PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Evaluation of phytochemical profile, and antioxidant, antidiabetic activities of indigenous Thai fruits
items: Estimation of reference evapotranspiration using some class-A pan evaporimeter pan coefficient estimation models in Mediterranean–Southeastern Anatolian transitional zone conditions of Turkey
items: Whole-brain radiation therapy plus simultaneous integrated boost for brain metastases from breast cancers
items: Impact of nitrogen fertilizer type and application rate on growth, nitrate accumulation, and postharvest quality of spinach
items: Meiofauna at a tropical sandy beach in the SW Atlantic: the influence of seasonality on diversity
items: Microplastic from beach sediment to tissue: a case study on burrowing crab Dotilla blanfordi
items: Analysis of measurement differences and causes of C, N, and P in river flooding areas—taking the Hailar River in China as an example
items: PKMYT1 knockdown inhibits cholesterol biosynthesis and promotes the drug sensitivity of triple-negative breast cancer cells to atorvastatin
items: Gut microbiome-immune interactions and their role in rheumatoid arthritis development
items: Early-life diet does not affect preference for fish in herring gulls (Larus argentatus)

Evaluation of phytochemical profile, and antioxidant, antidiabetic activities of indigenous Thai fruits
type: item
type: AcademicArticle
description: Background This research aims to explore the phenolics identification, phenolics quantification, antioxidant and potential biofunctional properties of lesser-known Thai fruits and their potency to treat type 2 diabetes mellitus (T2DM). Including, Antidesma puncticulatum, Dillenia indica, Diospyros decandra, Elaeagnus latifolia, Flacourtia indica, Garcinia dulcis, Lepisanthes fruticose, Mimusops elengi, Muntingia calabura, Phyllanthus reticulatus, Streblus asper, Syzygium cumini, Syzygium malaccense, Willughbeia edulis and Schleichera oleosa were analyzed by their phenolic and flavonoid content. These fruits have received limited scientific attention, prompting an investigation into their health benefits, particularly their relevance to diabetes management. Methods The study utilized methanolic crude extracts to measure phenolic and flavonoid levels. Additionally, UHPLC-DAD was utilized to identify and quantify phenolics. The methanolic extracts were assessed for antioxidant and antidiabetic abilities, including α-glucosidase and α-amylase inhibition. Results and Conclusion The study highlighted S. cumini as a rich source of phenolic (980.42 ± 0.89 mg GAE/g and flavonoid (3.55 ± 0.02 mg QE/g) compounds with strong antioxidant activity (IC50 by DPPH; 3.00 ± 0.01 µg/ml, IC50 by ABTS; 40 ± 0.01 µg/ml, FRAP; 898.63 ± 0.02 mg TE/ml). Additionally, S. cumini exhibited promising antidiabetic effects (S. cumini IC50; 0.13 ± 0.01 mg/ml for α-glucosidase inhibition, 3.91 ± 0.05 mg/ml for α-amylase inhibition), compared to Acarbose (IC50; 0.86 ± 0.01 mg/ml for α-glucosidase inhibition, 0.39 ± 0.05 mg/ml for α-amylase inhibition). Remarkably, compounds like catechins, gallic acid, kaempferol, and ellagic acid were identified in various quantities.This study suggests that these fruits, packed with phenolics, hold the potential to be included in an anti-diabetic diet and even pharmaceutical applications due to their health-promoting properties.
format: application/pdf
format: text/html
creator: Jirayupan Prakulanon
creator: Sutsawat Duangsrisai
creator: Srunya Vajrodaya
creator: Thanawat Thongchin
subject: Agricultural Science
subject: Biochemistry
subject: Food Science and Technology
subject: Plant Science
description: doi:10.7717/peerj.17681
publisher: PeerJ Inc.
rights: © 2024 Prakulanon et al.
abstract: Background This research aims to explore the phenolics identification, phenolics quantification, antioxidant and potential biofunctional properties of lesser-known Thai fruits and their potency to treat type 2 diabetes mellitus (T2DM). Including, Antidesma puncticulatum, Dillenia indica, Diospyros decandra, Elaeagnus latifolia, Flacourtia indica, Garcinia dulcis, Lepisanthes fruticose, Mimusops elengi, Muntingia calabura, Phyllanthus reticulatus, Streblus asper, Syzygium cumini, Syzygium malaccense, Willughbeia edulis and Schleichera oleosa were analyzed by their phenolic and flavonoid content. These fruits have received limited scientific attention, prompting an investigation into their health benefits, particularly their relevance to diabetes management. Methods The study utilized methanolic crude extracts to measure phenolic and flavonoid levels. Additionally, UHPLC-DAD was utilized to identify and quantify phenolics. The methanolic extracts were assessed for antioxidant and antidiabetic abilities, including α-glucosidase and α-amylase inhibition. Results and Conclusion The study highlighted S. cumini as a rich source of phenolic (980.42 ± 0.89 mg GAE/g and flavonoid (3.55 ± 0.02 mg QE/g) compounds with strong antioxidant activity (IC50 by DPPH; 3.00 ± 0.01 µg/ml, IC50 by ABTS; 40 ± 0.01 µg/ml, FRAP; 898.63 ± 0.02 mg TE/ml). Additionally, S. cumini exhibited promising antidiabetic effects (S. cumini IC50; 0.13 ± 0.01 mg/ml for α-glucosidase inhibition, 3.91 ± 0.05 mg/ml for α-amylase inhibition), compared to Acarbose (IC50; 0.86 ± 0.01 mg/ml for α-glucosidase inhibition, 0.39 ± 0.05 mg/ml for α-amylase inhibition). Remarkably, compounds like catechins, gallic acid, kaempferol, and ellagic acid were identified in various quantities.This study suggests that these fruits, packed with phenolics, hold the potential to be included in an anti-diabetic diet and even pharmaceutical applications due to their health-promoting properties.
bibliographic citation: Prakulanon et al. (2024) Evaluation of phytochemical profile, and antioxidant, antidiabetic activities of indigenous Thai fruits. PeerJ 12:e17681 https://doi.org/10.7717/peerj.17681
date submitted: 2024-02-14
date accepted: 2024-06-13
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Prakulanon
  given name: Jirayupan
author list: Agent
  family name: Duangsrisai
  given name: Sutsawat
author list: Agent
  family name: Vajrodaya
  given name: Srunya
author list: Agent
  family name: Thongchin
  given name: Thanawat
doi: 10.7717/peerj.17681
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: ©2024 Prakulanon et al.
attribution name: Prakulanon et al.

Estimation of reference evapotranspiration using some class-A pan evaporimeter pan coefficient estimation models in Mediterranean–Southeastern Anatolian transitional zone conditions of Turkey
type: item
type: AcademicArticle
description: Background Reference evapotranspiration (ETo), which is used as the basic data in many studies within the scope of hydrology, meteorology, irrigation and soil sciences, can be estimated by using the evaporation (Epan) measured from the class-A pan evaporimeter. However, this method requires reliable pan coefficients (Kp). Many empirical models are used to estimate Kp coefficients. The reliability of these models varies depending on climatic and environmental conditions. Therefore, they need to be tested in the local conditions where they will be used. In this study, conducted in Kahramanmaraş, which has a semi-arid Mediterranean climate in Turkey during the July–October periods of 2020 and 2021, aimed to determine the usability levels of six Kp models in estimating daily and monthly average ETo. Methods The Kp coefficients estimated by the models were multiplied with the daily Epan values, and the daily average ETo values were estimated on the basis of the model. The daily Epan values were measured using an ultrasonic sensor sensitive to the water surface placed on the class-A pan evaporimeter. The ultrasonic sensor was managed by a programmable logic controller (PLC). To enable the sensor to be managed by PLC, a software was prepared using the CODESYS programming language and uploaded to the PLC. The daily average ETo values determined by the FAO-56 Penman–Monteith equation were accepted as actual values. The ETo values estimated by the Kp models were compared with the actual ETo values using the mean absolute error (MAE), mean absolute percentage error (MAPE), root mean square error (RMSE) and determination coefficient (R2) statistical approaches. Results The Wahed & Snyder outperformed the other models in estimating daily (MAE = 0.78 mm day−1, MAPE = 14.40%, RMSE = 0.97 mm day−1, R2 = 0.82) and monthly (MAE = 0.32 mm day−1, MAPE = 5.88%, RMSE = 0.32 mm day−1, R2 = 0.99) average ETo. FAO-56 showed the nearest performance to Wahed & Snyder. The Snyder model present…
format: application/pdf
format: text/html
creator: Selçuk Usta
subject: Agricultural Science
subject: Plant Science
subject: Natural Resource Management
subject: Atmospheric Chemistry
subject: Ecohydrology
description: doi:10.7717/peerj.17685
publisher: PeerJ Inc.
rights: © 2024 Usta
abstract: Background Reference evapotranspiration (ETo), which is used as the basic data in many studies within the scope of hydrology, meteorology, irrigation and soil sciences, can be estimated by using the evaporation (Epan) measured from the class-A pan evaporimeter. However, this method requires reliable pan coefficients (Kp). Many empirical models are used to estimate Kp coefficients. The reliability of these models varies depending on climatic and environmental conditions. Therefore, they need to be tested in the local conditions where they will be used. In this study, conducted in Kahramanmaraş, which has a semi-arid Mediterranean climate in Turkey during the July–October periods of 2020 and 2021, aimed to determine the usability levels of six Kp models in estimating daily and monthly average ETo. Methods The Kp coefficients estimated by the models were multiplied with the daily Epan values, and the daily average ETo values were estimated on the basis of the model. The daily Epan values were measured using an ultrasonic sensor sensitive to the water surface placed on the class-A pan evaporimeter. The ultrasonic sensor was managed by a programmable logic controller (PLC). To enable the sensor to be managed by PLC, a software was prepared using the CODESYS programming language and uploaded to the PLC. The daily average ETo values determined by the FAO-56 Penman–Monteith equation were accepted as actual values. The ETo values estimated by the Kp models were compared with the actual ETo values using the mean absolute error (MAE), mean absolute percentage error (MAPE), root mean square error (RMSE) and determination coefficient (R2) statistical approaches. Results The Wahed & Snyder outperformed the other models in estimating daily (MAE = 0.78 mm day−1, MAPE = 14.40%, RMSE = 0.97 mm day−1, R2 = 0.82) and monthly (MAE = 0.32 mm day−1, MAPE = 5.88%, RMSE = 0.32 mm day−1, R2 = 0.99) average ETo. FAO-56 showed the nearest performance to Wahed & Snyder. The Snyder model present…
bibliographic citation: Usta (2024) Estimation of reference evapotranspiration using some class-A pan evaporimeter pan coefficient estimation models in Mediterranean–Southeastern Anatolian transitional zone conditions of Turkey. PeerJ 12:e17685 https://doi.org/10.7717/peerj.17685
date submitted: 2024-02-29
date accepted: 2024-06-13
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Usta
  given name: Selçuk
doi: 10.7717/peerj.17685
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: ©2024 Usta
attribution name: Usta

Whole-brain radiation therapy plus simultaneous integrated boost for brain metastases from breast cancers
type: item
type: AcademicArticle
description: Background The effect of whole-brain radiation therapy (WBRT) plus simultaneous integrated boost (SIB) in brain metastasis from breast cancers has not been demonstrated. Method In this single-center retrospective study, we reviewed consecutive breast cancer patients who developed brain metastasis and were treated with hypofractionated radiation therapy plus WBRT using intensity-modulated radiation therapy (IMRT)-SIB approaches. We analyzed clinical outcomes, prognostic factors and patterns of treatment failure. Result A total of 27 patients were eligible for analysis. Four (14.8%) patients achieved clinical complete response and 14 (51.9%) had partial response of brain lesions. The other nine patients were not evaluated for brain tumor response. The median brain progression-free survival was 8.60 (95% CI [6.43–13.33]) months and the median overall survival was 16.8 (95% CI [13.3–27.7]) months. Three patients had in-field failure, five had out-field failure and two had in-field and out-field failure. Conclusion WBRT plus SIB led to improved tumor control and clinical outcome in breast cancer patients with brain metastasis.
format: application/pdf
format: text/html
creator: Hongyan Zhang
creator: Qiuji Wu
creator: Li Li
creator: Linwei Wang
creator: Yahua Zhong
subject: Oncology
subject: Women’s Health
subject: Palliative Care
description: doi:10.7717/peerj.17696
publisher: PeerJ Inc.
rights: © 2024 Zhang et al.
abstract: Background The effect of whole-brain radiation therapy (WBRT) plus simultaneous integrated boost (SIB) in brain metastasis from breast cancers has not been demonstrated. Method In this single-center retrospective study, we reviewed consecutive breast cancer patients who developed brain metastasis and were treated with hypofractionated radiation therapy plus WBRT using intensity-modulated radiation therapy (IMRT)-SIB approaches. We analyzed clinical outcomes, prognostic factors and patterns of treatment failure. Result A total of 27 patients were eligible for analysis. Four (14.8%) patients achieved clinical complete response and 14 (51.9%) had partial response of brain lesions. The other nine patients were not evaluated for brain tumor response. The median brain progression-free survival was 8.60 (95% CI [6.43–13.33]) months and the median overall survival was 16.8 (95% CI [13.3–27.7]) months. Three patients had in-field failure, five had out-field failure and two had in-field and out-field failure. Conclusion WBRT plus SIB led to improved tumor control and clinical outcome in breast cancer patients with brain metastasis.
bibliographic citation: Zhang et al. (2024) Whole-brain radiation therapy plus simultaneous integrated boost for brain metastases from breast cancers. PeerJ 12:e17696 https://doi.org/10.7717/peerj.17696
date submitted: 2023-11-14
date accepted: 2024-06-14
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Hongyan
author list: Agent
  family name: Wu
  given name: Qiuji
author list: Agent
  family name: Li
  given name: Li
author list: Agent
  family name: Wang
  given name: Linwei
author list: Agent
  family name: Zhong
  given name: Yahua
doi: 10.7717/peerj.17696
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: © 2024 Zhang et al.
attribution name: Zhang et al.

Impact of nitrogen fertilizer type and application rate on growth, nitrate accumulation, and postharvest quality of spinach
type: item
type: AcademicArticle
description: Background A balanced supply of nitrogen is essential for spinach, supporting both optimal growth and appropriate nitrate (NO3−) levels for improved storage quality. Thus, choosing the correct nitrogen fertilizer type and application rate is key for successful spinach cultivation. This study investigated the effects of different nitrogen (N) fertilizer type and application rates on the growth, nitrate content, and storage quality of spinach plants. Methods Four fertilizer types were applied at five N doses (25, 50, 200, and 400 mg N kg−1) to plants grown in plastic pots at a greenhouse. The fertilizer types used in the experiment were ammonium sulphate (AS), slow-release ammonium sulphate (SRAS), calcium nitrate (CN), and yeast residue (YR). Spinach parameters like Soil Plant Analysis Development (SPAD) values (chlorophyll content), plant height, and fresh weight were measured. Nitrate content in leaves was analyzed after storage periods simulating post-harvest handling (0, 5, and 10 days). Results The application of nitrogen fertilizer significantly influenced spinach growth parameters and nitrate content. The YRx400 treatment yielded the largest leaves (10.3 ± 0.5 cm long, 5.3 ± 0.2 cm wide). SPAD values increased with higher N doses for AS, SRAS, and CN fertilizers, with AS×400 (58.1 ± 0.8) and SRAS×400 (62.0 ± 5.8) reaching the highest values. YR treatments showed a moderate SPAD increase. Fresh weight response depended on fertilizer type, N dose, and storage period. While fresh weight increased in all fertilizers till 200 mg kg−1 dose, a decrease was observed at the highest dose for AS and CN. SRAS exhibited a more gradual increase in fresh weight with increasing nitrogen dose, without the negative impact seen at the highest dose in AS and CN. Nitrate content in spinach leaves varied by fertilizer type, dose, and storage day. CNx400 resulted in the highest NO3− content (4,395 mg kg−1) at harvest (Day 0), exceeding the European Union’s safety limit. This level d…
format: application/pdf
format: text/html
creator: Kemal Yalçın Gülüt
creator: Gamze Güleç Şentürk
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.17726
publisher: PeerJ Inc.
rights: © 2024 Gülüt and Şentürk
abstract: Background A balanced supply of nitrogen is essential for spinach, supporting both optimal growth and appropriate nitrate (NO3−) levels for improved storage quality. Thus, choosing the correct nitrogen fertilizer type and application rate is key for successful spinach cultivation. This study investigated the effects of different nitrogen (N) fertilizer type and application rates on the growth, nitrate content, and storage quality of spinach plants. Methods Four fertilizer types were applied at five N doses (25, 50, 200, and 400 mg N kg−1) to plants grown in plastic pots at a greenhouse. The fertilizer types used in the experiment were ammonium sulphate (AS), slow-release ammonium sulphate (SRAS), calcium nitrate (CN), and yeast residue (YR). Spinach parameters like Soil Plant Analysis Development (SPAD) values (chlorophyll content), plant height, and fresh weight were measured. Nitrate content in leaves was analyzed after storage periods simulating post-harvest handling (0, 5, and 10 days). Results The application of nitrogen fertilizer significantly influenced spinach growth parameters and nitrate content. The YRx400 treatment yielded the largest leaves (10.3 ± 0.5 cm long, 5.3 ± 0.2 cm wide). SPAD values increased with higher N doses for AS, SRAS, and CN fertilizers, with AS×400 (58.1 ± 0.8) and SRAS×400 (62.0 ± 5.8) reaching the highest values. YR treatments showed a moderate SPAD increase. Fresh weight response depended on fertilizer type, N dose, and storage period. While fresh weight increased in all fertilizers till 200 mg kg−1 dose, a decrease was observed at the highest dose for AS and CN. SRAS exhibited a more gradual increase in fresh weight with increasing nitrogen dose, without the negative impact seen at the highest dose in AS and CN. Nitrate content in spinach leaves varied by fertilizer type, dose, and storage day. CNx400 resulted in the highest NO3− content (4,395 mg kg−1) at harvest (Day 0), exceeding the European Union’s safety limit. This level d…
bibliographic citation: Gülüt et al. (2024) Impact of nitrogen fertilizer type and application rate on growth, nitrate accumulation, and postharvest quality of spinach. PeerJ 12:e17726 https://doi.org/10.7717/peerj.17726
date submitted: 2024-04-18
date accepted: 2024-06-20
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gülüt
  given name: Kemal Yalçın
author list: Agent
  family name: Şentürk
  given name: Gamze Güleç
doi: 10.7717/peerj.17726
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: © 2024 Gülüt and Şentürk
attribution name: Gülüt and Şentürk

Meiofauna at a tropical sandy beach in the SW Atlantic: the influence of seasonality on diversity
type: item
type: AcademicArticle
description: Background Sandy beaches are dynamic environments housing a large diversity of organisms and providing important environmental services. Meiofaunal metazoan are small organisms that play a key role in the sediment. Their diversity, distribution and composition are driven by sedimentary and oceanographic parameters. Understanding the diversity patterns of marine meiofauna is critical in a changing world. Methods In this study, we investigate if there is seasonal difference in meiofaunal assemblage composition and diversity along 1 year and if the marine seascapes dynamics (water masses with particular biogeochemical features, characterized by temperature, salinity, absolute dynamic topography, chromophoric dissolved organic material, chlorophyll-a, and normalized fluorescent line height), rainfall, and sediment parameters (total organic matter, carbonate, carbohydrate, protein, lipids, protein-to-carbohydrate, carbohydrate-to-lipids, and biopolymeric carbon) affect significatively meiofaunal diversity at a tropical sandy beach. We tested two hypotheses here: (i) meiofaunal diversity is higher during warmer months and its composition changes significatively among seasons along a year at a tropical sandy beach, and (ii) meiofaunal diversity metrics are significantly explained by marine seascapes characteristics and sediment parameters. We used metabarcoding (V9 hypervariable region from 18S gene) from sediment samples to assess the meiofaunal assemblage composition and diversity (phylogenetic diversity and Shannon’s diversity) over a period of 1 year. Results Meiofauna was dominated by Crustacea (46% of sequence reads), Annelida (28% of sequence reads) and Nematoda (12% of sequence reads) in periods of the year with high temperatures (>25 °C), high salinity (>31.5 ppt), and calm waters. Our data support our initial hypotheses revealing a higher meiofaunal diversity (phylogenetic and Shannon’s Diversity) and different composition during warmer periods of the year. Meiof…
format: application/pdf
format: text/html
creator: Gabriel C. Coppo
creator: Araiene P. Pereira
creator: Sergio A. Netto
creator: Angelo F. Bernardino
subject: Biodiversity
subject: Ecology
subject: Genetics
subject: Genomics
subject: Marine Biology
description: doi:10.7717/peerj.17727
publisher: PeerJ Inc.
rights: © 2024 Coppo et al.
abstract: Background Sandy beaches are dynamic environments housing a large diversity of organisms and providing important environmental services. Meiofaunal metazoan are small organisms that play a key role in the sediment. Their diversity, distribution and composition are driven by sedimentary and oceanographic parameters. Understanding the diversity patterns of marine meiofauna is critical in a changing world. Methods In this study, we investigate if there is seasonal difference in meiofaunal assemblage composition and diversity along 1 year and if the marine seascapes dynamics (water masses with particular biogeochemical features, characterized by temperature, salinity, absolute dynamic topography, chromophoric dissolved organic material, chlorophyll-a, and normalized fluorescent line height), rainfall, and sediment parameters (total organic matter, carbonate, carbohydrate, protein, lipids, protein-to-carbohydrate, carbohydrate-to-lipids, and biopolymeric carbon) affect significatively meiofaunal diversity at a tropical sandy beach. We tested two hypotheses here: (i) meiofaunal diversity is higher during warmer months and its composition changes significatively among seasons along a year at a tropical sandy beach, and (ii) meiofaunal diversity metrics are significantly explained by marine seascapes characteristics and sediment parameters. We used metabarcoding (V9 hypervariable region from 18S gene) from sediment samples to assess the meiofaunal assemblage composition and diversity (phylogenetic diversity and Shannon’s diversity) over a period of 1 year. Results Meiofauna was dominated by Crustacea (46% of sequence reads), Annelida (28% of sequence reads) and Nematoda (12% of sequence reads) in periods of the year with high temperatures (>25 °C), high salinity (>31.5 ppt), and calm waters. Our data support our initial hypotheses revealing a higher meiofaunal diversity (phylogenetic and Shannon’s Diversity) and different composition during warmer periods of the year. Meiof…
bibliographic citation: Coppo et al. (2024) Meiofauna at a tropical sandy beach in the SW Atlantic: the influence of seasonality on diversity. PeerJ 12:e17727 https://doi.org/10.7717/peerj.17727
date submitted: 2023-11-08
date accepted: 2024-06-20
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Coppo
  given name: Gabriel C.
author list: Agent
  family name: Pereira
  given name: Araiene P.
author list: Agent
  family name: Netto
  given name: Sergio A.
author list: Agent
  family name: Bernardino
  given name: Angelo F.
doi: 10.7717/peerj.17727
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: © 2024 Coppo et al.
attribution name: Coppo et al.

Microplastic from beach sediment to tissue: a case study on burrowing crab Dotilla blanfordi
type: item
type: AcademicArticle
description: Background Microplastics (MPs) are pervasive pollutants in the marine environment, exhibiting persistence in coastal sediment over extended periods. However, the mechanism of their uptake by marine organisms and distribution in habitat is less understood. The objective of the present study was to investigate the presence of MP contamination in burrow sediment, feeding pellets, and tissue of Dotilla blanfordi in the Gulf of Kachchh, Gujarat State. Methods A total of 500 g of burrow sediment, 100 g of feeding pellets, and body tissue of 10 resident D. blanfordi were pooled as one replica. Such seven replicas from each site were analyzed for MP extraction from three sites, including Asharmata, Mandvi, and Serena, located in the Gulf of Kachchh. The standard protocol was used during the analysis of the collected samples in order to isolate MPs. Results The abundance of MP was found higher in burrow sediment, feeding pellets and tissue of D. blanfordi at study site Mandvi, followed by Serena and Asharmata. The abundance of MP was found higher in D. blanfordi tissue, followed by burrow sediment and feeding pellet. A significant variation was observed in MP abundance among burrow sediment, feeding pellets, and tissue. MPs with various shapes (fiber, film, and fragment), sizes (1–2, 2–3, 3–4, and 4–5 mm), and colors (blue, green, black, pink, purple, red transparent) were recorded from all the study sites. Polyurethane and polyvinyl chloride were recognized as the chemical profile of the extracted MPs. The current investigation revealed greater accumulation of MPs in D. blanfordi’s tissues compared to sediment and pellets, suggesting a risk of MP contamination in marine benthic fauna with a greater rate of bioaccumulation. D. blanfordi plays a significant role as a structuring agent for MP distribution in the intertidal flat through burrowing activity.
format: application/pdf
format: text/html
creator: Hiralba Zala
creator: Vasantkumar Rabari
creator: Krupal Patel
creator: Heris Patel
creator: Virendra Kumar Yadav
creator: Ashish Patel
creator: Dipak Kumar Sahoo
creator: Jigneshkumar Trivedi
subject: Ecology
subject: Marine Biology
subject: Toxicology
subject: Zoology
description: doi:10.7717/peerj.17738
publisher: PeerJ Inc.
rights: © 2024 Zala et al.
abstract: Background Microplastics (MPs) are pervasive pollutants in the marine environment, exhibiting persistence in coastal sediment over extended periods. However, the mechanism of their uptake by marine organisms and distribution in habitat is less understood. The objective of the present study was to investigate the presence of MP contamination in burrow sediment, feeding pellets, and tissue of Dotilla blanfordi in the Gulf of Kachchh, Gujarat State. Methods A total of 500 g of burrow sediment, 100 g of feeding pellets, and body tissue of 10 resident D. blanfordi were pooled as one replica. Such seven replicas from each site were analyzed for MP extraction from three sites, including Asharmata, Mandvi, and Serena, located in the Gulf of Kachchh. The standard protocol was used during the analysis of the collected samples in order to isolate MPs. Results The abundance of MP was found higher in burrow sediment, feeding pellets and tissue of D. blanfordi at study site Mandvi, followed by Serena and Asharmata. The abundance of MP was found higher in D. blanfordi tissue, followed by burrow sediment and feeding pellet. A significant variation was observed in MP abundance among burrow sediment, feeding pellets, and tissue. MPs with various shapes (fiber, film, and fragment), sizes (1–2, 2–3, 3–4, and 4–5 mm), and colors (blue, green, black, pink, purple, red transparent) were recorded from all the study sites. Polyurethane and polyvinyl chloride were recognized as the chemical profile of the extracted MPs. The current investigation revealed greater accumulation of MPs in D. blanfordi’s tissues compared to sediment and pellets, suggesting a risk of MP contamination in marine benthic fauna with a greater rate of bioaccumulation. D. blanfordi plays a significant role as a structuring agent for MP distribution in the intertidal flat through burrowing activity.
bibliographic citation: Zala et al. (2024) Microplastic from beach sediment to tissue: a case study on burrowing crab Dotilla blanfordi. PeerJ 12:e17738 https://doi.org/10.7717/peerj.17738
date submitted: 2023-11-13
date accepted: 2024-06-23
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zala
  given name: Hiralba
author list: Agent
  family name: Rabari
  given name: Vasantkumar
author list: Agent
  family name: Patel
  given name: Krupal
author list: Agent
  family name: Patel
  given name: Heris
author list: Agent
  family name: Yadav
  given name: Virendra Kumar
author list: Agent
  family name: Patel
  given name: Ashish
author list: Agent
  family name: Sahoo
  given name: Dipak Kumar
author list: Agent
  family name: Trivedi
  given name: Jigneshkumar
doi: 10.7717/peerj.17738
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: © 2024 Zala et al.
attribution name: Zala et al.

Analysis of measurement differences and causes of C, N, and P in river flooding areas—taking the Hailar River in China as an example
type: item
type: AcademicArticle
description: The Hailar River is located in the Inner Mongolia Autonomous Region of Northeast China. It is a connecting hub of the agricultural pastoral transitional zone on the Hulunbuir grassland, with abundant water and biodiversity resources, and important ecological conservation significance. This study takes the Hailar River as the research area to evaluate the impact and main influencing factors of soil C, N, and P ecological measurement from the upstream to downstream concave convex riverbanks of the Hailar River. The research results show that: (1) The average soil particle size shows differences in the upstream and downstream: the average soil particle size in Section 1 is 31.6–192.3 µm, Section 2 is 21–213 µm, Section 3 is 21–288 µm, and Section 4 is 42–206 µm; the pH value in the upstream area is generally low, while the pH value in the downstream area increases. The reason for this is that the convex bank area has sufficient water, which plays a role in inhibiting salt content; (2) the nutrient content in the concave bank is generally higher in the upstream region than in the downstream region, while the difference in nutrient content between the upstream and downstream regions is relatively small in the convex bank; (3) the nutrient content of concave banks is mostly positively correlated with soil moisture content, while convex banks are positively and negatively correlated with soil moisture content and soil particle size. Research has shown that different cross-sections upstream and downstream, as well as uneven riverbanks, significantly affect soil physicochemical properties and soil C, N, and P ecological measurements. Studying the content of soil C, N, and P in different riparian zones under typical cross-sections can provide new ideas for regional ecological protection and even global C, N, and P cycling.
format: application/pdf
format: text/html
creator: Xi Dong
creator: Chunming Hu
subject: Soil Science
subject: Aquatic and Marine Chemistry
subject: Biogeochemistry
subject: Ecohydrology
description: doi:10.7717/peerj.17745
publisher: PeerJ Inc.
rights: © 2024 Dong and Hu
abstract: The Hailar River is located in the Inner Mongolia Autonomous Region of Northeast China. It is a connecting hub of the agricultural pastoral transitional zone on the Hulunbuir grassland, with abundant water and biodiversity resources, and important ecological conservation significance. This study takes the Hailar River as the research area to evaluate the impact and main influencing factors of soil C, N, and P ecological measurement from the upstream to downstream concave convex riverbanks of the Hailar River. The research results show that: (1) The average soil particle size shows differences in the upstream and downstream: the average soil particle size in Section 1 is 31.6–192.3 µm, Section 2 is 21–213 µm, Section 3 is 21–288 µm, and Section 4 is 42–206 µm; the pH value in the upstream area is generally low, while the pH value in the downstream area increases. The reason for this is that the convex bank area has sufficient water, which plays a role in inhibiting salt content; (2) the nutrient content in the concave bank is generally higher in the upstream region than in the downstream region, while the difference in nutrient content between the upstream and downstream regions is relatively small in the convex bank; (3) the nutrient content of concave banks is mostly positively correlated with soil moisture content, while convex banks are positively and negatively correlated with soil moisture content and soil particle size. Research has shown that different cross-sections upstream and downstream, as well as uneven riverbanks, significantly affect soil physicochemical properties and soil C, N, and P ecological measurements. Studying the content of soil C, N, and P in different riparian zones under typical cross-sections can provide new ideas for regional ecological protection and even global C, N, and P cycling.
bibliographic citation: Dong et al. (2024) Analysis of measurement differences and causes of C, N, and P in river flooding areas—taking the Hailar River in China as an example. PeerJ 12:e17745 https://doi.org/10.7717/peerj.17745
date submitted: 2024-04-25
date accepted: 2024-06-24
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dong
  given name: Xi
author list: Agent
  family name: Hu
  given name: Chunming
doi: 10.7717/peerj.17745
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: ©2024 Dong and Hu
attribution name: Dong and Hu

PKMYT1 knockdown inhibits cholesterol biosynthesis and promotes the drug sensitivity of triple-negative breast cancer cells to atorvastatin
type: item
type: AcademicArticle
description: Triple negative breast cancer (TNBC) as the most aggressive molecular subtype of breast cancer is characterized by high cancer cell proliferation and poor patient prognosis. Abnormal lipid metabolism contributes to the malignant process of cancers. Study observed significantly enhanced cholesterol biosynthesis in TNBC. However, the mechanisms underlying the abnormal increase of cholesterol biosynthesis in TNBC are still unclear. Hence, we identified a member of the serine/threonine protein kinase family PKMYT1 as a key driver of cholesterol synthesis in TNBC cells. Aberrantly high-expressed PKMYT1 in TNBC was indicative of unfavorable prognostic outcomes. In addition, PKMYT1 promoted sterol regulatory element-binding protein 2 (SREBP2)-mediated expression of enzymes related to cholesterol biosynthesis through activating the TNF/ TNF receptor-associated factor 1 (TRAF1)/AKT pathway. Notably, downregulation of PKMYT1 significantly inhibited the feedback upregulation of statin-mediated cholesterol biosynthesis, whereas knockdown of PKMYT1 promoted the drug sensitivity of atorvastatin in TNBC cells. Overall, our study revealed a novel function of PKMYT1 in TNBC cholesterol biosynthesis, providing a new target for targeting tumor metabolic reprogramming in the cancer.
format: application/pdf
format: text/html
creator: Wei Gao
creator: Xin Guo
creator: Linlin Sun
creator: Jinwei Gai
creator: Yinan Cao
creator: Shuqun Zhang
subject: Cell Biology
subject: Molecular Biology
subject: Oncology
subject: Women’s Health
description: doi:10.7717/peerj.17749
publisher: PeerJ Inc.
rights: © 2024 Gao et al.
abstract: Triple negative breast cancer (TNBC) as the most aggressive molecular subtype of breast cancer is characterized by high cancer cell proliferation and poor patient prognosis. Abnormal lipid metabolism contributes to the malignant process of cancers. Study observed significantly enhanced cholesterol biosynthesis in TNBC. However, the mechanisms underlying the abnormal increase of cholesterol biosynthesis in TNBC are still unclear. Hence, we identified a member of the serine/threonine protein kinase family PKMYT1 as a key driver of cholesterol synthesis in TNBC cells. Aberrantly high-expressed PKMYT1 in TNBC was indicative of unfavorable prognostic outcomes. In addition, PKMYT1 promoted sterol regulatory element-binding protein 2 (SREBP2)-mediated expression of enzymes related to cholesterol biosynthesis through activating the TNF/ TNF receptor-associated factor 1 (TRAF1)/AKT pathway. Notably, downregulation of PKMYT1 significantly inhibited the feedback upregulation of statin-mediated cholesterol biosynthesis, whereas knockdown of PKMYT1 promoted the drug sensitivity of atorvastatin in TNBC cells. Overall, our study revealed a novel function of PKMYT1 in TNBC cholesterol biosynthesis, providing a new target for targeting tumor metabolic reprogramming in the cancer.
bibliographic citation: Gao et al. (2024) PKMYT1 knockdown inhibits cholesterol biosynthesis and promotes the drug sensitivity of triple-negative breast cancer cells to atorvastatin. PeerJ 12:e17749 https://doi.org/10.7717/peerj.17749
date submitted: 2024-02-06
date accepted: 2024-06-24
issued: 2024-07-12
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Gao
  given name: Wei
author list: Agent
  family name: Guo
  given name: Xin
author list: Agent
  family name: Sun
  given name: Linlin
author list: Agent
  family name: Gai
  given name: Jinwei
author list: Agent
  family name: Cao
  given name: Yinan
author list: Agent
  family name: Zhang
  given name: Shuqun
doi: 10.7717/peerj.17749
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-12
copyright: © 2024 Gao et al.
attribution name: Gao et al.

Gut microbiome-immune interactions and their role in rheumatoid arthritis development
type: item
type: AcademicArticle
description: Objective The primary objective is to study the impact of gut microbiota and their interactions with diverse immunological markers on the development of rheumatoid arthritis. Methods This study was performed in Astana, Kazakhstan, and included 77 Kazakh female patients older than 18 years, who met the American College of Rheumatology 2010 classification criteria for rheumatoid arthritis (RA), and 113 healthy controls. The DNA was extracted from fecal samples obtained from all study participants for subsequent sequencing at the 16S rRNA gene V1-V3 locus, facilitating the analysis of the gut microbiome. The Multiplex immunoassay was employed to measure the concentrations of inflammatory cytokines, chemokines, and immunoglobulins in both fecal and plasma samples. Results Our taxonomic analysis revealed significant differences in the composition of the gut microbiota between the healthy control cohort and the cohort with rheumatoid arthritis RA. Alpha diversity was significantly lower in the RA group. Lachnospiraceae were the most abundant taxon and found to be crucial, showing correlations with immunological markers such as IL5. Additionally, Lachnospiraceae and Oscillospiraceae exhibited the most predictable power and distinguished the composition of both study groups. Conclusion Our study identifies key differences in the gut microbiome of RA patients, revealing distinct microbial patterns and specific taxa abundance. We highlight potential biomarkers in immunological and bacterial pathways, offering insights into RA development and indicating possibilities for personalized treatment.
format: application/pdf
format: text/html
creator: Madiyar Nurgaziyev
creator: Argul Issilbayeva
creator: Rakhmetkazhi Bersimbaev
creator: Oralbek Ilderbayev
creator: Elizaveta Vinogradova
creator: Zharkyn Jarmukhanov
creator: Ayaulym Nurgozhina
creator: Shynggys Sergazy
creator: Nuray Kozhabergen
creator: Zhanar Akhmetova
creator: Assel Meiramova
creator: Laura Chulenbayeva
creator: Aigerim Ibrayeva
creator: Nurislam Mukhanbetzhanov
creator: Zhanel Mukhanbetzhanova
creator: Samat Kozhakhmetov
creator: Bayan Ainabekova
creator: Almagul Kushugulova
subject: Microbiology
subject: Molecular Biology
subject: Gastroenterology and Hepatology
subject: Immunology
subject: Rheumatology
description: doi:10.7717/peerj.17477
publisher: PeerJ Inc.
rights: © 2024 Nurgaziyev et al.
abstract: Objective The primary objective is to study the impact of gut microbiota and their interactions with diverse immunological markers on the development of rheumatoid arthritis. Methods This study was performed in Astana, Kazakhstan, and included 77 Kazakh female patients older than 18 years, who met the American College of Rheumatology 2010 classification criteria for rheumatoid arthritis (RA), and 113 healthy controls. The DNA was extracted from fecal samples obtained from all study participants for subsequent sequencing at the 16S rRNA gene V1-V3 locus, facilitating the analysis of the gut microbiome. The Multiplex immunoassay was employed to measure the concentrations of inflammatory cytokines, chemokines, and immunoglobulins in both fecal and plasma samples. Results Our taxonomic analysis revealed significant differences in the composition of the gut microbiota between the healthy control cohort and the cohort with rheumatoid arthritis RA. Alpha diversity was significantly lower in the RA group. Lachnospiraceae were the most abundant taxon and found to be crucial, showing correlations with immunological markers such as IL5. Additionally, Lachnospiraceae and Oscillospiraceae exhibited the most predictable power and distinguished the composition of both study groups. Conclusion Our study identifies key differences in the gut microbiome of RA patients, revealing distinct microbial patterns and specific taxa abundance. We highlight potential biomarkers in immunological and bacterial pathways, offering insights into RA development and indicating possibilities for personalized treatment.
bibliographic citation: Nurgaziyev et al. (2024) Gut microbiome-immune interactions and their role in rheumatoid arthritis development. PeerJ 12:e17477 https://doi.org/10.7717/peerj.17477
date submitted: 2024-01-19
date accepted: 2024-05-06
issued: 2024-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by-nc/4.0
author list: Agent
  family name: Nurgaziyev
  given name: Madiyar
author list: Agent
  family name: Issilbayeva
  given name: Argul
author list: Agent
  family name: Bersimbaev
  given name: Rakhmetkazhi
author list: Agent
  family name: Ilderbayev
  given name: Oralbek
author list: Agent
  family name: Vinogradova
  given name: Elizaveta
author list: Agent
  family name: Jarmukhanov
  given name: Zharkyn
author list: Agent
  family name: Nurgozhina
  given name: Ayaulym
author list: Agent
  family name: Sergazy
  given name: Shynggys
author list: Agent
  family name: Kozhabergen
  given name: Nuray
author list: Agent
  family name: Akhmetova
  given name: Zhanar
author list: Agent
  family name: Meiramova
  given name: Assel
author list: Agent
  family name: Chulenbayeva
  given name: Laura
author list: Agent
  family name: Ibrayeva
  given name: Aigerim
author list: Agent
  family name: Mukhanbetzhanov
  given name: Nurislam
author list: Agent
  family name: Mukhanbetzhanova
  given name: Zhanel
author list: Agent
  family name: Kozhakhmetov
  given name: Samat
author list: Agent
  family name: Ainabekova
  given name: Bayan
author list: Agent
  family name: Kushugulova
  given name: Almagul
doi: 10.7717/peerj.17477
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-11
copyright: © 2024 Nurgaziyev et al.
attribution name: Nurgaziyev et al.

Early-life diet does not affect preference for fish in herring gulls (Larus argentatus)
type: item
type: AcademicArticle
description: Urban populations of herring gulls (Larus argentatus) are increasing and causing human-wildlife conflict by exploiting anthropogenic resources. Gulls that breed in urban areas rely on varying amounts of terrestrial anthropogenic foods (e.g., domestic refuse, agricultural and commercial waste) to feed themselves. However, with the onset of hatching, many parent gulls switch to sourcing more marine than anthropogenic or terrestrial foods to provision their chicks. Although anthropogenic foods may meet chick calorific requirements for growth and development, some such foods (e.g., bread) may have lower levels of protein and other key nutrients compared to marine foods. However, whether this parental switch in chick diet is driven by chicks’ preference for marine foods, or whether chicks’ food preferences are shaped by the food types provisioned by their parents, remains untested. This study tests whether chick food preferences can be influenced by their provisioned diet by experimentally manipulating the ratio of time for which anthropogenic and marine foods were available (80:20 and vice versa) in the rearing diets of two treatment groups of rescued herring gull chicks. Each diet was randomly assigned to each of the 27 captive-reared chicks for the duration of the study. We tested chicks’ individual food preferences throughout their development in captivity using food arrays with four food choices (fish, cat food, mussels and brown bread). Regardless of the dietary treatment group, we found that all chicks preferred fish and almost all refused to eat most of the bread offered. Our findings suggest that early-life diet, manipulated by the ratio of time the different foods were available, did not influence gull chicks’ food preferences. Instead, chicks developed a strong and persistent preference for marine foods, which appears to match adult gulls’ dietary switch to marine foods upon chick hatching and may reinforce the provisioning of marine foods during chick develop…
format: application/pdf
format: text/html
creator: Emma Inzani
creator: Laura Kelley
creator: Robert Thomas
creator: Neeltje J. Boogert
subject: Animal Behavior
subject: Conservation Biology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.17565
publisher: PeerJ Inc.
rights: © 2024 Inzani et al.
abstract: Urban populations of herring gulls (Larus argentatus) are increasing and causing human-wildlife conflict by exploiting anthropogenic resources. Gulls that breed in urban areas rely on varying amounts of terrestrial anthropogenic foods (e.g., domestic refuse, agricultural and commercial waste) to feed themselves. However, with the onset of hatching, many parent gulls switch to sourcing more marine than anthropogenic or terrestrial foods to provision their chicks. Although anthropogenic foods may meet chick calorific requirements for growth and development, some such foods (e.g., bread) may have lower levels of protein and other key nutrients compared to marine foods. However, whether this parental switch in chick diet is driven by chicks’ preference for marine foods, or whether chicks’ food preferences are shaped by the food types provisioned by their parents, remains untested. This study tests whether chick food preferences can be influenced by their provisioned diet by experimentally manipulating the ratio of time for which anthropogenic and marine foods were available (80:20 and vice versa) in the rearing diets of two treatment groups of rescued herring gull chicks. Each diet was randomly assigned to each of the 27 captive-reared chicks for the duration of the study. We tested chicks’ individual food preferences throughout their development in captivity using food arrays with four food choices (fish, cat food, mussels and brown bread). Regardless of the dietary treatment group, we found that all chicks preferred fish and almost all refused to eat most of the bread offered. Our findings suggest that early-life diet, manipulated by the ratio of time the different foods were available, did not influence gull chicks’ food preferences. Instead, chicks developed a strong and persistent preference for marine foods, which appears to match adult gulls’ dietary switch to marine foods upon chick hatching and may reinforce the provisioning of marine foods during chick develop…
bibliographic citation: Inzani et al. (2024) Early-life diet does not affect preference for fish in herring gulls (Larus argentatus). PeerJ 12:e17565 https://doi.org/10.7717/peerj.17565
date submitted: 2023-12-22
date accepted: 2024-05-22
issued: 2024-07-11
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Inzani
  given name: Emma
author list: Agent
  family name: Kelley
  given name: Laura
author list: Agent
  family name: Thomas
  given name: Robert
author list: Agent
  family name: Boogert
  given name: Neeltje J.
doi: 10.7717/peerj.17565
volume: 12
issn: 2167-8359
publication name: PeerJ
publication date: 2024-07-11
copyright: © 2024 Inzani et al.
attribution name: Inzani et al.

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