PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2
items: Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand
items: Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan
items: Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye
items: Adult intussusception: a challenge to laparoscopic surgery?
items: Trichoderma longibrachiatum TG1 increases endogenous salicylic acid content and antioxidants activity in wheat seedlings under salinity stress
items: Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential
items: Supplementation of banana peel powder for the development of functional broiler nuggets
items: Correlation between religion, spirituality and perception of healthcare services utilisation in Poland during COVID-19 pandemic
items: Anatomy and behavior of Laternula elliptica, a keystone species of the Antarctic benthos (Bivalvia: Anomalodesmata: Laternulidae)

PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2
type: item
type: AcademicArticle
description: The optimization of resources for research in developing countries forces us to consider strategies in the wet lab that allow the reuse of molecular biology reagents to reduce costs. In this study, we used linear regression as a method for predictive modeling of coverage depth given the number of MinION reads sequenced to define the optimum number of reads necessary to obtain >200X coverage depth with a good lineage-clade assignment of SARS-CoV-2 genomes. The research aimed to create and implement a model based on machine learning algorithms to predict different variables (e.g., coverage depth) given the number of MinION reads produced by Nanopore sequencing to maximize the yield of high-quality SARS-CoV-2 genomes, determine the best sequencing runtime, and to be able to reuse the flow cell with the remaining nanopores available for sequencing in a new run. The best accuracy was −0.98 according to the R squared performance metric of the models. A demo version is available at https://genomicdashboard.herokuapp.com/.
format: application/pdf
format: text/html
creator: David E. Valencia-Valencia
creator: Diana Lopez-Alvarez
creator: Nelson Rivera-Franco
creator: Andres Castillo
creator: Johan S. Piña
creator: Carlos A. Pardo
creator: Beatriz Parra
subject: Bioinformatics
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
subject: COVID-19
description: doi:10.7717/peerj.14425
publisher: PeerJ Inc.
rights: © 2022 Valencia-Valencia et al.
abstract: The optimization of resources for research in developing countries forces us to consider strategies in the wet lab that allow the reuse of molecular biology reagents to reduce costs. In this study, we used linear regression as a method for predictive modeling of coverage depth given the number of MinION reads sequenced to define the optimum number of reads necessary to obtain >200X coverage depth with a good lineage-clade assignment of SARS-CoV-2 genomes. The research aimed to create and implement a model based on machine learning algorithms to predict different variables (e.g., coverage depth) given the number of MinION reads produced by Nanopore sequencing to maximize the yield of high-quality SARS-CoV-2 genomes, determine the best sequencing runtime, and to be able to reuse the flow cell with the remaining nanopores available for sequencing in a new run. The best accuracy was −0.98 according to the R squared performance metric of the models. A demo version is available at https://genomicdashboard.herokuapp.com/.
bibliographic citation: Valencia-Valencia et al. (2022) PredictION: a predictive model to establish the performance of Oxford sequencing reads of SARS-CoV-2. PeerJ 10:e14425 https://doi.org/10.7717/peerj.14425
date submitted: 2022-07-19
date accepted: 2022-10-30
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Valencia-Valencia
  given name: David E.
author list: Agent
  family name: Lopez-Alvarez
  given name: Diana
author list: Agent
  family name: Rivera-Franco
  given name: Nelson
author list: Agent
  family name: Castillo
  given name: Andres
author list: Agent
  family name: Piña
  given name: Johan S.
author list: Agent
  family name: Pardo
  given name: Carlos A.
author list: Agent
  family name: Parra
  given name: Beatriz
doi: 10.7717/peerj.14425
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: ©2022 Valencia-Valencia et al.
attribution name: Valencia-Valencia et al.

Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand
type: item
type: AcademicArticle
description: Background Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses. Methods Full-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4. Results ML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4. Conclusion H5N1 viruses existed, and were presuma…
format: application/pdf
format: text/html
creator: Pirom Noisumdaeng
creator: Juthamas Phadungsombat
creator: Sasrinakarn Weerated
creator: Witthawat Wiriyarat
creator: Pilaipan Puthavathana
subject: Bioinformatics
subject: Evolutionary Studies
subject: Microbiology
subject: Molecular Biology
subject: Virology
description: doi:10.7717/peerj.14419
publisher: PeerJ Inc.
rights: © 2022 Noisumdaeng et al.
abstract: Background Ongoing outbreaks of H5N1 highly pathogenic avian influenza (HPAI) viruses and the emergence of the genetic-related hemagglutinin (HA) gene of reassortant H5Nx viruses currently circulating in wild birds and poultries pose a great global public health concern. In this study, we comprehensively analyzed the genetic evolution of Thai H5N1 HA and neuraminidase (NA) genes between 2003 and 2010. The H5N1 Thailand virus clade 2.3.4 was also genetically compared to the currently circulating clade 2.3.4.4 of H5Nx viruses. Methods Full-length nucleotide sequences of 178 HA and 143 NA genes of H5N1 viruses circulating between 2003 and 2010 were phylogenetically analyzed using maximum likelihood (ML) phylogenetic construction. Bayesian phylogenetic trees were reconstructed using BEAST analysis with a Bayesian Markov chain Monte Carlo (MCMC) approach. The maximum clade credibility (MCC) tree was determined, and the time of the most recent common ancestor (tMRCA) was estimated. The H5N1 HA nucleotide sequences of clade 2.3.4 Thailand viruses were phylogenetically analyzed using ML phylogenetic tree construction and analyzed for nucleotide similarities with various subtypes of reassortant H5Nx HA clade 2.3.4.4. Results ML phylogenetic analysis revealed two distinct HA clades, clade 1 and clade 2.3.4, and two distinct NA groups within the corresponding H5 clade 1 viruses. Bayesian phylogenetic reconstruction for molecular clock suggested that the Thai H5N1 HA and NA emerged in 2001.87 (95% HPD: 2001.34-2002.49) and 2002.38 (95% HPD: 2001.99-2002.82), respectively, suggesting that the virus existed before it was first reported in 2004. The Thai H5N1 HA clade 2.3.4 was grouped into corresponding clades 2.3.4, 2.3.4.1, 2.3.4.2, and 2.3.4.3, and shared nucleotide similarities to reassortant H5Nx clade 2.3.4.4 ranged from 92.4-96.8%. Phylogenetic analysis revealed monophyletic H5Nx clade 2.3.4.4 evolved from H5N1 clade 2.3.4. Conclusion H5N1 viruses existed, and were presuma…
bibliographic citation: Noisumdaeng et al. (2022) Genetic evolution of hemagglutinin and neuraminidase genes of H5N1 highly pathogenic avian influenza viruses in Thailand. PeerJ 10:e14419 https://doi.org/10.7717/peerj.14419
date submitted: 2022-06-27
date accepted: 2022-10-28
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Noisumdaeng
  given name: Pirom
author list: Agent
  family name: Phadungsombat
  given name: Juthamas
author list: Agent
  family name: Weerated
  given name: Sasrinakarn
author list: Agent
  family name: Wiriyarat
  given name: Witthawat
author list: Agent
  family name: Puthavathana
  given name: Pilaipan
doi: 10.7717/peerj.14419
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: ©2022 Noisumdaeng et al.
attribution name: Noisumdaeng et al.

Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan
type: item
type: AcademicArticle
description: Nosemosis is the most common disease in honey bee Apis mellifera L., and is a major issue related to bee health worldwide. Therefore, the purpose of this research study was to determine prevalence of microsporidia parasitic infection of the genus Nosema spp. in East Kazakhstan Region (EKR). In the years of 2018 –2021, 394 honey bee samples were collected at 30 apiaries located in four districts of East Kazakhstan Region (Katon-Karagay, Urzhar, Borodulikhinsky, and Shemonaikhinsky). In order to determine the level of infestation, firstly, the presence of Nosema spp. spores was detected using optical microscopy, and then the average amount of spores per bee was counted using a hemocytometer. The degree of nosemosis prevalence was determined in points by means of a semi-quantitative method, and as a percentage from the total of samples and of the amount of positive tests. At the outcome of the study, microsporidia of the genus Nosema spp. were detected in 23.3% of cases (92 samples). Prevalence at its low degree was found in six samples (1.5%), at an average degree in 55 samples (14%), and at a high one in 31 samples (7.9%). This research study proved that microsporidia of the genus Nosema spp. are widely spread at the apiaries of East Kazakhstan Region in different orographic and climatic conditions. Notwithstanding that it was impossible to statistically determine any significant differences between the dependence of nosemosis prevalence and the apiary location, this indicator is actually higher in the mountainous regions than in the steppe. Concurrently, a close inverse correlation was recognized between the amount of spores in one bee and the level of infestation in bee families from the duration of the vegetation season at the apiary location. This gives grounds to assert that the environmental factors have an impact on formation and development of nosemosis. The results of the research presented in the article indicate the need for further research aimed at incre…
format: application/pdf
format: text/html
creator: Abdrakhman Baigazanov
creator: Yelena Tikhomirova
creator: Natalya Valitova
creator: Maral Nurkenova
creator: Ainur Koigeldinova
creator: Elmira Abdullina
creator: Olga Zaikovskaya
creator: Nurgul Ikimbayeva
creator: Dinara Zainettinova
creator: Lyailya Bauzhanova
subject: Agricultural Science
subject: Entomology
subject: Parasitology
subject: Zoology
description: doi:10.7717/peerj.14430
publisher: PeerJ Inc.
rights: © 2022 Baigazanov et al.
abstract: Nosemosis is the most common disease in honey bee Apis mellifera L., and is a major issue related to bee health worldwide. Therefore, the purpose of this research study was to determine prevalence of microsporidia parasitic infection of the genus Nosema spp. in East Kazakhstan Region (EKR). In the years of 2018 –2021, 394 honey bee samples were collected at 30 apiaries located in four districts of East Kazakhstan Region (Katon-Karagay, Urzhar, Borodulikhinsky, and Shemonaikhinsky). In order to determine the level of infestation, firstly, the presence of Nosema spp. spores was detected using optical microscopy, and then the average amount of spores per bee was counted using a hemocytometer. The degree of nosemosis prevalence was determined in points by means of a semi-quantitative method, and as a percentage from the total of samples and of the amount of positive tests. At the outcome of the study, microsporidia of the genus Nosema spp. were detected in 23.3% of cases (92 samples). Prevalence at its low degree was found in six samples (1.5%), at an average degree in 55 samples (14%), and at a high one in 31 samples (7.9%). This research study proved that microsporidia of the genus Nosema spp. are widely spread at the apiaries of East Kazakhstan Region in different orographic and climatic conditions. Notwithstanding that it was impossible to statistically determine any significant differences between the dependence of nosemosis prevalence and the apiary location, this indicator is actually higher in the mountainous regions than in the steppe. Concurrently, a close inverse correlation was recognized between the amount of spores in one bee and the level of infestation in bee families from the duration of the vegetation season at the apiary location. This gives grounds to assert that the environmental factors have an impact on formation and development of nosemosis. The results of the research presented in the article indicate the need for further research aimed at incre…
bibliographic citation: Baigazanov et al. (2022) Occurrence of Nosemosis in honey bee, Apis mellifera L. at the apiaries of East Kazakhstan. PeerJ 10:e14430 https://doi.org/10.7717/peerj.14430
date submitted: 2022-07-07
date accepted: 2022-10-30
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baigazanov
  given name: Abdrakhman
author list: Agent
  family name: Tikhomirova
  given name: Yelena
author list: Agent
  family name: Valitova
  given name: Natalya
author list: Agent
  family name: Nurkenova
  given name: Maral
author list: Agent
  family name: Koigeldinova
  given name: Ainur
author list: Agent
  family name: Abdullina
  given name: Elmira
author list: Agent
  family name: Zaikovskaya
  given name: Olga
author list: Agent
  family name: Ikimbayeva
  given name: Nurgul
author list: Agent
  family name: Zainettinova
  given name: Dinara
author list: Agent
  family name: Bauzhanova
  given name: Lyailya
doi: 10.7717/peerj.14430
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: ©2022 Baigazanov et al.
attribution name: Baigazanov et al.

Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye
type: item
type: AcademicArticle
description: Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is widely distributed in the high latitude areas of Eurasia. It plays an important role in grassland ecosystem maintenance, as well as being a valuable palatable forage species for livestock and wildlife. Russian wildrye germplasm has rich phenotypic and genetic diversity and has potential for improvement through crossbreeding. In this study, fifteen Russian wildrye hybrid combinations were produced and one F1 population with 123 putative hybrids was obtained by crossing two individual plants with significant differences in nutritional characteristics and reproductive tiller number. Twelve phenotypic traits of the F1 population were measured for three consecutive years, and ten of the twelve traits were in line with the genetic characteristics of quantitative traits. Hybrid superiority was revealed among F1 hybrids in both nutritional and reproductive traits. One non-recurrent parent plant with the highest PCA-synthesis score was selected and used to make a backcross with the ‘BOZOISKY SELECT’ male parent, and 143 putative BC1 hybrids were obtained. Sixteen pairs of EST-SSR primers were randomly selected from polymorphic primers derived from different expressed tiller trait related genes. Three primer pairs that amplified both the paternal and maternal characteristic band were used to assess the purity of the F1 population, and three primer pairs (with one shared primer pair) were used to identify the BC1 population. The hybrid purity was 96.75% for the F1 population and 95.80% for the BC1 population, and the results were confirmed by self-fertility test through bagging isolation. The genetic similarity coefficients between the F1 progeny and the male parent ranged from 0.500 to 0.895, and those between the BC1 progeny and the male parent ranged from 0.667 to 0.939. A subset of individuals in the BC1 population had closer genetic distance to the recurrent parent, and genetic variation within the BC1 populatio…
format: application/pdf
format: text/html
creator: Zhiqi Gao
creator: Lan Yun
creator: Zhen Li
creator: Qiyu Liu
creator: Chen Zhang
creator: Yingmei Ma
creator: Fengling Shi
subject: Agricultural Science
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.14442
publisher: PeerJ Inc.
rights: © 2022 Gao et al.
abstract: Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is widely distributed in the high latitude areas of Eurasia. It plays an important role in grassland ecosystem maintenance, as well as being a valuable palatable forage species for livestock and wildlife. Russian wildrye germplasm has rich phenotypic and genetic diversity and has potential for improvement through crossbreeding. In this study, fifteen Russian wildrye hybrid combinations were produced and one F1 population with 123 putative hybrids was obtained by crossing two individual plants with significant differences in nutritional characteristics and reproductive tiller number. Twelve phenotypic traits of the F1 population were measured for three consecutive years, and ten of the twelve traits were in line with the genetic characteristics of quantitative traits. Hybrid superiority was revealed among F1 hybrids in both nutritional and reproductive traits. One non-recurrent parent plant with the highest PCA-synthesis score was selected and used to make a backcross with the ‘BOZOISKY SELECT’ male parent, and 143 putative BC1 hybrids were obtained. Sixteen pairs of EST-SSR primers were randomly selected from polymorphic primers derived from different expressed tiller trait related genes. Three primer pairs that amplified both the paternal and maternal characteristic band were used to assess the purity of the F1 population, and three primer pairs (with one shared primer pair) were used to identify the BC1 population. The hybrid purity was 96.75% for the F1 population and 95.80% for the BC1 population, and the results were confirmed by self-fertility test through bagging isolation. The genetic similarity coefficients between the F1 progeny and the male parent ranged from 0.500 to 0.895, and those between the BC1 progeny and the male parent ranged from 0.667 to 0.939. A subset of individuals in the BC1 population had closer genetic distance to the recurrent parent, and genetic variation within the BC1 populatio…
bibliographic citation: Gao et al. (2022) Hybrid purity identification using EST-SSR markers and heterosis analysis of quantitative traits of Russian wildrye. PeerJ 10:e14442 https://doi.org/10.7717/peerj.14442
date submitted: 2021-09-01
date accepted: 2022-11-01
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gao
  given name: Zhiqi
author list: Agent
  family name: Yun
  given name: Lan
author list: Agent
  family name: Li
  given name: Zhen
author list: Agent
  family name: Liu
  given name: Qiyu
author list: Agent
  family name: Zhang
  given name: Chen
author list: Agent
  family name: Ma
  given name: Yingmei
author list: Agent
  family name: Shi
  given name: Fengling
doi: 10.7717/peerj.14442
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: © 2022 Gao et al.
attribution name: Gao et al.

Adult intussusception: a challenge to laparoscopic surgery?
type: item
type: AcademicArticle
description: Background Intussusception can occur at any age and is common in children but less common in adults. This study aimed to evaluate our experience of 51 adult intussusception and study the etiology, clinical manifestations, diagnosis, and treatment. Methods This analysis assessed the clinical manifestations, etiology, diagnosis, and treatment of adult intussusception in 51 adult patients at the Department of Gastrointestinal Surgery of China-Japan Union Hospital of Jilin University from January 2010 to December 2020. Results The mean age of the cohort was 54.43 ± 18.21 years, and 42 patients were diagnosed by abdominal ultrasonography and abdominal computed tomography (CT). Among them, 76.5% (39/51) had abdominal pain, 11.8% (6/51) had blood in stool, and 5.9% (3/51) had a palpable abdominal mass. Of these, 62.7% had tumors: malignant accounted for 39.2% (20/51) and benign accounted for 23.5% (12/51). CT is the preferred imaging method with a sensitivity of 92.2%, while colonoscopy provides a complementary diagnosis in patients involving the colon. All patients underwent surgical treatment, including 21.6% (11/51) laparoscopic surgery, 74.5% (38/51) open surgery, and 5.9% (3/51) intussusception reduction during the operation. The average operation time of the open group was 133.27 ± 43.75 min and the average hospital stay was 16.24 ± 12.55 days, while the average operation time of the laparoscopic group was 140.50 ± 46.15 mins, and the average hospital stay was 16.60 ± 16.98 days (P > 0.05). Conclusion Adult intussusception is a rare disease in clinic. Laparoscopic surgery can be useful and safe for adult intussusception.
format: application/pdf
format: text/html
creator: Mingze Sun
creator: Zhongmin Li
creator: Zhenbo Shu
creator: Qi Wu
creator: Xue Liu
subject: Gastroenterology and Hepatology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.14495
publisher: PeerJ Inc.
rights: © 2022 Sun et al.
abstract: Background Intussusception can occur at any age and is common in children but less common in adults. This study aimed to evaluate our experience of 51 adult intussusception and study the etiology, clinical manifestations, diagnosis, and treatment. Methods This analysis assessed the clinical manifestations, etiology, diagnosis, and treatment of adult intussusception in 51 adult patients at the Department of Gastrointestinal Surgery of China-Japan Union Hospital of Jilin University from January 2010 to December 2020. Results The mean age of the cohort was 54.43 ± 18.21 years, and 42 patients were diagnosed by abdominal ultrasonography and abdominal computed tomography (CT). Among them, 76.5% (39/51) had abdominal pain, 11.8% (6/51) had blood in stool, and 5.9% (3/51) had a palpable abdominal mass. Of these, 62.7% had tumors: malignant accounted for 39.2% (20/51) and benign accounted for 23.5% (12/51). CT is the preferred imaging method with a sensitivity of 92.2%, while colonoscopy provides a complementary diagnosis in patients involving the colon. All patients underwent surgical treatment, including 21.6% (11/51) laparoscopic surgery, 74.5% (38/51) open surgery, and 5.9% (3/51) intussusception reduction during the operation. The average operation time of the open group was 133.27 ± 43.75 min and the average hospital stay was 16.24 ± 12.55 days, while the average operation time of the laparoscopic group was 140.50 ± 46.15 mins, and the average hospital stay was 16.60 ± 16.98 days (P > 0.05). Conclusion Adult intussusception is a rare disease in clinic. Laparoscopic surgery can be useful and safe for adult intussusception.
bibliographic citation: Sun et al. (2022) Adult intussusception: a challenge to laparoscopic surgery?. PeerJ 10:e14495 https://doi.org/10.7717/peerj.14495
date submitted: 2022-07-28
date accepted: 2022-11-09
issued: 2022-11-30
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Mingze
author list: Agent
  family name: Li
  given name: Zhongmin
author list: Agent
  family name: Shu
  given name: Zhenbo
author list: Agent
  family name: Wu
  given name: Qi
author list: Agent
  family name: Liu
  given name: Xue
doi: 10.7717/peerj.14495
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-30
copyright: © 2022 Sun et al.
attribution name: Sun et al.

Trichoderma longibrachiatum TG1 increases endogenous salicylic acid content and antioxidants activity in wheat seedlings under salinity stress
type: item
type: AcademicArticle
description: Several studies have reported the deleterious effects of excessive salt stress on Triticum aestivum L. seedlings. Seed pretreatment with exogenous salicylic acid (SA) enhances plants to tolerate salt stress. Herein, the present study aims to investigate the potential of plant-growth-promoting fungus Trichoderma longibrachiatum (TG1) to increase the plant growth and enhance the salicylic acid (SA) contents and antioxidants activity in wheat seedlings under different concentrations of salt stress. Wheat seeds were pretreated in TG1 spore suspension before exposure to different salt stresses. Compared with 0, 50, 100, 150 salt stresses, the TG1 and NaCl increased the wheat seeds germination rate, germination potential and germination index significantly; the shoot height and root length were increased by an average of 39.45% and 29.73%, respectively. Compared to NaCl stress across the four concentrations (0, 50, 100, and 150 mM), the TG1 treated wheat seedlings increased SA concentration and phenylalanine ammonia-lyase activity (PAL) by an average of 55.87% and 24.10% respectively. In addition, the TG1+NaCl-treated seedlings increased superoxide dismutase (SOD), peroxidases (POD), and catalase (CAT) activities in the shoot by an average of 47.68%, 23.68%, and 38.65% respectively compared to NaCl-stressed seedlings. Significantly, the genes, SOD, CAT, and POD were relatively up-regulated in the salt-tolerant TG1-treated seedlings at all NaCl concentrations in comparison to the control. Wheat seedlings treated with TG1+NaCl increased the transcript levels of SOD, POD and CAT by 1.35, 1.85 and 1.04-fold at 50 mM NaCl concentration, respectively, compared with 0 mM NaCl concentration. Our results indicated that seeds pretreatment with TG1 could increase endogenous SA of plants and promote seedling growth under salt stress by improving enzymatic antioxidant activities and gene expression.
format: application/pdf
format: text/html
creator: Solomon Boamah
creator: Shuwu Zhang
creator: Bingliang Xu
creator: Tong Li
creator: Alejandro Calderón-Urrea
creator: Richard John Tiika
subject: Agricultural Science
subject: Mycology
subject: Plant Science
description: doi:10.7717/peerj.12923
publisher: PeerJ Inc.
rights: © 2022 Boamah et al.
abstract: Several studies have reported the deleterious effects of excessive salt stress on Triticum aestivum L. seedlings. Seed pretreatment with exogenous salicylic acid (SA) enhances plants to tolerate salt stress. Herein, the present study aims to investigate the potential of plant-growth-promoting fungus Trichoderma longibrachiatum (TG1) to increase the plant growth and enhance the salicylic acid (SA) contents and antioxidants activity in wheat seedlings under different concentrations of salt stress. Wheat seeds were pretreated in TG1 spore suspension before exposure to different salt stresses. Compared with 0, 50, 100, 150 salt stresses, the TG1 and NaCl increased the wheat seeds germination rate, germination potential and germination index significantly; the shoot height and root length were increased by an average of 39.45% and 29.73%, respectively. Compared to NaCl stress across the four concentrations (0, 50, 100, and 150 mM), the TG1 treated wheat seedlings increased SA concentration and phenylalanine ammonia-lyase activity (PAL) by an average of 55.87% and 24.10% respectively. In addition, the TG1+NaCl-treated seedlings increased superoxide dismutase (SOD), peroxidases (POD), and catalase (CAT) activities in the shoot by an average of 47.68%, 23.68%, and 38.65% respectively compared to NaCl-stressed seedlings. Significantly, the genes, SOD, CAT, and POD were relatively up-regulated in the salt-tolerant TG1-treated seedlings at all NaCl concentrations in comparison to the control. Wheat seedlings treated with TG1+NaCl increased the transcript levels of SOD, POD and CAT by 1.35, 1.85 and 1.04-fold at 50 mM NaCl concentration, respectively, compared with 0 mM NaCl concentration. Our results indicated that seeds pretreatment with TG1 could increase endogenous SA of plants and promote seedling growth under salt stress by improving enzymatic antioxidant activities and gene expression.
bibliographic citation: Boamah et al. (2022) Trichoderma longibrachiatum TG1 increases endogenous salicylic acid content and antioxidants activity in wheat seedlings under salinity stress. PeerJ 10:e12923 https://doi.org/10.7717/peerj.12923
date submitted: 2021-04-14
date accepted: 2022-01-20
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Boamah
  given name: Solomon
author list: Agent
  family name: Zhang
  given name: Shuwu
author list: Agent
  family name: Xu
  given name: Bingliang
author list: Agent
  family name: Li
  given name: Tong
author list: Agent
  family name: Calderón-Urrea
  given name: Alejandro
author list: Agent
  family name: John Tiika
  given name: Richard
doi: 10.7717/peerj.12923
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: © 2022 Boamah et al.
attribution name: Boamah et al.

Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential
type: item
type: AcademicArticle
description: Background Pea eggplant (Solanum torvum Swartz) commonly known as turkey berry or ‘terung pipit’ in Malay is a vegetable plant widely consumed by the local community in Malaysia. The shrub bears pea-like turkey berry fruits (TBFs), rich in phytochemicals of medicinal interest. The TBF phytochemicals hold a wide spectrum of pharmacological properties. In this study, the TBF phytochemicals’ potential inhibitory properties were evaluated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of the Coronavirus disease 2019 (COVID-19). The TBF polyphenols were screened against SARS-CoV receptors via molecular docking and the best receptor-ligand complex was validated further by molecular dynamics (MD) simulation. Method The SARS-CoV receptor structure files (viral structural components) were retrieved from the Protein Data Bank (PDB) database: membrane protein (PDB ID: 3I6G), main protease (PDB ID: 5RE4), and spike glycoproteins (PDB ID: 6VXX and 6VYB). The receptor binding pocket regions were identified by Discovery Studio (BIOVIA) for targeted docking with TBF polyphenols (genistin, kaempferol, mellein, rhoifolin and scutellarein). The ligand and SARS-CoV family receptor structure files were pre-processed using the AutoDock tools. Molecular docking was performed with the Lamarckian genetic algorithm using AutoDock Vina 4.2 software. The best pose (ligand-receptor complex) from the molecular docking analysis was selected based on the minimum binding energy (MBE) and extent of structural interactions, as indicated by BIOVIA visualization tool. The selected complex was validated by a 100 ns MD simulation run using the GROMACS software. The dynamic behaviour and stability of the receptor-ligand complex were evaluated by the root mean square displacement (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), solvent accessible surface volume (SASV) and number of hydrogen bonds. Results At RMSD = 0, the TB…
format: application/pdf
format: text/html
creator: Nisha Govender
creator: Norazura Syazlin Zulkifli
creator: Nurul Farhana Badrul Hisham
creator: Nur Syatila Ab Ghani
creator: Zeti-Azura Mohamed-Hussein
subject: Biochemistry
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: COVID-19
description: doi:10.7717/peerj.14168
publisher: PeerJ Inc.
rights: © 2022 Govender et al.
abstract: Background Pea eggplant (Solanum torvum Swartz) commonly known as turkey berry or ‘terung pipit’ in Malay is a vegetable plant widely consumed by the local community in Malaysia. The shrub bears pea-like turkey berry fruits (TBFs), rich in phytochemicals of medicinal interest. The TBF phytochemicals hold a wide spectrum of pharmacological properties. In this study, the TBF phytochemicals’ potential inhibitory properties were evaluated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) of the Coronavirus disease 2019 (COVID-19). The TBF polyphenols were screened against SARS-CoV receptors via molecular docking and the best receptor-ligand complex was validated further by molecular dynamics (MD) simulation. Method The SARS-CoV receptor structure files (viral structural components) were retrieved from the Protein Data Bank (PDB) database: membrane protein (PDB ID: 3I6G), main protease (PDB ID: 5RE4), and spike glycoproteins (PDB ID: 6VXX and 6VYB). The receptor binding pocket regions were identified by Discovery Studio (BIOVIA) for targeted docking with TBF polyphenols (genistin, kaempferol, mellein, rhoifolin and scutellarein). The ligand and SARS-CoV family receptor structure files were pre-processed using the AutoDock tools. Molecular docking was performed with the Lamarckian genetic algorithm using AutoDock Vina 4.2 software. The best pose (ligand-receptor complex) from the molecular docking analysis was selected based on the minimum binding energy (MBE) and extent of structural interactions, as indicated by BIOVIA visualization tool. The selected complex was validated by a 100 ns MD simulation run using the GROMACS software. The dynamic behaviour and stability of the receptor-ligand complex were evaluated by the root mean square displacement (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), solvent accessible surface volume (SASV) and number of hydrogen bonds. Results At RMSD = 0, the TB…
bibliographic citation: Govender et al. (2022) Pea eggplant (Solanum torvum Swartz) is a source of plant food polyphenols with SARS-CoV inhibiting potential. PeerJ 10:e14168 https://doi.org/10.7717/peerj.14168
date submitted: 2022-06-27
date accepted: 2022-09-12
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Govender
  given name: Nisha
author list: Agent
  family name: Zulkifli
  given name: Norazura Syazlin
author list: Agent
  family name: Badrul Hisham
  given name: Nurul Farhana
author list: Agent
  family name: Ab Ghani
  given name: Nur Syatila
author list: Agent
  family name: Mohamed-Hussein
  given name: Zeti-Azura
doi: 10.7717/peerj.14168
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: © 2022 Govender et al.
attribution name: Govender et al.

Supplementation of banana peel powder for the development of functional broiler nuggets
type: item
type: AcademicArticle
description: Banana peel powder is considered one of the most nutritive and effective waste product to be utilized as a functional additive in the food industry. This study aimed to determine the impact of banana peel powder at concentrations of 2%, 4%, and 6% on the nutritional composition, physicochemical parameters, antioxidant potential, cooking properties, microbial count, and organoleptic properties of functional nuggets during storage at refrigeration temperature for 21 days. Results showed a significant increase in nutritional content including ash and crude fiber ranging from 2.52 ± 0.017% to 6.45 ± 0.01% and 0.51 ± 0.01% to 2.13 ± 0.01%, respectively, whereas a significant decrease was observed in crude protein and crude fat ranging from 13.71 ± 0.02% to 8.92 ± 0.02% and 9.25 ± 0.02% to 4.51 ± 0.01%, respectively. The incorporation of banana peel powder significantly improved the Water Holding Capacity from 5.17% to 8.37%, cooking yield from 83.20 ± 0.20% to 87.73 ± 0.16% and cooking loss from 20.19 ± 0.290% to 13.98 ± 0.15%. Antioxidant potential was significantly improved as TPC of functional nuggets increased ranging from 3.73 ± 0.02 mg GAE/g to 8.53 ± 0.02 mg GAE/g while a decrease in TBARS (0.18 ± 0.02 mg malonaldehyde/kg to 0.14 ± 0.02 mg malonaldehyde/kg) was observed. Furthermore, functional broiler nuggets depicted a significantly reduced total plate count (3.06–4.20 × 105 CFU/g) than control, which is likely due to high amounts of phenolic compounds in BPP. Broiler nuggets supplemented with 2% BPP (T1) received the greatest sensory scores in terms of flavour, tenderness, and juiciness. Results of current study revealed the potential of BPP to be utilized as an effective natural source of fibre supplementation in food products along with enhanced antioxidant and anti-microbial properties.
format: application/pdf
format: text/html
creator: Tasleem Akram
creator: Sharmeen Mustafa
creator: Khola Ilyas
creator: Muhammad Rizwan Tariq
creator: Shinawar Waseem Ali
creator: Sajid Ali
creator: Muhammad Shafiq
creator: Maryam Rao
creator: Waseem Safdar
creator: Madiha Iftikhar
creator: Amna Hameed
creator: Mujahid Manzoor
creator: Madiha Akhtar
creator: Zujaja Umer
creator: Zunaira Basharat
subject: Agricultural Science
subject: Biotechnology
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.14364
publisher: PeerJ Inc.
rights: © 2022 Akram et al.
abstract: Banana peel powder is considered one of the most nutritive and effective waste product to be utilized as a functional additive in the food industry. This study aimed to determine the impact of banana peel powder at concentrations of 2%, 4%, and 6% on the nutritional composition, physicochemical parameters, antioxidant potential, cooking properties, microbial count, and organoleptic properties of functional nuggets during storage at refrigeration temperature for 21 days. Results showed a significant increase in nutritional content including ash and crude fiber ranging from 2.52 ± 0.017% to 6.45 ± 0.01% and 0.51 ± 0.01% to 2.13 ± 0.01%, respectively, whereas a significant decrease was observed in crude protein and crude fat ranging from 13.71 ± 0.02% to 8.92 ± 0.02% and 9.25 ± 0.02% to 4.51 ± 0.01%, respectively. The incorporation of banana peel powder significantly improved the Water Holding Capacity from 5.17% to 8.37%, cooking yield from 83.20 ± 0.20% to 87.73 ± 0.16% and cooking loss from 20.19 ± 0.290% to 13.98 ± 0.15%. Antioxidant potential was significantly improved as TPC of functional nuggets increased ranging from 3.73 ± 0.02 mg GAE/g to 8.53 ± 0.02 mg GAE/g while a decrease in TBARS (0.18 ± 0.02 mg malonaldehyde/kg to 0.14 ± 0.02 mg malonaldehyde/kg) was observed. Furthermore, functional broiler nuggets depicted a significantly reduced total plate count (3.06–4.20 × 105 CFU/g) than control, which is likely due to high amounts of phenolic compounds in BPP. Broiler nuggets supplemented with 2% BPP (T1) received the greatest sensory scores in terms of flavour, tenderness, and juiciness. Results of current study revealed the potential of BPP to be utilized as an effective natural source of fibre supplementation in food products along with enhanced antioxidant and anti-microbial properties.
bibliographic citation: Akram et al. (2022) Supplementation of banana peel powder for the development of functional broiler nuggets. PeerJ 10:e14364 https://doi.org/10.7717/peerj.14364
date submitted: 2022-08-25
date accepted: 2022-10-18
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Akram
  given name: Tasleem
author list: Agent
  family name: Mustafa
  given name: Sharmeen
author list: Agent
  family name: Ilyas
  given name: Khola
author list: Agent
  family name: Tariq
  given name: Muhammad Rizwan
author list: Agent
  family name: Ali
  given name: Shinawar Waseem
author list: Agent
  family name: Ali
  given name: Sajid
author list: Agent
  family name: Shafiq
  given name: Muhammad
author list: Agent
  family name: Rao
  given name: Maryam
author list: Agent
  family name: Safdar
  given name: Waseem
author list: Agent
  family name: Iftikhar
  given name: Madiha
author list: Agent
  family name: Hameed
  given name: Amna
author list: Agent
  family name: Manzoor
  given name: Mujahid
author list: Agent
  family name: Akhtar
  given name: Madiha
author list: Agent
  family name: Umer
  given name: Zujaja
author list: Agent
  family name: Basharat
  given name: Zunaira
doi: 10.7717/peerj.14364
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: © 2022 Akram et al.
attribution name: Akram et al.

Correlation between religion, spirituality and perception of healthcare services utilisation in Poland during COVID-19 pandemic
type: item
type: AcademicArticle
description: Background The worldwide transmission of SARS CoV-2 caused the COVID-19 pandemic and had an impact on healthcare provision. The disruption of reliance on the health system during the COVID-19 pandemic posed a clear threat to public trust. Religiosity, like spirituality, is believed to have a positive influence on people’s lives, enabling them to cope with illness, stress, and sudden life changes. In practice, although the terms religiosity and spirituality have similar meanings and are related, they are not identical concepts. The aim of this study is to compare the perceptions of the accessibility and quality of healthcare services provided before and during the COVID-19 pandemic in Poland by religious/spiritual people compared to those for whom religion and spirituality have little or no importance in their lives. Methodology This cross-sectional study was based on the authors’ questionnaire, carried out during the third wave of the COVID-19 pandemic in Poland. Participants in the study were people living in various regions of Poland over 18 who were willing to complete the questionnaire voluntarily. The number of people sampled was two hundred and sixty-four. Convenience sampling method was used for this study. Statistical calculations were performed using Statistica 13 software from TIBCO and PQStat from PQStat Software and were based on the Kruskal-Wallis test, multiple regression model, the chi2 test of independence or the Mann-Whitney test. The result was considered statistically significant when p < α. The significance level was taken as α = 0.05. Results Two hundred and sixty-three respondents answered the questionnaire. Among them, 181 (69%) were women, and 82 (31%) were men. It was shown that religion is more important for women than for men and women who report a high role of religion in their lives rated the quality of healthcare services better before and during the COVID-19 pandemic. It was also concluded that religious people for whom religion played…
format: application/pdf
format: text/html
creator: Magdalena Tuczyńska
creator: Maja Matthews-Kozanecka
creator: Ewa Baum
subject: Psychiatry and Psychology
subject: Public Health
subject: COVID-19
subject: Healthcare Services
description: doi:10.7717/peerj.14376
publisher: PeerJ Inc.
rights: © 2022 Tuczyńska et al.
abstract: Background The worldwide transmission of SARS CoV-2 caused the COVID-19 pandemic and had an impact on healthcare provision. The disruption of reliance on the health system during the COVID-19 pandemic posed a clear threat to public trust. Religiosity, like spirituality, is believed to have a positive influence on people’s lives, enabling them to cope with illness, stress, and sudden life changes. In practice, although the terms religiosity and spirituality have similar meanings and are related, they are not identical concepts. The aim of this study is to compare the perceptions of the accessibility and quality of healthcare services provided before and during the COVID-19 pandemic in Poland by religious/spiritual people compared to those for whom religion and spirituality have little or no importance in their lives. Methodology This cross-sectional study was based on the authors’ questionnaire, carried out during the third wave of the COVID-19 pandemic in Poland. Participants in the study were people living in various regions of Poland over 18 who were willing to complete the questionnaire voluntarily. The number of people sampled was two hundred and sixty-four. Convenience sampling method was used for this study. Statistical calculations were performed using Statistica 13 software from TIBCO and PQStat from PQStat Software and were based on the Kruskal-Wallis test, multiple regression model, the chi2 test of independence or the Mann-Whitney test. The result was considered statistically significant when p < α. The significance level was taken as α = 0.05. Results Two hundred and sixty-three respondents answered the questionnaire. Among them, 181 (69%) were women, and 82 (31%) were men. It was shown that religion is more important for women than for men and women who report a high role of religion in their lives rated the quality of healthcare services better before and during the COVID-19 pandemic. It was also concluded that religious people for whom religion played…
bibliographic citation: Tuczyńska et al. (2022) Correlation between religion, spirituality and perception of healthcare services utilisation in Poland during COVID-19 pandemic. PeerJ 10:e14376 https://doi.org/10.7717/peerj.14376
date submitted: 2022-07-06
date accepted: 2022-10-19
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tuczyńska
  given name: Magdalena
author list: Agent
  family name: Matthews-Kozanecka
  given name: Maja
author list: Agent
  family name: Baum
  given name: Ewa
doi: 10.7717/peerj.14376
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: ©2022 Tuczyńska et al.
attribution name: Tuczyńska et al.

Anatomy and behavior of Laternula elliptica, a keystone species of the Antarctic benthos (Bivalvia: Anomalodesmata: Laternulidae)
type: item
type: AcademicArticle
description: Laternula elliptica (P. P. King, 1832) is the sole representative of the anomalodesmatan family Laternulidae and the largest bivalve in the Antarctic and Subantarctic. A keystone species of the regional benthic communities, it has reached model status, having been studied in hundreds of scientific works across many biological disciplines. In contrast, its anatomy has remained poorly known, with prior published data limited to partial descriptions based on chemically preserved specimens. Based on observations of aquarium-maintained living animals at the Brazilian Comandante Ferraz Antarctic Station, gross-morphological dissections, and histological sectioning, the comparative anatomy, functional morphology, and aspects of behavior of L. elliptica are described and discussed. Special focus is placed on the pallial organs (including elucidation of cleansing and feeding sorting mechanisms in the mantle cavity) and the musculature. Among the noteworthy findings are the presence of well-developed siphons furnished with sensory tentacles at its tips, some of which bearing eyes; large, folded gills and labial palps capable of sorting the material entering the mantle cavity; an inter-chamber communication in the posterior region of the mantle cavity; an ample ventral mantle fusion with an anterior pedal gape; the absence of a 4th pallial opening; and the absence of a ligamental lithodesma in adult specimens. This study reevaluates the available anatomical data in the literature, both supplementing and correcting previously published accounts.
format: application/pdf
format: text/html
creator: Flávio Dias Passos
creator: André Fernando Sartori
creator: Osmar Domaneschi
creator: Rüdiger Bieler
subject: Animal Behavior
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.14380
publisher: PeerJ Inc.
rights: © 2022 Passos et al.
abstract: Laternula elliptica (P. P. King, 1832) is the sole representative of the anomalodesmatan family Laternulidae and the largest bivalve in the Antarctic and Subantarctic. A keystone species of the regional benthic communities, it has reached model status, having been studied in hundreds of scientific works across many biological disciplines. In contrast, its anatomy has remained poorly known, with prior published data limited to partial descriptions based on chemically preserved specimens. Based on observations of aquarium-maintained living animals at the Brazilian Comandante Ferraz Antarctic Station, gross-morphological dissections, and histological sectioning, the comparative anatomy, functional morphology, and aspects of behavior of L. elliptica are described and discussed. Special focus is placed on the pallial organs (including elucidation of cleansing and feeding sorting mechanisms in the mantle cavity) and the musculature. Among the noteworthy findings are the presence of well-developed siphons furnished with sensory tentacles at its tips, some of which bearing eyes; large, folded gills and labial palps capable of sorting the material entering the mantle cavity; an inter-chamber communication in the posterior region of the mantle cavity; an ample ventral mantle fusion with an anterior pedal gape; the absence of a 4th pallial opening; and the absence of a ligamental lithodesma in adult specimens. This study reevaluates the available anatomical data in the literature, both supplementing and correcting previously published accounts.
bibliographic citation: Passos et al. (2022) Anatomy and behavior of Laternula elliptica, a keystone species of the Antarctic benthos (Bivalvia: Anomalodesmata: Laternulidae). PeerJ 10:e14380 https://doi.org/10.7717/peerj.14380
date submitted: 2022-06-02
date accepted: 2022-10-20
issued: 2022-11-29
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Passos
  given name: Flávio Dias
author list: Agent
  family name: Sartori
  given name: André Fernando
author list: Agent
  family name: Domaneschi
  given name: Osmar
author list: Agent
  family name: Bieler
  given name: Rüdiger
doi: 10.7717/peerj.14380
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-11-29
copyright: © 2022 Passos et al.
attribution name: Passos et al.

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