leucine rich repeat domains. In addition, preliminary expression levels of TLR2 and TLR4 from transcriptome data showed overall low expression. Although it remains unclear whether infectious pathogens are a selective force acting on TLRs of Japanese frogs, our results support that certain sites in TLRs of these species may have experienced pathogen-mediated selection.
bibliographic citation: Lau et al. (2018) Selective constraint acting on TLR2 and TLR4 genes of Japanese Rana frogs. PeerJ 6:e4842 https://doi.org/10.7717/peerj.4842
date submitted: 2018-03-13
date accepted: 2018-05-06
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lau
  given name: Quintin
author list: Agent
  family name: Igawa
  given name: Takeshi
author list: Agent
  family name: Kosch
  given name: Tiffany A.
author list: Agent
  family name: Satta
  given name: Yoko
doi: 10.7717/peerj.4842
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Lau et al.
attribution name: Lau et al.

Shelters can negatively affect growth and welfare in lumpfish if feed is delivered continuously
type: item
type: AcademicArticle
description: Due to the socioeconomic importance of salmon farming in the North Atlantic and the economic impact of sea lice in this industry, there is high demand for novel pest control methods. One such method is the use of cleaner fish to remove the lice from the salmon. A cleaner fish that has recently gained in popularity due to its ability to work in cold water, is the lumpfish (Cyclopterus lumpus). This fish varies in efficiency, but when mortality is low and cleaning optimal, the fish are successful in keeping parasite burdens low. However, there is some concern for the welfare of lumpfish in the industry, because mortality is often high. This is sometimes attributed to inadequate feeding and shelter. Here we compare growth, body condition, and fin health of fish reared for four weeks in a crossed treatment design crossing shelter availability (shelter vs none) and feed delivery method (manual meal time feeds and continuous automated feeding). In terms of weight gain, shelter availability interacted with feeding method, with fish that had access to shelters and were fed using automated feeders gaining less weight than other fish. Fin health was not affected, but body condition was lowered both by access to shelter and being fed continuously. The results indicate a need to carefully consider how feeding method and shelter use is combined, both in cages and during rearing on land.
format: application/pdf
format: text/html
creator: Asa Johannesen
creator: Nakita E. Joensen
creator: Eyðfinn Magnussen
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
description: doi:10.7717/peerj.4837
publisher: PeerJ Inc.
rights: © 2018 Johannesen et al.
abstract: Due to the socioeconomic importance of salmon farming in the North Atlantic and the economic impact of sea lice in this industry, there is high demand for novel pest control methods. One such method is the use of cleaner fish to remove the lice from the salmon. A cleaner fish that has recently gained in popularity due to its ability to work in cold water, is the lumpfish (Cyclopterus lumpus). This fish varies in efficiency, but when mortality is low and cleaning optimal, the fish are successful in keeping parasite burdens low. However, there is some concern for the welfare of lumpfish in the industry, because mortality is often high. This is sometimes attributed to inadequate feeding and shelter. Here we compare growth, body condition, and fin health of fish reared for four weeks in a crossed treatment design crossing shelter availability (shelter vs none) and feed delivery method (manual meal time feeds and continuous automated feeding). In terms of weight gain, shelter availability interacted with feeding method, with fish that had access to shelters and were fed using automated feeders gaining less weight than other fish. Fin health was not affected, but body condition was lowered both by access to shelter and being fed continuously. The results indicate a need to carefully consider how feeding method and shelter use is combined, both in cages and during rearing on land.
bibliographic citation: Johannesen et al. (2018) Shelters can negatively affect growth and welfare in lumpfish if feed is delivered continuously. PeerJ 6:e4837 https://doi.org/10.7717/peerj.4837
date submitted: 2018-03-12
date accepted: 2018-05-04
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Johannesen
  given name: Asa
author list: Agent
  family name: Joensen
  given name: Nakita E.
author list: Agent
  family name: Magnussen
  given name: Eyðfinn
doi: 10.7717/peerj.4837
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Johannesen et al.
attribution name: Johannesen et al.

Fingerprinting snakes: paleontological and paleoecological implications of zygantral growth rings in Serpentes
type: item
type: AcademicArticle
description: We introduce a new non-destructive source of skeletochronological data with applications to species identification, associating disarticulated remains, assessing minimum number of individuals (MNI), and collection management of fossil snakes, but with potential implications for all bony vertebrates, extinct or extant. Study of a diverse sample of Recent henophidian snakes confirms that annual growth cycles (AGCs) visible on the surface of the vertebral zygantrum correspond to lines of arrested growth in osteohistological thin sections and accordingly reflect chronological age. None of the specimens considered here showed signs of remodelling of the zygantrum, suggesting that a complete, unaltered age record is preserved. We tested potential influences on AGCs with a single experimental organism, a male Bogertophis subocularis, that was raised at a controlled temperature and with constant access to mice and water. The conditions in which this individual was maintained, including that it had yet to live through a full reproductive cycle, enabled us to determine that its AGCs reflect only the annual solar cycle, and neither temperature, nor resource availability, nor energy diversion to gametogenesis could explain that it still exhibited lines of arrested growth. Moreover, growth lines in this specimen are deposited toward the end of the growth season in the fall, and not in the winter, during which this individual continued to feed and grow, even though this mid-latitude species would normally be hibernating and not growing. This suggests that growth lines are not caused by hibernation, but reflect the onset of a physiological cycle preparing Bogertophis subocularis for winter rest. That being said, hibernation and reproductive cycle could still influence the amount of time represented by an individual growth line. Growth-line number and AGC spacing-pattern, plus centrum length, are used to estimate MNI of the Early Eocene fossil snake Boavus occidentalis collected fr…
format: application/pdf
format: text/html
creator: Holger Petermann
creator: Jacques A. Gauthier
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.4819
publisher: PeerJ Inc.
rights: © 2018 Petermann and Gauthier
abstract: We introduce a new non-destructive source of skeletochronological data with applications to species identification, associating disarticulated remains, assessing minimum number of individuals (MNI), and collection management of fossil snakes, but with potential implications for all bony vertebrates, extinct or extant. Study of a diverse sample of Recent henophidian snakes confirms that annual growth cycles (AGCs) visible on the surface of the vertebral zygantrum correspond to lines of arrested growth in osteohistological thin sections and accordingly reflect chronological age. None of the specimens considered here showed signs of remodelling of the zygantrum, suggesting that a complete, unaltered age record is preserved. We tested potential influences on AGCs with a single experimental organism, a male Bogertophis subocularis, that was raised at a controlled temperature and with constant access to mice and water. The conditions in which this individual was maintained, including that it had yet to live through a full reproductive cycle, enabled us to determine that its AGCs reflect only the annual solar cycle, and neither temperature, nor resource availability, nor energy diversion to gametogenesis could explain that it still exhibited lines of arrested growth. Moreover, growth lines in this specimen are deposited toward the end of the growth season in the fall, and not in the winter, during which this individual continued to feed and grow, even though this mid-latitude species would normally be hibernating and not growing. This suggests that growth lines are not caused by hibernation, but reflect the onset of a physiological cycle preparing Bogertophis subocularis for winter rest. That being said, hibernation and reproductive cycle could still influence the amount of time represented by an individual growth line. Growth-line number and AGC spacing-pattern, plus centrum length, are used to estimate MNI of the Early Eocene fossil snake Boavus occidentalis collected fr…
bibliographic citation: Petermann et al. (2018) Fingerprinting snakes: paleontological and paleoecological implications of zygantral growth rings in Serpentes. PeerJ 6:e4819 https://doi.org/10.7717/peerj.4819
date submitted: 2017-10-09
date accepted: 2018-05-01
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Petermann
  given name: Holger
author list: Agent
  family name: Gauthier
  given name: Jacques A.
doi: 10.7717/peerj.4819
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Petermann and Gauthier
attribution name: Petermann and Gauthier

Feeding behavior and trophic interaction of three shark species in the Galapagos Marine Reserve
type: item
type: AcademicArticle
description: There is great concern about the future of sharks in Ecuador because of the lack of biological knowledge of most species that inhabit the region. This paper analyzes the feeding behavior of the pelagic thresher shark (Alopias pelagicus), the blue shark (Prionace glauca) and the silky shark (Carcharhinus falciformis) through the use of stable isotopes of carbon and nitrogen (δ13C and δ15N), with the aim of determining the degree of interaction between these species in the Galapagos Marine Reserve. No interspecific differences were found in use of oceanic vs. inshore feeding areas (δ13C: Kruskal–Wallis test, p = 0.09). The position in the hierarchy of the food web where A. pelagicus feeds differed from that of the other species (δ15N: Kruskal–Wallis test, p = 0.01). There were no significant differences in δ13C and δ15N values between males and females of the three species (Student’s t-test, p > 0.05), which suggests that both sexes have a similar feeding behavior. A specialist strategy was observed in P. glauca (trophic niche breadth TNB = 0.69), while the other species were found to be generalist (A. pelagicus TNB = 1.50 and C. falciformis TNB = 1.09). The estimated trophic level (TL) varied between the three species. C. falciformis occupied the highest trophic level (TL = 4.4), making it a quaternary predator in the region. The results of this study coincide with the identified behavior in these predators in other areas of the tropical Pacific (Colombia and Mexico), and suggest a pelagic foraging strategy with differential consumption of prey between the three species. These ecological aspects can provide timely information when implementing in conservation measures for these shark species in the Tropical Pacific and Galapagos Marine Reserve.
format: application/pdf
format: text/html
creator: Diego Páez-Rosas
creator: Paul Insuasti-Zarate
creator: Marjorie Riofrío-Lazo
creator: Felipe Galván-Magaña
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Conservation Biology
subject: Marine Biology
description: doi:10.7717/peerj.4818
publisher: PeerJ Inc.
rights: © 2018 Páez-Rosas et al.
abstract: There is great concern about the future of sharks in Ecuador because of the lack of biological knowledge of most species that inhabit the region. This paper analyzes the feeding behavior of the pelagic thresher shark (Alopias pelagicus), the blue shark (Prionace glauca) and the silky shark (Carcharhinus falciformis) through the use of stable isotopes of carbon and nitrogen (δ13C and δ15N), with the aim of determining the degree of interaction between these species in the Galapagos Marine Reserve. No interspecific differences were found in use of oceanic vs. inshore feeding areas (δ13C: Kruskal–Wallis test, p = 0.09). The position in the hierarchy of the food web where A. pelagicus feeds differed from that of the other species (δ15N: Kruskal–Wallis test, p = 0.01). There were no significant differences in δ13C and δ15N values between males and females of the three species (Student’s t-test, p > 0.05), which suggests that both sexes have a similar feeding behavior. A specialist strategy was observed in P. glauca (trophic niche breadth TNB = 0.69), while the other species were found to be generalist (A. pelagicus TNB = 1.50 and C. falciformis TNB = 1.09). The estimated trophic level (TL) varied between the three species. C. falciformis occupied the highest trophic level (TL = 4.4), making it a quaternary predator in the region. The results of this study coincide with the identified behavior in these predators in other areas of the tropical Pacific (Colombia and Mexico), and suggest a pelagic foraging strategy with differential consumption of prey between the three species. These ecological aspects can provide timely information when implementing in conservation measures for these shark species in the Tropical Pacific and Galapagos Marine Reserve.
bibliographic citation: Páez-Rosas et al. (2018) Feeding behavior and trophic interaction of three shark species in the Galapagos Marine Reserve. PeerJ 6:e4818 https://doi.org/10.7717/peerj.4818
date submitted: 2018-01-29
date accepted: 2018-05-01
issued: 2018-05-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Páez-Rosas
  given name: Diego
author list: Agent
  family name: Insuasti-Zarate
  given name: Paul
author list: Agent
  family name: Riofrío-Lazo
  given name: Marjorie
author list: Agent
  family name: Galván-Magaña
  given name: Felipe
doi: 10.7717/peerj.4818
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-05-25
copyright: ©2018 Páez-Rosas et al.
attribution name: Páez-Rosas et al.

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