PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods
items: Establishment and characterization of fantail goldfish fin (FtGF) cell line from goldfish, Carassius auratus for in vitro propagation of Cyprinid herpes virus-2 (CyHV-2)
items: https://peerj.com/articles/9381
items: Targeting secretory leukocyte protease inhibitor (SLPI) inhibits colorectal cancer cell growth, migration and invasion via downregulation of AKT
items: Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities
items: Utilization of brewery wastes in food industry
items: Correlation between emotional regulation and peripheral lymphocyte counts in colorectal cancer patients
items: Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding
items: https://peerj.com/articles/9529
items: Soil macro-fauna respond to environmental variations along a coastal-inland gradient

Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods
type: item
type: AcademicArticle
description: Background Alternative splicing (AS) is an important mechanism for regulating gene expression and proteome diversity. Tumor-alternative splicing can reveal a large class of new splicing-associated potential new antigens that may affect the immune response and can be used for immunotherapy. Methods The RNA-seq transcriptome data and clinical information of stomach adenocarcinoma (STAD) cohort were downloaded from The Cancer Genome Atlas (TCGA) database data portal, and data of splicing events were obtained from the SpliceSeq database. Predicting genes were validated by Asian cancer research group (ACRG) cohort and Oncomine database. RT-qPCR was used to analysis the expression of ECT2 in STAD. Results A total of 32,166 AS events were identified, among which 2,042 AS events were significantly associated with patients survival. Biological pathway analysis indicated that these genes play an important role in regulating gastric cancer-related processes such as GTPase activity and PI3K-Akt signaling pathway. Next, we derived a risk signature, using alternate acceptor, that is an independent prognostic marker. Moreover, high ECT2 expression was associated with poorer prognosis in STAD. Multivariate survival analysis demonstrated that high ECT2 expression was an independent risk factor for overall survival. Gene set enrichment analysis revealed that high ECT2 expression was enriched for hallmarks of malignant tumors. The ACRG cohort and Oncomine also showed that high ECT2 expression was associated with poorer prognosis in gastric cancer patients. Finally, RT-qPCR showed ECT2 expression was higher in STAD compared to the normal tissues. Conclusion This study excavated the alternative splicing events in gastric cancer, and found ECT2 might be a biomarkers for diagnosis and prognosis.
format: application/pdf
format: text/html
creator: Jie Liu
creator: Miao Zhou
creator: Yangyang Ouyang
creator: Laifeng Du
creator: Lingbo Xu
creator: Hongyun Li
subject: Bioinformatics
subject: Genomics
subject: Gastroenterology and Hepatology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9174
publisher: PeerJ Inc.
rights: © 2020 Liu et al.
abstract: Background Alternative splicing (AS) is an important mechanism for regulating gene expression and proteome diversity. Tumor-alternative splicing can reveal a large class of new splicing-associated potential new antigens that may affect the immune response and can be used for immunotherapy. Methods The RNA-seq transcriptome data and clinical information of stomach adenocarcinoma (STAD) cohort were downloaded from The Cancer Genome Atlas (TCGA) database data portal, and data of splicing events were obtained from the SpliceSeq database. Predicting genes were validated by Asian cancer research group (ACRG) cohort and Oncomine database. RT-qPCR was used to analysis the expression of ECT2 in STAD. Results A total of 32,166 AS events were identified, among which 2,042 AS events were significantly associated with patients survival. Biological pathway analysis indicated that these genes play an important role in regulating gastric cancer-related processes such as GTPase activity and PI3K-Akt signaling pathway. Next, we derived a risk signature, using alternate acceptor, that is an independent prognostic marker. Moreover, high ECT2 expression was associated with poorer prognosis in STAD. Multivariate survival analysis demonstrated that high ECT2 expression was an independent risk factor for overall survival. Gene set enrichment analysis revealed that high ECT2 expression was enriched for hallmarks of malignant tumors. The ACRG cohort and Oncomine also showed that high ECT2 expression was associated with poorer prognosis in gastric cancer patients. Finally, RT-qPCR showed ECT2 expression was higher in STAD compared to the normal tissues. Conclusion This study excavated the alternative splicing events in gastric cancer, and found ECT2 might be a biomarkers for diagnosis and prognosis.
bibliographic citation: Liu et al. (2020) Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods. PeerJ 8:e9174 https://doi.org/10.7717/peerj.9174
date submitted: 2019-12-19
date accepted: 2020-04-21
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Jie
author list: Agent
  family name: Zhou
  given name: Miao
author list: Agent
  family name: Ouyang
  given name: Yangyang
author list: Agent
  family name: Du
  given name: Laifeng
author list: Agent
  family name: Xu
  given name: Lingbo
author list: Agent
  family name: Li
  given name: Hongyun
doi: 10.7717/peerj.9174
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Liu et al.
attribution name: Liu et al.

Establishment and characterization of fantail goldfish fin (FtGF) cell line from goldfish, Carassius auratus for in vitro propagation of Cyprinid herpes virus-2 (CyHV-2)
type: item
type: AcademicArticle
description: Background Herpesviral hematopoietic necrosis disease, caused by cyprinid herpesvirus-2 (CyHV-2), is responsible for massive mortalities in the aquaculture of goldfish, Carassius auratus. Permissive cell lines for the isolation and propagation of CyHV-2 have been established from various goldfish tissues by sacrificing the fish. Here, we report the development of a cell line, FtGF (Fantail Goldfish Fin), from caudal fin of goldfish using non-lethal sampling. We also describe a simple protocol for successful establishment and characterization of a permissive cell line through explant method and continuous propagation of CyHV-2 with high viral titer using this cell line. Methods Caudal fin tissue samples were collected from goldfish without killing the fish. Cell culture of goldfish caudal fin cells was carried out using Leibovitz’s L-15 (L-15) medium containing 20% FBS and 1X concentration of antibiotic antimycotic solution, incubated at 28 °C. Cells were characterized and origin of the cells was confirmed by sequencing fragments of the 16S rRNA and COI genes. CyHV-2 was grown in the FtGF cells and passaged continuously 20 times. The infectivity of the CyHV-2 isolated using FtGF cells was confirmed by experimental infection of naïve goldfish. Results The cell line has been passaged up to 56 times in L-15 with 10% FBS. Karyotyping of FtGF cells at 30th, 40th and 56th passage indicated that modal chromosome number was 2n = 104. Species authentication of FtGF was performed by sequencing of the 16S rRNA and COI genes. The cell line was used for continuous propagation of CyHV-2 over 20 passages with high viral titer of 107.8±0.26 TCID50/mL. Following inoculation of CyHV-2 positive tissue homogenate, FtGF cells showed cytopathic effect by 2nd day post-inoculation (dpi) and complete destruction of cells was observed by the 10th dpi. An experimental infection of naïve goldfish using supernatant from infected FtGF cells caused 100% mortality and CyHV-2 infection in the challe…
format: application/pdf
format: text/html
creator: Arathi Dharmaratnam
creator: Raj Kumar
creator: Basheer Saidmuhammed Valaparambil
creator: Neeraj Sood
creator: Pravata Kumar Pradhan
creator: Sweta Das
creator: T. Raja Swaminathan
subject: Aquaculture, Fisheries and Fish Science
subject: Cell Biology
subject: Virology
subject: Zoology
description: doi:10.7717/peerj.9373
publisher: PeerJ Inc.
rights: © 2020 Dharmaratnam et al.
abstract: Background Herpesviral hematopoietic necrosis disease, caused by cyprinid herpesvirus-2 (CyHV-2), is responsible for massive mortalities in the aquaculture of goldfish, Carassius auratus. Permissive cell lines for the isolation and propagation of CyHV-2 have been established from various goldfish tissues by sacrificing the fish. Here, we report the development of a cell line, FtGF (Fantail Goldfish Fin), from caudal fin of goldfish using non-lethal sampling. We also describe a simple protocol for successful establishment and characterization of a permissive cell line through explant method and continuous propagation of CyHV-2 with high viral titer using this cell line. Methods Caudal fin tissue samples were collected from goldfish without killing the fish. Cell culture of goldfish caudal fin cells was carried out using Leibovitz’s L-15 (L-15) medium containing 20% FBS and 1X concentration of antibiotic antimycotic solution, incubated at 28 °C. Cells were characterized and origin of the cells was confirmed by sequencing fragments of the 16S rRNA and COI genes. CyHV-2 was grown in the FtGF cells and passaged continuously 20 times. The infectivity of the CyHV-2 isolated using FtGF cells was confirmed by experimental infection of naïve goldfish. Results The cell line has been passaged up to 56 times in L-15 with 10% FBS. Karyotyping of FtGF cells at 30th, 40th and 56th passage indicated that modal chromosome number was 2n = 104. Species authentication of FtGF was performed by sequencing of the 16S rRNA and COI genes. The cell line was used for continuous propagation of CyHV-2 over 20 passages with high viral titer of 107.8±0.26 TCID50/mL. Following inoculation of CyHV-2 positive tissue homogenate, FtGF cells showed cytopathic effect by 2nd day post-inoculation (dpi) and complete destruction of cells was observed by the 10th dpi. An experimental infection of naïve goldfish using supernatant from infected FtGF cells caused 100% mortality and CyHV-2 infection in the challe…
bibliographic citation: Dharmaratnam et al. (2020) Establishment and characterization of fantail goldfish fin (FtGF) cell line from goldfish, Carassius auratus for in vitro propagation of Cyprinid herpes virus-2 (CyHV-2). PeerJ 8:e9373 https://doi.org/10.7717/peerj.9373
date submitted: 2019-12-18
date accepted: 2020-05-27
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dharmaratnam
  given name: Arathi
author list: Agent
  family name: Kumar
  given name: Raj
author list: Agent
  family name: Valaparambil
  given name: Basheer Saidmuhammed
author list: Agent
  family name: Sood
  given name: Neeraj
author list: Agent
  family name: Pradhan
  given name: Pravata Kumar
author list: Agent
  family name: Das
  given name: Sweta
author list: Agent
  family name: Swaminathan
  given name: T. Raja
doi: 10.7717/peerj.9373
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: © 2020 Dharmaratnam et al.
attribution name: Dharmaratnam et al.

https://peerj.com/articles/9381
type: item
type: AcademicArticle
title: The validity of activity trackers is affected by walking speed: the criterion validity of Garmin Vivosmart® HR and StepWatch™ 3 for measuring steps at various walking speeds under controlled conditions
description: Introduction The use of activity trackers has increased both among private consumers and in healthcare. It is therefore relevant to consider whether a consumer-graded activity tracker is comparable to or may substitute a research-graded activity tracker, which could further increase the use of activity trackers in healthcare and rehabilitation. Such use will require knowledge of their accuracy as the clinical implications may be significant. Studies have indicated that activity trackers are not sufficiently accurate, especially at lower walking speeds. The present study seeks to inform decision makers and healthcare personnel considering implementing physical activity trackers in clinical practice. This study investigates the criterion validity of the consumer-graded Garmin Vivosmart® HR and the research-graded StepWatch™ 3 compared with manual step count (gold standard) at different walking speeds under controlled conditions. Methods Thirty participants, wearing Garmin Vivosmart® HR at the wrist and StepWatch™ 3 at the ankle, completed six trials on a treadmill at different walking speeds: 1.6 km/h, 2.4 km/h, 3.2 km/h, 4.0 km/h, 4.8 km/h, and 5.6 km/h. The participants were video recorded, and steps were registered by manual step count. Medians and inter-quartile ranges (IQR) were calculated for steps and differences in steps between manually counted steps and the two devices. In order to assess the clinical relevance of the tested devices, the mean absolute percentage error (MAPE) was determined at each speed. A MAPE ≤3% was considered to be clinically irrelevant. Furthermore, differences between manually counted steps and steps recorded by the two devices were presented in Bland–Altman style plots. Results The median of differences in steps between Garmin Vivosmart® HR and manual step count ranged from −49.5 (IQR = 101) at 1.6 km/h to −1 (IQR = 4) at 4.0 km/h. The median of differences in steps between StepWatch™ 3 and manual step count were 4 (IQR = 14) at 1.6 k…
format: application/pdf
format: text/html
creator: Frederik Rose Svarre
creator: Mads Møller Jensen
creator: Josephine Nielsen
creator: Morten Villumsen
subject: Kinesiology
subject: Public Health
subject: Translational Medicine
description: doi:10.7717/peerj.9381
publisher: PeerJ Inc.
rights: © 2020 Svarre et al.
abstract: Introduction The use of activity trackers has increased both among private consumers and in healthcare. It is therefore relevant to consider whether a consumer-graded activity tracker is comparable to or may substitute a research-graded activity tracker, which could further increase the use of activity trackers in healthcare and rehabilitation. Such use will require knowledge of their accuracy as the clinical implications may be significant. Studies have indicated that activity trackers are not sufficiently accurate, especially at lower walking speeds. The present study seeks to inform decision makers and healthcare personnel considering implementing physical activity trackers in clinical practice. This study investigates the criterion validity of the consumer-graded Garmin Vivosmart® HR and the research-graded StepWatch™ 3 compared with manual step count (gold standard) at different walking speeds under controlled conditions. Methods Thirty participants, wearing Garmin Vivosmart® HR at the wrist and StepWatch™ 3 at the ankle, completed six trials on a treadmill at different walking speeds: 1.6 km/h, 2.4 km/h, 3.2 km/h, 4.0 km/h, 4.8 km/h, and 5.6 km/h. The participants were video recorded, and steps were registered by manual step count. Medians and inter-quartile ranges (IQR) were calculated for steps and differences in steps between manually counted steps and the two devices. In order to assess the clinical relevance of the tested devices, the mean absolute percentage error (MAPE) was determined at each speed. A MAPE ≤3% was considered to be clinically irrelevant. Furthermore, differences between manually counted steps and steps recorded by the two devices were presented in Bland–Altman style plots. Results The median of differences in steps between Garmin Vivosmart® HR and manual step count ranged from −49.5 (IQR = 101) at 1.6 km/h to −1 (IQR = 4) at 4.0 km/h. The median of differences in steps between StepWatch™ 3 and manual step count were 4 (IQR = 14) at 1.6 k…
bibliographic citation: Svarre et al. (2020) The validity of activity trackers is affected by walking speed: the criterion validity of Garmin Vivosmart® HR and StepWatch™ 3 for measuring steps at various walking speeds under controlled conditions. PeerJ 8:e9381 https://doi.org/10.7717/peerj.9381
date submitted: 2020-02-06
date accepted: 2020-05-28
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Svarre
  given name: Frederik Rose
author list: Agent
  family name: Jensen
  given name: Mads Møller
author list: Agent
  family name: Nielsen
  given name: Josephine
author list: Agent
  family name: Villumsen
  given name: Morten
doi: 10.7717/peerj.9381
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: © 2020 Svarre et al.
attribution name: Svarre et al.

Targeting secretory leukocyte protease inhibitor (SLPI) inhibits colorectal cancer cell growth, migration and invasion via downregulation of AKT
type: item
type: AcademicArticle
description: The secretory leukocyte protease inhibitor (SLPI) is a serine protease inhibitor which plays important role in bacterial infection, inflammation, wound healing and epithelial proliferation. Dysregulation of SLPI has been reported in a variety of human cancers including glioblastoma, lung, breast, ovarian and colorectal carcinomas and is associated with tumor aggressiveness and metastatic potential. However, the pathogenic role of SLPI in colorectal cancer is still unclear. Here we showed that SLPI mRNA level was significantly upregulated in colorectal cancer tissues compared to adjacent normal controls. Targeting SLPI by siRNA inhibited proliferation, migration and invasion of colorectal cancer cells lines HT29 and HT116 in vitro. Mechanistically, blockage of cancer cell growth and metastasis after SLPI knockdown was associated with down-regulation of AKT signaling. In conclusion, SLPI regulated colorectal cell growth and metastasis via AKT signaling. SLPI may be a novel biomarker and therapeutic target for colorectal cancer. Targeting AKT signaling may be effective for colorectal cancer treatment.
format: application/pdf
format: text/html
creator: Zhijiang Wei
creator: Guiying Liu
creator: Rufu Jia
creator: Wei Zhang
creator: Li Li
creator: Yuanyuan Zhang
creator: Zhijing Wang
creator: Xiyong Bai
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.9400
publisher: PeerJ Inc.
rights: © 2020 Wei et al.
abstract: The secretory leukocyte protease inhibitor (SLPI) is a serine protease inhibitor which plays important role in bacterial infection, inflammation, wound healing and epithelial proliferation. Dysregulation of SLPI has been reported in a variety of human cancers including glioblastoma, lung, breast, ovarian and colorectal carcinomas and is associated with tumor aggressiveness and metastatic potential. However, the pathogenic role of SLPI in colorectal cancer is still unclear. Here we showed that SLPI mRNA level was significantly upregulated in colorectal cancer tissues compared to adjacent normal controls. Targeting SLPI by siRNA inhibited proliferation, migration and invasion of colorectal cancer cells lines HT29 and HT116 in vitro. Mechanistically, blockage of cancer cell growth and metastasis after SLPI knockdown was associated with down-regulation of AKT signaling. In conclusion, SLPI regulated colorectal cell growth and metastasis via AKT signaling. SLPI may be a novel biomarker and therapeutic target for colorectal cancer. Targeting AKT signaling may be effective for colorectal cancer treatment.
bibliographic citation: Wei et al. (2020) Targeting secretory leukocyte protease inhibitor (SLPI) inhibits colorectal cancer cell growth, migration and invasion via downregulation of AKT. PeerJ 8:e9400 https://doi.org/10.7717/peerj.9400
date submitted: 2020-04-24
date accepted: 2020-06-01
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wei
  given name: Zhijiang
author list: Agent
  family name: Liu
  given name: Guiying
author list: Agent
  family name: Jia
  given name: Rufu
author list: Agent
  family name: Zhang
  given name: Wei
author list: Agent
  family name: Li
  given name: Li
author list: Agent
  family name: Zhang
  given name: Yuanyuan
author list: Agent
  family name: Wang
  given name: Zhijing
author list: Agent
  family name: Bai
  given name: Xiyong
doi: 10.7717/peerj.9400
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Wei et al.
attribution name: Wei et al.

Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities
type: item
type: AcademicArticle
description: Paenibacillus triticisoli BJ-18, a N2-fixing bacterium, is able to promote plant growth, but the secondary metabolites that may play a role in promoting plant growth have never been characterized. In this study, untargeted metabolomics profiling of P. triticisoli BJ-18 indicated the existence of 101 known compounds, including N2-acetyl ornithine, which is the precursor of siderophores, plant growth regulators such as trehalose 6-phosphate, betaine and trigonelline, and other bioactive molecules such as oxymatrine, diosmetin, luotonin A, (-)-caryophyllene oxide and tetrahydrocurcumin. In addition, six compounds were also isolated from P. triticisoli BJ-18 using a combination of silica gel chromatography, sephadex LH-20, octadecyl silane (ODS), and high-performance liquid chromatography (HPLC). The compound structures were further analyzed by Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Electronic Circular Dichroism (ECD). The six compounds included three classical siderophore fusarinines identified as deshydroxylferritriacetylfusigen, desferritriacetylfusigen, and triacetylfusigen, and three indolic acids identified as paenibacillic acid A, 3-indoleacetic acid (IAA), and 3-indolepropionic acid (IPA). Both deshydroxylferritriacetylfusigen and paenibacillic acid A have new structures. Fusarinines, which normally occur in fungi, were isolated from bacterium for the first time in this study. Both siderophores (compounds 1 and 2) showed antimicrobial activity against Escherichia coli, Staphylococcus aureus and Bacillus subtilis, but did not show obvious inhibitory activity against yeast Candida albicans, whereas triacetylfusigen (compound 3) showed no antibiosis activity against these test microorganisms. Paenibacillic acid A, IAA, and IPA were shown to promote the growth of plant shoots and roots, and paenibacillic acid A also showed antimicrobial activity against S. aureus. Our study demonstrates that siderophores and indolic acids may play an important…
format: application/pdf
format: text/html
creator: Yunzhi Zhang
creator: Jinwei Ren
creator: Wenzhao Wang
creator: Baosong Chen
creator: Erwei Li
creator: Sanfeng Chen
subject: Agricultural Science
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.9403
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Paenibacillus triticisoli BJ-18, a N2-fixing bacterium, is able to promote plant growth, but the secondary metabolites that may play a role in promoting plant growth have never been characterized. In this study, untargeted metabolomics profiling of P. triticisoli BJ-18 indicated the existence of 101 known compounds, including N2-acetyl ornithine, which is the precursor of siderophores, plant growth regulators such as trehalose 6-phosphate, betaine and trigonelline, and other bioactive molecules such as oxymatrine, diosmetin, luotonin A, (-)-caryophyllene oxide and tetrahydrocurcumin. In addition, six compounds were also isolated from P. triticisoli BJ-18 using a combination of silica gel chromatography, sephadex LH-20, octadecyl silane (ODS), and high-performance liquid chromatography (HPLC). The compound structures were further analyzed by Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Electronic Circular Dichroism (ECD). The six compounds included three classical siderophore fusarinines identified as deshydroxylferritriacetylfusigen, desferritriacetylfusigen, and triacetylfusigen, and three indolic acids identified as paenibacillic acid A, 3-indoleacetic acid (IAA), and 3-indolepropionic acid (IPA). Both deshydroxylferritriacetylfusigen and paenibacillic acid A have new structures. Fusarinines, which normally occur in fungi, were isolated from bacterium for the first time in this study. Both siderophores (compounds 1 and 2) showed antimicrobial activity against Escherichia coli, Staphylococcus aureus and Bacillus subtilis, but did not show obvious inhibitory activity against yeast Candida albicans, whereas triacetylfusigen (compound 3) showed no antibiosis activity against these test microorganisms. Paenibacillic acid A, IAA, and IPA were shown to promote the growth of plant shoots and roots, and paenibacillic acid A also showed antimicrobial activity against S. aureus. Our study demonstrates that siderophores and indolic acids may play an important…
bibliographic citation: Zhang et al. (2020) Siderophore and indolic acid production by Paenibacillus triticisoli BJ-18 and their plant growth-promoting and antimicrobe abilities. PeerJ 8:e9403 https://doi.org/10.7717/peerj.9403
date submitted: 2019-11-08
date accepted: 2020-06-01
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Yunzhi
author list: Agent
  family name: Ren
  given name: Jinwei
author list: Agent
  family name: Wang
  given name: Wenzhao
author list: Agent
  family name: Chen
  given name: Baosong
author list: Agent
  family name: Li
  given name: Erwei
author list: Agent
  family name: Chen
  given name: Sanfeng
doi: 10.7717/peerj.9403
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Utilization of brewery wastes in food industry
type: item
type: AcademicArticle
description: Beer is the most popular low-alcohol beverage consumed in large amounts in many countries each year. The brewing industry is an important global business with huge annual revenues. It is profitable and important for the economies of many countries around the world. The brewing process involves several steps, which lead to fermentation of sugars contained in malt and conversion thereof into alcohol and carbon dioxide by yeasts. Beer brewing generates substantial amounts of by-products. The three main brewing industry wastes include brewer’s spent grain, hot trub, and residual brewer’s yeast. Proper management of these wastes may bring economical benefits and help to protect the environment from pollution caused by their excessive accumulation. The disposal of these wastes is cumbersome for the producers, however they are suitable for reuse in the food industry. Given their composition, they can serve as a low-cost and highly nutritional source of feed and food additives. They also have a potential to be a cheap material for extraction of compounds valuable for the food industry and a component of media used in biotechnological processes aimed at production of compounds and enzymes relevant for the food industry.
format: application/pdf
format: text/html
creator: Kamila Rachwał
creator: Adam Waśko
creator: Klaudia Gustaw
creator: Magdalena Polak-Berecka
subject: Agricultural Science
subject: Biotechnology
subject: Food Science and Technology
description: doi:10.7717/peerj.9427
publisher: PeerJ Inc.
rights: © 2020 Rachwałet al.
abstract: Beer is the most popular low-alcohol beverage consumed in large amounts in many countries each year. The brewing industry is an important global business with huge annual revenues. It is profitable and important for the economies of many countries around the world. The brewing process involves several steps, which lead to fermentation of sugars contained in malt and conversion thereof into alcohol and carbon dioxide by yeasts. Beer brewing generates substantial amounts of by-products. The three main brewing industry wastes include brewer’s spent grain, hot trub, and residual brewer’s yeast. Proper management of these wastes may bring economical benefits and help to protect the environment from pollution caused by their excessive accumulation. The disposal of these wastes is cumbersome for the producers, however they are suitable for reuse in the food industry. Given their composition, they can serve as a low-cost and highly nutritional source of feed and food additives. They also have a potential to be a cheap material for extraction of compounds valuable for the food industry and a component of media used in biotechnological processes aimed at production of compounds and enzymes relevant for the food industry.
bibliographic citation: Rachwał et al. (2020) Utilization of brewery wastes in food industry. PeerJ 8:e9427 https://doi.org/10.7717/peerj.9427
date submitted: 2020-03-18
date accepted: 2020-06-05
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rachwał
  given name: Kamila
author list: Agent
  family name: Waśko
  given name: Adam
author list: Agent
  family name: Gustaw
  given name: Klaudia
author list: Agent
  family name: Polak-Berecka
  given name: Magdalena
doi: 10.7717/peerj.9427
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Rachwałet al.
attribution name: Rachwałet al.

Correlation between emotional regulation and peripheral lymphocyte counts in colorectal cancer patients
type: item
type: AcademicArticle
description: Background Colorectal cancer is one of the most common cancers worldwide. Psychological morbidity has an important impact on quality of life and major clinical outcomes. Several data have shown that the immune system may be a key player on the relation between psychological features and cancer outcomes. Natural Killer (NK) cells have been shown to be influenced by psychological factors. The aim of this investigation was to assess the impact of anxiety, depression, and anger state, trait, and expression on the immune response, particularly, their effect on NK cells and CD8+ T cells in surgical colorectal cancer patients. Methods We studied 54 surgical colorectal cancer patients and assessed patients pre-surgically, post-surgically, and 12 months after surgery (follow-up). We applied the Hospital Anxiety and Depression Scale and the State-Trait Anger Expression Inventory and measured peripheral T cells, CD8+ T cells, and NK cells. We did a cross-sectional analysis as well as a longitudinal assessment of the variables during the follow-up period. Results Pre-surgical assessment: Trait anger, angry reaction, and anger-out had a significant negative correlation with NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety or depression. Post-surgical assessment: Patients without clinical anxiety had higher levels of T cells. Angry reaction was negatively correlated with NK cells. Lymphocytes values were unaffected by the presence of clinical depression. Follow-up assessment: Patients without clinical depression had higher T cell counts. Trait anger and angry reaction were negatively correlated with the levels of NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety. Longitudinal assessment: Angry-temperament, anger expression, and anger-in reduced significantly from the first to the second assessment. Anxiety, state anger, and trait anger significantly diminished from the pre-surgical to the follow-up assessment.…
format: application/pdf
format: text/html
creator: Estela Kakoo Brioso
creator: Sérgio Ferreira Cristina
creator: Luis Costa
creator: Silvia Ouakinin
subject: Allergy and Clinical Immunology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9475
publisher: PeerJ Inc.
rights: © 2020 Kakoo Brioso et al.
abstract: Background Colorectal cancer is one of the most common cancers worldwide. Psychological morbidity has an important impact on quality of life and major clinical outcomes. Several data have shown that the immune system may be a key player on the relation between psychological features and cancer outcomes. Natural Killer (NK) cells have been shown to be influenced by psychological factors. The aim of this investigation was to assess the impact of anxiety, depression, and anger state, trait, and expression on the immune response, particularly, their effect on NK cells and CD8+ T cells in surgical colorectal cancer patients. Methods We studied 54 surgical colorectal cancer patients and assessed patients pre-surgically, post-surgically, and 12 months after surgery (follow-up). We applied the Hospital Anxiety and Depression Scale and the State-Trait Anger Expression Inventory and measured peripheral T cells, CD8+ T cells, and NK cells. We did a cross-sectional analysis as well as a longitudinal assessment of the variables during the follow-up period. Results Pre-surgical assessment: Trait anger, angry reaction, and anger-out had a significant negative correlation with NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety or depression. Post-surgical assessment: Patients without clinical anxiety had higher levels of T cells. Angry reaction was negatively correlated with NK cells. Lymphocytes values were unaffected by the presence of clinical depression. Follow-up assessment: Patients without clinical depression had higher T cell counts. Trait anger and angry reaction were negatively correlated with the levels of NK cells. The lymphocytes values were unaffected by the presence of clinical anxiety. Longitudinal assessment: Angry-temperament, anger expression, and anger-in reduced significantly from the first to the second assessment. Anxiety, state anger, and trait anger significantly diminished from the pre-surgical to the follow-up assessment.…
bibliographic citation: Kakoo Brioso et al. (2020) Correlation between emotional regulation and peripheral lymphocyte counts in colorectal cancer patients. PeerJ 8:e9475 https://doi.org/10.7717/peerj.9475
date submitted: 2020-02-10
date accepted: 2020-06-12
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kakoo Brioso
  given name: Estela
author list: Agent
  family name: Ferreira Cristina
  given name: Sérgio
author list: Agent
  family name: Costa
  given name: Luis
author list: Agent
  family name: Ouakinin
  given name: Silvia
doi: 10.7717/peerj.9475
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Kakoo Brioso et al.
attribution name: Kakoo Brioso et al.

Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding
type: item
type: AcademicArticle
description: Environmental DNA (eDNA) metabarcoding is a cost-effective novel approach to estimate biodiversity in an ecosystem. In this study, the MiFish pipeline was employed to test if the system methodology is sufficiently reliable to estimate fish biodiversity in Korean rivers. A total of 125 unique haplotypes and 73 species were identified at the species level from 16 water samples collected from a single survey in four Korean rivers (Hyeongsan, Taehwa, Seomjin, and Nakdong). Among the four rivers, the highest species richness was recorded in the Seomjin River (52 species), followed by the Taehwa (42 species) and Hyeongsan (40 species) rivers. The Nakdong River (26 species) presented the lowest species richness and number of endemic species, presumably due to its metropolitan location and anthropogenic impacts, such as dams or weirs. We were also able to detect that five exotic species (Carassius cuvieri, Cyprinus carpio, Cyprinus megalophthalmus, Lepomis macrochirus, and Micropterus salmoides) are widely distributed in all surveyed rivers, a situation that might be problematic in terms of conservation. Our findings indicate that the eDNA metabarcoding technique is one of the most cost-effective scientific tools available for the management and conservation of the freshwater fish resources available in Korea. However, the low number of 12S sequences of endemic species in the database and low resolution of the MiFish region for differentiating several taxa should be upgraded for their wide use.
format: application/pdf
format: text/html
creator: Md Jobaidul Alam
creator: Nack-Keun Kim
creator: Sapto Andriyono
creator: Hee-kyu Choi
creator: Ji-Hyun Lee
creator: Hyun-Woo Kim
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.9508
publisher: PeerJ Inc.
rights: © 2020 Alam et al.
abstract: Environmental DNA (eDNA) metabarcoding is a cost-effective novel approach to estimate biodiversity in an ecosystem. In this study, the MiFish pipeline was employed to test if the system methodology is sufficiently reliable to estimate fish biodiversity in Korean rivers. A total of 125 unique haplotypes and 73 species were identified at the species level from 16 water samples collected from a single survey in four Korean rivers (Hyeongsan, Taehwa, Seomjin, and Nakdong). Among the four rivers, the highest species richness was recorded in the Seomjin River (52 species), followed by the Taehwa (42 species) and Hyeongsan (40 species) rivers. The Nakdong River (26 species) presented the lowest species richness and number of endemic species, presumably due to its metropolitan location and anthropogenic impacts, such as dams or weirs. We were also able to detect that five exotic species (Carassius cuvieri, Cyprinus carpio, Cyprinus megalophthalmus, Lepomis macrochirus, and Micropterus salmoides) are widely distributed in all surveyed rivers, a situation that might be problematic in terms of conservation. Our findings indicate that the eDNA metabarcoding technique is one of the most cost-effective scientific tools available for the management and conservation of the freshwater fish resources available in Korea. However, the low number of 12S sequences of endemic species in the database and low resolution of the MiFish region for differentiating several taxa should be upgraded for their wide use.
bibliographic citation: Alam et al. (2020) Assessment of fish biodiversity in four Korean rivers using environmental DNA metabarcoding. PeerJ 8:e9508 https://doi.org/10.7717/peerj.9508
date submitted: 2019-11-14
date accepted: 2020-06-18
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alam
  given name: Md Jobaidul
author list: Agent
  family name: Kim
  given name: Nack-Keun
author list: Agent
  family name: Andriyono
  given name: Sapto
author list: Agent
  family name: Choi
  given name: Hee-kyu
author list: Agent
  family name: Lee
  given name: Ji-Hyun
author list: Agent
  family name: Kim
  given name: Hyun-Woo
doi: 10.7717/peerj.9508
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Alam et al.
attribution name: Alam et al.

https://peerj.com/articles/9529
type: item
type: AcademicArticle
title: A novel histozoic myxosporean, Enteromyxum caesio n. sp., infecting the redbelly yellowtail fusilier, Caesio cuning, with the creation of the Enteromyxidae n. fam., to formally accommodate this commercially important genus
description: Gastrointestinal myxosporean parasites from the genus Enteromyxum are known to cause severe disease, resulting in high mortalities in numerous species of cultured marine fishes globally. Originally described as Myxidium spp., they were transferred to a new genus, Enteromyxum, to emphasize their novel characteristics. Their retention in the family Myxidiidae at the time was warranted, but more comprehensive phylogenetic analyses have since demonstrated the need for a new family for these parasites. We discovered a novel Enteromyxum in wild fish from Malaysia and herein describe the fourth species in the genus and erect a new family, the Enteromyxidae n. fam., to accommodate them. Enteromyxum caesio n. sp. is described infecting the tissues of the stomach in the redbelly yellowtail fusilier, Caesio cuning, from Malaysia. The new species is distinct from all others in the genus, as the myxospores although morphologically similar, are significantly smaller in size. Furthermore, small subunit ribosomal DNA sequence data reveal that E. caesio is <84% similar to others in the genus, but collectively they form a robust and discrete clade, the Enteromyxidae n. fam., which is placed as a sister taxon to other histozoic marine myxosporeans. In addition, we describe, using transmission electron microscopy, the epicellular stages of Enteromyxum fugu and show a scanning electron micrograph of a mature myxospore of E. caesio detailing the otherwise indistinct sutural line, features of the polar capsules and spore valve ridges. The Enteromyxidae n. fam. is a commercially important group of parasites infecting the gastrointestinal tract of marine fishes and the histozoic species can cause the disease enteromyxosis in intensive finfish aquaculture facilities. Epicellular and sloughed histozoic stages are responsible for fish-to-fish transmission in net pen aquaculture systems but actinospores from an annelid host are thought to be necessary for transmission to fish in the wild.
format: application/pdf
format: text/html
creator: Mark A. Freeman
creator: Tetsuya Yanagida
creator: Àrni Kristmundsson
subject: Aquaculture, Fisheries and Fish Science
subject: Biodiversity
subject: Parasitology
subject: Taxonomy
subject: Veterinary Medicine
description: doi:10.7717/peerj.9529
publisher: PeerJ Inc.
rights: © 2020 Freeman et al.
abstract: Gastrointestinal myxosporean parasites from the genus Enteromyxum are known to cause severe disease, resulting in high mortalities in numerous species of cultured marine fishes globally. Originally described as Myxidium spp., they were transferred to a new genus, Enteromyxum, to emphasize their novel characteristics. Their retention in the family Myxidiidae at the time was warranted, but more comprehensive phylogenetic analyses have since demonstrated the need for a new family for these parasites. We discovered a novel Enteromyxum in wild fish from Malaysia and herein describe the fourth species in the genus and erect a new family, the Enteromyxidae n. fam., to accommodate them. Enteromyxum caesio n. sp. is described infecting the tissues of the stomach in the redbelly yellowtail fusilier, Caesio cuning, from Malaysia. The new species is distinct from all others in the genus, as the myxospores although morphologically similar, are significantly smaller in size. Furthermore, small subunit ribosomal DNA sequence data reveal that E. caesio is <84% similar to others in the genus, but collectively they form a robust and discrete clade, the Enteromyxidae n. fam., which is placed as a sister taxon to other histozoic marine myxosporeans. In addition, we describe, using transmission electron microscopy, the epicellular stages of Enteromyxum fugu and show a scanning electron micrograph of a mature myxospore of E. caesio detailing the otherwise indistinct sutural line, features of the polar capsules and spore valve ridges. The Enteromyxidae n. fam. is a commercially important group of parasites infecting the gastrointestinal tract of marine fishes and the histozoic species can cause the disease enteromyxosis in intensive finfish aquaculture facilities. Epicellular and sloughed histozoic stages are responsible for fish-to-fish transmission in net pen aquaculture systems but actinospores from an annelid host are thought to be necessary for transmission to fish in the wild.
bibliographic citation: Freeman et al. (2020) A novel histozoic myxosporean, Enteromyxum caesio n. sp., infecting the redbelly yellowtail fusilier, Caesio cuning, with the creation of the Enteromyxidae n. fam., to formally accommodate this commercially important genus. PeerJ 8:e9529 https://doi.org/10.7717/peerj.9529
date submitted: 2020-04-16
date accepted: 2020-06-22
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Freeman
  given name: Mark A.
author list: Agent
  family name: Yanagida
  given name: Tetsuya
author list: Agent
  family name: Kristmundsson
  given name: Àrni
doi: 10.7717/peerj.9529
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Freeman et al.
attribution name: Freeman et al.

Soil macro-fauna respond to environmental variations along a coastal-inland gradient
type: item
type: AcademicArticle
description: Varied environmental conditions in coastal-inland zones tend to influence soil faunal communities. However, few studies have focused on the responses of soil fauna to environmental variations along the coastal-inland gradient. In order to better understand the aforementioned responses, a total of 80 soil macro-faunal samples were collected at the five different distances from the coastline of China’s Bohai Bay. The results revealed that the compositions, structural characteristics and diversity of the soil macro-fauna varied among the different habitats. With the increases in the distance from the sea, the individual density, richness and diversity levels of the soil macro-fauna all first increased and then decreased. The individual density, richness and diversity values were all at their maximum at 30 km from the sea. The Edge effect promoted unique and rare soil macro-faunal taxa. Formicidae, Curculionidae and Aphodiidae were found to be the edge taxa. Agelenidae, Liocranidae and Nematocera were considered to be indicator taxa of severe sea effects. Paradoxosomatidae was an indicator taxon of slight effects. Overall, the environmental variations along the coastal-inland gradient were found to have the potential to affect the soil macro-faunal communities, and the different taxa of the soil macro-fauna responded to those variations in different ways. This study further revealed the processes and mechanisms of the sea influencing the soil macro-faunal communities, which had been caused by the coastal-inland gradient. The results of this study also provided a theoretical basis for developing future biodiversity guidelines for coastal ecosystems.
format: application/pdf
format: text/html
creator: Xiaoxue Zheng
creator: Yan Tao
creator: Zhongqiang Wang
creator: Chen Ma
creator: Hong He
creator: Xiuqin Yin
subject: Biodiversity
subject: Ecology
subject: Entomology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.9532
publisher: PeerJ Inc.
rights: © 2020 Zheng et al.
abstract: Varied environmental conditions in coastal-inland zones tend to influence soil faunal communities. However, few studies have focused on the responses of soil fauna to environmental variations along the coastal-inland gradient. In order to better understand the aforementioned responses, a total of 80 soil macro-faunal samples were collected at the five different distances from the coastline of China’s Bohai Bay. The results revealed that the compositions, structural characteristics and diversity of the soil macro-fauna varied among the different habitats. With the increases in the distance from the sea, the individual density, richness and diversity levels of the soil macro-fauna all first increased and then decreased. The individual density, richness and diversity values were all at their maximum at 30 km from the sea. The Edge effect promoted unique and rare soil macro-faunal taxa. Formicidae, Curculionidae and Aphodiidae were found to be the edge taxa. Agelenidae, Liocranidae and Nematocera were considered to be indicator taxa of severe sea effects. Paradoxosomatidae was an indicator taxon of slight effects. Overall, the environmental variations along the coastal-inland gradient were found to have the potential to affect the soil macro-faunal communities, and the different taxa of the soil macro-fauna responded to those variations in different ways. This study further revealed the processes and mechanisms of the sea influencing the soil macro-faunal communities, which had been caused by the coastal-inland gradient. The results of this study also provided a theoretical basis for developing future biodiversity guidelines for coastal ecosystems.
bibliographic citation: Zheng et al. (2020) Soil macro-fauna respond to environmental variations along a coastal-inland gradient. PeerJ 8:e9532 https://doi.org/10.7717/peerj.9532
date submitted: 2020-04-28
date accepted: 2020-06-22
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zheng
  given name: Xiaoxue
author list: Agent
  family name: Tao
  given name: Yan
author list: Agent
  family name: Wang
  given name: Zhongqiang
author list: Agent
  family name: Ma
  given name: Chen
author list: Agent
  family name: He
  given name: Hong
author list: Agent
  family name: Yin
  given name: Xiuqin
doi: 10.7717/peerj.9532
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: © 2020 Zheng et al.
attribution name: Zheng et al.

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