PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: Predictive values of stool-based tests for mucosal healing among Taiwanese patients with ulcerative colitis: a retrospective cohort analysis
items: Bioinformatics analysis and identification of circular RNAs promoting the osteogenic differentiation of human bone marrow mesenchymal stem cells on titanium treated by surface mechanical attrition
items: High frequency direct shoot regeneration from Kazakh commercial potato cultivars

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.

Predictive values of stool-based tests for mucosal healing among Taiwanese patients with ulcerative colitis: a retrospective cohort analysis
type: item
type: AcademicArticle
description: Background/Purpose Over the past two decades, ulcerative colitis (UC) has emerged in the Asia Pacific area, and its treatment goal has shifted from symptom relief to endoscopic remission. Endoscopy is the gold standard for the assessment of mucosal healing; however, it is an invasive method. Fecal calprotectin (FC) is a non-invasive stool-based inflammatory marker which has been used to monitor mucosal healing status, but it is expensive. By contrast, the immune fecal occult blood test (iFOBT) is a widely utilized stool-based screening tool for colorectal cancer. In this study, we compared the predictive values of iFOBT and FC for mucosal healing in Taiwanese patients with UC. Methods A total of 50 patients with UC identified via the electronic clinical database of Changhua Christian Hospital, Taiwan, were retrospectively enrolled from January 2018 to July 2019. Results of iFOBT, FC level, and blood tests as well as Mayo scores were reviewed and analyzed. Colonic mucosa was evaluated using the endoscopic Mayo subscore. Results The average age of the patients was 46 years, and 62% of the patients were men. Disease distribution was as follows: E1 (26%), E2 (40%), and E3 (34%). Complete mucosal healing (Mayo score = 0) was observed in 30% of patients. Endoscopic mucosal healing with a Mayo score of 0 or 1 was observed in 62% of the patients. Results of FC and iFOBT were compared among patients with and without mucosal healing. Predictive cutoff values were analyzed using receiver operating characteristics curves. iFOBT and FC had similar area under the curve for both complete mucosal healing (0.813 vs. 0.769, respectively, p = 0.5581) and endoscopic mucosal healing (0.906 vs. 0.812, respectively, p = 0.1207). Conclusion In daily clinical practice, FC and iFOBT do not differ in terms of predictive values for mucosal healing among Taiwanese patients with UC.
format: application/pdf
format: text/html
creator: Hsu-Heng Yen
creator: Mei-Wen Chen
creator: Yu-Yao Chang
creator: Hsuan-Yuan Huang
creator: Tsui-Chun Hsu
creator: Yang-Yuan Chen
subject: Evidence Based Medicine
subject: Gastroenterology and Hepatology
subject: Hematology
subject: Pathology
description: doi:10.7717/peerj.9537
publisher: PeerJ Inc.
rights: © 2020 Yen et al.
abstract: Background/Purpose Over the past two decades, ulcerative colitis (UC) has emerged in the Asia Pacific area, and its treatment goal has shifted from symptom relief to endoscopic remission. Endoscopy is the gold standard for the assessment of mucosal healing; however, it is an invasive method. Fecal calprotectin (FC) is a non-invasive stool-based inflammatory marker which has been used to monitor mucosal healing status, but it is expensive. By contrast, the immune fecal occult blood test (iFOBT) is a widely utilized stool-based screening tool for colorectal cancer. In this study, we compared the predictive values of iFOBT and FC for mucosal healing in Taiwanese patients with UC. Methods A total of 50 patients with UC identified via the electronic clinical database of Changhua Christian Hospital, Taiwan, were retrospectively enrolled from January 2018 to July 2019. Results of iFOBT, FC level, and blood tests as well as Mayo scores were reviewed and analyzed. Colonic mucosa was evaluated using the endoscopic Mayo subscore. Results The average age of the patients was 46 years, and 62% of the patients were men. Disease distribution was as follows: E1 (26%), E2 (40%), and E3 (34%). Complete mucosal healing (Mayo score = 0) was observed in 30% of patients. Endoscopic mucosal healing with a Mayo score of 0 or 1 was observed in 62% of the patients. Results of FC and iFOBT were compared among patients with and without mucosal healing. Predictive cutoff values were analyzed using receiver operating characteristics curves. iFOBT and FC had similar area under the curve for both complete mucosal healing (0.813 vs. 0.769, respectively, p = 0.5581) and endoscopic mucosal healing (0.906 vs. 0.812, respectively, p = 0.1207). Conclusion In daily clinical practice, FC and iFOBT do not differ in terms of predictive values for mucosal healing among Taiwanese patients with UC.
bibliographic citation: Yen et al. (2020) Predictive values of stool-based tests for mucosal healing among Taiwanese patients with ulcerative colitis: a retrospective cohort analysis. PeerJ 8:e9537 https://doi.org/10.7717/peerj.9537
date submitted: 2020-05-07
date accepted: 2020-06-23
issued: 2020-07-14
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yen
  given name: Hsu-Heng
author list: Agent
  family name: Chen
  given name: Mei-Wen
author list: Agent
  family name: Chang
  given name: Yu-Yao
author list: Agent
  family name: Huang
  given name: Hsuan-Yuan
author list: Agent
  family name: Hsu
  given name: Tsui-Chun
author list: Agent
  family name: Chen
  given name: Yang-Yuan
doi: 10.7717/peerj.9537
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-14
copyright: ©2020 Yen et al.
attribution name: Yen et al.

Bioinformatics analysis and identification of circular RNAs promoting the osteogenic differentiation of human bone marrow mesenchymal stem cells on titanium treated by surface mechanical attrition
type: item
type: AcademicArticle
description: Background To analyze and identify the circular RNAs (circRNAs) involved in promoting the osteogenic differentiation of human bone mesenchymal stem cells (hBMSCs) on titanium by surface mechanical attrition treatment (SMAT). Methods The experimental material was SMAT titanium and the control material was annealed titanium. Cell Counting Kits-8 (CCK-8) was used to detect the proliferation of hBMSCs, and alkaline phosphatase (ALP) activity and alizarin red staining were used to detect the osteogenic differentiation of hBMSCs on the sample surfaces. The bioinformatics prediction software miwalk3.0 was used to construct competing endogenous RNA (ceRNA) networks by predicting circRNAs with osteogenesis-related messenger RNAs (mRNAs) and microRNAs (miRNAs). The circRNAs located at the key positions in the networks were selected and analyzed by quantitative real-time PCR (QRT-PCR). Results Compared with annealed titanium, SMAT titanium could promote the proliferation and osteogenic differentiation of hBMSCs. The total number of predicted circRNAs was 51. Among these, 30 circRNAs and 8 miRNAs constituted 6 ceRNA networks. Circ-LTBP2 was selected for verification. QRT-PCR results showed that the expression levels of hsa_circ_0032599, hsa_circ_0032600 and hsa_circ_0032601 were upregulated in the experimental group compared with those in the control group; the differential expression of hsa_circ_0032600 was the most obvious and statistically significant, with a fold change (FC) = 4.25 ± 1.60, p-values (p) < 0.05.
format: application/pdf
format: text/html
creator: Shanshan Zhu
creator: Yuhe Zhu
creator: Zhenbo Wang
creator: Chen Liang
creator: Nanjue Cao
creator: Ming Yan
creator: Fei Gao
creator: Jie Liu
creator: Wei Wang
subject: Bioinformatics
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Dentistry
description: doi:10.7717/peerj.9292
publisher: PeerJ Inc.
rights: © 2020 Zhu et al.
abstract: Background To analyze and identify the circular RNAs (circRNAs) involved in promoting the osteogenic differentiation of human bone mesenchymal stem cells (hBMSCs) on titanium by surface mechanical attrition treatment (SMAT). Methods The experimental material was SMAT titanium and the control material was annealed titanium. Cell Counting Kits-8 (CCK-8) was used to detect the proliferation of hBMSCs, and alkaline phosphatase (ALP) activity and alizarin red staining were used to detect the osteogenic differentiation of hBMSCs on the sample surfaces. The bioinformatics prediction software miwalk3.0 was used to construct competing endogenous RNA (ceRNA) networks by predicting circRNAs with osteogenesis-related messenger RNAs (mRNAs) and microRNAs (miRNAs). The circRNAs located at the key positions in the networks were selected and analyzed by quantitative real-time PCR (QRT-PCR). Results Compared with annealed titanium, SMAT titanium could promote the proliferation and osteogenic differentiation of hBMSCs. The total number of predicted circRNAs was 51. Among these, 30 circRNAs and 8 miRNAs constituted 6 ceRNA networks. Circ-LTBP2 was selected for verification. QRT-PCR results showed that the expression levels of hsa_circ_0032599, hsa_circ_0032600 and hsa_circ_0032601 were upregulated in the experimental group compared with those in the control group; the differential expression of hsa_circ_0032600 was the most obvious and statistically significant, with a fold change (FC) = 4.25 ± 1.60, p-values (p) < 0.05.
bibliographic citation: Zhu et al. (2020) Bioinformatics analysis and identification of circular RNAs promoting the osteogenic differentiation of human bone marrow mesenchymal stem cells on titanium treated by surface mechanical attrition. PeerJ 8:e9292 https://doi.org/10.7717/peerj.9292
date submitted: 2020-01-03
date accepted: 2020-05-13
issued: 2020-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhu
  given name: Shanshan
author list: Agent
  family name: Zhu
  given name: Yuhe
author list: Agent
  family name: Wang
  given name: Zhenbo
author list: Agent
  family name: Liang
  given name: Chen
author list: Agent
  family name: Cao
  given name: Nanjue
author list: Agent
  family name: Yan
  given name: Ming
author list: Agent
  family name: Gao
  given name: Fei
author list: Agent
  family name: Liu
  given name: Jie
author list: Agent
  family name: Wang
  given name: Wei
doi: 10.7717/peerj.9292
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-13
copyright: © 2020 Zhu et al.
attribution name: Zhu et al.

High frequency direct shoot regeneration from Kazakh commercial potato cultivars
type: item
type: AcademicArticle
description: Potato (Solanum tuberosum L.) is the third most economically important crop in the world and has a high nutritional value. In this study, the in vitro culture response of four widely grown in Kazakhstan potato cultivars, Astanalyk, Monument Kunaev, Tokhtar, and Aksor, was investigated using stem and leaf explants. Published protocols were evaluated and optimized to develop a more efficient protocol for the regeneration of plants from local potato cultivars in tissue culture, which is a prerequisite to facilitate potato genome modification. The explants were cultured on solid Murashige and Skoog medium supplemented with different concentrations and combinations of zeatin, 6-benzylaminopurine (BAP), gibberellic acid (GA3), 1-naphthaleneacetic acid (NAA) and indole-3-acetic acid (IAA). The maximum regeneration was induced from the stem internodal explants. A significant effect of the explant source on direct regeneration was confirmed with statistical analysis. The number of shoots obtained from the internode was 10.0 from cv. Aksor followed by cvs. Tokhtar and Astanalyk. The medium DRM-VIII with 1 mg/l zeatin, 0.1 mg/l IAA and 7.0 mg/l GA3 was considered the best for direct shoot regeneration and multiple shoot formation from all cultivars. To conclude, we outline a protocol for direct plant regeneration from four potato cultivars. Our findings suggest commercial cultivars Astanalyk and Aksor are good candidates for developing the genome-edited plants through direct shoot regeneration.
format: application/pdf
format: text/html
creator: Laura S. Abeuova
creator: Balnur R. Kali
creator: Aizhan O. Rakhimzhanova
creator: Sara S. Bekkuzhina
creator: Shuga A. Manabayeva
subject: Agricultural Science
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.9447
publisher: PeerJ Inc.
rights: © 2020 Abeuova et al.
abstract: Potato (Solanum tuberosum L.) is the third most economically important crop in the world and has a high nutritional value. In this study, the in vitro culture response of four widely grown in Kazakhstan potato cultivars, Astanalyk, Monument Kunaev, Tokhtar, and Aksor, was investigated using stem and leaf explants. Published protocols were evaluated and optimized to develop a more efficient protocol for the regeneration of plants from local potato cultivars in tissue culture, which is a prerequisite to facilitate potato genome modification. The explants were cultured on solid Murashige and Skoog medium supplemented with different concentrations and combinations of zeatin, 6-benzylaminopurine (BAP), gibberellic acid (GA3), 1-naphthaleneacetic acid (NAA) and indole-3-acetic acid (IAA). The maximum regeneration was induced from the stem internodal explants. A significant effect of the explant source on direct regeneration was confirmed with statistical analysis. The number of shoots obtained from the internode was 10.0 from cv. Aksor followed by cvs. Tokhtar and Astanalyk. The medium DRM-VIII with 1 mg/l zeatin, 0.1 mg/l IAA and 7.0 mg/l GA3 was considered the best for direct shoot regeneration and multiple shoot formation from all cultivars. To conclude, we outline a protocol for direct plant regeneration from four potato cultivars. Our findings suggest commercial cultivars Astanalyk and Aksor are good candidates for developing the genome-edited plants through direct shoot regeneration.
bibliographic citation: Abeuova et al. (2020) High frequency direct shoot regeneration from Kazakh commercial potato cultivars. PeerJ 8:e9447 https://doi.org/10.7717/peerj.9447
date submitted: 2020-02-13
date accepted: 2020-06-08
issued: 2020-07-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abeuova
  given name: Laura S.
author list: Agent
  family name: Kali
  given name: Balnur R.
author list: Agent
  family name: Rakhimzhanova
  given name: Aizhan O.
author list: Agent
  family name: Bekkuzhina
  given name: Sara S.
author list: Agent
  family name: Manabayeva
  given name: Shuga A.
doi: 10.7717/peerj.9447
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-07-13
copyright: ©2020 Abeuova et al.
attribution name: Abeuova et al.

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