PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Research progress on the bulb expansion and starch enrichment in taro (Colocasia esculenta (L). Schott)
items: Inflammatory auxo-action in the stem cell division theory of cancer
items: In vitro and in silico evaluation of the design of nano-phyto-drug candidate for oral use against Staphylococcus aureus
items: Partial substitution of exogenously applied phosphatic fertilizers by phosphate solubilizing bacteria in maize under calcareous soil
items: A miRNome analysis at the early postmortem interval
items: Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences
items: MFAP2 enhances cisplatin resistance in gastric cancer cells by regulating autophagy
items: Alterations in gene expressions of Caco-2 cell responses to LPS and ploy(I:C) stimulation
items: Endophytic fungus Biscogniauxia petrensis produces antibacterial substances
items: The introduction of an invasive weed was not followed by the introduction of ethnobotanical knowledge: a review on the ethnobotany of Centaurea solstitialis L. (Asteraceae)

Research progress on the bulb expansion and starch enrichment in taro (Colocasia esculenta (L). Schott)
type: item
type: AcademicArticle
description: Background Taro is an important potato crop, which can be used as food, vegetable, feed, and industrial raw material. The yield and quality of taro are primarily determined by the expansion degree of taro bulb and the filling condition of starch, whereas the expansion of taro bulb is a complex biological process. However, little information is reviewed on the research progress of bulb expansion and starch enrichment in taro. Methodology PubMed, Web of Science, and the China National Knowledge Infrastructure databases were searched for relevant articles. After removing duplicate articles and articles with little relevance, 73 articles were selected for review. Results This article introduces the formation and development of taro bulb for workers engaged in taro research. The content includes the process of amyloplast formation at the cytological level and changes in bulb expansion and starch enrichment at physiological levels, which involve endogenous hormones and key enzyme genes for starch synthesis. The effects of environment and cultivation methods on taro bulb expansion were also reviewed. Conclusions Future research directions and research focus about the development of taro bulb were proposed. Limited research has been conducted on the physiological mechanism and hormone regulatory pathway of taro growth and development, taro bulb expansion, key gene expression, and starch enrichment. Therefore, the abovementioned research will become the key research direction in the future.
format: application/pdf
format: text/html
creator: Erjin Zhang
creator: Wenyuan Shen
creator: Weijie Jiang
creator: Wenlong Li
creator: Xiaping Wan
creator: Xurun Yu
creator: Fei Xiong
subject: Agricultural Science
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.15400
publisher: PeerJ Inc.
rights: © 2023 Zhang et al.
abstract: Background Taro is an important potato crop, which can be used as food, vegetable, feed, and industrial raw material. The yield and quality of taro are primarily determined by the expansion degree of taro bulb and the filling condition of starch, whereas the expansion of taro bulb is a complex biological process. However, little information is reviewed on the research progress of bulb expansion and starch enrichment in taro. Methodology PubMed, Web of Science, and the China National Knowledge Infrastructure databases were searched for relevant articles. After removing duplicate articles and articles with little relevance, 73 articles were selected for review. Results This article introduces the formation and development of taro bulb for workers engaged in taro research. The content includes the process of amyloplast formation at the cytological level and changes in bulb expansion and starch enrichment at physiological levels, which involve endogenous hormones and key enzyme genes for starch synthesis. The effects of environment and cultivation methods on taro bulb expansion were also reviewed. Conclusions Future research directions and research focus about the development of taro bulb were proposed. Limited research has been conducted on the physiological mechanism and hormone regulatory pathway of taro growth and development, taro bulb expansion, key gene expression, and starch enrichment. Therefore, the abovementioned research will become the key research direction in the future.
bibliographic citation: Zhang et al. (2023) Research progress on the bulb expansion and starch enrichment in taro (Colocasia esculenta (L). Schott). PeerJ 11:e15400 https://doi.org/10.7717/peerj.15400
date submitted: 2022-09-14
date accepted: 2023-04-20
issued: 2023-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Erjin
author list: Agent
  family name: Shen
  given name: Wenyuan
author list: Agent
  family name: Jiang
  given name: Weijie
author list: Agent
  family name: Li
  given name: Wenlong
author list: Agent
  family name: Wan
  given name: Xiaping
author list: Agent
  family name: Yu
  given name: Xurun
author list: Agent
  family name: Xiong
  given name: Fei
doi: 10.7717/peerj.15400
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-08
copyright: ©2023 Zhang et al.
attribution name: Zhang et al.

Inflammatory auxo-action in the stem cell division theory of cancer
type: item
type: AcademicArticle
description: Acute inflammation is a beneficial response to the changes caused by pathogens or injuries that can eliminate the source of damage and restore homeostasis in damaged tissues. However, chronic inflammation causes malignant transformation and carcinogenic effects of cells through continuous exposure to pro-inflammatory cytokines and activation of inflammatory signaling pathways. According to the theory of stem cell division, the essential properties of stem cells, including long life span and self-renewal, make them vulnerable to accumulating genetic changes that can lead to cancer. Inflammation drives quiescent stem cells to enter the cell cycle and perform tissue repair functions. However, as cancer likely originates from DNA mutations that accumulate over time via normal stem cell division, inflammation may promote cancer development, even before the stem cells become cancerous. Numerous studies have reported that the mechanisms of inflammation in cancer formation and metastasis are diverse and complex; however, few studies have reviewed how inflammation affects cancer formation from the stem cell source. Based on the stem cell division theory of cancer, this review summarizes how inflammation affects normal stem cells, cancer stem cells, and cancer cells. We conclude that chronic inflammation leads to persistent stem cells activation, which can accumulate DNA damage and ultimately promote cancer. Additionally, inflammation not only facilitates the progression of stem cells into cancer cells, but also plays a positive role in cancer metastasis.
format: application/pdf
format: text/html
creator: Yi Luo
creator: Jian-Hui Xiao
subject: Biochemistry
subject: Cell Biology
subject: Oncology
description: doi:10.7717/peerj.15444
publisher: PeerJ Inc.
rights: © 2023 Luo and Xiao
abstract: Acute inflammation is a beneficial response to the changes caused by pathogens or injuries that can eliminate the source of damage and restore homeostasis in damaged tissues. However, chronic inflammation causes malignant transformation and carcinogenic effects of cells through continuous exposure to pro-inflammatory cytokines and activation of inflammatory signaling pathways. According to the theory of stem cell division, the essential properties of stem cells, including long life span and self-renewal, make them vulnerable to accumulating genetic changes that can lead to cancer. Inflammation drives quiescent stem cells to enter the cell cycle and perform tissue repair functions. However, as cancer likely originates from DNA mutations that accumulate over time via normal stem cell division, inflammation may promote cancer development, even before the stem cells become cancerous. Numerous studies have reported that the mechanisms of inflammation in cancer formation and metastasis are diverse and complex; however, few studies have reviewed how inflammation affects cancer formation from the stem cell source. Based on the stem cell division theory of cancer, this review summarizes how inflammation affects normal stem cells, cancer stem cells, and cancer cells. We conclude that chronic inflammation leads to persistent stem cells activation, which can accumulate DNA damage and ultimately promote cancer. Additionally, inflammation not only facilitates the progression of stem cells into cancer cells, but also plays a positive role in cancer metastasis.
bibliographic citation: Luo et al. (2023) Inflammatory auxo-action in the stem cell division theory of cancer. PeerJ 11:e15444 https://doi.org/10.7717/peerj.15444
date submitted: 2023-01-04
date accepted: 2023-05-01
issued: 2023-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Luo
  given name: Yi
author list: Agent
  family name: Xiao
  given name: Jian-Hui
doi: 10.7717/peerj.15444
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-08
copyright: ©2023 Luo and Xiao
attribution name: Luo and Xiao

In vitro and in silico evaluation of the design of nano-phyto-drug candidate for oral use against Staphylococcus aureus
type: item
type: AcademicArticle
description: Onopordum acanthium is a medicinal plant with many important properties, such as antibacterial, anticancer, and anti-hypotensive properties. Although various studies reported the biological activities of O. acanthium, there is no study on its nano-phyto-drug formulation. The aim of this study is to develop a candidate nano-drug based on phytotherapeutic constituents and evaluate its efficiency in vitro and in silico. In this context, poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) of O. acanthium extract (OAE) were synthesized and characterized. It was determined that the average particle size of OAE-PLGA-NPs was 214.9 ± 6.77 nm, and the zeta potential was −8.03 ± 0.85 mV, and PdI value was 0.064 ± 0.013. The encapsulation efficiency of OAE-PLGA-NPs was calculated as 91%, and the loading capacity as 75.83%. The in vitro drug release study showed that OAE was released from the PLGA NPs with 99.39% over the 6 days. Furthermore, the mutagenic and cytotoxic activity of free OAE and OAE-PLGA-NPs were evaluated by the Ames test and MTT test, respectively. Although 0.75 and 0.37 mg/mL free OAE concentrations caused both frameshift mutation and base pair substitution (p < 0.05), the administered OAE–PLGA NP concentrations were not mutagenic. It was determined with the MTT analysis that the doses of 0.75 and 1.5 mg/mL of free OAE had a cytotoxic effect on the L929 fibroblast cell line (p < 0.05), and OAE-PLGA-NPs had no cytotoxic effect. Moreover, the interaction between the OAE and S. aureus was also investigated using the molecular docking analysis method. The molecular docking and molecular dynamics (MD) results were implemented to elucidate the S. aureus MurE inhibition potential of OAE. It was shown that quercetin in the OAE content interacted significantly with the substantial residues in the catalytic pocket of the S. aureus MurE enzyme, and quercetin performed four hydrogen bond interactions corresponding to a low binding energy of −6.77 kcal/mol with catal…
format: application/pdf
format: text/html
creator: Yasemin Budama-Kilinc
creator: Bahar Gok
creator: Cigdem Cetin Aluc
creator: Serda Kecel-Gunduz
subject: Bioinformatics
subject: Biotechnology
subject: Cell Biology
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.15523
publisher: PeerJ Inc.
rights: © 2023 Budama-Kilinc et al.
abstract: Onopordum acanthium is a medicinal plant with many important properties, such as antibacterial, anticancer, and anti-hypotensive properties. Although various studies reported the biological activities of O. acanthium, there is no study on its nano-phyto-drug formulation. The aim of this study is to develop a candidate nano-drug based on phytotherapeutic constituents and evaluate its efficiency in vitro and in silico. In this context, poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) of O. acanthium extract (OAE) were synthesized and characterized. It was determined that the average particle size of OAE-PLGA-NPs was 214.9 ± 6.77 nm, and the zeta potential was −8.03 ± 0.85 mV, and PdI value was 0.064 ± 0.013. The encapsulation efficiency of OAE-PLGA-NPs was calculated as 91%, and the loading capacity as 75.83%. The in vitro drug release study showed that OAE was released from the PLGA NPs with 99.39% over the 6 days. Furthermore, the mutagenic and cytotoxic activity of free OAE and OAE-PLGA-NPs were evaluated by the Ames test and MTT test, respectively. Although 0.75 and 0.37 mg/mL free OAE concentrations caused both frameshift mutation and base pair substitution (p < 0.05), the administered OAE–PLGA NP concentrations were not mutagenic. It was determined with the MTT analysis that the doses of 0.75 and 1.5 mg/mL of free OAE had a cytotoxic effect on the L929 fibroblast cell line (p < 0.05), and OAE-PLGA-NPs had no cytotoxic effect. Moreover, the interaction between the OAE and S. aureus was also investigated using the molecular docking analysis method. The molecular docking and molecular dynamics (MD) results were implemented to elucidate the S. aureus MurE inhibition potential of OAE. It was shown that quercetin in the OAE content interacted significantly with the substantial residues in the catalytic pocket of the S. aureus MurE enzyme, and quercetin performed four hydrogen bond interactions corresponding to a low binding energy of −6.77 kcal/mol with catal…
bibliographic citation: Budama-Kilinc et al. (2023) In vitro and in silico evaluation of the design of nano-phyto-drug candidate for oral use against Staphylococcus aureus. PeerJ 11:e15523 https://doi.org/10.7717/peerj.15523
date submitted: 2022-10-16
date accepted: 2023-05-17
issued: 2023-06-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Budama-Kilinc
  given name: Yasemin
author list: Agent
  family name: Gok
  given name: Bahar
author list: Agent
  family name: Cetin Aluc
  given name: Cigdem
author list: Agent
  family name: Kecel-Gunduz
  given name: Serda
doi: 10.7717/peerj.15523
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-08
copyright: © 2023 Budama-Kilinc et al.
attribution name: Budama-Kilinc et al.

Partial substitution of exogenously applied phosphatic fertilizers by phosphate solubilizing bacteria in maize under calcareous soil
type: item
type: AcademicArticle
description: Phosphorus (P) availability is the major constrain in obtaining optimum crop yield in calcareous soils due to its precipitation as dicalcium and octacalcium phosphate by reacting with Ca+2 and Mg+2. Therefore, we explored the role of phosphate solubilizing bacteria (without and with PSB @ 2 kg ha−1) in optimizing maize yield and P availability from soluble and insoluble P sources applied @ of 100 kg P2O5 into calcareous soil. PSB inoculation significantly improved maize plant height (5.6%), 1,000 grain weight (11%), dry matter (7.5%), stover (10.8%) and grain yield (6.8%), plant P concentration (10.1%) and uptake (18.6%), extractable P (3.1%), agronomic (48%) and uptake (53%) P use efficiency over un-inoculated plots. Phosphorus application significantly improved maize yield, soil health and agronomic P use efficiency (4.84 times over control); however, its impact was more pronounced when applied as 50% P each from farmyard manure (FYM) and single super phosphate (SSP). On the basis of overall performance, the sources were ranked as 50% FYM + 50% SSP >50% rock phosphate (RP) + 50% SSP > 100% SSP > 75% FYM + 25% SSP > 75% RP +25% SSP > 100% FYM > 100 RP > control. Interactively, a significant and maximum increased over absolute control in most of the soil and plant tested characteristics were observed when 100 kg P2O5 ha−1 was supplemented 50% each as FYM and SSP along with PSB inoculation which was followed by 50% P each as FYM and SSP demonstrating that PSB were effective in enhancing RP solubilization under calcareous soil. Maximum value cost ratio of 3.1 was observed for 50% P each as FYM and SSP + PSB which was similar to 100% P as FYM + PSB and 75% FYM+ 25% SSP + PSB. Therefore, in calcareous soil P shall be amended 50% each as organic and mineral sources with PSB for its efficient utilization and obtaining optimum yield of maize.
format: application/pdf
format: text/html
creator: Hajira
creator: Yousaf Jamal
creator: Muhammad Adnan
creator: Manzoor Ahmad
creator: Maria Mussarat
creator: Muhammad Hamzah Saleem
creator: Beena Saeed
creator: Fazli Wahid
creator: Rafi Ullah
creator: Shah Fahad
creator: Baber Ali
creator: Imtiaz Khan
creator: Sezai Ercisli
creator: Kirill S. Golokhvast
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.15038
publisher: PeerJ Inc.
rights: © 2023 Hajira et al.
abstract: Phosphorus (P) availability is the major constrain in obtaining optimum crop yield in calcareous soils due to its precipitation as dicalcium and octacalcium phosphate by reacting with Ca+2 and Mg+2. Therefore, we explored the role of phosphate solubilizing bacteria (without and with PSB @ 2 kg ha−1) in optimizing maize yield and P availability from soluble and insoluble P sources applied @ of 100 kg P2O5 into calcareous soil. PSB inoculation significantly improved maize plant height (5.6%), 1,000 grain weight (11%), dry matter (7.5%), stover (10.8%) and grain yield (6.8%), plant P concentration (10.1%) and uptake (18.6%), extractable P (3.1%), agronomic (48%) and uptake (53%) P use efficiency over un-inoculated plots. Phosphorus application significantly improved maize yield, soil health and agronomic P use efficiency (4.84 times over control); however, its impact was more pronounced when applied as 50% P each from farmyard manure (FYM) and single super phosphate (SSP). On the basis of overall performance, the sources were ranked as 50% FYM + 50% SSP >50% rock phosphate (RP) + 50% SSP > 100% SSP > 75% FYM + 25% SSP > 75% RP +25% SSP > 100% FYM > 100 RP > control. Interactively, a significant and maximum increased over absolute control in most of the soil and plant tested characteristics were observed when 100 kg P2O5 ha−1 was supplemented 50% each as FYM and SSP along with PSB inoculation which was followed by 50% P each as FYM and SSP demonstrating that PSB were effective in enhancing RP solubilization under calcareous soil. Maximum value cost ratio of 3.1 was observed for 50% P each as FYM and SSP + PSB which was similar to 100% P as FYM + PSB and 75% FYM+ 25% SSP + PSB. Therefore, in calcareous soil P shall be amended 50% each as organic and mineral sources with PSB for its efficient utilization and obtaining optimum yield of maize.
bibliographic citation: Hajira et al. (2023) Partial substitution of exogenously applied phosphatic fertilizers by phosphate solubilizing bacteria in maize under calcareous soil. PeerJ 11:e15038 https://doi.org/10.7717/peerj.15038
date submitted: 2022-11-14
date accepted: 2023-04-26
issued: 2023-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hajira
author list: Agent
  family name: Jamal
  given name: Yousaf
author list: Agent
  family name: Adnan
  given name: Muhammad
author list: Agent
  family name: Ahmad
  given name: Manzoor
author list: Agent
  family name: Mussarat
  given name: Maria
author list: Agent
  family name: Saleem
  given name: Muhammad Hamzah
author list: Agent
  family name: Saeed
  given name: Beena
author list: Agent
  family name: Wahid
  given name: Fazli
author list: Agent
  family name: Ullah
  given name: Rafi
author list: Agent
  family name: Fahad
  given name: Shah
author list: Agent
  family name: Ali
  given name: Baber
author list: Agent
  family name: Khan
  given name: Imtiaz
author list: Agent
  family name: Ercisli
  given name: Sezai
author list: Agent
  family name: Golokhvast
  given name: Kirill S.
doi: 10.7717/peerj.15038
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-07
copyright: ©2023 Hajira et al.
attribution name: Hajira et al.

A miRNome analysis at the early postmortem interval
type: item
type: AcademicArticle
description: The postmortem interval (PMI) is the time elapsing since the death of an individual until the body is examined. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI as they can better support degradation. In the present work, we analyzed the miRNome at early PMI in rats’ skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 microarrays. We found 156 dysregulated miRNAs in rats’ skeletal muscle at 24 h of PMI, out of which 84 were downregulated, and 72 upregulated. The miRNA most significantly downregulated was miR-139-5p (FC = −160, p = 9.97 × 10−11), while the most upregulated was rno-miR-92b-5p (FC = 241.18, p = 2.39 × 10−6). Regarding the targets of these dysregulated miRNAs, the rno-miR-125b-5p and rno-miR-138-5p were the miRNAs with more mRNA targets. The mRNA targets that we found in the present study participate in several biological processes such as interleukin secretion regulation, translation regulation, cell growth, or low oxygen response. In addition, we found a downregulation of SIRT1 mRNA and an upregulation of TGFBR2 mRNA at 24 h of PMI. These results suggest there is an active participation of miRNAs at early PMI which could be further explored to identify potential biomarkers for PMI estimation.
format: application/pdf
format: text/html
creator: Mariano Guardado-Estrada
creator: Christian A. Cárdenas-Monroy
creator: Vanessa Martínez-Rivera
creator: Fernanda Cortez
creator: Carlos Pedraza-Lara
creator: Oliver Millan-Catalan
creator: Carlos Pérez-Plasencia
subject: Biochemistry
subject: Genomics
subject: Molecular Biology
description: doi:10.7717/peerj.15409
publisher: PeerJ Inc.
rights: © 2023 Guardado-Estrada et al.
abstract: The postmortem interval (PMI) is the time elapsing since the death of an individual until the body is examined. Different molecules have been analyzed to better estimate the PMI with variable results. The miRNAs draw attention in the forensic field to estimate the PMI as they can better support degradation. In the present work, we analyzed the miRNome at early PMI in rats’ skeletal muscle using the Affymetrix GeneChip™ miRNA 4.0 microarrays. We found 156 dysregulated miRNAs in rats’ skeletal muscle at 24 h of PMI, out of which 84 were downregulated, and 72 upregulated. The miRNA most significantly downregulated was miR-139-5p (FC = −160, p = 9.97 × 10−11), while the most upregulated was rno-miR-92b-5p (FC = 241.18, p = 2.39 × 10−6). Regarding the targets of these dysregulated miRNAs, the rno-miR-125b-5p and rno-miR-138-5p were the miRNAs with more mRNA targets. The mRNA targets that we found in the present study participate in several biological processes such as interleukin secretion regulation, translation regulation, cell growth, or low oxygen response. In addition, we found a downregulation of SIRT1 mRNA and an upregulation of TGFBR2 mRNA at 24 h of PMI. These results suggest there is an active participation of miRNAs at early PMI which could be further explored to identify potential biomarkers for PMI estimation.
bibliographic citation: Guardado-Estrada et al. (2023) A miRNome analysis at the early postmortem interval. PeerJ 11:e15409 https://doi.org/10.7717/peerj.15409
date submitted: 2023-01-24
date accepted: 2023-04-23
issued: 2023-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guardado-Estrada
  given name: Mariano
author list: Agent
  family name: Cárdenas-Monroy
  given name: Christian A.
author list: Agent
  family name: Martínez-Rivera
  given name: Vanessa
author list: Agent
  family name: Cortez
  given name: Fernanda
author list: Agent
  family name: Pedraza-Lara
  given name: Carlos
author list: Agent
  family name: Millan-Catalan
  given name: Oliver
author list: Agent
  family name: Pérez-Plasencia
  given name: Carlos
doi: 10.7717/peerj.15409
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-07
copyright: © 2023 Guardado-Estrada et al.
attribution name: Guardado-Estrada et al.

Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences
type: item
type: AcademicArticle
description: Background Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea. Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16%…
format: application/pdf
format: text/html
creator: Tsuyoshi Watanabe
creator: Junya Hirai
creator: Sirje Sildever
creator: Kazuaki Tadokoro
creator: Kiyotaka Hidaka
creator: Iwao Tanita
creator: Koh Nishiuchi
creator: Naoki Iguchi
creator: Hiromi Kasai
creator: Noriko Nishi
creator: Seiji Katakura
creator: Yukiko Taniuchi
creator: Taketoshi Kodama
creator: Satokuni Tashiro
creator: Misato Nakae
creator: Yuji Okazaki
creator: Satoshi Kitajima
creator: Sayaka Sogawa
creator: Toru Hasegawa
creator: Tomonori Azumaya
creator: Yutaka Hiroe
creator: Daisuke Ambe
creator: Takashi Setou
creator: Daiki Ito
creator: Akira Kusaka
creator: Takeshi Okunishi
creator: Takahiro Tanaka
creator: Akira Kuwata
creator: Daisuke Hasegawa
creator: Shigeho Kakehi
creator: Yugo Shimizu
creator: Satoshi Nagai
subject: Ecology
subject: Marine Biology
subject: Molecular Biology
subject: Zoology
subject: Biological Oceanography
description: doi:10.7717/peerj.15427
publisher: PeerJ Inc.
rights: © 2023 Watanabe et al.
abstract: Background Zooplankton plays an important role in the marine ecosystem. A high level of taxonomic expertise is necessary for accurate species identification based on morphological characteristics. As an alternative method to morphological classification, we focused on a molecular approach using 18S and 28S ribosomal RNA (rRNA) gene sequences. This study investigates how the accuracy of species identification by metabarcoding improves when taxonomically verified sequences of dominant zooplankton species are added to the public database. The improvement was tested by using natural zooplankton samples. Methods rRNA gene sequences were obtained from dominant zooplankton species from six sea areas around Japan and registered in the public database for improving the accuracy of taxonomic classifications. Two reference databases with and without newly registered sequences were created. Comparison of detected OTUs associated with single species between the two references was done using field-collected zooplankton samples from the Sea of Okhotsk for metabarcoding analysis to verify whether or not the newly registered sequences improved the accuracy of taxonomic classifications. Results A total of 166 sequences in 96 species based on the 18S marker and 165 sequences in 95 species based on the 28S marker belonging to Arthropoda (mostly Copepoda) and Chaetognatha were registered in the public database. The newly registered sequences were mainly composed of small non-calanoid copepods, such as species belonging to Oithona and Oncaea. Based on the metabarcoding analysis of field samples, a total of 18 out of 92 OTUs were identified at the species level based on newly registered sequences in the data obtained by the 18S marker. Based on the 28S marker, 42 out of 89 OTUs were classified at the species level based on taxonomically verified sequences. Thanks to the newly registered sequences, the number of OTUs associated with a single species based on the 18S marker increased by 16%…
bibliographic citation: Watanabe et al. (2023) Improving taxonomic classification of marine zooplankton by molecular approach: registration of taxonomically verified 18S and 28S rRNA gene sequences. PeerJ 11:e15427 https://doi.org/10.7717/peerj.15427
date submitted: 2022-08-17
date accepted: 2023-04-25
issued: 2023-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Watanabe
  given name: Tsuyoshi
author list: Agent
  family name: Hirai
  given name: Junya
author list: Agent
  family name: Sildever
  given name: Sirje
author list: Agent
  family name: Tadokoro
  given name: Kazuaki
author list: Agent
  family name: Hidaka
  given name: Kiyotaka
author list: Agent
  family name: Tanita
  given name: Iwao
author list: Agent
  family name: Nishiuchi
  given name: Koh
author list: Agent
  family name: Iguchi
  given name: Naoki
author list: Agent
  family name: Kasai
  given name: Hiromi
author list: Agent
  family name: Nishi
  given name: Noriko
author list: Agent
  family name: Katakura
  given name: Seiji
author list: Agent
  family name: Taniuchi
  given name: Yukiko
author list: Agent
  family name: Kodama
  given name: Taketoshi
author list: Agent
  family name: Tashiro
  given name: Satokuni
author list: Agent
  family name: Nakae
  given name: Misato
author list: Agent
  family name: Okazaki
  given name: Yuji
author list: Agent
  family name: Kitajima
  given name: Satoshi
author list: Agent
  family name: Sogawa
  given name: Sayaka
author list: Agent
  family name: Hasegawa
  given name: Toru
author list: Agent
  family name: Azumaya
  given name: Tomonori
author list: Agent
  family name: Hiroe
  given name: Yutaka
doi: 10.7717/peerj.15427
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-07
copyright: ©2023 Watanabe et al.
attribution name: Watanabe et al.

MFAP2 enhances cisplatin resistance in gastric cancer cells by regulating autophagy
type: item
type: AcademicArticle
description: Background Cisplatin (CDDP) is of importance in cancer treatment and widely used in advanced gastric cancer (GC). However, its clinical usage is limited due to its resistance, and the regulatory mechanism of CDDP resistance in GC has not yet been fully elucidated. In this study, we first conducted a comprehensive study to investigate the role of MFAP2 through bioinformatics analysis. Methods The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were applied to downloadgene expression data and clinicopathologic data, and the differentially expressed genes (DEGs) were further analyzed. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and survival analysis were conducted. Furthermore, according to the clinicopathological characteristics of TCGA, clinical correlation analysis was conducted, and a receiver operating characteristic curve (ROC) was plotted. Results We revealed that FAP, INHBA and MFAP2 were good diagnostic factors of GC. However, the mechanism of MFAP2 in GC remains elusive, especially in the aspect of chemotherapy resistance. We developed the CDDP-resistant cell line, and found that MFAP2 was upregulated in CDDP-resistant cells, and MFAP2-knockdown improved CDDP sensitivity. Finally, we found that MFAP2 enhanced CDDP resistance by inducing autophagy in drug-resistant cell lines. Conclusions The above results suggested that MFAP2 could affect the chemotherapy resistance by altering the level of autophagy in GC patients as a potential therapeutic target.
format: application/pdf
format: text/html
creator: Meng Li
creator: Hong-Yi Zhang
creator: Rong-Gui Zhang
subject: Bioinformatics
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.15441
publisher: PeerJ Inc.
rights: © 2023 Li et al.
abstract: Background Cisplatin (CDDP) is of importance in cancer treatment and widely used in advanced gastric cancer (GC). However, its clinical usage is limited due to its resistance, and the regulatory mechanism of CDDP resistance in GC has not yet been fully elucidated. In this study, we first conducted a comprehensive study to investigate the role of MFAP2 through bioinformatics analysis. Methods The Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were applied to downloadgene expression data and clinicopathologic data, and the differentially expressed genes (DEGs) were further analyzed. Then, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and survival analysis were conducted. Furthermore, according to the clinicopathological characteristics of TCGA, clinical correlation analysis was conducted, and a receiver operating characteristic curve (ROC) was plotted. Results We revealed that FAP, INHBA and MFAP2 were good diagnostic factors of GC. However, the mechanism of MFAP2 in GC remains elusive, especially in the aspect of chemotherapy resistance. We developed the CDDP-resistant cell line, and found that MFAP2 was upregulated in CDDP-resistant cells, and MFAP2-knockdown improved CDDP sensitivity. Finally, we found that MFAP2 enhanced CDDP resistance by inducing autophagy in drug-resistant cell lines. Conclusions The above results suggested that MFAP2 could affect the chemotherapy resistance by altering the level of autophagy in GC patients as a potential therapeutic target.
bibliographic citation: Li et al. (2023) MFAP2 enhances cisplatin resistance in gastric cancer cells by regulating autophagy. PeerJ 11:e15441 https://doi.org/10.7717/peerj.15441
date submitted: 2023-02-03
date accepted: 2023-04-28
issued: 2023-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Meng
author list: Agent
  family name: Zhang
  given name: Hong-Yi
author list: Agent
  family name: Zhang
  given name: Rong-Gui
doi: 10.7717/peerj.15441
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-07
copyright: ©2023 Li et al.
attribution name: Li et al.

Alterations in gene expressions of Caco-2 cell responses to LPS and ploy(I:C) stimulation
type: item
type: AcademicArticle
description: The intestinal epithelium barrier serves as a highly dynamic immunologic frontier in the defense against invading pathogenic bacteria and viruses. Hence, understanding of the complicated underlying relationship between enteric pathogens and the intestinal epithelium barrier is vital for developing strategies to improve the intestinal health of farm animals. To this end, Caco-2 cells were stimulated by 1 µg/ml lipopolysaccharide (LPS) for 24 h and 5 µg/ml polyinosinic-polycytidylic acid (ploy(I:C)) for 4 h to imitate bacterial and viral infection processes, respectively. The specific alterations in gene expression of Caco-2 cells after stimulation were characterized by transcriptome sequencing. Seventy differentially expressed genes (DEGs) were identified under LPS exposure, and 17 DEGs were observed under ploy(I:C) exposure. We found that most DEGs were specific, and only one common DEG SPAG7 was observed. Gene Ontology (GO) annotation analysis indicated that all DEGs identified in the different treatments were mainly derived from GO terms related to the maintenance of cellular homeostasis. Moreover, specific DEGs such as SLC39A10, MT2A, and MT1E regulated by LPS treatment, while IFIT2 and RUNX2 mediated by ploy(I:C) treatment, which are derived from immune function modulation related GO terms, were confirmed by both transcriptome sequencing and qRT-PCR. In addition, both transcriptome sequencing and qRT-PCR results verified that LPS specifically down-regulated the DEGs INHBE and ARF6, which are involved in inflammation responses related to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway including the TGF-beta signaling pathways and the Ras signaling pathway. Ploy(I:C) uniquely suppressed the DEGs GABARAP and LAMTOR3, which participated in viral replication-associated pathways including autophagy and mTOR signaling pathway.
format: application/pdf
format: text/html
creator: Ge Qin
creator: Yuanjie Zhao
creator: Yating Gan
creator: Xiaomei Yu
creator: Yifan Zhao
creator: Hui Peng
creator: Shaoming Fang
subject: Biochemistry
subject: Cell Biology
subject: Genomics
subject: Molecular Biology
subject: Veterinary Medicine
description: doi:10.7717/peerj.15459
publisher: PeerJ Inc.
rights: © 2023 Qin et al.
abstract: The intestinal epithelium barrier serves as a highly dynamic immunologic frontier in the defense against invading pathogenic bacteria and viruses. Hence, understanding of the complicated underlying relationship between enteric pathogens and the intestinal epithelium barrier is vital for developing strategies to improve the intestinal health of farm animals. To this end, Caco-2 cells were stimulated by 1 µg/ml lipopolysaccharide (LPS) for 24 h and 5 µg/ml polyinosinic-polycytidylic acid (ploy(I:C)) for 4 h to imitate bacterial and viral infection processes, respectively. The specific alterations in gene expression of Caco-2 cells after stimulation were characterized by transcriptome sequencing. Seventy differentially expressed genes (DEGs) were identified under LPS exposure, and 17 DEGs were observed under ploy(I:C) exposure. We found that most DEGs were specific, and only one common DEG SPAG7 was observed. Gene Ontology (GO) annotation analysis indicated that all DEGs identified in the different treatments were mainly derived from GO terms related to the maintenance of cellular homeostasis. Moreover, specific DEGs such as SLC39A10, MT2A, and MT1E regulated by LPS treatment, while IFIT2 and RUNX2 mediated by ploy(I:C) treatment, which are derived from immune function modulation related GO terms, were confirmed by both transcriptome sequencing and qRT-PCR. In addition, both transcriptome sequencing and qRT-PCR results verified that LPS specifically down-regulated the DEGs INHBE and ARF6, which are involved in inflammation responses related to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway including the TGF-beta signaling pathways and the Ras signaling pathway. Ploy(I:C) uniquely suppressed the DEGs GABARAP and LAMTOR3, which participated in viral replication-associated pathways including autophagy and mTOR signaling pathway.
bibliographic citation: Qin et al. (2023) Alterations in gene expressions of Caco-2 cell responses to LPS and ploy(I:C) stimulation. PeerJ 11:e15459 https://doi.org/10.7717/peerj.15459
date submitted: 2022-10-13
date accepted: 2023-05-03
issued: 2023-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Qin
  given name: Ge
author list: Agent
  family name: Zhao
  given name: Yuanjie
author list: Agent
  family name: Gan
  given name: Yating
author list: Agent
  family name: Yu
  given name: Xiaomei
author list: Agent
  family name: Zhao
  given name: Yifan
author list: Agent
  family name: Peng
  given name: Hui
author list: Agent
  family name: Fang
  given name: Shaoming
doi: 10.7717/peerj.15459
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-07
copyright: ©2023 Qin et al.
attribution name: Qin et al.

Endophytic fungus Biscogniauxia petrensis produces antibacterial substances
type: item
type: AcademicArticle
description: Widespread drug resistance and limited antibiotics challenge the treatment of pathogenic bacteria, which leads to a focus on searching for new antimicrobial lead compounds. We found the endophytic fungus Biscogniauxia petrensis MFLUCC14-0151 from the medicinal plant Dendrobium harveyanum had antibacterial activity for the first time. This work aimed to reveal the capacity of Biscogniauxia petrensis MFLUCC14-0151 against foodborne pathogenic bacteria and identify its bioactive substances. Bioassay-guided isolation led to the discovery of six infrequent active monomers, including (10R)-Xylariterpenoid B (1), Xylariterpenoid C (2), Tricycloalternarene 1b (3), Tricycloalternarene 3b (4), Funicin (5) and Vinetorin (6) from MFLUCC14-0151 for the first time. The results of antibacterial tests showed that (10R)-Xylariterpenoid B and Xylariterpenoid C exhibited inhibitory activities against Streptococcus agalactiae with MIC values ranging from 99.21 to 100.00 μM, and against Streptococcus aureus with MIC values ranging from 49.60 to 50.00 μM. Tricycloalternarene 1b and Tricycloalternarene 3b showed inhibitory effects on Streptococcus agalactiae with MIC values ranging from 36.13 to 75.76 μM. Unexpectedly, Funicin and Vinetorin exhibited remarkable antagonistic activities against Streptococcus agalactiae with MIC values of 10.35 and 10.21 μM, respectively, and against Streptococcus aureus with MIC values of 5.17 and 20.42 μM, respectively. In conclusion, we suggest that the isolated compounds Funicin and Vinetorin may be promising lead compounds for natural antibacterial agents.
format: application/pdf
format: text/html
creator: Long Han
creator: Wen Zheng
creator: Zhangjiang He
creator: Shengyan Qian
creator: Xiaoya Ma
creator: Jichuan Kang
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.15461
publisher: PeerJ Inc.
rights: © 2023 Han et al.
abstract: Widespread drug resistance and limited antibiotics challenge the treatment of pathogenic bacteria, which leads to a focus on searching for new antimicrobial lead compounds. We found the endophytic fungus Biscogniauxia petrensis MFLUCC14-0151 from the medicinal plant Dendrobium harveyanum had antibacterial activity for the first time. This work aimed to reveal the capacity of Biscogniauxia petrensis MFLUCC14-0151 against foodborne pathogenic bacteria and identify its bioactive substances. Bioassay-guided isolation led to the discovery of six infrequent active monomers, including (10R)-Xylariterpenoid B (1), Xylariterpenoid C (2), Tricycloalternarene 1b (3), Tricycloalternarene 3b (4), Funicin (5) and Vinetorin (6) from MFLUCC14-0151 for the first time. The results of antibacterial tests showed that (10R)-Xylariterpenoid B and Xylariterpenoid C exhibited inhibitory activities against Streptococcus agalactiae with MIC values ranging from 99.21 to 100.00 μM, and against Streptococcus aureus with MIC values ranging from 49.60 to 50.00 μM. Tricycloalternarene 1b and Tricycloalternarene 3b showed inhibitory effects on Streptococcus agalactiae with MIC values ranging from 36.13 to 75.76 μM. Unexpectedly, Funicin and Vinetorin exhibited remarkable antagonistic activities against Streptococcus agalactiae with MIC values of 10.35 and 10.21 μM, respectively, and against Streptococcus aureus with MIC values of 5.17 and 20.42 μM, respectively. In conclusion, we suggest that the isolated compounds Funicin and Vinetorin may be promising lead compounds for natural antibacterial agents.
bibliographic citation: Han et al. (2023) Endophytic fungus Biscogniauxia petrensis produces antibacterial substances. PeerJ 11:e15461 https://doi.org/10.7717/peerj.15461
date submitted: 2022-11-11
date accepted: 2023-05-03
issued: 2023-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Long
author list: Agent
  family name: Zheng
  given name: Wen
author list: Agent
  family name: He
  given name: Zhangjiang
author list: Agent
  family name: Qian
  given name: Shengyan
author list: Agent
  family name: Ma
  given name: Xiaoya
author list: Agent
  family name: Kang
  given name: Jichuan
doi: 10.7717/peerj.15461
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-07
copyright: © 2023 Han et al.
attribution name: Han et al.

The introduction of an invasive weed was not followed by the introduction of ethnobotanical knowledge: a review on the ethnobotany of Centaurea solstitialis L. (Asteraceae)
type: item
type: AcademicArticle
description: Invasive plants are known for their impacts to ecosystems and societies, but their potential cultural use tend to be unexplored. One important mechanism of plant invasion is the use of “allelochemicals” or “novel weapons”: chemical defenses which are new to their invaded habitats and that confer them competitive advantages. However, these chemicals are precisely what confers them ethnobotanical and medicinal properties. We reviewed the literature assessing the biogeography of the cultural uses of the model invasive plant yellow-starthistle (Centaurea solstitialis L.; Asteraceae), and assessed the extent to which the introduction of a weed native to Eurasia into several non-native world regions was paralleled by the spread of cultural uses from its native range. We found that the species was rich in pharmaceutically active compounds and that the species had been traditionally used for medicinal purposes, as raw material, and as food. However, ethnobotanical uses were reported almost exclusively in its native range, with no uses described for the non-native range, apart from honey production in California, Argentina, and Australia. Our study exemplifies how, when plant introductions are not paralleled synchronously by significant human migrations, cultural adoption can be extremely slow, even within the native range of the species. Invasive species can provide real-time insights into the cultural processes by which humans learn to use plants. This case study highlights how biological invasions and cultural expansions can be subjected to different constraints.
format: application/pdf
format: text/html
creator: Soraia Branco
creator: Ramona E. Irimia
creator: Daniel Montesinos
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.15489
publisher: PeerJ Inc.
rights: © 2023 Branco et al.
abstract: Invasive plants are known for their impacts to ecosystems and societies, but their potential cultural use tend to be unexplored. One important mechanism of plant invasion is the use of “allelochemicals” or “novel weapons”: chemical defenses which are new to their invaded habitats and that confer them competitive advantages. However, these chemicals are precisely what confers them ethnobotanical and medicinal properties. We reviewed the literature assessing the biogeography of the cultural uses of the model invasive plant yellow-starthistle (Centaurea solstitialis L.; Asteraceae), and assessed the extent to which the introduction of a weed native to Eurasia into several non-native world regions was paralleled by the spread of cultural uses from its native range. We found that the species was rich in pharmaceutically active compounds and that the species had been traditionally used for medicinal purposes, as raw material, and as food. However, ethnobotanical uses were reported almost exclusively in its native range, with no uses described for the non-native range, apart from honey production in California, Argentina, and Australia. Our study exemplifies how, when plant introductions are not paralleled synchronously by significant human migrations, cultural adoption can be extremely slow, even within the native range of the species. Invasive species can provide real-time insights into the cultural processes by which humans learn to use plants. This case study highlights how biological invasions and cultural expansions can be subjected to different constraints.
bibliographic citation: Branco et al. (2023) The introduction of an invasive weed was not followed by the introduction of ethnobotanical knowledge: a review on the ethnobotany of Centaurea solstitialis L. (Asteraceae). PeerJ 11:e15489 https://doi.org/10.7717/peerj.15489
date submitted: 2022-08-02
date accepted: 2023-05-10
issued: 2023-06-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Branco
  given name: Soraia
author list: Agent
  family name: Irimia
  given name: Ramona E.
author list: Agent
  family name: Montesinos
  given name: Daniel
doi: 10.7717/peerj.15489
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-06-07
copyright: ©2023 Branco et al.
attribution name: Branco et al.

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

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family name: Tanaka
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given name: Akira

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family name: Hasegawa
given name: Daisuke

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