PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: KIT is involved in melanocyte proliferation, apoptosis and melanogenesis in the Rex Rabbit
items: Habitual and ready positions in female table tennis players and their relation to the prevalence of back pain
items: Image database of Japanese food samples with nutrition information
items: Legacy effects of historical grazing alter leaf stomatal characteristics in progeny plants
items: Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan
items: Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process
items: Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China
items: Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China
items: Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma
items: Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice

KIT is involved in melanocyte proliferation, apoptosis and melanogenesis in the Rex Rabbit
type: item
type: AcademicArticle
description: Background Melanocytes play an extremely important role in the process of skin and coat colors in mammals which is regulated by melanin-related genes. Previous studies have demonstrated that KIT is implicated in the process of determining the color of the coat in Rex rabbits. However, the effect of KIT on the proliferation and apoptosis of melanocytes and melanogenesis has not been clarified. Methods The mRNA and protein expression levels of KIT were quantified in different coat colored rabbits by qRT-PCR and a Wes assay. To identify whether KIT functions by regulating of melanogenesis, KIT overexpression and knockdown was conducted in melanocytes, and KIT mRNA expression and melanin-related genes TYR, MITF, PMEL and DCT were quantified by qRT-PCR. To further confirm whether KIT influences melanogenesis in melanocytes, melanin content was quantified using NaOH lysis after overexpression and knockdown of KIT. Melanocyte proliferation was estimated using a CCK-8 assay at 0, 24, 48 and 72 h after transfection, and the rate of apoptosis of melanocytes was measured by fluorescence-activated cell sorting. Results KITmRNA and protein expression levels were significantly different in the skin of Rex rabbits with different color coats (P < 0.05), the greatest levels observed in those with black skin. The mRNA expression levels of KIT significantly affected the mRNA expression of the pigmentation-related genes TYR, MITF, PMEL and DCT (P < 0.01). Melanin content was evidently regulated by the change in expression patterns of KIT (P < 0.01). In addition, KIT clearly promoted melanocyte proliferation, but inhibited apoptosis. Conclusions Our results reveal that KIT is a critical gene in the regulation of melanogenesis, controlling proliferation and apoptosis in melanocytes, providing additional evidence for the mechanism of pigmentation of animal fur.
format: application/pdf
format: text/html
creator: Shuaishuai Hu
creator: Yang Chen
creator: Bohao Zhao
creator: Naisu Yang
creator: Shi Chen
creator: Jinyu Shen
creator: Guolian Bao
creator: Xinsheng Wu
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.9402
publisher: PeerJ Inc.
rights: © 2020 Hu et al.
abstract: Background Melanocytes play an extremely important role in the process of skin and coat colors in mammals which is regulated by melanin-related genes. Previous studies have demonstrated that KIT is implicated in the process of determining the color of the coat in Rex rabbits. However, the effect of KIT on the proliferation and apoptosis of melanocytes and melanogenesis has not been clarified. Methods The mRNA and protein expression levels of KIT were quantified in different coat colored rabbits by qRT-PCR and a Wes assay. To identify whether KIT functions by regulating of melanogenesis, KIT overexpression and knockdown was conducted in melanocytes, and KIT mRNA expression and melanin-related genes TYR, MITF, PMEL and DCT were quantified by qRT-PCR. To further confirm whether KIT influences melanogenesis in melanocytes, melanin content was quantified using NaOH lysis after overexpression and knockdown of KIT. Melanocyte proliferation was estimated using a CCK-8 assay at 0, 24, 48 and 72 h after transfection, and the rate of apoptosis of melanocytes was measured by fluorescence-activated cell sorting. Results KITmRNA and protein expression levels were significantly different in the skin of Rex rabbits with different color coats (P < 0.05), the greatest levels observed in those with black skin. The mRNA expression levels of KIT significantly affected the mRNA expression of the pigmentation-related genes TYR, MITF, PMEL and DCT (P < 0.01). Melanin content was evidently regulated by the change in expression patterns of KIT (P < 0.01). In addition, KIT clearly promoted melanocyte proliferation, but inhibited apoptosis. Conclusions Our results reveal that KIT is a critical gene in the regulation of melanogenesis, controlling proliferation and apoptosis in melanocytes, providing additional evidence for the mechanism of pigmentation of animal fur.
bibliographic citation: Hu et al. (2020) KIT is involved in melanocyte proliferation, apoptosis and melanogenesis in the Rex Rabbit. PeerJ 8:e9402 https://doi.org/10.7717/peerj.9402
date submitted: 2019-11-27
date accepted: 2020-06-01
issued: 2020-06-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hu
  given name: Shuaishuai
author list: Agent
  family name: Chen
  given name: Yang
author list: Agent
  family name: Zhao
  given name: Bohao
author list: Agent
  family name: Yang
  given name: Naisu
author list: Agent
  family name: Chen
  given name: Shi
author list: Agent
  family name: Shen
  given name: Jinyu
author list: Agent
  family name: Bao
  given name: Guolian
author list: Agent
  family name: Wu
  given name: Xinsheng
doi: 10.7717/peerj.9402
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-18
copyright: ©2020 Hu et al.
attribution name: Hu et al.

Habitual and ready positions in female table tennis players and their relation to the prevalence of back pain
type: item
type: AcademicArticle
description: Background The current body of knowledge shows that there is very little research into the occurrence and scale of asymmetry or postural defects in table tennis. It is interesting which regions of the spine are exposed to the greatest changes in the shape of its curvatures and whether the asymmetrical position of the shoulder and pelvic girdles in table tennis players changes when adopting the ready position. Consequently, can overload occur in certain parts of the spine and can the asymmetry deepen as a response of adopting this position? The reply to these questions may be an indication of the need for appropriate compensatory or corrective measures. Therefore, the aim of the study was to evaluate the effect of body position during play on the change in the shape of anterior–posterior spinal curvatures and trunk asymmetry in table tennis players. Methods To evaluate body posture the photogrammetric method based on the Moiré phenomenon with equipment by CQ electronic was applied. The study involved 22 female players practicing competitive table tennis (the age of 17 ± 4.5, with the average training experience of 7 ± 4.3 years, body mass of 47.8 ± 15.8, and body height of 161.2 ± 10.4). Each participant completed an author’s own questionnaire on spinal pain. The shape of curvatures in the sagittal and frontal plane was evaluated in the participant in the habitual standing position and in the table tennis ready position. Descriptive statistical analysis was performed and the significance of differences was tested using the Mann–Whitney U test. Results and Conclusions This study demonstrated the dominance of kyphotic body posture in table tennis players, which can be caused by many hours of using the ready position during playing. After adopting this position, there are significant differences in the angles of anterior and posterior spinal curvatures compared to the habitual posture. This may be the cause of overloads and pain complaints reported by the study particip…
format: application/pdf
format: text/html
creator: Ziemowit Bańkosz
creator: Katarzyna Barczyk-Pawelec
subject: Anatomy and Physiology
subject: Kinesiology
description: doi:10.7717/peerj.9170
publisher: PeerJ Inc.
rights: © 2020 Bańkosz and Barczyk-Pawelec
abstract: Background The current body of knowledge shows that there is very little research into the occurrence and scale of asymmetry or postural defects in table tennis. It is interesting which regions of the spine are exposed to the greatest changes in the shape of its curvatures and whether the asymmetrical position of the shoulder and pelvic girdles in table tennis players changes when adopting the ready position. Consequently, can overload occur in certain parts of the spine and can the asymmetry deepen as a response of adopting this position? The reply to these questions may be an indication of the need for appropriate compensatory or corrective measures. Therefore, the aim of the study was to evaluate the effect of body position during play on the change in the shape of anterior–posterior spinal curvatures and trunk asymmetry in table tennis players. Methods To evaluate body posture the photogrammetric method based on the Moiré phenomenon with equipment by CQ electronic was applied. The study involved 22 female players practicing competitive table tennis (the age of 17 ± 4.5, with the average training experience of 7 ± 4.3 years, body mass of 47.8 ± 15.8, and body height of 161.2 ± 10.4). Each participant completed an author’s own questionnaire on spinal pain. The shape of curvatures in the sagittal and frontal plane was evaluated in the participant in the habitual standing position and in the table tennis ready position. Descriptive statistical analysis was performed and the significance of differences was tested using the Mann–Whitney U test. Results and Conclusions This study demonstrated the dominance of kyphotic body posture in table tennis players, which can be caused by many hours of using the ready position during playing. After adopting this position, there are significant differences in the angles of anterior and posterior spinal curvatures compared to the habitual posture. This may be the cause of overloads and pain complaints reported by the study particip…
bibliographic citation: Bańkosz et al. (2020) Habitual and ready positions in female table tennis players and their relation to the prevalence of back pain. PeerJ 8:e9170 https://doi.org/10.7717/peerj.9170
date submitted: 2019-12-10
date accepted: 2020-04-20
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bańkosz
  given name: Ziemowit
author list: Agent
  family name: Barczyk-Pawelec
  given name: Katarzyna
doi: 10.7717/peerj.9170
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Bańkosz and Barczyk-Pawelec
attribution name: Bańkosz and Barczyk-Pawelec

Image database of Japanese food samples with nutrition information
type: item
type: AcademicArticle
description: Background Visual processing of food plays an important role in controlling eating behaviors. Several studies have developed image databases of food to investigate visual food processing. However, few databases include non-Western foods and objective nutrition information on the foods. Methods We developed an image database of Japanese food samples that has detailed nutrition information, including calorie, carbohydrate, fat and protein contents. To validate the database, we presented the images, together with Western food images selected from an existing database and had Japanese participants rate their affective (valence, arousal, liking and wanting) and cognitive (naturalness, recognizability and familiarity) appraisals and estimates of nutrition. Results The results showed that all affective and cognitive appraisals (except arousal) of the Japanese food images were higher than those of Western food. Correlational analyses found positive associations between the objective nutrition information and subjective estimates of the nutrition information, and between the objective calorie/fat content and affective appraisals. Conclusions These data suggest that by using our image database, researchers can investigate the visual processing of Japanese food and the relationships between objective nutrition information and the psychological/neural processing of food.
format: application/pdf
format: text/html
creator: Wataru Sato
creator: Kazusa Minemoto
creator: Reiko Sawada
creator: Yoshiko Miyazaki
creator: Tohru Fushiki
subject: Food Science and Technology
subject: Nutrition
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.9206
publisher: PeerJ Inc.
rights: © 2020 Sato et al.
abstract: Background Visual processing of food plays an important role in controlling eating behaviors. Several studies have developed image databases of food to investigate visual food processing. However, few databases include non-Western foods and objective nutrition information on the foods. Methods We developed an image database of Japanese food samples that has detailed nutrition information, including calorie, carbohydrate, fat and protein contents. To validate the database, we presented the images, together with Western food images selected from an existing database and had Japanese participants rate their affective (valence, arousal, liking and wanting) and cognitive (naturalness, recognizability and familiarity) appraisals and estimates of nutrition. Results The results showed that all affective and cognitive appraisals (except arousal) of the Japanese food images were higher than those of Western food. Correlational analyses found positive associations between the objective nutrition information and subjective estimates of the nutrition information, and between the objective calorie/fat content and affective appraisals. Conclusions These data suggest that by using our image database, researchers can investigate the visual processing of Japanese food and the relationships between objective nutrition information and the psychological/neural processing of food.
bibliographic citation: Sato et al. (2020) Image database of Japanese food samples with nutrition information. PeerJ 8:e9206 https://doi.org/10.7717/peerj.9206
date submitted: 2019-12-04
date accepted: 2020-04-27
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sato
  given name: Wataru
author list: Agent
  family name: Minemoto
  given name: Kazusa
author list: Agent
  family name: Sawada
  given name: Reiko
author list: Agent
  family name: Miyazaki
  given name: Yoshiko
author list: Agent
  family name: Fushiki
  given name: Tohru
doi: 10.7717/peerj.9206
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Sato et al.
attribution name: Sato et al.

Legacy effects of historical grazing alter leaf stomatal characteristics in progeny plants
type: item
type: AcademicArticle
description: Grazing, one of the primary utilization modes of grassland, is the main cause of grassland degradation. Historical overgrazing results in dwarf phenotype and decreased photosynthesis of perennial plants. However, it remains unknown what the mechanism underlying of this legacy effect is, and the role of stomata in the resulting decreased photosynthesis also remains unclear. To address these questions, differences in stomatal density, length and width on both adaxial and abaxial epidermis were compared between overgrazing and ungrazed Leymus chinensis offspring by using rhizome buds cultivated in a greenhouse, and the correlation between photosynthetic capacity and stomatal behavior was also investigated. Our results showed that historical grazing significantly impacted phenotype, photosynthesis and stomatal traits of L. chinensis. The offspring plants taken from overgrazed parents were dwarfed compared to those taken from ungrazed parents, and the photosynthesis and stomatal conductance of plants with a grazing history decreased by 28.6% and 21.3%, respectively. In addition, stomatal density and length on adaxial and abaxial leaf surfaces were significantly increased; however, stomatal width on abaxial leaf surfaces of overgrazed L. chinensis was significantly decreased compared with ungrazed individuals. Moreover, the expression patterns of eight genes related to stomatal regulation were tested: seven were down-regulated (2–18 times) and one was up-regulated (three times). Genes, involved in ABC transporter and receptor-like serine/threonine protein kinase were down-regulated. These results suggest that legacy effects of historical grazing affect the stomatal conductance by decreasing the stomatal width in progeny plants, which thus results in lower photosynthesis. Furthermore, changes of stomatal traits and function were regulated by the inhibition of ABC transporter and serine/threonine protein kinase. These findings are helpful for future exploration of the possi…
format: application/pdf
format: text/html
creator: Jingjing Yin
creator: Xiliang Li
creator: Huiqin Guo
creator: Jize Zhang
creator: Lingqi Kong
creator: Weibo Ren
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.9266
publisher: PeerJ Inc.
rights: © 2020 Yin et al.
abstract: Grazing, one of the primary utilization modes of grassland, is the main cause of grassland degradation. Historical overgrazing results in dwarf phenotype and decreased photosynthesis of perennial plants. However, it remains unknown what the mechanism underlying of this legacy effect is, and the role of stomata in the resulting decreased photosynthesis also remains unclear. To address these questions, differences in stomatal density, length and width on both adaxial and abaxial epidermis were compared between overgrazing and ungrazed Leymus chinensis offspring by using rhizome buds cultivated in a greenhouse, and the correlation between photosynthetic capacity and stomatal behavior was also investigated. Our results showed that historical grazing significantly impacted phenotype, photosynthesis and stomatal traits of L. chinensis. The offspring plants taken from overgrazed parents were dwarfed compared to those taken from ungrazed parents, and the photosynthesis and stomatal conductance of plants with a grazing history decreased by 28.6% and 21.3%, respectively. In addition, stomatal density and length on adaxial and abaxial leaf surfaces were significantly increased; however, stomatal width on abaxial leaf surfaces of overgrazed L. chinensis was significantly decreased compared with ungrazed individuals. Moreover, the expression patterns of eight genes related to stomatal regulation were tested: seven were down-regulated (2–18 times) and one was up-regulated (three times). Genes, involved in ABC transporter and receptor-like serine/threonine protein kinase were down-regulated. These results suggest that legacy effects of historical grazing affect the stomatal conductance by decreasing the stomatal width in progeny plants, which thus results in lower photosynthesis. Furthermore, changes of stomatal traits and function were regulated by the inhibition of ABC transporter and serine/threonine protein kinase. These findings are helpful for future exploration of the possi…
bibliographic citation: Yin et al. (2020) Legacy effects of historical grazing alter leaf stomatal characteristics in progeny plants. PeerJ 8:e9266 https://doi.org/10.7717/peerj.9266
date submitted: 2019-12-20
date accepted: 2020-05-10
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Jingjing
author list: Agent
  family name: Li
  given name: Xiliang
author list: Agent
  family name: Guo
  given name: Huiqin
author list: Agent
  family name: Zhang
  given name: Jize
author list: Agent
  family name: Kong
  given name: Lingqi
author list: Agent
  family name: Ren
  given name: Weibo
doi: 10.7717/peerj.9266
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Yin et al.
attribution name: Yin et al.

Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan
type: item
type: AcademicArticle
description: Coronavirus disease 2019 has become a worldwide pandemic. By April 7, 2020, approximately 1,279,722 confirmed cases were reported worldwide including those in Asia, European Region, African Region and Region of the Americas. Rapid and accurate detection of Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) is critical for patient care and implementing public health measures to control the spread of infection. In this study, we developed and validated a rapid total nucleic acid extraction method based on real‐time RT-PCR for reliable, high‐throughput identification of SARS-CoV-2 using the BD MAX platform. For clinical validation, 300 throat swab and 100 sputum clinical samples were examined by both the BD MAX platform and in-house real-time RT-PCR methods, which showed 100% concordant results. This BD MAX protocol is fully automated and the turnaround time from sample to results is approximately 2.5 h for 24 samples compared to 4.8 h by in-house real-time RT-PCR. Our developed BD MAX RT-PCR assay can accurately identify SARS-CoV-2 infection and shorten the turnaround time to increase the effectiveness of control and prevention measures for this emerging infectious disease.
format: application/pdf
format: text/html
creator: Cherng-Lih Perng
creator: Ming-Jr Jian
creator: Chih-Kai Chang
creator: Jung-Chung Lin
creator: Kuo-Ming Yeh
creator: Chien-Wen Chen
creator: Sheng-Kang Chiu
creator: Hsing-Yi Chung
creator: Yi-Hui Wang
creator: Shu-Jung Liao
creator: Shih-Yi Li
creator: Shan-Shan Hsieh
creator: Shih-Hung Tsai
creator: Feng-Yee Chang
creator: Hung-Sheng Shang
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.9318
publisher: PeerJ Inc.
rights: © 2020 Perng et al.
abstract: Coronavirus disease 2019 has become a worldwide pandemic. By April 7, 2020, approximately 1,279,722 confirmed cases were reported worldwide including those in Asia, European Region, African Region and Region of the Americas. Rapid and accurate detection of Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) is critical for patient care and implementing public health measures to control the spread of infection. In this study, we developed and validated a rapid total nucleic acid extraction method based on real‐time RT-PCR for reliable, high‐throughput identification of SARS-CoV-2 using the BD MAX platform. For clinical validation, 300 throat swab and 100 sputum clinical samples were examined by both the BD MAX platform and in-house real-time RT-PCR methods, which showed 100% concordant results. This BD MAX protocol is fully automated and the turnaround time from sample to results is approximately 2.5 h for 24 samples compared to 4.8 h by in-house real-time RT-PCR. Our developed BD MAX RT-PCR assay can accurately identify SARS-CoV-2 infection and shorten the turnaround time to increase the effectiveness of control and prevention measures for this emerging infectious disease.
bibliographic citation: Perng et al. (2020) Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan. PeerJ 8:e9318 https://doi.org/10.7717/peerj.9318
date submitted: 2020-04-20
date accepted: 2020-05-17
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Perng
  given name: Cherng-Lih
author list: Agent
  family name: Jian
  given name: Ming-Jr
author list: Agent
  family name: Chang
  given name: Chih-Kai
author list: Agent
  family name: Lin
  given name: Jung-Chung
author list: Agent
  family name: Yeh
  given name: Kuo-Ming
author list: Agent
  family name: Chen
  given name: Chien-Wen
author list: Agent
  family name: Chiu
  given name: Sheng-Kang
author list: Agent
  family name: Chung
  given name: Hsing-Yi
author list: Agent
  family name: Wang
  given name: Yi-Hui
author list: Agent
  family name: Liao
  given name: Shu-Jung
author list: Agent
  family name: Li
  given name: Shih-Yi
author list: Agent
  family name: Hsieh
  given name: Shan-Shan
author list: Agent
  family name: Tsai
  given name: Shih-Hung
author list: Agent
  family name: Chang
  given name: Feng-Yee
author list: Agent
  family name: Shang
  given name: Hung-Sheng
doi: 10.7717/peerj.9318
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Perng et al.
attribution name: Perng et al.

Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process
type: item
type: AcademicArticle
description: Reduction of the greenhouse effect is primarily associated with the reduction of greenhouse gas (GHG) emissions. Carbon dioxide (CO2) is one of the gases that increases the greenhouse effect - it is responsible for about half of the greenhouse effect. Significant sources of CO2 are wastewater treatment plants (WWTPs) and waste management, with about 3% contribution to global emissions. CO2 is produced mainly in the aerobic stage of wastewater purification and is a consequence of activated sludge activity. Although the roles of activated sludge components in the purification process have been studied quite well, their quantitative contribution to CO2 emissions is still unknown. The emission of CO2 caused by prokaryotes and eukaryotes over the course of a year (taking into account subsequent seasons) in model sequencing batch reactors (SBR) is presented in this study. In this work, for the first time, we aimed to quantify this contribution of eukaryotic organisms to total CO2 emissions during the WWTP process. It is of the order of several or more ppm. The contribution of CO2 produced by different components of activated sludge in WWTPs can improve estimation of the emissions of GHGs in this area of human activity.
format: application/pdf
format: text/html
creator: Katarzyna Jaromin-Gleń
creator: Roman Babko
creator: Tatiana Kuzmina
creator: Yaroslav Danko
creator: Grzegorz Łagód
creator: Cezary Polakowski
creator: Joanna Szulżyk-Cieplak
creator: Andrzej Bieganowski
subject: Agricultural Science
subject: Climate Change Biology
description: doi:10.7717/peerj.9325
publisher: PeerJ Inc.
rights: © 2020 Jaromin-Gleń et al.
abstract: Reduction of the greenhouse effect is primarily associated with the reduction of greenhouse gas (GHG) emissions. Carbon dioxide (CO2) is one of the gases that increases the greenhouse effect - it is responsible for about half of the greenhouse effect. Significant sources of CO2 are wastewater treatment plants (WWTPs) and waste management, with about 3% contribution to global emissions. CO2 is produced mainly in the aerobic stage of wastewater purification and is a consequence of activated sludge activity. Although the roles of activated sludge components in the purification process have been studied quite well, their quantitative contribution to CO2 emissions is still unknown. The emission of CO2 caused by prokaryotes and eukaryotes over the course of a year (taking into account subsequent seasons) in model sequencing batch reactors (SBR) is presented in this study. In this work, for the first time, we aimed to quantify this contribution of eukaryotic organisms to total CO2 emissions during the WWTP process. It is of the order of several or more ppm. The contribution of CO2 produced by different components of activated sludge in WWTPs can improve estimation of the emissions of GHGs in this area of human activity.
bibliographic citation: Jaromin-Gleń et al. (2020) Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process. PeerJ 8:e9325 https://doi.org/10.7717/peerj.9325
date submitted: 2019-12-03
date accepted: 2020-05-18
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jaromin-Gleń
  given name: Katarzyna
author list: Agent
  family name: Babko
  given name: Roman
author list: Agent
  family name: Kuzmina
  given name: Tatiana
author list: Agent
  family name: Danko
  given name: Yaroslav
author list: Agent
  family name: Łagód
  given name: Grzegorz
author list: Agent
  family name: Polakowski
  given name: Cezary
author list: Agent
  family name: Szulżyk-Cieplak
  given name: Joanna
author list: Agent
  family name: Bieganowski
  given name: Andrzej
doi: 10.7717/peerj.9325
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: © 2020 Jaromin-Gleń et al.
attribution name: Jaromin-Gleń et al.

Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China
type: item
type: AcademicArticle
description: Given their complexity, targeted care and management of different areas and tree species are necessary for enhancing the natural regeneration of forests. Thus, an understanding of changes in the overstory and understory is essential for ensuring successful regeneration. Promoting the natural regeneration of Larix principis-rupprechtii plantations is considered challenging; indeed, regional sustainable development through natural regeneration of many stands has often been considered unattainable. Here, we studied several plots with varying extents of regeneration to identify the most important factors that affect regeneration. The plots were divided into three forest types based on the number of regenerating plants. For each type of plot, we measured various factors that might potentially affect regeneration. Representational difference analysis was used to identify the most important factors >9% contribution). Based on these factors, multiple corrections were made to construct a structural equation model of topography, stand structure, soil properties and litter to identify the most important factors driving variation in regeneration. Positive correlations were detected between regeneration with diameter at breast height (0.21) and litter thickness (0.57). Regeneration was negatively correlated with soil (−0.54) and slope (−0.48). Additionally, the number of regenerating plants and the height of regenerating plants were strongly positively correlated. However, there was no significant relationship between regeneration and litter accumulation, stand density, altitude, average tree height, total P and total N. Overall, our study showed that key factors for promoting natural regeneration include appropriate litter thickness, strong parent trees, a gentle slope and sufficient quantities of soil nutrients. Moreover, our findings provide a reference for the design of effective management and restoration plans.
format: application/pdf
format: text/html
creator: Wenjun Liang
creator: Xi Wei
subject: Ecology
subject: Ecosystem Science
subject: Plant Science
subject: Forestry
description: doi:10.7717/peerj.9339
publisher: PeerJ Inc.
rights: © 2020 Liang and Wei
abstract: Given their complexity, targeted care and management of different areas and tree species are necessary for enhancing the natural regeneration of forests. Thus, an understanding of changes in the overstory and understory is essential for ensuring successful regeneration. Promoting the natural regeneration of Larix principis-rupprechtii plantations is considered challenging; indeed, regional sustainable development through natural regeneration of many stands has often been considered unattainable. Here, we studied several plots with varying extents of regeneration to identify the most important factors that affect regeneration. The plots were divided into three forest types based on the number of regenerating plants. For each type of plot, we measured various factors that might potentially affect regeneration. Representational difference analysis was used to identify the most important factors >9% contribution). Based on these factors, multiple corrections were made to construct a structural equation model of topography, stand structure, soil properties and litter to identify the most important factors driving variation in regeneration. Positive correlations were detected between regeneration with diameter at breast height (0.21) and litter thickness (0.57). Regeneration was negatively correlated with soil (−0.54) and slope (−0.48). Additionally, the number of regenerating plants and the height of regenerating plants were strongly positively correlated. However, there was no significant relationship between regeneration and litter accumulation, stand density, altitude, average tree height, total P and total N. Overall, our study showed that key factors for promoting natural regeneration include appropriate litter thickness, strong parent trees, a gentle slope and sufficient quantities of soil nutrients. Moreover, our findings provide a reference for the design of effective management and restoration plans.
bibliographic citation: Liang et al. (2020) Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China. PeerJ 8:e9339 https://doi.org/10.7717/peerj.9339
date submitted: 2020-02-17
date accepted: 2020-05-20
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Wenjun
author list: Agent
  family name: Wei
  given name: Xi
doi: 10.7717/peerj.9339
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 Liang and Wei
attribution name: Liang and Wei

Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China
type: item
type: AcademicArticle
description: Endophytic fungi have been emerged as fruitful resources for producing structurally fascinating and biologically active secondary metabolites. However, endophytic fungi from medicinal plants of Qinling Mountains–the most important natural climatic boundary between the subtropical and warm temperate zones of China with an astonishingly high level of biodiversity–have rarely been explored as potential sources of novel fungal species and active secondary metabolites. In this study, a total of 371 fungal colonies were successfully isolated from 510 tissue segments of the medicinal Tupistra chinensis Baker collected from Qinling Mountains, China. Roots of T. chinensis Baker are used as a folk medicine to ameliorate pharyngitis and treat rheumatic diseases. A total of 100 representative morphotype strains were identified according to ITS rDNA sequence analyses and were grouped into three phyla (Ascomycota, Basidiomycota, Mucoromycota), seven classes (Dothideomycetes, Sordariomycetes, Eurotiomycetes, Microbotryomycetes, Agaricomycetes, Leotiomycetes, Mortierellomycetes), and at least 35 genera. The genera of Collectotrichum (IF, 29.92%), Fusarium (IF, 8.36%), Aspergillus (IF, 8.09%), and Dactylonectria (IF, 5.39%) were most frequently isolated from the tissues of T. chinensis Baker. The Species Richness Index (S, 65) and the Shannon-Wiener Index (H′, 3.7914) indicated that T. chinensis Baker harbored abundant fungal resources. Moreover, five isolates were potential new taxa because of low similarity of ITS sequences ranged from 95.09%∼96.61%. Fifteen out of 100 endophytic fungal ethyl acetate extracts exhibited inhibitory activities against at least one pathogenic bacterium or fungus. Two important lead compounds produced by two stains (F8047 and F8075) with high antimicrobial activities were identified using high performance liquid chromatography (HPLC) and ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC–QTOF MS) analyses. In addi…
format: application/pdf
format: text/html
creator: Chao An
creator: Saijian Ma
creator: Xinwei Shi
creator: Wenjiao Xue
creator: Chen Liu
creator: Hao Ding
subject: Biodiversity
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.9342
publisher: PeerJ Inc.
rights: © 2020 An et al.
abstract: Endophytic fungi have been emerged as fruitful resources for producing structurally fascinating and biologically active secondary metabolites. However, endophytic fungi from medicinal plants of Qinling Mountains–the most important natural climatic boundary between the subtropical and warm temperate zones of China with an astonishingly high level of biodiversity–have rarely been explored as potential sources of novel fungal species and active secondary metabolites. In this study, a total of 371 fungal colonies were successfully isolated from 510 tissue segments of the medicinal Tupistra chinensis Baker collected from Qinling Mountains, China. Roots of T. chinensis Baker are used as a folk medicine to ameliorate pharyngitis and treat rheumatic diseases. A total of 100 representative morphotype strains were identified according to ITS rDNA sequence analyses and were grouped into three phyla (Ascomycota, Basidiomycota, Mucoromycota), seven classes (Dothideomycetes, Sordariomycetes, Eurotiomycetes, Microbotryomycetes, Agaricomycetes, Leotiomycetes, Mortierellomycetes), and at least 35 genera. The genera of Collectotrichum (IF, 29.92%), Fusarium (IF, 8.36%), Aspergillus (IF, 8.09%), and Dactylonectria (IF, 5.39%) were most frequently isolated from the tissues of T. chinensis Baker. The Species Richness Index (S, 65) and the Shannon-Wiener Index (H′, 3.7914) indicated that T. chinensis Baker harbored abundant fungal resources. Moreover, five isolates were potential new taxa because of low similarity of ITS sequences ranged from 95.09%∼96.61%. Fifteen out of 100 endophytic fungal ethyl acetate extracts exhibited inhibitory activities against at least one pathogenic bacterium or fungus. Two important lead compounds produced by two stains (F8047 and F8075) with high antimicrobial activities were identified using high performance liquid chromatography (HPLC) and ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC–QTOF MS) analyses. In addi…
bibliographic citation: An et al. (2020) Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China. PeerJ 8:e9342 https://doi.org/10.7717/peerj.9342
date submitted: 2019-08-30
date accepted: 2020-05-21
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: An
  given name: Chao
author list: Agent
  family name: Ma
  given name: Saijian
author list: Agent
  family name: Shi
  given name: Xinwei
author list: Agent
  family name: Xue
  given name: Wenjiao
author list: Agent
  family name: Liu
  given name: Chen
author list: Agent
  family name: Ding
  given name: Hao
doi: 10.7717/peerj.9342
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 An et al.
attribution name: An et al.

Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Increasing bodies of evidence reveal that targeting a programmed cell death protein 1 (PD-1) monoclonal antibody is a promising immunotherapy for lung adenocarcinoma. Although PD receptor ligand 1 (PDL1) expression is widely recognized as the most powerful predictive biomarker for anti-PD-1 therapy, its regulatory mechanisms in lung adenocarcinoma remain unclear. Therefore, we conducted this study to explore differentially expressed genes (DEGs) and elucidate the regulatory mechanism of PDL1 in lung adenocarcinoma. Methods The GSE99995 data set was obtained from the Gene Expression Omnibus (GEO) database. Patients with and without PDL1 expression were divided into PDL1-positive and PDL1-negative groups, respectively. DEGs were screened using R. The Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed using the Database for Annotation, Visualization and Integrated Discovery. Protein–protein interaction (PPI) networks of DEGs was visualized using Cytoscape, and the MNC algorithm was applied to screen hub genes. A survival analysis involving Gene Expression Profiling Interactive Analysis was used to verify the GEO results. Mutation characteristics of the hub genes were further analyzed in a combined study of five datasets in The Cancer Genome Atlas (TCGA) database. Results In total, 869 DEGs were identified, 387 in the PDL1-positive group and 482 in the PDL1-negative group. GO and KEGG analysis results of the PDL1-positive group mainly exhibited enrichment of biological processes and pathways related to cell adhesion and the peroxisome proliferators-activated receptors (PPAR) signaling pathway, whereas biological process and pathways associated with cell division and repair were mainly enriched in the PDL1-negative group. The top 10 hub genes were screened during the PPI network analysis. Notably, survival analysis revealed BRCA1, mainly involved in cell cycle and DNA damage responses, to be a novel prognostic indicato…
format: application/pdf
format: text/html
creator: Xiaoguang Qi
creator: Chunyan Qi
creator: Xindan Kang
creator: Yi Hu
creator: Weidong Han
subject: Bioinformatics
subject: Immunology
subject: Oncology
subject: Respiratory Medicine
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.9362
publisher: PeerJ Inc.
rights: © 2020 Qi et al.
abstract: Background Increasing bodies of evidence reveal that targeting a programmed cell death protein 1 (PD-1) monoclonal antibody is a promising immunotherapy for lung adenocarcinoma. Although PD receptor ligand 1 (PDL1) expression is widely recognized as the most powerful predictive biomarker for anti-PD-1 therapy, its regulatory mechanisms in lung adenocarcinoma remain unclear. Therefore, we conducted this study to explore differentially expressed genes (DEGs) and elucidate the regulatory mechanism of PDL1 in lung adenocarcinoma. Methods The GSE99995 data set was obtained from the Gene Expression Omnibus (GEO) database. Patients with and without PDL1 expression were divided into PDL1-positive and PDL1-negative groups, respectively. DEGs were screened using R. The Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed using the Database for Annotation, Visualization and Integrated Discovery. Protein–protein interaction (PPI) networks of DEGs was visualized using Cytoscape, and the MNC algorithm was applied to screen hub genes. A survival analysis involving Gene Expression Profiling Interactive Analysis was used to verify the GEO results. Mutation characteristics of the hub genes were further analyzed in a combined study of five datasets in The Cancer Genome Atlas (TCGA) database. Results In total, 869 DEGs were identified, 387 in the PDL1-positive group and 482 in the PDL1-negative group. GO and KEGG analysis results of the PDL1-positive group mainly exhibited enrichment of biological processes and pathways related to cell adhesion and the peroxisome proliferators-activated receptors (PPAR) signaling pathway, whereas biological process and pathways associated with cell division and repair were mainly enriched in the PDL1-negative group. The top 10 hub genes were screened during the PPI network analysis. Notably, survival analysis revealed BRCA1, mainly involved in cell cycle and DNA damage responses, to be a novel prognostic indicato…
bibliographic citation: Qi et al. (2020) Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma. PeerJ 8:e9362 https://doi.org/10.7717/peerj.9362
date submitted: 2020-02-14
date accepted: 2020-05-25
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qi
  given name: Xiaoguang
author list: Agent
  family name: Qi
  given name: Chunyan
author list: Agent
  family name: Kang
  given name: Xindan
author list: Agent
  family name: Hu
  given name: Yi
author list: Agent
  family name: Han
  given name: Weidong
doi: 10.7717/peerj.9362
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 Qi et al.
attribution name: Qi et al.

Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice
type: item
type: AcademicArticle
description: Noise induced hearing loss (NIHL) is accompanied by a reduction of cochlear hair cells and spiral ganglion neurons. Different approaches have been applied to prevent noise induced apoptosis / necrosis. Physical intervention is one technique currently under investigation. Specific wavelengths within the near-infrared light (NIR)-spectrum are known to influence cytochrome-c-oxidase activity, which leads in turn to a decrease in apoptotic mechanisms. It has been shown recently that NIR can significantly decrease the cochlear hair cell loss if applied daily for 12 days after a noise exposure. However, it is still unclear if a single NIR-treatment, just before a noise exposure, could induce similar protective effects. Therefore, the present study was conducted to investigate the effect of a single NIR-pre-treatment aimed at preventing or limiting NIHL. The cochleae of adult NMRI-mice were pre-treated with NIR-light (808 nm, 120 mW) for 5, 10, 20, 30 or 40 minutes via the external ear canal. All animals were noised exposed immediately after the pre-treatment by broad band noise (5–20 kHz) for 30 minutes at 115 dB SPL. Frequency specific ABR-recordings to determine auditory threshold shift were carried out before the pre-treatment and two weeks after the noise exposure. The amplitude increase for wave IV and cochlear hair cell loss were determined. A further group of similar mice was noise exposed only and served as a control for the NIR pre-exposed groups. Two weeks after noise exposure, the ABR threshold shifts of NIR-treated animals were significantly lower (p < 0.05) than those of the control animals. The significance was at three frequencies for the 5-minute pre-treatment group and across the entire frequency range for all other treatment groups. Due to NIR light, the amplitude of wave four deteriorates significantly less after noise exposure than in controls. The NIR pre-treatment had no effect on the loss of outer hair cells, which was just as high with or without N…
format: application/pdf
format: text/html
creator: Dietmar Basta
creator: Moritz Gröschel
creator: Ira Strübing
creator: Patrick Boyle
creator: Felix Fröhlich
creator: Arne Ernst
creator: Rainer Seidl
subject: Neuroscience
subject: Neurology
subject: Otorhinolaryngology
description: doi:10.7717/peerj.9384
publisher: PeerJ Inc.
rights: © 2020 Basta et al.
abstract: Noise induced hearing loss (NIHL) is accompanied by a reduction of cochlear hair cells and spiral ganglion neurons. Different approaches have been applied to prevent noise induced apoptosis / necrosis. Physical intervention is one technique currently under investigation. Specific wavelengths within the near-infrared light (NIR)-spectrum are known to influence cytochrome-c-oxidase activity, which leads in turn to a decrease in apoptotic mechanisms. It has been shown recently that NIR can significantly decrease the cochlear hair cell loss if applied daily for 12 days after a noise exposure. However, it is still unclear if a single NIR-treatment, just before a noise exposure, could induce similar protective effects. Therefore, the present study was conducted to investigate the effect of a single NIR-pre-treatment aimed at preventing or limiting NIHL. The cochleae of adult NMRI-mice were pre-treated with NIR-light (808 nm, 120 mW) for 5, 10, 20, 30 or 40 minutes via the external ear canal. All animals were noised exposed immediately after the pre-treatment by broad band noise (5–20 kHz) for 30 minutes at 115 dB SPL. Frequency specific ABR-recordings to determine auditory threshold shift were carried out before the pre-treatment and two weeks after the noise exposure. The amplitude increase for wave IV and cochlear hair cell loss were determined. A further group of similar mice was noise exposed only and served as a control for the NIR pre-exposed groups. Two weeks after noise exposure, the ABR threshold shifts of NIR-treated animals were significantly lower (p < 0.05) than those of the control animals. The significance was at three frequencies for the 5-minute pre-treatment group and across the entire frequency range for all other treatment groups. Due to NIR light, the amplitude of wave four deteriorates significantly less after noise exposure than in controls. The NIR pre-treatment had no effect on the loss of outer hair cells, which was just as high with or without N…
bibliographic citation: Basta et al. (2020) Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice. PeerJ 8:e9384 https://doi.org/10.7717/peerj.9384
date submitted: 2020-01-07
date accepted: 2020-05-28
issued: 2020-06-17
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Basta
  given name: Dietmar
author list: Agent
  family name: Gröschel
  given name: Moritz
author list: Agent
  family name: Strübing
  given name: Ira
author list: Agent
  family name: Boyle
  given name: Patrick
author list: Agent
  family name: Fröhlich
  given name: Felix
author list: Agent
  family name: Ernst
  given name: Arne
author list: Agent
  family name: Seidl
  given name: Rainer
doi: 10.7717/peerj.9384
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-06-17
copyright: ©2020 Basta et al.
attribution name: Basta et al.

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