PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Laying the foundations for selective-fish guidance using electricity: multi-species response to pulsed direct currents
items: An unusual Cretaceous beetle with affinity to Anamorphidae (Coleoptera: Coccinelloidea)
items: Effects of direction specific exercise training on athletic performance: a systematic review and meta-analysis
items: MME and PTPRC: key renal biomarkers in lupus nephritis
items: Walking on different inclines affects gait symmetry differently in the anterior-posterior and vertical directions: implication for future sensorimotor training
items: Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama‘ehuakanaloa Seamount
items: The burgeoning spatial multi-omics in human gastrointestinal cancers
items: Seasonal mouse cadaver microbial study: rupture time and postmortem interval estimation model construction
items: Eukaryotic plankton species diversity and community structure in the Xiao Jiang River (the primary tributary of Upper Yangtze River), Yunnan
items: Potential acetylcholine-based communication in honeybee haemocytes and its modulation by a neonicotinoid insecticide

Laying the foundations for selective-fish guidance using electricity: multi-species response to pulsed direct currents
type: item
type: AcademicArticle
description: To develop effective technology that employs electric fields to simultaneously guide valued freshwater fish whilst limiting the range expansion of undesirable invasive species, there is a need to quantify the electrosensitivity of multiple families. This experimental study quantified the electrosensitivity of two carp species that, in UK, are invasive (grass carp, Ctenopharyngodon idella, and common carp, Cyprinus carpio) and compared the values with those previously obtained for adult European eel (Anguilla anguilla), a species of conservation concern in Europe. Electric field strengths (V/cm) required to elicit physiological responses (twitch, loss of orientation and tetany) were identified across four pulsed direct current (PDC) electric waveforms (single pulse-2 Hz, double pulse-2 Hz, single pulse-3 Hz and double pulse-3 Hz). Grass carp were sensitive to differences in waveform with tetany exhibited at lower field strengths in the single pulse-2 Hz treatment. Both cyprinid species responded similarly and were less sensitive to PDC than adult European eel, although loss of orientation occurred at lower field strengths for grass than common carp in the single pulse-3 Hz waveform treatment. This variation in electrosensitivity, likely due to differences in body length, indicates potential for electric fields to selectively guide fish in areas where invasive and native species occur in sympatry.
format: application/pdf
format: text/html
creator: Mhairi Miller
creator: Suleiman M. Sharkh
creator: Paul S. Kemp
subject: Animal Behavior
subject: Aquaculture, Fisheries and Fish Science
subject: Bioengineering
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.17962
publisher: PeerJ Inc.
rights: © 2024 Miller et al.
abstract: To develop effective technology that employs electric fields to simultaneously guide valued freshwater fish whilst limiting the range expansion of undesirable invasive species, there is a need to quantify the electrosensitivity of multiple families. This experimental study quantified the electrosensitivity of two carp species that, in UK, are invasive (grass carp, Ctenopharyngodon idella, and common carp, Cyprinus carpio) and compared the values with those previously obtained for adult European eel (Anguilla anguilla), a species of conservation concern in Europe. Electric field strengths (V/cm) required to elicit physiological responses (twitch, loss of orientation and tetany) were identified across four pulsed direct current (PDC) electric waveforms (single pulse-2 Hz, double pulse-2 Hz, single pulse-3 Hz and double pulse-3 Hz). Grass carp were sensitive to differences in waveform with tetany exhibited at lower field strengths in the single pulse-2 Hz treatment. Both cyprinid species responded similarly and were less sensitive to PDC than adult European eel, although loss of orientation occurred at lower field strengths for grass than common carp in the single pulse-3 Hz waveform treatment. This variation in electrosensitivity, likely due to differences in body length, indicates potential for electric fields to selectively guide fish in areas where invasive and native species occur in sympatry.
bibliographic citation: Miller et al. (2024) Laying the foundations for selective-fish guidance using electricity: multi-species response to pulsed direct currents. PeerJ 12:e17962 https://doi.org/10.7717/peerj.17962
date submitted: 2024-01-25
date accepted: 2024-08-01
issued: 2024-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Miller
  given name: Mhairi
author list: Agent
  family name: Sharkh
  given name: Suleiman M.
author list: Agent
  family name: Kemp
  given name: Paul S.
doi: 10.7717/peerj.17962
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-16
copyright: ©2024 Miller et al.
attribution name: Miller et al.

An unusual Cretaceous beetle with affinity to Anamorphidae (Coleoptera: Coccinelloidea)
type: item
type: AcademicArticle
description: Coccinelloid beetles have a sparse fossil record in the Mesozoic. Here, we describe and illustrate an unusual coccinelloid beetle, Yassibum yoshitomii gen. et sp. nov., from mid-Cretaceous Kachin amber. Yassibum stands out within the Coccinelloidea due to its notched profemora and the presence of antennal grooves on the elytral epipleura. Based on our phylogenetic analyses, we suggest that Yassibum is most likely related to the family Anamorphidae. The alternative placements are critically evaluated based on our comparison of the morphology.
format: application/pdf
format: text/html
creator: Yan-Da Li
creator: Wioletta Tomaszewska
creator: Emmanuel Arriaga-Varela
creator: Di-Ying Huang
creator: Chen-Yang Cai
subject: Entomology
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.18008
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: Coccinelloid beetles have a sparse fossil record in the Mesozoic. Here, we describe and illustrate an unusual coccinelloid beetle, Yassibum yoshitomii gen. et sp. nov., from mid-Cretaceous Kachin amber. Yassibum stands out within the Coccinelloidea due to its notched profemora and the presence of antennal grooves on the elytral epipleura. Based on our phylogenetic analyses, we suggest that Yassibum is most likely related to the family Anamorphidae. The alternative placements are critically evaluated based on our comparison of the morphology.
bibliographic citation: Li et al. (2024) An unusual Cretaceous beetle with affinity to Anamorphidae (Coleoptera: Coccinelloidea). PeerJ 12:e18008 https://doi.org/10.7717/peerj.18008
date submitted: 2024-05-07
date accepted: 2024-08-09
issued: 2024-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Yan-Da
author list: Agent
  family name: Tomaszewska
  given name: Wioletta
author list: Agent
  family name: Arriaga-Varela
  given name: Emmanuel
author list: Agent
  family name: Huang
  given name: Di-Ying
author list: Agent
  family name: Cai
  given name: Chen-Yang
doi: 10.7717/peerj.18008
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-16
copyright: © 2024 Li et al.
attribution name: Li et al.

Effects of direction specific exercise training on athletic performance: a systematic review and meta-analysis
type: item
type: AcademicArticle
description: Background The similarity between movement patterns and force-vector specificity of training exercises and the target movement will likely result in the greatest transfer of the practiced skills and physical abilities to the intended sports skill performance. Therefore, this review aimed to investigate whether specific adaptations in athletic performance would be observed following direction specific exercise training. Methodology The literature search was performed in PubMed, Web of Science, and MEDLINE. Studies comparing acute (post-activation potentiation enhancement) and short-term (>2 weeks) effects of horizontally vs. vertically oriented resistance and plyometric training on athletic performance of recreationally active participants of either sex were included. The effect sizes were determined using a robust variance estimation random-effects model and were reported as Hedge’s g. Results Twenty-two studies were included. For acute studies (n = 4), a small non-significant effect favoring horizontal training (HT) for sprint performance improvements (g = −0.19, p = 0.17) was evident. For short-term studies (n = 18), the results showed non-significant, small to large differences between HT and vertical training (VT) in pooled vertical and horizontal jump improvements (g = 0.06, p = 0.67), vertical (g = 0.21, p = 0.17) and horizontal jump (g = −0.15, p = 0.40), pooled vertical and horizontal maximal strength (g = 0.27, p = 0.42), horizontal (g = −0.83, p = 0.16) and vertical maximal strength (g = 0.78, p = 0.28), pooled short and medium distance sprint (g = −0.23, p = 0.16), short (g = −0.33 [−0.85, 0.19], p = 0.19) and medium (g = −0.12 [−0.37, 0.13], p = 0.28) distance sprint, and COD speed and maneuverability (g = −0.45, p = 0.26). Conclusions HT and VT were both equally effective in improving vertically and horizontally athletic performance, potentially refuting the theory of directional specificity of training on athletic performance outcomes.
format: application/pdf
format: text/html
creator: Jiaru Huang
creator: Tibor Hortobágyi
creator: Thomas Dos’Santos
creator: Yu Shi
creator: Yilin Que
creator: Junlei Lin
creator: Yuying Su
creator: Wei Li
subject: Kinesiology
subject: Sports Medicine
description: doi:10.7717/peerj.18047
publisher: PeerJ Inc.
rights: © 2024 Huang et al.
abstract: Background The similarity between movement patterns and force-vector specificity of training exercises and the target movement will likely result in the greatest transfer of the practiced skills and physical abilities to the intended sports skill performance. Therefore, this review aimed to investigate whether specific adaptations in athletic performance would be observed following direction specific exercise training. Methodology The literature search was performed in PubMed, Web of Science, and MEDLINE. Studies comparing acute (post-activation potentiation enhancement) and short-term (>2 weeks) effects of horizontally vs. vertically oriented resistance and plyometric training on athletic performance of recreationally active participants of either sex were included. The effect sizes were determined using a robust variance estimation random-effects model and were reported as Hedge’s g. Results Twenty-two studies were included. For acute studies (n = 4), a small non-significant effect favoring horizontal training (HT) for sprint performance improvements (g = −0.19, p = 0.17) was evident. For short-term studies (n = 18), the results showed non-significant, small to large differences between HT and vertical training (VT) in pooled vertical and horizontal jump improvements (g = 0.06, p = 0.67), vertical (g = 0.21, p = 0.17) and horizontal jump (g = −0.15, p = 0.40), pooled vertical and horizontal maximal strength (g = 0.27, p = 0.42), horizontal (g = −0.83, p = 0.16) and vertical maximal strength (g = 0.78, p = 0.28), pooled short and medium distance sprint (g = −0.23, p = 0.16), short (g = −0.33 [−0.85, 0.19], p = 0.19) and medium (g = −0.12 [−0.37, 0.13], p = 0.28) distance sprint, and COD speed and maneuverability (g = −0.45, p = 0.26). Conclusions HT and VT were both equally effective in improving vertically and horizontally athletic performance, potentially refuting the theory of directional specificity of training on athletic performance outcomes.
bibliographic citation: Huang et al. (2024) Effects of direction specific exercise training on athletic performance: a systematic review and meta-analysis. PeerJ 12:e18047 https://doi.org/10.7717/peerj.18047
date submitted: 2024-06-10
date accepted: 2024-08-14
issued: 2024-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Huang
  given name: Jiaru
author list: Agent
  family name: Hortobágyi
  given name: Tibor
author list: Agent
  family name: Dos’Santos
  given name: Thomas
author list: Agent
  family name: Shi
  given name: Yu
author list: Agent
  family name: Que
  given name: Yilin
author list: Agent
  family name: Lin
  given name: Junlei
author list: Agent
  family name: Su
  given name: Yuying
author list: Agent
  family name: Li
  given name: Wei
doi: 10.7717/peerj.18047
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-16
copyright: © 2024 Huang et al.
attribution name: Huang et al.

MME and PTPRC: key renal biomarkers in lupus nephritis
type: item
type: AcademicArticle
description: Background Lupus nephritis (LN) is an autoimmune-related kidney disease with a poor prognosis, however the potential pathogenic mechanism remains unclear and there is a lack of precise biomarkers. Therefore, a thorough screening and identification of renal markers in LN are immensely beneficial to the research on its pathogenic mechanisms and treatment strategies. Methods We utilized bioinformatics to analyze the differentially expressed genes (DEGs) at the transcriptome level of three clusters: total renal, glomeruli, and renal tubulointerstitium in the GEO database to discover potential renal biomarkers of LN. We utilized NephroSeq datasets and measured mRNA and protein levels in the kidneys of MRL/lpr mice to confirm the expression of key DEGs. Results Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis. The seven hot differential genes were verified to have consistent change trends using three datasets from NephroSeq database. The receiver operating characteristic (ROC) curve indicated that five DEGs (PTPRC, MX1, EGR1, MME and RORC) exhibited a higher diagnostic ROC value in both the glomerulus and tubulointerstitium group. Validation of core genes using MRL/lpr mice showed that MME and PTPRC exhibit significantly differential mRNA and protein expression patterns in mouse kidneys like the datasets. Conclusions This study identified seven key renal biomarkers through bioinformatics analysis using the GEO and NephroSeq databases. It was identified that MME and PTPRC may have a high predictive value as renal biomarkers in the pathogenesis of LN, as confirmed by animal validation.
format: application/pdf
format: text/html
creator: Min Wen
creator: Marady Hun
creator: Mingyi Zhao
creator: Qingnan He
subject: Genetics
subject: Molecular Biology
subject: Nephrology
subject: Histology
description: doi:10.7717/peerj.18070
publisher: PeerJ Inc.
rights: © 2024 Wen et al.
abstract: Background Lupus nephritis (LN) is an autoimmune-related kidney disease with a poor prognosis, however the potential pathogenic mechanism remains unclear and there is a lack of precise biomarkers. Therefore, a thorough screening and identification of renal markers in LN are immensely beneficial to the research on its pathogenic mechanisms and treatment strategies. Methods We utilized bioinformatics to analyze the differentially expressed genes (DEGs) at the transcriptome level of three clusters: total renal, glomeruli, and renal tubulointerstitium in the GEO database to discover potential renal biomarkers of LN. We utilized NephroSeq datasets and measured mRNA and protein levels in the kidneys of MRL/lpr mice to confirm the expression of key DEGs. Results Seven significantly differential genes (EGR1, MME, PTPRC, RORC, MX1, ZBTB16, FKBP5) were revealed from the transcriptome database of GSE200306, which were mostly enriched in the pathway of the hematopoietic cell lineage and T cell differentiation respectively by KEGG and GO analysis. The seven hot differential genes were verified to have consistent change trends using three datasets from NephroSeq database. The receiver operating characteristic (ROC) curve indicated that five DEGs (PTPRC, MX1, EGR1, MME and RORC) exhibited a higher diagnostic ROC value in both the glomerulus and tubulointerstitium group. Validation of core genes using MRL/lpr mice showed that MME and PTPRC exhibit significantly differential mRNA and protein expression patterns in mouse kidneys like the datasets. Conclusions This study identified seven key renal biomarkers through bioinformatics analysis using the GEO and NephroSeq databases. It was identified that MME and PTPRC may have a high predictive value as renal biomarkers in the pathogenesis of LN, as confirmed by animal validation.
bibliographic citation: Wen et al. (2024) MME and PTPRC: key renal biomarkers in lupus nephritis. PeerJ 12:e18070 https://doi.org/10.7717/peerj.18070
date submitted: 2024-04-16
date accepted: 2024-08-19
issued: 2024-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wen
  given name: Min
author list: Agent
  family name: Hun
  given name: Marady
author list: Agent
  family name: Zhao
  given name: Mingyi
author list: Agent
  family name: He
  given name: Qingnan
doi: 10.7717/peerj.18070
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-16
copyright: ©2024 Wen et al.
attribution name: Wen et al.

Walking on different inclines affects gait symmetry differently in the anterior-posterior and vertical directions: implication for future sensorimotor training
type: item
type: AcademicArticle
description: A symmetric gait pattern in humans reflects near-identical movement in bilateral limbs during walking. However, little is known about how gait symmetry changes on different inclines. This study aimed to address this knowledge gap using the central pattern generator and internal model hypotheses. Eighteen healthy young adults underwent five 2-minute walking trials (inclines of +15%, +8%, 0%, −8%, and −15%). Dependent variables included step time, step length, step width, maximum heel clearance, time to peaks of maximum heel clearance, their corresponding coefficients of variation (CV), and respective symmetry indices (SI). Significant differences were observed in SI of step length (p = .022), step length variability (p < .001), step width variability (p =.001), maximum heel clearance (p < .001), and maximum heel clearance variability (p = .049). Compared to level walking, walking at −8% and −15% inclines increased SI of step length (p = .011, p = .039 respectively) but decreased SI of maximum heel clearance (p = .025, p = .019 respectively). These observations suggested that incline walking affected gait symmetry differently, possibly due to varied internal models used in locomotion. Downhill walking improved vertical gait symmetry but reduced anterior-posterior symmetry compared to level walking. Downhill walking may be a preferable rehabilitation protocol for enhancing gait symmetry, as it activates internal model controls. Even slight downhill inclines could increase active control loading, beneficial for the elderly and those with impaired gait.
format: application/pdf
format: text/html
creator: Haoyu Xie
creator: Jung H. Chien
subject: Kinesiology
subject: Biomechanics
subject: Rehabilitation
description: doi:10.7717/peerj.18096
publisher: PeerJ Inc.
rights: © 2024 Xie and Chien
abstract: A symmetric gait pattern in humans reflects near-identical movement in bilateral limbs during walking. However, little is known about how gait symmetry changes on different inclines. This study aimed to address this knowledge gap using the central pattern generator and internal model hypotheses. Eighteen healthy young adults underwent five 2-minute walking trials (inclines of +15%, +8%, 0%, −8%, and −15%). Dependent variables included step time, step length, step width, maximum heel clearance, time to peaks of maximum heel clearance, their corresponding coefficients of variation (CV), and respective symmetry indices (SI). Significant differences were observed in SI of step length (p = .022), step length variability (p < .001), step width variability (p =.001), maximum heel clearance (p < .001), and maximum heel clearance variability (p = .049). Compared to level walking, walking at −8% and −15% inclines increased SI of step length (p = .011, p = .039 respectively) but decreased SI of maximum heel clearance (p = .025, p = .019 respectively). These observations suggested that incline walking affected gait symmetry differently, possibly due to varied internal models used in locomotion. Downhill walking improved vertical gait symmetry but reduced anterior-posterior symmetry compared to level walking. Downhill walking may be a preferable rehabilitation protocol for enhancing gait symmetry, as it activates internal model controls. Even slight downhill inclines could increase active control loading, beneficial for the elderly and those with impaired gait.
bibliographic citation: Xie et al. (2024) Walking on different inclines affects gait symmetry differently in the anterior-posterior and vertical directions: implication for future sensorimotor training. PeerJ 12:e18096 https://doi.org/10.7717/peerj.18096
date submitted: 2024-05-31
date accepted: 2024-08-23
issued: 2024-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xie
  given name: Haoyu
author list: Agent
  family name: Chien
  given name: Jung H.
doi: 10.7717/peerj.18096
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-16
copyright: ©2024 Xie and Chien
attribution name: Xie and Chien

Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama‘ehuakanaloa Seamount
type: item
type: AcademicArticle
description: The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene was assessed for use on environmental samples from microbial mats surrounding Kama‘ehuakanaloa Seamount, an iron-dominated hydrothermal vent system. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities were elucidated, and both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at Kama‘ehuakanaloa Seamount.
format: application/pdf
format: text/html
creator: Lindsey Smith
creator: Heather Fullerton
creator: Craig L. Moyer
subject: Ecology
subject: Microbiology
subject: Computational Science
subject: Biogeochemistry
subject: Biological Oceanography
description: doi:10.7717/peerj.18099
publisher: PeerJ Inc.
rights: © 2024 Smith et al.
abstract: The microbiota of hydrothermal vents has been widely implicated in the dynamics of oceanic biogeochemical cycling. Lithotrophic organisms utilize reduced chemicals in the vent effluent for energy, which fuels carbon fixation, and their metabolic byproducts can then support higher trophic levels and high-biomass ecosystems. However, despite the important role these microorganisms play in our oceans, they are difficult to study. Most are resistant to culturing in a lab setting, so culture-independent methods are necessary to examine community composition. Targeted amplicon surveying has become the standard practice for assessing the structure and diversity of hydrothermal vent microbial communities. Here, the performance of primer pairs targeting the V3V4 and V4V5 variable regions of the SSU rRNA gene was assessed for use on environmental samples from microbial mats surrounding Kama‘ehuakanaloa Seamount, an iron-dominated hydrothermal vent system. Using the amplicon sequence variant (ASV) approach to taxonomic identification, the structure and diversity of microbial communities were elucidated, and both primer pairs generated robust data and comparable alpha diversity profiles. However, several distinct differences in community composition were identified between primer sets, including differential relative abundances of both bacterial and archaeal phyla. The primer choice was determined to be a significant driver of variation among the taxonomic profiles generated. Based on the higher quality of the raw sequences generated and on the breadth of abundant taxa found using the V4V5 primer set, it is determined as the most efficacious primer pair for whole-community surveys of microbial mats at Kama‘ehuakanaloa Seamount.
bibliographic citation: Smith et al. (2024) Complex hydrothermal vent microbial mat communities used to assess primer selection for targeted amplicon surveys from Kama‘ehuakanaloa Seamount. PeerJ 12:e18099 https://doi.org/10.7717/peerj.18099
date submitted: 2024-04-12
date accepted: 2024-08-26
issued: 2024-09-16
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Smith
  given name: Lindsey
author list: Agent
  family name: Fullerton
  given name: Heather
author list: Agent
  family name: Moyer
  given name: Craig L.
doi: 10.7717/peerj.18099
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-16
copyright: © 2024 Smith et al.
attribution name: Smith et al.

The burgeoning spatial multi-omics in human gastrointestinal cancers
type: item
type: AcademicArticle
description: The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome, transcriptome, proteome, metabolome, and epigenome, with single-cell resolution and spatial information within the body’s three-dimensional context, is essential. This foundational information serves as the basis for deciphering cellular and molecular mechanisms. Although single-cell multi-omics technology can provide biological information such as genome, transcriptome, proteome, metabolome, and epigenome with single-cell resolution, the sample preparation process leads to the loss of spatial information. Spatial multi-omics technology, however, facilitates the characterization of biological data, such as genome, transcriptome, proteome, metabolome, and epigenome in tissue samples, while retaining their spatial context. Consequently, these techniques significantly enhance our understanding of individual development and disease pathology. Currently, spatial multi-omics technology has played a vital role in elucidating various processes in tumor biology, including tumor occurrence, development, and metastasis, particularly in the realms of tumor immunity and the heterogeneity of the tumor microenvironment. Therefore, this article provides a comprehensive overview of spatial transcriptomics, spatial proteomics, and spatial metabolomics-related technologies and their application in research concerning esophageal cancer, gastric cancer, and colorectal cancer. The objective is to foster the research and implementation of spatial multi-omics technology in digestive tumor diseases. This review will provide new technical insights for molecular biology researchers.
format: application/pdf
format: text/html
creator: Weizheng Liang
creator: Zhenpeng Zhu
creator: Dandan Xu
creator: Peng Wang
creator: Fei Guo
creator: Haoshan Xiao
creator: Chenyang Hou
creator: Jun Xue
creator: Xuejun Zhi
creator: Rensen Ran
subject: Biotechnology
subject: Genomics
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.17860
publisher: PeerJ Inc.
rights: © 2024 Liang et al.
abstract: The development and progression of diseases in multicellular organisms unfold within the intricate three-dimensional body environment. Thus, to comprehensively understand the molecular mechanisms governing individual development and disease progression, precise acquisition of biological data, including genome, transcriptome, proteome, metabolome, and epigenome, with single-cell resolution and spatial information within the body’s three-dimensional context, is essential. This foundational information serves as the basis for deciphering cellular and molecular mechanisms. Although single-cell multi-omics technology can provide biological information such as genome, transcriptome, proteome, metabolome, and epigenome with single-cell resolution, the sample preparation process leads to the loss of spatial information. Spatial multi-omics technology, however, facilitates the characterization of biological data, such as genome, transcriptome, proteome, metabolome, and epigenome in tissue samples, while retaining their spatial context. Consequently, these techniques significantly enhance our understanding of individual development and disease pathology. Currently, spatial multi-omics technology has played a vital role in elucidating various processes in tumor biology, including tumor occurrence, development, and metastasis, particularly in the realms of tumor immunity and the heterogeneity of the tumor microenvironment. Therefore, this article provides a comprehensive overview of spatial transcriptomics, spatial proteomics, and spatial metabolomics-related technologies and their application in research concerning esophageal cancer, gastric cancer, and colorectal cancer. The objective is to foster the research and implementation of spatial multi-omics technology in digestive tumor diseases. This review will provide new technical insights for molecular biology researchers.
bibliographic citation: Liang et al. (2024) The burgeoning spatial multi-omics in human gastrointestinal cancers. PeerJ 12:e17860 https://doi.org/10.7717/peerj.17860
date submitted: 2024-03-27
date accepted: 2024-07-14
issued: 2024-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liang
  given name: Weizheng
author list: Agent
  family name: Zhu
  given name: Zhenpeng
author list: Agent
  family name: Xu
  given name: Dandan
author list: Agent
  family name: Wang
  given name: Peng
author list: Agent
  family name: Guo
  given name: Fei
author list: Agent
  family name: Xiao
  given name: Haoshan
author list: Agent
  family name: Hou
  given name: Chenyang
author list: Agent
  family name: Xue
  given name: Jun
author list: Agent
  family name: Zhi
  given name: Xuejun
author list: Agent
  family name: Ran
  given name: Rensen
doi: 10.7717/peerj.17860
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-13
copyright: ©2024 Liang et al.
attribution name: Liang et al.

Seasonal mouse cadaver microbial study: rupture time and postmortem interval estimation model construction
type: item
type: AcademicArticle
description: The estimation of postmortem interval (PMI) has long been a focal point in the field of forensic science. Following the death of an organism, microorganisms exhibit a clock-like proliferation pattern during the course of cadaver decomposition, forming the foundation for utilizing microbiology in PMI estimation. The establishment of PMI estimation models based on datasets from different seasons is of great practical significance. In this experiment, we conducted microbiota sequencing and analysis on gravesoil and mouse intestinal contents collected during both the winter and summer seasons and constructed a PMI estimation model using the Random Forest algorithm. The results showed that the MAE of the gut microbiota model in summer was 0.47 ± 0.26 d, R2 = 0.991, and the MAE of the gravesoil model in winter was 1.04 ± 0.22 d, R2 = 0.998. We propose that, in practical applications, it is advantageous to selectively build PMI estimation models based on seasonal variations. Additionally, through a combination of morphological observations, gravesoil microbiota sequencing results, and soil physicochemical data, we identified the time of cadaveric rupture for mouse cadavers, occurring at around days 24–27 in winter and days 6–9 in summer. This study not only confirms previous research findings but also introduces novel insights, contributing to the foundational knowledge necessary to advance the utilization of microbiota for PMI estimation.
format: application/pdf
format: text/html
creator: Xingchun Zhao
creator: Fengqin Yang
creator: Fan Yang
creator: Hao Nie
creator: Sheng Hu
creator: Peng Gui
creator: Yadong Guo
creator: Changquan Zhang
subject: Microbiology
subject: Pathology
description: doi:10.7717/peerj.17932
publisher: PeerJ Inc.
rights: © 2024 Zhao et al.
abstract: The estimation of postmortem interval (PMI) has long been a focal point in the field of forensic science. Following the death of an organism, microorganisms exhibit a clock-like proliferation pattern during the course of cadaver decomposition, forming the foundation for utilizing microbiology in PMI estimation. The establishment of PMI estimation models based on datasets from different seasons is of great practical significance. In this experiment, we conducted microbiota sequencing and analysis on gravesoil and mouse intestinal contents collected during both the winter and summer seasons and constructed a PMI estimation model using the Random Forest algorithm. The results showed that the MAE of the gut microbiota model in summer was 0.47 ± 0.26 d, R2 = 0.991, and the MAE of the gravesoil model in winter was 1.04 ± 0.22 d, R2 = 0.998. We propose that, in practical applications, it is advantageous to selectively build PMI estimation models based on seasonal variations. Additionally, through a combination of morphological observations, gravesoil microbiota sequencing results, and soil physicochemical data, we identified the time of cadaveric rupture for mouse cadavers, occurring at around days 24–27 in winter and days 6–9 in summer. This study not only confirms previous research findings but also introduces novel insights, contributing to the foundational knowledge necessary to advance the utilization of microbiota for PMI estimation.
bibliographic citation: Zhao et al. (2024) Seasonal mouse cadaver microbial study: rupture time and postmortem interval estimation model construction. PeerJ 12:e17932 https://doi.org/10.7717/peerj.17932
date submitted: 2024-05-12
date accepted: 2024-07-25
issued: 2024-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Zhao
  given name: Xingchun
author list: Agent
  family name: Yang
  given name: Fengqin
author list: Agent
  family name: Yang
  given name: Fan
author list: Agent
  family name: Nie
  given name: Hao
author list: Agent
  family name: Hu
  given name: Sheng
author list: Agent
  family name: Gui
  given name: Peng
author list: Agent
  family name: Guo
  given name: Yadong
author list: Agent
  family name: Zhang
  given name: Changquan
doi: 10.7717/peerj.17932
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-13
copyright: ©2024 Zhao et al.
attribution name: Zhao et al.

Eukaryotic plankton species diversity and community structure in the Xiao Jiang River (the primary tributary of Upper Yangtze River), Yunnan
type: item
type: AcademicArticle
description: The Xiao Jiang River, as a crucial element of ecological restoration in the upper reaches of the Yangtze River, plays an indispensable role in agricultural water utilization and water ecology within its watersheds. The water quality status of the Xiao Jiang River not only impacts local water-ecological equilibrium and economic benefits but also holds paramount importance for sustaining ecosystem health in the Yangtze River basin. Plankton surveys and environmental physicochemical detection were conducted in the major channel region of the Xiao Jiang River in dry and wet periods in 2022 to better understand the diversity of eukaryotic plankton and its community structure characteristics. Environmental DNA is an emerging method that combines traditional ecology with second-generation sequencing technology. It can detect species from a single sample that are difficult to find by traditional microscopy, making the results of plankton diversity studies more comprehensive. For the first time, environmental DNA was used to investigate eukaryotic plankton in the Xiao Jiang River . The results showed that a total of 881 species of plankton from 592 genera in 17 phyla were observed. During the dry period, 480 species belonging to 384 genera within17 phyla were detected, while, during the wet period, a total of 805 species belonging to 463 genera within 17 phyla were recorded. The phylum Ciliophora dominated the zooplankton, while the phylum Chlorophyta and Bacillariophyta dominated the phytoplankton. The presence of these dominant species indicate that the water quality conditions in the study area are oligotrophic and mesotrophic. Principal coordinate analysis and difference test showed that the number of plankton ASVs, abundance, species richness, dominating species, and diversity indices differed between the dry and wet periods. Spearman correlation analysis and redundancy analysis (RDA) of relative abundance data with environmental physicochemical factors revealed that wa…
format: application/pdf
format: text/html
creator: XueRong Li
creator: JiShan Wang
creator: YunRui He
creator: XiaoJun Yang
creator: Mo Wang
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.17972
publisher: PeerJ Inc.
rights: © 2024 Li et al.
abstract: The Xiao Jiang River, as a crucial element of ecological restoration in the upper reaches of the Yangtze River, plays an indispensable role in agricultural water utilization and water ecology within its watersheds. The water quality status of the Xiao Jiang River not only impacts local water-ecological equilibrium and economic benefits but also holds paramount importance for sustaining ecosystem health in the Yangtze River basin. Plankton surveys and environmental physicochemical detection were conducted in the major channel region of the Xiao Jiang River in dry and wet periods in 2022 to better understand the diversity of eukaryotic plankton and its community structure characteristics. Environmental DNA is an emerging method that combines traditional ecology with second-generation sequencing technology. It can detect species from a single sample that are difficult to find by traditional microscopy, making the results of plankton diversity studies more comprehensive. For the first time, environmental DNA was used to investigate eukaryotic plankton in the Xiao Jiang River . The results showed that a total of 881 species of plankton from 592 genera in 17 phyla were observed. During the dry period, 480 species belonging to 384 genera within17 phyla were detected, while, during the wet period, a total of 805 species belonging to 463 genera within 17 phyla were recorded. The phylum Ciliophora dominated the zooplankton, while the phylum Chlorophyta and Bacillariophyta dominated the phytoplankton. The presence of these dominant species indicate that the water quality conditions in the study area are oligotrophic and mesotrophic. Principal coordinate analysis and difference test showed that the number of plankton ASVs, abundance, species richness, dominating species, and diversity indices differed between the dry and wet periods. Spearman correlation analysis and redundancy analysis (RDA) of relative abundance data with environmental physicochemical factors revealed that wa…
bibliographic citation: Li et al. (2024) Eukaryotic plankton species diversity and community structure in the Xiao Jiang River (the primary tributary of Upper Yangtze River), Yunnan. PeerJ 12:e17972 https://doi.org/10.7717/peerj.17972
date submitted: 2023-03-10
date accepted: 2024-08-05
issued: 2024-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Li
  given name: XueRong
author list: Agent
  family name: Wang
  given name: JiShan
author list: Agent
  family name: He
  given name: YunRui
author list: Agent
  family name: Yang
  given name: XiaoJun
author list: Agent
  family name: Wang
  given name: Mo
doi: 10.7717/peerj.17972
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-13
copyright: ©2024 Li et al.
attribution name: Li et al.

Potential acetylcholine-based communication in honeybee haemocytes and its modulation by a neonicotinoid insecticide
type: item
type: AcademicArticle
description: There is growing concern that some managed and wild insect pollinator populations are in decline, potentially threatening biodiversity and sustainable food production on a global scale. In recent years, there has been increasing evidence that sub-lethal exposure to neurotoxic, neonicotinoid pesticides can negatively affect pollinator immunocompetence and could amplify the effects of diseases, likely contributing to pollinator declines. However, a direct pathway connecting neonicotinoids and immune functions remains elusive. In this study we show that haemocytes and non-neural tissues of the honeybee Apis mellifera express the building blocks of the nicotinic acetylcholine receptors that are the target of neonicotinoids. In addition, we demonstrate that the haemocytes, which form the cellular arm of the innate immune system, actively express choline acetyltransferase, a key enzyme necessary to synthesize acetylcholine. In a last step, we show that the expression of this key enzyme is affected by field-realistic doses of clothianidin, a widely used neonicotinoid. These results support a potential mechanistic framework to explain the effects of sub-lethal doses of neonicotinoids on the immune function of pollinators.
format: application/pdf
format: text/html
creator: Tobias Pamminger
creator: Kate Basley
creator: Dave Goulson
creator: William O. H. Hughes
subject: Entomology
description: doi:10.7717/peerj.17978
publisher: PeerJ Inc.
rights: © 2024 Pamminger et al.
abstract: There is growing concern that some managed and wild insect pollinator populations are in decline, potentially threatening biodiversity and sustainable food production on a global scale. In recent years, there has been increasing evidence that sub-lethal exposure to neurotoxic, neonicotinoid pesticides can negatively affect pollinator immunocompetence and could amplify the effects of diseases, likely contributing to pollinator declines. However, a direct pathway connecting neonicotinoids and immune functions remains elusive. In this study we show that haemocytes and non-neural tissues of the honeybee Apis mellifera express the building blocks of the nicotinic acetylcholine receptors that are the target of neonicotinoids. In addition, we demonstrate that the haemocytes, which form the cellular arm of the innate immune system, actively express choline acetyltransferase, a key enzyme necessary to synthesize acetylcholine. In a last step, we show that the expression of this key enzyme is affected by field-realistic doses of clothianidin, a widely used neonicotinoid. These results support a potential mechanistic framework to explain the effects of sub-lethal doses of neonicotinoids on the immune function of pollinators.
bibliographic citation: Pamminger et al. (2024) Potential acetylcholine-based communication in honeybee haemocytes and its modulation by a neonicotinoid insecticide. PeerJ 12:e17978 https://doi.org/10.7717/peerj.17978
date submitted: 2018-03-03
date accepted: 2024-08-06
issued: 2024-09-13
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Pamminger
  given name: Tobias
author list: Agent
  family name: Basley
  given name: Kate
author list: Agent
  family name: Goulson
  given name: Dave
author list: Agent
  family name: Hughes
  given name: William O. H.
doi: 10.7717/peerj.17978
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-09-13
copyright: © 2024 Pamminger et al.
attribution name: Pamminger et al.

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