PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Salinity and temperature significantly influence seed germination, seedling establishment, and seedling growth of eelgrass Zostera marina L.
items: The scavenger receptor repertoire in six cnidarian species and its putative role in cnidarian-dinoflagellate symbiosis
items: Assessing pollinators’ use of floral resource subsidies in agri-environment schemes: An illustration using Phacelia tanacetifolia and honeybees
items: Zebra mussel beds: an effective feeding ground for Ponto-Caspian gobies or suitable shelter for their prey?
items: Lithocholic acid induces endoplasmic reticulum stress, autophagy and mitochondrial dysfunction in human prostate cancer cells
items: Identification of phenolic secondary metabolites from Schotia brachypetala Sond. (Fabaceae) and demonstration of their antioxidant activities in Caenorhabditis elegans
items: Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)
items: https://peerj.com/articles/2701
items: Induced pluripotent stem cells from human hair follicle keratinocytes as a potential source for in vitro hair follicle cloning
items: Reanalysis of the anthrax epidemic in Rhodesia, 1978–1984

Salinity and temperature significantly influence seed germination, seedling establishment, and seedling growth of eelgrass Zostera marina L.
type: item
type: AcademicArticle
description: Globally, seagrass beds have been recognized as critical yet declining coastal habitats. To mitigate seagrass losses, seagrass restorations have been conducted in worldwide over the past two decades. Seed utilization is considered to be an important approach in seagrass restoration efforts. In this study, we investigated the effects of salinity and temperature on seed germination, seedling establishment, and seedling growth of eelgrass Zostera marina L. (Swan Lake, northern China). We initially tested the effects of salinity (0, 5, 10, 15, 20, 25, 30, 35, and 40 ppt) and water temperature (5, 10, 15, and 20 °C) on seed germination to identify optimal levels. To identify levels of salinity that could potentially limit survival and growth, and, consequently, the spatial distribution of seedlings in temperate estuaries, we then examined the effect of freshwater and other salinity levels (10, 20, and 30 ppt) on seedling growth and establishment to confirm suitable conditions for seedling development. Finally, we examined the effect of transferring germinated seeds from freshwater or low salinity levels (1, 5, and 15 ppt) to natural seawater (32 ppt) on seedling establishment rate (SER) at 15 °C. In our research, we found that: (1) Mature seeds had a considerably lower moisture content than immature seeds; therefore, moisture content may be a potential indicator of Z. marina seed maturity; (2) Seed germination significantly increased at low salinity (p < 0.001) and high temperature (p < 0.001). Salinity had a much stronger influence on seed germination than temperature. Maximum seed germination (88.67 ± 5.77%) was recorded in freshwater at 15 °C; (3) Freshwater and low salinity levels (< 20 ppt) increased germination but had a strong negative effect on seedling morphology (number of leaves per seedling reduced from 2 to 0, and maximum seedling leaf length reduced from 4.48 to 0 cm) and growth (seedling biomass reduced by 46.15–66.67% and maximum seedling length reduced b…
format: application/pdf
format: text/html
creator: Shaochun Xu
creator: Yi Zhou
creator: Pengmei Wang
creator: Feng Wang
creator: Xiaomei Zhang
creator: Ruiting Gu
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.2697
publisher: PeerJ Inc.
rights: © 2016 Xu et al.
abstract: Globally, seagrass beds have been recognized as critical yet declining coastal habitats. To mitigate seagrass losses, seagrass restorations have been conducted in worldwide over the past two decades. Seed utilization is considered to be an important approach in seagrass restoration efforts. In this study, we investigated the effects of salinity and temperature on seed germination, seedling establishment, and seedling growth of eelgrass Zostera marina L. (Swan Lake, northern China). We initially tested the effects of salinity (0, 5, 10, 15, 20, 25, 30, 35, and 40 ppt) and water temperature (5, 10, 15, and 20 °C) on seed germination to identify optimal levels. To identify levels of salinity that could potentially limit survival and growth, and, consequently, the spatial distribution of seedlings in temperate estuaries, we then examined the effect of freshwater and other salinity levels (10, 20, and 30 ppt) on seedling growth and establishment to confirm suitable conditions for seedling development. Finally, we examined the effect of transferring germinated seeds from freshwater or low salinity levels (1, 5, and 15 ppt) to natural seawater (32 ppt) on seedling establishment rate (SER) at 15 °C. In our research, we found that: (1) Mature seeds had a considerably lower moisture content than immature seeds; therefore, moisture content may be a potential indicator of Z. marina seed maturity; (2) Seed germination significantly increased at low salinity (p < 0.001) and high temperature (p < 0.001). Salinity had a much stronger influence on seed germination than temperature. Maximum seed germination (88.67 ± 5.77%) was recorded in freshwater at 15 °C; (3) Freshwater and low salinity levels (< 20 ppt) increased germination but had a strong negative effect on seedling morphology (number of leaves per seedling reduced from 2 to 0, and maximum seedling leaf length reduced from 4.48 to 0 cm) and growth (seedling biomass reduced by 46.15–66.67% and maximum seedling length reduced b…
bibliographic citation: Xu et al. (2016) Salinity and temperature significantly influence seed germination, seedling establishment, and seedling growth of eelgrass Zostera marina L.. PeerJ 4:e2697 https://doi.org/10.7717/peerj.2697
date submitted: 2016-06-28
date accepted: 2016-10-18
issued: 2016-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Shaochun
author list: Agent
  family name: Zhou
  given name: Yi
author list: Agent
  family name: Wang
  given name: Pengmei
author list: Agent
  family name: Wang
  given name: Feng
author list: Agent
  family name: Zhang
  given name: Xiaomei
author list: Agent
  family name: Gu
  given name: Ruiting
doi: 10.7717/peerj.2697
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-15
copyright: © 2016 Xu et al.
attribution name: Xu et al.

The scavenger receptor repertoire in six cnidarian species and its putative role in cnidarian-dinoflagellate symbiosis
type: item
type: AcademicArticle
description: Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians have diverse and complex innate immune repertoires that are just beginning to be described. Scavenger receptors (SR) are a diverse superfamily of innate immunity genes that recognize a broad array of microbial ligands and participate in phagocytosis of invading microbes. The superfamily includes subclades named SR-A through SR-I that are categorized based on the arrangement of sequence domains including the scavenger receptor cysteine rich (SRCR), the C-type lectin (CTLD) and the CD36 domains. Previous functional and gene expression studies on cnidarian-dinoflagellate symbiosis have implicated SR-like proteins in interpartner communication and regulation. In this study, we characterized the SR repertoire from a combination of genomic and transcriptomic resources from six cnidarian species in the Class Anthozoa. We combined these bioinformatic analyses with functional experiments using the SR inhibitor fucoidan to explore a role for SRs in cnidarian symbiosis and immunity. Bioinformatic searches revealed a large diversity of SR-like genes that resembled SR-As, SR-Bs, SR-Es and SR-Is. SRCRs, CTLDs and CD36 domains were identified in multiple sequences in combinations that were highly homologous to vertebrate SRs as well as in proteins with novel domain combinations. Phylogenetic analyses of CD36 domains of the SR-B-like sequences from a diversity of metazoans grouped cnidarian with bilaterian sequences separate from other basal metazoans. All cnidarian sequences grouped together with moderate support in a subclade separately from bilaterian sequences. Functional experiments were carried out on the sea anemone Aiptasia pallida that engages in a symbiosis with Symbiodinium minutum (clade B1). Experimenta…
format: application/pdf
format: text/html
creator: Emilie F. Neubauer
creator: Angela Z. Poole
creator: Olivier Detournay
creator: Virginia M. Weis
creator: Simon K. Davy
subject: Cell Biology
subject: Evolutionary Studies
subject: Genomics
subject: Marine Biology
description: doi:10.7717/peerj.2692
publisher: PeerJ Inc.
rights: © 2016 Neubauer et al.
abstract: Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians have diverse and complex innate immune repertoires that are just beginning to be described. Scavenger receptors (SR) are a diverse superfamily of innate immunity genes that recognize a broad array of microbial ligands and participate in phagocytosis of invading microbes. The superfamily includes subclades named SR-A through SR-I that are categorized based on the arrangement of sequence domains including the scavenger receptor cysteine rich (SRCR), the C-type lectin (CTLD) and the CD36 domains. Previous functional and gene expression studies on cnidarian-dinoflagellate symbiosis have implicated SR-like proteins in interpartner communication and regulation. In this study, we characterized the SR repertoire from a combination of genomic and transcriptomic resources from six cnidarian species in the Class Anthozoa. We combined these bioinformatic analyses with functional experiments using the SR inhibitor fucoidan to explore a role for SRs in cnidarian symbiosis and immunity. Bioinformatic searches revealed a large diversity of SR-like genes that resembled SR-As, SR-Bs, SR-Es and SR-Is. SRCRs, CTLDs and CD36 domains were identified in multiple sequences in combinations that were highly homologous to vertebrate SRs as well as in proteins with novel domain combinations. Phylogenetic analyses of CD36 domains of the SR-B-like sequences from a diversity of metazoans grouped cnidarian with bilaterian sequences separate from other basal metazoans. All cnidarian sequences grouped together with moderate support in a subclade separately from bilaterian sequences. Functional experiments were carried out on the sea anemone Aiptasia pallida that engages in a symbiosis with Symbiodinium minutum (clade B1). Experimenta…
bibliographic citation: Neubauer et al. (2016) The scavenger receptor repertoire in six cnidarian species and its putative role in cnidarian-dinoflagellate symbiosis. PeerJ 4:e2692 https://doi.org/10.7717/peerj.2692
date submitted: 2016-08-03
date accepted: 2016-10-15
issued: 2016-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Neubauer
  given name: Emilie F.
author list: Agent
  family name: Poole
  given name: Angela Z.
author list: Agent
  family name: Detournay
  given name: Olivier
author list: Agent
  family name: Weis
  given name: Virginia M.
author list: Agent
  family name: Davy
  given name: Simon K.
doi: 10.7717/peerj.2692
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-15
copyright: ©2016 Neubauer et al.
attribution name: Neubauer et al.

Assessing pollinators’ use of floral resource subsidies in agri-environment schemes: An illustration using Phacelia tanacetifolia and honeybees
type: item
type: AcademicArticle
description: Background Honeybees (Apis mellifera L.) are frequently used in agriculture for pollination services because of their abundance, generalist floral preferences, ease of management and hive transport. However, their populations are declining in many countries. Agri-Environment Schemes (AES) are being implemented in agricultural systems to combat the decline in populations of pollinators and other insects. Despite AES being increasingly embedded in policy and budgets, scientific assessments of many of these schemes still are lacking, and only a few studies have examined the extent to which insect pollinators use the floral enhancements that are part of AES and on which floral components they feed (i.e., pollen and/or nectar). Methods In the present work, we used a combination of observations on honeybee foraging for nectar/pollen from the Californian annual plant Phacelia tanacetifolia in the field, collection of pollen pellets from hives, and pollen identification, to assess the value of adding phacelia to an agro-ecosystem to benefit honeybees. Results It was found that phacelia pollen was almost never taken by honeybees. The work here demonstrates that honeybees may not use the floral enhancements added to a landscape as expected and points to the need for more careful assessments of what resources are used by honeybees in AES and understanding the role, if any, which AES play in enhancing pollinator fitness. Discussion We recommend using the methodology in this paper to explore the efficacy of AES before particular flowering species are adopted more widely to give a more complete illustration of the actual efficacy of AES.
format: application/pdf
format: text/html
creator: Rowan Sprague
creator: Stéphane Boyer
creator: Georgia M. Stevenson
creator: Steve D. Wratten
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Science Policy
description: doi:10.7717/peerj.2677
publisher: PeerJ Inc.
rights: © 2016 Sprague et al.
abstract: Background Honeybees (Apis mellifera L.) are frequently used in agriculture for pollination services because of their abundance, generalist floral preferences, ease of management and hive transport. However, their populations are declining in many countries. Agri-Environment Schemes (AES) are being implemented in agricultural systems to combat the decline in populations of pollinators and other insects. Despite AES being increasingly embedded in policy and budgets, scientific assessments of many of these schemes still are lacking, and only a few studies have examined the extent to which insect pollinators use the floral enhancements that are part of AES and on which floral components they feed (i.e., pollen and/or nectar). Methods In the present work, we used a combination of observations on honeybee foraging for nectar/pollen from the Californian annual plant Phacelia tanacetifolia in the field, collection of pollen pellets from hives, and pollen identification, to assess the value of adding phacelia to an agro-ecosystem to benefit honeybees. Results It was found that phacelia pollen was almost never taken by honeybees. The work here demonstrates that honeybees may not use the floral enhancements added to a landscape as expected and points to the need for more careful assessments of what resources are used by honeybees in AES and understanding the role, if any, which AES play in enhancing pollinator fitness. Discussion We recommend using the methodology in this paper to explore the efficacy of AES before particular flowering species are adopted more widely to give a more complete illustration of the actual efficacy of AES.
bibliographic citation: Sprague et al. (2016) Assessing pollinators’ use of floral resource subsidies in agri-environment schemes: An illustration using Phacelia tanacetifolia and honeybees. PeerJ 4:e2677 https://doi.org/10.7717/peerj.2677
date submitted: 2016-06-27
date accepted: 2016-10-12
issued: 2016-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sprague
  given name: Rowan
author list: Agent
  family name: Boyer
  given name: Stéphane
author list: Agent
  family name: Stevenson
  given name: Georgia M.
author list: Agent
  family name: Wratten
  given name: Steve D.
doi: 10.7717/peerj.2677
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-15
copyright: © 2016 Sprague et al.
attribution name: Sprague et al.

Zebra mussel beds: an effective feeding ground for Ponto-Caspian gobies or suitable shelter for their prey?
type: item
type: AcademicArticle
description: Aggregations of the Ponto-Caspian invasive zebra mussel (Dreissena polymorpha) constitute a suitable habitat for macroinvertebrates, considerably increasing their abundance and providing effective antipredator protection. Thus, the overall effect of a mussel bed on particular predator species may vary from positive to negative, depending on both prey density increase and predator ability to prey in a structurally complex habitat. Alien Ponto-Caspian goby fish are likely to be facilitated when introduced into new areas by zebra mussels, provided that they are capable of utilizing mussel beds as habitat and feeding grounds. We ran laboratory experiments to find which prey (chironomid larvae) densities (from ca. 500 to 2,000 individuals m−2) in a mussel bed make it a more beneficial feeding ground for the racer goby Babka gymnotrachelus (RG) and western tubenose goby Proterorhinus semilunaris (WTG) compared to sandy and stone substrata (containing the basic prey density of 500 ind. m−2). Moreover, we checked how food availability affects habitat selection by fish. Mussel beds became more suitable for fish than alternative mineral substrata when food abundance was at least two times higher (1,000 vs. 500 ind. m−2), regardless of fish size and species. WTG was associated with mussel beds regardless of its size and prey density, whereas RG switched to this habitat when it became a better feeding ground than alternative substrata. Larger RG exhibited a stronger affinity for mussels than small individuals. WTG fed more efficiently from a mussel bed at high food abundances than RG. A literature review has shown that increasing chironomid density, which in our study was sufficient to make a mussel habitat an attractive feeding ground for the gobies, is commonly observed in mussel beds in the field. Therefore, we conclude that zebra mussels may positively affect the alien goby species and are likely to facilitate their establishment in novel areas, contributing to an invasiona…
format: application/pdf
format: text/html
creator: Jarosław Kobak
creator: Małgorzata Poznańska
creator: Łukasz Jermacz
creator: Tomasz Kakareko
creator: Daniel Prądzynski
creator: Małgorzata Łodygowska
creator: Karolina Montowska
creator: Karolina Bącela-Spychalska
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.2672
publisher: PeerJ Inc.
rights: © 2016 Kobak et al.
abstract: Aggregations of the Ponto-Caspian invasive zebra mussel (Dreissena polymorpha) constitute a suitable habitat for macroinvertebrates, considerably increasing their abundance and providing effective antipredator protection. Thus, the overall effect of a mussel bed on particular predator species may vary from positive to negative, depending on both prey density increase and predator ability to prey in a structurally complex habitat. Alien Ponto-Caspian goby fish are likely to be facilitated when introduced into new areas by zebra mussels, provided that they are capable of utilizing mussel beds as habitat and feeding grounds. We ran laboratory experiments to find which prey (chironomid larvae) densities (from ca. 500 to 2,000 individuals m−2) in a mussel bed make it a more beneficial feeding ground for the racer goby Babka gymnotrachelus (RG) and western tubenose goby Proterorhinus semilunaris (WTG) compared to sandy and stone substrata (containing the basic prey density of 500 ind. m−2). Moreover, we checked how food availability affects habitat selection by fish. Mussel beds became more suitable for fish than alternative mineral substrata when food abundance was at least two times higher (1,000 vs. 500 ind. m−2), regardless of fish size and species. WTG was associated with mussel beds regardless of its size and prey density, whereas RG switched to this habitat when it became a better feeding ground than alternative substrata. Larger RG exhibited a stronger affinity for mussels than small individuals. WTG fed more efficiently from a mussel bed at high food abundances than RG. A literature review has shown that increasing chironomid density, which in our study was sufficient to make a mussel habitat an attractive feeding ground for the gobies, is commonly observed in mussel beds in the field. Therefore, we conclude that zebra mussels may positively affect the alien goby species and are likely to facilitate their establishment in novel areas, contributing to an invasiona…
bibliographic citation: Kobak et al. (2016) Zebra mussel beds: an effective feeding ground for Ponto-Caspian gobies or suitable shelter for their prey?. PeerJ 4:e2672 https://doi.org/10.7717/peerj.2672
date submitted: 2016-07-13
date accepted: 2016-10-09
issued: 2016-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kobak
  given name: Jarosław
author list: Agent
  family name: Poznańska
  given name: Małgorzata
author list: Agent
  family name: Jermacz
  given name: Łukasz
author list: Agent
  family name: Kakareko
  given name: Tomasz
author list: Agent
  family name: Prądzynski
  given name: Daniel
author list: Agent
  family name: Łodygowska
  given name: Małgorzata
author list: Agent
  family name: Montowska
  given name: Karolina
author list: Agent
  family name: Bącela-Spychalska
  given name: Karolina
doi: 10.7717/peerj.2672
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-15
copyright: © 2016 Kobak et al.
attribution name: Kobak et al.

Lithocholic acid induces endoplasmic reticulum stress, autophagy and mitochondrial dysfunction in human prostate cancer cells
type: item
type: AcademicArticle
description: Lithocholic acid (LCA) is a secondary bile acid that is selectively toxic to human neuroblastoma, breast and prostate cancer cells, whilst sparing normal cells. We previously reported that LCA inhibited cell viability and proliferation and induced apoptosis and necrosis of androgen-dependent LNCaP and androgen-independent PC-3 human prostate cancer cells. In the present study, we investigated the roles of endoplasmic reticulum (ER) stress, autophagy and mitochondrial dysfunction in the toxicity of LCA in PC-3 and autophagy deficient, androgen-independent DU-145 cells. LCA induced ER stress-related proteins, such as CCAAT-enhancer-binding protein homologous protein (CHOP), and the phosphorylation of eukaryotic initiation factor 2-alpha (p-eIF2α) and c-Jun N-terminal kinases (p-JNK) in both cancer cell-types. The p53 upregulated modulator of apoptosis (PUMA) and B cell lymphoma-like protein 11 (BIM) levels were decreased at overtly toxic LCA concentrations, although PUMA levels increased at lower LCA concentrations in both cell lines. LCA induced autophagy-related conversion of microtubule-associated proteins 1A/1B light chain 3B (LC3BI–LC3BII), and autophagy-related protein ATG5 in PC-3 cells, but not in autophagy-deficient DU-145 cells. LCA (>10 µM) increased levels of reactive oxygen species (ROS) concentration-dependently in PC-3 cells, whereas ROS levels were not affected in DU-145 cells. Salubrinal, an inhibitor of eIF2α dephosphorylation and ER stress, reduced LCA-induced CHOP levels slightly in PC-3, but not DU-145 cells. Salubrinal pre-treatment increased the cytotoxicity of LCA in PC-3 and DU-145 cells and resulted in a statistically significant loss of cell viability at normally non-toxic concentrations of LCA. The late-stage autophagy inhibitor bafilomycin A1 exacerbated LCA toxicity at subtoxic LCA concentrations in PC-3 cells. The antioxidant α-tocotrienol strongly inhibited the toxicity of LCA in PC-3 cells, but not in DU-145 cells. Collectively, althou…
format: application/pdf
format: text/html
creator: Ahmed A. Gafar
creator: Hossam M. Draz
creator: Alexander A. Goldberg
creator: Mohamed A. Bashandy
creator: Sayed Bakry
creator: Mahmoud A. Khalifa
creator: Walid AbuShair
creator: Vladimir I. Titorenko
creator: J. Thomas Sanderson
subject: Toxicology
subject: Oncology
description: doi:10.7717/peerj.2445
publisher: PeerJ Inc.
rights: © 2016 Gafar et al.
abstract: Lithocholic acid (LCA) is a secondary bile acid that is selectively toxic to human neuroblastoma, breast and prostate cancer cells, whilst sparing normal cells. We previously reported that LCA inhibited cell viability and proliferation and induced apoptosis and necrosis of androgen-dependent LNCaP and androgen-independent PC-3 human prostate cancer cells. In the present study, we investigated the roles of endoplasmic reticulum (ER) stress, autophagy and mitochondrial dysfunction in the toxicity of LCA in PC-3 and autophagy deficient, androgen-independent DU-145 cells. LCA induced ER stress-related proteins, such as CCAAT-enhancer-binding protein homologous protein (CHOP), and the phosphorylation of eukaryotic initiation factor 2-alpha (p-eIF2α) and c-Jun N-terminal kinases (p-JNK) in both cancer cell-types. The p53 upregulated modulator of apoptosis (PUMA) and B cell lymphoma-like protein 11 (BIM) levels were decreased at overtly toxic LCA concentrations, although PUMA levels increased at lower LCA concentrations in both cell lines. LCA induced autophagy-related conversion of microtubule-associated proteins 1A/1B light chain 3B (LC3BI–LC3BII), and autophagy-related protein ATG5 in PC-3 cells, but not in autophagy-deficient DU-145 cells. LCA (>10 µM) increased levels of reactive oxygen species (ROS) concentration-dependently in PC-3 cells, whereas ROS levels were not affected in DU-145 cells. Salubrinal, an inhibitor of eIF2α dephosphorylation and ER stress, reduced LCA-induced CHOP levels slightly in PC-3, but not DU-145 cells. Salubrinal pre-treatment increased the cytotoxicity of LCA in PC-3 and DU-145 cells and resulted in a statistically significant loss of cell viability at normally non-toxic concentrations of LCA. The late-stage autophagy inhibitor bafilomycin A1 exacerbated LCA toxicity at subtoxic LCA concentrations in PC-3 cells. The antioxidant α-tocotrienol strongly inhibited the toxicity of LCA in PC-3 cells, but not in DU-145 cells. Collectively, althou…
bibliographic citation: Gafar et al. (2016) Lithocholic acid induces endoplasmic reticulum stress, autophagy and mitochondrial dysfunction in human prostate cancer cells. PeerJ 4:e2445 https://doi.org/10.7717/peerj.2445
date submitted: 2016-01-21
date accepted: 2016-08-13
issued: 2016-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gafar
  given name: Ahmed A.
author list: Agent
  family name: Draz
  given name: Hossam M.
author list: Agent
  family name: Goldberg
  given name: Alexander A.
author list: Agent
  family name: Bashandy
  given name: Mohamed A.
author list: Agent
  family name: Bakry
  given name: Sayed
author list: Agent
  family name: Khalifa
  given name: Mahmoud A.
author list: Agent
  family name: AbuShair
  given name: Walid
author list: Agent
  family name: Titorenko
  given name: Vladimir I.
author list: Agent
  family name: Sanderson
  given name: J. Thomas
doi: 10.7717/peerj.2445
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-15
copyright: ©2016 Gafar et al.
attribution name: Gafar et al.

Identification of phenolic secondary metabolites from Schotia brachypetala Sond. (Fabaceae) and demonstration of their antioxidant activities in Caenorhabditis elegans
type: item
type: AcademicArticle
description: Background Schotia brachypetala Sond. (Fabaceae) is an endemic tree of Southern Africa whose phytochemistry and pharmacology were slightly studied. The present work aimed at profiling the major phenolics compounds present in the hydro-alcohol extract from S. brachypetala leaves (SBE) using LC/HRESI/MS/MS and NMR and prove their antioxidant capabilities using novel methods. Methods In vitro assays; DPPH, TEAC persulfate decolorizing kinetic and FRAP assays, and in vivo assays: Caenorhabditis elegans strains maintenance, Intracellular ROS in C. elegans, Survival assay, GFP expression and Subcellular DAF-16 localization were employed to evaluate the antioxidant activity. Results More than forty polyphenols, including flavonoid glycosides, galloylated flavonoid glycosides, isoflavones, dihydrochalcones, procyanidins, anthocyanins, hydroxy benzoic acid derivatives, hydrolysable tannins, and traces of methylated and acetylated flavonoid derivatives were identified. Three compounds were isolated and identified from the genus Schotia for the first time, namely gallic acid, myricetin-3-O-α-L-1C4-rhamnoside and quercetin-3-O-L-1C4-rhamnoside. The total phenolics content of SBE was (376 mg CAE/g), followed by flavonoids (67.87 QE/g). In vitro antioxidant activity of SBE was evidenced by DPPH radical scavenging activity (IC50 of 9 µg/mL), FRAP ferric reducing activity (5,000 mol Fe2+ E/mg) and ABTS peroxide inhibiting activity (1,054 mM Trolox E/mg). The tested extract was able to protect the worms against juglone induced oxidative stress, an increased survival rate (up to 41%) was recorded, when compared with the control group (11%) and attenuate the reactive oxygen species (ROS) accumulation in dose-dependent and reached up to 72% for the highest tested concentration. SBE was also able to attenuate the levels of heat shock protein (HSP) expression in dose-dependent up to 60% in the 150 µg SBE/mL group. In DAF-16 Subcellular localization SBE treated worms showed nuclear locali…
format: application/pdf
format: text/html
creator: Mansour Sobeh
creator: Esraa ElHawary
creator: Herbenya Peixoto
creator: Rola M. Labib
creator: Heba Handoussa
creator: Noha Swilam
creator: Ahmed H. El-Khatib
creator: Farukh Sharapov
creator: Tamer Mohamed
creator: Sonja Krstin
creator: Michael W. Linscheid
creator: Abdel Nasser Singab
creator: Michael Wink
creator: Nahla Ayoub
subject: Plant Science
subject: Pharmacology
description: doi:10.7717/peerj.2404
publisher: PeerJ Inc.
rights: © 2016 Sobeh et al.
abstract: Background Schotia brachypetala Sond. (Fabaceae) is an endemic tree of Southern Africa whose phytochemistry and pharmacology were slightly studied. The present work aimed at profiling the major phenolics compounds present in the hydro-alcohol extract from S. brachypetala leaves (SBE) using LC/HRESI/MS/MS and NMR and prove their antioxidant capabilities using novel methods. Methods In vitro assays; DPPH, TEAC persulfate decolorizing kinetic and FRAP assays, and in vivo assays: Caenorhabditis elegans strains maintenance, Intracellular ROS in C. elegans, Survival assay, GFP expression and Subcellular DAF-16 localization were employed to evaluate the antioxidant activity. Results More than forty polyphenols, including flavonoid glycosides, galloylated flavonoid glycosides, isoflavones, dihydrochalcones, procyanidins, anthocyanins, hydroxy benzoic acid derivatives, hydrolysable tannins, and traces of methylated and acetylated flavonoid derivatives were identified. Three compounds were isolated and identified from the genus Schotia for the first time, namely gallic acid, myricetin-3-O-α-L-1C4-rhamnoside and quercetin-3-O-L-1C4-rhamnoside. The total phenolics content of SBE was (376 mg CAE/g), followed by flavonoids (67.87 QE/g). In vitro antioxidant activity of SBE was evidenced by DPPH radical scavenging activity (IC50 of 9 µg/mL), FRAP ferric reducing activity (5,000 mol Fe2+ E/mg) and ABTS peroxide inhibiting activity (1,054 mM Trolox E/mg). The tested extract was able to protect the worms against juglone induced oxidative stress, an increased survival rate (up to 41%) was recorded, when compared with the control group (11%) and attenuate the reactive oxygen species (ROS) accumulation in dose-dependent and reached up to 72% for the highest tested concentration. SBE was also able to attenuate the levels of heat shock protein (HSP) expression in dose-dependent up to 60% in the 150 µg SBE/mL group. In DAF-16 Subcellular localization SBE treated worms showed nuclear locali…
bibliographic citation: Sobeh et al. (2016) Identification of phenolic secondary metabolites from Schotia brachypetala Sond. (Fabaceae) and demonstration of their antioxidant activities in Caenorhabditis elegans. PeerJ 4:e2404 https://doi.org/10.7717/peerj.2404
date submitted: 2016-02-20
date accepted: 2016-08-03
issued: 2016-11-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sobeh
  given name: Mansour
author list: Agent
  family name: ElHawary
  given name: Esraa
author list: Agent
  family name: Peixoto
  given name: Herbenya
author list: Agent
  family name: Labib
  given name: Rola M.
author list: Agent
  family name: Handoussa
  given name: Heba
author list: Agent
  family name: Swilam
  given name: Noha
author list: Agent
  family name: El-Khatib
  given name: Ahmed H.
author list: Agent
  family name: Sharapov
  given name: Farukh
author list: Agent
  family name: Mohamed
  given name: Tamer
author list: Agent
  family name: Krstin
  given name: Sonja
author list: Agent
  family name: Linscheid
  given name: Michael W.
author list: Agent
  family name: Singab
  given name: Abdel Nasser
author list: Agent
  family name: Wink
  given name: Michael
author list: Agent
  family name: Ayoub
  given name: Nahla
doi: 10.7717/peerj.2404
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-15
copyright: ©2016 Sobeh et al.
attribution name: Sobeh et al.

Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae)
type: item
type: AcademicArticle
description: The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.
format: application/pdf
format: text/html
creator: Wenpan Dong
creator: Chao Xu
creator: Delu Li
creator: Xiaobai Jin
creator: Ruili Li
creator: Qi Lu
creator: Zhili Suo
subject: Biodiversity
subject: Biotechnology
subject: Genetics
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.2699
publisher: PeerJ Inc.
rights: © 2016 Dong et al.
abstract: The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.
bibliographic citation: Dong et al. (2016) Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae). PeerJ 4:e2699 https://doi.org/10.7717/peerj.2699
date submitted: 2016-08-02
date accepted: 2016-10-18
issued: 2016-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Wenpan
author list: Agent
  family name: Xu
  given name: Chao
author list: Agent
  family name: Li
  given name: Delu
author list: Agent
  family name: Jin
  given name: Xiaobai
author list: Agent
  family name: Li
  given name: Ruili
author list: Agent
  family name: Lu
  given name: Qi
author list: Agent
  family name: Suo
  given name: Zhili
doi: 10.7717/peerj.2699
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-10
copyright: ©2016 Dong et al.
attribution name: Dong et al.

https://peerj.com/articles/2701
type: item
type: AcademicArticle
title: Soymilk residue (okara) as a natural immobilization carrier for Lactobacillus plantarum cells enhances soymilk fermentation, glucosidic isoflavone bioconversion, and cell survival under simulated gastric and intestinal conditions
description: Cell immobilization is an alternative to microencapsulation for the maintenance of cells in a liquid medium. However, artificial immobilization carriers are expensive and pose a high safety risk. Okara, a food-grade byproduct from soymilk production, is rich in prebiotics. Lactobacilli could provide health enhancing effects to the host. This study aimed to evaluate the potential of okara as a natural immobilizer for L. plantarum 70810 cells. The study also aimed to evaluate the effects of okara-immobilized L. plantarum 70810 cells (IL) on soymilk fermentation, glucosidic isoflavone bioconversion, and cell resistance to simulated gastric and intestinal stresses. Scanning electron microscopy (SEM) was used to show cells adherence to the surface of okara. Lactic acid, acetic acid and isoflavone analyses in unfermented and fermented soymilk were performed by HPLC with UV detection. Viability and growth kinetics of immobilized and free L. plantarum 70810 cells (FL) were followed during soymilk fermentation. Moreover, changes in pH, titrable acidity and viscosity were measured by conventional methods. For in vitro testing of simulated gastrointestinal resistance, fermented soymilk was inoculated with FL or IL and an aliquot incubated into acidic MRS broth which was conveniently prepared to simulate gastric, pancreatic juices and bile salts. Survival to simulated gastric and intestinal stresses was evaluated by plate count of colony forming units on MRS agar. SEM revealed that the lactobacilli cells attached and bound to the surface of okara. Compared with FL, IL exhibited a significantly higher specific growth rate, shorter lag phase of growth, higher productions of lactic and acetic acids, a faster decrease in pH and increase in titrable acidity, and a higher soymilk viscosity. Similarly, IL in soymilk showed higher productions of daizein and genistein compared with the control. Compared with FL, IL showed reinforced resistance to simulatedgastric and intestinal stresses…
format: application/pdf
format: text/html
creator: Xia Xiudong
creator: Wang Ying
creator: Liu Xiaoli
creator: Li Ying
creator: Zhou Jianzhong
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.2701
publisher: PeerJ Inc.
rights: © 2016 Xiudong et al.
abstract: Cell immobilization is an alternative to microencapsulation for the maintenance of cells in a liquid medium. However, artificial immobilization carriers are expensive and pose a high safety risk. Okara, a food-grade byproduct from soymilk production, is rich in prebiotics. Lactobacilli could provide health enhancing effects to the host. This study aimed to evaluate the potential of okara as a natural immobilizer for L. plantarum 70810 cells. The study also aimed to evaluate the effects of okara-immobilized L. plantarum 70810 cells (IL) on soymilk fermentation, glucosidic isoflavone bioconversion, and cell resistance to simulated gastric and intestinal stresses. Scanning electron microscopy (SEM) was used to show cells adherence to the surface of okara. Lactic acid, acetic acid and isoflavone analyses in unfermented and fermented soymilk were performed by HPLC with UV detection. Viability and growth kinetics of immobilized and free L. plantarum 70810 cells (FL) were followed during soymilk fermentation. Moreover, changes in pH, titrable acidity and viscosity were measured by conventional methods. For in vitro testing of simulated gastrointestinal resistance, fermented soymilk was inoculated with FL or IL and an aliquot incubated into acidic MRS broth which was conveniently prepared to simulate gastric, pancreatic juices and bile salts. Survival to simulated gastric and intestinal stresses was evaluated by plate count of colony forming units on MRS agar. SEM revealed that the lactobacilli cells attached and bound to the surface of okara. Compared with FL, IL exhibited a significantly higher specific growth rate, shorter lag phase of growth, higher productions of lactic and acetic acids, a faster decrease in pH and increase in titrable acidity, and a higher soymilk viscosity. Similarly, IL in soymilk showed higher productions of daizein and genistein compared with the control. Compared with FL, IL showed reinforced resistance to simulatedgastric and intestinal stresses…
bibliographic citation: Xiudong et al. (2016) Soymilk residue (okara) as a natural immobilization carrier for Lactobacillus plantarum cells enhances soymilk fermentation, glucosidic isoflavone bioconversion, and cell survival under simulated gastric and intestinal conditions. PeerJ 4:e2701 https://doi.org/10.7717/peerj.2701
date submitted: 2016-08-11
date accepted: 2016-10-18
issued: 2016-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xiudong
  given name: Xia
author list: Agent
  family name: Ying
  given name: Wang
author list: Agent
  family name: Xiaoli
  given name: Liu
author list: Agent
  family name: Ying
  given name: Li
author list: Agent
  family name: Jianzhong
  given name: Zhou
doi: 10.7717/peerj.2701
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-10
copyright: ©2016 Xiudong et al.
attribution name: Xiudong et al.

Induced pluripotent stem cells from human hair follicle keratinocytes as a potential source for in vitro hair follicle cloning
type: item
type: AcademicArticle
description: Background Human hair follicles are important for the renewal of new hairs and their development. The generation of induced pluripotent stem cells (iPSCs) from hair follicles is easy due to its accessibility and availability. The pluripotent cells derived from hair follicles not only have a higher tendency to re-differentiate into hair follicles, but are also more suited for growth in hair scalp tissue microenvironment. Methods In this study, human hair follicular keratinocytes were used to generate iPSCs, which were then further differentiated in vitro into keratinocytes. The derived iPSCs were characterised by using immunofluorescence staining, flow cytometry, and reverse-transcription PCR to check for its pluripotency markers expression. Results The iPSC clones expressed pluripotency markers such as TRA-1-60, TRA-1-81, SSEA4, OCT4, SOX2, NANOG, LEFTY, and GABRB. The well-formed three germ layers were observed during differentiation using iPSCs derived from hair follicles. The successful formation of keratioctyes from iPSCs was confirmed by the expression of cytokeratin 14 marker. Discussion Hair follicles represent a valuable keratinocytes source for in vitro hair cloning for use in treating hair balding or grafting in burn patients. Our significant findings in this report proved that hair follicles could be used to produce pluripotent stem cells and suggested that the genetic and micro-environmental elements of hair follicles might trigger higher and more efficient hair follicles re-differentiation.
format: application/pdf
format: text/html
creator: Sheng Jye Lim
creator: Shu Cheow Ho
creator: Pooi Ling Mok
creator: Kian Lee Tan
creator: Alan H.K. Ong
creator: Seng Chiew Gan
subject: Cell Biology
subject: Molecular Biology
subject: Translational Medicine
description: doi:10.7717/peerj.2695
publisher: PeerJ Inc.
rights: © 2016 Lim et al.
abstract: Background Human hair follicles are important for the renewal of new hairs and their development. The generation of induced pluripotent stem cells (iPSCs) from hair follicles is easy due to its accessibility and availability. The pluripotent cells derived from hair follicles not only have a higher tendency to re-differentiate into hair follicles, but are also more suited for growth in hair scalp tissue microenvironment. Methods In this study, human hair follicular keratinocytes were used to generate iPSCs, which were then further differentiated in vitro into keratinocytes. The derived iPSCs were characterised by using immunofluorescence staining, flow cytometry, and reverse-transcription PCR to check for its pluripotency markers expression. Results The iPSC clones expressed pluripotency markers such as TRA-1-60, TRA-1-81, SSEA4, OCT4, SOX2, NANOG, LEFTY, and GABRB. The well-formed three germ layers were observed during differentiation using iPSCs derived from hair follicles. The successful formation of keratioctyes from iPSCs was confirmed by the expression of cytokeratin 14 marker. Discussion Hair follicles represent a valuable keratinocytes source for in vitro hair cloning for use in treating hair balding or grafting in burn patients. Our significant findings in this report proved that hair follicles could be used to produce pluripotent stem cells and suggested that the genetic and micro-environmental elements of hair follicles might trigger higher and more efficient hair follicles re-differentiation.
bibliographic citation: Lim et al. (2016) Induced pluripotent stem cells from human hair follicle keratinocytes as a potential source for in vitro hair follicle cloning. PeerJ 4:e2695 https://doi.org/10.7717/peerj.2695
date submitted: 2016-07-28
date accepted: 2016-10-14
issued: 2016-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lim
  given name: Sheng Jye
author list: Agent
  family name: Ho
  given name: Shu Cheow
author list: Agent
  family name: Mok
  given name: Pooi Ling
author list: Agent
  family name: Tan
  given name: Kian Lee
author list: Agent
  family name: Ong
  given name: Alan H.K.
author list: Agent
  family name: Gan
  given name: Seng Chiew
doi: 10.7717/peerj.2695
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-10
copyright: ©2016 Lim et al.
attribution name: Lim et al.

Reanalysis of the anthrax epidemic in Rhodesia, 1978–1984
type: item
type: AcademicArticle
description: In the mid-1980s, the largest epidemic of anthrax of the last 200 years was documented in a little known series of studies by Davies in The Central African Journal of Medicine. This epidemic involved thousands of cattle and 10,738 human cases with 200 fatalities in Rhodesia during the Counterinsurgency. Grossly unusual epidemiological features were noted that, to this day, have not been definitively explained. This study performed a historical reanalysis of the data to reveal an estimated geographic involvement of 245,750 km2, with 171,990 cattle and 17,199 human cases. Here we present the first documented geotemporal visualization of the human anthrax epidemic.
format: application/pdf
format: text/html
creator: James M. Wilson
creator: Walter Brediger
creator: Thomas P. Albright
creator: Julie Smith-Gagen
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
description: doi:10.7717/peerj.2686
publisher: PeerJ Inc.
rights: © 2016 Wilson et al.
abstract: In the mid-1980s, the largest epidemic of anthrax of the last 200 years was documented in a little known series of studies by Davies in The Central African Journal of Medicine. This epidemic involved thousands of cattle and 10,738 human cases with 200 fatalities in Rhodesia during the Counterinsurgency. Grossly unusual epidemiological features were noted that, to this day, have not been definitively explained. This study performed a historical reanalysis of the data to reveal an estimated geographic involvement of 245,750 km2, with 171,990 cattle and 17,199 human cases. Here we present the first documented geotemporal visualization of the human anthrax epidemic.
bibliographic citation: Wilson et al. (2016) Reanalysis of the anthrax epidemic in Rhodesia, 1978–1984. PeerJ 4:e2686 https://doi.org/10.7717/peerj.2686
date submitted: 2016-06-15
date accepted: 2016-10-14
issued: 2016-11-10
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilson
  given name: James M.
author list: Agent
  family name: Brediger
  given name: Walter
author list: Agent
  family name: Albright
  given name: Thomas P.
author list: Agent
  family name: Smith-Gagen
  given name: Julie
doi: 10.7717/peerj.2686
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-10
copyright: © 2016 Wilson et al.
attribution name: Wilson et al.

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