PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center
items: Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis
items: Effects of species-dominated patches on soil organic carbon and total nitrogen storage in a degraded grassland in China
items: Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China
items: Combining UAV-based hyperspectral imagery and machine learning algorithms for soil moisture content monitoring
items: Cytotoxic and apoptosis-inducing effects of wildtype and mutated Hydra actinoporin-like toxin 1 (HALT-1) on various cancer cell lines
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

Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center
type: item
type: AcademicArticle
description: Background The objective of this study is to investigate small cell neuroendocrine carcinoma of the cervix (SCCC), using a retrospective clinicopathological characteristic and treatment approach. Method We retrospectively analyzed cases of early-stage SCCC, identified between 2006 and 2016, in women who received radical surgery and adjuvant chemotherapy with or without radiotherapy. Kaplan–Meier and one-way ANOVA analyses were performed. Result A total of 37 cases of SCCC are presented in this study, of which 21 had stage IB1 SCCC, 12 had stage IB2, 3 had stage IIA1, and 1 had stage IIA2. All patients were treated with radical surgery and adjuvant chemotherapy, specifically, 26 with radical surgery followed by adjuvant chemotherapy plus radiation and 11 with neoadjuvant chemotherapy (NACT) followed by radical surgery. After a median follow-up time of 27 months (range, 8–115 months), the 2-year and 5-year disease-free survival rate for all patients was 51.9% and 34.1%, respectively, and the overall survival rate was 60.3% and 38.6%, respectively. Univariate analysis showed that International Federation of Gynecology and Obstetrics (FIGO) stage and tumor size may be a predictor of a poor prognosis. NACT and adjuvant radiation did not improve survival over adjuvant chemotherapy alone but should not be a significant independent prognostic factor for survival. Conclusion Even in patients with early-stage SCCC, the prognosis is poor, although FIGO stage and tumor size may act as surrogate factors prognostic of survival.
format: application/pdf
format: text/html
creator: Dandan Zhang
creator: Xiaoxin Ma
subject: Gynecology and Obstetrics
subject: Oncology
description: doi:10.7717/peerj.6868
publisher: PeerJ Inc.
rights: © 2019 Zhang and Ma
abstract: Background The objective of this study is to investigate small cell neuroendocrine carcinoma of the cervix (SCCC), using a retrospective clinicopathological characteristic and treatment approach. Method We retrospectively analyzed cases of early-stage SCCC, identified between 2006 and 2016, in women who received radical surgery and adjuvant chemotherapy with or without radiotherapy. Kaplan–Meier and one-way ANOVA analyses were performed. Result A total of 37 cases of SCCC are presented in this study, of which 21 had stage IB1 SCCC, 12 had stage IB2, 3 had stage IIA1, and 1 had stage IIA2. All patients were treated with radical surgery and adjuvant chemotherapy, specifically, 26 with radical surgery followed by adjuvant chemotherapy plus radiation and 11 with neoadjuvant chemotherapy (NACT) followed by radical surgery. After a median follow-up time of 27 months (range, 8–115 months), the 2-year and 5-year disease-free survival rate for all patients was 51.9% and 34.1%, respectively, and the overall survival rate was 60.3% and 38.6%, respectively. Univariate analysis showed that International Federation of Gynecology and Obstetrics (FIGO) stage and tumor size may be a predictor of a poor prognosis. NACT and adjuvant radiation did not improve survival over adjuvant chemotherapy alone but should not be a significant independent prognostic factor for survival. Conclusion Even in patients with early-stage SCCC, the prognosis is poor, although FIGO stage and tumor size may act as surrogate factors prognostic of survival.
bibliographic citation: Zhang et al. (2019) Prognostic factors and outcomes of early-stage small cell neuroendocrine carcinoma of the cervix: 37 cases from a single center. PeerJ 7:e6868 https://doi.org/10.7717/peerj.6868
date submitted: 2018-11-15
date accepted: 2019-03-29
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Dandan
author list: Agent
  family name: Ma
  given name: Xiaoxin
doi: 10.7717/peerj.6868
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Zhang and Ma
attribution name: Zhang and Ma

Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis
type: item
type: AcademicArticle
description: Background Elaiosomes are specialized fleshy and edible seed appendages dispersed by ants. Lipids are the primary components of elaiosomes. Chelidonium majus is a well-known plant, the seeds of which are dispersed by ants. Previous studies have identified the presence of primary fatty acids in its elaiosomes and seeds. However, the molecular mechanisms underlying fatty acid biosynthesis in elaiosomes remain unknown. Methods In order to gain a comprehensive transcriptional profile of the elaiosomes and seeds of C. majus, and understand the expression patterns of genes associated with fatty acid biosynthesis, four different developmental stages, including the flower-bud (Ch01), flowering (Ch02), young seed (Ch03), and mature seed (Ch04) stages, were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing). Results A total of 63,064 unigenes were generated from 12 libraries. Of these, 7,323, 258, and 11,540 unigenes were annotated with 25 Cluster of Orthologous Groups, 43 Gene Ontology terms, and 373 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. In addition, 322 genes were involved in lipid transport and metabolism, and 508 genes were involved in the lipid metabolism pathways. A total of 41 significantly differentially expressed genes (DEGs) involved in the lipid metabolism pathways were identified, most of which were upregulated in Ch03 compared to Ch02, indicating that fatty acid biosynthesis primarily occurs during the flowering to the young seed stages. Of the DEGs, acyl-ACP thioesterases, acyl carrier protein desaturase (DESA1), and malonyl CoA-ACP transacylase were involved in palmitic acid synthesis; stearoyl-CoA desaturase and DESA1 were involved in oleic acid synthesis, and acyl-lipid omega-6 desaturase was involved in linoleic acid synthesis.
format: application/pdf
format: text/html
creator: Jiayue Wu
creator: Linlin Peng
creator: Shubin Dong
creator: Xiaofei Xia
creator: Liangcheng Zhao
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6871
publisher: PeerJ Inc.
rights: © 2019 Wu et al.
abstract: Background Elaiosomes are specialized fleshy and edible seed appendages dispersed by ants. Lipids are the primary components of elaiosomes. Chelidonium majus is a well-known plant, the seeds of which are dispersed by ants. Previous studies have identified the presence of primary fatty acids in its elaiosomes and seeds. However, the molecular mechanisms underlying fatty acid biosynthesis in elaiosomes remain unknown. Methods In order to gain a comprehensive transcriptional profile of the elaiosomes and seeds of C. majus, and understand the expression patterns of genes associated with fatty acid biosynthesis, four different developmental stages, including the flower-bud (Ch01), flowering (Ch02), young seed (Ch03), and mature seed (Ch04) stages, were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing). Results A total of 63,064 unigenes were generated from 12 libraries. Of these, 7,323, 258, and 11,540 unigenes were annotated with 25 Cluster of Orthologous Groups, 43 Gene Ontology terms, and 373 Kyoto Encyclopedia of Genes and Genomes pathways, respectively. In addition, 322 genes were involved in lipid transport and metabolism, and 508 genes were involved in the lipid metabolism pathways. A total of 41 significantly differentially expressed genes (DEGs) involved in the lipid metabolism pathways were identified, most of which were upregulated in Ch03 compared to Ch02, indicating that fatty acid biosynthesis primarily occurs during the flowering to the young seed stages. Of the DEGs, acyl-ACP thioesterases, acyl carrier protein desaturase (DESA1), and malonyl CoA-ACP transacylase were involved in palmitic acid synthesis; stearoyl-CoA desaturase and DESA1 were involved in oleic acid synthesis, and acyl-lipid omega-6 desaturase was involved in linoleic acid synthesis.
bibliographic citation: Wu et al. (2019) Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis. PeerJ 7:e6871 https://doi.org/10.7717/peerj.6871
date submitted: 2018-12-14
date accepted: 2019-03-25
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Jiayue
author list: Agent
  family name: Peng
  given name: Linlin
author list: Agent
  family name: Dong
  given name: Shubin
author list: Agent
  family name: Xia
  given name: Xiaofei
author list: Agent
  family name: Zhao
  given name: Liangcheng
doi: 10.7717/peerj.6871
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Wu et al.
attribution name: Wu et al.

Effects of species-dominated patches on soil organic carbon and total nitrogen storage in a degraded grassland in China
type: item
type: AcademicArticle
description: Background Patchy vegetation is a very common phenomenon due to long-term overgrazing in degraded steppe grasslands, which results in substantial uncertainty associated with soil carbon (C) and nitrogen (N) dynamics because of changes in the amount of litter accumulation and nutrition input into soil. Methods We investigated soil C and N stocks beneath three types of monodominant species patches according to community dominance. Stipa krylovii patches, Artemisia frigida patches, and Potentilla acaulis patches represent better to worse vegetation conditions in a grassland in northern China. Results The results revealed that the soil C stock (0–40 cm) changed significantly, from 84.7 to 95.7 Mg ha−1, and that the soil organic carbon content (0–10 cm) and microbial biomass carbon (0–10 and 10–20 cm) varied remarkably among the different monodominant species communities (P < 0.05). However, soil total nitrogen and microbial biomass nitrogen showed no significant differences among different plant patches in the top 0–20 cm of topsoil. The soil C stocks under the P. acaulis and S. krylovii patches were greater than that under the A. frigida patch. Our study implies that accurate estimates of soil C and N storage in degenerated grassland require integrated analyses of the concurrent effects of differences in plant community composition.
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creator: Yujuan Zhang
creator: Shiming Tang
creator: Shu Xie
creator: Kesi Liu
creator: Jinsheng Li
creator: Qian Chen
creator: Ding Huang
creator: Kun Wang
subject: Agricultural Science
subject: Ecology
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.6897
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Background Patchy vegetation is a very common phenomenon due to long-term overgrazing in degraded steppe grasslands, which results in substantial uncertainty associated with soil carbon (C) and nitrogen (N) dynamics because of changes in the amount of litter accumulation and nutrition input into soil. Methods We investigated soil C and N stocks beneath three types of monodominant species patches according to community dominance. Stipa krylovii patches, Artemisia frigida patches, and Potentilla acaulis patches represent better to worse vegetation conditions in a grassland in northern China. Results The results revealed that the soil C stock (0–40 cm) changed significantly, from 84.7 to 95.7 Mg ha−1, and that the soil organic carbon content (0–10 cm) and microbial biomass carbon (0–10 and 10–20 cm) varied remarkably among the different monodominant species communities (P < 0.05). However, soil total nitrogen and microbial biomass nitrogen showed no significant differences among different plant patches in the top 0–20 cm of topsoil. The soil C stocks under the P. acaulis and S. krylovii patches were greater than that under the A. frigida patch. Our study implies that accurate estimates of soil C and N storage in degenerated grassland require integrated analyses of the concurrent effects of differences in plant community composition.
bibliographic citation: Zhang et al. (2019) Effects of species-dominated patches on soil organic carbon and total nitrogen storage in a degraded grassland in China. PeerJ 7:e6897 https://doi.org/10.7717/peerj.6897
date submitted: 2018-10-26
date accepted: 2019-04-02
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yujuan
author list: Agent
  family name: Tang
  given name: Shiming
author list: Agent
  family name: Xie
  given name: Shu
author list: Agent
  family name: Liu
  given name: Kesi
author list: Agent
  family name: Li
  given name: Jinsheng
author list: Agent
  family name: Chen
  given name: Qian
author list: Agent
  family name: Huang
  given name: Ding
author list: Agent
  family name: Wang
  given name: Kun
doi: 10.7717/peerj.6897
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China
type: item
type: AcademicArticle
description: Background This study aims to describe the epidemiological patterns of influenza-like illness (ILI) in Huludao, China and seek scientific evidence on the link of ILI activity with weather factors. Methods Surveillance data of ILI cases between January 2012 and December 2015 was collected in Huludao Central Hospital, meteorological data was obtained from the China Meteorological Data Service Center. Generalized additive model (GAM) was used to seek the relationship between the number of ILI cases and the meteorological factors. Multiple Smoothing parameter estimation was made on the basis of Poisson distribution, where the number of weekly ILI cases was treated as response, and the smoothness of weather was treated as covariates. Lag time was determined by the smallest Akaike information criterion (AIC). Smoothing coefficients were estimated for the prediction of the number of ILI cases. Results A total of 29, 622 ILI cases were observed during the study period, with children ILI cases constituted 86.77%. The association between ILI activity and meteorological factors varied across different lag periods. The lag time for average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity were 2, 2, 1, 1 and 0 weeks, respectively. Average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity could explain 16.5%, 9.5%, 18.0%, 15.9% and 7.7% of the deviance, respectively. Among the temperature indexes, the minimum temperature played the most important role. The number of ILI cases peaked when minimum temperature was around −13 °C in winter and 18 °C in summer. The number of cases peaked when the relative humidity was equal to 43% and then began to decrease with the increase of relative humidity. When the humidity exceeded 76%, the number of ILI cases began to rise. Conclusions The present study first analyzed the relationship between meteorological factors and ILI cases with sp…
format: application/pdf
format: text/html
creator: Ying-Long Bai
creator: De-Sheng Huang
creator: Jing Liu
creator: De-Qiang Li
creator: Peng Guan
subject: Epidemiology
subject: Health Policy
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.6919
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background This study aims to describe the epidemiological patterns of influenza-like illness (ILI) in Huludao, China and seek scientific evidence on the link of ILI activity with weather factors. Methods Surveillance data of ILI cases between January 2012 and December 2015 was collected in Huludao Central Hospital, meteorological data was obtained from the China Meteorological Data Service Center. Generalized additive model (GAM) was used to seek the relationship between the number of ILI cases and the meteorological factors. Multiple Smoothing parameter estimation was made on the basis of Poisson distribution, where the number of weekly ILI cases was treated as response, and the smoothness of weather was treated as covariates. Lag time was determined by the smallest Akaike information criterion (AIC). Smoothing coefficients were estimated for the prediction of the number of ILI cases. Results A total of 29, 622 ILI cases were observed during the study period, with children ILI cases constituted 86.77%. The association between ILI activity and meteorological factors varied across different lag periods. The lag time for average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity were 2, 2, 1, 1 and 0 weeks, respectively. Average air temperature, maximum air temperature, minimum air temperature, vapor pressure and relative humidity could explain 16.5%, 9.5%, 18.0%, 15.9% and 7.7% of the deviance, respectively. Among the temperature indexes, the minimum temperature played the most important role. The number of ILI cases peaked when minimum temperature was around −13 °C in winter and 18 °C in summer. The number of cases peaked when the relative humidity was equal to 43% and then began to decrease with the increase of relative humidity. When the humidity exceeded 76%, the number of ILI cases began to rise. Conclusions The present study first analyzed the relationship between meteorological factors and ILI cases with sp…
bibliographic citation: Bai et al. (2019) Effect of meteorological factors on influenza-like illness from 2012 to 2015 in Huludao, a northeastern city in China. PeerJ 7:e6919 https://doi.org/10.7717/peerj.6919
date submitted: 2019-01-31
date accepted: 2019-04-06
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Ying-Long
author list: Agent
  family name: Huang
  given name: De-Sheng
author list: Agent
  family name: Liu
  given name: Jing
author list: Agent
  family name: Li
  given name: De-Qiang
author list: Agent
  family name: Guan
  given name: Peng
doi: 10.7717/peerj.6919
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: ©2019 Bai et al.
attribution name: Bai et al.

Combining UAV-based hyperspectral imagery and machine learning algorithms for soil moisture content monitoring
type: item
type: AcademicArticle
description: Soil moisture content (SMC) is an important factor that affects agricultural development in arid regions. Compared with the space-borne remote sensing system, the unmanned aerial vehicle (UAV) has been widely used because of its stronger controllability and higher resolution. It also provides a more convenient method for monitoring SMC than normal measurement methods that includes field sampling and oven-drying techniques. However, research based on UAV hyperspectral data has not yet formed a standard procedure in arid regions. Therefore, a universal processing scheme is required. We hypothesized that combining pretreatments of UAV hyperspectral imagery under optimal indices and a set of field observations within a machine learning framework will yield a highly accurate estimate of SMC. Optimal 2D spectral indices act as indispensable variables and allow us to characterize a model’s SMC performance and spatial distribution. For this purpose, we used hyperspectral imagery and a total of 70 topsoil samples (0–10 cm) from the farmland (2.5 × 104 m2) of Fukang City, Xinjiang Uygur AutonomousRegion, China. The random forest (RF) method and extreme learning machine (ELM) were used to estimate the SMC using six methods of pretreatments combined with four optimal spectral indices. The validation accuracy of the estimated method clearly increased compared with that of linear models. The combination of pretreatments and indices by our assessment effectively eliminated the interference and the noises. Comparing two machine learning algorithms showed that the RF models were superior to the ELM models, and the best model was PIR (R2val = 0.907, RMSEP = 1.477, and RPD = 3.396). The SMC map predicted via the best scheme was highly similar to the SMC map measured. We conclude that combining preprocessed spectral indices and machine learning algorithms allows estimation of SMC with high accuracy (R2val = 0.907) via UAV hyperspectral imagery on a regional scale. Ultimately, our progr…
format: application/pdf
format: text/html
creator: Xiangyu Ge
creator: Jingzhe Wang
creator: Jianli Ding
creator: Xiaoyi Cao
creator: Zipeng Zhang
creator: Jie Liu
creator: Xiaohang Li
subject: Ecosystem Science
subject: Soil Science
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.6926
publisher: PeerJ Inc.
rights: © 2019 Ge et al.
abstract: Soil moisture content (SMC) is an important factor that affects agricultural development in arid regions. Compared with the space-borne remote sensing system, the unmanned aerial vehicle (UAV) has been widely used because of its stronger controllability and higher resolution. It also provides a more convenient method for monitoring SMC than normal measurement methods that includes field sampling and oven-drying techniques. However, research based on UAV hyperspectral data has not yet formed a standard procedure in arid regions. Therefore, a universal processing scheme is required. We hypothesized that combining pretreatments of UAV hyperspectral imagery under optimal indices and a set of field observations within a machine learning framework will yield a highly accurate estimate of SMC. Optimal 2D spectral indices act as indispensable variables and allow us to characterize a model’s SMC performance and spatial distribution. For this purpose, we used hyperspectral imagery and a total of 70 topsoil samples (0–10 cm) from the farmland (2.5 × 104 m2) of Fukang City, Xinjiang Uygur AutonomousRegion, China. The random forest (RF) method and extreme learning machine (ELM) were used to estimate the SMC using six methods of pretreatments combined with four optimal spectral indices. The validation accuracy of the estimated method clearly increased compared with that of linear models. The combination of pretreatments and indices by our assessment effectively eliminated the interference and the noises. Comparing two machine learning algorithms showed that the RF models were superior to the ELM models, and the best model was PIR (R2val = 0.907, RMSEP = 1.477, and RPD = 3.396). The SMC map predicted via the best scheme was highly similar to the SMC map measured. We conclude that combining preprocessed spectral indices and machine learning algorithms allows estimation of SMC with high accuracy (R2val = 0.907) via UAV hyperspectral imagery on a regional scale. Ultimately, our progr…
bibliographic citation: Ge et al. (2019) Combining UAV-based hyperspectral imagery and machine learning algorithms for soil moisture content monitoring. PeerJ 7:e6926 https://doi.org/10.7717/peerj.6926
date submitted: 2019-01-03
date accepted: 2019-04-01
issued: 2019-05-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ge
  given name: Xiangyu
author list: Agent
  family name: Wang
  given name: Jingzhe
author list: Agent
  family name: Ding
  given name: Jianli
author list: Agent
  family name: Cao
  given name: Xiaoyi
author list: Agent
  family name: Zhang
  given name: Zipeng
author list: Agent
  family name: Liu
  given name: Jie
author list: Agent
  family name: Li
  given name: Xiaohang
doi: 10.7717/peerj.6926
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-03
copyright: © 2019 Ge et al.
attribution name: Ge et al.

Cytotoxic and apoptosis-inducing effects of wildtype and mutated Hydra actinoporin-like toxin 1 (HALT-1) on various cancer cell lines
type: item
type: AcademicArticle
description: Background Hydra actinoporin like toxin -1 (HALT-1), is a small 18.5 kDa pore forming toxin derived from Hydra magnipapillata which has been shown to elicit strong haemolytic and cytolytic activity when in contact with cell membranes. Due to its cytotoxic potency, HALT-1 was further investigated for its potential as a toxin moiety candidate in immunotoxin developmental efforts, ideally as a form of targeted therapy against cancer. Methods In this study, wtHALT-1 (wild type) and its Y110A mutated binding domain counterpart (mHALT-1) were produced and evaluated for their cytotoxic and apoptotic effects on various cancer cell lines. A total of seven different tumour and non-tumour cell lines including HeLa, HepG2, SW-620, MCF-7, CCD841CoN, NHDF and HCT116 were used. Immunofluorescence assays were used to observe membrane binding and localization changes between both HALT-1 recombinant proteins based on 6xHis-tag detection. Result Based on MTT data, mHALT-1 demonstrated a significant reduction of 82% ± 12.21% in cytotoxic activity across all cell lines after the membrane recognition domain had been mutated in comparison to the wtHALT-1. Annexin V FITC/PI assay data also indicated that HeLa, HepG2 and MCF-7 demonstrated an apoptosis-mediated cell death after being treated with wtHALT-1. Additionally, a notable difference between wtHALT-1 and mHALT-1 binding affinity was clearly observed where emission of green fluorescence along the cell membrane was observed only in wtHALT-1 treated cells. Discussion These results suggest that mHALT-1 (Y110A) can be potentially developed as a toxin-moiety candidate for the development of future immunotoxins against various human cell-based diseases.
format: application/pdf
format: text/html
creator: Teng Jia Ng
creator: Michelle Yee Mun Teo
creator: Dek Shen Liew
creator: Paul Etim Effiong
creator: Jung Shan Hwang
creator: Crystale Siew Ying Lim
creator: Lionel L.A. In
subject: Biotechnology
subject: Cell Biology
subject: Molecular Biology
subject: Immunology
description: doi:10.7717/peerj.6639
publisher: PeerJ Inc.
rights: © 2019 Ng et al.
abstract: Background Hydra actinoporin like toxin -1 (HALT-1), is a small 18.5 kDa pore forming toxin derived from Hydra magnipapillata which has been shown to elicit strong haemolytic and cytolytic activity when in contact with cell membranes. Due to its cytotoxic potency, HALT-1 was further investigated for its potential as a toxin moiety candidate in immunotoxin developmental efforts, ideally as a form of targeted therapy against cancer. Methods In this study, wtHALT-1 (wild type) and its Y110A mutated binding domain counterpart (mHALT-1) were produced and evaluated for their cytotoxic and apoptotic effects on various cancer cell lines. A total of seven different tumour and non-tumour cell lines including HeLa, HepG2, SW-620, MCF-7, CCD841CoN, NHDF and HCT116 were used. Immunofluorescence assays were used to observe membrane binding and localization changes between both HALT-1 recombinant proteins based on 6xHis-tag detection. Result Based on MTT data, mHALT-1 demonstrated a significant reduction of 82% ± 12.21% in cytotoxic activity across all cell lines after the membrane recognition domain had been mutated in comparison to the wtHALT-1. Annexin V FITC/PI assay data also indicated that HeLa, HepG2 and MCF-7 demonstrated an apoptosis-mediated cell death after being treated with wtHALT-1. Additionally, a notable difference between wtHALT-1 and mHALT-1 binding affinity was clearly observed where emission of green fluorescence along the cell membrane was observed only in wtHALT-1 treated cells. Discussion These results suggest that mHALT-1 (Y110A) can be potentially developed as a toxin-moiety candidate for the development of future immunotoxins against various human cell-based diseases.
bibliographic citation: Ng et al. (2019) Cytotoxic and apoptosis-inducing effects of wildtype and mutated Hydra actinoporin-like toxin 1 (HALT-1) on various cancer cell lines. PeerJ 7:e6639 https://doi.org/10.7717/peerj.6639
date submitted: 2018-09-26
date accepted: 2019-02-18
issued: 2019-05-02
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ng
  given name: Teng Jia
author list: Agent
  family name: Teo
  given name: Michelle Yee Mun
author list: Agent
  family name: Liew
  given name: Dek Shen
author list: Agent
  family name: Effiong
  given name: Paul Etim
author list: Agent
  family name: Hwang
  given name: Jung Shan
author list: Agent
  family name: Lim
  given name: Crystale Siew Ying
author list: Agent
  family name: In
  given name: Lionel L.A.
doi: 10.7717/peerj.6639
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-05-02
copyright: ©2019 Ng et al.
attribution name: Ng et al.

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.

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