PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Emergent trees in Colophospermum mopane woodland: influence of elephant density on persistence versus attrition
items: TICI: a taxon-independent community index for eDNA-based ecological health assessment
items: Different ecological demands shape differences in population structure and behaviour among the two generations of the small pearl-bordered fritillary
items: Genome-wide association studies reveal stable loci for wheat grain size under different sowing dates
items: Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment
items: Multiscale transport and 4D time-lapse imaging in precision-cut liver slices (PCLS)
items: An alternative peptone preparation using Hermetia illucens (Black soldier fly) hydrolysis: process optimization and performance evaluation
items: moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud
items: New records of immature aquatic Diptera from the Foulden Maar Fossil-Lagerstätte, New Zealand, and their biogeographic implications
items: Spatiotemporal variables comparison between drop jump and horizontal drop jump in elite jumpers and sprinters

Emergent trees in Colophospermum mopane woodland: influence of elephant density on persistence versus attrition
type: item
type: AcademicArticle
description: Colophospermum mopane (mopane) forms mono-dominant woodlands covering extensive areas of southern Africa. Mopane provides a staple foodstuff for elephants, who hedge woodland by reducing trees to small trees or shrubs, leaving emergent trees which are too large to be pollarded. Emergent trees are important for supporting faunal biodiversity, but they can be killed by ringbarking. This study first examined the influence of elephant density on woodland transformation and the height distribution of canopy volume, and, second, whether canopy volume is maintained, and tall emergent trees too large to be broken can persist, under chronic elephant utilisation. Three regimes of 0.23, 0.59 and 2.75 elephants km−2 differed in vegetation structure and the height structure of trees. Areas under the highest elephant density supported the lowest total canopy volume owing to less canopy for plants >3 m in height, shorter trees, loss of most trees 6–10 m in height, but trees >10 m in height (>45 cm stem diameter) persisted. Under eight years of chronic utilisation by elephants, transformed mopane woodland maintained its plant density and canopy volume. Plant density was greatest for the 0–1 m height class, whereas the 3.1–6 m height class provided the bulk of canopy volume, and the 1.1–3 m height layer contained the most canopy volume. Emergent trees (>10 m in height) suffered a loss of 1.4% per annum as a result of debarking. Canopy dieback of emergent trees increased conspicuously when more than 50% of a stem was debarked, and such trees could be toppled by windthrow before being ringbarked. Thus relict emergent trees will slowly be eliminated but will not be replaced whilst smaller trees are being maintained in a pollarded state. Woodland transformation has not markedly reduced canopy volume available to elephants, but the slow attrition of emergent trees may affect supported biota, especially cavity-dependent vertebrate species, making use of these trees.
format: application/pdf
format: text/html
creator: Timothy O’Connor
creator: Angela Ferguson
creator: Bruce W. Clegg
creator: Nita Pallett
creator: Jeremy J. Midgley
creator: Julius Shimbani
subject: Conservation Biology
subject: Ecology
subject: Plant Science
subject: Zoology
subject: Natural Resource Management
description: doi:10.7717/peerj.16961
publisher: PeerJ Inc.
rights: © 2024 O’Connor et al.
abstract: Colophospermum mopane (mopane) forms mono-dominant woodlands covering extensive areas of southern Africa. Mopane provides a staple foodstuff for elephants, who hedge woodland by reducing trees to small trees or shrubs, leaving emergent trees which are too large to be pollarded. Emergent trees are important for supporting faunal biodiversity, but they can be killed by ringbarking. This study first examined the influence of elephant density on woodland transformation and the height distribution of canopy volume, and, second, whether canopy volume is maintained, and tall emergent trees too large to be broken can persist, under chronic elephant utilisation. Three regimes of 0.23, 0.59 and 2.75 elephants km−2 differed in vegetation structure and the height structure of trees. Areas under the highest elephant density supported the lowest total canopy volume owing to less canopy for plants >3 m in height, shorter trees, loss of most trees 6–10 m in height, but trees >10 m in height (>45 cm stem diameter) persisted. Under eight years of chronic utilisation by elephants, transformed mopane woodland maintained its plant density and canopy volume. Plant density was greatest for the 0–1 m height class, whereas the 3.1–6 m height class provided the bulk of canopy volume, and the 1.1–3 m height layer contained the most canopy volume. Emergent trees (>10 m in height) suffered a loss of 1.4% per annum as a result of debarking. Canopy dieback of emergent trees increased conspicuously when more than 50% of a stem was debarked, and such trees could be toppled by windthrow before being ringbarked. Thus relict emergent trees will slowly be eliminated but will not be replaced whilst smaller trees are being maintained in a pollarded state. Woodland transformation has not markedly reduced canopy volume available to elephants, but the slow attrition of emergent trees may affect supported biota, especially cavity-dependent vertebrate species, making use of these trees.
bibliographic citation: O’Connor et al. (2024) Emergent trees in Colophospermum mopane woodland: influence of elephant density on persistence versus attrition. PeerJ 12:e16961 https://doi.org/10.7717/peerj.16961
date submitted: 2023-11-16
date accepted: 2024-01-26
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: O’Connor
  given name: Timothy
author list: Agent
  family name: Ferguson
  given name: Angela
author list: Agent
  family name: Clegg
  given name: Bruce W.
author list: Agent
  family name: Pallett
  given name: Nita
author list: Agent
  family name: Midgley
  given name: Jeremy J.
author list: Agent
  family name: Shimbani
  given name: Julius
doi: 10.7717/peerj.16961
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 O’Connor et al.
attribution name: O’Connor et al.

TICI: a taxon-independent community index for eDNA-based ecological health assessment
type: item
type: AcademicArticle
description: Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to…
format: application/pdf
format: text/html
creator: Shaun P. Wilkinson
creator: Amy A. Gault
creator: Susan A. Welsh
creator: Joshua P. Smith
creator: Bruno O. David
creator: Andy S. Hicks
creator: Daniel R. Fake
creator: Alastair M. Suren
creator: Megan R. Shaffer
creator: Simon N. Jarman
creator: Michael Bunce
subject: Biodiversity
subject: Bioinformatics
subject: Ecology
subject: Molecular Biology
subject: Freshwater Biology
description: doi:10.7717/peerj.16963
publisher: PeerJ Inc.
rights: © 2024 Wilkinson et al.
abstract: Global biodiversity is declining at an ever-increasing rate. Yet effective policies to mitigate or reverse these declines require ecosystem condition data that are rarely available. Morphology-based bioassessment methods are difficult to scale, limited in scope, suffer prohibitive costs, require skilled taxonomists, and can be applied inconsistently between practitioners. Environmental DNA (eDNA) metabarcoding offers a powerful, reproducible and scalable solution that can survey across the tree-of-life with relatively low cost and minimal expertise for sample collection. However, there remains a need to condense the complex, multidimensional community information into simple, interpretable metrics of ecological health for environmental management purposes. We developed a riverine taxon-independent community index (TICI) that objectively assigns indicator values to amplicon sequence variants (ASVs), and significantly improves the statistical power and utility of eDNA-based bioassessments. The TICI model training step uses the Chessman iterative learning algorithm to assign health indicator scores to a large number of ASVs that are commonly encountered across a wide geographic range. New sites can then be evaluated for ecological health by averaging the indicator value of the ASVs present at the site. We trained a TICI model on an eDNA dataset from 53 well-studied riverine monitoring sites across New Zealand, each sampled with a high level of biological replication (n = 16). Eight short-amplicon metabarcoding assays were used to generate data from a broad taxonomic range, including bacteria, microeukaryotes, fungi, plants, and animals. Site-specific TICI scores were strongly correlated with historical stream condition scores from macroinvertebrate assessments (macroinvertebrate community index or MCI; R2 = 0.82), and TICI variation between sample replicates was minimal (CV = 0.013). Taken together, this demonstrates the potential for taxon-independent eDNA analysis to…
bibliographic citation: Wilkinson et al. (2024) TICI: a taxon-independent community index for eDNA-based ecological health assessment. PeerJ 12:e16963 https://doi.org/10.7717/peerj.16963
date submitted: 2023-03-31
date accepted: 2024-01-26
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wilkinson
  given name: Shaun P.
author list: Agent
  family name: Gault
  given name: Amy A.
author list: Agent
  family name: Welsh
  given name: Susan A.
author list: Agent
  family name: Smith
  given name: Joshua P.
author list: Agent
  family name: David
  given name: Bruno O.
author list: Agent
  family name: Hicks
  given name: Andy S.
author list: Agent
  family name: Fake
  given name: Daniel R.
author list: Agent
  family name: Suren
  given name: Alastair M.
author list: Agent
  family name: Shaffer
  given name: Megan R.
author list: Agent
  family name: Jarman
  given name: Simon N.
author list: Agent
  family name: Bunce
  given name: Michael
doi: 10.7717/peerj.16963
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Wilkinson et al.
attribution name: Wilkinson et al.

Different ecological demands shape differences in population structure and behaviour among the two generations of the small pearl-bordered fritillary
type: item
type: AcademicArticle
description: The population structure and behaviour of univoltine butterfly species have been studied intensively. However, much less is known about bivoltine species. In particular, in-depth studies of the differences in population structure, behaviour, and ecology between these two generations are largely lacking. Therefore, we here present a mark-release-recapture study of two successive generations of the fritillary butterfly Boloria selene performed in eastern Brandenburg (Germany). We revealed intersexual and intergenerational differences regarding behaviour, dispersal, population characteristics, and protandry. The observed population densities were higher in the second generation. The flight activity of females decreased in the second generation, but remained unchanged in males. This was further supported by the rate of wing decay. The first generation displayed a linear correlation between wing decay and passed time in both sexes, whereas the linear correlation was lost in second-generation females. The proportion of resting individuals in both sexes increased in the second generation, as well as the number of nectaring females. The choice of plant genera used for nectaring seems to be more specialised in the first and more opportunistic in the second generation. The average flight distances were generally higher for females than for males and overall higher in the first generation. Predictions of long-distance movements based on the inverse power function were also generally higher in females than in males but lower in the first generation. Additionally, we found protandry only in the first but not in the second generation, which might correlate with the different developmental pathways of the two generations. These remarkable differences between both generations might reflect an adaptation to the different ecological demands during the flight season and the different tasks they have, i.e., growth in the spring season; dispersal and colonisation of new habitats during …
format: application/pdf
format: text/html
creator: Ann-Kathrin Sing
creator: Laura Guderjan
creator: Klara Lemke
creator: Martin Wiemers
creator: Thomas Schmitt
creator: Martin Wendt
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Entomology
subject: Population Biology
description: doi:10.7717/peerj.16965
publisher: PeerJ Inc.
rights: © 2024 Sing et al.
abstract: The population structure and behaviour of univoltine butterfly species have been studied intensively. However, much less is known about bivoltine species. In particular, in-depth studies of the differences in population structure, behaviour, and ecology between these two generations are largely lacking. Therefore, we here present a mark-release-recapture study of two successive generations of the fritillary butterfly Boloria selene performed in eastern Brandenburg (Germany). We revealed intersexual and intergenerational differences regarding behaviour, dispersal, population characteristics, and protandry. The observed population densities were higher in the second generation. The flight activity of females decreased in the second generation, but remained unchanged in males. This was further supported by the rate of wing decay. The first generation displayed a linear correlation between wing decay and passed time in both sexes, whereas the linear correlation was lost in second-generation females. The proportion of resting individuals in both sexes increased in the second generation, as well as the number of nectaring females. The choice of plant genera used for nectaring seems to be more specialised in the first and more opportunistic in the second generation. The average flight distances were generally higher for females than for males and overall higher in the first generation. Predictions of long-distance movements based on the inverse power function were also generally higher in females than in males but lower in the first generation. Additionally, we found protandry only in the first but not in the second generation, which might correlate with the different developmental pathways of the two generations. These remarkable differences between both generations might reflect an adaptation to the different ecological demands during the flight season and the different tasks they have, i.e., growth in the spring season; dispersal and colonisation of new habitats during …
bibliographic citation: Sing et al. (2024) Different ecological demands shape differences in population structure and behaviour among the two generations of the small pearl-bordered fritillary. PeerJ 12:e16965 https://doi.org/10.7717/peerj.16965
date submitted: 2023-11-16
date accepted: 2024-01-26
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sing
  given name: Ann-Kathrin
author list: Agent
  family name: Guderjan
  given name: Laura
author list: Agent
  family name: Lemke
  given name: Klara
author list: Agent
  family name: Wiemers
  given name: Martin
author list: Agent
  family name: Schmitt
  given name: Thomas
author list: Agent
  family name: Wendt
  given name: Martin
doi: 10.7717/peerj.16965
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Sing et al.
attribution name: Sing et al.

Genome-wide association studies reveal stable loci for wheat grain size under different sowing dates
type: item
type: AcademicArticle
description: Background Wheat (Tritium aestivum L.) production is critical for global food security. In recent years, due to climate change and the prolonged growing period of rice varieties, the delayed sowing of wheat has resulted in a loss of grain yield in the area of the middle and lower reaches of the Yangtze River. It is of great significance to screen for natural germplasm resources of wheat that are resistant to late sowing and to explore genetic loci that stably control grain size and yield. Methods A collection of 327 wheat accessions from diverse sources were subjected to genome-wide association studies using genotyping-by-sequencing. Field trials were conducted under normal, delayed, and seriously delayed sowing conditions for grain length, width, and thousand-grain weight at two sites. Additionally, the additive main effects and multiplicative interaction (AMMI) model was applied to evaluate the stability of thousand-grain weight of 327 accessions across multiple sowing dates. Results Four wheat germplasm resources have been screened, demonstrating higher stability of thousand-grain weight. A total of 43, 35, and 39 significant MTAs were determined across all chromosomes except for 4D under the three sowing dates, respectively. A total of 10.31% of MTAs that stably affect wheat grain size could be repeatedly identified in at least two sowing dates, with PVE ranging from 0.03% to 38.06%. Among these, six were for GL, three for GW, and one for TGW. There were three novel and stable loci (4A_598189950, 4B_307707920, 2D_622241054) located in conserved regions of the genome, which provide excellent genetic resources for pyramid breeding strategies of superior loci. Our findings offer a theoretical basis for cultivar improvement and marker-assisted selection in wheat breeding practices.
format: application/pdf
format: text/html
creator: Yi Hong
creator: Mengna Zhang
creator: Zechen Yuan
creator: Juan Zhu
creator: Chao Lv
creator: Baojian Guo
creator: Feifei Wang
creator: Rugen Xu
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.16984
publisher: PeerJ Inc.
rights: © 2024 Hong et al.
abstract: Background Wheat (Tritium aestivum L.) production is critical for global food security. In recent years, due to climate change and the prolonged growing period of rice varieties, the delayed sowing of wheat has resulted in a loss of grain yield in the area of the middle and lower reaches of the Yangtze River. It is of great significance to screen for natural germplasm resources of wheat that are resistant to late sowing and to explore genetic loci that stably control grain size and yield. Methods A collection of 327 wheat accessions from diverse sources were subjected to genome-wide association studies using genotyping-by-sequencing. Field trials were conducted under normal, delayed, and seriously delayed sowing conditions for grain length, width, and thousand-grain weight at two sites. Additionally, the additive main effects and multiplicative interaction (AMMI) model was applied to evaluate the stability of thousand-grain weight of 327 accessions across multiple sowing dates. Results Four wheat germplasm resources have been screened, demonstrating higher stability of thousand-grain weight. A total of 43, 35, and 39 significant MTAs were determined across all chromosomes except for 4D under the three sowing dates, respectively. A total of 10.31% of MTAs that stably affect wheat grain size could be repeatedly identified in at least two sowing dates, with PVE ranging from 0.03% to 38.06%. Among these, six were for GL, three for GW, and one for TGW. There were three novel and stable loci (4A_598189950, 4B_307707920, 2D_622241054) located in conserved regions of the genome, which provide excellent genetic resources for pyramid breeding strategies of superior loci. Our findings offer a theoretical basis for cultivar improvement and marker-assisted selection in wheat breeding practices.
bibliographic citation: Hong et al. (2024) Genome-wide association studies reveal stable loci for wheat grain size under different sowing dates. PeerJ 12:e16984 https://doi.org/10.7717/peerj.16984
date submitted: 2023-11-30
date accepted: 2024-01-30
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Yi
author list: Agent
  family name: Zhang
  given name: Mengna
author list: Agent
  family name: Yuan
  given name: Zechen
author list: Agent
  family name: Zhu
  given name: Juan
author list: Agent
  family name: Lv
  given name: Chao
author list: Agent
  family name: Guo
  given name: Baojian
author list: Agent
  family name: Wang
  given name: Feifei
author list: Agent
  family name: Xu
  given name: Rugen
doi: 10.7717/peerj.16984
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Hong et al.
attribution name: Hong et al.

Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment
type: item
type: AcademicArticle
description: Background Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community. Methods In this study, nine PGPR strains, belonging to the genera Pseudomonas and Buttiauxella, were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson’s correlation, Kendall’s tau correlation and Spearman’s rank correlation analysis methods. Results The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community. Discussio…
format: application/pdf
format: text/html
creator: Mengjiao Wang
creator: Xinlong Yang
subject: Agricultural Science
subject: Microbiology
subject: Molecular Biology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.16992
publisher: PeerJ Inc.
rights: © 2024 Wang and Yang
abstract: Background Plant growth-promoting rhizobacteria (PGPR) have a specific symbiotic relationship with plants and rhizosphere soil. The purpose of this study was to evaluate the effects of PGPR on blueberry plant growth, rhizospheric soil nutrients and the microbial community. Methods In this study, nine PGPR strains, belonging to the genera Pseudomonas and Buttiauxella, were selected and added into the soil in which the blueberry cuttings were planted. All the physiological indexes of the cuttings and all rhizospheric soil element contents were determined on day 6 after the quartic root irrigation experiments were completed. The microbial diversity in the soil was determined using high-throughput amplicon sequencing technology. The correlations between phosphorus solubilization, the auxin production of PGPR strains, and the physiological indexes of blueberry plants, and the correlation between rhizospheric microbial diversity and soil element contents were determined using the Pearson’s correlation, Kendall’s tau correlation and Spearman’s rank correlation analysis methods. Results The branch number, leaf number, chlorophyllcontentand plant height of the treated blueberry group were significantly higher than those of the control group. The rhizospheric soil element contents also increased after PGPR root irrigation. The rhizospheric microbial community structure changed significantly under the PGPR of root irrigation. The dominant phyla, except Actinomycetota, in the soil samples had the greatest correlation with phosphorus solubilization and the auxin production of PGPR strains. The branch number, leaf number, and chlorophyllcontent had a positive correlation with the phosphorus solubilization and auxin production of PGPR strains and soil element contents. In conclusion, plant growth could be promoted by the root irrigation of PGPR to improve rhizospheric soil nutrients and the microenvironment, with modification of the rhizospheric soil microbial community. Discussio…
bibliographic citation: Wang et al. (2024) Effects of plant growth-promoting rhizobacteria on blueberry growth and rhizosphere soil microenvironment. PeerJ 12:e16992 https://doi.org/10.7717/peerj.16992
date submitted: 2023-06-15
date accepted: 2024-01-31
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Mengjiao
author list: Agent
  family name: Yang
  given name: Xinlong
doi: 10.7717/peerj.16992
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Wang and Yang
attribution name: Wang and Yang

Multiscale transport and 4D time-lapse imaging in precision-cut liver slices (PCLS)
type: item
type: AcademicArticle
description: Background Monitoring cellular processes across different levels of complexity, from the cellular to the tissue scale, is important for understanding tissue structure and function. However, it is challenging to monitor and estimate these structural and dynamic interactions within three-dimensional (3D) tissue models. Objective The aim of this study was to design a method for imaging, tracking, and quantifying 3D changes in cell morphology (shape and size) within liver tissue, specifically a precision-cut liver slice (PCLS). A PCLS is a 3D model of the liver that allows the study of the structure and function of liver cells in their native microenvironment. Methods Here, we present a method for imaging liver tissue during anisosmotic exposure in a multispectral four-dimensional manner. Three metrics of tissue morphology were measured to quantify the effects of osmotic stress on liver tissue. We estimated the changes in the volume of whole precision cut liver slices, quantified the changes in nuclei position, and calculated the changes in volumetric responses of tissue-embedded cells. Results During equilibration with cell-membrane-permeating and non-permeating solutes, the whole tissue experiences shrinkage and expansion. As nuclei showed a change in position and directional displacement under osmotic stress, we demonstrate that nuclei could be used as a probe to measure local osmotic and mechanical stress. Moreover, we demonstrate that cells change their volume within tissue slices as a result of osmotic perturbation and that this change in volume is dependent on the position of the cell within the tissue and the duration of the exposure. Conclusion The results of this study have implications for a better understanding of multiscale transport, mechanobiology, and triggered biological responses within complex biological structures.
format: application/pdf
format: text/html
creator: Iqra Azam
creator: James D. Benson
subject: Bioengineering
subject: Biophysics
subject: Cell Biology
description: doi:10.7717/peerj.16994
publisher: PeerJ Inc.
rights: © 2024 Azam and Benson
abstract: Background Monitoring cellular processes across different levels of complexity, from the cellular to the tissue scale, is important for understanding tissue structure and function. However, it is challenging to monitor and estimate these structural and dynamic interactions within three-dimensional (3D) tissue models. Objective The aim of this study was to design a method for imaging, tracking, and quantifying 3D changes in cell morphology (shape and size) within liver tissue, specifically a precision-cut liver slice (PCLS). A PCLS is a 3D model of the liver that allows the study of the structure and function of liver cells in their native microenvironment. Methods Here, we present a method for imaging liver tissue during anisosmotic exposure in a multispectral four-dimensional manner. Three metrics of tissue morphology were measured to quantify the effects of osmotic stress on liver tissue. We estimated the changes in the volume of whole precision cut liver slices, quantified the changes in nuclei position, and calculated the changes in volumetric responses of tissue-embedded cells. Results During equilibration with cell-membrane-permeating and non-permeating solutes, the whole tissue experiences shrinkage and expansion. As nuclei showed a change in position and directional displacement under osmotic stress, we demonstrate that nuclei could be used as a probe to measure local osmotic and mechanical stress. Moreover, we demonstrate that cells change their volume within tissue slices as a result of osmotic perturbation and that this change in volume is dependent on the position of the cell within the tissue and the duration of the exposure. Conclusion The results of this study have implications for a better understanding of multiscale transport, mechanobiology, and triggered biological responses within complex biological structures.
bibliographic citation: Azam et al. (2024) Multiscale transport and 4D time-lapse imaging in precision-cut liver slices (PCLS). PeerJ 12:e16994 https://doi.org/10.7717/peerj.16994
date submitted: 2023-09-21
date accepted: 2024-02-01
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Azam
  given name: Iqra
author list: Agent
  family name: Benson
  given name: James D.
doi: 10.7717/peerj.16994
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Azam and Benson
attribution name: Azam and Benson

An alternative peptone preparation using Hermetia illucens (Black soldier fly) hydrolysis: process optimization and performance evaluation
type: item
type: AcademicArticle
description: Background Hermetia illucens (HI), commonly known as the black soldier fly, has been recognized for its prowess in resource utilization and environmental protection because of its ability to transform organic waste into animal feed for livestock, poultry, and aquaculture. However, the potential of the black soldier fly’s high protein content for more than cheap feedstock is still largely unexplored. Methods This study innovatively explores the potential of H. illucens larvae (HIL) protein as a peptone substitute for microbial culture media. Four commercial proteases (alkaline protease, trypsin, trypsase, and papain) were explored to hydrolyze the defatted HIL, and the experimental conditions were optimized via response surface methodology experimental design. The hydrolysate of the defatted HIL was subsequently vacuum freeze-dried and deployed as a growth medium for three bacterial strains (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli) to determine the growth kinetics between the HIL peptone and commercial peptone. Results The optimal conditions were 1.70% w/w complex enzyme (alkaline protease: trypsin at 1:1 ratio) at pH 7.0 and 54 °C for a duration of 4 h. Under these conditions, the hydrolysis of defatted HIL yielded 19.25% ±0.49%. A growth kinetic analysis showed no significant difference in growth parameters (μmax, Xmax, and λ) between the HIL peptone and commercial peptone, demonstrating that the HIL hydrolysate could serve as an effective, low-cost alternative to commercial peptone. This study introduces an innovative approach to HIL protein resource utilization, broadening its application beyond its current use in animal feed.
format: application/pdf
format: text/html
creator: Gaoqiang Liu
creator: Ming Foong Tiang
creator: Shixia Ma
creator: Zeyan Wei
creator: Xiaolin Liang
creator: Mohd Shaiful Sajab
creator: Peer Mohamed Abdul
creator: Xueyan Zhou
creator: Zhongren Ma
creator: Gongtao Ding
subject: Bioengineering
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.16995
publisher: PeerJ Inc.
rights: © 2024 Liu et al.
abstract: Background Hermetia illucens (HI), commonly known as the black soldier fly, has been recognized for its prowess in resource utilization and environmental protection because of its ability to transform organic waste into animal feed for livestock, poultry, and aquaculture. However, the potential of the black soldier fly’s high protein content for more than cheap feedstock is still largely unexplored. Methods This study innovatively explores the potential of H. illucens larvae (HIL) protein as a peptone substitute for microbial culture media. Four commercial proteases (alkaline protease, trypsin, trypsase, and papain) were explored to hydrolyze the defatted HIL, and the experimental conditions were optimized via response surface methodology experimental design. The hydrolysate of the defatted HIL was subsequently vacuum freeze-dried and deployed as a growth medium for three bacterial strains (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli) to determine the growth kinetics between the HIL peptone and commercial peptone. Results The optimal conditions were 1.70% w/w complex enzyme (alkaline protease: trypsin at 1:1 ratio) at pH 7.0 and 54 °C for a duration of 4 h. Under these conditions, the hydrolysis of defatted HIL yielded 19.25% ±0.49%. A growth kinetic analysis showed no significant difference in growth parameters (μmax, Xmax, and λ) between the HIL peptone and commercial peptone, demonstrating that the HIL hydrolysate could serve as an effective, low-cost alternative to commercial peptone. This study introduces an innovative approach to HIL protein resource utilization, broadening its application beyond its current use in animal feed.
bibliographic citation: Liu et al. (2024) An alternative peptone preparation using Hermetia illucens (Black soldier fly) hydrolysis: process optimization and performance evaluation. PeerJ 12:e16995 https://doi.org/10.7717/peerj.16995
date submitted: 2023-10-10
date accepted: 2024-02-01
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Gaoqiang
author list: Agent
  family name: Tiang
  given name: Ming Foong
author list: Agent
  family name: Ma
  given name: Shixia
author list: Agent
  family name: Wei
  given name: Zeyan
author list: Agent
  family name: Liang
  given name: Xiaolin
author list: Agent
  family name: Sajab
  given name: Mohd Shaiful
author list: Agent
  family name: Abdul
  given name: Peer Mohamed
author list: Agent
  family name: Zhou
  given name: Xueyan
author list: Agent
  family name: Ma
  given name: Zhongren
author list: Agent
  family name: Ding
  given name: Gongtao
doi: 10.7717/peerj.16995
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: ©2024 Liu et al.
attribution name: Liu et al.

moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud
type: item
type: AcademicArticle
description: Single-cell omics sequencing has rapidly advanced, enabling the quantification of diverse omics profiles at a single-cell resolution. To facilitate comprehensive biological insights, such as cellular differentiation trajectories, precise annotation of cell subtypes is essential. Conventional methods involve clustering cells and manually assigning subtypes based on canonical markers, a labor-intensive and expert-dependent process. Hence, an automated computational prediction framework is crucial. While several classification frameworks for predicting cell subtypes from single-cell RNA sequencing datasets exist, these methods solely rely on single-omics data, offering insights at a single molecular level. They often miss inter-omic correlations and a holistic understanding of cellular processes. To address this, the integration of multi-omics datasets from individual cells is essential for accurate subtype annotation. This article introduces moSCminer, a novel framework for classifying cell subtypes that harnesses the power of single-cell multi-omics sequencing datasets through an attention-based neural network operating at the omics level. By integrating three distinct omics datasets—gene expression, DNA methylation, and DNA accessibility—while accounting for their biological relationships, moSCminer excels at learning the relative significance of each omics feature. It then transforms this knowledge into a novel representation for cell subtype classification. Comparative evaluations against standard machine learning-based classifiers demonstrate moSCminer’s superior performance, consistently achieving the highest average performance on real datasets. The efficacy of multi-omics integration is further corroborated through an in-depth analysis of the omics-level attention module, which identifies potential markers for cell subtype annotation. To enhance accessibility and scalability, moSCminer is accessible as a user-friendly web-based platform seamlessly connected to…
format: application/pdf
format: text/html
creator: Joung Min Choi
creator: Chaelin Park
creator: Heejoon Chae
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.17006
publisher: PeerJ Inc.
rights: © 2024 Choi et al.
abstract: Single-cell omics sequencing has rapidly advanced, enabling the quantification of diverse omics profiles at a single-cell resolution. To facilitate comprehensive biological insights, such as cellular differentiation trajectories, precise annotation of cell subtypes is essential. Conventional methods involve clustering cells and manually assigning subtypes based on canonical markers, a labor-intensive and expert-dependent process. Hence, an automated computational prediction framework is crucial. While several classification frameworks for predicting cell subtypes from single-cell RNA sequencing datasets exist, these methods solely rely on single-omics data, offering insights at a single molecular level. They often miss inter-omic correlations and a holistic understanding of cellular processes. To address this, the integration of multi-omics datasets from individual cells is essential for accurate subtype annotation. This article introduces moSCminer, a novel framework for classifying cell subtypes that harnesses the power of single-cell multi-omics sequencing datasets through an attention-based neural network operating at the omics level. By integrating three distinct omics datasets—gene expression, DNA methylation, and DNA accessibility—while accounting for their biological relationships, moSCminer excels at learning the relative significance of each omics feature. It then transforms this knowledge into a novel representation for cell subtype classification. Comparative evaluations against standard machine learning-based classifiers demonstrate moSCminer’s superior performance, consistently achieving the highest average performance on real datasets. The efficacy of multi-omics integration is further corroborated through an in-depth analysis of the omics-level attention module, which identifies potential markers for cell subtype annotation. To enhance accessibility and scalability, moSCminer is accessible as a user-friendly web-based platform seamlessly connected to…
bibliographic citation: Choi et al. (2024) moSCminer: a cell subtype classification framework based on the attention neural network integrating the single-cell multi-omics dataset on the cloud. PeerJ 12:e17006 https://doi.org/10.7717/peerj.17006
date submitted: 2023-11-22
date accepted: 2024-02-05
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Choi
  given name: Joung Min
author list: Agent
  family name: Park
  given name: Chaelin
author list: Agent
  family name: Chae
  given name: Heejoon
doi: 10.7717/peerj.17006
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Choi et al.
attribution name: Choi et al.

New records of immature aquatic Diptera from the Foulden Maar Fossil-Lagerstätte, New Zealand, and their biogeographic implications
type: item
type: AcademicArticle
description: Background The biogeographical and ecological history of true flies (Diptera) in New Zealand is little known due to a scarcity of fossil specimens. Here, we report a fauna of immature aquatic dipterans from freshwater diatomites of the early Miocene Foulden Maar Fossil-Lagerstätte in southern New Zealand. Methods We document 30 specimens of immature dipterans, mostly pupae, and compare their external morphology to extant aquatic Diptera. Based on the reconstructed paleoenvironment of Foulden Maar, we discuss taxonomic, ecological and taphonomic implications of this early Miocene fauna. Results Among Chironomidae, one pupal morphotype is attributed to Tanypodinae, one pupal morphotype and one larval morphotype are placed into Chironomus (Chironominae) and a further morphotype into Chironominae incertae sedis. Chaoboridae are represented by a pupal morphotype congeneric or very close to the extant Chaoborus, today globally distributed except for New Zealand. Additional immature specimens are likely larvae and puparia of brachyceran flies but cannot be identified to a narrower range. These finds document an aquatic dipteran fauna in New Zealand in the earliest Miocene and highlight Neogene extinction as a factor in shaping the extant Diptera fauna in New Zealand. Immature aquatic dipterans were a common and likely ecologically important component of the early Miocene Foulden Maar lake. Preservation of larvae and pupae may have been promoted by diatomaceous microbial mats and the light colour of the diatomite likely facilitated spotting of these minute fossils in the field.
format: application/pdf
format: text/html
creator: Viktor O. Baranov
creator: Joachim T. Haug
creator: Uwe Kaulfuss
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.17014
publisher: PeerJ Inc.
rights: © 2024 Baranov et al.
abstract: Background The biogeographical and ecological history of true flies (Diptera) in New Zealand is little known due to a scarcity of fossil specimens. Here, we report a fauna of immature aquatic dipterans from freshwater diatomites of the early Miocene Foulden Maar Fossil-Lagerstätte in southern New Zealand. Methods We document 30 specimens of immature dipterans, mostly pupae, and compare their external morphology to extant aquatic Diptera. Based on the reconstructed paleoenvironment of Foulden Maar, we discuss taxonomic, ecological and taphonomic implications of this early Miocene fauna. Results Among Chironomidae, one pupal morphotype is attributed to Tanypodinae, one pupal morphotype and one larval morphotype are placed into Chironomus (Chironominae) and a further morphotype into Chironominae incertae sedis. Chaoboridae are represented by a pupal morphotype congeneric or very close to the extant Chaoborus, today globally distributed except for New Zealand. Additional immature specimens are likely larvae and puparia of brachyceran flies but cannot be identified to a narrower range. These finds document an aquatic dipteran fauna in New Zealand in the earliest Miocene and highlight Neogene extinction as a factor in shaping the extant Diptera fauna in New Zealand. Immature aquatic dipterans were a common and likely ecologically important component of the early Miocene Foulden Maar lake. Preservation of larvae and pupae may have been promoted by diatomaceous microbial mats and the light colour of the diatomite likely facilitated spotting of these minute fossils in the field.
bibliographic citation: Baranov et al. (2024) New records of immature aquatic Diptera from the Foulden Maar Fossil-Lagerstätte, New Zealand, and their biogeographic implications. PeerJ 12:e17014 https://doi.org/10.7717/peerj.17014
date submitted: 2023-11-21
date accepted: 2024-02-05
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baranov
  given name: Viktor O.
author list: Agent
  family name: Haug
  given name: Joachim T.
author list: Agent
  family name: Kaulfuss
  given name: Uwe
doi: 10.7717/peerj.17014
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Baranov et al.
attribution name: Baranov et al.

Spatiotemporal variables comparison between drop jump and horizontal drop jump in elite jumpers and sprinters
type: item
type: AcademicArticle
description: Background General expectations speculated that there are differences between drop jump (DJ) and horizontal drop jump (HDJ) exercises. While these criteria may be valid, we have yet to find a report that explores these differences in competitive level athletes. Objective The study aimed to compare spatiotemporal variables in the drop jump (DJ) vs. the horizontal drop jump (HDJ) in elite jumpers and sprinters. Methods Sixteen international-level male athletes performed two DJ attempts at different fall heights 0.3, 0.4, and 0.5 m (DJ30, DJ40, and DJ50), and after 2 h, they performed two HDJ attempts (HDJ30, HDJ40, HDJ50). All jumps were performed on a Kistler force plate. The variables analyzed were ground contact time (GCT), flight time (FT), eccentric phase time, concentric phase time, and time to peak concentric force. Results The GCT was found to be significantly shorter in DJ vs. HDJ (Z = 4.980; p = 0.0001; ES = 3.11). FT was significantly lower in DJ30 versus HDJ30 (Z = 4.845; p = 0.0001, d = 3.79), but significantly higher in DJ40 vs. HDJ40 (Z = 4.437; p ≤ 0.0001, d = 3.70) and in DJ50 vs. HDJ50 (Z = 4.549; p ≤ 0.0001, d = 4.72). Conclusions It is concluded that the HDJ requires more time for force production, that the eccentric component requires more time than the concentric and that it is not recommended to use the HDJ over the DJ for reactive purposes. This is the first study that comprehensively compare the differences between DJ and HDJ, which will assist coaches and researchers in the design of future training strategies.
format: application/pdf
format: text/html
creator: Raynier Montoro-Bombú
creator: Paulo Miranda-Oliveira
creator: Maria João Valamatos
creator: Filipa João
creator: Tom JW Buurke
creator: Amândio Cupido Santos
creator: Luis Rama
subject: Sports Medicine
description: doi:10.7717/peerj.17026
publisher: PeerJ Inc.
rights: © 2024 Montoro-Bombú et al.
abstract: Background General expectations speculated that there are differences between drop jump (DJ) and horizontal drop jump (HDJ) exercises. While these criteria may be valid, we have yet to find a report that explores these differences in competitive level athletes. Objective The study aimed to compare spatiotemporal variables in the drop jump (DJ) vs. the horizontal drop jump (HDJ) in elite jumpers and sprinters. Methods Sixteen international-level male athletes performed two DJ attempts at different fall heights 0.3, 0.4, and 0.5 m (DJ30, DJ40, and DJ50), and after 2 h, they performed two HDJ attempts (HDJ30, HDJ40, HDJ50). All jumps were performed on a Kistler force plate. The variables analyzed were ground contact time (GCT), flight time (FT), eccentric phase time, concentric phase time, and time to peak concentric force. Results The GCT was found to be significantly shorter in DJ vs. HDJ (Z = 4.980; p = 0.0001; ES = 3.11). FT was significantly lower in DJ30 versus HDJ30 (Z = 4.845; p = 0.0001, d = 3.79), but significantly higher in DJ40 vs. HDJ40 (Z = 4.437; p ≤ 0.0001, d = 3.70) and in DJ50 vs. HDJ50 (Z = 4.549; p ≤ 0.0001, d = 4.72). Conclusions It is concluded that the HDJ requires more time for force production, that the eccentric component requires more time than the concentric and that it is not recommended to use the HDJ over the DJ for reactive purposes. This is the first study that comprehensively compare the differences between DJ and HDJ, which will assist coaches and researchers in the design of future training strategies.
bibliographic citation: Montoro-Bombú et al. (2024) Spatiotemporal variables comparison between drop jump and horizontal drop jump in elite jumpers and sprinters. PeerJ 12:e17026 https://doi.org/10.7717/peerj.17026
date submitted: 2023-11-06
date accepted: 2024-02-07
issued: 2024-02-26
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Montoro-Bombú
  given name: Raynier
author list: Agent
  family name: Miranda-Oliveira
  given name: Paulo
author list: Agent
  family name: Valamatos
  given name: Maria João
author list: Agent
  family name: João
  given name: Filipa
author list: Agent
  family name: Buurke
  given name: Tom JW
author list: Agent
  family name: Cupido Santos
  given name: Amândio
author list: Agent
  family name: Rama
  given name: Luis
doi: 10.7717/peerj.17026
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-02-26
copyright: © 2024 Montoro-Bombú et al.
attribution name: Montoro-Bombú et al.

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