PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Century-scale changes in phytoplankton phenology in the Gulf of Maine
items: Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters
items: Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)
items: Coupling and metabolic analysis of urbanization and environment between two resource-based cities in North China
items: How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species
items: Galantamine plasma concentration and cognitive response in Alzheimer’s disease
items: A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast
items: The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment
items: Predicting gene expression using DNA methylation in three human populations
items: Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids

Century-scale changes in phytoplankton phenology in the Gulf of Maine
type: item
type: AcademicArticle
description: The phenology of major seasonal events is an important indicator of climate. We analyzed multiple datasets of in situ chlorophyll measurements from the Gulf of Maine dating back to the early 20th century in order to detect climate-scale changes in phenology. The seasonal cycle was consistently characterized by a two-bloom pattern, with spring and autumn blooms. The timing of both spring and autumn blooms has shifted later in the year at rates ranging from ∼1 to 9 days per decade since 1960, depending on the phenology metric, and trends only emerged at time scales of >40 years. Bloom phenology had only weak correlations with major climate indices. There were stronger associations between bloom timing and physical and chemical variables. Autumn bloom initiation correlated strongly with surface temperature and salinity, and spring bloom with nutrients. A later spring bloom also correlated with an increased cohort of Calanus finmarchicus, suggesting broader ecosystem implications of phytoplankton phenology.
format: application/pdf
format: text/html
creator: Nicholas R. Record
creator: William M. Balch
creator: Karen Stamieszkin
subject: Climate Change Biology
subject: Biological Oceanography
description: doi:10.7717/peerj.6735
publisher: PeerJ Inc.
rights: © 2019 Record et al.
abstract: The phenology of major seasonal events is an important indicator of climate. We analyzed multiple datasets of in situ chlorophyll measurements from the Gulf of Maine dating back to the early 20th century in order to detect climate-scale changes in phenology. The seasonal cycle was consistently characterized by a two-bloom pattern, with spring and autumn blooms. The timing of both spring and autumn blooms has shifted later in the year at rates ranging from ∼1 to 9 days per decade since 1960, depending on the phenology metric, and trends only emerged at time scales of >40 years. Bloom phenology had only weak correlations with major climate indices. There were stronger associations between bloom timing and physical and chemical variables. Autumn bloom initiation correlated strongly with surface temperature and salinity, and spring bloom with nutrients. A later spring bloom also correlated with an increased cohort of Calanus finmarchicus, suggesting broader ecosystem implications of phytoplankton phenology.
bibliographic citation: Record et al. (2019) Century-scale changes in phytoplankton phenology in the Gulf of Maine. PeerJ 7:e6735 https://doi.org/10.7717/peerj.6735
date submitted: 2018-11-05
date accepted: 2019-03-07
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Record
  given name: Nicholas R.
author list: Agent
  family name: Balch
  given name: William M.
author list: Agent
  family name: Stamieszkin
  given name: Karen
doi: 10.7717/peerj.6735
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Record et al.
attribution name: Record et al.

Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters
type: item
type: AcademicArticle
description: A 2016 collaborative survey of commercial fish parasites in Moreton Bay, Queensland, Australia led to the discovery of two new species of parasitic copepods belonging to the family Bomolochidae. Females of Nothobomolochus johndaveorum n. sp. were found attached to the gill filaments of Gerres subfasciatus and Gerres oyena. The new species most closely resembles N. leiognathicola and N. quadriceros. All 3 species possess 3 modified setae on the first antennulary segment that are approximately the same length and have a robust seta on the second antennulary segment adjacent to the 3 modified setae giving a superficial appearance of 4 modified setae on the antennule. The new species can be distinguished from these two species in its possession of longer inner setae on the first two endopodal segments of leg 4: the seta on endopodal segment 1 extends past the midline of the distal segment in the new species vs to the proximal margin of the distal segment in the other two species, and the seta on segment 2 extends well beyond the distal margin of the endopod in the new species vs just to the margin in the other two species. Females and males of Unicolax longicrus n. sp. were found in the nasal sinuses of Sillago maculata and Sillago ciliata. The new species differs from 6 of its 7 congeners in having a leg 4 exopod formula of II, I, 4 rather than II, I, 3 or II, I, 5. The new species resembles U. anonymous in this feature, but differs in its possession of a leg 5 that is relatively longer and less wide, and, whereas U. anonymous possesses inner and outer distal spines on leg 5 that are approximately the same length, those of the new species are relatively longer and asymmetrical. Unicolax longicrus n. sp. is unique among its congeners in its possession of a leg 4 with highly elongated endopodal segments 2 and 3, from which its name is derived. In addition to describing the two new species, host and locality reports for all species of Nothobomolochus and Unicolax are revi…
format: application/pdf
format: text/html
creator: James P. Bernot
creator: Geoffrey A. Boxshall
subject: Biodiversity
subject: Marine Biology
subject: Parasitology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6858
publisher: PeerJ Inc.
rights: © 2019 Bernot and Boxshall
abstract: A 2016 collaborative survey of commercial fish parasites in Moreton Bay, Queensland, Australia led to the discovery of two new species of parasitic copepods belonging to the family Bomolochidae. Females of Nothobomolochus johndaveorum n. sp. were found attached to the gill filaments of Gerres subfasciatus and Gerres oyena. The new species most closely resembles N. leiognathicola and N. quadriceros. All 3 species possess 3 modified setae on the first antennulary segment that are approximately the same length and have a robust seta on the second antennulary segment adjacent to the 3 modified setae giving a superficial appearance of 4 modified setae on the antennule. The new species can be distinguished from these two species in its possession of longer inner setae on the first two endopodal segments of leg 4: the seta on endopodal segment 1 extends past the midline of the distal segment in the new species vs to the proximal margin of the distal segment in the other two species, and the seta on segment 2 extends well beyond the distal margin of the endopod in the new species vs just to the margin in the other two species. Females and males of Unicolax longicrus n. sp. were found in the nasal sinuses of Sillago maculata and Sillago ciliata. The new species differs from 6 of its 7 congeners in having a leg 4 exopod formula of II, I, 4 rather than II, I, 3 or II, I, 5. The new species resembles U. anonymous in this feature, but differs in its possession of a leg 5 that is relatively longer and less wide, and, whereas U. anonymous possesses inner and outer distal spines on leg 5 that are approximately the same length, those of the new species are relatively longer and asymmetrical. Unicolax longicrus n. sp. is unique among its congeners in its possession of a leg 4 with highly elongated endopodal segments 2 and 3, from which its name is derived. In addition to describing the two new species, host and locality reports for all species of Nothobomolochus and Unicolax are revi…
bibliographic citation: Bernot et al. (2019) Two new species of parasitic copepods from the genera Nothobomolochus and Unicolax (Cyclopoida: Bomolochidae) from Australian waters. PeerJ 7:e6858 https://doi.org/10.7717/peerj.6858
date submitted: 2019-01-17
date accepted: 2019-03-27
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bernot
  given name: James P.
author list: Agent
  family name: Boxshall
  given name: Geoffrey A.
doi: 10.7717/peerj.6858
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Bernot and Boxshall
attribution name: Bernot and Boxshall

Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae)
type: item
type: AcademicArticle
description: A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.
format: application/pdf
format: text/html
creator: Gengyun Niu
creator: Yaoyao Zhang
creator: Zhenyi Li
creator: Meicai Wei
subject: Entomology
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.6866
publisher: PeerJ Inc.
rights: © 2019 Niu et al.
abstract: A new genus with a new species of the tribe Hoplocampini of Hoplocampinae was described from China: Analcellicampa xanthosoma Wei & Niu, gen. et sp. nov. Hoplocampa danfengensis G. Xiao 1994 was designated as the type species of the new genus. The characters of Analcellicampa danfengensis (G. Xiao) comb. nov. were briefly discussed. A key to the tribes and known genera of Hoplocampinae was provided. The nearly complete mitochondrial genome of A. xanthosoma was characterized as having a length of 15,512 bp and containing 37 genes (22 tRNAs, 13 protein-coding genes (PCGs), and 2 rRNAs). The gene order of this new specimen was the same as that in the inferred insect ancestral mitochondrial genome. All PCGs were initiated by ATN codons and ended with TAA or T stop codons. All tRNAs had a typical cloverleaf secondary structure, except for trnS1. Remarkably, the helices H991 of rrnS and H47 of rrnL were redundant, while helix H563 of rrnL was highly conserved. A phylogeny based on previously reported symphytan mitochondrial genomes showed that A. xanthosoma is a sister group to Monocellicampa pruni, with high support values. We suggest that A. xanthosoma and M. pruni belong to the tribe Hoplocampini of Hoplocampinae.
bibliographic citation: Niu et al. (2019) Characterization of the mitochondrial genome of Analcellicampa xanthosoma gen. et sp. nov. (Hymenoptera: Tenthredinidae). PeerJ 7:e6866 https://doi.org/10.7717/peerj.6866
date submitted: 2018-10-10
date accepted: 2019-03-28
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Niu
  given name: Gengyun
author list: Agent
  family name: Zhang
  given name: Yaoyao
author list: Agent
  family name: Li
  given name: Zhenyi
author list: Agent
  family name: Wei
  given name: Meicai
doi: 10.7717/peerj.6866
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Niu et al.
attribution name: Niu et al.

Coupling and metabolic analysis of urbanization and environment between two resource-based cities in North China
type: item
type: AcademicArticle
description: Background The complex relationship between urbanization and environment in resource-based cities is of increasing concern. Methods As typical examples of rapid economic growth, obvious urbanization, and successful transformed production models, the cities of Dongying and Binzhou in Yellow River Delta High-tech Economic Zone were chosen for research. First, this study examines the coupling relationship between urbanization and the environment over the last seventeen years using the coupling degree model. Second, the emergy analysis method is used to further study the energy metabolism and environmental load in the two cities to reveal these couplings. Results Dongying and Binzhou were well-coupled and the coupling coordination degree was in the stage of mild coordination coupling showing an upward trend. The total metabolic energy of the two cities increased yearly from 2000 to 2016, and the emergy extroversion ratio data showed the cities’ dependence on external elements such as continuously increased imported resources. The total emergy used in the two cities showed an upward trend during 2000 and 2016, while the emergy per capita consumption increased significantly, suggesting that the society’s energy efficiency improved. During the same period, the environmental loading ratio increased gradually, and the elements causing the environmental load shifted from internal to external. Discussion The study shows that the factors of environmental load in developing cities are gradually shifting from internal to external, which is vital to understanding the impact of urban transformation and upgrading of resource-based cities on the environment.
format: application/pdf
format: text/html
creator: Hao Chen
creator: Linyu Xu
creator: Qingqing Cao
creator: Miansong Huang
creator: Minghua Song
creator: Quan Quan
creator: Jian Liu
subject: Ecology
subject: Ecosystem Science
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Atmospheric Chemistry
description: doi:10.7717/peerj.6869
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Background The complex relationship between urbanization and environment in resource-based cities is of increasing concern. Methods As typical examples of rapid economic growth, obvious urbanization, and successful transformed production models, the cities of Dongying and Binzhou in Yellow River Delta High-tech Economic Zone were chosen for research. First, this study examines the coupling relationship between urbanization and the environment over the last seventeen years using the coupling degree model. Second, the emergy analysis method is used to further study the energy metabolism and environmental load in the two cities to reveal these couplings. Results Dongying and Binzhou were well-coupled and the coupling coordination degree was in the stage of mild coordination coupling showing an upward trend. The total metabolic energy of the two cities increased yearly from 2000 to 2016, and the emergy extroversion ratio data showed the cities’ dependence on external elements such as continuously increased imported resources. The total emergy used in the two cities showed an upward trend during 2000 and 2016, while the emergy per capita consumption increased significantly, suggesting that the society’s energy efficiency improved. During the same period, the environmental loading ratio increased gradually, and the elements causing the environmental load shifted from internal to external. Discussion The study shows that the factors of environmental load in developing cities are gradually shifting from internal to external, which is vital to understanding the impact of urban transformation and upgrading of resource-based cities on the environment.
bibliographic citation: Chen et al. (2019) Coupling and metabolic analysis of urbanization and environment between two resource-based cities in North China. PeerJ 7:e6869 https://doi.org/10.7717/peerj.6869
date submitted: 2018-12-18
date accepted: 2019-03-29
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Hao
author list: Agent
  family name: Xu
  given name: Linyu
author list: Agent
  family name: Cao
  given name: Qingqing
author list: Agent
  family name: Huang
  given name: Miansong
author list: Agent
  family name: Song
  given name: Minghua
author list: Agent
  family name: Quan
  given name: Quan
author list: Agent
  family name: Liu
  given name: Jian
doi: 10.7717/peerj.6869
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Chen et al.
attribution name: Chen et al.

How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species
type: item
type: AcademicArticle
description: Restoration of depleted populations is an important method in biological conservation. Reintroduction strategies frequently aim to restore stable, increasing, self-sustaining populations. Knowledge of asymptotic system dynamics may provide advantage in selecting reintroduction strategies. We introduce interactive software that is designed to identify strategies for release of females that are immediately aligned with stable population dynamics from species represented by 2-, 3-, 4-, and 5-stage life history strategies. The software allows managers to input a matrix of interest, the desired number of breeding females, and the desired management timeline, and calls upon stable population theory to give release strategies that are in concert with both stable population status and the management goals. We demonstrate how the software can aid in assessing various strategies ahead of a hypothetical restoration. For the purpose of demonstration of the tool only, we use published vital rates of an ungulate species, but remark that the selection of species for demonstration is not central to the use of this tool. Adaption of this tool to real-life restorations of any 2-, 3-, 4-, or 5-stage iteroparous species may aid in understanding how to minimize undesirable recovery complications that may naturally arise from transient population dynamics. The software is freely available at: https//cwhl.vet.cornell.edu/tools/stapopd.
format: application/pdf
format: text/html
creator: Brenda J. Hanley
creator: Elizabeth M. Bunting
creator: Krysten L. Schuler
subject: Mathematical Biology
subject: Natural Resource Management
subject: Population Biology
description: doi:10.7717/peerj.6873
publisher: PeerJ Inc.
rights: © 2019 Hanley et al.
abstract: Restoration of depleted populations is an important method in biological conservation. Reintroduction strategies frequently aim to restore stable, increasing, self-sustaining populations. Knowledge of asymptotic system dynamics may provide advantage in selecting reintroduction strategies. We introduce interactive software that is designed to identify strategies for release of females that are immediately aligned with stable population dynamics from species represented by 2-, 3-, 4-, and 5-stage life history strategies. The software allows managers to input a matrix of interest, the desired number of breeding females, and the desired management timeline, and calls upon stable population theory to give release strategies that are in concert with both stable population status and the management goals. We demonstrate how the software can aid in assessing various strategies ahead of a hypothetical restoration. For the purpose of demonstration of the tool only, we use published vital rates of an ungulate species, but remark that the selection of species for demonstration is not central to the use of this tool. Adaption of this tool to real-life restorations of any 2-, 3-, 4-, or 5-stage iteroparous species may aid in understanding how to minimize undesirable recovery complications that may naturally arise from transient population dynamics. The software is freely available at: https//cwhl.vet.cornell.edu/tools/stapopd.
bibliographic citation: Hanley et al. (2019) How can we augment the few that remain? Using stable population dynamics to aid reintroduction planning of an iteroparous species. PeerJ 7:e6873 https://doi.org/10.7717/peerj.6873
date submitted: 2018-10-24
date accepted: 2019-03-30
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hanley
  given name: Brenda J.
author list: Agent
  family name: Bunting
  given name: Elizabeth M.
author list: Agent
  family name: Schuler
  given name: Krysten L.
doi: 10.7717/peerj.6873
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Hanley et al.
attribution name: Hanley et al.

Galantamine plasma concentration and cognitive response in Alzheimer’s disease
type: item
type: AcademicArticle
description: Background Galantamine has been approved for the treatment of Alzheimer’s disease (AD). However, there are few studies which have reported the association between cognitive responses and galantamine plasma concentration. The aim of this study was to determine the correlation between galantamine plasma concentration and the subsequent cognitive response following treatment in AD patients. Methods AD sufferers who continuously took 8 mg/d galantamine for at least 6 months without previous exposure to other kinds of AChEI such as donepezil, rivastigmine, or memantine were included in this cohort study. The assessments included the Mini Mental Status Examination (MMSE), Clinical Dementia Rating Scale (CDR) and the Cognitive Assessment Screening Instrument (CASI). Each subdomain of the CASI assessment was conducted at baseline and after 6 months of galantamine. The plasma concentrations of galantamine were measured by capillary electrophoresis after 6 months of the treatment. Logistic regression was performed to adjust for age, gender, apolipoprotein E ε4 genotype status, and baseline score to investigate the association between galantamine plasma concentrations and the cognitive response. Results The total sample consisted of 33 clinically diagnosed AD patients taking galantamine 8 mg/d for 6 months. There was no linear correlation between galantamine concentration and cognitive response in patients. However, 22 patients were responsive to the treatment in the long-term memory domain. In CASI subset domain, concentration improved during the 6 months follow up. Conclusions In the limited samples study, galantamine mostly benefitted the cognitive domain of long-term memory. The benefits were not related to the galantamine plasma concentration. Objective intra-individual evaluation of therapeutic response should be encouraged.
format: application/pdf
format: text/html
creator: Yi-Ting Lin
creator: Mei-Chuan Chou
creator: Shyh-Jong Wu
creator: Yuan-Han Yang
subject: Cognitive Disorders
subject: Neurology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.6887
publisher: PeerJ Inc.
rights: © 2019 Lin et al.
abstract: Background Galantamine has been approved for the treatment of Alzheimer’s disease (AD). However, there are few studies which have reported the association between cognitive responses and galantamine plasma concentration. The aim of this study was to determine the correlation between galantamine plasma concentration and the subsequent cognitive response following treatment in AD patients. Methods AD sufferers who continuously took 8 mg/d galantamine for at least 6 months without previous exposure to other kinds of AChEI such as donepezil, rivastigmine, or memantine were included in this cohort study. The assessments included the Mini Mental Status Examination (MMSE), Clinical Dementia Rating Scale (CDR) and the Cognitive Assessment Screening Instrument (CASI). Each subdomain of the CASI assessment was conducted at baseline and after 6 months of galantamine. The plasma concentrations of galantamine were measured by capillary electrophoresis after 6 months of the treatment. Logistic regression was performed to adjust for age, gender, apolipoprotein E ε4 genotype status, and baseline score to investigate the association between galantamine plasma concentrations and the cognitive response. Results The total sample consisted of 33 clinically diagnosed AD patients taking galantamine 8 mg/d for 6 months. There was no linear correlation between galantamine concentration and cognitive response in patients. However, 22 patients were responsive to the treatment in the long-term memory domain. In CASI subset domain, concentration improved during the 6 months follow up. Conclusions In the limited samples study, galantamine mostly benefitted the cognitive domain of long-term memory. The benefits were not related to the galantamine plasma concentration. Objective intra-individual evaluation of therapeutic response should be encouraged.
bibliographic citation: Lin et al. (2019) Galantamine plasma concentration and cognitive response in Alzheimer’s disease. PeerJ 7:e6887 https://doi.org/10.7717/peerj.6887
date submitted: 2018-12-18
date accepted: 2019-04-02
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lin
  given name: Yi-Ting
author list: Agent
  family name: Chou
  given name: Mei-Chuan
author list: Agent
  family name: Wu
  given name: Shyh-Jong
author list: Agent
  family name: Yang
  given name: Yuan-Han
doi: 10.7717/peerj.6887
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Lin et al.
attribution name: Lin et al.

A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast
type: item
type: AcademicArticle
description: Benthic–pelagic coupling refers to the ecological relationships between benthic and pelagic environments. Studying such links is particularly useful to understand biological variation in intertidal organisms along marine coasts. Filter-feeding invertebrates are ecologically important on marine rocky shores, so they have often been used to investigate benthic–pelagic coupling. Most studies, however, have been conducted on eastern ocean boundaries. To evaluate benthic–pelagic coupling on a western ocean boundary, we conducted a 5-year study spanning 415 km of the Atlantic coast of Nova Scotia (Canada). We hypothesized that the summer size of intertidal barnacles (Semibalanus balanoides) recruited in the preceding spring would be positively related to the nearshore abundance (biomass) of phytoplankton, as phytoplankton constitutes food for the nauplius larvae and benthic stages of barnacles. Every year between 2014 and 2018, we measured summer barnacle size in clearings created before spring recruitment on the rocky substrate at eight wave-exposed locations along this coast. We then examined the annual relationships between barnacle size and chlorophyll-a concentration (Chl-a), a proxy for phytoplankton biomass. For every year and location, we used satellite data to calculate Chl-a averages for a period ranging from the early spring (when most barnacle larvae were in the water) to the summer (when barnacle size was measured after weeks of growth following spring benthic recruitment). The relationships were always positive, Chl-a explaining nearly half, or more, of the variation in barnacle size in four of the five studied years. These are remarkable results because they were based on a relatively limited number of locations (which often curtails statistical power) and point to the relevance of pelagic food supply to explain variation in intertidal barnacle size along this western ocean boundary coast.
format: application/pdf
format: text/html
creator: Ricardo A. Scrosati
creator: Julius A. Ellrich
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.6892
publisher: PeerJ Inc.
rights: © 2019 Scrosati and Ellrich
abstract: Benthic–pelagic coupling refers to the ecological relationships between benthic and pelagic environments. Studying such links is particularly useful to understand biological variation in intertidal organisms along marine coasts. Filter-feeding invertebrates are ecologically important on marine rocky shores, so they have often been used to investigate benthic–pelagic coupling. Most studies, however, have been conducted on eastern ocean boundaries. To evaluate benthic–pelagic coupling on a western ocean boundary, we conducted a 5-year study spanning 415 km of the Atlantic coast of Nova Scotia (Canada). We hypothesized that the summer size of intertidal barnacles (Semibalanus balanoides) recruited in the preceding spring would be positively related to the nearshore abundance (biomass) of phytoplankton, as phytoplankton constitutes food for the nauplius larvae and benthic stages of barnacles. Every year between 2014 and 2018, we measured summer barnacle size in clearings created before spring recruitment on the rocky substrate at eight wave-exposed locations along this coast. We then examined the annual relationships between barnacle size and chlorophyll-a concentration (Chl-a), a proxy for phytoplankton biomass. For every year and location, we used satellite data to calculate Chl-a averages for a period ranging from the early spring (when most barnacle larvae were in the water) to the summer (when barnacle size was measured after weeks of growth following spring benthic recruitment). The relationships were always positive, Chl-a explaining nearly half, or more, of the variation in barnacle size in four of the five studied years. These are remarkable results because they were based on a relatively limited number of locations (which often curtails statistical power) and point to the relevance of pelagic food supply to explain variation in intertidal barnacle size along this western ocean boundary coast.
bibliographic citation: Scrosati et al. (2019) A 5-year study (2014–2018) of the relationship between coastal phytoplankton abundance and intertidal barnacle size along the Atlantic Canadian coast. PeerJ 7:e6892 https://doi.org/10.7717/peerj.6892
date submitted: 2019-01-09
date accepted: 2019-04-01
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Scrosati
  given name: Ricardo A.
author list: Agent
  family name: Ellrich
  given name: Julius A.
doi: 10.7717/peerj.6892
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Scrosati and Ellrich
attribution name: Scrosati and Ellrich

The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment
type: item
type: AcademicArticle
description: Background The increasing production of sewage sludge (SS) engenders the problem of its responsible utilization and disposal. Likewise, urban sediments (SED) are deposited at the bottom of urban reservoirs and sedimentation ponds, and these require periodical dredging and utilization. However, while the SS and SED deposits often contain nutrients such as nitrogen and phosphorus; however, they also contain a variety of hazardous compounds including heavy metals, Persistent Organic Pollutants (POPs) and microbial pollutants. Fortunately, some species of Cucurbitaceae can accumulate high levels of POPs, such as polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF) and polychlorinated biphenyls (PCB), in their tissues. Methods SS was collected from the Lodz Municipal Wastewater Treatment Plant and SED from the Sokołówka Sequential Biofiltration System. The SS and SED samples were added to soil in flower pots at three concentrations (1.8 g, 5.4 g and 10.8 g per flower pot), and one pot was left as an unamended control (C). Soil PCB concentrations were determined before cucumber planting, and after five weeks of growth. Also, total soluble protein, total chlorophyll content, chlorophyll a/b ratio and degree of lipid peroxidation (TBARS) were examined in the leaves of the cucumber plants (Cucumis sativus L.) cv. Cezar after five weeks. Antioxidative response was assessed by ascorbate peroxidase (APx) and catalase (CAT) assay. Results The initial PCB concentration in soil after application of SS or SED was dependent on the applied dose. After five weeks, PCB concentration fell significantly for all samples and confirmed that the dose of SS/SED had a strong effect. Soil remediation was found to be more effective after SS application. Total soluble protein content in the cucumber leaf tissues was dependent on both the type and the dose of the applied amendments, and increased with greater SS doses in the soil. The total chlorophyll content remained un…
format: application/pdf
format: text/html
creator: Anna Wyrwicka
creator: Magdalena Urbaniak
creator: Mirosław Przybylski
subject: Agricultural Science
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6743
publisher: PeerJ Inc.
rights: © 2019 Wyrwicka et al.
abstract: Background The increasing production of sewage sludge (SS) engenders the problem of its responsible utilization and disposal. Likewise, urban sediments (SED) are deposited at the bottom of urban reservoirs and sedimentation ponds, and these require periodical dredging and utilization. However, while the SS and SED deposits often contain nutrients such as nitrogen and phosphorus; however, they also contain a variety of hazardous compounds including heavy metals, Persistent Organic Pollutants (POPs) and microbial pollutants. Fortunately, some species of Cucurbitaceae can accumulate high levels of POPs, such as polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF) and polychlorinated biphenyls (PCB), in their tissues. Methods SS was collected from the Lodz Municipal Wastewater Treatment Plant and SED from the Sokołówka Sequential Biofiltration System. The SS and SED samples were added to soil in flower pots at three concentrations (1.8 g, 5.4 g and 10.8 g per flower pot), and one pot was left as an unamended control (C). Soil PCB concentrations were determined before cucumber planting, and after five weeks of growth. Also, total soluble protein, total chlorophyll content, chlorophyll a/b ratio and degree of lipid peroxidation (TBARS) were examined in the leaves of the cucumber plants (Cucumis sativus L.) cv. Cezar after five weeks. Antioxidative response was assessed by ascorbate peroxidase (APx) and catalase (CAT) assay. Results The initial PCB concentration in soil after application of SS or SED was dependent on the applied dose. After five weeks, PCB concentration fell significantly for all samples and confirmed that the dose of SS/SED had a strong effect. Soil remediation was found to be more effective after SS application. Total soluble protein content in the cucumber leaf tissues was dependent on both the type and the dose of the applied amendments, and increased with greater SS doses in the soil. The total chlorophyll content remained un…
bibliographic citation: Wyrwicka et al. (2019) The response of cucumber plants (Cucumis sativus L.) to the application of PCB-contaminated sewage sludge and urban sediment. PeerJ 7:e6743 https://doi.org/10.7717/peerj.6743
date submitted: 2018-07-19
date accepted: 2019-03-06
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wyrwicka
  given name: Anna
author list: Agent
  family name: Urbaniak
  given name: Magdalena
author list: Agent
  family name: Przybylski
  given name: Mirosław
doi: 10.7717/peerj.6743
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: ©2019 Wyrwicka et al.
attribution name: Wyrwicka et al.

Predicting gene expression using DNA methylation in three human populations
type: item
type: AcademicArticle
description: Background DNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative correlation in the promoter region. However, its correlation with gene expression across genome at human population level has not been well studied. In particular, it is unclear if genome-wide DNA methylation profile of an individual can predict her/his gene expression profile. Previous studies were mostly limited to association analyses between single CpG site methylation and gene expression. It is not known whether DNA methylation of a gene has enough prediction power to serve as a surrogate for gene expression in existing human study cohorts with DNA samples other than RNA samples. Results We examined DNA methylation in the gene region for predicting gene expression across individuals in non-cancer tissues of three human population datasets, adipose tissue of the Multiple Tissue Human Expression Resource Projects (MuTHER), peripheral blood mononuclear cell (PBMC) from Asthma and normal control study participates, and lymphoblastoid cell lines (LCL) from healthy individuals. Three prediction models were investigated, single linear regression, multiple linear regression, and least absolute shrinkage and selection operator (LASSO) penalized regression. Our results showed that LASSO regression has superior performance among these methods. However, the prediction power is generally low and varies across datasets. Only 30 and 42 genes were found to have cross-validation R2 greater than 0.3 in the PBMC and Adipose datasets, respectively. A substantially larger number of genes (258) were identified in the LCL dataset, which was generated from a more homogeneous cell line sample source. We also demonstrated that it gives better prediction power not to exclude any CpG probe due to cross hybridization or SNP effect. Conclusion In our three population analyses DNA methylation of CpG sites at gene region have limited prediction power for …
format: application/pdf
format: text/html
creator: Huan Zhong
creator: Soyeon Kim
creator: Degui Zhi
creator: Xiangqin Cui
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Epidemiology
subject: Statistics
description: doi:10.7717/peerj.6757
publisher: PeerJ Inc.
rights: © 2019 Zhong et al.
abstract: Background DNA methylation, an important epigenetic mark, is well known for its regulatory role in gene expression, especially the negative correlation in the promoter region. However, its correlation with gene expression across genome at human population level has not been well studied. In particular, it is unclear if genome-wide DNA methylation profile of an individual can predict her/his gene expression profile. Previous studies were mostly limited to association analyses between single CpG site methylation and gene expression. It is not known whether DNA methylation of a gene has enough prediction power to serve as a surrogate for gene expression in existing human study cohorts with DNA samples other than RNA samples. Results We examined DNA methylation in the gene region for predicting gene expression across individuals in non-cancer tissues of three human population datasets, adipose tissue of the Multiple Tissue Human Expression Resource Projects (MuTHER), peripheral blood mononuclear cell (PBMC) from Asthma and normal control study participates, and lymphoblastoid cell lines (LCL) from healthy individuals. Three prediction models were investigated, single linear regression, multiple linear regression, and least absolute shrinkage and selection operator (LASSO) penalized regression. Our results showed that LASSO regression has superior performance among these methods. However, the prediction power is generally low and varies across datasets. Only 30 and 42 genes were found to have cross-validation R2 greater than 0.3 in the PBMC and Adipose datasets, respectively. A substantially larger number of genes (258) were identified in the LCL dataset, which was generated from a more homogeneous cell line sample source. We also demonstrated that it gives better prediction power not to exclude any CpG probe due to cross hybridization or SNP effect. Conclusion In our three population analyses DNA methylation of CpG sites at gene region have limited prediction power for …
bibliographic citation: Zhong et al. (2019) Predicting gene expression using DNA methylation in three human populations. PeerJ 7:e6757 https://doi.org/10.7717/peerj.6757
date submitted: 2018-07-19
date accepted: 2019-03-10
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Huan
author list: Agent
  family name: Kim
  given name: Soyeon
author list: Agent
  family name: Zhi
  given name: Degui
author list: Agent
  family name: Cui
  given name: Xiangqin
doi: 10.7717/peerj.6757
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: ©2019 Zhong et al.
attribution name: Zhong et al.

Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids
type: item
type: AcademicArticle
description: Knowledge of the early evolution of sea turtles (Chelonioidea) has been limited by conflicting phylogenetic hypotheses resulting from sparse taxon sampling and a superficial understanding of the morphology of key taxa. This limits our understanding of evolutionary adaptation to marine life in turtles, and in amniotes more broadly. One problematic group are the protostegids, Early–Late Cretaceous marine turtles that have been hypothesised to be either stem-cryptodires, stem-chelonioids, or crown-chelonioids. Different phylogenetic hypotheses for protostegids suggest different answers to key questions, including (1) the number of transitions to marine life in turtles, (2) the age of the chelonioid crown-group, and (3) patterns of skeletal evolution during marine adaptation. We present a detailed anatomical study of one of the earliest protostegids, Rhinochelys pulchriceps from the early Late Cretaceous of Europe, using high-resolution μCT. We synonymise all previously named European species and document the variation seen among them. A phylogeny of turtles with increased chelonioid taxon sampling and revised postcranial characters is provided, recovering protostegids as stem-chelonioids. Our results imply a mid Early Cretaceous origin of total-group chelonioids and an early Late Cretaceous age for crown-chelonioids, which may inform molecular clock analyses in future. Specialisations of the chelonioid flipper evolved in a stepwise-fashion, with innovations clustered into pulses at the origin of total-group chelonioids, and subsequently among dermochelyids, crown-cheloniids, and gigantic protostegids from the Late Cretaceous.
format: application/pdf
format: text/html
creator: Serjoscha W. Evers
creator: Paul M. Barrett
creator: Roger B. J. Benson
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6811
publisher: PeerJ Inc.
rights: © 2019 Evers et al.
abstract: Knowledge of the early evolution of sea turtles (Chelonioidea) has been limited by conflicting phylogenetic hypotheses resulting from sparse taxon sampling and a superficial understanding of the morphology of key taxa. This limits our understanding of evolutionary adaptation to marine life in turtles, and in amniotes more broadly. One problematic group are the protostegids, Early–Late Cretaceous marine turtles that have been hypothesised to be either stem-cryptodires, stem-chelonioids, or crown-chelonioids. Different phylogenetic hypotheses for protostegids suggest different answers to key questions, including (1) the number of transitions to marine life in turtles, (2) the age of the chelonioid crown-group, and (3) patterns of skeletal evolution during marine adaptation. We present a detailed anatomical study of one of the earliest protostegids, Rhinochelys pulchriceps from the early Late Cretaceous of Europe, using high-resolution μCT. We synonymise all previously named European species and document the variation seen among them. A phylogeny of turtles with increased chelonioid taxon sampling and revised postcranial characters is provided, recovering protostegids as stem-chelonioids. Our results imply a mid Early Cretaceous origin of total-group chelonioids and an early Late Cretaceous age for crown-chelonioids, which may inform molecular clock analyses in future. Specialisations of the chelonioid flipper evolved in a stepwise-fashion, with innovations clustered into pulses at the origin of total-group chelonioids, and subsequently among dermochelyids, crown-cheloniids, and gigantic protostegids from the Late Cretaceous.
bibliographic citation: Evers et al. (2019) Anatomy of Rhinochelys pulchriceps (Protostegidae) and marine adaptation during the early evolution of chelonioids. PeerJ 7:e6811 https://doi.org/10.7717/peerj.6811
date submitted: 2018-10-23
date accepted: 2019-03-19
issued: 2019-05-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Evers
  given name: Serjoscha W.
author list: Agent
  family name: Barrett
  given name: Paul M.
author list: Agent
  family name: Benson
  given name: Roger B. J.
doi: 10.7717/peerj.6811
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-01
copyright: © 2019 Evers et al.
attribution name: Evers et al.

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