PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Experimental lung injury induces cerebral cytokine mRNA production in pigs
items: Assessment of the effects of ischaemia/ hypoxia on angiogenesis in rat myofascial trigger points using colour Doppler flow imaging
items: Oncolytic effects of the recombinant Newcastle disease virus, rAF-IL12, against colon cancer cells in vitro and in tumor-challenged NCr-Foxn1nu nude mice
items: Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico
items: Insights into dog owner perspectives on risks, benefits, and nutritional value of raw diets compared to commercial cooked diets
items: Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods
items: Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
items: Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot
items: Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet
items: Pro-inflammatory effect of obesity on rats with burn wounds

Experimental lung injury induces cerebral cytokine mRNA production in pigs
type: item
type: AcademicArticle
description: Background Acute respiratory distress syndrome (ARDS) is an important disease with a high incidence among patients admitted to intensive care units. Over the last decades, the survival of critically ill patients has improved; however, cognitive deficits are among the long-term sequelae. We hypothesize that acute lung injury leads to upregulation of cerebral cytokine synthesis. Methods After approval of the institutional and animal care committee, 20 male pigs were randomized to one of three groups: (1) Lung injury by oleic acid injection (OAI), (2) ventilation only (CTR) or (3) untreated. We compared neuronal numbers, proportion of neurons with markers for apoptosis, activation state of Iba-1 stained microglia cells and cerebral mRNA levels of different cytokines between the groups 18 hours after onset of lung injury. Results We found an increase in hippocampal TNFalpha (p < 0.05) and IL-6 (p < 0.05) messenger RNA (mRNA) in the OAI compared to untreated group as well as higher hippocampal IL-6 mRNA compared to control (p < 0.05). IL-8 and IL-1beta mRNA showed no differences between the groups. We found histologic markers for beginning apoptosis in OAI compared to untreated (p < 0.05) and more active microglia cells in OAI and CTR compared to untreated (p < 0.001 each). Conclusion Hippocampal cytokine transcription increases within 18 hours after the induction of acute lung injury with histological evidence of neuronal damage. It remains to be elucidated if increased cytokine mRNA synthesis plays a role in the cognitive decline observed in survivors of ARDS.
format: application/pdf
format: text/html
creator: Jens Kamuf
creator: Andreas Garcia Bardon
creator: Alexander Ziebart
creator: Katrin Frauenknecht
creator: Konstantin Folkert
creator: Johannes Schwab
creator: Robert Ruemmler
creator: Miriam Renz
creator: Denis Cana
creator: Serge C. Thal
creator: Erik K. Hartmann
subject: Cognitive Disorders
subject: Emergency and Critical Care
subject: Neurology
subject: Respiratory Medicine
description: doi:10.7717/peerj.10471
publisher: PeerJ Inc.
rights: © 2020 Kamuf et al.
abstract: Background Acute respiratory distress syndrome (ARDS) is an important disease with a high incidence among patients admitted to intensive care units. Over the last decades, the survival of critically ill patients has improved; however, cognitive deficits are among the long-term sequelae. We hypothesize that acute lung injury leads to upregulation of cerebral cytokine synthesis. Methods After approval of the institutional and animal care committee, 20 male pigs were randomized to one of three groups: (1) Lung injury by oleic acid injection (OAI), (2) ventilation only (CTR) or (3) untreated. We compared neuronal numbers, proportion of neurons with markers for apoptosis, activation state of Iba-1 stained microglia cells and cerebral mRNA levels of different cytokines between the groups 18 hours after onset of lung injury. Results We found an increase in hippocampal TNFalpha (p < 0.05) and IL-6 (p < 0.05) messenger RNA (mRNA) in the OAI compared to untreated group as well as higher hippocampal IL-6 mRNA compared to control (p < 0.05). IL-8 and IL-1beta mRNA showed no differences between the groups. We found histologic markers for beginning apoptosis in OAI compared to untreated (p < 0.05) and more active microglia cells in OAI and CTR compared to untreated (p < 0.001 each). Conclusion Hippocampal cytokine transcription increases within 18 hours after the induction of acute lung injury with histological evidence of neuronal damage. It remains to be elucidated if increased cytokine mRNA synthesis plays a role in the cognitive decline observed in survivors of ARDS.
bibliographic citation: Kamuf et al. (2020) Experimental lung injury induces cerebral cytokine mRNA production in pigs. PeerJ 8:e10471 https://doi.org/10.7717/peerj.10471
date submitted: 2020-04-07
date accepted: 2020-11-11
issued: 2020-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kamuf
  given name: Jens
author list: Agent
  family name: Garcia Bardon
  given name: Andreas
author list: Agent
  family name: Ziebart
  given name: Alexander
author list: Agent
  family name: Frauenknecht
  given name: Katrin
author list: Agent
  family name: Folkert
  given name: Konstantin
author list: Agent
  family name: Schwab
  given name: Johannes
author list: Agent
  family name: Ruemmler
  given name: Robert
author list: Agent
  family name: Renz
  given name: Miriam
author list: Agent
  family name: Cana
  given name: Denis
author list: Agent
  family name: Thal
  given name: Serge C.
author list: Agent
  family name: Hartmann
  given name: Erik K.
doi: 10.7717/peerj.10471
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-09
copyright: ©2020 Kamuf et al.
attribution name: Kamuf et al.

Assessment of the effects of ischaemia/ hypoxia on angiogenesis in rat myofascial trigger points using colour Doppler flow imaging
type: item
type: AcademicArticle
description: Background & Aims Myofascial pain syndrome (MPS) is a common non-articular disorder of the musculoskeletal system that is characterized by the presence of myofascial trigger points (MTrPs). Despite the high prevalence of MPS, its pathogenesis, which induces the onset and maintenance of MTrPs, is still not completely understood. To date, no studies have investigated the changes in the biochemical milieu caused by ischaemia/hypoxia in the MTrP regions of muscle that are proposed in the integrated hypothesis. Therefore, this study investigated whether ischaemic/hypoxic conditions participate in the formation of active MTrPs and affect angiogenesis using colour Doppler flow imaging (CDFI). Methods Twenty-five Sprague-Dawley rats were randomly divided into a model group and a normal control group. A model of active MTrPs was established by a blunt strike combined with eccentric exercise. Enzyme-linked immunosorbent assays (ELISAs) were employed to detect the levels of HIF-1α and VEGF. Microvessel density (MVD) was evaluated using immunohistochemistry. CDFI was applied to observe the blood flow signals in the MTrPs, which were classified into four grades based on their strengths. Results Compared with the control group, the active MTrP group exhibited significantly higher HIF-1α and VEGF levels and MVD values. These differences were accompanied by increased blood flow signals. In the active MTrP group, the blood flow signal grade was positively correlated with the MVD (P < 0.05) and independently correlated with the VEGF level (P < 0.05) but was not correlated with the expression of HIF-1α (P > 0.05). Conclusion Ischaemic/hypoxic conditions may be involved in the formation of MTrPs. CDFI is useful for detection of the features of angiogenesis in or surrounding MTrPs via assessment of blood flow signals.
format: application/pdf
format: text/html
creator: Fangyan Jiang
creator: Shuangcheng Yu
creator: Haiqing Su
creator: Shangyong Zhu
subject: Anesthesiology and Pain Management
subject: Cardiology
subject: Hematology
subject: Radiology and Medical Imaging
description: doi:10.7717/peerj.10481
publisher: PeerJ Inc.
rights: © 2020 Jiang et al.
abstract: Background & Aims Myofascial pain syndrome (MPS) is a common non-articular disorder of the musculoskeletal system that is characterized by the presence of myofascial trigger points (MTrPs). Despite the high prevalence of MPS, its pathogenesis, which induces the onset and maintenance of MTrPs, is still not completely understood. To date, no studies have investigated the changes in the biochemical milieu caused by ischaemia/hypoxia in the MTrP regions of muscle that are proposed in the integrated hypothesis. Therefore, this study investigated whether ischaemic/hypoxic conditions participate in the formation of active MTrPs and affect angiogenesis using colour Doppler flow imaging (CDFI). Methods Twenty-five Sprague-Dawley rats were randomly divided into a model group and a normal control group. A model of active MTrPs was established by a blunt strike combined with eccentric exercise. Enzyme-linked immunosorbent assays (ELISAs) were employed to detect the levels of HIF-1α and VEGF. Microvessel density (MVD) was evaluated using immunohistochemistry. CDFI was applied to observe the blood flow signals in the MTrPs, which were classified into four grades based on their strengths. Results Compared with the control group, the active MTrP group exhibited significantly higher HIF-1α and VEGF levels and MVD values. These differences were accompanied by increased blood flow signals. In the active MTrP group, the blood flow signal grade was positively correlated with the MVD (P < 0.05) and independently correlated with the VEGF level (P < 0.05) but was not correlated with the expression of HIF-1α (P > 0.05). Conclusion Ischaemic/hypoxic conditions may be involved in the formation of MTrPs. CDFI is useful for detection of the features of angiogenesis in or surrounding MTrPs via assessment of blood flow signals.
bibliographic citation: Jiang et al. (2020) Assessment of the effects of ischaemia/ hypoxia on angiogenesis in rat myofascial trigger points using colour Doppler flow imaging. PeerJ 8:e10481 https://doi.org/10.7717/peerj.10481
date submitted: 2020-06-25
date accepted: 2020-11-12
issued: 2020-12-09
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Fangyan
author list: Agent
  family name: Yu
  given name: Shuangcheng
author list: Agent
  family name: Su
  given name: Haiqing
author list: Agent
  family name: Zhu
  given name: Shangyong
doi: 10.7717/peerj.10481
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-09
copyright: ©2020 Jiang et al.
attribution name: Jiang et al.

Oncolytic effects of the recombinant Newcastle disease virus, rAF-IL12, against colon cancer cells in vitro and in tumor-challenged NCr-Foxn1nu nude mice
type: item
type: AcademicArticle
description: Colon cancer remains one of the main cancers causing death in men and women worldwide as certain colon cancer subtypes are resistant to conventional treatments and the development of new cancer therapies remains elusive. Alternative modalities such as the use of viral-based therapeutic cancer vaccine is still limited, with only the herpes simplex virus (HSV) expressing granulocyte-macrophage colony- stimulating factor (GM-CSF) or talimogene laherparepvec (T-Vec) being approved in the USA and Europe so far. Therefore, it is imperative to continue the search for a new treatment modality. This current study evaluates a combinatorial therapy between the oncolytic Newcastle disease virus (NDV) and interleukin-12 (IL-12) cytokine as a potential therapeutic vaccine to the current anti-cancer drugs. Several in vitro analyses such as MTT assay, Annexin V/FITC flow cytometry, and cell cycle assay were performed to evaluate the cytotoxicity effect of recombinant NDV, rAF-IL12. Meanwhile, serum cytokine, serum biochemical, histopathology of organs and TUNEL assay were carried out to assess the anti-tumoral effects of rAF-IL12 in HT29 tumor-challenged nude mice. The apoptosis mechanism underlying the effect of rAF-IL12 treatment was also investigated using NanoString Gene expression analysis. The recombinant NDV, rAF-IL12 replicated in HT29 colon cancer cells as did its parental virus, AF2240-i. The rAF-IL12 treatment had slightly better cytotoxicity effects towards HT29 cancer cells when compared to the AF2240-i as revealed by the MTT, Annexin V FITC and cell cycle assay. Meanwhile, the 28-day treatment with rAF-IL12 had significantly (p < 0.05) perturbed the growth and progression of HT29 tumor in NCr-Foxn1nu nude mice when compared to the untreated and parental wild-type NDV strain AF2240-i. The rAF-IL12 also modulated the immune system in nude mice by significantly (p < 0.05) increased the level of IL-2, IL-12, and IFN-γ cytokines. Treatment with rAF-IL12 had also significan…
format: application/pdf
format: text/html
creator: Syed Umar Faruq Syed Najmuddin
creator: Zahiah Mohamed Amin
creator: Sheau Wei Tan
creator: Swee Keong Yeap
creator: Jeevanathan Kalyanasundram
creator: Abhimanyu Veerakumarasivam
creator: Soon Choy Chan
creator: Suet Lin Chia
creator: Khatijah Yusoff
creator: Noorjahan Banu Alitheen
subject: Biochemistry
subject: Cell Biology
subject: Virology
subject: Oncology
subject: Histology
description: doi:10.7717/peerj.9761
publisher: PeerJ Inc.
rights: © 2020 Syed Najmuddin et al.
abstract: Colon cancer remains one of the main cancers causing death in men and women worldwide as certain colon cancer subtypes are resistant to conventional treatments and the development of new cancer therapies remains elusive. Alternative modalities such as the use of viral-based therapeutic cancer vaccine is still limited, with only the herpes simplex virus (HSV) expressing granulocyte-macrophage colony- stimulating factor (GM-CSF) or talimogene laherparepvec (T-Vec) being approved in the USA and Europe so far. Therefore, it is imperative to continue the search for a new treatment modality. This current study evaluates a combinatorial therapy between the oncolytic Newcastle disease virus (NDV) and interleukin-12 (IL-12) cytokine as a potential therapeutic vaccine to the current anti-cancer drugs. Several in vitro analyses such as MTT assay, Annexin V/FITC flow cytometry, and cell cycle assay were performed to evaluate the cytotoxicity effect of recombinant NDV, rAF-IL12. Meanwhile, serum cytokine, serum biochemical, histopathology of organs and TUNEL assay were carried out to assess the anti-tumoral effects of rAF-IL12 in HT29 tumor-challenged nude mice. The apoptosis mechanism underlying the effect of rAF-IL12 treatment was also investigated using NanoString Gene expression analysis. The recombinant NDV, rAF-IL12 replicated in HT29 colon cancer cells as did its parental virus, AF2240-i. The rAF-IL12 treatment had slightly better cytotoxicity effects towards HT29 cancer cells when compared to the AF2240-i as revealed by the MTT, Annexin V FITC and cell cycle assay. Meanwhile, the 28-day treatment with rAF-IL12 had significantly (p < 0.05) perturbed the growth and progression of HT29 tumor in NCr-Foxn1nu nude mice when compared to the untreated and parental wild-type NDV strain AF2240-i. The rAF-IL12 also modulated the immune system in nude mice by significantly (p < 0.05) increased the level of IL-2, IL-12, and IFN-γ cytokines. Treatment with rAF-IL12 had also significan…
bibliographic citation: Syed Najmuddin et al. (2020) Oncolytic effects of the recombinant Newcastle disease virus, rAF-IL12, against colon cancer cells in vitro and in tumor-challenged NCr-Foxn1nu nude mice. PeerJ 8:e9761 https://doi.org/10.7717/peerj.9761
date submitted: 2020-05-01
date accepted: 2020-07-28
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Syed Najmuddin
  given name: Syed Umar Faruq
author list: Agent
  family name: Amin
  given name: Zahiah Mohamed
author list: Agent
  family name: Tan
  given name: Sheau Wei
author list: Agent
  family name: Yeap
  given name: Swee Keong
author list: Agent
  family name: Kalyanasundram
  given name: Jeevanathan
author list: Agent
  family name: Veerakumarasivam
  given name: Abhimanyu
author list: Agent
  family name: Chan
  given name: Soon Choy
author list: Agent
  family name: Chia
  given name: Suet Lin
author list: Agent
  family name: Yusoff
  given name: Khatijah
author list: Agent
  family name: Alitheen
  given name: Noorjahan Banu
doi: 10.7717/peerj.9761
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: © 2020 Syed Najmuddin et al.
attribution name: Syed Najmuddin et al.

Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico
type: item
type: AcademicArticle
description: Background Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites. Methods The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation. Results We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.
format: application/pdf
format: text/html
creator: Pablo Suárez-Moo
creator: Araceli Lamelas
creator: Itza Garcia-Bautista
creator: Luis Felipe Barahona-Pérez
creator: Gloria Sandoval-Flores
creator: David Valdes-Lozano
creator: Tanit Toledano-Thompson
creator: Erik Polanco-Lugo
creator: Ruby Valdez-Ojeda
subject: Microbiology
subject: Molecular Biology
subject: Aquatic and Marine Chemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.10339
publisher: PeerJ Inc.
rights: © 2020 Suárez-Moo et al.
abstract: Background Coastal ecosystems are prone to hydrocarbon pollution due to human activities, and this issue has a tremendous impact on the environment, socioeconomic consequences, and represents a hazard to humans. Bioremediation relies on the ability of bacteria to metabolize hydrocarbons with the aim of cleaning up polluted sites. Methods The potential of naturally occurring microbial communities as oil degraders was investigated in Sisal and Progreso, two port locations in the southeast Gulf of Mexico, both with a low level of hydrocarbon pollution. To do so, we determined the diversity and composition of bacterial communities in the marine sediment during the dry and rainy seasons using 16S rRNA sequencing. Functional profile analysis (PICRUTSt2) was used to predict metabolic functions associated with hydrocarbon degradation. Results We found a large bacterial taxonomic diversity, including some genera reported as hydrocarbon-degraders. Analyses of the alpha and beta diversity did not detect significant differences between sites or seasons, suggesting that location, season, and the contamination level detected here do not represent determining factors in the structure of the microbial communities. PICRUTSt2 predicted 10 metabolic functions associated with hydrocarbon degradation. Most bacterial genera with potential hydrocarbon bioremediation activity were generalists likely capable of degrading different hydrocarbon compounds. The bacterial composition and diversity reported here represent an initial attempt to characterize sites with low levels of contamination. This information is crucial for understanding the impact of eventual rises in hydrocarbon pollution.
bibliographic citation: Suárez-Moo et al. (2020) Characterization of sediment microbial communities at two sites with low hydrocarbon pollution in the southeast Gulf of Mexico. PeerJ 8:e10339 https://doi.org/10.7717/peerj.10339
date submitted: 2020-07-27
date accepted: 2020-10-20
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Suárez-Moo
  given name: Pablo
author list: Agent
  family name: Lamelas
  given name: Araceli
author list: Agent
  family name: Garcia-Bautista
  given name: Itza
author list: Agent
  family name: Barahona-Pérez
  given name: Luis Felipe
author list: Agent
  family name: Sandoval-Flores
  given name: Gloria
author list: Agent
  family name: Valdes-Lozano
  given name: David
author list: Agent
  family name: Toledano-Thompson
  given name: Tanit
author list: Agent
  family name: Polanco-Lugo
  given name: Erik
author list: Agent
  family name: Valdez-Ojeda
  given name: Ruby
doi: 10.7717/peerj.10339
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Suárez-Moo et al.
attribution name: Suárez-Moo et al.

Insights into dog owner perspectives on risks, benefits, and nutritional value of raw diets compared to commercial cooked diets
type: item
type: AcademicArticle
description: Background The practice of feeding a raw meat-based diet (RMBD) to dogs is a topic of increasing interest to owners and veterinary professionals alike. Despite the research around the practice, particularly about the risk of nutritional imbalances and microbial contamination, an increasing number of dog owners are adopting a raw diet for their dogs. This study expands the research into owner motivations for feeding RMBDs and cooked diets and asks them their opinions about risk and nutritional value. Methods An anonymized, online, internationally accessible questionnaire was developed to ascertain owner perspectives on the risks, benefits, and nutritional value of commercially prepared and homemade RMBDs as compared with commercially prepared cooked diets (CCDs). Results The questionnaire was completed by 419 dog owners of diverse backgrounds across the world. Of the participants, 25.3% fed RMBDs. Just over 70.0% of all participants had spoken to their veterinarian about their dog’s nutrition. Owners who fed RMBDs ranked their veterinarian’s knowledge lower and their own knowledge of canine nutrition higher than owners who fed CCDs. They rated commercial and homemade RMBDs as highly nutritious 83.5% and 73.6% of the time, respectively, while only 12.5% rated CCDs as highly nutritious. Owners who fed CCDs ranked RMBDs as highly nutritious less often, but also only ranked CCDs as highly nutritious 52.7% of the time. All participants agreed that CCDs were low risk to human health. Owners who fed RMBDs ranked raw diets as highly risky to human or dog health under 20.0% of the time but deemed CCDs risky to animal health over 65.0% of the time. When asked about benefits of raw diets, the most repeated words offered by owners were “health”, “better”, “coat” and “teeth”. The most repeated risks presented were “bacteria”, “nutrition”, “risk” and “Salmonella”. Owners who fed RMBDs tended to use vague terminology like “health” and “better” when asked why they fed a raw diet. Ow…
format: application/pdf
format: text/html
creator: Alysia Empert-Gallegos
creator: Sally Hill
creator: Philippa S. Yam
subject: Veterinary Medicine
subject: Zoology
subject: Nutrition
subject: Public Health
description: doi:10.7717/peerj.10383
publisher: PeerJ Inc.
rights: © 2020 Empert-Gallegos et al.
abstract: Background The practice of feeding a raw meat-based diet (RMBD) to dogs is a topic of increasing interest to owners and veterinary professionals alike. Despite the research around the practice, particularly about the risk of nutritional imbalances and microbial contamination, an increasing number of dog owners are adopting a raw diet for their dogs. This study expands the research into owner motivations for feeding RMBDs and cooked diets and asks them their opinions about risk and nutritional value. Methods An anonymized, online, internationally accessible questionnaire was developed to ascertain owner perspectives on the risks, benefits, and nutritional value of commercially prepared and homemade RMBDs as compared with commercially prepared cooked diets (CCDs). Results The questionnaire was completed by 419 dog owners of diverse backgrounds across the world. Of the participants, 25.3% fed RMBDs. Just over 70.0% of all participants had spoken to their veterinarian about their dog’s nutrition. Owners who fed RMBDs ranked their veterinarian’s knowledge lower and their own knowledge of canine nutrition higher than owners who fed CCDs. They rated commercial and homemade RMBDs as highly nutritious 83.5% and 73.6% of the time, respectively, while only 12.5% rated CCDs as highly nutritious. Owners who fed CCDs ranked RMBDs as highly nutritious less often, but also only ranked CCDs as highly nutritious 52.7% of the time. All participants agreed that CCDs were low risk to human health. Owners who fed RMBDs ranked raw diets as highly risky to human or dog health under 20.0% of the time but deemed CCDs risky to animal health over 65.0% of the time. When asked about benefits of raw diets, the most repeated words offered by owners were “health”, “better”, “coat” and “teeth”. The most repeated risks presented were “bacteria”, “nutrition”, “risk” and “Salmonella”. Owners who fed RMBDs tended to use vague terminology like “health” and “better” when asked why they fed a raw diet. Ow…
bibliographic citation: Empert-Gallegos et al. (2020) Insights into dog owner perspectives on risks, benefits, and nutritional value of raw diets compared to commercial cooked diets. PeerJ 8:e10383 https://doi.org/10.7717/peerj.10383
date submitted: 2020-06-12
date accepted: 2020-10-27
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Empert-Gallegos
  given name: Alysia
author list: Agent
  family name: Hill
  given name: Sally
author list: Agent
  family name: Yam
  given name: Philippa S.
doi: 10.7717/peerj.10383
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: © 2020 Empert-Gallegos et al.
attribution name: Empert-Gallegos et al.

Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods
type: item
type: AcademicArticle
description: Background Existing studies of PLK1 in cervical cancer had several flaws. The methods adopted by those studies of detecting PLK1 expression in cervical cancer were single and there lacks comprehensive evaluation of the clinico-pathological significance of PLK1 in cervical cancer. Methods A total of 303 cervical tissue samples were collected for in-house tissue microarrays. Immunohistochemistry was performed for evaluating PLK1 expression between cervical cancer (including cervical squamous cell carcinoma (CESC) and cervical adenocarcinoma) and non-cancer samples. The Expression Atlas database was searched for querying PLK1 expression in different cervical cancer cell lines and different tissues in the context of pan-cancer. Standard mean difference (SMD) was calculated and the summarized receiver’s operating characteristics (SROC) curves were plotted for integrated tissue microarrays, exterior high-throughput microarrays and RNA sequencing data as further verification. The effect of PLK1 expression on the overall survival, disease-free survival and event-free survival of cervical cancer patients was analyzed through Kaplan Meier survival curves for cervical cancer patients from RNA-seq and GSE44001 datasets. The gene mutation and alteration status of PLK1 in cervical cancer was inspected in COSMIC and cBioPortal databases. Functional enrichment analysis was performed for genes correlated with PLK1 from aggregated RNA-seq and microarrays. Results A total of 963 cervical cancer samples and 178 non-cancer samples were collected from in-house tissue microarrays and exterior microarrays and RNA-seq datasets. The combined expression analysis supported overexpression of PLK1 in CESC, cervical adenocarcinoma and all types of cervical cancer (SMD = 1.59, 95%CI [0.56–2.63]; SMD = 2.99, 95%CI [0.75–5.24]; SMD = 1.57, 95% CI [0.85–2.29]) and the significant power of PLK1 expression in distinguishing CESC or all types of cervical cancer samples from non-cancer samples (AUC = 0.9…
format: application/pdf
format: text/html
creator: Li Gao
creator: Yu-Yan Pang
creator: Xian-Yu Guo
creator: Jing-Jing Zeng
creator: Zhong-Qing Tang
creator: Dan-Dan Xiong
creator: Xia Yang
creator: Ying Li
creator: Fu-Chao Ma
creator: Lin-Jiang Pan
creator: Zhen-Bo Feng
creator: Gang Chen
subject: Computational Biology
subject: Genetics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.10458
publisher: PeerJ Inc.
rights: © 2020 Gao et al.
abstract: Background Existing studies of PLK1 in cervical cancer had several flaws. The methods adopted by those studies of detecting PLK1 expression in cervical cancer were single and there lacks comprehensive evaluation of the clinico-pathological significance of PLK1 in cervical cancer. Methods A total of 303 cervical tissue samples were collected for in-house tissue microarrays. Immunohistochemistry was performed for evaluating PLK1 expression between cervical cancer (including cervical squamous cell carcinoma (CESC) and cervical adenocarcinoma) and non-cancer samples. The Expression Atlas database was searched for querying PLK1 expression in different cervical cancer cell lines and different tissues in the context of pan-cancer. Standard mean difference (SMD) was calculated and the summarized receiver’s operating characteristics (SROC) curves were plotted for integrated tissue microarrays, exterior high-throughput microarrays and RNA sequencing data as further verification. The effect of PLK1 expression on the overall survival, disease-free survival and event-free survival of cervical cancer patients was analyzed through Kaplan Meier survival curves for cervical cancer patients from RNA-seq and GSE44001 datasets. The gene mutation and alteration status of PLK1 in cervical cancer was inspected in COSMIC and cBioPortal databases. Functional enrichment analysis was performed for genes correlated with PLK1 from aggregated RNA-seq and microarrays. Results A total of 963 cervical cancer samples and 178 non-cancer samples were collected from in-house tissue microarrays and exterior microarrays and RNA-seq datasets. The combined expression analysis supported overexpression of PLK1 in CESC, cervical adenocarcinoma and all types of cervical cancer (SMD = 1.59, 95%CI [0.56–2.63]; SMD = 2.99, 95%CI [0.75–5.24]; SMD = 1.57, 95% CI [0.85–2.29]) and the significant power of PLK1 expression in distinguishing CESC or all types of cervical cancer samples from non-cancer samples (AUC = 0.9…
bibliographic citation: Gao et al. (2020) Polo like kinase 1 expression in cervical cancer tissues generated from multiple detection methods. PeerJ 8:e10458 https://doi.org/10.7717/peerj.10458
date submitted: 2020-08-20
date accepted: 2020-11-10
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Li
author list: Agent
  family name: Pang
  given name: Yu-Yan
author list: Agent
  family name: Guo
  given name: Xian-Yu
author list: Agent
  family name: Zeng
  given name: Jing-Jing
author list: Agent
  family name: Tang
  given name: Zhong-Qing
author list: Agent
  family name: Xiong
  given name: Dan-Dan
author list: Agent
  family name: Yang
  given name: Xia
author list: Agent
  family name: Li
  given name: Ying
author list: Agent
  family name: Ma
  given name: Fu-Chao
author list: Agent
  family name: Pan
  given name: Lin-Jiang
author list: Agent
  family name: Feng
  given name: Zhen-Bo
author list: Agent
  family name: Chen
  given name: Gang
doi: 10.7717/peerj.10458
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Gao et al.
attribution name: Gao et al.

Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers
type: item
type: AcademicArticle
description: Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.
format: application/pdf
format: text/html
creator: Zhixin Wang
creator: Yalin Sun
creator: Xinfang Huang
creator: Feng Li
creator: Yuping Liu
creator: Honglian Zhu
creator: Zhengwei Liu
creator: Weidong Ke
subject: Biodiversity
subject: Conservation Biology
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10485
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.
bibliographic citation: Wang et al. (2020) Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers. PeerJ 8:e10485 https://doi.org/10.7717/peerj.10485
date submitted: 2020-07-13
date accepted: 2020-11-12
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Zhixin
author list: Agent
  family name: Sun
  given name: Yalin
author list: Agent
  family name: Huang
  given name: Xinfang
author list: Agent
  family name: Li
  given name: Feng
author list: Agent
  family name: Liu
  given name: Yuping
author list: Agent
  family name: Zhu
  given name: Honglian
author list: Agent
  family name: Liu
  given name: Zhengwei
author list: Agent
  family name: Ke
  given name: Weidong
doi: 10.7717/peerj.10485
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Wang et al.
attribution name: Wang et al.

Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot
type: item
type: AcademicArticle
description: Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants.
format: application/pdf
format: text/html
creator: Ahmed Khadr
creator: Guang-Long Wang
creator: Ya-Hui Wang
creator: Rong-Rong Zhang
creator: Xin-Rui Wang
creator: Zhi-Sheng Xu
creator: Yong-Sheng Tian
creator: Ai-Sheng Xiong
subject: Agricultural Science
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.10492
publisher: PeerJ Inc.
rights: © 2020 Khadr et al.
abstract: Carrot is an important root vegetable crop abundant in bioactive compounds including carotenoids, vitamins, and dietary fibers. Carrot intake and its products are gradually growing owing to its high antioxidant activity. Auxins are a class of plant hormones that control many processes of plant growth and development. Yet, the effects of exogenous application of auxin on lignin biosynthesis and gene expression profiles of lignin-related genes in carrot taproot are still unclear. In order to investigate the effect of exogenous indole-3-butyric acid (IBA) on lignin-related gene profiles, lignin accumulation, anatomical structures and morphological characteristics in carrot taproots, carrots were treated with different concentrations of IBA (0, 50, 100, and 150 µM). The results showed that IBA application significantly improved the growth parameters of carrot. The 100 or 150 µM IBA treatment increased the number and area of xylem vessels, whereas transcript levels of lignin-related genes were restricted, resulting in a decline in lignin content in carrot taproots. The results indicate that taproot development and lignin accumulation may be influenced by the auxin levels within carrot plants.
bibliographic citation: Khadr et al. (2020) Effects of auxin (indole-3-butyric acid) on growth characteristics, lignification, and expression profiles of genes involved in lignin biosynthesis in carrot taproot. PeerJ 8:e10492 https://doi.org/10.7717/peerj.10492
date submitted: 2020-06-05
date accepted: 2020-11-13
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Khadr
  given name: Ahmed
author list: Agent
  family name: Wang
  given name: Guang-Long
author list: Agent
  family name: Wang
  given name: Ya-Hui
author list: Agent
  family name: Zhang
  given name: Rong-Rong
author list: Agent
  family name: Wang
  given name: Xin-Rui
author list: Agent
  family name: Xu
  given name: Zhi-Sheng
author list: Agent
  family name: Tian
  given name: Yong-Sheng
author list: Agent
  family name: Xiong
  given name: Ai-Sheng
doi: 10.7717/peerj.10492
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Khadr et al.
attribution name: Khadr et al.

Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet
type: item
type: AcademicArticle
description: Seagrasses are critical habitats for the recruitment and growth of juvenile penaeid shrimps within estuaries and coastal lagoons. The location of a seagrass bed within the lagoon can determine the value of a particular bed for shrimp populations. Consequently, differences in the abundance of shrimp can be found in seagrasses depending on their location. As shrimp density increases, density-dependent effects on biological parameters are more likely to occur. However, knowledge about density-dependent processes on shrimp populations in nursery habitats remains limited. The present investigation was undertaken to examine the effects of population density on shrimp condition in two selected seagrass beds, located at different distance from a tidal inlet, one 25 km away (distant) and the other 1 km away (nearby), in a subtropical coastal lagoon. The study was based on monthly samplings during one year in Laguna Madre (Mexico), performing a total of 36 shrimp trawls (100 m2 each one) within each seagrass bed (n = 3 trawls per bed per month for 12 months). Shrimp density was related to the proximity to the tidal inlet (higher density was consistently observed in the nearby seagrass bed), which in turn adversely affected the condition of both species studied (Penaeus aztecus and P. duorarum). In this regard, the present study provides the first evidence of density-dependent effects on shrimp condition inhabiting a nursery habitat. Both shrimp species exhibited a negative relationship between condition and shrimp density. However, this pattern differed depending on the proximity to the tidal inlet, suggesting that shrimp populations inhabiting the nearby seagrass bed are exposed to density-dependent effects on condition; whereas, such effects were not detected in the distant seagrass bed. Shrimp density within the distant seagrass bed was probably below carrying capacity, which is suggested by the better shrimp condition observed in that area of the lagoon. Intra and intersp…
format: application/pdf
format: text/html
creator: Zeferino Blanco-Martínez
creator: Roberto Pérez-Castañeda
creator: Jesús Genaro Sánchez-Martínez
creator: Flaviano Benavides-González
creator: Jaime Luis Rábago-Castro
creator: María de la Luz Vázquez-Sauceda
creator: Lorena Garrido-Olvera
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.10496
publisher: PeerJ Inc.
rights: © 2020 Blanco-Martínez et al.
abstract: Seagrasses are critical habitats for the recruitment and growth of juvenile penaeid shrimps within estuaries and coastal lagoons. The location of a seagrass bed within the lagoon can determine the value of a particular bed for shrimp populations. Consequently, differences in the abundance of shrimp can be found in seagrasses depending on their location. As shrimp density increases, density-dependent effects on biological parameters are more likely to occur. However, knowledge about density-dependent processes on shrimp populations in nursery habitats remains limited. The present investigation was undertaken to examine the effects of population density on shrimp condition in two selected seagrass beds, located at different distance from a tidal inlet, one 25 km away (distant) and the other 1 km away (nearby), in a subtropical coastal lagoon. The study was based on monthly samplings during one year in Laguna Madre (Mexico), performing a total of 36 shrimp trawls (100 m2 each one) within each seagrass bed (n = 3 trawls per bed per month for 12 months). Shrimp density was related to the proximity to the tidal inlet (higher density was consistently observed in the nearby seagrass bed), which in turn adversely affected the condition of both species studied (Penaeus aztecus and P. duorarum). In this regard, the present study provides the first evidence of density-dependent effects on shrimp condition inhabiting a nursery habitat. Both shrimp species exhibited a negative relationship between condition and shrimp density. However, this pattern differed depending on the proximity to the tidal inlet, suggesting that shrimp populations inhabiting the nearby seagrass bed are exposed to density-dependent effects on condition; whereas, such effects were not detected in the distant seagrass bed. Shrimp density within the distant seagrass bed was probably below carrying capacity, which is suggested by the better shrimp condition observed in that area of the lagoon. Intra and intersp…
bibliographic citation: Blanco-Martínez et al. (2020) Density-dependent condition of juvenile penaeid shrimps in seagrass-dominated aquatic vegetation beds located at different distance from a tidal inlet. PeerJ 8:e10496 https://doi.org/10.7717/peerj.10496
date submitted: 2020-07-06
date accepted: 2020-11-14
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Blanco-Martínez
  given name: Zeferino
author list: Agent
  family name: Pérez-Castañeda
  given name: Roberto
author list: Agent
  family name: Sánchez-Martínez
  given name: Jesús Genaro
author list: Agent
  family name: Benavides-González
  given name: Flaviano
author list: Agent
  family name: Rábago-Castro
  given name: Jaime Luis
author list: Agent
  family name: Vázquez-Sauceda
  given name: María de la Luz
author list: Agent
  family name: Garrido-Olvera
  given name: Lorena
doi: 10.7717/peerj.10496
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Blanco-Martínez et al.
attribution name: Blanco-Martínez et al.

Pro-inflammatory effect of obesity on rats with burn wounds
type: item
type: AcademicArticle
description: Objective A burn is an inflammatory injury to the skin or other tissue due to contact with thermal, radioactive, electric, or chemical agents. Burn injury is an important cause of disability and death worldwide. Obesity is a significant public health problem, often causing underlying systemic inflammation. Studying the combined impact of burn injuries on obese patients has become critical to the successful treatment of these patients. The aim of this paper is to highlight the effect of inflammation associated with burn injuries on several body weight group in a rat study. Materials and methods Different degrees of obesity and burns were established in rats and divided into a normal weight group, overweight group, obese group, second-degree burn group, third-degree burn group, over-weight second-degree burn group, over-weight third-degree burn group, obese second-degree burn group, and obese third-degree burn group (20 rats per group). Changes in inflammatory factors and growth factor were measured on the 1st, 3rd, 7th and 14th days after burns were inflicted. Results The ELISA test showed that in the unburned control group, MCP-1, IL-1β and TNF-α protein expressions in the obese and over-weight groups were higher than the normal-weight group (P < 0.05). RT-PCR test showed that the expressions of MCP-1, IL-1β and TNF-α genes in the obese group were higher compared to the overweight and normal weight groups (P < 0.05). Three and 7 days after burns were inflicted, the level of VEGF in the normal weight group was higher than the obese group (P < 0.05), however increased VEGF was not observed on days 1 and 14. Conclusion Burn injury and obesity have a mutually synergistic effect on the body’s inflammatory response.
format: application/pdf
format: text/html
creator: Chan Nie
creator: Huiting Yu
creator: Xue Wang
creator: Xiahong Li
creator: Zairong Wei
creator: Xiuquan Shi
subject: Molecular Biology
subject: Dermatology
subject: Internal Medicine
subject: Metabolic Sciences
description: doi:10.7717/peerj.10499
publisher: PeerJ Inc.
rights: © 2020 Nie et al.
abstract: Objective A burn is an inflammatory injury to the skin or other tissue due to contact with thermal, radioactive, electric, or chemical agents. Burn injury is an important cause of disability and death worldwide. Obesity is a significant public health problem, often causing underlying systemic inflammation. Studying the combined impact of burn injuries on obese patients has become critical to the successful treatment of these patients. The aim of this paper is to highlight the effect of inflammation associated with burn injuries on several body weight group in a rat study. Materials and methods Different degrees of obesity and burns were established in rats and divided into a normal weight group, overweight group, obese group, second-degree burn group, third-degree burn group, over-weight second-degree burn group, over-weight third-degree burn group, obese second-degree burn group, and obese third-degree burn group (20 rats per group). Changes in inflammatory factors and growth factor were measured on the 1st, 3rd, 7th and 14th days after burns were inflicted. Results The ELISA test showed that in the unburned control group, MCP-1, IL-1β and TNF-α protein expressions in the obese and over-weight groups were higher than the normal-weight group (P < 0.05). RT-PCR test showed that the expressions of MCP-1, IL-1β and TNF-α genes in the obese group were higher compared to the overweight and normal weight groups (P < 0.05). Three and 7 days after burns were inflicted, the level of VEGF in the normal weight group was higher than the obese group (P < 0.05), however increased VEGF was not observed on days 1 and 14. Conclusion Burn injury and obesity have a mutually synergistic effect on the body’s inflammatory response.
bibliographic citation: Nie et al. (2020) Pro-inflammatory effect of obesity on rats with burn wounds. PeerJ 8:e10499 https://doi.org/10.7717/peerj.10499
date submitted: 2020-07-23
date accepted: 2020-11-15
issued: 2020-12-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nie
  given name: Chan
author list: Agent
  family name: Yu
  given name: Huiting
author list: Agent
  family name: Wang
  given name: Xue
author list: Agent
  family name: Li
  given name: Xiahong
author list: Agent
  family name: Wei
  given name: Zairong
author list: Agent
  family name: Shi
  given name: Xiuquan
doi: 10.7717/peerj.10499
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-12-08
copyright: ©2020 Nie et al.
attribution name: Nie et al.

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