PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum
items: CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks
items: A divergence between underlying and final causes of death in selected conditions: an analysis of death registries in Peru
items: Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens)
items: Late Cretaceous sauropod tooth morphotypes may provide supporting evidence for faunal connections between North Africa and Southern Europe
items: First evidence of asexual recruitment of Pocillopora acuta in Okinawa Island using genotypic identification
items: Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles
items: An index of non-sampling error in area frame sampling based on remote sensing data
items: Interaction between Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis
items: Nutrition of marine mesograzers: integrating feeding behavior, nutrient intake and performance of an herbivorous amphipod

Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum
type: item
type: AcademicArticle
description: Background In our previous study, Melaleuca alternifolia essential oil (EO) was considered to have an insecticidal effect by acting on the mitochondrial respiratory chain in insects. However, the mode of action is not fully understood. Methods In this study, we investigated the insecticidal efficacy of the M. alternifolia EO against another major stored-product pest, Tribolium confusum Jacquelin du Val. Rarefaction and vacuolization of the mitochondrial matrix were evident in oil-fumigated T. confusum adults. Results Alterations to the mitochondria confirmed the insecticidal effect of the M. alternifolia EO. Furthermore, comparative transcriptome analysis of T. confusum using RNA-seq indicated that most of the differentially expressed genes were involved in insecticide detoxification and mitochondrial function. The biochemical analysis showed that the intracellular NAD+/NADH ratio is involved in the differential effect of the M. alternifolia EO. Discussion These results led us to conclude that NAD+/NADH dehydrogenase may be the prime target site for the M. alternifolia EO in insects, leading to blocking of the mitochondrial respiratory chain.
format: application/pdf
format: text/html
creator: Min Liao
creator: Qian-Qian Yang
creator: Jin-Jing Xiao
creator: Yong Huang
creator: Li-Jun Zhou
creator: Ri-Mao Hua
creator: Hai-Qun Cao
subject: Bioinformatics
subject: Entomology
subject: Toxicology
description: doi:10.7717/peerj.5693
publisher: PeerJ Inc.
rights: © 2018 Liao et al.
abstract: Background In our previous study, Melaleuca alternifolia essential oil (EO) was considered to have an insecticidal effect by acting on the mitochondrial respiratory chain in insects. However, the mode of action is not fully understood. Methods In this study, we investigated the insecticidal efficacy of the M. alternifolia EO against another major stored-product pest, Tribolium confusum Jacquelin du Val. Rarefaction and vacuolization of the mitochondrial matrix were evident in oil-fumigated T. confusum adults. Results Alterations to the mitochondria confirmed the insecticidal effect of the M. alternifolia EO. Furthermore, comparative transcriptome analysis of T. confusum using RNA-seq indicated that most of the differentially expressed genes were involved in insecticide detoxification and mitochondrial function. The biochemical analysis showed that the intracellular NAD+/NADH ratio is involved in the differential effect of the M. alternifolia EO. Discussion These results led us to conclude that NAD+/NADH dehydrogenase may be the prime target site for the M. alternifolia EO in insects, leading to blocking of the mitochondrial respiratory chain.
bibliographic citation: Liao et al. (2018) Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum. PeerJ 6:e5693 https://doi.org/10.7717/peerj.5693
date submitted: 2018-05-02
date accepted: 2018-09-05
issued: 2018-11-13
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Min
author list: Agent
  family name: Yang
  given name: Qian-Qian
author list: Agent
  family name: Xiao
  given name: Jin-Jing
author list: Agent
  family name: Huang
  given name: Yong
author list: Agent
  family name: Zhou
  given name: Li-Jun
author list: Agent
  family name: Hua
  given name: Ri-Mao
author list: Agent
  family name: Cao
  given name: Hai-Qun
doi: 10.7717/peerj.5693
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-13
copyright: © 2018 Liao et al.
attribution name: Liao et al.

CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks
type: item
type: AcademicArticle
description: Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many diseases including cancer. A unified picture of regulatory interactions of these regulators and their joint target genes would shed light on cancer studies. Although online resources developed to support probing of TF-gene and miRNA-gene interactions are available, online applications for miRNA-TF co-regulatory analysis, especially with a focus on cancers, are lacking. In light of this, we developed a web tool, namely CMTCN (freely available at http://www.cbportal.org/CMTCN), which constructs miRNA-TF co-regulatory networks and conducts comprehensive analyses within the context of particular cancer types. With its user-friendly provision of topological and functional analyses, CMTCN promises to be a reliable and indispensable web tool for biomedical studies.
format: application/pdf
format: text/html
creator: Ruijiang Li
creator: Hebing Chen
creator: Shuai Jiang
creator: Wanying Li
creator: Hao Li
creator: Zhuo Zhang
creator: Hao Hong
creator: Xin Huang
creator: Chenghui Zhao
creator: Yiming Lu
creator: Xiaochen Bo
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Computational Science
description: doi:10.7717/peerj.5951
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: Transcription factors (TFs) and microRNAs (miRNAs) are well-characterized trans-acting essential players in gene expression regulation. Growing evidence indicates that TFs and miRNAs can work cooperatively, and their dysregulation has been associated with many diseases including cancer. A unified picture of regulatory interactions of these regulators and their joint target genes would shed light on cancer studies. Although online resources developed to support probing of TF-gene and miRNA-gene interactions are available, online applications for miRNA-TF co-regulatory analysis, especially with a focus on cancers, are lacking. In light of this, we developed a web tool, namely CMTCN (freely available at http://www.cbportal.org/CMTCN), which constructs miRNA-TF co-regulatory networks and conducts comprehensive analyses within the context of particular cancer types. With its user-friendly provision of topological and functional analyses, CMTCN promises to be a reliable and indispensable web tool for biomedical studies.
bibliographic citation: Li et al. (2018) CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks. PeerJ 6:e5951 https://doi.org/10.7717/peerj.5951
date submitted: 2018-08-22
date accepted: 2018-10-14
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Ruijiang
author list: Agent
  family name: Chen
  given name: Hebing
author list: Agent
  family name: Jiang
  given name: Shuai
author list: Agent
  family name: Li
  given name: Wanying
author list: Agent
  family name: Li
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Zhuo
author list: Agent
  family name: Hong
  given name: Hao
author list: Agent
  family name: Huang
  given name: Xin
author list: Agent
  family name: Zhao
  given name: Chenghui
author list: Agent
  family name: Lu
  given name: Yiming
author list: Agent
  family name: Bo
  given name: Xiaochen
doi: 10.7717/peerj.5951
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: ©2018 Li et al.
attribution name: Li et al.

A divergence between underlying and final causes of death in selected conditions: an analysis of death registries in Peru
type: item
type: AcademicArticle
description: Background The underlying cause of death is used to study country and global mortality trends and profiles. The final cause of death could also inform the ultimately cause of death in individuals with underlying conditions. Whether there is a pattern between the underlying and final cause of death has not been explored using national death registries. We studied what final causes of death were most common among selected underlying causes using national death registries in Peru, 2015. Methods Underlying and final causes of death were classified according to their ICD-10 codes. Underlying causes included chronic kidney disease (CKD), chronic obstructive pulmonary disease (COPD), hypertension (HTN), diabetes, and selected cancers (cervix, breast, stomach, prostate, and lung). Final causes were categorized as: communicable, cardiovascular, and cancers. Descriptive statistics were used. Results A total of 77,065 death registries were analyzed; cases had a mean age of 69.4 (SD: 19.3) years at death and were mostly men (53.9%). When the underlying cause was HTN, the most frequent final cause was cardiovascular diseases (82.3%). For all the other underlying causes, the most frequent final cause was communicable diseases: COPD (86.4%), CKD (79.3%), cancer (76.5%), and diabetes (68.3%). Conclusions In four selected underlying causes of death there was a divergence with respect to the final cause, suggesting there was a shift from non-communicable to communicable causes. Although efforts should be deployed to prevent underlying non-communicable diseases, potential communicable complications should not be neglected.
format: application/pdf
format: text/html
creator: Rodrigo M. Carrillo-Larco
creator: Antonio Bernabe-Ortiz
subject: Epidemiology
subject: Evidence Based Medicine
subject: Global Health
description: doi:10.7717/peerj.5948
publisher: PeerJ Inc.
rights: © 2018 Carrillo-Larco and Bernabe-Ortiz
abstract: Background The underlying cause of death is used to study country and global mortality trends and profiles. The final cause of death could also inform the ultimately cause of death in individuals with underlying conditions. Whether there is a pattern between the underlying and final cause of death has not been explored using national death registries. We studied what final causes of death were most common among selected underlying causes using national death registries in Peru, 2015. Methods Underlying and final causes of death were classified according to their ICD-10 codes. Underlying causes included chronic kidney disease (CKD), chronic obstructive pulmonary disease (COPD), hypertension (HTN), diabetes, and selected cancers (cervix, breast, stomach, prostate, and lung). Final causes were categorized as: communicable, cardiovascular, and cancers. Descriptive statistics were used. Results A total of 77,065 death registries were analyzed; cases had a mean age of 69.4 (SD: 19.3) years at death and were mostly men (53.9%). When the underlying cause was HTN, the most frequent final cause was cardiovascular diseases (82.3%). For all the other underlying causes, the most frequent final cause was communicable diseases: COPD (86.4%), CKD (79.3%), cancer (76.5%), and diabetes (68.3%). Conclusions In four selected underlying causes of death there was a divergence with respect to the final cause, suggesting there was a shift from non-communicable to communicable causes. Although efforts should be deployed to prevent underlying non-communicable diseases, potential communicable complications should not be neglected.
bibliographic citation: Carrillo-Larco et al. (2018) A divergence between underlying and final causes of death in selected conditions: an analysis of death registries in Peru. PeerJ 6:e5948 https://doi.org/10.7717/peerj.5948
date submitted: 2018-08-14
date accepted: 2018-10-17
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carrillo-Larco
  given name: Rodrigo M.
author list: Agent
  family name: Bernabe-Ortiz
  given name: Antonio
doi: 10.7717/peerj.5948
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: © 2018 Carrillo-Larco and Bernabe-Ortiz
attribution name: Carrillo-Larco and Bernabe-Ortiz

Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens)
type: item
type: AcademicArticle
description: Background Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak. Methods A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy–Weinberg equilibrium without linkage disequilibrium. Results Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak. Discussion Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were s…
format: application/pdf
format: text/html
creator: Jie Pei
creator: Pengjia Bao
creator: Min Chu
creator: Chunnian Liang
creator: Xuezhi Ding
creator: Hongbo Wang
creator: Xiaoyun Wu
creator: Xian Guo
creator: Ping Yan
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.5946
publisher: PeerJ Inc.
rights: © 2018 Pei et al.
abstract: Background Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak. Methods A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy–Weinberg equilibrium without linkage disequilibrium. Results Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak. Discussion Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were s…
bibliographic citation: Pei et al. (2018) Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak (Bos grunniens). PeerJ 6:e5946 https://doi.org/10.7717/peerj.5946
date submitted: 2018-01-08
date accepted: 2018-10-17
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pei
  given name: Jie
author list: Agent
  family name: Bao
  given name: Pengjia
author list: Agent
  family name: Chu
  given name: Min
author list: Agent
  family name: Liang
  given name: Chunnian
author list: Agent
  family name: Ding
  given name: Xuezhi
author list: Agent
  family name: Wang
  given name: Hongbo
author list: Agent
  family name: Wu
  given name: Xiaoyun
author list: Agent
  family name: Guo
  given name: Xian
author list: Agent
  family name: Yan
  given name: Ping
doi: 10.7717/peerj.5946
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: © 2018 Pei et al.
attribution name: Pei et al.

Late Cretaceous sauropod tooth morphotypes may provide supporting evidence for faunal connections between North Africa and Southern Europe
type: item
type: AcademicArticle
description: The Cretaceous Kem Kem beds of Morocco and equivalent beds in Algeria have produced a rich fossil assemblage, yielding, amongst others, isolated sauropod teeth, which can be used in species diversity studies. These Albian-Cenomanian (∼113–93.9 Ma) strata rarely yield sauropod body fossils, therefore, isolated teeth can help to elucidate the faunal assemblages from North Africa, and their relations with those of contemporaneous beds and geographically close assemblages. Eighteen isolated sauropod teeth from three localities (Erfoud and Taouz, Morocco, and Algeria) are studied here, to assess whether the teeth can be ascribed to a specific clade, and whether different tooth morphotypes can be found in the samples. Two general morphotypes are found, based on enamel wrinkling and general tooth morphology. Morphotype I, with mainly rugose enamel wrinkling, pronounced carinae, lemon-shaped to (sub)cylindrical cross-section and mesiodistal tapering towards an apical tip, shows affinities to titanosauriforms and titanosaurs. Morphotype II, characterized by more smooth enamel, cylindrical cross-section, rectangular teeth with no apical tapering and both labial and lingual wear facets, shows similarities to rebbachisaurids. Moreover, similarities are found between these northwest African tooth morphotypes, and tooth morphotypes from titanosaurs and rebbachisaurids from both contemporaneous finds from north and central Africa, as well as from the latest Cretaceous (Campanian–Maastrichtian, 83.6 Ma–66.0 Ma) of the Ibero-Armorican Island. These results support previous hypotheses from earlier studies on faunal exchange and continental connections between North Africa and Southern Europe in the Cretaceous.
format: application/pdf
format: text/html
creator: Femke M. Holwerda
creator: Verónica Díez Díaz
creator: Alejandro Blanco
creator: Roel Montie
creator: Jelle W.F. Reumer
subject: Biodiversity
subject: Biogeography
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.5925
publisher: PeerJ Inc.
rights: © 2018 Holwerda et al.
abstract: The Cretaceous Kem Kem beds of Morocco and equivalent beds in Algeria have produced a rich fossil assemblage, yielding, amongst others, isolated sauropod teeth, which can be used in species diversity studies. These Albian-Cenomanian (∼113–93.9 Ma) strata rarely yield sauropod body fossils, therefore, isolated teeth can help to elucidate the faunal assemblages from North Africa, and their relations with those of contemporaneous beds and geographically close assemblages. Eighteen isolated sauropod teeth from three localities (Erfoud and Taouz, Morocco, and Algeria) are studied here, to assess whether the teeth can be ascribed to a specific clade, and whether different tooth morphotypes can be found in the samples. Two general morphotypes are found, based on enamel wrinkling and general tooth morphology. Morphotype I, with mainly rugose enamel wrinkling, pronounced carinae, lemon-shaped to (sub)cylindrical cross-section and mesiodistal tapering towards an apical tip, shows affinities to titanosauriforms and titanosaurs. Morphotype II, characterized by more smooth enamel, cylindrical cross-section, rectangular teeth with no apical tapering and both labial and lingual wear facets, shows similarities to rebbachisaurids. Moreover, similarities are found between these northwest African tooth morphotypes, and tooth morphotypes from titanosaurs and rebbachisaurids from both contemporaneous finds from north and central Africa, as well as from the latest Cretaceous (Campanian–Maastrichtian, 83.6 Ma–66.0 Ma) of the Ibero-Armorican Island. These results support previous hypotheses from earlier studies on faunal exchange and continental connections between North Africa and Southern Europe in the Cretaceous.
bibliographic citation: Holwerda et al. (2018) Late Cretaceous sauropod tooth morphotypes may provide supporting evidence for faunal connections between North Africa and Southern Europe. PeerJ 6:e5925 https://doi.org/10.7717/peerj.5925
date submitted: 2018-03-14
date accepted: 2018-10-13
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Holwerda
  given name: Femke M.
author list: Agent
  family name: Díez Díaz
  given name: Verónica
author list: Agent
  family name: Blanco
  given name: Alejandro
author list: Agent
  family name: Montie
  given name: Roel
author list: Agent
  family name: Reumer
  given name: Jelle W.F.
doi: 10.7717/peerj.5925
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: ©2018 Holwerda et al.
attribution name: Holwerda et al.

First evidence of asexual recruitment of Pocillopora acuta in Okinawa Island using genotypic identification
type: item
type: AcademicArticle
description: Okinawa Island is located near the center of the Nansei Islands (∼24–31°N), at a relatively high latitude for coral reefs. Nevertheless, more than 80 coral genera (over 400 species) are abundant in the Nansei Islands. Since March, 2017, scleractinian corals have been held in an outdoor tank at the OIST Marine Science Station at Seragaki, Onna with natural sea water flow-through in order to be used in molecular biological and physiological studies. In January, 2018, we found small pocilloporid-like colonies suspected to have originated asexually. We collected 25 small colonies and measured their sizes and weights. Also, we validated the classification and clonality of the colonies using a mitochondrial locus and nine microsatellite loci. Almost all of the small colonies collected in the outdoor tank were ≤1 cm in both width and height. The weight of dried skeletons ranged from 0.0287 to 0.1807 g. Genetic analysis determined that they were, in fact, Pocillopora acuta. Only one mitochondrial haplotype was shared and two microsatellite multilocus genotypes were detected (20 colonies of one and four colonies of the other). The mitochondrial haplotype and one microsatellite multilocus genotype for 20 colonies corresponded to those of one P. acuta colony being kept in the tank. One small colony matched both multilocus genotypes. This may have been a chimeric colony resulting from allogenic fusion. These small colonies were not produced sexually, because the only potential parent in the tank was the aforementioned P. acuta colony. Instead, they were more likely derived from asexual planula release or polyp bail-out. Corals as Pocillopora acuta have the capacity to produce clonal offspring rapidly and to adapt readily to local environments. This is the first report of asexual reproduction by planulae or expelled polyps in P. acuta at Okinawa Island.
format: application/pdf
format: text/html
creator: Yuichi Nakajima
creator: Po-Shun Chuang
creator: Nobuo Ueda
creator: Satoshi Mitarai
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Marine Biology
subject: Population Biology
description: doi:10.7717/peerj.5915
publisher: PeerJ Inc.
rights: © 2018 Nakajima et al.
abstract: Okinawa Island is located near the center of the Nansei Islands (∼24–31°N), at a relatively high latitude for coral reefs. Nevertheless, more than 80 coral genera (over 400 species) are abundant in the Nansei Islands. Since March, 2017, scleractinian corals have been held in an outdoor tank at the OIST Marine Science Station at Seragaki, Onna with natural sea water flow-through in order to be used in molecular biological and physiological studies. In January, 2018, we found small pocilloporid-like colonies suspected to have originated asexually. We collected 25 small colonies and measured their sizes and weights. Also, we validated the classification and clonality of the colonies using a mitochondrial locus and nine microsatellite loci. Almost all of the small colonies collected in the outdoor tank were ≤1 cm in both width and height. The weight of dried skeletons ranged from 0.0287 to 0.1807 g. Genetic analysis determined that they were, in fact, Pocillopora acuta. Only one mitochondrial haplotype was shared and two microsatellite multilocus genotypes were detected (20 colonies of one and four colonies of the other). The mitochondrial haplotype and one microsatellite multilocus genotype for 20 colonies corresponded to those of one P. acuta colony being kept in the tank. One small colony matched both multilocus genotypes. This may have been a chimeric colony resulting from allogenic fusion. These small colonies were not produced sexually, because the only potential parent in the tank was the aforementioned P. acuta colony. Instead, they were more likely derived from asexual planula release or polyp bail-out. Corals as Pocillopora acuta have the capacity to produce clonal offspring rapidly and to adapt readily to local environments. This is the first report of asexual reproduction by planulae or expelled polyps in P. acuta at Okinawa Island.
bibliographic citation: Nakajima et al. (2018) First evidence of asexual recruitment of Pocillopora acuta in Okinawa Island using genotypic identification. PeerJ 6:e5915 https://doi.org/10.7717/peerj.5915
date submitted: 2018-06-29
date accepted: 2018-10-10
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nakajima
  given name: Yuichi
author list: Agent
  family name: Chuang
  given name: Po-Shun
author list: Agent
  family name: Ueda
  given name: Nobuo
author list: Agent
  family name: Mitarai
  given name: Satoshi
doi: 10.7717/peerj.5915
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: ©2018 Nakajima et al.
attribution name: Nakajima et al.

Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles
type: item
type: AcademicArticle
description: Four species of true crocodile (genus Crocodylus) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions—Crocodylus intermedius in South America, C. moreletii along the Caribbean coast of Mesoamerica, and C. rhombifer confined to Cuba. The fourth, C. acutus, is narrowly sympatric with each of the other three species. In this study, we sampled 113 crocodiles across Crocodylus populations in Cuba, as well as exemplar populations in Belize and Florida (USA), and sequenced three regions of the mitochondrial genome (D-loop, cytochrome b, cytochrome oxidase I; 3,626 base pair long dataset) that overlapped with published data previously collected from Colombia, Jamaica, and the Cayman Islands. Phylogenetic analyses of these data revealed two, paraphyletic lineages of C. acutus. One lineage, found in the continental Americas, is the sister taxon to C. intermedius, while the Greater Antillean lineage is most closely related to C. rhombifer. In addition to the paraphyly of the two C. acutus lineages, we recovered a 5.4% estimate of Tamura-Nei genetic divergence between the Antillean and continental clades. The reconstructed paraphyly, distinct phylogenetic affinities and high genetic divergence between Antillean and continental C. acutus populations are consistent with interspecific differentiation within the genus and suggest that the current taxon recognized as C. acutus is more likely a complex of cryptic species warranting a reassessment of current taxonomy. Moreover, the inclusion, for the first time, of samples from the western population of the American crocodile in Cuba revealed evidence for continental mtDNA haplotypes in the Antilles, suggesting this area may constitute a transition zone between distinct lineages of C. acutus. Further study using nuclear character data is warranted to more fully characterize this cryptic diversity, resolve taxonomic uncertainty, and inform conservation planning in this system.
format: application/pdf
format: text/html
creator: Yoamel Milián-García
creator: Michael A. Russello
creator: Jessica Castellanos-Labarcena
creator: Martin Cichon
creator: Vikas Kumar
creator: Georgina Espinosa
creator: Natalia Rossi
creator: Frank Mazzotti
creator: Evon Hekkala
creator: George Amato
creator: Axel Janke
subject: Evolutionary Studies
subject: Genetics
description: doi:10.7717/peerj.5836
publisher: PeerJ Inc.
rights: © 2018 Milián-García et al.
abstract: Four species of true crocodile (genus Crocodylus) have been described from the Americas. Three of these crocodile species exhibit non-overlapping distributions—Crocodylus intermedius in South America, C. moreletii along the Caribbean coast of Mesoamerica, and C. rhombifer confined to Cuba. The fourth, C. acutus, is narrowly sympatric with each of the other three species. In this study, we sampled 113 crocodiles across Crocodylus populations in Cuba, as well as exemplar populations in Belize and Florida (USA), and sequenced three regions of the mitochondrial genome (D-loop, cytochrome b, cytochrome oxidase I; 3,626 base pair long dataset) that overlapped with published data previously collected from Colombia, Jamaica, and the Cayman Islands. Phylogenetic analyses of these data revealed two, paraphyletic lineages of C. acutus. One lineage, found in the continental Americas, is the sister taxon to C. intermedius, while the Greater Antillean lineage is most closely related to C. rhombifer. In addition to the paraphyly of the two C. acutus lineages, we recovered a 5.4% estimate of Tamura-Nei genetic divergence between the Antillean and continental clades. The reconstructed paraphyly, distinct phylogenetic affinities and high genetic divergence between Antillean and continental C. acutus populations are consistent with interspecific differentiation within the genus and suggest that the current taxon recognized as C. acutus is more likely a complex of cryptic species warranting a reassessment of current taxonomy. Moreover, the inclusion, for the first time, of samples from the western population of the American crocodile in Cuba revealed evidence for continental mtDNA haplotypes in the Antilles, suggesting this area may constitute a transition zone between distinct lineages of C. acutus. Further study using nuclear character data is warranted to more fully characterize this cryptic diversity, resolve taxonomic uncertainty, and inform conservation planning in this system.
bibliographic citation: Milián-García et al. (2018) Genetic evidence supports a distinct lineage of American crocodile (Crocodylus acutus) in the Greater Antilles. PeerJ 6:e5836 https://doi.org/10.7717/peerj.5836
date submitted: 2018-06-25
date accepted: 2018-09-27
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Milián-García
  given name: Yoamel
author list: Agent
  family name: Russello
  given name: Michael A.
author list: Agent
  family name: Castellanos-Labarcena
  given name: Jessica
author list: Agent
  family name: Cichon
  given name: Martin
author list: Agent
  family name: Kumar
  given name: Vikas
author list: Agent
  family name: Espinosa
  given name: Georgina
author list: Agent
  family name: Rossi
  given name: Natalia
author list: Agent
  family name: Mazzotti
  given name: Frank
author list: Agent
  family name: Hekkala
  given name: Evon
author list: Agent
  family name: Amato
  given name: George
author list: Agent
  family name: Janke
  given name: Axel
doi: 10.7717/peerj.5836
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: © 2018 Milián-García et al.
attribution name: Milián-García et al.

An index of non-sampling error in area frame sampling based on remote sensing data
type: item
type: AcademicArticle
description: Agricultural areas are often surveyed using area frame sampling. Using non-updated area sampling frame causes significant non-sampling errors when land cover and usage changes between updates. To address this problem, a novel method is proposed to estimate non-sampling errors in crop area statistics. Three parameters used in stratified sampling that are affected by land use changes were monitored using satellite remote sensing imagery: (1) the total number of sampling units; (2) the number of sampling units in each stratum; and (3) the mean value of selected sampling units in each stratum. A new index, called the non-sampling error by land use change index (NELUCI), was defined to estimate non-sampling errors. Using this method, the sizes of cropping areas in Bole, Xinjiang, China, were estimated with a coefficient of variation of 0.0237 and NELUCI of 0.0379. These are 0.0474 and 0.0994 lower, respectively, than errors calculated by traditional methods based on non-updated area sampling frame and selected sampling units.
format: application/pdf
format: text/html
creator: Mingquan Wu
creator: Dailiang Peng
creator: Yuchu Qin
creator: Zheng Niu
creator: Chenghai Yang
creator: Wang Li
creator: Pengyu Hao
creator: Chunyang Zhang
subject: Agricultural Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5824
publisher: PeerJ Inc.
rights: © 2018 Wu et al.
abstract: Agricultural areas are often surveyed using area frame sampling. Using non-updated area sampling frame causes significant non-sampling errors when land cover and usage changes between updates. To address this problem, a novel method is proposed to estimate non-sampling errors in crop area statistics. Three parameters used in stratified sampling that are affected by land use changes were monitored using satellite remote sensing imagery: (1) the total number of sampling units; (2) the number of sampling units in each stratum; and (3) the mean value of selected sampling units in each stratum. A new index, called the non-sampling error by land use change index (NELUCI), was defined to estimate non-sampling errors. Using this method, the sizes of cropping areas in Bole, Xinjiang, China, were estimated with a coefficient of variation of 0.0237 and NELUCI of 0.0379. These are 0.0474 and 0.0994 lower, respectively, than errors calculated by traditional methods based on non-updated area sampling frame and selected sampling units.
bibliographic citation: Wu et al. (2018) An index of non-sampling error in area frame sampling based on remote sensing data. PeerJ 6:e5824 https://doi.org/10.7717/peerj.5824
date submitted: 2018-05-22
date accepted: 2018-09-25
issued: 2018-11-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Mingquan
author list: Agent
  family name: Peng
  given name: Dailiang
author list: Agent
  family name: Qin
  given name: Yuchu
author list: Agent
  family name: Niu
  given name: Zheng
author list: Agent
  family name: Yang
  given name: Chenghai
author list: Agent
  family name: Li
  given name: Wang
author list: Agent
  family name: Hao
  given name: Pengyu
author list: Agent
  family name: Zhang
  given name: Chunyang
doi: 10.7717/peerj.5824
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-12
copyright: ©2018 Wu et al.
attribution name: Wu et al.

Interaction between Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis
type: item
type: AcademicArticle
description: Background Cystic fibrosis (CF) is a disease characterized by chronic airway infection with a high incidence and poor prognosis. Pseudomonas aeruginosa and Aspergillus fumigatus are pathogens commonly found in CF patients. Clinically, these two microorganisms often coexist in the airway of CF patients. Combined infection with P. aeruginosa and A. fumigatus results in worsening lung function and clinical condition. Methods In this review, we focus on the mutual inhibition and promotion mechanisms of P. aeruginosa and A. fumigatus in CF patients. We also summarized the mechanisms of the interaction between these pathogenic microorganisms. Results P. aeruginosa inhibits A. fumigatus growth through the effects of phenazines, the quorum sensing system, iron competition, bacteriophages, and small colony variants. P. aeruginosa induces A. fumigatus growth through volatile organic compounds and subbacteriostatic concentrations of phenazines. A. fumigatus interferes with P. aeruginosa, affecting its metabolic growth via phenazine metabolic transformation, gliotoxin production, and reduced antibiotic sensitivity. Discussion Coexistence of P. aeruginosa and A. fumigatus can lead to both mutual inhibition and promotion. In different stages of CF disease, the interaction between these two pathogenic microorganisms may shift between promotion and inhibition. A discussion of the mechanisms of P. aeruginosa and A. fumigatus interaction can be beneficial for further treatment of CF patients and for improving the prognosis of the disease.
format: application/pdf
format: text/html
creator: Jingming Zhao
creator: Wencheng Yu
subject: Microbiology
subject: Infectious Diseases
subject: Internal Medicine
subject: Respiratory Medicine
subject: Science and Medical Education
description: doi:10.7717/peerj.5931
publisher: PeerJ Inc.
rights: © 2018 Zhao and Yu
abstract: Background Cystic fibrosis (CF) is a disease characterized by chronic airway infection with a high incidence and poor prognosis. Pseudomonas aeruginosa and Aspergillus fumigatus are pathogens commonly found in CF patients. Clinically, these two microorganisms often coexist in the airway of CF patients. Combined infection with P. aeruginosa and A. fumigatus results in worsening lung function and clinical condition. Methods In this review, we focus on the mutual inhibition and promotion mechanisms of P. aeruginosa and A. fumigatus in CF patients. We also summarized the mechanisms of the interaction between these pathogenic microorganisms. Results P. aeruginosa inhibits A. fumigatus growth through the effects of phenazines, the quorum sensing system, iron competition, bacteriophages, and small colony variants. P. aeruginosa induces A. fumigatus growth through volatile organic compounds and subbacteriostatic concentrations of phenazines. A. fumigatus interferes with P. aeruginosa, affecting its metabolic growth via phenazine metabolic transformation, gliotoxin production, and reduced antibiotic sensitivity. Discussion Coexistence of P. aeruginosa and A. fumigatus can lead to both mutual inhibition and promotion. In different stages of CF disease, the interaction between these two pathogenic microorganisms may shift between promotion and inhibition. A discussion of the mechanisms of P. aeruginosa and A. fumigatus interaction can be beneficial for further treatment of CF patients and for improving the prognosis of the disease.
bibliographic citation: Zhao et al. (2018) Interaction between Pseudomonas aeruginosa and Aspergillus fumigatus in cystic fibrosis. PeerJ 6:e5931 https://doi.org/10.7717/peerj.5931
date submitted: 2018-05-17
date accepted: 2018-10-13
issued: 2018-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhao
  given name: Jingming
author list: Agent
  family name: Yu
  given name: Wencheng
doi: 10.7717/peerj.5931
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-09
copyright: © 2018 Zhao and Yu
attribution name: Zhao and Yu

Nutrition of marine mesograzers: integrating feeding behavior, nutrient intake and performance of an herbivorous amphipod
type: item
type: AcademicArticle
description: Consumers can regulate the acquisition and use of nutrients through behavioral and physiological mechanisms. Here, we present an experimental approach that simultaneously integrates multiple nutritional traits, feeding assays, and juvenile performance to assess whether a marine herbivore (the amphipod Ampithoe valida) regulates the intake of elements (carbon and nitrogen), macronutrients (protein and non-protein) or both when offered freeze-dried tissues of seaweeds varying in nutritional content. We assessed behavioral regulation of nutrients in three ways. First, during no-choice assays, we found that amphipods ingested similar amounts of carbon, but not nitrogen, non-protein and protein, across algal diets. Second, herbivore intake rates of carbon, protein and non-protein components across no-choice assays was similar to intake rates when offered a choice of foods. Third, variation in intake rates of carbon and non-protein components among algal diets was significantly greater than was tissue content of these components, while variation in intake rates of nitrogen was significantly lower; differences in protein intake variation was equivocal. While these analytical approaches are not uniformly consistent, carbon and nitrogen seem to emerge as the nutrient components that are more strongly regulated by A. valida. Juveniles reared on single diets shown patterns of survivorship, growth and reproduction that could not be predicted by these feeding preferences, nor nutrient content. We conclude that an integrative approach that considers the intake of multiple nutrients potentially yields insights into feeding behavior and its performance consequences.
format: application/pdf
format: text/html
creator: Glauco B.O. Machado
creator: Fosca P.P. Leite
creator: Erik E. Sotka
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.5929
publisher: PeerJ Inc.
rights: © 2018 Machado et al.
abstract: Consumers can regulate the acquisition and use of nutrients through behavioral and physiological mechanisms. Here, we present an experimental approach that simultaneously integrates multiple nutritional traits, feeding assays, and juvenile performance to assess whether a marine herbivore (the amphipod Ampithoe valida) regulates the intake of elements (carbon and nitrogen), macronutrients (protein and non-protein) or both when offered freeze-dried tissues of seaweeds varying in nutritional content. We assessed behavioral regulation of nutrients in three ways. First, during no-choice assays, we found that amphipods ingested similar amounts of carbon, but not nitrogen, non-protein and protein, across algal diets. Second, herbivore intake rates of carbon, protein and non-protein components across no-choice assays was similar to intake rates when offered a choice of foods. Third, variation in intake rates of carbon and non-protein components among algal diets was significantly greater than was tissue content of these components, while variation in intake rates of nitrogen was significantly lower; differences in protein intake variation was equivocal. While these analytical approaches are not uniformly consistent, carbon and nitrogen seem to emerge as the nutrient components that are more strongly regulated by A. valida. Juveniles reared on single diets shown patterns of survivorship, growth and reproduction that could not be predicted by these feeding preferences, nor nutrient content. We conclude that an integrative approach that considers the intake of multiple nutrients potentially yields insights into feeding behavior and its performance consequences.
bibliographic citation: Machado et al. (2018) Nutrition of marine mesograzers: integrating feeding behavior, nutrient intake and performance of an herbivorous amphipod. PeerJ 6:e5929 https://doi.org/10.7717/peerj.5929
date submitted: 2018-03-07
date accepted: 2018-10-14
issued: 2018-11-09
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Machado
  given name: Glauco B.O.
author list: Agent
  family name: Leite
  given name: Fosca P.P.
author list: Agent
  family name: Sotka
  given name: Erik E.
doi: 10.7717/peerj.5929
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-09
copyright: ©2018 Machado et al.
attribution name: Machado et al.

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