PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest
items: Minimizing the variables of voiding spot assay for comparison between laboratories
items: Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer
items: Determination of the affinity constants for phage display albumin-binding peptides
items: Effects of in-situ stroboscopic training on visual, visuomotor and reactive agility in youth volleyball players
items: Description and life cycle of a new species of the genus Arachnanthus (Cnidaria: Anthozoa: Ceriantharia) from the Southwestern Atlantic Ocean
items: Comparative morpho-anatomical study on Leptadenia pyrotechnica (Apocynaceae) growing in the hyper-arid and arid habitats of Saudi Arabia
items: Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach
items: Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion
items: Optimising sampling of fish assemblages on intertidal reefs using remote underwater video

Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest
type: item
type: AcademicArticle
description: Background Soil microenvironmental variables showed an important key in α and β-tree diversity in Neotropical montane oak forest. Thus, understanding the microenvironment fluctuation at small-fragment effects on tree diversity is crucial in maintaining the montane oak ecosystems. In this study, we hypothesized that within a relatively small-fragment (151.63 ha), tree α and β-diversity fluctuate and specific soil microenvironmental factors could influence tree species diversity to answer three questions: Do tree α and β-diversity differ among transects, even in a short-distance between them? Do microenvironmental variables influence tree diversity composition that occurs within a relict Neotropical montane oak forest? Is there a particular microenvironmental variable influencing tree species-specific? Methods We established four permanent transects during a year in a relict Neotropical montane oak forest, we assessed tree diversity and specific microenvironmental variables (soil moisture, soil temperature, pH, depth litterfall and light incidence). This allowed us to evaluate how microenvironmental variables at small-fragment influence α and β-tree diversity and tree species-specific. Results Our results showed that α-diversity was not different among transects; however, β-diversity of tree species was mostly explained by turnover and soil moisture, soil temperature, and light incidence were the microenvironmental variables that triggered the replacement (i.e., one species by another). Those variables also had effect on tree species-specific: Mexican beech (Fagus mexicana), Quebracho (Quercus delgadoana), Pezma (Cyathea fulva), Aguacatillo (Beilschmiedia mexicana), Pezma (Dicksonia sellowiana var. arachneosa), and Mountain magnolia (Magnolia schiedeana). Discussion Our results confirm our hypothesis related to β-diversity but not with α-diversity; however, the tree community structure of the diversity was similar among transects. Our study represents the first effort…
format: application/pdf
format: text/html
creator: Luis F. López-Calvillo
creator: Pilar Carbó-Ramírez
creator: Ernesto C. Rodríguez-Ramírez
subject: Biodiversity
subject: Ecology
subject: Plant Science
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.15415
publisher: PeerJ Inc.
rights: © 2023 López-Calvillo et al.
abstract: Background Soil microenvironmental variables showed an important key in α and β-tree diversity in Neotropical montane oak forest. Thus, understanding the microenvironment fluctuation at small-fragment effects on tree diversity is crucial in maintaining the montane oak ecosystems. In this study, we hypothesized that within a relatively small-fragment (151.63 ha), tree α and β-diversity fluctuate and specific soil microenvironmental factors could influence tree species diversity to answer three questions: Do tree α and β-diversity differ among transects, even in a short-distance between them? Do microenvironmental variables influence tree diversity composition that occurs within a relict Neotropical montane oak forest? Is there a particular microenvironmental variable influencing tree species-specific? Methods We established four permanent transects during a year in a relict Neotropical montane oak forest, we assessed tree diversity and specific microenvironmental variables (soil moisture, soil temperature, pH, depth litterfall and light incidence). This allowed us to evaluate how microenvironmental variables at small-fragment influence α and β-tree diversity and tree species-specific. Results Our results showed that α-diversity was not different among transects; however, β-diversity of tree species was mostly explained by turnover and soil moisture, soil temperature, and light incidence were the microenvironmental variables that triggered the replacement (i.e., one species by another). Those variables also had effect on tree species-specific: Mexican beech (Fagus mexicana), Quebracho (Quercus delgadoana), Pezma (Cyathea fulva), Aguacatillo (Beilschmiedia mexicana), Pezma (Dicksonia sellowiana var. arachneosa), and Mountain magnolia (Magnolia schiedeana). Discussion Our results confirm our hypothesis related to β-diversity but not with α-diversity; however, the tree community structure of the diversity was similar among transects. Our study represents the first effort…
bibliographic citation: López-Calvillo et al. (2023) Small-fragment, high turnover: soil microenvironment fluctuation effect on tree diversity in a Neotropical montane oak forest. PeerJ 11:e15415 https://doi.org/10.7717/peerj.15415
date submitted: 2022-12-30
date accepted: 2023-04-24
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: López-Calvillo
  given name: Luis F.
author list: Agent
  family name: Carbó-Ramírez
  given name: Pilar
author list: Agent
  family name: Rodríguez-Ramírez
  given name: Ernesto C.
doi: 10.7717/peerj.15415
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: ©2023 López-Calvillo et al.
attribution name: López-Calvillo et al.

Minimizing the variables of voiding spot assay for comparison between laboratories
type: item
type: AcademicArticle
description: The voiding spot assay (VSA) is increasingly being adopted as a standard method for assessing mouse urinary function. However, VSA outcomes are highly sensitive to housing environment and procedural parameters. Many variables exist among laboratories, including analytical software, type of daily housing cage, transportation, and the time of the day. Some of these variables, such as the time of VSA and analytical software, have been shown to result in inconsistency and incomparability of data. In this study, we evaluated whether the results of VSA can be compared across laboratories by minimizing these variables. We found that analytical tools between Fiji and MATLAB are in good agreement in the quantification of VSA parameters, especially primary voiding spot (PVS) parameters. Unexpectedly, we found that mice housed in different daily home cages did not alter voiding patterns in a standard VSA cage. Nonetheless, we still recommend acclimation when performing VSA in unfamiliar cages. Notably, mice are highly sensitive to transportation and the time in the morning versus afternoon, which can induce significant changes in voiding patterns. Therefore, a standardized period among laboratories and allowing 2–3 days of rest for mice acclimation after transportation are necessary for VSA. Finally, we performed VSA using identical procedural parameters in two laboratories from two geographical locations to compare the results of VSA and concluded that it is possible to generate limited comparable VSA data, such as PVS volume.
format: application/pdf
format: text/html
creator: Chuang Luo
creator: Juan Liu
creator: Jiali Yang
creator: Xiang Xie
creator: Weiqun Yu
creator: Huan Chen
subject: Animal Behavior
subject: Biochemistry
subject: Zoology
description: doi:10.7717/peerj.15420
publisher: PeerJ Inc.
rights: © 2023 Luo et al.
abstract: The voiding spot assay (VSA) is increasingly being adopted as a standard method for assessing mouse urinary function. However, VSA outcomes are highly sensitive to housing environment and procedural parameters. Many variables exist among laboratories, including analytical software, type of daily housing cage, transportation, and the time of the day. Some of these variables, such as the time of VSA and analytical software, have been shown to result in inconsistency and incomparability of data. In this study, we evaluated whether the results of VSA can be compared across laboratories by minimizing these variables. We found that analytical tools between Fiji and MATLAB are in good agreement in the quantification of VSA parameters, especially primary voiding spot (PVS) parameters. Unexpectedly, we found that mice housed in different daily home cages did not alter voiding patterns in a standard VSA cage. Nonetheless, we still recommend acclimation when performing VSA in unfamiliar cages. Notably, mice are highly sensitive to transportation and the time in the morning versus afternoon, which can induce significant changes in voiding patterns. Therefore, a standardized period among laboratories and allowing 2–3 days of rest for mice acclimation after transportation are necessary for VSA. Finally, we performed VSA using identical procedural parameters in two laboratories from two geographical locations to compare the results of VSA and concluded that it is possible to generate limited comparable VSA data, such as PVS volume.
bibliographic citation: Luo et al. (2023) Minimizing the variables of voiding spot assay for comparison between laboratories. PeerJ 11:e15420 https://doi.org/10.7717/peerj.15420
date submitted: 2023-01-10
date accepted: 2023-04-25
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Chuang
author list: Agent
  family name: Liu
  given name: Juan
author list: Agent
  family name: Yang
  given name: Jiali
author list: Agent
  family name: Xie
  given name: Xiang
author list: Agent
  family name: Yu
  given name: Weiqun
author list: Agent
  family name: Chen
  given name: Huan
doi: 10.7717/peerj.15420
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: ©2023 Luo et al.
attribution name: Luo et al.

Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer
type: item
type: AcademicArticle
description: Among the Arctic seas, the largest volume of river runoff (~45% of the total river-water inflow into the Arctic Ocean) enters the Siberian Kara Sea. The viral communities of the Kara Sea are important for the functioning of the marine ecosystem. Studies of virus–prokaryote interactions on the Kara Sea shelf have been conducted only in spring and autumn. Here, we investigated the abundance of free viruses, viruses attached to prokaryotes, and pico-sized detrital particles; the morphology (shape and size) of the viruses, viral infection and virus-mediated mortality of prokaryotes in early summer, i.e., during a seasonal ice melting period and maximum inflow of river-water volumes with high concentrations of dissolved and suspended organic carbon. Seawater samples for microbial analyses were collected across the Kara Sea shelf zone on board the Norilskiy Nickel as a research platform from June 29 to July 15, 2018. Abundances of prokaryotes (range (0.6–25.3) × 105 cells mL−1) and free viruses (range (10–117) × 105 viruses mL−1) were correlated (r = 0.63, p = 0.005) with an average virus: prokaryote ratio of 23.9 ± 5.3. The abundance of free viruses and viral-mediated mortality of prokaryotes were significantly higher in early summer than in early spring and autumn. Free viruses with a capsid diameter of 16–304 nm were recorded in the examined water samples. Waters in the Kara Sea shelf contained high concentrations of suspended organic particles 0.25–4.0 µm in size (range (0.6–25.3) × 105 particles mL−1). The proportions of free viruses, viruses attached to prokaryotes, and viruses attached to pico-sized detrital particles were 89.8 ± 6.0%, 2.2 ± 0.6% and 8.0 ± 1.3%, respectively, of the total virioplankton abundance (on average (61.5 ± 6.2) × 105 viruses mL−1). Viruses smaller than 60 nm clearly dominated at all studied sites. The majority of free viruses were not tailed. We estimated that an average of 1.4% (range 0.4–3.5%) of the prokaryote community was visibly infe…
format: application/pdf
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creator: Alexander Ivanovich Kopylov
creator: Elena Anatoliyevna Zabotkina
creator: Andrey Fiodorovich Sazhin
creator: Nadezda Romanova
creator: Nikolay Belyaev
creator: Anastasia Drozdova
subject: Ecology
subject: Ecosystem Science
subject: Marine Biology
subject: Microbiology
subject: Virology
description: doi:10.7717/peerj.15457
publisher: PeerJ Inc.
rights: © 2023 Kopylov et al.
abstract: Among the Arctic seas, the largest volume of river runoff (~45% of the total river-water inflow into the Arctic Ocean) enters the Siberian Kara Sea. The viral communities of the Kara Sea are important for the functioning of the marine ecosystem. Studies of virus–prokaryote interactions on the Kara Sea shelf have been conducted only in spring and autumn. Here, we investigated the abundance of free viruses, viruses attached to prokaryotes, and pico-sized detrital particles; the morphology (shape and size) of the viruses, viral infection and virus-mediated mortality of prokaryotes in early summer, i.e., during a seasonal ice melting period and maximum inflow of river-water volumes with high concentrations of dissolved and suspended organic carbon. Seawater samples for microbial analyses were collected across the Kara Sea shelf zone on board the Norilskiy Nickel as a research platform from June 29 to July 15, 2018. Abundances of prokaryotes (range (0.6–25.3) × 105 cells mL−1) and free viruses (range (10–117) × 105 viruses mL−1) were correlated (r = 0.63, p = 0.005) with an average virus: prokaryote ratio of 23.9 ± 5.3. The abundance of free viruses and viral-mediated mortality of prokaryotes were significantly higher in early summer than in early spring and autumn. Free viruses with a capsid diameter of 16–304 nm were recorded in the examined water samples. Waters in the Kara Sea shelf contained high concentrations of suspended organic particles 0.25–4.0 µm in size (range (0.6–25.3) × 105 particles mL−1). The proportions of free viruses, viruses attached to prokaryotes, and viruses attached to pico-sized detrital particles were 89.8 ± 6.0%, 2.2 ± 0.6% and 8.0 ± 1.3%, respectively, of the total virioplankton abundance (on average (61.5 ± 6.2) × 105 viruses mL−1). Viruses smaller than 60 nm clearly dominated at all studied sites. The majority of free viruses were not tailed. We estimated that an average of 1.4% (range 0.4–3.5%) of the prokaryote community was visibly infe…
bibliographic citation: Kopylov et al. (2023) Virioplankton and virus-induced mortality of prokaryotes in the Kara Sea (Arctic) in summer. PeerJ 11:e15457 https://doi.org/10.7717/peerj.15457
date submitted: 2022-11-04
date accepted: 2023-05-03
issued: 2023-05-23
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kopylov
  given name: Alexander Ivanovich
author list: Agent
  family name: Zabotkina
  given name: Elena Anatoliyevna
author list: Agent
  family name: Sazhin
  given name: Andrey Fiodorovich
author list: Agent
  family name: Romanova
  given name: Nadezda
author list: Agent
  family name: Belyaev
  given name: Nikolay
author list: Agent
  family name: Drozdova
  given name: Anastasia
doi: 10.7717/peerj.15457
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-23
copyright: © 2023 Kopylov et al.
attribution name: Kopylov et al.

Determination of the affinity constants for phage display albumin-binding peptides
type: item
type: AcademicArticle
description: Background Phage display technology has been established as a powerful screening approach to select ligands or peptides for binding to proteins. Despite rapid growth in the field, there has been a relative dearth of quantitative criteria to measure the effectiveness of the process of phage display screening. Since human serum albumin (HSA) has been extensively studied as a drug carrier to extend the plasma half-life of protein therapeutics, the use of phage display technology is required for identifying albumin-binding peptides as the very promising strategy of albumin-binding against albumin fusion. The construction of albumin-binding drug requires the assessment of a large quantity of HSA-binding peptide (HSA binder) candidates for conjugation with therapeutic proteins. The use of the linear epitope mapping method has allowed researchers to discover many HSA-binding peptides. However, it may be inefficient to select these peptides based on sequence identity via randomly sequencing individual phage clones from enrichment pools. Method Here, a simple assessment method to facilitate phage display selection of HSA-binding peptides was recommended. With experimentally determined phage titer, one can calculate the specificity ratios, the recovery yields and the relative dissociation constants, which are defined as quantitative criteria for panning and characterization of the binding phage fused peptides. Results Consequently, this approach may not only enable more rapid and low-cost phage display screening, but also efficiently reduce pseudo-positive phages selected as HSA binders for conjugation with therapeutic proteins.
format: application/pdf
format: text/html
creator: Yi-Feng Shi
subject: Biochemistry
subject: Bioengineering
subject: Biotechnology
subject: Molecular Biology
subject: Synthetic Biology
description: doi:10.7717/peerj.15078
publisher: PeerJ Inc.
rights: © 2023 Shi
abstract: Background Phage display technology has been established as a powerful screening approach to select ligands or peptides for binding to proteins. Despite rapid growth in the field, there has been a relative dearth of quantitative criteria to measure the effectiveness of the process of phage display screening. Since human serum albumin (HSA) has been extensively studied as a drug carrier to extend the plasma half-life of protein therapeutics, the use of phage display technology is required for identifying albumin-binding peptides as the very promising strategy of albumin-binding against albumin fusion. The construction of albumin-binding drug requires the assessment of a large quantity of HSA-binding peptide (HSA binder) candidates for conjugation with therapeutic proteins. The use of the linear epitope mapping method has allowed researchers to discover many HSA-binding peptides. However, it may be inefficient to select these peptides based on sequence identity via randomly sequencing individual phage clones from enrichment pools. Method Here, a simple assessment method to facilitate phage display selection of HSA-binding peptides was recommended. With experimentally determined phage titer, one can calculate the specificity ratios, the recovery yields and the relative dissociation constants, which are defined as quantitative criteria for panning and characterization of the binding phage fused peptides. Results Consequently, this approach may not only enable more rapid and low-cost phage display screening, but also efficiently reduce pseudo-positive phages selected as HSA binders for conjugation with therapeutic proteins.
bibliographic citation: Shi (2023) Determination of the affinity constants for phage display albumin-binding peptides. PeerJ 11:e15078 https://doi.org/10.7717/peerj.15078
date submitted: 2020-12-21
date accepted: 2023-02-24
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shi
  given name: Yi-Feng
doi: 10.7717/peerj.15078
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: ©2023 Shi
attribution name: Shi

Effects of in-situ stroboscopic training on visual, visuomotor and reactive agility in youth volleyball players
type: item
type: AcademicArticle
description: Background Stroboscopic training is based on an exercise with intermittent visual stimuli that force a greater demand on the visuomotor processing for improving performance under normal vision. While the stroboscopic effect is used as an effective tool to improve information processing in general perceptual-cognitive tasks, there is still a lack of research focused on identifying training protocols for sport-specific settings. Therefore, we aimed at assessing the effects of in-situ stroboscopic training on visual, visuomotor and reactive agility in young volleyball players. Methods Fifty young volleyball athletes (26 males and 24 females; mean age, 16.5 ± 0.6 years) participated in this study and were each divided randomly into an experimental group and a control group, who then both performed identical volleyball-specific tasks, with the experimental group under stroboscopic influence. The participants were evaluated three times using laboratory based tests for simple and complex reaction speed, sensory sensitivity and saccade dynamics; before the after the 6-week-long training (short-term effect) and 4 weeks later (long-term effect). In addition, a field test investigated the effects of the training on reactive agility. Results A significant TIME vs GROUP effect was observed for (1) simple motor time (p = 0.020, ηp2 = 0.08), with improvement in the stroboscopic group in the post-test and retention test (p = 0.003, d = 0.42 and p = 0.027, d = 0.35, respectively); (2) complex reaction speed (p < 0.001, ηp2 = 0.22), with a large post-test effect in the stroboscopic group (p < 0.001, d = 0.87) and a small effect in the non-stroboscopic group (p = 0.010, d = 0.31); (3) saccade dynamics (p = 0.011, ηp2 = 0.09), with post-hoc tests in the stroboscopic group not reaching significance (p = 0.083, d = 0.54); and (4) reactive agility (p = 0.039, ηp2 = 0.07), with a post-test improvement in the stroboscopic group (p = 0.017, d = 0.49). Neither sensory sensitivity nor simple r…
format: application/pdf
format: text/html
creator: Michał Zwierko
creator: Wojciech Jedziniak
creator: Marek Popowczak
creator: Andrzej Rokita
subject: Kinesiology
subject: Psychiatry and Psychology
subject: Sports Medicine
description: doi:10.7717/peerj.15213
publisher: PeerJ Inc.
rights: © 2023 Zwierko et al.
abstract: Background Stroboscopic training is based on an exercise with intermittent visual stimuli that force a greater demand on the visuomotor processing for improving performance under normal vision. While the stroboscopic effect is used as an effective tool to improve information processing in general perceptual-cognitive tasks, there is still a lack of research focused on identifying training protocols for sport-specific settings. Therefore, we aimed at assessing the effects of in-situ stroboscopic training on visual, visuomotor and reactive agility in young volleyball players. Methods Fifty young volleyball athletes (26 males and 24 females; mean age, 16.5 ± 0.6 years) participated in this study and were each divided randomly into an experimental group and a control group, who then both performed identical volleyball-specific tasks, with the experimental group under stroboscopic influence. The participants were evaluated three times using laboratory based tests for simple and complex reaction speed, sensory sensitivity and saccade dynamics; before the after the 6-week-long training (short-term effect) and 4 weeks later (long-term effect). In addition, a field test investigated the effects of the training on reactive agility. Results A significant TIME vs GROUP effect was observed for (1) simple motor time (p = 0.020, ηp2 = 0.08), with improvement in the stroboscopic group in the post-test and retention test (p = 0.003, d = 0.42 and p = 0.027, d = 0.35, respectively); (2) complex reaction speed (p < 0.001, ηp2 = 0.22), with a large post-test effect in the stroboscopic group (p < 0.001, d = 0.87) and a small effect in the non-stroboscopic group (p = 0.010, d = 0.31); (3) saccade dynamics (p = 0.011, ηp2 = 0.09), with post-hoc tests in the stroboscopic group not reaching significance (p = 0.083, d = 0.54); and (4) reactive agility (p = 0.039, ηp2 = 0.07), with a post-test improvement in the stroboscopic group (p = 0.017, d = 0.49). Neither sensory sensitivity nor simple r…
bibliographic citation: Zwierko et al. (2023) Effects of in-situ stroboscopic training on visual, visuomotor and reactive agility in youth volleyball players. PeerJ 11:e15213 https://doi.org/10.7717/peerj.15213
date submitted: 2022-12-16
date accepted: 2023-03-20
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zwierko
  given name: Michał
author list: Agent
  family name: Jedziniak
  given name: Wojciech
author list: Agent
  family name: Popowczak
  given name: Marek
author list: Agent
  family name: Rokita
  given name: Andrzej
doi: 10.7717/peerj.15213
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Zwierko et al.
attribution name: Zwierko et al.

Description and life cycle of a new species of the genus Arachnanthus (Cnidaria: Anthozoa: Ceriantharia) from the Southwestern Atlantic Ocean
type: item
type: AcademicArticle
description: Background Ceriantharia is a subclass of the phylum Cnidaria, which comprises tube-dwelling marine invertebrates. This subclass is composed of three families, including Arachnactidae, with two known genera. Currently, the genus Arachnanthus has five valid species recorded from Australia, the Mediterranean Sea and both the Southern and Northern Pacific Ocean. However, at the moment, there is no record of organisms of this family from the South Atlantic Ocean. Besides that, the life cycle of any species of the genus Arachnanthus is known. The present study describes a new species of the genus Arachnanthus and its life cycle, based on specimens from Uruguay and South of Brazil. Methods Larvae were collected by plankton net in Rio Grande—Brazil and the development and external morphology of these specimens were observed in the laboratory during two years, and subsequently described. Additionally, nine adult ceriantharians correspondent to the larvae from Rio Grande were collected in Uruguay and their external and internal anatomies, and cnidome were described. Results Arachnanthus errans sp. nov. exhibited a free-swimming, short-lived cerinula larvae that spent short-time on the plankton. The larva developed into small and translucent polyps with a short actinopharynx, one pair of mesenteries attached to a siphonoglyph, and a medium first pair of metamesenteries. Further, the adult polyp displayed an unprecedented locomotion behavior in Ceriantharia that is first reported here, it can crawl under and in between the sediment.
format: application/pdf
format: text/html
creator: Celine S.S. Lopes
creator: Fabrizio Scarabino
creator: Alvar Carranza
creator: Ricardo González Muñoz
creator: André C. Morandini
creator: Renato Mitsuo Nagata
creator: Sérgio Nascimento Stampar
subject: Biodiversity
subject: Developmental Biology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.15290
publisher: PeerJ Inc.
rights: © 2023 S S Lopes et al.
abstract: Background Ceriantharia is a subclass of the phylum Cnidaria, which comprises tube-dwelling marine invertebrates. This subclass is composed of three families, including Arachnactidae, with two known genera. Currently, the genus Arachnanthus has five valid species recorded from Australia, the Mediterranean Sea and both the Southern and Northern Pacific Ocean. However, at the moment, there is no record of organisms of this family from the South Atlantic Ocean. Besides that, the life cycle of any species of the genus Arachnanthus is known. The present study describes a new species of the genus Arachnanthus and its life cycle, based on specimens from Uruguay and South of Brazil. Methods Larvae were collected by plankton net in Rio Grande—Brazil and the development and external morphology of these specimens were observed in the laboratory during two years, and subsequently described. Additionally, nine adult ceriantharians correspondent to the larvae from Rio Grande were collected in Uruguay and their external and internal anatomies, and cnidome were described. Results Arachnanthus errans sp. nov. exhibited a free-swimming, short-lived cerinula larvae that spent short-time on the plankton. The larva developed into small and translucent polyps with a short actinopharynx, one pair of mesenteries attached to a siphonoglyph, and a medium first pair of metamesenteries. Further, the adult polyp displayed an unprecedented locomotion behavior in Ceriantharia that is first reported here, it can crawl under and in between the sediment.
bibliographic citation: S.S. Lopes et al. (2023) Description and life cycle of a new species of the genus Arachnanthus (Cnidaria: Anthozoa: Ceriantharia) from the Southwestern Atlantic Ocean. PeerJ 11:e15290 https://doi.org/10.7717/peerj.15290
date submitted: 2023-01-27
date accepted: 2023-04-04
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: S.S. Lopes
  given name: Celine
author list: Agent
  family name: Scarabino
  given name: Fabrizio
author list: Agent
  family name: Carranza
  given name: Alvar
author list: Agent
  family name: González Muñoz
  given name: Ricardo
author list: Agent
  family name: C. Morandini
  given name: André
author list: Agent
  family name: Nagata
  given name: Renato Mitsuo
author list: Agent
  family name: Nascimento Stampar
  given name: Sérgio
doi: 10.7717/peerj.15290
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: ©2023 S S Lopes et al.
attribution name: S S Lopes et al.

Comparative morpho-anatomical study on Leptadenia pyrotechnica (Apocynaceae) growing in the hyper-arid and arid habitats of Saudi Arabia
type: item
type: AcademicArticle
description: The use of wild plants is considered to be an eco-friendly and promising natural resource. In sandy desert habitats, Leptadenia pyrotechnica flourishes as a xerophytic shrub with high biomass production. As a dominant shrub in the arid sand dune habitats of Saudi Arabia, Leptadenia pyrotechnica (Forssk.) Decne (Asclepiadaceae) is one of the most common xerophytes; the many medicinal uses of this plant include treating allergies, productive coughs, abortions, diabetes, stomach disorders, fevers, kidney disorders, and stones. In such a distribution, morpho-anatomical characteristics, among other adaptive traits, play an important role. This study aims to characterize some morpho-anatomical adaptations of L. pyrotechnica in two stressful habitats: the hyper-arid inland sand dunes of the Empty Quarter (EQ) and the arid coastal sand dunes of Jazan. A morpho-anatomical analysis of plant stems and roots from both habitats was conducted using light microscopy (LM) and scanning electron microscopy (SEM). The outcomes indicated similar characteristics, a low surface-to-volume ratio (S/V), a thin boundary layer (δbl), an epidermis with many layers of hypodermis, bundles of sclerenchymatous cells around vascular tissue, and storage starch grains in ray parenchyma between xylem conduits. On the other hand, the L. pyrotechnica stem from the hyper-arid habitat of the Empty Quarter revealed more encrypted stomata, more elongated palisade cells, less calcium oxalate crystals with low Ca percentage, and a high vulnerability index of xylem vessels compared with the same traits of the stem from the Jazan coastal sand dunes habitat. Roots of L. pyrotechnica from both habitats revealed similar features of general anatomy. However, differences in specific anatomical traits were observed, especially in xylem vessel characters. The vulnerability index of root xylem vessels from the Empty Quarter habitat was more than that from the Jazan coastal sand dunes habitat. Furthermore, vestured bord…
format: application/pdf
format: text/html
creator: Najla A. Al Shaye
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Plant Science
description: doi:10.7717/peerj.15320
publisher: PeerJ Inc.
rights: © 2023 Al Shaye
abstract: The use of wild plants is considered to be an eco-friendly and promising natural resource. In sandy desert habitats, Leptadenia pyrotechnica flourishes as a xerophytic shrub with high biomass production. As a dominant shrub in the arid sand dune habitats of Saudi Arabia, Leptadenia pyrotechnica (Forssk.) Decne (Asclepiadaceae) is one of the most common xerophytes; the many medicinal uses of this plant include treating allergies, productive coughs, abortions, diabetes, stomach disorders, fevers, kidney disorders, and stones. In such a distribution, morpho-anatomical characteristics, among other adaptive traits, play an important role. This study aims to characterize some morpho-anatomical adaptations of L. pyrotechnica in two stressful habitats: the hyper-arid inland sand dunes of the Empty Quarter (EQ) and the arid coastal sand dunes of Jazan. A morpho-anatomical analysis of plant stems and roots from both habitats was conducted using light microscopy (LM) and scanning electron microscopy (SEM). The outcomes indicated similar characteristics, a low surface-to-volume ratio (S/V), a thin boundary layer (δbl), an epidermis with many layers of hypodermis, bundles of sclerenchymatous cells around vascular tissue, and storage starch grains in ray parenchyma between xylem conduits. On the other hand, the L. pyrotechnica stem from the hyper-arid habitat of the Empty Quarter revealed more encrypted stomata, more elongated palisade cells, less calcium oxalate crystals with low Ca percentage, and a high vulnerability index of xylem vessels compared with the same traits of the stem from the Jazan coastal sand dunes habitat. Roots of L. pyrotechnica from both habitats revealed similar features of general anatomy. However, differences in specific anatomical traits were observed, especially in xylem vessel characters. The vulnerability index of root xylem vessels from the Empty Quarter habitat was more than that from the Jazan coastal sand dunes habitat. Furthermore, vestured bord…
bibliographic citation: Al Shaye (2023) Comparative morpho-anatomical study on Leptadenia pyrotechnica (Apocynaceae) growing in the hyper-arid and arid habitats of Saudi Arabia. PeerJ 11:e15320 https://doi.org/10.7717/peerj.15320
date submitted: 2023-01-18
date accepted: 2023-04-10
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Al Shaye
  given name: Najla A.
doi: 10.7717/peerj.15320
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Al Shaye
attribution name: Al Shaye

Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach
type: item
type: AcademicArticle
description: Background Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant. Methods Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods. Results Our results suggest that using our subsampling approach, identifying less than 10% of a sample’s contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.
format: application/pdf
format: text/html
creator: Caroline Chimeno
creator: Björn Rulik
creator: Alessandro Manfrin
creator: Gregor Kalinkat
creator: Franz Hölker
creator: Viktor Baranov
subject: Biodiversity
subject: Entomology
subject: Molecular Biology
subject: Taxonomy
subject: Freshwater Biology
description: doi:10.7717/peerj.15336
publisher: PeerJ Inc.
rights: © 2023 Chimeno et al.
abstract: Background Integrative taxonomy is becoming ever more significant in biodiversity research as scientists are tackling increasingly taxonomically challenging groups. Implementing a combined approach not only guarantees more accurate species identification, but also helps overcome limitations that each method presents when applied on its own. In this study, we present one application of integrative taxonomy for the highly abundant and particularly diverse fly taxon Chironomidae (Diptera). Although non-biting midges are key organisms in merolimnic systems, they are often cast aside in ecological surveys because they are very challenging to identify and extremely abundant. Methods Here, we demonstrate one way of applying integrative methods to tackle this highly diverse taxon. We present a three-level subsampling method to drastically reduce the workload of bulk sample processing, then apply morphological and molecular identification methods in parallel to evaluate species diversity and to examine inconsistencies across methods. Results Our results suggest that using our subsampling approach, identifying less than 10% of a sample’s contents can reliably detect >90% of its diversity. However, despite reducing the processing workload drastically, the performance of our taxonomist was affected by mistakes, caused by large amounts of material. We conducted misidentifications for 9% of vouchers, which may not have been recovered had we not applied a second identification method. On the other hand, we were able to provide species information in cases where molecular methods could not, which was the case for 14% of vouchers. Therefore, we conclude that when wanting to implement non-biting midges into ecological frameworks, it is imperative to use an integrative approach.
bibliographic citation: Chimeno et al. (2023) Facing the infinity: tackling large samples of challenging Chironomidae (Diptera) with an integrative approach. PeerJ 11:e15336 https://doi.org/10.7717/peerj.15336
date submitted: 2023-01-10
date accepted: 2023-04-11
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chimeno
  given name: Caroline
author list: Agent
  family name: Rulik
  given name: Björn
author list: Agent
  family name: Manfrin
  given name: Alessandro
author list: Agent
  family name: Kalinkat
  given name: Gregor
author list: Agent
  family name: Hölker
  given name: Franz
author list: Agent
  family name: Baranov
  given name: Viktor
doi: 10.7717/peerj.15336
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Chimeno et al.
attribution name: Chimeno et al.

Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion
type: item
type: AcademicArticle
description: Background The effects of FBXO43 on hepatocellular carcinoma (HCC) and its clinical significance have not yet been determined. This study aims to determine the clinical significance of FBXO43 in HCC and its impact on the biological functions of HCC cells. Methods Data from TCGA database were downloaded to investigate the expression of FBXO43 in HCC and its correlation with prognosis and immune infiltration. Immunohistochemical staining images of FBXO43 in HCC were acquired from the HPA website. HCC cells (BEL-7404 and SMMC-7721) were transfected with the lentivirus targeting FBXO43 to decrease FBXO43 expression in HCC cells. Western blotting assay was conducted to evaluate the expression level of FBXO43 protein. MTT assay was used to detect the proliferation of HCC cells. The migration and invasion of HCC cells were investigated by performing scratch wound-healing and Transwell invasion assays, respectively. Results In comparison to normal tissues, FBXO43 is overexpressed in HCC tissue, and high FBXO43 expression is linked to late T stage, TNM stage and tumor grade. Elevated FBXO43 expression is a risk factor for HCC. In patients with high FBXO43 expression, the overall survival, disease-specific survival, progression-free survival and disease-free survival are poorer. The proliferation, migration and invasion of HCC cells are significantly attenuated in FBXO43 knockdown cells. Also, TCGA data analysis reveals that FBXO43 exhibits a positive correlation with immunosuppression of HCC. Conclusion FBXO43 is overexpressed in HCC, and is linked to late tumor stage, worse prognosis and tumor immunosuppression. FBXO43 knockdown restrains the proliferation, migration and invasion of HCC.
format: application/pdf
format: text/html
creator: Rulan Ma
creator: Wenbo Liu
creator: Tuanhe Sun
creator: Chengxue Dang
creator: Kang Li
subject: Bioinformatics
subject: Cell Biology
subject: Gastroenterology and Hepatology
subject: Oncology
subject: Medical Genetics
description: doi:10.7717/peerj.15373
publisher: PeerJ Inc.
rights: © 2023 Ma et al.
abstract: Background The effects of FBXO43 on hepatocellular carcinoma (HCC) and its clinical significance have not yet been determined. This study aims to determine the clinical significance of FBXO43 in HCC and its impact on the biological functions of HCC cells. Methods Data from TCGA database were downloaded to investigate the expression of FBXO43 in HCC and its correlation with prognosis and immune infiltration. Immunohistochemical staining images of FBXO43 in HCC were acquired from the HPA website. HCC cells (BEL-7404 and SMMC-7721) were transfected with the lentivirus targeting FBXO43 to decrease FBXO43 expression in HCC cells. Western blotting assay was conducted to evaluate the expression level of FBXO43 protein. MTT assay was used to detect the proliferation of HCC cells. The migration and invasion of HCC cells were investigated by performing scratch wound-healing and Transwell invasion assays, respectively. Results In comparison to normal tissues, FBXO43 is overexpressed in HCC tissue, and high FBXO43 expression is linked to late T stage, TNM stage and tumor grade. Elevated FBXO43 expression is a risk factor for HCC. In patients with high FBXO43 expression, the overall survival, disease-specific survival, progression-free survival and disease-free survival are poorer. The proliferation, migration and invasion of HCC cells are significantly attenuated in FBXO43 knockdown cells. Also, TCGA data analysis reveals that FBXO43 exhibits a positive correlation with immunosuppression of HCC. Conclusion FBXO43 is overexpressed in HCC, and is linked to late tumor stage, worse prognosis and tumor immunosuppression. FBXO43 knockdown restrains the proliferation, migration and invasion of HCC.
bibliographic citation: Ma et al. (2023) Clinical significance of FBXO43 in hepatocellular carcinoma and its impact on tumor cell proliferation, migration and invasion. PeerJ 11:e15373 https://doi.org/10.7717/peerj.15373
date submitted: 2023-02-17
date accepted: 2023-04-18
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Rulan
author list: Agent
  family name: Liu
  given name: Wenbo
author list: Agent
  family name: Sun
  given name: Tuanhe
author list: Agent
  family name: Dang
  given name: Chengxue
author list: Agent
  family name: Li
  given name: Kang
doi: 10.7717/peerj.15373
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: ©2023 Ma et al.
attribution name: Ma et al.

Optimising sampling of fish assemblages on intertidal reefs using remote underwater video
type: item
type: AcademicArticle
description: Background Assessing fish assemblages in subtidal and intertidal habitats is challenging due to the structural complexity of many of these systems. Trapping and collecting are regarded as optimal ways to sample these assemblages, but this method is costly and destructive, so researchers also use video techniques. Underwater visual census and baited remote underwater video stations are commonly used to characterise fish communities in these systems. More passive techniques such as remote underwater video (RUV) may be more appropriate for behavioural studies, or for comparing proximal habitats where the broad attraction caused by bait plumes could be an issue. However, data processing for RUVs can be time consuming and create processing bottlenecks. Methods Here, we identified the optimal subsampling method to assess fish assemblages on intertidal oyster reefs using RUV footage and bootstrapping techniques. We quantified how video subsampling effort and method (systematic vs random) affect the accuracy and precision of three different fish assemblage metrics; species richness and two proxies for the total abundance of fish, MaxNT and MeanCountT, which have not been evaluated previously for complex intertidal habitats. Results Results suggest that MaxNT and species richness should be recorded in real time, whereas optimal sampling for MeanCountT is every 60 s. Systematic sampling proved to be more accurate and precise than random sampling. This study provides valuable methodology recommendations which are relevant for the use of RUV to assess fish assemblages in a variety of shallow intertidal habitats.
format: application/pdf
format: text/html
creator: Katherine R. Erickson
creator: Ana B. Bugnot
creator: Will F. Figueira
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Marine Biology
description: doi:10.7717/peerj.15426
publisher: PeerJ Inc.
rights: © 2023 Erickson et al.
abstract: Background Assessing fish assemblages in subtidal and intertidal habitats is challenging due to the structural complexity of many of these systems. Trapping and collecting are regarded as optimal ways to sample these assemblages, but this method is costly and destructive, so researchers also use video techniques. Underwater visual census and baited remote underwater video stations are commonly used to characterise fish communities in these systems. More passive techniques such as remote underwater video (RUV) may be more appropriate for behavioural studies, or for comparing proximal habitats where the broad attraction caused by bait plumes could be an issue. However, data processing for RUVs can be time consuming and create processing bottlenecks. Methods Here, we identified the optimal subsampling method to assess fish assemblages on intertidal oyster reefs using RUV footage and bootstrapping techniques. We quantified how video subsampling effort and method (systematic vs random) affect the accuracy and precision of three different fish assemblage metrics; species richness and two proxies for the total abundance of fish, MaxNT and MeanCountT, which have not been evaluated previously for complex intertidal habitats. Results Results suggest that MaxNT and species richness should be recorded in real time, whereas optimal sampling for MeanCountT is every 60 s. Systematic sampling proved to be more accurate and precise than random sampling. This study provides valuable methodology recommendations which are relevant for the use of RUV to assess fish assemblages in a variety of shallow intertidal habitats.
bibliographic citation: Erickson et al. (2023) Optimising sampling of fish assemblages on intertidal reefs using remote underwater video. PeerJ 11:e15426 https://doi.org/10.7717/peerj.15426
date submitted: 2022-11-21
date accepted: 2023-04-25
issued: 2023-05-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Erickson
  given name: Katherine R.
author list: Agent
  family name: Bugnot
  given name: Ana B.
author list: Agent
  family name: Figueira
  given name: Will F.
doi: 10.7717/peerj.15426
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-05-22
copyright: © 2023 Erickson et al.
attribution name: Erickson et al.

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