PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Cafeteria diet increased adiposity in comparison to high fat diet in young male rats
items: Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica
items: Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore
items: HERVs, immunity, and autoimmunity: understanding the connection
items: Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells
items: Noninvasive and safe cell viability assay for Euglena gracilis using natural food pigment
items: Photo-hydrogen and lipid production from lactate, acetate, butyrate, and sugar manufacturing wastewater with an alternative nitrogen source by Rhodobacter sp. KKU-PS1
items: Hematological parameters in largemouth bass (Micropterus salmoides) with formalin-preservation: comparison between wild tournament-caught and captive-raised fish
items: Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission
items: Association and diagnostic value of serum SPINK4 in colorectal cancer

Cafeteria diet increased adiposity in comparison to high fat diet in young male rats
type: item
type: AcademicArticle
description: Background Dietary intervention studies in animal models of obesity are crucial to elucidate the mechanistic effects of specific nutrients and diets. Although several models of diet induced obesity have been examined in rodents to assess obesity, there are few studies that have researched influence of different high fat and/or westernized diets. The aim of this study was to compare a high fat diet and a cafeteria diet on obesity related biochemical and physiological parameters in young male rats. Methods Five week old Wistar male rats were fed a control chow diet (C), butter-based high fat diet (HF) or cafeteria diet (CAF) for twelve weeks. In HF, 40% of energy came from fat and this ratio was 46% in CAF. CAF composed of highly energetic and palatable human foods along with chow diet. At the end of the feeding protocol all animals were culled using CO2 asphyxia and cervical dislocation after an overnight fasting. Results Total energy and fat intake of CAF was significantly higher than C and HF. CAF was more effective in inducing obesity, as demonstrated by increased weight gain, Lee index, fat depot weights and total body fat in comparison to C and HF. Despite increased adiposity in CAF, plasma glucose, insulin and HOMA-IR levels were similar between the groups. Plasma leptin and cholesterol levels were markedly higher in CAF than C and HF. Discussion We have demonstrated that there are differential effects of high fat diet and cafeteria diet upon obesity and obesity-related parameters, with CAF leading to a more pronounced adiposity in comparison to high fat diet in young male rats. Future studies should consider the varied outcomes of different diet induced obesity models and development of a standardized approach in similar research practices.
format: application/pdf
format: text/html
creator: Yucel Buyukdere
creator: Atila Gulec
creator: Asli Akyol
subject: Animal Behavior
subject: Nutrition
description: doi:10.7717/peerj.6656
publisher: PeerJ Inc.
rights: © 2019 Buyukdere et al.
abstract: Background Dietary intervention studies in animal models of obesity are crucial to elucidate the mechanistic effects of specific nutrients and diets. Although several models of diet induced obesity have been examined in rodents to assess obesity, there are few studies that have researched influence of different high fat and/or westernized diets. The aim of this study was to compare a high fat diet and a cafeteria diet on obesity related biochemical and physiological parameters in young male rats. Methods Five week old Wistar male rats were fed a control chow diet (C), butter-based high fat diet (HF) or cafeteria diet (CAF) for twelve weeks. In HF, 40% of energy came from fat and this ratio was 46% in CAF. CAF composed of highly energetic and palatable human foods along with chow diet. At the end of the feeding protocol all animals were culled using CO2 asphyxia and cervical dislocation after an overnight fasting. Results Total energy and fat intake of CAF was significantly higher than C and HF. CAF was more effective in inducing obesity, as demonstrated by increased weight gain, Lee index, fat depot weights and total body fat in comparison to C and HF. Despite increased adiposity in CAF, plasma glucose, insulin and HOMA-IR levels were similar between the groups. Plasma leptin and cholesterol levels were markedly higher in CAF than C and HF. Discussion We have demonstrated that there are differential effects of high fat diet and cafeteria diet upon obesity and obesity-related parameters, with CAF leading to a more pronounced adiposity in comparison to high fat diet in young male rats. Future studies should consider the varied outcomes of different diet induced obesity models and development of a standardized approach in similar research practices.
bibliographic citation: Buyukdere et al. (2019) Cafeteria diet increased adiposity in comparison to high fat diet in young male rats. PeerJ 7:e6656 https://doi.org/10.7717/peerj.6656
date submitted: 2018-10-30
date accepted: 2019-02-21
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Buyukdere
  given name: Yucel
author list: Agent
  family name: Gulec
  given name: Atila
author list: Agent
  family name: Akyol
  given name: Asli
doi: 10.7717/peerj.6656
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Buyukdere et al.
attribution name: Buyukdere et al.

Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica
type: item
type: AcademicArticle
description: Background Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic. Methods LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Amine oxidase activity has been measured fluorometrically as hydrogen peroxide release coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting. Results Cultured H. turkmenica has no detectable amine oxidase activity. HTU-LOX may be expressed in E. coli with a high protein yield. The full-length protein gives no catalytic activity. For this reason, we hypothesized that the hydrophobic N-terminal region may interfere with proper folding and its removal may be beneficial. Indeed, truncated His-tagged HTU-LOX lacking the N-terminal hydrophobic signal peptide purified under denaturing conditions can be successfully refolded into an active enzyme, and a larger N-terminal truncation further increases the amine oxidase activity. Refolding is optimal in the presence of Cu2+ at pH 6.2 and is not sensitive to salt. HTU-LOX is sensitive to LOX inhibitor 3-aminopropionitrile. HTU-LOX deaminates usual substrates of mammalian LOX such as lysine-containing polypeptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed substrate specificity of the former. HTU-LOX readily oxidizes various primary amines including such compounds as taurine and glycine, benzylamine being a poor substrate. Of note, HTU-LOX is also active towards several aminoglycoside antibiotics and polymyxin. Western blotting indicates that epitopes for the anti-HTU-LOX polyclonal antibodies coincide with a high molecula…
format: application/pdf
format: text/html
creator: Nikolay B. Pestov
creator: Daniel V. Kalinovsky
creator: Tatyana D. Larionova
creator: Alia Z. Zakirova
creator: Nikolai N. Modyanov
creator: Irina A. Okkelman
creator: Tatyana V. Korneenko
subject: Biochemistry
subject: Biotechnology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6691
publisher: PeerJ Inc.
rights: © 2019 Pestov et al.
abstract: Background Lysyl oxidases (LOX) have been extensively studied in mammals, whereas properties and functions of recently found homologues in prokaryotic genomes remain enigmatic. Methods LOX open reading frame was cloned from Haloterrigena turkmenica in an E. coli expression vector. Recombinant Haloterrigena turkmenica lysyl oxidase (HTU-LOX) proteins were purified using metal affinity chromatography under denaturing conditions followed by refolding. Amine oxidase activity has been measured fluorometrically as hydrogen peroxide release coupled with the oxidation of 10-acetyl-3,7-dihydroxyphenoxazine in the presence of horseradish peroxidase. Rabbit polyclonal antibodies were obtained and used in western blotting. Results Cultured H. turkmenica has no detectable amine oxidase activity. HTU-LOX may be expressed in E. coli with a high protein yield. The full-length protein gives no catalytic activity. For this reason, we hypothesized that the hydrophobic N-terminal region may interfere with proper folding and its removal may be beneficial. Indeed, truncated His-tagged HTU-LOX lacking the N-terminal hydrophobic signal peptide purified under denaturing conditions can be successfully refolded into an active enzyme, and a larger N-terminal truncation further increases the amine oxidase activity. Refolding is optimal in the presence of Cu2+ at pH 6.2 and is not sensitive to salt. HTU-LOX is sensitive to LOX inhibitor 3-aminopropionitrile. HTU-LOX deaminates usual substrates of mammalian LOX such as lysine-containing polypeptides and polymers. The major difference between HTU-LOX and mammalian LOX is a relaxed substrate specificity of the former. HTU-LOX readily oxidizes various primary amines including such compounds as taurine and glycine, benzylamine being a poor substrate. Of note, HTU-LOX is also active towards several aminoglycoside antibiotics and polymyxin. Western blotting indicates that epitopes for the anti-HTU-LOX polyclonal antibodies coincide with a high molecula…
bibliographic citation: Pestov et al. (2019) Properties of a cryptic lysyl oxidase from haloarchaeon Haloterrigena turkmenica. PeerJ 7:e6691 https://doi.org/10.7717/peerj.6691
date submitted: 2018-01-02
date accepted: 2019-02-26
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pestov
  given name: Nikolay B.
author list: Agent
  family name: Kalinovsky
  given name: Daniel V.
author list: Agent
  family name: Larionova
  given name: Tatyana D.
author list: Agent
  family name: Zakirova
  given name: Alia Z.
author list: Agent
  family name: Modyanov
  given name: Nikolai N.
author list: Agent
  family name: Okkelman
  given name: Irina A.
author list: Agent
  family name: Korneenko
  given name: Tatyana V.
doi: 10.7717/peerj.6691
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Pestov et al.
attribution name: Pestov et al.

Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore
type: item
type: AcademicArticle
description: Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale’s stomach contents. Plastic debris was also found in the whale’s stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.
format: application/pdf
format: text/html
creator: Marcus A.H. Chua
creator: David J.W. Lane
creator: Seng Keat Ooi
creator: Serene H.X. Tay
creator: Tsunemi Kubodera
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.6705
publisher: PeerJ Inc.
rights: © 2019 Chua et al.
abstract: Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale’s stomach contents. Plastic debris was also found in the whale’s stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.
bibliographic citation: Chua et al. (2019) Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore. PeerJ 7:e6705 https://doi.org/10.7717/peerj.6705
date submitted: 2018-12-15
date accepted: 2019-03-03
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chua
  given name: Marcus A.H.
author list: Agent
  family name: Lane
  given name: David J.W.
author list: Agent
  family name: Ooi
  given name: Seng Keat
author list: Agent
  family name: Tay
  given name: Serene H.X.
author list: Agent
  family name: Kubodera
  given name: Tsunemi
doi: 10.7717/peerj.6705
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Chua et al.
attribution name: Chua et al.

HERVs, immunity, and autoimmunity: understanding the connection
type: item
type: AcademicArticle
description: Since their discovery in the 1960s, further investigation into endogenous retroviruses (ERVs) has challenged the conventional view of viral sequences as exclusively parasitic elements. Once presumed to be a group of passive genetic relics, it is becoming increasingly clear that this view of ERVs, while generally accurate, is incorrect in many specific cases. Research has identified ERV genes that appear to be co-opted by their mammalian hosts, but the biological function of ERV elements in humans remains a controversial subject. One area that has attracted some attention in this domain is the role of co-opted ERV elements in mammalian immune systems. The relationship between ERVs and human autoimmune diseases has also been investigated, but has historically been treated as a separate topic. This review will summarize the current evidence concerning the phenotypic significance of ERVs, both in the healthy immune system and in manifestations of autoimmunity. Furthermore, it will evaluate the relationship between these fields of study, and propose previously-unexplored molecular mechanisms through which human endogenous retroviruses might contribute to certain autoimmune pathologies. Investigation into these novel mechanisms could further our understanding of the molecular basis of autoimmune disease, and may one day provide new targets for treatment.
format: application/pdf
format: text/html
creator: Matthew Greenig
subject: Molecular Biology
subject: Virology
subject: Allergy and Clinical Immunology
subject: Immunology
description: doi:10.7717/peerj.6711
publisher: PeerJ Inc.
rights: © 2019 Greenig
abstract: Since their discovery in the 1960s, further investigation into endogenous retroviruses (ERVs) has challenged the conventional view of viral sequences as exclusively parasitic elements. Once presumed to be a group of passive genetic relics, it is becoming increasingly clear that this view of ERVs, while generally accurate, is incorrect in many specific cases. Research has identified ERV genes that appear to be co-opted by their mammalian hosts, but the biological function of ERV elements in humans remains a controversial subject. One area that has attracted some attention in this domain is the role of co-opted ERV elements in mammalian immune systems. The relationship between ERVs and human autoimmune diseases has also been investigated, but has historically been treated as a separate topic. This review will summarize the current evidence concerning the phenotypic significance of ERVs, both in the healthy immune system and in manifestations of autoimmunity. Furthermore, it will evaluate the relationship between these fields of study, and propose previously-unexplored molecular mechanisms through which human endogenous retroviruses might contribute to certain autoimmune pathologies. Investigation into these novel mechanisms could further our understanding of the molecular basis of autoimmune disease, and may one day provide new targets for treatment.
bibliographic citation: Greenig (2019) HERVs, immunity, and autoimmunity: understanding the connection. PeerJ 7:e6711 https://doi.org/10.7717/peerj.6711
date submitted: 2018-11-09
date accepted: 2019-02-28
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greenig
  given name: Matthew
doi: 10.7717/peerj.6711
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Greenig
attribution name: Greenig

Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells
type: item
type: AcademicArticle
description: The function of long non-coding RNA H19 (H19) on cell proliferation has been observed in various cell types, and the increased expression of H19 was also found in the lipopolysaccharide (LPS)-induced inflammatory bovine mammary epithelial cells (MAC-T). However, the roles of H19 in the inflammatory response and physiological functions of bovine mammary epithelial cell are not clear. In the present study, we found that overexpression of H19 in MAC-T cells significantly promoted cell proliferation, increased the protein and mRNA level of β-casein, and enhanced the expression of tight junction (TJ)-related proteins while inhibited staphylococcus aureus adhesion to cells. In addition, results demonstrated that overexpression of H19 affected the LPS-induced immune response of MAC-T cells by promoting expressions of inflammatory factors, including TNF-α, IL-6, CXCL2 and CCL5, and activating the NF-κB signal pathway. Our findings indicate that H19 is likely to play an important role in maintaining normal functions and regulating immune response of bovine mammary epithelial cells.
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format: text/html
creator: Xuezhong Li
creator: Hao Wang
creator: Yanfen Zhang
creator: Jinjing Zhang
creator: Shaopei Qi
creator: Yong Zhang
creator: Ming-Qing Gao
subject: Cell Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6715
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: The function of long non-coding RNA H19 (H19) on cell proliferation has been observed in various cell types, and the increased expression of H19 was also found in the lipopolysaccharide (LPS)-induced inflammatory bovine mammary epithelial cells (MAC-T). However, the roles of H19 in the inflammatory response and physiological functions of bovine mammary epithelial cell are not clear. In the present study, we found that overexpression of H19 in MAC-T cells significantly promoted cell proliferation, increased the protein and mRNA level of β-casein, and enhanced the expression of tight junction (TJ)-related proteins while inhibited staphylococcus aureus adhesion to cells. In addition, results demonstrated that overexpression of H19 affected the LPS-induced immune response of MAC-T cells by promoting expressions of inflammatory factors, including TNF-α, IL-6, CXCL2 and CCL5, and activating the NF-κB signal pathway. Our findings indicate that H19 is likely to play an important role in maintaining normal functions and regulating immune response of bovine mammary epithelial cells.
bibliographic citation: Li et al. (2019) Overexpression of lncRNA H19 changes basic characteristics and affects immune response of bovine mammary epithelial cells. PeerJ 7:e6715 https://doi.org/10.7717/peerj.6715
date submitted: 2018-10-20
date accepted: 2019-03-05
issued: 2019-04-05
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Xuezhong
author list: Agent
  family name: Wang
  given name: Hao
author list: Agent
  family name: Zhang
  given name: Yanfen
author list: Agent
  family name: Zhang
  given name: Jinjing
author list: Agent
  family name: Qi
  given name: Shaopei
author list: Agent
  family name: Zhang
  given name: Yong
author list: Agent
  family name: Gao
  given name: Ming-Qing
doi: 10.7717/peerj.6715
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-05
copyright: ©2019 Li et al.
attribution name: Li et al.

Noninvasive and safe cell viability assay for Euglena gracilis using natural food pigment
type: item
type: AcademicArticle
description: Noninvasive and safe cell viability assay is required in many fields such as regenerative medicine, genetic engineering, single-cell analysis, and microbial food culture. In this case, a safe and inexpensive method which is a small load on cells and the environment is preferable without requiring expensive and space-consuming equipment and a technician to operate. We examined eight typical natural food pigments to find Monascus pigment (MP) or anthocyanin pigment (AP) works as a good viability indicator of dye exclusion test (DET) for Euglena gracilis which is an edible photosynthetic green microalga. This is the first report using natural food pigments as cell viability assay. Euglena gracilis stained by MP or AP can be visually judged with a bright field microscope. This was spectrally confirmed by scan-free, non-invasive absorbance spectral imaging A(x, y, λ) microscopy of single live cells and principal component analysis (PCA). To confirm the ability of staining dead cells and examine the load on the cells, these two natural pigments were compared with trypan blue (TB) and methylene blue (MP), which are synthetic dyes conventionally used for DET. As a result, MP and AP had as good ability of staining dead cells treated with microwave as TB and MB and showed faster and more uniform staining for dead cells in benzalkonium chloride than them. The growth curve and the ratio of dead cells in the culture showed that the synthetic dyes inhibit the growth of E. gracilis, but the natural pigments do not. As the cell density increased, however, AP increased the ratio of stained cells, which was prevented by the addition of glucose. MP can stain dead cells in a shorter time than AP, while AP is more stable in color against long-term irradiation of intense light than MP. Due to the low toxicity of these pigments, viability of cells in culture can be monitored with them over a long period.
format: application/pdf
format: text/html
creator: Kyohei Yamashita
creator: Koji Yamada
creator: Kengo Suzuki
creator: Eiji Tokunaga
subject: Cell Biology
subject: Food Science and Technology
subject: Microbiology
subject: Plant Science
subject: Pharmacology
description: doi:10.7717/peerj.6636
publisher: PeerJ Inc.
rights: © 2019 Yamashita et al.
abstract: Noninvasive and safe cell viability assay is required in many fields such as regenerative medicine, genetic engineering, single-cell analysis, and microbial food culture. In this case, a safe and inexpensive method which is a small load on cells and the environment is preferable without requiring expensive and space-consuming equipment and a technician to operate. We examined eight typical natural food pigments to find Monascus pigment (MP) or anthocyanin pigment (AP) works as a good viability indicator of dye exclusion test (DET) for Euglena gracilis which is an edible photosynthetic green microalga. This is the first report using natural food pigments as cell viability assay. Euglena gracilis stained by MP or AP can be visually judged with a bright field microscope. This was spectrally confirmed by scan-free, non-invasive absorbance spectral imaging A(x, y, λ) microscopy of single live cells and principal component analysis (PCA). To confirm the ability of staining dead cells and examine the load on the cells, these two natural pigments were compared with trypan blue (TB) and methylene blue (MP), which are synthetic dyes conventionally used for DET. As a result, MP and AP had as good ability of staining dead cells treated with microwave as TB and MB and showed faster and more uniform staining for dead cells in benzalkonium chloride than them. The growth curve and the ratio of dead cells in the culture showed that the synthetic dyes inhibit the growth of E. gracilis, but the natural pigments do not. As the cell density increased, however, AP increased the ratio of stained cells, which was prevented by the addition of glucose. MP can stain dead cells in a shorter time than AP, while AP is more stable in color against long-term irradiation of intense light than MP. Due to the low toxicity of these pigments, viability of cells in culture can be monitored with them over a long period.
bibliographic citation: Yamashita et al. (2019) Noninvasive and safe cell viability assay for Euglena gracilis using natural food pigment. PeerJ 7:e6636 https://doi.org/10.7717/peerj.6636
date submitted: 2018-10-07
date accepted: 2019-02-18
issued: 2019-04-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yamashita
  given name: Kyohei
author list: Agent
  family name: Yamada
  given name: Koji
author list: Agent
  family name: Suzuki
  given name: Kengo
author list: Agent
  family name: Tokunaga
  given name: Eiji
doi: 10.7717/peerj.6636
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-04
copyright: ©2019 Yamashita et al.
attribution name: Yamashita et al.

Photo-hydrogen and lipid production from lactate, acetate, butyrate, and sugar manufacturing wastewater with an alternative nitrogen source by Rhodobacter sp. KKU-PS1
type: item
type: AcademicArticle
description: Photo-hydrogen and lipid production from individual synthetic volatile fatty acids (VFAs) and sugar manufacturing wastewater (SMW) by Rhodobacter sp. KKU-PS1 with sodium glutamate or Aji-L (i.e., waste from the process of crystallizing monosodium glutamate) as a nitrogen source was investigated. Using individual synthetic VFAs, the maximum hydrogen production was achieved with Aji-L as a nitrogen source rather than sodium glutamate. The maximum hydrogen production was 1,727, 754 and 1,353 mL H2/L, respectively, using 25 mM of lactate, 40 mM of acetate and 15mM of butyrate as substrates. Under these conditions, lipid was produced in the range of 10.6–16.9% (w/w). Subsequently, photo-hydrogen and lipid production from SMW using Aji-L as nitrogen source was conducted. Maximal hydrogen production and hydrogen yields of 1,672 mL H2/L and 1.92 mol H2/mol substrate, respectively, were obtained. Additionally, lipid content and lipid production of 21.3% (w/w) and 475 mg lipid/L were achieved. The analysis of the lipid and fatty acid components revealed that triacyglycerol (TAG) and C18:1 methyl ester were the main lipid and fatty acid components, respectively, found in Rhodobacter sp. KKU-PS1 cells.
format: application/pdf
format: text/html
creator: Thitirut Assawamongkholsiri
creator: Alissara Reungsang
creator: Sureewan Sittijunda
subject: Biotechnology
subject: Food, Water and Energy Nexus
description: doi:10.7717/peerj.6653
publisher: PeerJ Inc.
rights: © 2019 Assawamongkholsiri et al.
abstract: Photo-hydrogen and lipid production from individual synthetic volatile fatty acids (VFAs) and sugar manufacturing wastewater (SMW) by Rhodobacter sp. KKU-PS1 with sodium glutamate or Aji-L (i.e., waste from the process of crystallizing monosodium glutamate) as a nitrogen source was investigated. Using individual synthetic VFAs, the maximum hydrogen production was achieved with Aji-L as a nitrogen source rather than sodium glutamate. The maximum hydrogen production was 1,727, 754 and 1,353 mL H2/L, respectively, using 25 mM of lactate, 40 mM of acetate and 15mM of butyrate as substrates. Under these conditions, lipid was produced in the range of 10.6–16.9% (w/w). Subsequently, photo-hydrogen and lipid production from SMW using Aji-L as nitrogen source was conducted. Maximal hydrogen production and hydrogen yields of 1,672 mL H2/L and 1.92 mol H2/mol substrate, respectively, were obtained. Additionally, lipid content and lipid production of 21.3% (w/w) and 475 mg lipid/L were achieved. The analysis of the lipid and fatty acid components revealed that triacyglycerol (TAG) and C18:1 methyl ester were the main lipid and fatty acid components, respectively, found in Rhodobacter sp. KKU-PS1 cells.
bibliographic citation: Assawamongkholsiri et al. (2019) Photo-hydrogen and lipid production from lactate, acetate, butyrate, and sugar manufacturing wastewater with an alternative nitrogen source by Rhodobacter sp. KKU-PS1. PeerJ 7:e6653 https://doi.org/10.7717/peerj.6653
date submitted: 2018-10-15
date accepted: 2019-02-21
issued: 2019-04-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Assawamongkholsiri
  given name: Thitirut
author list: Agent
  family name: Reungsang
  given name: Alissara
author list: Agent
  family name: Sittijunda
  given name: Sureewan
doi: 10.7717/peerj.6653
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-04
copyright: ©2019 Assawamongkholsiri et al.
attribution name: Assawamongkholsiri et al.

Hematological parameters in largemouth bass (Micropterus salmoides) with formalin-preservation: comparison between wild tournament-caught and captive-raised fish
type: item
type: AcademicArticle
description: Background Largemouth bass (Micropterus salmoides) are an economically important freshwater fish species that have been investigated for both the short and long-term effects of stress, secondary to angling. Limited data has been published on the hematological parameters of this species and blood sample stability is a notable limitation of hematologic field studies. A relatively novel technique using 10% neutral buffered formalin preserves heparinized whole blood and maintains blood cell stability beyond one month in striped bass. The objective of this study was to evaluate the differences in hematological parameters between tournament-caught and captive-raised largemouth bass using whole blood preservation with neutral buffered formalin. Methods Two populations of largemouth bass (n = 26 wild; n = 29 captive) underwent coccygeal venipuncture to collect heparinized whole blood for packed cell volume, total solids, and manual differential. Formalin preservation of heparinized whole blood facilitated manual hemocytometer analysis. Results were compared between the populations (tournament-caught, and captive-raised) with Wilcoxon rank sum test, a Hotelling’s T2 test, and Bonferroni simultaneous 95% confidence intervals to determine significance. Results The mean packed cell volume (44.9 ± 5.4%) and total solids (7.2 ± 1.1 g/dL) were significantly higher, while the total leukocyte count (7.08 ± 1.86 × 103/µL) was significantly lower in the wild tournament-caught population of largemouth bass, as compared to the captive-raised counterparts (PCV 34.4 ± 7.2%; TS 5.2 ± 1.0 g/dL; WBC 16.43 ± 8.37 × 103/µL). The wild population demonstrated a significantly distinct leukogram characterized by a neutropenia (24.1 ± 12.7%), lymphocytosis (67.7 ± 13.0%), and monocytopenia (8.3 ± 2.9%), while the erythrocyte and thrombocyte counts were not significantly different between populations. Discussion Numerous factors have been demonstrated to influence hematologic parameters in fish incl…
format: application/pdf
format: text/html
creator: Michelle C. Whitehead
creator: Chelsey L. Vanetten
creator: Yaxin Zheng
creator: Gregory A. Lewbart
subject: Aquaculture, Fisheries and Fish Science
subject: Veterinary Medicine
description: doi:10.7717/peerj.6669
publisher: PeerJ Inc.
rights: © 2019 Whitehead et al.
abstract: Background Largemouth bass (Micropterus salmoides) are an economically important freshwater fish species that have been investigated for both the short and long-term effects of stress, secondary to angling. Limited data has been published on the hematological parameters of this species and blood sample stability is a notable limitation of hematologic field studies. A relatively novel technique using 10% neutral buffered formalin preserves heparinized whole blood and maintains blood cell stability beyond one month in striped bass. The objective of this study was to evaluate the differences in hematological parameters between tournament-caught and captive-raised largemouth bass using whole blood preservation with neutral buffered formalin. Methods Two populations of largemouth bass (n = 26 wild; n = 29 captive) underwent coccygeal venipuncture to collect heparinized whole blood for packed cell volume, total solids, and manual differential. Formalin preservation of heparinized whole blood facilitated manual hemocytometer analysis. Results were compared between the populations (tournament-caught, and captive-raised) with Wilcoxon rank sum test, a Hotelling’s T2 test, and Bonferroni simultaneous 95% confidence intervals to determine significance. Results The mean packed cell volume (44.9 ± 5.4%) and total solids (7.2 ± 1.1 g/dL) were significantly higher, while the total leukocyte count (7.08 ± 1.86 × 103/µL) was significantly lower in the wild tournament-caught population of largemouth bass, as compared to the captive-raised counterparts (PCV 34.4 ± 7.2%; TS 5.2 ± 1.0 g/dL; WBC 16.43 ± 8.37 × 103/µL). The wild population demonstrated a significantly distinct leukogram characterized by a neutropenia (24.1 ± 12.7%), lymphocytosis (67.7 ± 13.0%), and monocytopenia (8.3 ± 2.9%), while the erythrocyte and thrombocyte counts were not significantly different between populations. Discussion Numerous factors have been demonstrated to influence hematologic parameters in fish incl…
bibliographic citation: Whitehead et al. (2019) Hematological parameters in largemouth bass (Micropterus salmoides) with formalin-preservation: comparison between wild tournament-caught and captive-raised fish. PeerJ 7:e6669 https://doi.org/10.7717/peerj.6669
date submitted: 2018-11-19
date accepted: 2019-02-23
issued: 2019-04-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Whitehead
  given name: Michelle C.
author list: Agent
  family name: Vanetten
  given name: Chelsey L.
author list: Agent
  family name: Zheng
  given name: Yaxin
author list: Agent
  family name: Lewbart
  given name: Gregory A.
doi: 10.7717/peerj.6669
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-04
copyright: ©2019 Whitehead et al.
attribution name: Whitehead et al.

Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission
type: item
type: AcademicArticle
description: Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.
format: application/pdf
format: text/html
creator: Yanqing Zhang
creator: Zaohai Zeng
creator: Chengjie Chen
creator: Caiqin Li
creator: Rui Xia
creator: Jianguo Li
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6677
publisher: PeerJ Inc.
rights: © 2019 Zhang et al.
abstract: Auxin response factors (ARFs) play fundamental roles in modulating various biological processes including fruit development and abscission via regulating the expression of auxin response genes. Currently, little is known about roles of ARFs in litchi (Litchi chinensis Sonn.), an economically important subtropical fruit tree whose production is suffering from fruit abscission. In this study, a genome-wide analysis of ARFs was conducted for litchi, 39 ARF genes (LcARFs) were identified. Conserved domain analysis showed that all the LcARFs identified have the signature B3 DNA-binding (B3) and ARF (Aux_rep) domains, with only 23 members having the dimerization domain (Aux_IAA). The number of exons in LcARF genes ranges from 2 to 16, suggesting a large variation for the gene structure of LcARFs. Phylogenetic analysis showed that the 39 LcARFs could be divided into three main groups: class I, II, and III. In total, 23 LcARFs were found to be potential targets of small RNAs, with three conserved and one novel miRNA-ARF (miRN43-ARF9) regulatory pathways discovered in litchi. Expression patterns were used to evaluate candidate LcARFs involved in various developmental processes, especially in flower formation and organ abscission. The results revealed that most ARF genes likely acted as repressors in litchi fruit abscission, that is, ARF2D/2E, 7A/7B, 9A/9B, 16A/16B, while a few LcARFs, such as LcARF5A/B, might be positively involved in this process. These findings provide useful information and resources for further studies on the roles of ARF genes in litchi growth and development, especially in the process of fruit abscission.
bibliographic citation: Zhang et al. (2019) Genome-wide characterization of the auxin response factor (ARF) gene family of litchi (Litchi chinensis Sonn.): phylogenetic analysis, miRNA regulation and expression changes during fruit abscission. PeerJ 7:e6677 https://doi.org/10.7717/peerj.6677
date submitted: 2018-12-17
date accepted: 2019-02-25
issued: 2019-04-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yanqing
author list: Agent
  family name: Zeng
  given name: Zaohai
author list: Agent
  family name: Chen
  given name: Chengjie
author list: Agent
  family name: Li
  given name: Caiqin
author list: Agent
  family name: Xia
  given name: Rui
author list: Agent
  family name: Li
  given name: Jianguo
doi: 10.7717/peerj.6677
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-04
copyright: © 2019 Zhang et al.
attribution name: Zhang et al.

Association and diagnostic value of serum SPINK4 in colorectal cancer
type: item
type: AcademicArticle
description: The role of serum serine peptidase inhibitor, Kazal type 4 (SPINK4), in colorectal cancer (CRC) is largely unknown. This study aimed to explore the association and diagnostic value of serum SPINK4 in CRC. A total of 70 preoperative CRC patients, 30 postoperative CRC patients, 30 gastric cancer patients, and 30 healthy controls were enrolled. Using enzyme-linked immunosorbent assays, we found that the serum SPINK4 level was significantly increased in preoperative CRC compared with postoperative CRC patients, gastric cancer patients, and healthy controls (p < 0.05). The serum SPINK4 level was remarkably elevated in colon cancer compared with rectal cancer and was enhanced in the M1 stage compared with the M0 stage (p < 0.05). The area under the receiver operating characteristic curve of serum SPINK4 level in the diagnosis of CRC was 0.9186, with a sensitivity and specificity of 0.886 and 0.900, respectively, and a cut-off value of 2.065. There was no significant difference between high and low expression of serum SPINK4 regarding the overall survival time and disease-free survival (p > 0.05). This study demonstrated that the serum SPINK4 level increased in CRC and was associated with the location and distant metastasis of CRC. It had a high diagnostic value in CRC but was not associated with the survival of CRC patients.
format: application/pdf
format: text/html
creator: Mingzhi Xie
creator: Kezhi Li
creator: Jilin Li
creator: Dongcheng Lu
creator: Bangli Hu
subject: Gastroenterology and Hepatology
description: doi:10.7717/peerj.6679
publisher: PeerJ Inc.
rights: © 2019 Xie et al.
abstract: The role of serum serine peptidase inhibitor, Kazal type 4 (SPINK4), in colorectal cancer (CRC) is largely unknown. This study aimed to explore the association and diagnostic value of serum SPINK4 in CRC. A total of 70 preoperative CRC patients, 30 postoperative CRC patients, 30 gastric cancer patients, and 30 healthy controls were enrolled. Using enzyme-linked immunosorbent assays, we found that the serum SPINK4 level was significantly increased in preoperative CRC compared with postoperative CRC patients, gastric cancer patients, and healthy controls (p < 0.05). The serum SPINK4 level was remarkably elevated in colon cancer compared with rectal cancer and was enhanced in the M1 stage compared with the M0 stage (p < 0.05). The area under the receiver operating characteristic curve of serum SPINK4 level in the diagnosis of CRC was 0.9186, with a sensitivity and specificity of 0.886 and 0.900, respectively, and a cut-off value of 2.065. There was no significant difference between high and low expression of serum SPINK4 regarding the overall survival time and disease-free survival (p > 0.05). This study demonstrated that the serum SPINK4 level increased in CRC and was associated with the location and distant metastasis of CRC. It had a high diagnostic value in CRC but was not associated with the survival of CRC patients.
bibliographic citation: Xie et al. (2019) Association and diagnostic value of serum SPINK4 in colorectal cancer. PeerJ 7:e6679 https://doi.org/10.7717/peerj.6679
date submitted: 2018-12-30
date accepted: 2019-02-21
issued: 2019-04-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Mingzhi
author list: Agent
  family name: Li
  given name: Kezhi
author list: Agent
  family name: Li
  given name: Jilin
author list: Agent
  family name: Lu
  given name: Dongcheng
author list: Agent
  family name: Hu
  given name: Bangli
doi: 10.7717/peerj.6679
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-04
copyright: ©2019 Xie et al.
attribution name: Xie et al.

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