PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Antioxidant-rich leaf extract of Barringtonia racemosa significantly alters the in vitro expression of genes encoding enzymes that are involved in methylglyoxal degradation III
items: Rapid induction of GFP expression by the nitrate reductase promoter in the diatom Phaeodactylum tricornutum
items: Morpho-histological characterisation of the alimentary canal of an important food fish, Asian seabass (Lates calcarifer)
items: The incidence rates of endometrial hyperplasia and endometrial cancer: a four-year population-based study
items: Effects of yearling, juvenile and adult survival on reef manta ray (Manta alfredi) demography
items: Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species
items: Fine structure of the spermatozoon in three species of Cambaridae (Arthropoda: Crustacea: Decapoda) Cambarus robustus, Orconectes propinquus and Orconectes rusticus: a comparative biometrical study
items: Transmission of a heterologous clade C Symbiodinium in a model anemone infection system via asexual reproduction
items: Taxonomic revision of Eoalligator (Crocodylia, Brevirostres) and the paleogeographic origins of the Chinese alligatoroids
items: Anxiolytic effects of fluoxetine and nicotine exposure on exploratory behavior in zebrafish

Antioxidant-rich leaf extract of Barringtonia racemosa significantly alters the in vitro expression of genes encoding enzymes that are involved in methylglyoxal degradation III
type: item
type: AcademicArticle
description: Background Barringtonia racemosa is a medicinal plant belonging to the Lecythidaceae family. The water extract of B. racemosa leaf (BLE) has been shown to be rich in polyphenols. Despite the diverse medicinal properties of B. racemosa, information on its major biological effects and the underlying molecular mechanisms are still lacking. Methods In this study, the effect of the antioxidant-rich BLE on gene expression in HepG2 cells was investigated using microarray analysis in order to shed more light on the molecular mechanism associated with the medicinal properties of the plant. Results Microarray analysis showed that a total of 138 genes were significantly altered in response to BLE treatment (p < 0.05) with a fold change difference of at least 1.5. SERPINE1 was the most significantly up-regulated gene at 2.8-fold while HAMP was the most significantly down-regulated gene at 6.5-fold. Ingenuity Pathways Analysis (IPA) revealed that “Cancer, cell death and survival, cellular movement” was the top network affected by the BLE with a score of 44. The top five canonical pathways associated with BLE were Methylglyoxal Degradation III followed by VDR/RXR activation, TR/RXR activation, PXR/RXR activation and gluconeogenesis. The expression of genes that encode for enzymes involved in methylglyoxal degradation (ADH4, AKR1B10 and AKR1C2) and glycolytic process (ENO3, ALDOC and SLC2A1) was significantly regulated. Owing to the Warburg effect, aerobic glycolysis in cancer cells may increase the level of methylglyoxal, a cytotoxic compound. Conclusions BLE has the potential to be developed into a novel chemopreventive agent provided that the cytotoxic effects related to methylglyoxal accumulation are minimized in normal cells that rely on aerobic glycolysis for energy supply.
format: application/pdf
format: text/html
creator: Kin Weng Kong
creator: Azlina Abdul Aziz
creator: Nurhanani Razali
creator: Norhaniza Aminuddin
creator: Sarni Mat Junit
subject: Molecular Biology
subject: Pharmacology
description: doi:10.7717/peerj.2379
publisher: PeerJ Inc.
rights: © 2016 Kong et al.
abstract: Background Barringtonia racemosa is a medicinal plant belonging to the Lecythidaceae family. The water extract of B. racemosa leaf (BLE) has been shown to be rich in polyphenols. Despite the diverse medicinal properties of B. racemosa, information on its major biological effects and the underlying molecular mechanisms are still lacking. Methods In this study, the effect of the antioxidant-rich BLE on gene expression in HepG2 cells was investigated using microarray analysis in order to shed more light on the molecular mechanism associated with the medicinal properties of the plant. Results Microarray analysis showed that a total of 138 genes were significantly altered in response to BLE treatment (p < 0.05) with a fold change difference of at least 1.5. SERPINE1 was the most significantly up-regulated gene at 2.8-fold while HAMP was the most significantly down-regulated gene at 6.5-fold. Ingenuity Pathways Analysis (IPA) revealed that “Cancer, cell death and survival, cellular movement” was the top network affected by the BLE with a score of 44. The top five canonical pathways associated with BLE were Methylglyoxal Degradation III followed by VDR/RXR activation, TR/RXR activation, PXR/RXR activation and gluconeogenesis. The expression of genes that encode for enzymes involved in methylglyoxal degradation (ADH4, AKR1B10 and AKR1C2) and glycolytic process (ENO3, ALDOC and SLC2A1) was significantly regulated. Owing to the Warburg effect, aerobic glycolysis in cancer cells may increase the level of methylglyoxal, a cytotoxic compound. Conclusions BLE has the potential to be developed into a novel chemopreventive agent provided that the cytotoxic effects related to methylglyoxal accumulation are minimized in normal cells that rely on aerobic glycolysis for energy supply.
bibliographic citation: Kong et al. (2016) Antioxidant-rich leaf extract of Barringtonia racemosa significantly alters the in vitro expression of genes encoding enzymes that are involved in methylglyoxal degradation III. PeerJ 4:e2379 https://doi.org/10.7717/peerj.2379
date submitted: 2016-04-21
date accepted: 2016-07-29
issued: 2016-08-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kong
  given name: Kin Weng
author list: Agent
  family name: Abdul Aziz
  given name: Azlina
author list: Agent
  family name: Razali
  given name: Nurhanani
author list: Agent
  family name: Aminuddin
  given name: Norhaniza
author list: Agent
  family name: Mat Junit
  given name: Sarni
doi: 10.7717/peerj.2379
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-25
copyright: ©2016 Kong et al.
attribution name: Kong et al.

Rapid induction of GFP expression by the nitrate reductase promoter in the diatom Phaeodactylum tricornutum
type: item
type: AcademicArticle
description: An essential prerequisite for a controlled transgene expression is the choice of a suitable promoter. In the model diatom Phaeodactylum tricornutum, the most commonly used promoters for trans-gene expression are the light dependent lhcf1 promoters (derived from two endogenous genes encoding fucoxanthin chlorophyll a/c binding proteins) and the nitrate dependent nr promoter (derived from the endogenous nitrate reductase gene). In this study, we investigated the time dependent expression of the green fluorescent protein (GFP) reporter under control of the nitrate reductase promoter in independently genetically transformed P. tricornutum cell lines following induction of expression by change of the nitrogen source in the medium via flow cytometry, microscopy and western blotting. In all investigated cell lines, GFP fluorescence started to increase 1 h after change of the medium, the fastest increase rates were observed between 2 and 3 h. Fluorescence continued to increase slightly for up to 7 h even after transfer of the cells to ammonium medium. The subsequent decrease of GFP fluorescence was much slower than the increase, probably due to the stability of GFP. The investigation of several cell lines transformed with nr based constructs revealed that, also in the absence of nitrate, the promoter may show residual activity. Furthermore, we observed a strong variation of gene expression between independent cell lines, emphasising the importance of a thorough characterisation of genetically modified cell lines and their individual expression patterns.
format: application/pdf
format: text/html
creator: Lili Chu
creator: Daniela Ewe
creator: Carolina Río Bártulos
creator: Peter G. Kroth
creator: Ansgar Gruber
subject: Aquaculture, Fisheries and Fish Science
subject: Biotechnology
subject: Genetics
subject: Marine Biology
subject: Plant Science
description: doi:10.7717/peerj.2344
publisher: PeerJ Inc.
rights: © 2016 Chu et al.
abstract: An essential prerequisite for a controlled transgene expression is the choice of a suitable promoter. In the model diatom Phaeodactylum tricornutum, the most commonly used promoters for trans-gene expression are the light dependent lhcf1 promoters (derived from two endogenous genes encoding fucoxanthin chlorophyll a/c binding proteins) and the nitrate dependent nr promoter (derived from the endogenous nitrate reductase gene). In this study, we investigated the time dependent expression of the green fluorescent protein (GFP) reporter under control of the nitrate reductase promoter in independently genetically transformed P. tricornutum cell lines following induction of expression by change of the nitrogen source in the medium via flow cytometry, microscopy and western blotting. In all investigated cell lines, GFP fluorescence started to increase 1 h after change of the medium, the fastest increase rates were observed between 2 and 3 h. Fluorescence continued to increase slightly for up to 7 h even after transfer of the cells to ammonium medium. The subsequent decrease of GFP fluorescence was much slower than the increase, probably due to the stability of GFP. The investigation of several cell lines transformed with nr based constructs revealed that, also in the absence of nitrate, the promoter may show residual activity. Furthermore, we observed a strong variation of gene expression between independent cell lines, emphasising the importance of a thorough characterisation of genetically modified cell lines and their individual expression patterns.
bibliographic citation: Chu et al. (2016) Rapid induction of GFP expression by the nitrate reductase promoter in the diatom Phaeodactylum tricornutum. PeerJ 4:e2344 https://doi.org/10.7717/peerj.2344
date submitted: 2016-02-17
date accepted: 2016-07-19
issued: 2016-08-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chu
  given name: Lili
author list: Agent
  family name: Ewe
  given name: Daniela
author list: Agent
  family name: Río Bártulos
  given name: Carolina
author list: Agent
  family name: Kroth
  given name: Peter G.
author list: Agent
  family name: Gruber
  given name: Ansgar
doi: 10.7717/peerj.2344
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-25
copyright: © 2016 Chu et al.
attribution name: Chu et al.

Morpho-histological characterisation of the alimentary canal of an important food fish, Asian seabass (Lates calcarifer)
type: item
type: AcademicArticle
description: Asian seabass (Lates calcarifer) is a food fish of increasing aquaculture importance. In order to improve our understanding on the digestive system and feeding of this species, morphological and histological features of the gut were studied. Morphologically, the Asian seabass gut is defined by a short and muscular esophagus, well-developed stomach and comparatively short intestine. Mucous secreting goblet cells reactive to PAS (Periodic Acid Schiff) and AB (Alcian Blue) stain were present throughout the esophagus. The stomach was sac-like and could be distinguished into the cardiac, fundic and pyloric regions. Gastric glands and mucus cells were predominately present in the cardiac and fundic regions. Five finger-like pyloric caeca were present between the stomach and intestine. The intestine was a short, tubular structure with no morphological differences between the various regions. Histologically, the intestinal regions were similar, the main difference being in the number of goblet cells that increased from anterior to posterior intestine, with 114 ± 9, 153 ± 7 and 317 ± 21 goblet cells in the anterior, mid and posterior regions, respectively. The intestinal epithelium stained positively for PAS, but the staining was stronger for acidic glycoproteins. The rectum was similar to intestine, except for increased goblet cell numbers (anterior rectum: 529 ± 26; posterior rectum: 745 ± 29). Gut morpho-histology did not respond to salinity changes, however, there was a significant reduction of mucosal height, goblet cell numbers and muscularis thickness upon food deprivation.
format: application/pdf
format: text/html
creator: Kathiresan Purushothaman
creator: Doreen Lau
creator: Jolly M. Saju
creator: Syed Musthaq SK
creator: Declan Patrick Lunny
creator: Shubha Vij
creator: László Orbán
subject: Aquaculture, Fisheries and Fish Science
subject: Marine Biology
subject: Histology
description: doi:10.7717/peerj.2377
publisher: PeerJ Inc.
rights: © 2016 Purushothaman et al.
abstract: Asian seabass (Lates calcarifer) is a food fish of increasing aquaculture importance. In order to improve our understanding on the digestive system and feeding of this species, morphological and histological features of the gut were studied. Morphologically, the Asian seabass gut is defined by a short and muscular esophagus, well-developed stomach and comparatively short intestine. Mucous secreting goblet cells reactive to PAS (Periodic Acid Schiff) and AB (Alcian Blue) stain were present throughout the esophagus. The stomach was sac-like and could be distinguished into the cardiac, fundic and pyloric regions. Gastric glands and mucus cells were predominately present in the cardiac and fundic regions. Five finger-like pyloric caeca were present between the stomach and intestine. The intestine was a short, tubular structure with no morphological differences between the various regions. Histologically, the intestinal regions were similar, the main difference being in the number of goblet cells that increased from anterior to posterior intestine, with 114 ± 9, 153 ± 7 and 317 ± 21 goblet cells in the anterior, mid and posterior regions, respectively. The intestinal epithelium stained positively for PAS, but the staining was stronger for acidic glycoproteins. The rectum was similar to intestine, except for increased goblet cell numbers (anterior rectum: 529 ± 26; posterior rectum: 745 ± 29). Gut morpho-histology did not respond to salinity changes, however, there was a significant reduction of mucosal height, goblet cell numbers and muscularis thickness upon food deprivation.
bibliographic citation: Purushothaman et al. (2016) Morpho-histological characterisation of the alimentary canal of an important food fish, Asian seabass (Lates calcarifer). PeerJ 4:e2377 https://doi.org/10.7717/peerj.2377
date submitted: 2016-03-22
date accepted: 2016-07-29
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Purushothaman
  given name: Kathiresan
author list: Agent
  family name: Lau
  given name: Doreen
author list: Agent
  family name: Saju
  given name: Jolly M.
author list: Agent
  family name: Musthaq SK
  given name: Syed
author list: Agent
  family name: Lunny
  given name: Declan Patrick
author list: Agent
  family name: Vij
  given name: Shubha
author list: Agent
  family name: Orbán
  given name: László
doi: 10.7717/peerj.2377
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Purushothaman et al.
attribution name: Purushothaman et al.

The incidence rates of endometrial hyperplasia and endometrial cancer: a four-year population-based study
type: item
type: AcademicArticle
description: Introduction The aim of this study was to determine the incidence rates of endometrial hyperplasia (EH) and endometrial cancer (EC) in the Republic of Korea using national insurance claim data generated from 2009 to 2012. Materials and Methods Data that were generated from 2009 to 2012 were sourced from the Korean Health Insurance Review and Assessment Service-National Inpatients Sample database. The data from women who were assigned diagnosis codes representing EH or EC within 1 month of being assigned codes that corresponded to procedures that included endometrial biopsies and several types of gynecologic surgeries to obtain endometrial pathology samples, were selected for analysis. Results Data from 2,477,424 women were entered into the database between 2009 and 2012, and the data from 1,868 women with EH and 868 women with EC were extracted for analysis. The mean ages of the patients were 44.1 ± 0.4 years for those with EH and 52.7 ± 0.6 years for those with EC. The EH and EC incidence rates were 37 per 100,000 woman-years and 8 per 100,000 woman-years, respectively. The EH and EC incidence rates peaked when the women were in their late forties and fifties, respectively. Conclusions The EH and EC incidence rates determined in this study were somewhat lower than those determined from previous studies. Further studies are required that adjust the data for race, menopausal hormone therapy, and obesity.
format: application/pdf
format: text/html
creator: Jin-Sung Yuk
subject: Epidemiology
subject: Gynecology and Obstetrics
subject: Women's Health
description: doi:10.7717/peerj.2374
publisher: PeerJ Inc.
rights: © 2016 Yuk
abstract: Introduction The aim of this study was to determine the incidence rates of endometrial hyperplasia (EH) and endometrial cancer (EC) in the Republic of Korea using national insurance claim data generated from 2009 to 2012. Materials and Methods Data that were generated from 2009 to 2012 were sourced from the Korean Health Insurance Review and Assessment Service-National Inpatients Sample database. The data from women who were assigned diagnosis codes representing EH or EC within 1 month of being assigned codes that corresponded to procedures that included endometrial biopsies and several types of gynecologic surgeries to obtain endometrial pathology samples, were selected for analysis. Results Data from 2,477,424 women were entered into the database between 2009 and 2012, and the data from 1,868 women with EH and 868 women with EC were extracted for analysis. The mean ages of the patients were 44.1 ± 0.4 years for those with EH and 52.7 ± 0.6 years for those with EC. The EH and EC incidence rates were 37 per 100,000 woman-years and 8 per 100,000 woman-years, respectively. The EH and EC incidence rates peaked when the women were in their late forties and fifties, respectively. Conclusions The EH and EC incidence rates determined in this study were somewhat lower than those determined from previous studies. Further studies are required that adjust the data for race, menopausal hormone therapy, and obesity.
bibliographic citation: Yuk (2016) The incidence rates of endometrial hyperplasia and endometrial cancer: a four-year population-based study. PeerJ 4:e2374 https://doi.org/10.7717/peerj.2374
date submitted: 2016-03-25
date accepted: 2016-07-26
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuk
  given name: Jin-Sung
doi: 10.7717/peerj.2374
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Yuk
attribution name: Yuk

Effects of yearling, juvenile and adult survival on reef manta ray (Manta alfredi) demography
type: item
type: AcademicArticle
description: Background The trade in manta ray gill plates has considerably increased over the last two decades. The resulting increases in ray mortality, in addition to mortality caused by by-catch, has caused many ray populations to decrease in size. The aim of this study was to ascertain how yearling and juvenile growth and survival, and adult survival and reproduction affect reef manta ray (Manta alfredi) population change, to increase our understanding of manta ray demography and thereby improve conservation research and measures for these fish. Methods We developed a population projection model for reef manta rays, and used published life history data on yearling and juvenile growth and adult reproduction to parameterise the model. Because little is known about reef manta ray yearling and juvenile survival, we conducted our analyses using a range of plausible survival rate values for yearlings, juveniles and adults. Results The model accurately captured observed variation in population growth rate, lifetime reproductive success and cohort generation time in different reef manta ray populations. Our demographic analyses revealed a range of population consequences in response to variation in demographic rates. For example, an increase in yearling or adult survival rates always elicited greater responses in population growth rate, lifetime reproductive success and cohort generation time than the same increase in juvenile survival rate. The population growth rate increased linearly, but lifetime reproductive success and cohort generation time increased at an accelerating rate with increasing yearling or adult survival rates. Hence, even a small increase in survival rate could increase lifetime reproductive success by one pup, and cohort generation time by several years. Elasticity analyses revealed that, depending on survival rate values of all life stages, the population growth rate is either most sensitive to changes in the rate with which juveniles survive but stay juvenile…
format: application/pdf
format: text/html
creator: Isabel M. Smallegange
creator: Isabelle B.C. van der Ouderaa
creator: Yara Tibiriçá
subject: Biosphere Interactions
subject: Conservation Biology
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
description: doi:10.7717/peerj.2370
publisher: PeerJ Inc.
rights: © 2016 Smallegange et al.
abstract: Background The trade in manta ray gill plates has considerably increased over the last two decades. The resulting increases in ray mortality, in addition to mortality caused by by-catch, has caused many ray populations to decrease in size. The aim of this study was to ascertain how yearling and juvenile growth and survival, and adult survival and reproduction affect reef manta ray (Manta alfredi) population change, to increase our understanding of manta ray demography and thereby improve conservation research and measures for these fish. Methods We developed a population projection model for reef manta rays, and used published life history data on yearling and juvenile growth and adult reproduction to parameterise the model. Because little is known about reef manta ray yearling and juvenile survival, we conducted our analyses using a range of plausible survival rate values for yearlings, juveniles and adults. Results The model accurately captured observed variation in population growth rate, lifetime reproductive success and cohort generation time in different reef manta ray populations. Our demographic analyses revealed a range of population consequences in response to variation in demographic rates. For example, an increase in yearling or adult survival rates always elicited greater responses in population growth rate, lifetime reproductive success and cohort generation time than the same increase in juvenile survival rate. The population growth rate increased linearly, but lifetime reproductive success and cohort generation time increased at an accelerating rate with increasing yearling or adult survival rates. Hence, even a small increase in survival rate could increase lifetime reproductive success by one pup, and cohort generation time by several years. Elasticity analyses revealed that, depending on survival rate values of all life stages, the population growth rate is either most sensitive to changes in the rate with which juveniles survive but stay juvenile…
bibliographic citation: Smallegange et al. (2016) Effects of yearling, juvenile and adult survival on reef manta ray (Manta alfredi) demography. PeerJ 4:e2370 https://doi.org/10.7717/peerj.2370
date submitted: 2015-11-07
date accepted: 2016-07-26
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smallegange
  given name: Isabel M.
author list: Agent
  family name: van der Ouderaa
  given name: Isabelle B.C.
author list: Agent
  family name: Tibiriçá
  given name: Yara
doi: 10.7717/peerj.2370
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Smallegange et al.
attribution name: Smallegange et al.

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species
type: item
type: AcademicArticle
description: Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%). Discussion Our results suggest that individual samples from…
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creator: Isabelle Laforest-Lapointe
creator: Christian Messier
creator: Steven W. Kembel
subject: Ecology
subject: Genomics
subject: Microbiology
subject: Plant Science
description: doi:10.7717/peerj.2367
publisher: PeerJ Inc.
rights: © 2016 Laforest-Lapointe et al.
abstract: Background The diversity and composition of the microbial community of tree leaves (the phyllosphere) varies among trees and host species and along spatial, temporal, and environmental gradients. Phyllosphere community variation within the canopy of an individual tree exists but the importance of this variation relative to among-tree and among-species variation is poorly understood. Sampling techniques employed for phyllosphere studies include picking leaves from one canopy location to mixing randomly selected leaves from throughout the canopy. In this context, our goal was to characterize the relative importance of intra-individual variation in phyllosphere communities across multiple species, and compare this variation to inter-individual and interspecific variation of phyllosphere epiphytic bacterial communities in a natural temperate forest in Quebec, Canada. Methods We targeted five dominant temperate forest tree species including angiosperms and gymnosperms: Acer saccharum, Acer rubrum, Betula papyrifera, Abies balsamea and Picea glauca. For one randomly selected tree of each species, we sampled microbial communities at six distinct canopy locations: bottom-canopy (1–2 m height), the four cardinal points of mid-canopy (2–4 m height), and the top-canopy (4–6 m height). We also collected bottom-canopy leaves from five additional trees from each species. Results Based on an analysis of bacterial community structure measured via Illumina sequencing of the bacterial 16S gene, we demonstrate that 65% of the intra-individual variation in leaf bacterial community structure could be attributed to the effect of inter-individual and inter-specific differences while the effect of canopy location was not significant. In comparison, host species identity explains 47% of inter-individual and inter-specific variation in leaf bacterial community structure followed by individual identity (32%) and canopy location (6%). Discussion Our results suggest that individual samples from…
bibliographic citation: Laforest-Lapointe et al. (2016) Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species. PeerJ 4:e2367 https://doi.org/10.7717/peerj.2367
date submitted: 2016-05-15
date accepted: 2016-07-25
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Laforest-Lapointe
  given name: Isabelle
author list: Agent
  family name: Messier
  given name: Christian
author list: Agent
  family name: Kembel
  given name: Steven W.
doi: 10.7717/peerj.2367
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Laforest-Lapointe et al.
attribution name: Laforest-Lapointe et al.

Fine structure of the spermatozoon in three species of Cambaridae (Arthropoda: Crustacea: Decapoda) Cambarus robustus, Orconectes propinquus and Orconectes rusticus: a comparative biometrical study
type: item
type: AcademicArticle
description: The ultrastructure of spermatozoa in three species of cambarid crayfish, Cambarus robustus, Orconectes propinquus, and Orconectes rusticus, were studied and compared with eight previously studied species from different crayfish families using morphological features and biometrical data. The ultrastructure of spermatozoa show a generally conserved pattern including an acrosome and nucleus in the anterior and posterior parts of the cell, respectively, radial arms that wrap around the nucleus, and the whole cell is enclosed by an extracellular capsule. The most outstanding morphological feature in spermatozoa of three studied cambarid crayfish is the crest-like protrusions in the anterior part of the acrosome that can be used as one of the features for distinguishing the members of this family. Results of biometrical data reveal that acrosome size in the representatives of Parastacidae are the smallest, while representatives of Astacidae show the biggest acrosome. The acrosome size in species belonging to Cambaridae occupy an intermediate position between the two other families of freshwater crayfish. In conclusion, a combination of morphological features and biometrical data of spermatozoa can help distinguishing different species of the freshwater crayfish.
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format: text/html
creator: Buket Yazicioglu
creator: Přemek Hamr
creator: Pavel Kozák
creator: Antonín Kouba
creator: Hamid Niksirat
subject: Biodiversity
subject: Zoology
description: doi:10.7717/peerj.2363
publisher: PeerJ Inc.
rights: © 2016 Yazicioglu et al.
abstract: The ultrastructure of spermatozoa in three species of cambarid crayfish, Cambarus robustus, Orconectes propinquus, and Orconectes rusticus, were studied and compared with eight previously studied species from different crayfish families using morphological features and biometrical data. The ultrastructure of spermatozoa show a generally conserved pattern including an acrosome and nucleus in the anterior and posterior parts of the cell, respectively, radial arms that wrap around the nucleus, and the whole cell is enclosed by an extracellular capsule. The most outstanding morphological feature in spermatozoa of three studied cambarid crayfish is the crest-like protrusions in the anterior part of the acrosome that can be used as one of the features for distinguishing the members of this family. Results of biometrical data reveal that acrosome size in the representatives of Parastacidae are the smallest, while representatives of Astacidae show the biggest acrosome. The acrosome size in species belonging to Cambaridae occupy an intermediate position between the two other families of freshwater crayfish. In conclusion, a combination of morphological features and biometrical data of spermatozoa can help distinguishing different species of the freshwater crayfish.
bibliographic citation: Yazicioglu et al. (2016) Fine structure of the spermatozoon in three species of Cambaridae (Arthropoda: Crustacea: Decapoda) Cambarus robustus, Orconectes propinquus and Orconectes rusticus: a comparative biometrical study. PeerJ 4:e2363 https://doi.org/10.7717/peerj.2363
date submitted: 2016-05-25
date accepted: 2016-07-23
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yazicioglu
  given name: Buket
author list: Agent
  family name: Hamr
  given name: Přemek
author list: Agent
  family name: Kozák
  given name: Pavel
author list: Agent
  family name: Kouba
  given name: Antonín
author list: Agent
  family name: Niksirat
  given name: Hamid
doi: 10.7717/peerj.2363
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Yazicioglu et al.
attribution name: Yazicioglu et al.

Transmission of a heterologous clade C Symbiodinium in a model anemone infection system via asexual reproduction
type: item
type: AcademicArticle
description: Anemones of genus Exaiptasia are used as model organisms for the study of cnidarian-dinoflagellate (genus Symbiodinium) endosymbiosis. However, while most reef-building corals harbor Symbiodinium of clade C, Exaiptasia spp. anemones mainly harbor clade B Symbiodinium (ITS2 type B1) populations. In this study, we reveal for the first time that bleached Exaiptasia pallida anemones can establish a symbiotic relationship with a clade C Symbiodinium (ITS2 type C1). We further found that anemones can transmit the exogenously supplied clade C Symbiodinium cells to their offspring by asexual reproduction (pedal laceration). In order to corroborate the establishment of stable symbiosis, we used microscopic techniques and genetic analyses to examine several generations of anemones, and the results of these endeavors confirmed the sustainability of the system. These findings provide a framework for understanding the differences in infection dynamics between homologous and heterologous dinoflagellate types using a model anemone infection system.
format: application/pdf
format: text/html
creator: Wan-Nan U. Chen
creator: Ya-Ju Hsiao
creator: Anderson B. Mayfield
creator: Ryan Young
creator: Ling-Lan Hsu
creator: Shao-En Peng
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2358
publisher: PeerJ Inc.
rights: © 2016 Chen et al.
abstract: Anemones of genus Exaiptasia are used as model organisms for the study of cnidarian-dinoflagellate (genus Symbiodinium) endosymbiosis. However, while most reef-building corals harbor Symbiodinium of clade C, Exaiptasia spp. anemones mainly harbor clade B Symbiodinium (ITS2 type B1) populations. In this study, we reveal for the first time that bleached Exaiptasia pallida anemones can establish a symbiotic relationship with a clade C Symbiodinium (ITS2 type C1). We further found that anemones can transmit the exogenously supplied clade C Symbiodinium cells to their offspring by asexual reproduction (pedal laceration). In order to corroborate the establishment of stable symbiosis, we used microscopic techniques and genetic analyses to examine several generations of anemones, and the results of these endeavors confirmed the sustainability of the system. These findings provide a framework for understanding the differences in infection dynamics between homologous and heterologous dinoflagellate types using a model anemone infection system.
bibliographic citation: Chen et al. (2016) Transmission of a heterologous clade C Symbiodinium in a model anemone infection system via asexual reproduction. PeerJ 4:e2358 https://doi.org/10.7717/peerj.2358
date submitted: 2016-05-21
date accepted: 2016-07-22
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Wan-Nan U.
author list: Agent
  family name: Hsiao
  given name: Ya-Ju
author list: Agent
  family name: Mayfield
  given name: Anderson B.
author list: Agent
  family name: Young
  given name: Ryan
author list: Agent
  family name: Hsu
  given name: Ling-Lan
author list: Agent
  family name: Peng
  given name: Shao-En
doi: 10.7717/peerj.2358
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Chen et al.
attribution name: Chen et al.

Taxonomic revision of Eoalligator (Crocodylia, Brevirostres) and the paleogeographic origins of the Chinese alligatoroids
type: item
type: AcademicArticle
description: Background. The primarily Neotropical distribution of living alligatoroids raises questions as to when and how the ancestors of Alligator sinensis migrated to China. As phylogeny provides a necessary framework for historical biogeographic issues, determining the phylogenetic positions of the Chinese alligatoroids is a crucial step towards understanding global alligatoroid paleobiogeography. Besides the unnamed alligatoroids from the Eocene of Guangdong Province, three Chinese fossil taxa have been referred to Alligatoroidea: Alligator luicus, Eoalligator chunyii and Eoalligator huiningensis. However, none of these fossil taxa has been included in a phylogenetic analysis. The genus Eoalligator was established to accommodate E. chunyii from Guangdong Province. E. huiningensis from Anhui Province was later erected as a second species, despite no distinctive similarities with E. chunyii. By contrast, the putative crocodyline Asiatosuchus nanlingensis was established based on material from Guangdong Province, close to the E. chunyii specimens geographically and stratigraphically. Furthermore, specimens of A. nanlingensis and E. chunyii share four distinctive characters, but display no evident differences. As a result, the taxonomic relationships of these three species require restudy. Methods. In this paper, all specimens of E. chunyii and E. huiningensis are reassessed in detail, and compared to specimens of A. nanlingensis. Detailed re-descriptions and revised diagnoses are provided, and a cladistic analysis is carried out to assess the phylogenetic positions of E. chunyii, E. huiningensis and A. nanlingensis. Results. The analysis recovers E. chunyii and A. nanlingensis as sister taxa among basal Crocodylidae, while P. huiningensis is posited as an alligatoroid. Two key characters support the monophyly E. chunyii + A. nanlingensis: sulcus within surangular, and anteroposteriorly oriented surangular-articular suture. The former character is unique to E. chunyii and A. …
format: application/pdf
format: text/html
creator: Yan-yin Wang
creator: Corwin Sullivan
creator: Jun Liu
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.2356
publisher: PeerJ Inc.
rights: © 2016 Wang et al.
abstract: Background. The primarily Neotropical distribution of living alligatoroids raises questions as to when and how the ancestors of Alligator sinensis migrated to China. As phylogeny provides a necessary framework for historical biogeographic issues, determining the phylogenetic positions of the Chinese alligatoroids is a crucial step towards understanding global alligatoroid paleobiogeography. Besides the unnamed alligatoroids from the Eocene of Guangdong Province, three Chinese fossil taxa have been referred to Alligatoroidea: Alligator luicus, Eoalligator chunyii and Eoalligator huiningensis. However, none of these fossil taxa has been included in a phylogenetic analysis. The genus Eoalligator was established to accommodate E. chunyii from Guangdong Province. E. huiningensis from Anhui Province was later erected as a second species, despite no distinctive similarities with E. chunyii. By contrast, the putative crocodyline Asiatosuchus nanlingensis was established based on material from Guangdong Province, close to the E. chunyii specimens geographically and stratigraphically. Furthermore, specimens of A. nanlingensis and E. chunyii share four distinctive characters, but display no evident differences. As a result, the taxonomic relationships of these three species require restudy. Methods. In this paper, all specimens of E. chunyii and E. huiningensis are reassessed in detail, and compared to specimens of A. nanlingensis. Detailed re-descriptions and revised diagnoses are provided, and a cladistic analysis is carried out to assess the phylogenetic positions of E. chunyii, E. huiningensis and A. nanlingensis. Results. The analysis recovers E. chunyii and A. nanlingensis as sister taxa among basal Crocodylidae, while P. huiningensis is posited as an alligatoroid. Two key characters support the monophyly E. chunyii + A. nanlingensis: sulcus within surangular, and anteroposteriorly oriented surangular-articular suture. The former character is unique to E. chunyii and A. …
bibliographic citation: Wang et al. (2016) Taxonomic revision of Eoalligator (Crocodylia, Brevirostres) and the paleogeographic origins of the Chinese alligatoroids. PeerJ 4:e2356 https://doi.org/10.7717/peerj.2356
date submitted: 2016-03-20
date accepted: 2016-07-22
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yan-yin
author list: Agent
  family name: Sullivan
  given name: Corwin
author list: Agent
  family name: Liu
  given name: Jun
doi: 10.7717/peerj.2356
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Wang et al.
attribution name: Wang et al.

Anxiolytic effects of fluoxetine and nicotine exposure on exploratory behavior in zebrafish
type: item
type: AcademicArticle
description: Zebrafish (Danio rerio) have emerged as a popular model for studying the pharmacology and behavior of anxiety. While there have been numerous studies documenting the anxiolytic and anxiogenic effects of common drugs in zebrafish, many do not report or test for behavioral differences between the sexes. Previous studies have indicated that males and females differ in their baseline level of anxiety. In this study, we test for a sex interaction with fluoxetine and nicotine. We exposed fish to system water (control), 10 mg/L fluoxetine, or 1 mg/L nicotine for three minutes prior to being subjected to four minutes in an open-field drop test. Video recordings were tracked using ProAnalyst. Fish from both drug treatments reduced swimming speed, increased vertical position, and increased use of the top half of the open field when compared with the control, though fluoxetine had a larger effect on depth related behaviors while nicotine mostly affected swimming speed. A significant sex effect was observed where females swam at a slower and more constant speed than males, however neither drug produced a sex-dependent response.
format: application/pdf
format: text/html
creator: Matthew L. Singer
creator: Kris Oreschak
creator: Zachariah Rhinehart
creator: Barrie D. Robison
subject: Animal Behavior
subject: Zoology
subject: Pharmacology
description: doi:10.7717/peerj.2352
publisher: PeerJ Inc.
rights: © 2016 Singer et al.
abstract: Zebrafish (Danio rerio) have emerged as a popular model for studying the pharmacology and behavior of anxiety. While there have been numerous studies documenting the anxiolytic and anxiogenic effects of common drugs in zebrafish, many do not report or test for behavioral differences between the sexes. Previous studies have indicated that males and females differ in their baseline level of anxiety. In this study, we test for a sex interaction with fluoxetine and nicotine. We exposed fish to system water (control), 10 mg/L fluoxetine, or 1 mg/L nicotine for three minutes prior to being subjected to four minutes in an open-field drop test. Video recordings were tracked using ProAnalyst. Fish from both drug treatments reduced swimming speed, increased vertical position, and increased use of the top half of the open field when compared with the control, though fluoxetine had a larger effect on depth related behaviors while nicotine mostly affected swimming speed. A significant sex effect was observed where females swam at a slower and more constant speed than males, however neither drug produced a sex-dependent response.
bibliographic citation: Singer et al. (2016) Anxiolytic effects of fluoxetine and nicotine exposure on exploratory behavior in zebrafish. PeerJ 4:e2352 https://doi.org/10.7717/peerj.2352
date submitted: 2016-02-05
date accepted: 2016-07-20
issued: 2016-08-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Singer
  given name: Matthew L.
author list: Agent
  family name: Oreschak
  given name: Kris
author list: Agent
  family name: Rhinehart
  given name: Zachariah
author list: Agent
  family name: Robison
  given name: Barrie D.
doi: 10.7717/peerj.2352
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-08-24
copyright: ©2016 Singer et al.
attribution name: Singer et al.

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