PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, ʻōpeʻapeʻa, across the Hawaiian Islands
items: Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development
items: Evidence of validity and reliability of Jumpo 2 and MyJump 2 for estimating vertical jump variables
items: Facilitation of a free-roaming apex predator in working lands: evaluating factors that influence leopard spatial dynamics and prey availability in a South African biodiversity hotspot
items: Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study
items: Combination of Vitamin C and Lenvatinib potentiates antitumor effects in hepatocellular carcinoma cells in vitro
items: Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep
items: Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance
items: Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells
items: Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing

Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, ʻōpeʻapeʻa, across the Hawaiian Islands
type: item
type: AcademicArticle
description: Island bat species are disproportionately at risk of extinction, and Hawaiʻi’s only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as ʻōpeʻapeʻa, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988–2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawaiʻi, Maui, Oʻahu, and Kauaʻi. Genetic differentiation occurred between Hawaiʻi and Maui, both of which were differentiated from Oʻahu and Kauaʻi. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawaiʻi and Kauaʻi. Contemporary genetic effective population sizes were smaller on Oʻahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawaiʻi. Our study provides population-level estimates for the genetic diversity and geographic structure of ‘ōpeʻapeʻa, that could be used by agencies tasked with wildlife conservation in Hawaiʻi.
format: application/pdf
format: text/html
creator: Corinna A. Pinzari
creator: M. Renee Bellinger
creator: Donald Price
creator: Frank J. Bonaccorso
subject: Conservation Biology
subject: Ecology
subject: Genetics
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.14365
publisher: PeerJ Inc.
rights: © 2023
abstract: Island bat species are disproportionately at risk of extinction, and Hawaiʻi’s only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as ʻōpeʻapeʻa, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988–2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawaiʻi, Maui, Oʻahu, and Kauaʻi. Genetic differentiation occurred between Hawaiʻi and Maui, both of which were differentiated from Oʻahu and Kauaʻi. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawaiʻi and Kauaʻi. Contemporary genetic effective population sizes were smaller on Oʻahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawaiʻi. Our study provides population-level estimates for the genetic diversity and geographic structure of ‘ōpeʻapeʻa, that could be used by agencies tasked with wildlife conservation in Hawaiʻi.
bibliographic citation: Pinzari et al. (2023) Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, ʻōpeʻapeʻa, across the Hawaiian Islands. PeerJ 11:e14365 https://doi.org/10.7717/peerj.14365
date submitted: 2022-01-17
date accepted: 2022-10-19
issued: 2023-01-25
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Pinzari
  given name: Corinna A.
author list: Agent
  family name: Bellinger
  given name: M. Renee
author list: Agent
  family name: Price
  given name: Donald
author list: Agent
  family name: Bonaccorso
  given name: Frank J.
doi: 10.7717/peerj.14365
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25

Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development
type: item
type: AcademicArticle
description: Glutathione S-transferase (GSTs), a large and diverse group of multi-functional enzymes (EC 2.5.1.18), are associated with cellular detoxification, various biotic and abiotic stress responses, as well as secondary metabolites transportation. Here, 53 members of the FcGST gene family were screened from the genome database of fig (Ficus carica), which were further classified into five subfamilies, and the tau and phi were the major subfamilies. These genes were unevenly distributed over all the 13 chromosomes, and 12 tandem and one segmental duplication may contribute to this family expansion. Syntenic analysis revealed that FcGST shared closer genetic evolutionary origin relationship with species from the Ficus genus of the Moraceae family, such as F. microcarpa and F. hispida. The FcGST members of the same subfamily shared similar gene structure and motif distribution. The α helices were the chief structure element in predicted secondary and tertiary structure of FcGSTs proteins. GO and KEGG indicated that FcGSTs play multiple roles in glutathione metabolism and stress reactions as well as flavonoid metabolism. Predictive promoter analysis indicated that FcGSTs gene may be responsive to light, hormone, stress stimulation, development signaling, and regulated by MYB or WRKY. RNA-seq analysis showed that several FcGSTs that mainly expressed in the female flower tissue and peel during ‘Purple-Peel’ fig fruit development. Compared with ‘Green Peel’, FcGSTF1, and FcGSTU5/6/7 exhibited high expression abundance in the mature fruit purple peel. Additionally, results of phylogenetic sequences analysis, multiple sequences alignment, and anthocyanin content together showed that the expression changes of FcGSTF1, and FcGSTU5/6/7 may play crucial roles in fruit peel color alteration during fruit ripening. Our study provides a comprehensive overview of the GST gene family in fig, thus facilitating the further clarification of the molecular function and breeding utilization.
format: application/pdf
format: text/html
creator: Longbo Liu
creator: Shuxuan Zheng
creator: Dekun Yang
creator: Jie Zheng
subject: Agricultural Science
subject: Bioinformatics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14406
publisher: PeerJ Inc.
rights: © 2023 Liu et al.
abstract: Glutathione S-transferase (GSTs), a large and diverse group of multi-functional enzymes (EC 2.5.1.18), are associated with cellular detoxification, various biotic and abiotic stress responses, as well as secondary metabolites transportation. Here, 53 members of the FcGST gene family were screened from the genome database of fig (Ficus carica), which were further classified into five subfamilies, and the tau and phi were the major subfamilies. These genes were unevenly distributed over all the 13 chromosomes, and 12 tandem and one segmental duplication may contribute to this family expansion. Syntenic analysis revealed that FcGST shared closer genetic evolutionary origin relationship with species from the Ficus genus of the Moraceae family, such as F. microcarpa and F. hispida. The FcGST members of the same subfamily shared similar gene structure and motif distribution. The α helices were the chief structure element in predicted secondary and tertiary structure of FcGSTs proteins. GO and KEGG indicated that FcGSTs play multiple roles in glutathione metabolism and stress reactions as well as flavonoid metabolism. Predictive promoter analysis indicated that FcGSTs gene may be responsive to light, hormone, stress stimulation, development signaling, and regulated by MYB or WRKY. RNA-seq analysis showed that several FcGSTs that mainly expressed in the female flower tissue and peel during ‘Purple-Peel’ fig fruit development. Compared with ‘Green Peel’, FcGSTF1, and FcGSTU5/6/7 exhibited high expression abundance in the mature fruit purple peel. Additionally, results of phylogenetic sequences analysis, multiple sequences alignment, and anthocyanin content together showed that the expression changes of FcGSTF1, and FcGSTU5/6/7 may play crucial roles in fruit peel color alteration during fruit ripening. Our study provides a comprehensive overview of the GST gene family in fig, thus facilitating the further clarification of the molecular function and breeding utilization.
bibliographic citation: Liu et al. (2023) Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development. PeerJ 11:e14406 https://doi.org/10.7717/peerj.14406
date submitted: 2022-02-15
date accepted: 2022-10-26
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Longbo
author list: Agent
  family name: Zheng
  given name: Shuxuan
author list: Agent
  family name: Yang
  given name: Dekun
author list: Agent
  family name: Zheng
  given name: Jie
doi: 10.7717/peerj.14406
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Liu et al.
attribution name: Liu et al.

Evidence of validity and reliability of Jumpo 2 and MyJump 2 for estimating vertical jump variables
type: item
type: AcademicArticle
description: Background We investigated the concurrent validity and test-retest reliability of the Jumpo 2 and MyJump 2 apps for estimating jump height, and the mean values of force, velocity, and power produced during countermovement (CMJ) and squat jumps (SJ). Methods Physically active university aged men (n = 10, 20 ± 3 years, 176 ± 6 cm, 68 ± 9 kg) jumped on a force plate (i.e., criterion) while being recorded by a smartphone slow-motion camera. The videos were analyzed using Jumpo 2 and MyJump 2 using a Samsung Galaxy S7 powered by the Android system. Validity and reliability were determined by regression analysis, typical error of estimates and measurements, and intraclass correlation coefficients. Results Both apps provided a reliable estimate of jump height and the mean values of force, velocity, and power. Furthermore, estimates of jump height for CMJ and SJ and the mean force of the CMJ were valid. However, the apps presented impractical or poor validity correlations for velocity and power. Compared with criterion, the apps underestimated the velocity of the CMJ. Conclusions Therefore, Jumpo 2 and MyJump 2 both provide a valid measure of jump height, but the remaining variables provided by these apps must be viewed with caution since the validity of force depends on jump type, while velocity (and as consequence power) could not be well estimated from the apps.
format: application/pdf
format: text/html
creator: Amilton Vieira
creator: Gabriela L. Ribeiro
creator: Victor Macedo
creator: Valdinar de Araújo Rocha Junior
creator: Roberto de Souza Baptista
creator: Carlos Gonçalves
creator: Rafael Cunha
creator: James Tufano
subject: Biomechanics
subject: Sports Medicine
description: doi:10.7717/peerj.14558
publisher: PeerJ Inc.
rights: © 2023 Vieira et al.
abstract: Background We investigated the concurrent validity and test-retest reliability of the Jumpo 2 and MyJump 2 apps for estimating jump height, and the mean values of force, velocity, and power produced during countermovement (CMJ) and squat jumps (SJ). Methods Physically active university aged men (n = 10, 20 ± 3 years, 176 ± 6 cm, 68 ± 9 kg) jumped on a force plate (i.e., criterion) while being recorded by a smartphone slow-motion camera. The videos were analyzed using Jumpo 2 and MyJump 2 using a Samsung Galaxy S7 powered by the Android system. Validity and reliability were determined by regression analysis, typical error of estimates and measurements, and intraclass correlation coefficients. Results Both apps provided a reliable estimate of jump height and the mean values of force, velocity, and power. Furthermore, estimates of jump height for CMJ and SJ and the mean force of the CMJ were valid. However, the apps presented impractical or poor validity correlations for velocity and power. Compared with criterion, the apps underestimated the velocity of the CMJ. Conclusions Therefore, Jumpo 2 and MyJump 2 both provide a valid measure of jump height, but the remaining variables provided by these apps must be viewed with caution since the validity of force depends on jump type, while velocity (and as consequence power) could not be well estimated from the apps.
bibliographic citation: Vieira et al. (2023) Evidence of validity and reliability of Jumpo 2 and MyJump 2 for estimating vertical jump variables. PeerJ 11:e14558 https://doi.org/10.7717/peerj.14558
date submitted: 2022-08-05
date accepted: 2022-11-21
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vieira
  given name: Amilton
author list: Agent
  family name: Ribeiro
  given name: Gabriela L.
author list: Agent
  family name: Macedo
  given name: Victor
author list: Agent
  family name: de Araújo Rocha Junior
  given name: Valdinar
author list: Agent
  family name: Baptista
  given name: Roberto de Souza
author list: Agent
  family name: Gonçalves
  given name: Carlos
author list: Agent
  family name: Cunha
  given name: Rafael
author list: Agent
  family name: Tufano
  given name: James
doi: 10.7717/peerj.14558
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Vieira et al.
attribution name: Vieira et al.

Facilitation of a free-roaming apex predator in working lands: evaluating factors that influence leopard spatial dynamics and prey availability in a South African biodiversity hotspot
type: item
type: AcademicArticle
description: Apex predators ideally require vast intact spaces that support sufficient prey abundances to sustain them. In a developing world, however, it is becoming extremely difficult to maintain large enough areas to facilitate apex predators outside of protected regions. Free-roaming leopards (Panthera pardus) are the last remaining apex predator in the Greater Cape Floristic Region, South Africa, and face a multitude of threats attributable to competition for space and resources with humans. Using camera-trap data, we investigated the influence of anthropogenic land modification on leopards and the availability of their natural prey species in two contrasting communities—primarily protected (Cederberg) and agriculturally transformed (Piketberg). Potential prey species composition and diversity were determined, to indicate prey availability in each region. Factors influencing spatial utilisation by leopards and their main prey species were also assessed. Estimated potential prey species richness (Cederberg = 27, Piketberg = 26) and diversity indices (Cederberg—H′ = 2.64, Ds = 0.90; Piketberg—H′ = 2.46, Ds = 0.89), supported by both the Jaccard’s Index (J = 0.73) and Sørensen’s Coefficient (CC = 0.85), suggested high levels of similarity across the two regions. Main leopard prey species were present in both regions, but their relative abundances differed. Grey rhebok, klipspringer, and rock hyrax were more abundant in the Cederberg, while Cape grysbok, Cape porcupine, chacma baboon, and common duiker were more abundant in Piketberg. Leopards persisted across the agriculturally transformed landscape despite these differences. Occupancy modelling revealed that the spatial dynamics of leopards differed between the two regions, except for both populations preferring areas further away from human habitation. Overall, anthropogenic factors played a greater role in affecting spatial utilisation by leopards and their main prey species in the transformed region, whereas environmental…
format: application/pdf
format: text/html
creator: Eugene Greyling
creator: Jessica Comley
creator: Michael I. Cherry
creator: Alison J. Leslie
creator: Lana Müller
subject: Animal Behavior
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.14575
publisher: PeerJ Inc.
rights: © 2023 Greyling et al.
abstract: Apex predators ideally require vast intact spaces that support sufficient prey abundances to sustain them. In a developing world, however, it is becoming extremely difficult to maintain large enough areas to facilitate apex predators outside of protected regions. Free-roaming leopards (Panthera pardus) are the last remaining apex predator in the Greater Cape Floristic Region, South Africa, and face a multitude of threats attributable to competition for space and resources with humans. Using camera-trap data, we investigated the influence of anthropogenic land modification on leopards and the availability of their natural prey species in two contrasting communities—primarily protected (Cederberg) and agriculturally transformed (Piketberg). Potential prey species composition and diversity were determined, to indicate prey availability in each region. Factors influencing spatial utilisation by leopards and their main prey species were also assessed. Estimated potential prey species richness (Cederberg = 27, Piketberg = 26) and diversity indices (Cederberg—H′ = 2.64, Ds = 0.90; Piketberg—H′ = 2.46, Ds = 0.89), supported by both the Jaccard’s Index (J = 0.73) and Sørensen’s Coefficient (CC = 0.85), suggested high levels of similarity across the two regions. Main leopard prey species were present in both regions, but their relative abundances differed. Grey rhebok, klipspringer, and rock hyrax were more abundant in the Cederberg, while Cape grysbok, Cape porcupine, chacma baboon, and common duiker were more abundant in Piketberg. Leopards persisted across the agriculturally transformed landscape despite these differences. Occupancy modelling revealed that the spatial dynamics of leopards differed between the two regions, except for both populations preferring areas further away from human habitation. Overall, anthropogenic factors played a greater role in affecting spatial utilisation by leopards and their main prey species in the transformed region, whereas environmental…
bibliographic citation: Greyling et al. (2023) Facilitation of a free-roaming apex predator in working lands: evaluating factors that influence leopard spatial dynamics and prey availability in a South African biodiversity hotspot. PeerJ 11:e14575 https://doi.org/10.7717/peerj.14575
date submitted: 2022-06-04
date accepted: 2022-11-28
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Greyling
  given name: Eugene
author list: Agent
  family name: Comley
  given name: Jessica
author list: Agent
  family name: Cherry
  given name: Michael I.
author list: Agent
  family name: Leslie
  given name: Alison J.
author list: Agent
  family name: Müller
  given name: Lana
doi: 10.7717/peerj.14575
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Greyling et al.
attribution name: Greyling et al.

Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study
type: item
type: AcademicArticle
description: Background and Objective Epidemiological studies report associations between coronavirus disease 2019 (COVID-19) and periodontitis; however, causality has not been proven. The aim of this study is to assess the associations between COVID-19 susceptibility and periodontitis with two-sample Mendelian randomization (MR) analyses. Methods A two-sample summary MR analysis was performed using data for outcome and exposure from the OpenGWAS database on people of European descent. Periodontal complex traits (PCTs) were chosen as a proxy for the periodontitis phenotype. The causal association between PCT3 (Aggregatibacter actinomycetemcomitans), PCT5 (Porphyromonas gingivalis), and gingival crevicular fluid (GCF) interleukin-1β (IL-1β) and COVID-19 were considered. Genome-wide association study (GWAS) data with the two largest sample sizes were selected as COVID-19 outcomes (datasets ebi-a-GCST010776 and ebi-a-GCST010777). Single-nucleotide polymorphisms (SNPs) associated with PCT3, PCT5, and GCF IL-1β at statistical significance at genome-wide level (P < 5 × 10−8) were identified as genetic instruments. We used two-sample summary MR methods and tested the existence of a pleiotropic effect with MR-Egger. Results Inverse-variance weighted (IVW) estimates showed that there was a positive association between COVID-19 risk and periodontitis (ebi-a-GCST010776: odds ratio [OR] = 1.02 (95% confidence interval (CI), 1.00–1.05), P = 0.0171; ebi-a-GCST010777: OR = 1.03 (95% CI, 1.00–1.05), P = 0.0397). The weighted median also showed directionally similar estimates. Exploration of the causal associations between other PCTs and COVID-19 identified a slight effect of local inflammatory response (GCF IL-1β) on COVID-19 risk across the two datasets (ebi-a-GCST010776: IVW OR = 1.02 (95% CI, [1.01–1.03]), P < 0.001; ebi-a-GCST010777: IVW OR = 1.03 (95% CI, [1.02–1.04]), P < 0.001). The intercepts of MR-Egger yielded no proof for significant directional pleiotropy for either dataset (ebi-a-G…
format: application/pdf
format: text/html
creator: Zhaoqiang Meng
creator: Yujia Ma
creator: Wenjing Li
creator: Xuliang Deng
subject: Dentistry
subject: Medical Genetics
description: doi:10.7717/peerj.14595
publisher: PeerJ Inc.
rights: © 2023 Meng et al.
abstract: Background and Objective Epidemiological studies report associations between coronavirus disease 2019 (COVID-19) and periodontitis; however, causality has not been proven. The aim of this study is to assess the associations between COVID-19 susceptibility and periodontitis with two-sample Mendelian randomization (MR) analyses. Methods A two-sample summary MR analysis was performed using data for outcome and exposure from the OpenGWAS database on people of European descent. Periodontal complex traits (PCTs) were chosen as a proxy for the periodontitis phenotype. The causal association between PCT3 (Aggregatibacter actinomycetemcomitans), PCT5 (Porphyromonas gingivalis), and gingival crevicular fluid (GCF) interleukin-1β (IL-1β) and COVID-19 were considered. Genome-wide association study (GWAS) data with the two largest sample sizes were selected as COVID-19 outcomes (datasets ebi-a-GCST010776 and ebi-a-GCST010777). Single-nucleotide polymorphisms (SNPs) associated with PCT3, PCT5, and GCF IL-1β at statistical significance at genome-wide level (P < 5 × 10−8) were identified as genetic instruments. We used two-sample summary MR methods and tested the existence of a pleiotropic effect with MR-Egger. Results Inverse-variance weighted (IVW) estimates showed that there was a positive association between COVID-19 risk and periodontitis (ebi-a-GCST010776: odds ratio [OR] = 1.02 (95% confidence interval (CI), 1.00–1.05), P = 0.0171; ebi-a-GCST010777: OR = 1.03 (95% CI, 1.00–1.05), P = 0.0397). The weighted median also showed directionally similar estimates. Exploration of the causal associations between other PCTs and COVID-19 identified a slight effect of local inflammatory response (GCF IL-1β) on COVID-19 risk across the two datasets (ebi-a-GCST010776: IVW OR = 1.02 (95% CI, [1.01–1.03]), P < 0.001; ebi-a-GCST010777: IVW OR = 1.03 (95% CI, [1.02–1.04]), P < 0.001). The intercepts of MR-Egger yielded no proof for significant directional pleiotropy for either dataset (ebi-a-G…
bibliographic citation: Meng et al. (2023) Association between periodontitis and COVID-19 infection: a two-sample Mendelian randomization study. PeerJ 11:e14595 https://doi.org/10.7717/peerj.14595
date submitted: 2022-04-29
date accepted: 2022-11-28
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Meng
  given name: Zhaoqiang
author list: Agent
  family name: Ma
  given name: Yujia
author list: Agent
  family name: Li
  given name: Wenjing
author list: Agent
  family name: Deng
  given name: Xuliang
doi: 10.7717/peerj.14595
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Meng et al.
attribution name: Meng et al.

Combination of Vitamin C and Lenvatinib potentiates antitumor effects in hepatocellular carcinoma cells in vitro
type: item
type: AcademicArticle
description: Lenvatinib has become a first-line drug in the treatment of advanced hepatocellular carcinoma (HCC). Investigating its use in combination with other agents is of great significance to improve the sensitivity and durable response of Lenvatinib in advanced HCC patients. Vitamin C (L-ascorbic acid, ascorbate, VC) is an important natural antioxidant, which has been reported to show suppressive effects in cancer treatment. Here, we investigated the effect of the combination of VC and Lenvatinib in HCC cells in vitro. We found that treatment of VC alone significantly inhibited the proliferation, migration and invasion in HCC cells. Additionally, VC was strongly synergistic with Lenvatinib in inhibition of the proliferative, migratory and invasive capacities of HCC cells in vitro. In conclusion, our results demonstrate that the combination of VC and Lenvatinib has synergistic antitumor activities against HCC cells, providing a promising therapeutic strategy to improve the prognosis of HCC patients.
format: application/pdf
format: text/html
creator: Xinyue Wang
creator: Songyi Qian
creator: Siyi Wang
creator: Sheng Jia
creator: Nishang Zheng
creator: Qing Yao
creator: Jian Gao
subject: Biochemistry
subject: Cell Biology
description: doi:10.7717/peerj.14610
publisher: PeerJ Inc.
rights: © 2023 Wang et al.
abstract: Lenvatinib has become a first-line drug in the treatment of advanced hepatocellular carcinoma (HCC). Investigating its use in combination with other agents is of great significance to improve the sensitivity and durable response of Lenvatinib in advanced HCC patients. Vitamin C (L-ascorbic acid, ascorbate, VC) is an important natural antioxidant, which has been reported to show suppressive effects in cancer treatment. Here, we investigated the effect of the combination of VC and Lenvatinib in HCC cells in vitro. We found that treatment of VC alone significantly inhibited the proliferation, migration and invasion in HCC cells. Additionally, VC was strongly synergistic with Lenvatinib in inhibition of the proliferative, migratory and invasive capacities of HCC cells in vitro. In conclusion, our results demonstrate that the combination of VC and Lenvatinib has synergistic antitumor activities against HCC cells, providing a promising therapeutic strategy to improve the prognosis of HCC patients.
bibliographic citation: Wang et al. (2023) Combination of Vitamin C and Lenvatinib potentiates antitumor effects in hepatocellular carcinoma cells in vitro. PeerJ 11:e14610 https://doi.org/10.7717/peerj.14610
date submitted: 2022-10-05
date accepted: 2022-11-30
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Wang
  given name: Xinyue
author list: Agent
  family name: Qian
  given name: Songyi
author list: Agent
  family name: Wang
  given name: Siyi
author list: Agent
  family name: Jia
  given name: Sheng
author list: Agent
  family name: Zheng
  given name: Nishang
author list: Agent
  family name: Yao
  given name: Qing
author list: Agent
  family name: Gao
  given name: Jian
doi: 10.7717/peerj.14610
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Wang et al.
attribution name: Wang et al.

Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep
type: item
type: AcademicArticle
description: Background Stevia straw is a byproduct of sugar crop stevia. It is a good feed material because of richness in nutrients and active substances (steviosides and flavonoids). However, due to improper utilization such as piling, burning and so on, it became a large amount of wasted straw resources and lead to environmental pollution. Methods We added 0%, 0.2%, 0.4%, 0.6%, 0.8%, 1.0% and 1.5% of stevia stalk to study the effects of different stevia stalk concentrations on nutrient utilization and rumen fermentation in sheep (based on sheep diet). In vitro fermentation method was used, with 17 repetitions for each treatment. All fermentation substrate based on sheep diet with different stevia stalk concentrations were fermented for 2 h, 6 h, 12 h, 24 h and 48 h, then the gas production, dry matter degradability (DMD), crude protein degradability (CPD), neutral detergent fiber degradability (NDFD), acid detergent fiber degradability (ADFD), pH, ammonia nitrogen (NH3-N) and volatile fatty acids (VFAs) were determined. Results The results showed that at different fermentation time, the change trend of gas production in each teatment was basically same, but the maximum occurred in 1.0% treatment at 48 h. The DMD, CPD, NDFD and ADFD of sheep diets increased with fermentation time increasing, especially the CPD48h, NDFD48h and ADFD48h of diets in 0.8%, 1.0% and 1.5% treatments were significantly higher than those in control (P < 0.05). The pH of fermentation substrate in each treatment remained within the normal range of 6.21∼7.25. NH3-N24h–48hin 0.8%, 1.0% and 1.5% treatments were higher than that in control. At 6 h–12 h, the total acid content of 0.8% and 1.0% treatments were significantly higher than those of other treatments (P < 0.05), it reached the highest in 1.0% treatment. According to overall evaluation, effect ranking of stevia stalk on sheep nutrient utilization was as follows: 1.0% >0.8% >1.5% >0.4% >0.6% >0.2%. Overall, 1.0% stevia stalk could promote nutrient de…
format: application/pdf
format: text/html
creator: Xia Zhang
creator: Ting Jiao
creator: Shumin Ma
creator: Xin Chen
creator: Zhengwen Wang
creator: Shengguo Zhao
creator: Yue Ren
subject: Agricultural Science
subject: Biochemistry
subject: Plant Science
subject: Zoology
description: doi:10.7717/peerj.14689
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Background Stevia straw is a byproduct of sugar crop stevia. It is a good feed material because of richness in nutrients and active substances (steviosides and flavonoids). However, due to improper utilization such as piling, burning and so on, it became a large amount of wasted straw resources and lead to environmental pollution. Methods We added 0%, 0.2%, 0.4%, 0.6%, 0.8%, 1.0% and 1.5% of stevia stalk to study the effects of different stevia stalk concentrations on nutrient utilization and rumen fermentation in sheep (based on sheep diet). In vitro fermentation method was used, with 17 repetitions for each treatment. All fermentation substrate based on sheep diet with different stevia stalk concentrations were fermented for 2 h, 6 h, 12 h, 24 h and 48 h, then the gas production, dry matter degradability (DMD), crude protein degradability (CPD), neutral detergent fiber degradability (NDFD), acid detergent fiber degradability (ADFD), pH, ammonia nitrogen (NH3-N) and volatile fatty acids (VFAs) were determined. Results The results showed that at different fermentation time, the change trend of gas production in each teatment was basically same, but the maximum occurred in 1.0% treatment at 48 h. The DMD, CPD, NDFD and ADFD of sheep diets increased with fermentation time increasing, especially the CPD48h, NDFD48h and ADFD48h of diets in 0.8%, 1.0% and 1.5% treatments were significantly higher than those in control (P < 0.05). The pH of fermentation substrate in each treatment remained within the normal range of 6.21∼7.25. NH3-N24h–48hin 0.8%, 1.0% and 1.5% treatments were higher than that in control. At 6 h–12 h, the total acid content of 0.8% and 1.0% treatments were significantly higher than those of other treatments (P < 0.05), it reached the highest in 1.0% treatment. According to overall evaluation, effect ranking of stevia stalk on sheep nutrient utilization was as follows: 1.0% >0.8% >1.5% >0.4% >0.6% >0.2%. Overall, 1.0% stevia stalk could promote nutrient de…
bibliographic citation: Zhang et al. (2023) Effects of different proportions of stevia stalk on nutrient utilization and rumen fermentation in ruminal fluid derived from sheep. PeerJ 11:e14689 https://doi.org/10.7717/peerj.14689
date submitted: 2022-10-06
date accepted: 2022-12-13
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Xia
author list: Agent
  family name: Jiao
  given name: Ting
author list: Agent
  family name: Ma
  given name: Shumin
author list: Agent
  family name: Chen
  given name: Xin
author list: Agent
  family name: Wang
  given name: Zhengwen
author list: Agent
  family name: Zhao
  given name: Shengguo
author list: Agent
  family name: Ren
  given name: Yue
doi: 10.7717/peerj.14689
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance
type: item
type: AcademicArticle
description: Acinetobacter baumannii is one of the most successful pathogens that can cause difficult-to-treat nosocomial infections. Outbreaks and infections caused by multi-drug resistant A. baumannii are prevalent worldwide, with only a few antibiotics are currently available for treatments. Plasmids represent an ideal vehicle for acquiring and transferring resistance genes in A. baumannii. Five extensively drug-resistant A. baumannii clinical isolates from three major Jordanian hospitals were fully sequenced. Whole-Genome Sequences (WGS) were used to study the antimicrobial resistance and virulence genes, sequence types, and phylogenetic relationship of the isolates. Plasmids were characterized In-silico, followed by conjugation, and plasmid curing experiments. Eight plasmids were recovered; resistance plasmids carrying either aminoglycosides or sulfonamide genes were detected. Chromosomal resistance genes included blaOXA-66, blaOXA-91, and blaOXA-23,and the detected virulence factors were involved in biofilm formation, adhesion, and many other mechanisms. Conjugation and plasmid curing experiments resulted in the transfer or loss of several resistance phenotypes. Plasmid profiling along with phylogenetic analyses revealed high similarities between two A. baumannii isolates recovered from two different intensive care units (ICU). The high similarities between the isolates of the study, especially the two ICU isolates, suggest that there is a common A. baumannii strain prevailing in different ICU wards in Jordanian hospitals. Three resistance genes were plasmid-borne, and the transfer of the resistance phenotype emphasizes the role and importance of conjugative plasmids in spreading resistance among A. baumannii clinical strains.
format: application/pdf
format: text/html
creator: Qutaiba Ababneh
creator: Sara Al Sbei
creator: Ziad Jaradat
creator: Sebawe Syaj
creator: Neda’a Aldaken
creator: Hamza Ababneh
creator: Zeina Inaya
subject: Genomics
subject: Microbiology
subject: Molecular Biology
subject: Infectious Diseases
description: doi:10.7717/peerj.14709
publisher: PeerJ Inc.
rights: © 2023 Ababneh et al.
abstract: Acinetobacter baumannii is one of the most successful pathogens that can cause difficult-to-treat nosocomial infections. Outbreaks and infections caused by multi-drug resistant A. baumannii are prevalent worldwide, with only a few antibiotics are currently available for treatments. Plasmids represent an ideal vehicle for acquiring and transferring resistance genes in A. baumannii. Five extensively drug-resistant A. baumannii clinical isolates from three major Jordanian hospitals were fully sequenced. Whole-Genome Sequences (WGS) were used to study the antimicrobial resistance and virulence genes, sequence types, and phylogenetic relationship of the isolates. Plasmids were characterized In-silico, followed by conjugation, and plasmid curing experiments. Eight plasmids were recovered; resistance plasmids carrying either aminoglycosides or sulfonamide genes were detected. Chromosomal resistance genes included blaOXA-66, blaOXA-91, and blaOXA-23,and the detected virulence factors were involved in biofilm formation, adhesion, and many other mechanisms. Conjugation and plasmid curing experiments resulted in the transfer or loss of several resistance phenotypes. Plasmid profiling along with phylogenetic analyses revealed high similarities between two A. baumannii isolates recovered from two different intensive care units (ICU). The high similarities between the isolates of the study, especially the two ICU isolates, suggest that there is a common A. baumannii strain prevailing in different ICU wards in Jordanian hospitals. Three resistance genes were plasmid-borne, and the transfer of the resistance phenotype emphasizes the role and importance of conjugative plasmids in spreading resistance among A. baumannii clinical strains.
bibliographic citation: Ababneh et al. (2023) Extensively drug-resistant Acinetobacter baumannii: role of conjugative plasmids in transferring resistance. PeerJ 11:e14709 https://doi.org/10.7717/peerj.14709
date submitted: 2022-01-28
date accepted: 2022-12-15
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ababneh
  given name: Qutaiba
author list: Agent
  family name: Al Sbei
  given name: Sara
author list: Agent
  family name: Jaradat
  given name: Ziad
author list: Agent
  family name: Syaj
  given name: Sebawe
author list: Agent
  family name: Aldaken
  given name: Neda’a
author list: Agent
  family name: Ababneh
  given name: Hamza
author list: Agent
  family name: Inaya
  given name: Zeina
doi: 10.7717/peerj.14709
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: ©2023 Ababneh et al.
attribution name: Ababneh et al.

Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells
type: item
type: AcademicArticle
description: Background S100 calcium-binding protein A9 (S100A9) is a commonly known pro-inflammatory factor involved in various inflammatory responses. Clostridium perfringens (C. perfringens ) type C is known to cause diarrhea in piglets. However, the role of S100A9 in C. perfringens type C-induced infectious diarrhea is unclear. Methods Here, the S100A9 gene was overexpressed and knocked down in the IPEC-J2 cells, which were treated with C. perfringens beta2 (CPB2) toxin. The role of S100A9 in CPB2 toxin-induced injury in IPEC-J2 cells was assessed by measuring the levels of inflammatory cytokines, reactive oxygen species (ROS), lactate dehydrogenase (LDH), cell proliferation, and tight junction-related proteins. Results The results showed elevated expression of S100A9 in diarrhea-affected piglet tissues, and the elevation of S100A9 expression after CPB2 toxin treatment of IPEC-J2 was time-dependent. In CPB2 toxin-induced IPEC-J2 cells, overexpression of S100A9 had the following effects: the relative expression of inflammatory factors IL-6, IL8, TNF-α, and IL-1β was increased; the ROS levels and LDH viability were significantly increased; cell viability and proliferation were inhibited; the G0/G1 phase cell ratio was significantly increased. Furthermore, overexpression of S100A9 reduced the expression of tight junction proteins in CPB2-induced IPEC-J2 cells. The knockdown of S100A9 had an inverse effect. In conclusion, our results confirmed that S100A9 exacerbated inflammatory injury in CPB2 toxin-induced IPEC-J2 cells, inhibited cell viability and cell proliferation, and disrupted the tight junctions between cells. Thus, decreased S100A9 expression alleviates CPB2 toxin-induced inflammatory injury in IPEC-J2 cells.
format: application/pdf
format: text/html
creator: Jie Li
creator: Xiaoyu Huang
creator: Kaihui Xie
creator: Juanli Zhang
creator: Jiaojiao Yang
creator: Zunqiang Yan
creator: Shuangbao Gun
subject: Biochemistry
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
subject: Toxicology
description: doi:10.7717/peerj.14722
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background S100 calcium-binding protein A9 (S100A9) is a commonly known pro-inflammatory factor involved in various inflammatory responses. Clostridium perfringens (C. perfringens ) type C is known to cause diarrhea in piglets. However, the role of S100A9 in C. perfringens type C-induced infectious diarrhea is unclear. Methods Here, the S100A9 gene was overexpressed and knocked down in the IPEC-J2 cells, which were treated with C. perfringens beta2 (CPB2) toxin. The role of S100A9 in CPB2 toxin-induced injury in IPEC-J2 cells was assessed by measuring the levels of inflammatory cytokines, reactive oxygen species (ROS), lactate dehydrogenase (LDH), cell proliferation, and tight junction-related proteins. Results The results showed elevated expression of S100A9 in diarrhea-affected piglet tissues, and the elevation of S100A9 expression after CPB2 toxin treatment of IPEC-J2 was time-dependent. In CPB2 toxin-induced IPEC-J2 cells, overexpression of S100A9 had the following effects: the relative expression of inflammatory factors IL-6, IL8, TNF-α, and IL-1β was increased; the ROS levels and LDH viability were significantly increased; cell viability and proliferation were inhibited; the G0/G1 phase cell ratio was significantly increased. Furthermore, overexpression of S100A9 reduced the expression of tight junction proteins in CPB2-induced IPEC-J2 cells. The knockdown of S100A9 had an inverse effect. In conclusion, our results confirmed that S100A9 exacerbated inflammatory injury in CPB2 toxin-induced IPEC-J2 cells, inhibited cell viability and cell proliferation, and disrupted the tight junctions between cells. Thus, decreased S100A9 expression alleviates CPB2 toxin-induced inflammatory injury in IPEC-J2 cells.
bibliographic citation: Li et al. (2023) Decreased S100A9 expression alleviates Clostridium perfringens beta2 toxin-induced inflammatory injury in IPEC-J2 cells. PeerJ 11:e14722 https://doi.org/10.7717/peerj.14722
date submitted: 2022-09-30
date accepted: 2022-12-19
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jie
author list: Agent
  family name: Huang
  given name: Xiaoyu
author list: Agent
  family name: Xie
  given name: Kaihui
author list: Agent
  family name: Zhang
  given name: Juanli
author list: Agent
  family name: Yang
  given name: Jiaojiao
author list: Agent
  family name: Yan
  given name: Zunqiang
author list: Agent
  family name: Gun
  given name: Shuangbao
doi: 10.7717/peerj.14722
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Li et al.
attribution name: Li et al.

Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing
type: item
type: AcademicArticle
description: Background The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated. Methods In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function. Results After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.
format: application/pdf
format: text/html
creator: Shifang Wu
creator: Xiaoli Yang
creator: Haina Gao
creator: Chengrui Shi
creator: Longlin Wang
creator: Deyuan Lu
creator: Yiheng Li
creator: Jinliang Zhang
creator: Weibing Zhang
creator: Pengcheng Wen
subject: Food Science and Technology
subject: Microbiology
description: doi:10.7717/peerj.14733
publisher: PeerJ Inc.
rights: © 2023 Wu et al.
abstract: Background The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated. Methods In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function. Results After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.
bibliographic citation: Wu et al. (2023) Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing. PeerJ 11:e14733 https://doi.org/10.7717/peerj.14733
date submitted: 2022-09-22
date accepted: 2022-12-21
issued: 2023-01-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Shifang
author list: Agent
  family name: Yang
  given name: Xiaoli
author list: Agent
  family name: Gao
  given name: Haina
author list: Agent
  family name: Shi
  given name: Chengrui
author list: Agent
  family name: Wang
  given name: Longlin
author list: Agent
  family name: Lu
  given name: Deyuan
author list: Agent
  family name: Li
  given name: Yiheng
author list: Agent
  family name: Zhang
  given name: Jinliang
author list: Agent
  family name: Zhang
  given name: Weibing
author list: Agent
  family name: Wen
  given name: Pengcheng
doi: 10.7717/peerj.14733
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-01-25
copyright: © 2023 Wu et al.
attribution name: Wu et al.

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