PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Location angle of second mesio-buccal canal in maxillary molars of an Indian population: an in vivo retrospective CBCT evaluation and proposal of a new classification
items: Physique and performance in male sitting volleyball players: implications for classification and training
items: Changes in whistle parameters of two common bottlenose dolphin ecotypes as a result of the physical presence of the research vessel
items: Dynamics of the gut microbiota in rats after hypobaric hypoxia exposure
items: Comparative assessment of enamel remineralisation on the surface microhardness of demineralized enamel - an in vitro study
items: Interactions between two functionally distinct aquatic invertebrate herbivores complicate ecosystem- and population-level resilience
items: Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations
items: Deep ploughing in the summer fallow season and optimizing nitrogen rate can increase yield, water, and nitrogen efficiencies of rain-fed winter wheat in the Loess Plateau region of China
items: Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench)
items: Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil

Location angle of second mesio-buccal canal in maxillary molars of an Indian population: an in vivo retrospective CBCT evaluation and proposal of a new classification
type: item
type: AcademicArticle
description: Background The current investigation was designed for predicting the location angle of second mesio-buccal root canal in permanent maxillary (first and second) molars with the aid of proposed measuring points and line using cone beam computed tomography in an Indian population. Methods Three-hundred and twenty-four scans of permanent maxillary (first (n = 162) and second (n = 162)) molars with mesio-buccal 2 root canals and unassociated to the current evaluation were acquired. The maxillary molars were viewed with CSI imaging software. The images were captured and were further assessed using 3D Slicer. The assessment included of measuring the distance between the main mesio-buccal and mesio-buccal 2 canal and the angle at which the MB2 it is located utilizing proposed lines joining the disto-buccal and palatal canals. The data was tabulated for the incidence of various angles where the MB2 is located and MB-MB2 distance was determined. The angles denoted were either positive; I (0.1° to 1.9°), II (2° to 4°), III (>4°) or negative I (−0.1° to −1.9°), II (−2° to −4°), III (>−4°). On the data tabulated a new Banga Vhorkate and Pawar’s (BVP’s) angular classification for maxillary molars was proposed. Results The existence of positive angle III was found in 41.35% of maxillary first molars (36 right and 31 left of 162), whereas positive angle II appeared in 41.98% of maxillary second molars (32 right and 36 left of 162). The MB1–MB2 in maxillary 1st molar is seen to be 3.12–3.31 mm and this distance in maxillary 2nd molar is 2.8–3.1 mm. The disto-buccal to palatal canal orifice mean distance was 5.06–5.22 mm in maxillary first molars and 4.9–5.8 mm in maxillary second molars. Conclusion Accurate diagnosis of the location of second mesio-buccal canal increases the success rate of endodontic treatment and a better prognosis. The new proposed classification may be considerably helpful in the urge to locate the mesio-buccal 2 canal.
format: application/pdf
format: text/html
creator: Kishor Vhorkate
creator: Kulvinder Banga
creator: Ajinkya M. Pawar
creator: Shugufta Mir
creator: Suraj Arora
creator: Dian Agustin Wahjuningrum
creator: Anuj Bhardwaj
creator: Alexander Maniangat Luke
subject: Anatomy and Physiology
subject: Dentistry
description: doi:10.7717/peerj.14234
publisher: PeerJ Inc.
rights: © 2022 Vhorkate et al.
abstract: Background The current investigation was designed for predicting the location angle of second mesio-buccal root canal in permanent maxillary (first and second) molars with the aid of proposed measuring points and line using cone beam computed tomography in an Indian population. Methods Three-hundred and twenty-four scans of permanent maxillary (first (n = 162) and second (n = 162)) molars with mesio-buccal 2 root canals and unassociated to the current evaluation were acquired. The maxillary molars were viewed with CSI imaging software. The images were captured and were further assessed using 3D Slicer. The assessment included of measuring the distance between the main mesio-buccal and mesio-buccal 2 canal and the angle at which the MB2 it is located utilizing proposed lines joining the disto-buccal and palatal canals. The data was tabulated for the incidence of various angles where the MB2 is located and MB-MB2 distance was determined. The angles denoted were either positive; I (0.1° to 1.9°), II (2° to 4°), III (>4°) or negative I (−0.1° to −1.9°), II (−2° to −4°), III (>−4°). On the data tabulated a new Banga Vhorkate and Pawar’s (BVP’s) angular classification for maxillary molars was proposed. Results The existence of positive angle III was found in 41.35% of maxillary first molars (36 right and 31 left of 162), whereas positive angle II appeared in 41.98% of maxillary second molars (32 right and 36 left of 162). The MB1–MB2 in maxillary 1st molar is seen to be 3.12–3.31 mm and this distance in maxillary 2nd molar is 2.8–3.1 mm. The disto-buccal to palatal canal orifice mean distance was 5.06–5.22 mm in maxillary first molars and 4.9–5.8 mm in maxillary second molars. Conclusion Accurate diagnosis of the location of second mesio-buccal canal increases the success rate of endodontic treatment and a better prognosis. The new proposed classification may be considerably helpful in the urge to locate the mesio-buccal 2 canal.
bibliographic citation: Vhorkate et al. (2022) Location angle of second mesio-buccal canal in maxillary molars of an Indian population: an in vivo retrospective CBCT evaluation and proposal of a new classification. PeerJ 10:e14234 https://doi.org/10.7717/peerj.14234
date submitted: 2022-06-22
date accepted: 2022-09-22
issued: 2022-10-10
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vhorkate
  given name: Kishor
author list: Agent
  family name: Banga
  given name: Kulvinder
author list: Agent
  family name: Pawar
  given name: Ajinkya M.
author list: Agent
  family name: Mir
  given name: Shugufta
author list: Agent
  family name: Arora
  given name: Suraj
author list: Agent
  family name: Wahjuningrum
  given name: Dian Agustin
author list: Agent
  family name: Bhardwaj
  given name: Anuj
author list: Agent
  family name: Luke
  given name: Alexander Maniangat
doi: 10.7717/peerj.14234
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-10
copyright: © 2022 Vhorkate et al.
attribution name: Vhorkate et al.

Physique and performance in male sitting volleyball players: implications for classification and training
type: item
type: AcademicArticle
description: Background This study assessed whether anthropometry, physical fitness and sport-specific sprint performance vary across the three groups of sitting volleyball (SV) athletes (athletes with a disability (VS1), athletes with a minimal disability (VS2) and able-bodied SV athletes (AB)) in order to explore the validity of the current system of classification. This study also investigated how the anthropometric and physical fitness characteristics of athletes relate to their sprint performance. Methods Thirty-five SV male athletes aged 37.4 ± 10.8 years and practicing SV at a national/international level volunteered for this study. Testing consisted in the evaluation of linear anthropometry, physical fitness (body composition by-means of dual-energy X-ray absorptiometry and upper-body strength) and sprint performance (5-meter sprint tests, agility test and speed and endurance test). Results Athletes in the three groups differed in fat mass percentage (%FM) which was higher in VS1 versus AB at the sub-total level (+9%), in the arms (+15%) and in the non-impaired leg (+8%) regions. Greater hand span, greater length of the impaired lower leg, lower %FM at both the sub-total and regional level and a higher level of strength in the upper body are all associated with better performances in the considered sprint tests (P < 0.05 for all). These results do not confirm the validity of the current system of classification of athletes adopted in SV. Professionals dealing with SV athletes should include specific exercises aimed at improving whole-body and regional body composition and the strength of the trunk and upper limbs in their training programs.
format: application/pdf
format: text/html
creator: Valentina Cavedon
creator: Chiara Brugnoli
creator: Marco Sandri
creator: Luciano Bertinato
creator: Lorenzo Giacobbi
creator: Filip Bolčević
creator: Carlo Zancanaro
creator: Chiara Milanese
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.14013
publisher: PeerJ Inc.
rights: © 2022 Cavedon et al.
abstract: Background This study assessed whether anthropometry, physical fitness and sport-specific sprint performance vary across the three groups of sitting volleyball (SV) athletes (athletes with a disability (VS1), athletes with a minimal disability (VS2) and able-bodied SV athletes (AB)) in order to explore the validity of the current system of classification. This study also investigated how the anthropometric and physical fitness characteristics of athletes relate to their sprint performance. Methods Thirty-five SV male athletes aged 37.4 ± 10.8 years and practicing SV at a national/international level volunteered for this study. Testing consisted in the evaluation of linear anthropometry, physical fitness (body composition by-means of dual-energy X-ray absorptiometry and upper-body strength) and sprint performance (5-meter sprint tests, agility test and speed and endurance test). Results Athletes in the three groups differed in fat mass percentage (%FM) which was higher in VS1 versus AB at the sub-total level (+9%), in the arms (+15%) and in the non-impaired leg (+8%) regions. Greater hand span, greater length of the impaired lower leg, lower %FM at both the sub-total and regional level and a higher level of strength in the upper body are all associated with better performances in the considered sprint tests (P < 0.05 for all). These results do not confirm the validity of the current system of classification of athletes adopted in SV. Professionals dealing with SV athletes should include specific exercises aimed at improving whole-body and regional body composition and the strength of the trunk and upper limbs in their training programs.
bibliographic citation: Cavedon et al. (2022) Physique and performance in male sitting volleyball players: implications for classification and training. PeerJ 10:e14013 https://doi.org/10.7717/peerj.14013
date submitted: 2022-06-20
date accepted: 2022-08-15
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cavedon
  given name: Valentina
author list: Agent
  family name: Brugnoli
  given name: Chiara
author list: Agent
  family name: Sandri
  given name: Marco
author list: Agent
  family name: Bertinato
  given name: Luciano
author list: Agent
  family name: Giacobbi
  given name: Lorenzo
author list: Agent
  family name: Bolčević
  given name: Filip
author list: Agent
  family name: Zancanaro
  given name: Carlo
author list: Agent
  family name: Milanese
  given name: Chiara
doi: 10.7717/peerj.14013
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Cavedon et al.
attribution name: Cavedon et al.

Changes in whistle parameters of two common bottlenose dolphin ecotypes as a result of the physical presence of the research vessel
type: item
type: AcademicArticle
description: In the presence of vessels, dolphins have been found to change their habitat, behavior, group composition and whistle repertoire. The modification of the whistle parameters is generally considered to be a response to the engine noise. Little is known about the impact of the physical presence of vessels on dolphin acoustics. Whistle parameters of the coastal and oceanic ecotypes of common bottlenose dolphins in La Paz Bay, Mexico, were measured after the approach of the research vessel and its engine shutdown. Recordings of 10 min were made immediately after turning off the engine. For analysis, these recordings were divided from minute 0 to minute 5, and from minute 5:01 to minute 10. The whistles of the oceanic ecotype showed higher maximum, minimum and peak frequency in the second time interval compared to the first one. The whistle rate decreased in the second time interval. The whistles of the coastal ecotype showed no difference between the two time intervals. The physical presence of the research vessel could have induced a change in the whistle parameters of the oceanic dolphins until habituation to the vessel disturbance. The oceanic ecotype could increase the whistle rate and decrease the whistle frequencies to maintain acoustic contact more frequently and for longer distances. The coastal ecotype, showing no significant changes in the whistle parameters, could be more habituated to the presence of vessels and display a higher tolerance.
format: application/pdf
format: text/html
creator: Simone Antichi
creator: Jorge Urbán R.
creator: Sergio Martínez-Aguilar
creator: Lorena Viloria-Gómora
subject: Animal Behavior
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.14074
publisher: PeerJ Inc.
rights: © 2022 Antichi et al.
abstract: In the presence of vessels, dolphins have been found to change their habitat, behavior, group composition and whistle repertoire. The modification of the whistle parameters is generally considered to be a response to the engine noise. Little is known about the impact of the physical presence of vessels on dolphin acoustics. Whistle parameters of the coastal and oceanic ecotypes of common bottlenose dolphins in La Paz Bay, Mexico, were measured after the approach of the research vessel and its engine shutdown. Recordings of 10 min were made immediately after turning off the engine. For analysis, these recordings were divided from minute 0 to minute 5, and from minute 5:01 to minute 10. The whistles of the oceanic ecotype showed higher maximum, minimum and peak frequency in the second time interval compared to the first one. The whistle rate decreased in the second time interval. The whistles of the coastal ecotype showed no difference between the two time intervals. The physical presence of the research vessel could have induced a change in the whistle parameters of the oceanic dolphins until habituation to the vessel disturbance. The oceanic ecotype could increase the whistle rate and decrease the whistle frequencies to maintain acoustic contact more frequently and for longer distances. The coastal ecotype, showing no significant changes in the whistle parameters, could be more habituated to the presence of vessels and display a higher tolerance.
bibliographic citation: Antichi et al. (2022) Changes in whistle parameters of two common bottlenose dolphin ecotypes as a result of the physical presence of the research vessel. PeerJ 10:e14074 https://doi.org/10.7717/peerj.14074
date submitted: 2022-05-19
date accepted: 2022-08-27
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Antichi
  given name: Simone
author list: Agent
  family name: Urbán R.
  given name: Jorge
author list: Agent
  family name: Martínez-Aguilar
  given name: Sergio
author list: Agent
  family name: Viloria-Gómora
  given name: Lorena
doi: 10.7717/peerj.14074
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Antichi et al.
attribution name: Antichi et al.

Dynamics of the gut microbiota in rats after hypobaric hypoxia exposure
type: item
type: AcademicArticle
description: Background Gut microbiota plays an important role in host health and is influenced by multiple factors. Hypobaric hypoxia usually existing at high altitude conditions can adversely affect normal physiological functions. However, the dynamic changes of gut microbiota influenced by hypobaric hypoxia have not been elucidated. Methods In this study, we collected fecal samples from seven rats at 14 time points from entering the hypobaric chamber (eight time points) to leaving the chamber (six time points) and five rats served as normoxic controls. Metagenome sequencing was performed on all samples and the dynamics of taxa and functions were analyzed. Results We found that the α-diversity was changed in the first 5 days after entering or leaving the hypobaric chamber. The β-diversity analysis revealed that gut microbiota structure was significantly separated among 14 time points. After entering the chamber, the relative abundance of Bacteroides decreased and the most abundant genus turned into Prevotella. The abundance of Firmicutes and Bacteroidetes showed an opposite trend and both have a significant change within 5 days after entering or leaving the hypobaric hypoxia chamber. Some obligate anaerobic bacteria belonging to Desulfovibrio and Alistipes were significantly enriched after entering the chamber for 5 weeks, whereas Probiotics like Bifidobacterium and Lactococcus, and short-chain fatty acids producers like Butyrivibrio and Pseudobutyrivibrio were significantly enriched after leaving the chamber for 3 weeks. Microbial functions like ‘Two-component regulatory system’, ‘beta-carotene biosynthesis’ and ‘Fatty acid biosynthesis’ were significantly enriched after entering the chamber for 5 weeks. Hypobaric hypoxia conditions could deeply affect the diversity and structure of gut microbiota. The alterations of abundance of dominant taxa (Firmicutes and Bacteroidetes), increased anaerobes and decreased probiotics induced by hypobaric hypoxia conditions might affect the …
format: application/pdf
format: text/html
creator: Yang Han
creator: Jiayu Xu
creator: Yan Yan
creator: Xiaojing Zhao
subject: Biochemistry
subject: Bioinformatics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.14090
publisher: PeerJ Inc.
rights: © 2022 Han et al.
abstract: Background Gut microbiota plays an important role in host health and is influenced by multiple factors. Hypobaric hypoxia usually existing at high altitude conditions can adversely affect normal physiological functions. However, the dynamic changes of gut microbiota influenced by hypobaric hypoxia have not been elucidated. Methods In this study, we collected fecal samples from seven rats at 14 time points from entering the hypobaric chamber (eight time points) to leaving the chamber (six time points) and five rats served as normoxic controls. Metagenome sequencing was performed on all samples and the dynamics of taxa and functions were analyzed. Results We found that the α-diversity was changed in the first 5 days after entering or leaving the hypobaric chamber. The β-diversity analysis revealed that gut microbiota structure was significantly separated among 14 time points. After entering the chamber, the relative abundance of Bacteroides decreased and the most abundant genus turned into Prevotella. The abundance of Firmicutes and Bacteroidetes showed an opposite trend and both have a significant change within 5 days after entering or leaving the hypobaric hypoxia chamber. Some obligate anaerobic bacteria belonging to Desulfovibrio and Alistipes were significantly enriched after entering the chamber for 5 weeks, whereas Probiotics like Bifidobacterium and Lactococcus, and short-chain fatty acids producers like Butyrivibrio and Pseudobutyrivibrio were significantly enriched after leaving the chamber for 3 weeks. Microbial functions like ‘Two-component regulatory system’, ‘beta-carotene biosynthesis’ and ‘Fatty acid biosynthesis’ were significantly enriched after entering the chamber for 5 weeks. Hypobaric hypoxia conditions could deeply affect the diversity and structure of gut microbiota. The alterations of abundance of dominant taxa (Firmicutes and Bacteroidetes), increased anaerobes and decreased probiotics induced by hypobaric hypoxia conditions might affect the …
bibliographic citation: Han et al. (2022) Dynamics of the gut microbiota in rats after hypobaric hypoxia exposure. PeerJ 10:e14090 https://doi.org/10.7717/peerj.14090
date submitted: 2022-04-11
date accepted: 2022-08-30
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Yang
author list: Agent
  family name: Xu
  given name: Jiayu
author list: Agent
  family name: Yan
  given name: Yan
author list: Agent
  family name: Zhao
  given name: Xiaojing
doi: 10.7717/peerj.14090
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Han et al.
attribution name: Han et al.

Comparative assessment of enamel remineralisation on the surface microhardness of demineralized enamel - an in vitro study
type: item
type: AcademicArticle
description: Objective The main objective of the study was to compare two different remineralising materials containing casein phosphopeptide-amorphous calcium phosphate, bioactive glass on enamel surface microhardness. Materials and Methods Thirty premolars were used for specimen preparation. Group 1 (the control group) consisted of intact enamel samples, group 2: CPP-ACPF (Tooth Mousse Plus), group 3: bioenamel remineralising gel (Prevest DenPro). All specimens were subjected to demineralisation except the control group, followed by which remineralising agents were applied. A universal hardness tester was used to assess the surface microhardness of all samples. Results were analysed using one-way ANOVA test and comparison was analysed using Scheffe’s post hoc least significant difference (LSD) test. Results Both remineralising agents used in groups 2 and 3 have shown significant outcome in terms of improving the surface microhardness in comparison with the control group. Group 2 increased the enamel hardness by 8.34 where P = 0.023 whereas group 3 increased the hardness by 5.87, where P = 0.01. Conclusion Group 2 has a superior hardness value than group 3; however, no statistically significant results were obtained between both the groups.
format: application/pdf
format: text/html
creator: Bhavika Bhavsar
creator: Mary Vijo
creator: Pranjely Sharma
creator: Tulika Patnaik
creator: Mohammad Khursheed Alam
creator: Santosh Patil
subject: Biochemistry
subject: Anatomy and Physiology
subject: Dentistry
subject: Drugs and Devices
subject: Biomechanics
description: doi:10.7717/peerj.14098
publisher: PeerJ Inc.
rights: © 2022 Bhavsar et al.
abstract: Objective The main objective of the study was to compare two different remineralising materials containing casein phosphopeptide-amorphous calcium phosphate, bioactive glass on enamel surface microhardness. Materials and Methods Thirty premolars were used for specimen preparation. Group 1 (the control group) consisted of intact enamel samples, group 2: CPP-ACPF (Tooth Mousse Plus), group 3: bioenamel remineralising gel (Prevest DenPro). All specimens were subjected to demineralisation except the control group, followed by which remineralising agents were applied. A universal hardness tester was used to assess the surface microhardness of all samples. Results were analysed using one-way ANOVA test and comparison was analysed using Scheffe’s post hoc least significant difference (LSD) test. Results Both remineralising agents used in groups 2 and 3 have shown significant outcome in terms of improving the surface microhardness in comparison with the control group. Group 2 increased the enamel hardness by 8.34 where P = 0.023 whereas group 3 increased the hardness by 5.87, where P = 0.01. Conclusion Group 2 has a superior hardness value than group 3; however, no statistically significant results were obtained between both the groups.
bibliographic citation: Bhavsar et al. (2022) Comparative assessment of enamel remineralisation on the surface microhardness of demineralized enamel - an in vitro study. PeerJ 10:e14098 https://doi.org/10.7717/peerj.14098
date submitted: 2022-04-26
date accepted: 2022-08-31
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bhavsar
  given name: Bhavika
author list: Agent
  family name: Vijo
  given name: Mary
author list: Agent
  family name: Sharma
  given name: Pranjely
author list: Agent
  family name: Patnaik
  given name: Tulika
author list: Agent
  family name: Alam
  given name: Mohammad Khursheed
author list: Agent
  family name: Patil
  given name: Santosh
doi: 10.7717/peerj.14098
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Bhavsar et al.
attribution name: Bhavsar et al.

Interactions between two functionally distinct aquatic invertebrate herbivores complicate ecosystem- and population-level resilience
type: item
type: AcademicArticle
description: Resilience, the capacity for a system to bounce-back after a perturbation, is critical for conservation and restoration efforts. Different functional traits have differential effects on system-level resilience. We test this experimentally in a lab system consisting of algae consumed by zooplankton, snails, or both, using an eutrophication event as a perturbation. We examined seston settlement load, chlorophyll-a and ammonium concentration as gauges of resilience. We find that Daphnia magna increased our measures of resilience. But this effect is not consistent across ecosystem measures; in fact, D. magna increased the difference between disturbed and undisturbed treatments in seston settlement loads. We have some evidence of shifting reproductive strategy in response to perturbation in D. magna and in the presence of Physa sp. These shifts correspond with altered population levels in D. magna, suggesting feedback loops between the herbivore species. While these results suggest only an ambiguous connection between functional traits to ecosystem resilience, they point to the difficulties in establishing such a link: indirect effects of one species on reproduction of another and different scales of response among components of the system, are just two examples that may compromise the power of simple predictions.
format: application/pdf
format: text/html
creator: Jo A. Werba
creator: Alexander C. Phong
creator: Lakhdeep Brar
creator: Acacia Frempong-Manso
creator: Ofure Vanessa Oware
creator: Jurek Kolasa
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.14103
publisher: PeerJ Inc.
rights: © 2022 Werba et al.
abstract: Resilience, the capacity for a system to bounce-back after a perturbation, is critical for conservation and restoration efforts. Different functional traits have differential effects on system-level resilience. We test this experimentally in a lab system consisting of algae consumed by zooplankton, snails, or both, using an eutrophication event as a perturbation. We examined seston settlement load, chlorophyll-a and ammonium concentration as gauges of resilience. We find that Daphnia magna increased our measures of resilience. But this effect is not consistent across ecosystem measures; in fact, D. magna increased the difference between disturbed and undisturbed treatments in seston settlement loads. We have some evidence of shifting reproductive strategy in response to perturbation in D. magna and in the presence of Physa sp. These shifts correspond with altered population levels in D. magna, suggesting feedback loops between the herbivore species. While these results suggest only an ambiguous connection between functional traits to ecosystem resilience, they point to the difficulties in establishing such a link: indirect effects of one species on reproduction of another and different scales of response among components of the system, are just two examples that may compromise the power of simple predictions.
bibliographic citation: Werba et al. (2022) Interactions between two functionally distinct aquatic invertebrate herbivores complicate ecosystem- and population-level resilience. PeerJ 10:e14103 https://doi.org/10.7717/peerj.14103
date submitted: 2022-02-28
date accepted: 2022-09-01
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Werba
  given name: Jo A.
author list: Agent
  family name: Phong
  given name: Alexander C.
author list: Agent
  family name: Brar
  given name: Lakhdeep
author list: Agent
  family name: Frempong-Manso
  given name: Acacia
author list: Agent
  family name: Oware
  given name: Ofure Vanessa
author list: Agent
  family name: Kolasa
  given name: Jurek
doi: 10.7717/peerj.14103
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Werba et al.
attribution name: Werba et al.

Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations
type: item
type: AcademicArticle
description: The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.
format: application/pdf
format: text/html
creator: Hossam Nada
creator: Ahmed Elkamhawy
creator: Kyeong Lee
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Computational Science
subject: COVID-19
description: doi:10.7717/peerj.14120
publisher: PeerJ Inc.
rights: © 2022 Nada et al.
abstract: The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth molecular docking studies and MM-GBSA calculations over SARS-COV-2 Mpro. Finally, the most promising hit, compound (1), and the potent standard (III) were subjected to 100 ns molecular dynamics (MD) simulations and in silico ADME study. The result of the MD analysis as well as the in silico pharmacokinetic study reveal compound 1 to be a promising SARS-Cov-2 MPro inhibitor suitable for further development.
bibliographic citation: Nada et al. (2022) Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations. PeerJ 10:e14120 https://doi.org/10.7717/peerj.14120
date submitted: 2022-06-10
date accepted: 2022-09-05
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nada
  given name: Hossam
author list: Agent
  family name: Elkamhawy
  given name: Ahmed
author list: Agent
  family name: Lee
  given name: Kyeong
doi: 10.7717/peerj.14120
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Nada et al.
attribution name: Nada et al.

Deep ploughing in the summer fallow season and optimizing nitrogen rate can increase yield, water, and nitrogen efficiencies of rain-fed winter wheat in the Loess Plateau region of China
type: item
type: AcademicArticle
description: Background About 60% of the annual precipitation in the Loess Plateau occurs during the summer fallow season, and does not align with the wheat growing season. In addition, the nitrogen use efficiency is low in this area because nutrient availability is affected by drought. As a result, rainwater storage during the summer fallow season is very important to increasing nitrogen use efficiency, and to the stable production of dryland wheat in the Loess Plateau. Methods A 3-year field experiment in the eastern part of the Loess Plateau was conducted with two tillage methods (no tillage (NT) and deep ploughing (DP)) and five N rates (0, 120, 150, 180, and 210 kg N ha−1) to study the effect of tillage on soil water utilization, plant nitrogen utilization, and wheat yield. Result Compared to NT, DP showed a larger increase in soil water storage (SWSf) and precipitation storage efficiency (PSEf) during the two dry summer fallow seasons than in the normal summer fallow season. DP substantially increased the pre-anthesis soil water consumption (SWCpre) and N translocation. The average yield under DP was 12.46% and 14.92–18.29% higher than under NT in the normal and dry seasons, respectively. A 1 mm increase in SWCpre could increase grain yield by 25.28 kg ha−1, water use efficiency (WUE) by 0.069 kg ha−1 mm−1, and nitrogen utilization efficiency (NUtE) by 0.029 kg kg−1. DP could reduce the N rate by 11.49–53.34% in the normal seasons and 40.97–65.07% in the dry seasons compared to the same highest point of yield, WUE, and NUtE under NT. Conclusion Deep ploughing in the summer fallow season, paired with optimized N application, could help increase wheat yield and nitrogen efficiency in dryland.
format: application/pdf
format: text/html
creator: Rongrong Zhang
creator: Peiru Wang
creator: Wenxiang Wang
creator: Aixia Ren
creator: Hafeez Noor
creator: Rong Zhong
creator: Zhiqiang Gao
creator: Min Sun
subject: Agricultural Science
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.14153
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: Background About 60% of the annual precipitation in the Loess Plateau occurs during the summer fallow season, and does not align with the wheat growing season. In addition, the nitrogen use efficiency is low in this area because nutrient availability is affected by drought. As a result, rainwater storage during the summer fallow season is very important to increasing nitrogen use efficiency, and to the stable production of dryland wheat in the Loess Plateau. Methods A 3-year field experiment in the eastern part of the Loess Plateau was conducted with two tillage methods (no tillage (NT) and deep ploughing (DP)) and five N rates (0, 120, 150, 180, and 210 kg N ha−1) to study the effect of tillage on soil water utilization, plant nitrogen utilization, and wheat yield. Result Compared to NT, DP showed a larger increase in soil water storage (SWSf) and precipitation storage efficiency (PSEf) during the two dry summer fallow seasons than in the normal summer fallow season. DP substantially increased the pre-anthesis soil water consumption (SWCpre) and N translocation. The average yield under DP was 12.46% and 14.92–18.29% higher than under NT in the normal and dry seasons, respectively. A 1 mm increase in SWCpre could increase grain yield by 25.28 kg ha−1, water use efficiency (WUE) by 0.069 kg ha−1 mm−1, and nitrogen utilization efficiency (NUtE) by 0.029 kg kg−1. DP could reduce the N rate by 11.49–53.34% in the normal seasons and 40.97–65.07% in the dry seasons compared to the same highest point of yield, WUE, and NUtE under NT. Conclusion Deep ploughing in the summer fallow season, paired with optimized N application, could help increase wheat yield and nitrogen efficiency in dryland.
bibliographic citation: Zhang et al. (2022) Deep ploughing in the summer fallow season and optimizing nitrogen rate can increase yield, water, and nitrogen efficiencies of rain-fed winter wheat in the Loess Plateau region of China. PeerJ 10:e14153 https://doi.org/10.7717/peerj.14153
date submitted: 2022-05-30
date accepted: 2022-09-07
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Rongrong
author list: Agent
  family name: Wang
  given name: Peiru
author list: Agent
  family name: Wang
  given name: Wenxiang
author list: Agent
  family name: Ren
  given name: Aixia
author list: Agent
  family name: Noor
  given name: Hafeez
author list: Agent
  family name: Zhong
  given name: Rong
author list: Agent
  family name: Gao
  given name: Zhiqiang
author list: Agent
  family name: Sun
  given name: Min
doi: 10.7717/peerj.14153
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: © 2022 Zhang et al.
attribution name: Zhang et al.

Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench)
type: item
type: AcademicArticle
description: The aboveground parts of plants are covered with cuticle, a hydrophobic layer composed of cutin polyester and cuticular wax that can protect plants from various environmental stresses. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. Although the properties of KCS family genes have been investigated in many plant species, the understanding of this gene family in sorghum is still limited. Here, a total of 25 SbKCS genes were identified in the sorghum genome, which were named from SbKCS1 to SbKCS25. Evolutionary analysis among different species divided the KCS family into five subfamilies and the SbKCSs were more closely related to maize, implying a closer evolutionary relationship between sorghum and maize. All SbKCS genes were located on chromosomes 1, 2, 3, 4, 5, 6, 9 and 10, respectively, while Chr 1 and Chr 10 contained more KCS genes than other chromosomes. The prediction results of subcellular localization showed that SbKCSs were mainly expressed in the plasma membrane and mitochondria. Gene structure analysis revealed that there was 0–1 intron in the sorghum KCS family and SbKCSs within the same subgroup were similar. Multiple cis-acting elements related to abiotic stress, light and hormone response were enriched in the promoters of SbKCS genes, which indicated the functional diversity among these genes. The three-dimensional structure analysis showed that a compact spherical space structure was formed by various secondary bonds to maintain the stability of SbKCS proteins, which was necessary for their biological activity. qRT-PCR results revealed that nine randomly selected SbKCS genes expressed differently under drought and salt treatments, among which SbKCS8 showed the greatest fold of expression difference at 12 h after drought and salt stresses, which suggested that the SbKCS genes played a potential role in abiotic stress responses. Taken together, these results provided an insight into investigating the functions of …
format: application/pdf
format: text/html
creator: Aixia Zhang
creator: Jingjing Xu
creator: Xin Xu
creator: Junping Wu
creator: Ping Li
creator: Baohua Wang
creator: Hui Fang
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14156
publisher: PeerJ Inc.
rights: © 2022 Zhang et al.
abstract: The aboveground parts of plants are covered with cuticle, a hydrophobic layer composed of cutin polyester and cuticular wax that can protect plants from various environmental stresses. β-Ketoacyl-CoA synthase (KCS) is the key rate-limiting enzyme in plant wax synthesis. Although the properties of KCS family genes have been investigated in many plant species, the understanding of this gene family in sorghum is still limited. Here, a total of 25 SbKCS genes were identified in the sorghum genome, which were named from SbKCS1 to SbKCS25. Evolutionary analysis among different species divided the KCS family into five subfamilies and the SbKCSs were more closely related to maize, implying a closer evolutionary relationship between sorghum and maize. All SbKCS genes were located on chromosomes 1, 2, 3, 4, 5, 6, 9 and 10, respectively, while Chr 1 and Chr 10 contained more KCS genes than other chromosomes. The prediction results of subcellular localization showed that SbKCSs were mainly expressed in the plasma membrane and mitochondria. Gene structure analysis revealed that there was 0–1 intron in the sorghum KCS family and SbKCSs within the same subgroup were similar. Multiple cis-acting elements related to abiotic stress, light and hormone response were enriched in the promoters of SbKCS genes, which indicated the functional diversity among these genes. The three-dimensional structure analysis showed that a compact spherical space structure was formed by various secondary bonds to maintain the stability of SbKCS proteins, which was necessary for their biological activity. qRT-PCR results revealed that nine randomly selected SbKCS genes expressed differently under drought and salt treatments, among which SbKCS8 showed the greatest fold of expression difference at 12 h after drought and salt stresses, which suggested that the SbKCS genes played a potential role in abiotic stress responses. Taken together, these results provided an insight into investigating the functions of …
bibliographic citation: Zhang et al. (2022) Genome-wide identification and characterization of the KCS gene family in sorghum (Sorghum bicolor (L.) Moench). PeerJ 10:e14156 https://doi.org/10.7717/peerj.14156
date submitted: 2022-03-15
date accepted: 2022-09-08
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Aixia
author list: Agent
  family name: Xu
  given name: Jingjing
author list: Agent
  family name: Xu
  given name: Xin
author list: Agent
  family name: Wu
  given name: Junping
author list: Agent
  family name: Li
  given name: Ping
author list: Agent
  family name: Wang
  given name: Baohua
author list: Agent
  family name: Fang
  given name: Hui
doi: 10.7717/peerj.14156
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Zhang et al.
attribution name: Zhang et al.

Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil
type: item
type: AcademicArticle
description: Humic acids (HAs) are complex organic substances with abundant functional groups (e.g., carboxyl, phenolic-OH, etc.). They are commonly distributed in the soil environment and exert a double-edged sword effect in controlling the migration and transformation of uranium. However, the effects of HAs on dynamic processes associated with uranium transformation are still unclear. In this study, we used HAs derived from leonardite (L-HA) and commercial HA (C-HA) as exogenous organic matter and C-HA as the reference. UO2, UO3, and UO2(NO3)2 were used as the sources of U to explore the fractionations of uranium in the soil. We also studied the behavior of the HA. The incubation experiments were designed to investigate the effects of HA on the soil pH, uranium fraction transformation, dynamic behavior of exchangeable, weak acid, and labile uranium. The observations were made for one month. The results showed that soil pH decreased for L-HA but increased for C-HA. Under these conditions, uranium tended to transform into an inactive fraction. The dynamic behavior of exchangeable, weak acid, and labile uranium varied with the sources of HA and uranium. This study highlighted that HA could affect soil pH and the dynamic redistribution of U fractions. The results suggest that the sources of HA and U should be considered when using HA as the remediation material for uranium-contaminated soils.
format: application/pdf
format: text/html
creator: Fande Meng
creator: Qiuxiang Huang
creator: Yongbing Cai
creator: Guodong Yuan
creator: Liang Xiao
creator: Fengxiang X. Han
subject: Soil Science
subject: Ecotoxicology
subject: Biogeochemistry
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.14162
publisher: PeerJ Inc.
rights: © 2022 Meng et al.
abstract: Humic acids (HAs) are complex organic substances with abundant functional groups (e.g., carboxyl, phenolic-OH, etc.). They are commonly distributed in the soil environment and exert a double-edged sword effect in controlling the migration and transformation of uranium. However, the effects of HAs on dynamic processes associated with uranium transformation are still unclear. In this study, we used HAs derived from leonardite (L-HA) and commercial HA (C-HA) as exogenous organic matter and C-HA as the reference. UO2, UO3, and UO2(NO3)2 were used as the sources of U to explore the fractionations of uranium in the soil. We also studied the behavior of the HA. The incubation experiments were designed to investigate the effects of HA on the soil pH, uranium fraction transformation, dynamic behavior of exchangeable, weak acid, and labile uranium. The observations were made for one month. The results showed that soil pH decreased for L-HA but increased for C-HA. Under these conditions, uranium tended to transform into an inactive fraction. The dynamic behavior of exchangeable, weak acid, and labile uranium varied with the sources of HA and uranium. This study highlighted that HA could affect soil pH and the dynamic redistribution of U fractions. The results suggest that the sources of HA and U should be considered when using HA as the remediation material for uranium-contaminated soils.
bibliographic citation: Meng et al. (2022) Effect of humic acid derived from leonardite on the redistribution of uranium fractions in soil. PeerJ 10:e14162 https://doi.org/10.7717/peerj.14162
date submitted: 2022-07-28
date accepted: 2022-09-09
issued: 2022-10-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Fande
author list: Agent
  family name: Huang
  given name: Qiuxiang
author list: Agent
  family name: Cai
  given name: Yongbing
author list: Agent
  family name: Yuan
  given name: Guodong
author list: Agent
  family name: Xiao
  given name: Liang
author list: Agent
  family name: Han
  given name: Fengxiang X.
doi: 10.7717/peerj.14162
volume: 10
issn: 2167-8359
publication name: PeerJ
publication date: 2022-10-07
copyright: ©2022 Meng et al.
attribution name: Meng et al.

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