PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Comparative characterization of biochars produced at three selected pyrolysis temperatures from common woody and herbaceous waste streams
items: Marine biodiversity research in the Ryukyu Islands, Japan: current status and trends
items: Do the regular annual extreme water level changes affect the seasonal appearance of Anabaena in Poyang Lake?
items: Comparison of long-term kidney functions after radical nephrectomy and simple nephrectomy
items: The prevalence of Pseudomonas aeruginosa and multidrug resistant Pseudomonas aeruginosa in healthy captive ophidian
items: Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii)
items: An experimental study on the early diagnosis of traumatic brain injury in rabbits based on a noncontact and portable system
items: Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis
items: Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana
items: Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods

Comparative characterization of biochars produced at three selected pyrolysis temperatures from common woody and herbaceous waste streams
type: item
type: AcademicArticle
description: Biochar, the product of biomass pyrolysis, has been explored as a soil amendment and carbon capture vessel. Recent literature has aligned biochar as a novel sorbent for a host of environmental contaminants. Through the variation of pyrolysis conditions, biochars can be engineered to have qualities desirable in sorbents whilst maintaining their agronomic benefits. This study focuses on identifying the effects that feedstock type and process temperature have on biochar characteristics which may in turn shed light on their potential environmental applications. Using this approach, six biochars were created from two waste biomasses. The biochars exhibited wide ranges of pH (5.6–11.1), surface area (16.2–397.4 m2/g), electrical conductivity (19–2,826 µS/cm), fixed carbon (72–97%), heavy metal and polycyclic aromatic hydrocarbons (PAHs). Statistically significant trends (P < 0.05) in biochar characteristics dependent upon increasing pyrolysis temperature and feedstock type were identified. Arsenic (>13 mg/kg), chromium (>93 mg/kg), copper (>143 mg/kg) and PAH (>6 mg/kg) concentrations presented themselves as obstacles to land application in a small number of biochars with respects to International Biochar Initiative (IBI) guidelines. However, it was demonstrated that these could be eliminated through employing pyrolysis processes which encompass higher temperatures (>500 °C) and ensuring the use of contaminant-free feedstocks. The variation in surface areas, carbonized fractions and surface functional groups achieved suggest that using the correct feedstock and process, biochar could be produced in Victoria (Australia) from common organic waste streams to the ends of acting as a sorbent, soil enhancer, and a waste management strategy.
format: application/pdf
format: text/html
creator: Matthew Askeland
creator: Bradley Clarke
creator: Jorge Paz-Ferreiro
subject: Soil Science
subject: Natural Resource Management
description: doi:10.7717/peerj.6784
publisher: PeerJ Inc.
rights: © 2019 Askeland et al.
abstract: Biochar, the product of biomass pyrolysis, has been explored as a soil amendment and carbon capture vessel. Recent literature has aligned biochar as a novel sorbent for a host of environmental contaminants. Through the variation of pyrolysis conditions, biochars can be engineered to have qualities desirable in sorbents whilst maintaining their agronomic benefits. This study focuses on identifying the effects that feedstock type and process temperature have on biochar characteristics which may in turn shed light on their potential environmental applications. Using this approach, six biochars were created from two waste biomasses. The biochars exhibited wide ranges of pH (5.6–11.1), surface area (16.2–397.4 m2/g), electrical conductivity (19–2,826 µS/cm), fixed carbon (72–97%), heavy metal and polycyclic aromatic hydrocarbons (PAHs). Statistically significant trends (P < 0.05) in biochar characteristics dependent upon increasing pyrolysis temperature and feedstock type were identified. Arsenic (>13 mg/kg), chromium (>93 mg/kg), copper (>143 mg/kg) and PAH (>6 mg/kg) concentrations presented themselves as obstacles to land application in a small number of biochars with respects to International Biochar Initiative (IBI) guidelines. However, it was demonstrated that these could be eliminated through employing pyrolysis processes which encompass higher temperatures (>500 °C) and ensuring the use of contaminant-free feedstocks. The variation in surface areas, carbonized fractions and surface functional groups achieved suggest that using the correct feedstock and process, biochar could be produced in Victoria (Australia) from common organic waste streams to the ends of acting as a sorbent, soil enhancer, and a waste management strategy.
bibliographic citation: Askeland et al. (2019) Comparative characterization of biochars produced at three selected pyrolysis temperatures from common woody and herbaceous waste streams. PeerJ 7:e6784 https://doi.org/10.7717/peerj.6784
date submitted: 2019-01-02
date accepted: 2019-03-14
issued: 2019-04-15
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Askeland
  given name: Matthew
author list: Agent
  family name: Clarke
  given name: Bradley
author list: Agent
  family name: Paz-Ferreiro
  given name: Jorge
doi: 10.7717/peerj.6784
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-15
copyright: ©2019 Askeland et al.
attribution name: Askeland et al.

Marine biodiversity research in the Ryukyu Islands, Japan: current status and trends
type: item
type: AcademicArticle
description: Marine biodiversity and derived ecosystem services are critical to the healthy functioning of marine ecosystems, and to human economic and societal well-being. Thus, an understanding of marine biodiversity in different ecosystems is necessary for their conservation and management. Coral reefs in particular are noted for their high levels of biodiversity, and among the world’s coral reefs, the subtropical Ryukyu Islands (RYS; also known as the Nansei Islands) in Japan have been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of English language scientific literature in the Web of Science (WoS; 1995–2017) on six selected representative taxa spanning protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate a need to address ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), particularly sub-regions away from marine research stations. Second, we compared the numbers of English language scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAR), Great Barrier Reef (GBR), and the Red Sea (RES). As expected, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, rese…
format: application/pdf
format: text/html
creator: James Davis Reimer
creator: Piera Biondi
creator: Yee Wah Lau
creator: Giovanni Diego Masucci
creator: Xuan Hoa Nguyen
creator: Maria E.A. Santos
creator: Hin Boo Wee
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
description: doi:10.7717/peerj.6532
publisher: PeerJ Inc.
rights: © 2019 Reimer et al.
abstract: Marine biodiversity and derived ecosystem services are critical to the healthy functioning of marine ecosystems, and to human economic and societal well-being. Thus, an understanding of marine biodiversity in different ecosystems is necessary for their conservation and management. Coral reefs in particular are noted for their high levels of biodiversity, and among the world’s coral reefs, the subtropical Ryukyu Islands (RYS; also known as the Nansei Islands) in Japan have been shown to harbor very high levels of marine biodiversity. This study provides an overview of the state of marine biodiversity research in the RYS. First, we examined the amount of English language scientific literature in the Web of Science (WoS; 1995–2017) on six selected representative taxa spanning protists to vertebrates across six geographic sub-regions in the RYS. Our results show clear taxonomic and sub-region bias, with research on Pisces, Cnidaria, and Crustacea to be much more common than on Dinoflagellata, Echinodermata, and Mollusca. Such research was more commonly conducted in sub-regions with larger human populations (Okinawa, Yaeyama). Additional analyses with the Ocean Biogeographic Information System (OBIS) records show that within sub-regions, records are concentrated in areas directly around marine research stations and institutes (if present), further showing geographical bias within sub-regions. While not surprising, the results indicate a need to address ‘understudied’ taxa in ‘understudied sub-regions’ (Tokara, Miyako, Yakutane, Amami Oshima), particularly sub-regions away from marine research stations. Second, we compared the numbers of English language scientific papers on eight ecological topics for the RYS with numbers from selected major coral reef regions of the world; the Caribbean (CAR), Great Barrier Reef (GBR), and the Red Sea (RES). As expected, the numbers for all topics in the RYS were well below numbers from all other regions, yet within this disparity, rese…
bibliographic citation: Reimer et al. (2019) Marine biodiversity research in the Ryukyu Islands, Japan: current status and trends. PeerJ 7:e6532 https://doi.org/10.7717/peerj.6532
date submitted: 2018-07-10
date accepted: 2019-01-27
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Reimer
  given name: James Davis
author list: Agent
  family name: Biondi
  given name: Piera
author list: Agent
  family name: Lau
  given name: Yee Wah
author list: Agent
  family name: Masucci
  given name: Giovanni Diego
author list: Agent
  family name: Nguyen
  given name: Xuan Hoa
author list: Agent
  family name: Santos
  given name: Maria E.A.
author list: Agent
  family name: Wee
  given name: Hin Boo
doi: 10.7717/peerj.6532
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: ©2019 Reimer et al.
attribution name: Reimer et al.

Do the regular annual extreme water level changes affect the seasonal appearance of Anabaena in Poyang Lake?
type: item
type: AcademicArticle
description: Background Poyang Lake is an ecosystem experiencing annual variations in water level of up to 14 m. Water level changes were 8.03 and 11.22 m, respectively, in the years 2013 and 2014. The biomass and heterocyst frequency of Anabaena increased in the summers of recent years. Methods A weekly to bi-weekly monitoring from June to November 2013 and 2014 was set up to explain the variations of Anabaena appearance in different phases of the water level. Results Anabaena was present in the lake throughout the year. The average relative biomass of Anabaena in the present study was over 40%, being most abundant in summer. The average heterocyst frequency was 0.23% in 2013 and 0.76% in 2014. Correlation analysis indicated a positive trend of Anabaena biomass with water temperature and water level and a negative one with total nitrogen (TN), which is the reason for the increase of heterocyst frequency in 2013 and 2014. Heterocyst frequency of Anabaena was positively correlated with water temperature, water level and PO4-P, and negatively with dissolved inorganic nitrogen (DIN/DIP), NO3-N and TN. Moreover, water temperature and DIN/DIP were significantly correlated with water level, indicating that water level changes have a direct effect on Anabaena and heterocyst formation in Poyang Lake. Conclusions The results of this study support the hypothesis that increasing biomass and heterocyst formation of Anabaena can be primarily caused by seasonal changes of the water level in Poyang Lake.
format: application/pdf
format: text/html
creator: Kuimei Qian
creator: Martin Dokulil
creator: Yuwei Chen
subject: Ecology
subject: Freshwater Biology
subject: Ecohydrology
description: doi:10.7717/peerj.6608
publisher: PeerJ Inc.
rights: © 2019 Qian et al.
abstract: Background Poyang Lake is an ecosystem experiencing annual variations in water level of up to 14 m. Water level changes were 8.03 and 11.22 m, respectively, in the years 2013 and 2014. The biomass and heterocyst frequency of Anabaena increased in the summers of recent years. Methods A weekly to bi-weekly monitoring from June to November 2013 and 2014 was set up to explain the variations of Anabaena appearance in different phases of the water level. Results Anabaena was present in the lake throughout the year. The average relative biomass of Anabaena in the present study was over 40%, being most abundant in summer. The average heterocyst frequency was 0.23% in 2013 and 0.76% in 2014. Correlation analysis indicated a positive trend of Anabaena biomass with water temperature and water level and a negative one with total nitrogen (TN), which is the reason for the increase of heterocyst frequency in 2013 and 2014. Heterocyst frequency of Anabaena was positively correlated with water temperature, water level and PO4-P, and negatively with dissolved inorganic nitrogen (DIN/DIP), NO3-N and TN. Moreover, water temperature and DIN/DIP were significantly correlated with water level, indicating that water level changes have a direct effect on Anabaena and heterocyst formation in Poyang Lake. Conclusions The results of this study support the hypothesis that increasing biomass and heterocyst formation of Anabaena can be primarily caused by seasonal changes of the water level in Poyang Lake.
bibliographic citation: Qian et al. (2019) Do the regular annual extreme water level changes affect the seasonal appearance of Anabaena in Poyang Lake?. PeerJ 7:e6608 https://doi.org/10.7717/peerj.6608
date submitted: 2018-11-23
date accepted: 2019-02-02
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qian
  given name: Kuimei
author list: Agent
  family name: Dokulil
  given name: Martin
author list: Agent
  family name: Chen
  given name: Yuwei
doi: 10.7717/peerj.6608
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: © 2019 Qian et al.
attribution name: Qian et al.

Comparison of long-term kidney functions after radical nephrectomy and simple nephrectomy
type: item
type: AcademicArticle
description: Objective To determine if there is a difference in proceeding to CKD between patients who had undergone radical nephrectomy (RN) and simple nephrectomy (SN) for different indications by comparing the short- and long-term renal function. Materials and Methods We retrospectively analyzed the records of all patients who underwent nephrectomy (either for malign or benign indications) in our clinic between January 2007 and September 2017. The patients were divided into 2 groups according the type of surgery: 1) Radical nephrectomy Group, 2) Simple Nephrectomy Group. Renal function was evaluated with Glomerular Filtration Rate (GFR) calculated using the MDRD formula. Results A total of 276 patients were included in the study. There were 202 patients in RN Group and 74 patients in SN Group. The mean age of the patients in RN Group and SN Group were age 59,2 ± 11,5 and 49,9 ± 15,1 years, respectively (p = 0.001). GFR levels of patients in RN Group versus SN Group were as follows: Preoperative period: 84.9 vs. 81 mL/min/1.73 m2; postoperative 1st day: 60.5 vs. 84.4 mL/min/1.73 m2, postoperative 1st month 58.9 vs. 76 mL/min/1.73 m2, postoperative 1st year: 59.5 vs. 74.1 mL/min/1.73 m2; at last control 60.3 and 76.1 mL/min/1.73 m2. While preoperative GFR was found to be similar in two groups (p = 0.26), postoperative GFR values were found to be significantly lower in Group RN (p < 0.001). In comparison of the decrease in GFR in two groups at last follow-up, significantly higher decrease was observed in RN Group, 29% vs. 6%, (p < 0.05). Conclusion The decrease in GFR exists more common and intensive after RN compared to SN. In long-term, compensation mechanisms that develop after sudden nephron loss like radical nephrectomy deteriorates kidney function more than gradual nephron loss as in benign etiologies which indicates simple nephrectomy.
format: application/pdf
format: text/html
creator: Erkan Olcucuoglu
creator: Senol Tonyali
creator: Sedat Tastemur
creator: Yusuf Kasap
creator: Mehmet Emin Sirin
creator: Eymen Gazel
creator: Esin Olcucuoglu
creator: Oner Odabas
creator: Can Ates
creator: Mahmut Taha Olcucu
subject: Nephrology
subject: Surgery and Surgical Specialties
subject: Urology
description: doi:10.7717/peerj.6701
publisher: PeerJ Inc.
rights: © 2019 Olcucuoglu et al.
abstract: Objective To determine if there is a difference in proceeding to CKD between patients who had undergone radical nephrectomy (RN) and simple nephrectomy (SN) for different indications by comparing the short- and long-term renal function. Materials and Methods We retrospectively analyzed the records of all patients who underwent nephrectomy (either for malign or benign indications) in our clinic between January 2007 and September 2017. The patients were divided into 2 groups according the type of surgery: 1) Radical nephrectomy Group, 2) Simple Nephrectomy Group. Renal function was evaluated with Glomerular Filtration Rate (GFR) calculated using the MDRD formula. Results A total of 276 patients were included in the study. There were 202 patients in RN Group and 74 patients in SN Group. The mean age of the patients in RN Group and SN Group were age 59,2 ± 11,5 and 49,9 ± 15,1 years, respectively (p = 0.001). GFR levels of patients in RN Group versus SN Group were as follows: Preoperative period: 84.9 vs. 81 mL/min/1.73 m2; postoperative 1st day: 60.5 vs. 84.4 mL/min/1.73 m2, postoperative 1st month 58.9 vs. 76 mL/min/1.73 m2, postoperative 1st year: 59.5 vs. 74.1 mL/min/1.73 m2; at last control 60.3 and 76.1 mL/min/1.73 m2. While preoperative GFR was found to be similar in two groups (p = 0.26), postoperative GFR values were found to be significantly lower in Group RN (p < 0.001). In comparison of the decrease in GFR in two groups at last follow-up, significantly higher decrease was observed in RN Group, 29% vs. 6%, (p < 0.05). Conclusion The decrease in GFR exists more common and intensive after RN compared to SN. In long-term, compensation mechanisms that develop after sudden nephron loss like radical nephrectomy deteriorates kidney function more than gradual nephron loss as in benign etiologies which indicates simple nephrectomy.
bibliographic citation: Olcucuoglu et al. (2019) Comparison of long-term kidney functions after radical nephrectomy and simple nephrectomy. PeerJ 7:e6701 https://doi.org/10.7717/peerj.6701
date submitted: 2018-10-08
date accepted: 2019-03-01
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Olcucuoglu
  given name: Erkan
author list: Agent
  family name: Tonyali
  given name: Senol
author list: Agent
  family name: Tastemur
  given name: Sedat
author list: Agent
  family name: Kasap
  given name: Yusuf
author list: Agent
  family name: Sirin
  given name: Mehmet Emin
author list: Agent
  family name: Gazel
  given name: Eymen
author list: Agent
  family name: Olcucuoglu
  given name: Esin
author list: Agent
  family name: Odabas
  given name: Oner
author list: Agent
  family name: Ates
  given name: Can
author list: Agent
  family name: Olcucu
  given name: Mahmut Taha
doi: 10.7717/peerj.6701
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: ©2019 Olcucuoglu et al.
attribution name: Olcucuoglu et al.

The prevalence of Pseudomonas aeruginosa and multidrug resistant Pseudomonas aeruginosa in healthy captive ophidian
type: item
type: AcademicArticle
description: Background Snakes are globally considered as pet animals, and millions of ophidians are bred in captivity. Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium that can act as an opportunistic pathogen of man and animals and is frequently present in the oral and cloacal microbiota of healthy ophidians. It can cause severe clinical diseases and often shows antibiotic resistance. The aim of this study was to evaluate the prevalence and antibiotic resistance profiles of P. aeruginosa isolated from the cloacal microbiota of a large population sample of healthy captive ophidians and to evaluate the statistical associations with farming conditions. Methods A total of 419 cloacal swabs were collected from snakes belonging to the Boidae (n = 45), Colubridae (n = 48) and Pythonidae (n = 326) families and inoculated onto complete culture media. Food, water and bedding samples were also analyzed. The antimicrobial susceptibility of P. aeruginosa isolates was evaluated through the Kirby-Bauer agar diffusion test. Statistical analyses were performed with the chi-square test. Results The prevalence of P. aeruginosa was 59.9%, and 35.5% of these strains were multidrug resistant (MDR). The prevalence of MDR P. aeruginosa was significantly higher in adult samples than in young samples, and widespread resistance to Cephalosporins, Polymyxins and Sulfonamides was observed. Statistically significant differences in the prevalence of P. aeruginosa were observed depending on the farm size and snake family. Feeding thawed prey was associated with a higher P. aeruginosa and MDR P. aeruginosa prevalence. Moreover, snakes fed home-raised prey had a significantly higher MDR P. aeruginosa prevalence than snakes fed commercially available feed. Less frequent terrarium cleaning was associated with a higher MDR P. aeruginosa prevalence. On the other hand, snake reproductive status was not significantly associated with P. aeruginosa or MDR P. aeruginosa prevalence. All food, water and bed…
format: application/pdf
format: text/html
creator: Andrea Sala
creator: Francesco Di Ianni
creator: Igor Pelizzone
creator: Mara Bertocchi
creator: Davide Santospirito
creator: Francesco Rogato
creator: Sara Flisi
creator: Costanza Spadini
creator: Tiziano Iemmi
creator: Emanuele Moggia
creator: Enrico Parmigiani
creator: Sandro Cavirani
creator: Simone Taddei
creator: Clotilde S. Cabassi
subject: Microbiology
subject: Veterinary Medicine
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.6706
publisher: PeerJ Inc.
rights: © 2019 Sala et al.
abstract: Background Snakes are globally considered as pet animals, and millions of ophidians are bred in captivity. Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium that can act as an opportunistic pathogen of man and animals and is frequently present in the oral and cloacal microbiota of healthy ophidians. It can cause severe clinical diseases and often shows antibiotic resistance. The aim of this study was to evaluate the prevalence and antibiotic resistance profiles of P. aeruginosa isolated from the cloacal microbiota of a large population sample of healthy captive ophidians and to evaluate the statistical associations with farming conditions. Methods A total of 419 cloacal swabs were collected from snakes belonging to the Boidae (n = 45), Colubridae (n = 48) and Pythonidae (n = 326) families and inoculated onto complete culture media. Food, water and bedding samples were also analyzed. The antimicrobial susceptibility of P. aeruginosa isolates was evaluated through the Kirby-Bauer agar diffusion test. Statistical analyses were performed with the chi-square test. Results The prevalence of P. aeruginosa was 59.9%, and 35.5% of these strains were multidrug resistant (MDR). The prevalence of MDR P. aeruginosa was significantly higher in adult samples than in young samples, and widespread resistance to Cephalosporins, Polymyxins and Sulfonamides was observed. Statistically significant differences in the prevalence of P. aeruginosa were observed depending on the farm size and snake family. Feeding thawed prey was associated with a higher P. aeruginosa and MDR P. aeruginosa prevalence. Moreover, snakes fed home-raised prey had a significantly higher MDR P. aeruginosa prevalence than snakes fed commercially available feed. Less frequent terrarium cleaning was associated with a higher MDR P. aeruginosa prevalence. On the other hand, snake reproductive status was not significantly associated with P. aeruginosa or MDR P. aeruginosa prevalence. All food, water and bed…
bibliographic citation: Sala et al. (2019) The prevalence of Pseudomonas aeruginosa and multidrug resistant Pseudomonas aeruginosa in healthy captive ophidian. PeerJ 7:e6706 https://doi.org/10.7717/peerj.6706
date submitted: 2018-06-29
date accepted: 2019-03-02
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sala
  given name: Andrea
author list: Agent
  family name: Di Ianni
  given name: Francesco
author list: Agent
  family name: Pelizzone
  given name: Igor
author list: Agent
  family name: Bertocchi
  given name: Mara
author list: Agent
  family name: Santospirito
  given name: Davide
author list: Agent
  family name: Rogato
  given name: Francesco
author list: Agent
  family name: Flisi
  given name: Sara
author list: Agent
  family name: Spadini
  given name: Costanza
author list: Agent
  family name: Iemmi
  given name: Tiziano
author list: Agent
  family name: Moggia
  given name: Emanuele
author list: Agent
  family name: Parmigiani
  given name: Enrico
author list: Agent
  family name: Cavirani
  given name: Sandro
author list: Agent
  family name: Taddei
  given name: Simone
author list: Agent
  family name: Cabassi
  given name: Clotilde S.
doi: 10.7717/peerj.6706
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: ©2019 Sala et al.
attribution name: Sala et al.

Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii)
type: item
type: AcademicArticle
description: Objective Sturgeons are considered living fossils, and have a very high conservation and economic value. Studies on the molecular mechanism of sturgeon gonadal development and sex differentiation would not only aid in understanding vertebrate sex determination but also benefit sturgeon aquaculture. Piwi-interacting RNAs (piRNAs) have been shown to function in germline or gonadal development. In this study, we performed small RNA deep sequencing and microarray hybridization to identify potential sturgeon piRNAs. Methods Male and female sturgeon gonads were collected and used for small RNA sequencing on an Illumina HiSeq platform with the validation of piRNA expression by microarray chip. The program Bowtie and k-mer scheme were performed to filter small RNA reads and discover potential sturgeon piRNAs. A known piRNA database, the coding sequence (CDS), 5′ and 3′ untranslated region (UTR) database of the A. Schrenckii transcriptome, Gene Ontology (GO) database and KEGG pathway database were searched subsequently to analyze the potential bio-function of sturgeon piRNAs. Results A total of 875,679 putative sturgeon piRNAs were obtained, including 93 homologous to known piRNAs and hundreds showing sex-specific and sex-biased expression. Further analysis showed that they are predominant in both the ovaries and testes and those with a sex-specific expression pattern are nearly equally distribution between sexes. This may imply a relevant role in sturgeon gonadal development. KEGG pathway and GO annotation analyses indicated that they may be related to sturgeon reproductive processes. Conclusion Our study provides the first insights into the gonadal piRNAs in a sturgeon species and should serve as a useful resource for further elucidation of the gene regulation involved in the sex differentiation of vertebrates. These results should also facilitate the technological development of early sex identification in sturgeon aquaculture.
format: application/pdf
format: text/html
creator: Lihong Yuan
creator: Linmiao Li
creator: Xiujuan Zhang
creator: Haiying Jiang
creator: Jinping Chen
subject: Aquaculture, Fisheries and Fish Science
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
description: doi:10.7717/peerj.6709
publisher: PeerJ Inc.
rights: © 2019 Yuan et al.
abstract: Objective Sturgeons are considered living fossils, and have a very high conservation and economic value. Studies on the molecular mechanism of sturgeon gonadal development and sex differentiation would not only aid in understanding vertebrate sex determination but also benefit sturgeon aquaculture. Piwi-interacting RNAs (piRNAs) have been shown to function in germline or gonadal development. In this study, we performed small RNA deep sequencing and microarray hybridization to identify potential sturgeon piRNAs. Methods Male and female sturgeon gonads were collected and used for small RNA sequencing on an Illumina HiSeq platform with the validation of piRNA expression by microarray chip. The program Bowtie and k-mer scheme were performed to filter small RNA reads and discover potential sturgeon piRNAs. A known piRNA database, the coding sequence (CDS), 5′ and 3′ untranslated region (UTR) database of the A. Schrenckii transcriptome, Gene Ontology (GO) database and KEGG pathway database were searched subsequently to analyze the potential bio-function of sturgeon piRNAs. Results A total of 875,679 putative sturgeon piRNAs were obtained, including 93 homologous to known piRNAs and hundreds showing sex-specific and sex-biased expression. Further analysis showed that they are predominant in both the ovaries and testes and those with a sex-specific expression pattern are nearly equally distribution between sexes. This may imply a relevant role in sturgeon gonadal development. KEGG pathway and GO annotation analyses indicated that they may be related to sturgeon reproductive processes. Conclusion Our study provides the first insights into the gonadal piRNAs in a sturgeon species and should serve as a useful resource for further elucidation of the gene regulation involved in the sex differentiation of vertebrates. These results should also facilitate the technological development of early sex identification in sturgeon aquaculture.
bibliographic citation: Yuan et al. (2019) Identification and differential expression of piRNAs in the gonads of Amur sturgeon (Acipenser schrenckii). PeerJ 7:e6709 https://doi.org/10.7717/peerj.6709
date submitted: 2018-10-08
date accepted: 2019-03-04
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yuan
  given name: Lihong
author list: Agent
  family name: Li
  given name: Linmiao
author list: Agent
  family name: Zhang
  given name: Xiujuan
author list: Agent
  family name: Jiang
  given name: Haiying
author list: Agent
  family name: Chen
  given name: Jinping
doi: 10.7717/peerj.6709
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: ©2019 Yuan et al.
attribution name: Yuan et al.

An experimental study on the early diagnosis of traumatic brain injury in rabbits based on a noncontact and portable system
type: item
type: AcademicArticle
description: Closed cerebral hemorrhage (CCH) is a common symptom in traumatic brain injury (TBI) patients who suffer intracranial hemorrhage with the dura mater remaining intact. The diagnosis of CCH patients prior to hospitalization and in the early stage of the disease can help patients get earlier treatments that improve outcomes. In this study, a noncontact, portable system for early TBI-induced CCH detection was constructed that measures the magnetic induction phase shift (MIPS), which is associated with the mean brain conductivity caused by the ratio between the liquid (blood/CSF and the intracranial tissues) change. To evaluate the performance of this system, a rabbit CCH model with two severity levels was established based on the horizontal biological impactor BIM-II, whose feasibility was verified by computed tomography images of three sections and three serial slices. There were two groups involved in the experiments (group 1 with 10 TBI rabbits were simulated by hammer hit with air pressure of 600 kPa by BIM-II and group 2 with 10 TBI rabbits were simulated with 650 kPa). The MIPS values of the two groups were obtained within 30 min before and after injury. In group 1, the MIPS values showed a constant downward trend with a minimum value of −11.17 ± 2.91° at the 30th min after 600 kPa impact by BIM-II. After the 650 kPa impact, the MIPS values in group 2 showed a constant downward trend until the 25th min, with a minimum value of −16.81 ± 2.10°. Unlike group 1, the MIPS values showed an upward trend after that point. Before the injury, the MIPS values in both group 1 and group 2 did not obviously change within the 30 min measurement. Using a support vector machine at the same time point after injury, the classification accuracy of the two types of severity was shown to be beyond 90%. Combined with CCH pathological mechanisms, this system can not only achieve the detection of early functional changes in CCH but can also distinguish different severities of CCH.
format: application/pdf
format: text/html
creator: Jun Yang
creator: Hui Zhao
creator: Gen Li
creator: Qisheng Ran
creator: Jingbo Chen
creator: Zelin Bai
creator: Gui Jin
creator: Jian Sun
creator: Jia Xu
creator: Mingxin Qin
creator: Mingsheng Chen
subject: Bioengineering
subject: Biophysics
subject: Radiology and Medical Imaging
subject: Computational Science
description: doi:10.7717/peerj.6717
publisher: PeerJ Inc.
rights: © 2019 Yang et al.
abstract: Closed cerebral hemorrhage (CCH) is a common symptom in traumatic brain injury (TBI) patients who suffer intracranial hemorrhage with the dura mater remaining intact. The diagnosis of CCH patients prior to hospitalization and in the early stage of the disease can help patients get earlier treatments that improve outcomes. In this study, a noncontact, portable system for early TBI-induced CCH detection was constructed that measures the magnetic induction phase shift (MIPS), which is associated with the mean brain conductivity caused by the ratio between the liquid (blood/CSF and the intracranial tissues) change. To evaluate the performance of this system, a rabbit CCH model with two severity levels was established based on the horizontal biological impactor BIM-II, whose feasibility was verified by computed tomography images of three sections and three serial slices. There were two groups involved in the experiments (group 1 with 10 TBI rabbits were simulated by hammer hit with air pressure of 600 kPa by BIM-II and group 2 with 10 TBI rabbits were simulated with 650 kPa). The MIPS values of the two groups were obtained within 30 min before and after injury. In group 1, the MIPS values showed a constant downward trend with a minimum value of −11.17 ± 2.91° at the 30th min after 600 kPa impact by BIM-II. After the 650 kPa impact, the MIPS values in group 2 showed a constant downward trend until the 25th min, with a minimum value of −16.81 ± 2.10°. Unlike group 1, the MIPS values showed an upward trend after that point. Before the injury, the MIPS values in both group 1 and group 2 did not obviously change within the 30 min measurement. Using a support vector machine at the same time point after injury, the classification accuracy of the two types of severity was shown to be beyond 90%. Combined with CCH pathological mechanisms, this system can not only achieve the detection of early functional changes in CCH but can also distinguish different severities of CCH.
bibliographic citation: Yang et al. (2019) An experimental study on the early diagnosis of traumatic brain injury in rabbits based on a noncontact and portable system. PeerJ 7:e6717 https://doi.org/10.7717/peerj.6717
date submitted: 2018-12-20
date accepted: 2019-03-05
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yang
  given name: Jun
author list: Agent
  family name: Zhao
  given name: Hui
author list: Agent
  family name: Li
  given name: Gen
author list: Agent
  family name: Ran
  given name: Qisheng
author list: Agent
  family name: Chen
  given name: Jingbo
author list: Agent
  family name: Bai
  given name: Zelin
author list: Agent
  family name: Jin
  given name: Gui
author list: Agent
  family name: Sun
  given name: Jian
author list: Agent
  family name: Xu
  given name: Jia
author list: Agent
  family name: Qin
  given name: Mingxin
author list: Agent
  family name: Chen
  given name: Mingsheng
doi: 10.7717/peerj.6717
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: © 2019 Yang et al.
attribution name: Yang et al.

Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis
type: item
type: AcademicArticle
description: The anthrax toxin is a virulence factor produced by the bacterium Bacillus anthracis. Transcription of anthrax toxin genes is controlled by the transcription factor AtxA. Thus, AtxA is thought to be a key factor for the pathogenicity of B. anthracis. Despite its important role in B. anthracis infection, the molecular mechanism by which AtxA controls expression of anthrax toxin remains unclear. This study aimed to characterize the molecular mechanism of AtxA-mediated regulation of protective antigen (PA), a component of anthrax toxin encoded by the pagA gene. First, the interaction between the upstream region of pagA and AtxA was evaluated in vivo by constructing a transcriptional fusion of the upstream region with an auxotrophic marker. The results showed that (i) the upstream region of pagA suppressed transcription of the downstream gene and (ii) AtxA recovered suppressed transcription. Second, in vitro analysis using a gel mobility shift assay was performed to evaluate binding specificity of the AtxA–DNA interaction. The result showed sequence-independent binding of AtxA to DNA. Taken together, our findings suggest that the expression of PA was suppressed by the upstream region of pagA and that an interaction of AtxA and the upstream region releases the suppression.
format: application/pdf
format: text/html
creator: Kochi Toyomane
creator: Yoshikazu Furuta
creator: Daisuke Fujikura
creator: Hideaki Higashi
subject: Genetics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6718
publisher: PeerJ Inc.
rights: © 2019 Toyomane et al.
abstract: The anthrax toxin is a virulence factor produced by the bacterium Bacillus anthracis. Transcription of anthrax toxin genes is controlled by the transcription factor AtxA. Thus, AtxA is thought to be a key factor for the pathogenicity of B. anthracis. Despite its important role in B. anthracis infection, the molecular mechanism by which AtxA controls expression of anthrax toxin remains unclear. This study aimed to characterize the molecular mechanism of AtxA-mediated regulation of protective antigen (PA), a component of anthrax toxin encoded by the pagA gene. First, the interaction between the upstream region of pagA and AtxA was evaluated in vivo by constructing a transcriptional fusion of the upstream region with an auxotrophic marker. The results showed that (i) the upstream region of pagA suppressed transcription of the downstream gene and (ii) AtxA recovered suppressed transcription. Second, in vitro analysis using a gel mobility shift assay was performed to evaluate binding specificity of the AtxA–DNA interaction. The result showed sequence-independent binding of AtxA to DNA. Taken together, our findings suggest that the expression of PA was suppressed by the upstream region of pagA and that an interaction of AtxA and the upstream region releases the suppression.
bibliographic citation: Toyomane et al. (2019) Upstream sequence-dependent suppression and AtxA-dependent activation of protective antigens in Bacillus anthracis. PeerJ 7:e6718 https://doi.org/10.7717/peerj.6718
date submitted: 2018-10-26
date accepted: 2019-03-05
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Toyomane
  given name: Kochi
author list: Agent
  family name: Furuta
  given name: Yoshikazu
author list: Agent
  family name: Fujikura
  given name: Daisuke
author list: Agent
  family name: Higashi
  given name: Hideaki
doi: 10.7717/peerj.6718
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: © 2019 Toyomane et al.
attribution name: Toyomane et al.

Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana
type: item
type: AcademicArticle
description: Genome sequencing has uncovered tremendous sequence variation within and between species. In plants, in addition to large variations in genome size, a great deal of sequence polymorphism is also evident in several large multi-gene families, including those involved in the ubiquitin-26S proteasome protein degradation system. However, the biological function of this sequence variation is yet not clear. In this work, we explicitly demonstrated a single origin of retroposed Arabidopsis Skp1-Like (ASK) genes using an improved phylogenetic analysis. Taking advantage of the 1,001 genomes project, we here provide several lines of polymorphism evidence showing both adaptive and degenerative evolutionary processes in ASK genes. Yeast two-hybrid quantitative interaction assays further suggested that recent neutral changes in the ASK2 coding sequence weakened its interactions with some F-box proteins. The trend that highly polymorphic upstream regions of ASK1 yield high levels of expression implied negative expression regulation of ASK1 by an as-yet-unknown transcriptional suppression mechanism, which may contribute to the polymorphic roles of Skp1-CUL1-F-box complexes. Taken together, this study provides new evolutionary evidence to guide future functional genomic studies of SCF-mediated protein ubiquitylation.
format: application/pdf
format: text/html
creator: Zhihua Hua
creator: Zhenyu Gao
subject: Biochemistry
subject: Bioinformatics
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.6740
publisher: PeerJ Inc.
rights: © 2019 Hua and Gao
abstract: Genome sequencing has uncovered tremendous sequence variation within and between species. In plants, in addition to large variations in genome size, a great deal of sequence polymorphism is also evident in several large multi-gene families, including those involved in the ubiquitin-26S proteasome protein degradation system. However, the biological function of this sequence variation is yet not clear. In this work, we explicitly demonstrated a single origin of retroposed Arabidopsis Skp1-Like (ASK) genes using an improved phylogenetic analysis. Taking advantage of the 1,001 genomes project, we here provide several lines of polymorphism evidence showing both adaptive and degenerative evolutionary processes in ASK genes. Yeast two-hybrid quantitative interaction assays further suggested that recent neutral changes in the ASK2 coding sequence weakened its interactions with some F-box proteins. The trend that highly polymorphic upstream regions of ASK1 yield high levels of expression implied negative expression regulation of ASK1 by an as-yet-unknown transcriptional suppression mechanism, which may contribute to the polymorphic roles of Skp1-CUL1-F-box complexes. Taken together, this study provides new evolutionary evidence to guide future functional genomic studies of SCF-mediated protein ubiquitylation.
bibliographic citation: Hua et al. (2019) Adaptive and degenerative evolution of the S-Phase Kinase-Associated Protein 1-Like family in Arabidopsis thaliana. PeerJ 7:e6740 https://doi.org/10.7717/peerj.6740
date submitted: 2019-02-08
date accepted: 2019-03-07
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hua
  given name: Zhihua
author list: Agent
  family name: Gao
  given name: Zhenyu
doi: 10.7717/peerj.6740
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: © 2019 Hua and Gao
attribution name: Hua and Gao

Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods
type: item
type: AcademicArticle
description: Background The application of an appropriate extraction method is a relevant factor for the success of all molecular studies. Methods Seven different DNA extraction methods suitable for high-throughput DNA sequencing with very small arthropods were compared by applying nine different protocols: three silica gel based spin methods, two cetyltrimethyl ammonium bromide (CTAB) based ones (one with an additional silica membrane), a protein precipitation method and a method based on a chelating resin (applying different protocols). The quantity (concentration) and quality (degradation, contamination, polymerase chain reaction (PCR) and sequencing success) of the extracted DNA as well as the costs, preparation times, user friendliness, and required supplies were compared across these methods. To assess the DNA quantity, two different DNA concentration measurements were applied. Additionally, the effect of varying amounts of starting material (different body sizes), variable lysis temperatures and mixing during DNA extraction was evaluated. Results Although low DNA concentrations were measured for all methods, the results showed that—with the exception of two methods—the PCR success was 100%. However, other parameters show vast differences. The time taken to perform DNA extraction varied from 20 min to 2.5 h (Chelex vs. CTAB) and the costs from 0.02 to 3.46 € (Chelex vs. QIAamp kit) per sample. High quality genomic DNA was only gained from four methods. Results of DNA quantity measurements further indicated that some devices cannot deal with small amounts of DNA and show variant results. Discussion In conclusion, using Chelex (chelating resin) turned out as a rapid, low-cost method which can provide high quality DNA for different kinds of molecular investigations.
format: application/pdf
format: text/html
creator: Andrea Lienhard
creator: Sylvia Schäffer
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.6753
publisher: PeerJ Inc.
rights: © 2019 Lienhard and Schäffer
abstract: Background The application of an appropriate extraction method is a relevant factor for the success of all molecular studies. Methods Seven different DNA extraction methods suitable for high-throughput DNA sequencing with very small arthropods were compared by applying nine different protocols: three silica gel based spin methods, two cetyltrimethyl ammonium bromide (CTAB) based ones (one with an additional silica membrane), a protein precipitation method and a method based on a chelating resin (applying different protocols). The quantity (concentration) and quality (degradation, contamination, polymerase chain reaction (PCR) and sequencing success) of the extracted DNA as well as the costs, preparation times, user friendliness, and required supplies were compared across these methods. To assess the DNA quantity, two different DNA concentration measurements were applied. Additionally, the effect of varying amounts of starting material (different body sizes), variable lysis temperatures and mixing during DNA extraction was evaluated. Results Although low DNA concentrations were measured for all methods, the results showed that—with the exception of two methods—the PCR success was 100%. However, other parameters show vast differences. The time taken to perform DNA extraction varied from 20 min to 2.5 h (Chelex vs. CTAB) and the costs from 0.02 to 3.46 € (Chelex vs. QIAamp kit) per sample. High quality genomic DNA was only gained from four methods. Results of DNA quantity measurements further indicated that some devices cannot deal with small amounts of DNA and show variant results. Discussion In conclusion, using Chelex (chelating resin) turned out as a rapid, low-cost method which can provide high quality DNA for different kinds of molecular investigations.
bibliographic citation: Lienhard et al. (2019) Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods. PeerJ 7:e6753 https://doi.org/10.7717/peerj.6753
date submitted: 2018-08-23
date accepted: 2019-03-09
issued: 2019-04-12
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Lienhard
  given name: Andrea
author list: Agent
  family name: Schäffer
  given name: Sylvia
doi: 10.7717/peerj.6753
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-04-12
copyright: © 2019 Lienhard and Schäffer
attribution name: Lienhard and Schäffer

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