PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Response of soil extracellular enzyme activity and stoichiometry to short-term warming and phosphorus addition in desert steppe
items: Similarities and differences in the microbial structure of surface soils of different vegetation types
items: Association between sports expertise and visual attention in male and female soccer players
items: Tissue-specific expression of senescence biomarkers in spontaneously hypertensive rats: evidence of premature aging in hypertension
items: A systematic review on physical mutagens in rice breeding in Southeast Asia
items: Contact-independent exposure to Rhodococcus rhodochrous DAP96253 volatiles does not improve the survival rate of Myotis lucifugus (little brown bats) affected by White-nose Syndrome
items: Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding
items: Delineating the calling pattern of Oecanthus indicus from native and non-native plant species
items: The effects of anthropogenic disturbance and seasonality on the ant communities of Lang Tengah Island
items: Effects of nanoscale zinc oxide treatment on growth, rhizosphere microbiota, and metabolism of Aconitum carmichaelii

Response of soil extracellular enzyme activity and stoichiometry to short-term warming and phosphorus addition in desert steppe
type: item
type: AcademicArticle
description: Background Phosphorus (P) is regarded as one of the major limiting factors in grassland ecosystems. Soil available phosphorus deficiency could affect soil extracellular enzyme activity, which is essential for microbial metabolism. Yet it is still unclear how soil available phosphorus affects soil extracellular enzyme activity and microbial nutrient limitation of desert steppe in the context of climate warming. Methods This study carried out a short-term open-top chambers (OTCs) experiment in a desert steppe to examine the effects of warming, P addition, and their interaction on soil properties, the activities of soil extracellular enzymes, and stoichiometries. Results The findings demonstrated that soil acquisition enzyme stoichiometry of C: N: P was 1.2:1:1.5 in this experiment region, which deviated from the global mean scale (1:1:1). Warming increased soil AN (ammonium nitrogen and nitrate nitrogen) contents and decreased microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Phosphorus addition raised soil available phosphorus and microbial biomass phosphorus (MBP) contents. Soil extracellular enzyme activities and stoichiometries in desert steppe are largely impacted by soil AN, MBC: MBP, and MBN: MBP. These results revealed that the changes of soil available nutrients and stoichiometries induced by short-term warming and P addition could influence soil microbial activities and alleviate soil microbial carbon and phosphorus limitation. Our findings highlight that soil available phosphorus played a critical role in regulating soil extracellular enzyme activity and microbial nutrient limitation of desert steppe. Further research on soil microbial communities should explore the microbiological mechanisms underlying these findings.
format: application/pdf
format: text/html
creator: Lingxia Feng
creator: Bing Cao
creator: Xiaojia Wang
subject: Agricultural Science
subject: Ecology
subject: Soil Science
subject: Biogeochemistry
description: doi:10.7717/peerj.16227
publisher: PeerJ Inc.
rights: © 2023 Feng et al.
abstract: Background Phosphorus (P) is regarded as one of the major limiting factors in grassland ecosystems. Soil available phosphorus deficiency could affect soil extracellular enzyme activity, which is essential for microbial metabolism. Yet it is still unclear how soil available phosphorus affects soil extracellular enzyme activity and microbial nutrient limitation of desert steppe in the context of climate warming. Methods This study carried out a short-term open-top chambers (OTCs) experiment in a desert steppe to examine the effects of warming, P addition, and their interaction on soil properties, the activities of soil extracellular enzymes, and stoichiometries. Results The findings demonstrated that soil acquisition enzyme stoichiometry of C: N: P was 1.2:1:1.5 in this experiment region, which deviated from the global mean scale (1:1:1). Warming increased soil AN (ammonium nitrogen and nitrate nitrogen) contents and decreased microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN). Phosphorus addition raised soil available phosphorus and microbial biomass phosphorus (MBP) contents. Soil extracellular enzyme activities and stoichiometries in desert steppe are largely impacted by soil AN, MBC: MBP, and MBN: MBP. These results revealed that the changes of soil available nutrients and stoichiometries induced by short-term warming and P addition could influence soil microbial activities and alleviate soil microbial carbon and phosphorus limitation. Our findings highlight that soil available phosphorus played a critical role in regulating soil extracellular enzyme activity and microbial nutrient limitation of desert steppe. Further research on soil microbial communities should explore the microbiological mechanisms underlying these findings.
bibliographic citation: Feng et al. (2023) Response of soil extracellular enzyme activity and stoichiometry to short-term warming and phosphorus addition in desert steppe. PeerJ 11:e16227 https://doi.org/10.7717/peerj.16227
date submitted: 2023-04-11
date accepted: 2023-09-12
issued: 2023-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Feng
  given name: Lingxia
author list: Agent
  family name: Cao
  given name: Bing
author list: Agent
  family name: Wang
  given name: Xiaojia
doi: 10.7717/peerj.16227
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-19
copyright: ©2023 Feng et al.
attribution name: Feng et al.

Similarities and differences in the microbial structure of surface soils of different vegetation types
type: item
type: AcademicArticle
description: Background Soil microbial community diversity serves as a highly sensitive indicator for assessing the response of terrestrial ecosystems to various changes, and it holds significant ecological relevance in terms of indicating ecological alterations. At the global scale, vegetation type acts as a major driving force behind the diversity of soil microbial communities, encompassing both bacterial and fungal components. Modifications in vegetation type not only induce transformations in the visual appearance of land, but also influence the soil ecosystem’s material cycle and energy flow, resulting in substantial impacts on the composition and performance of soil microbes. Methods In order to examine the disparities in the structure and diversity of soil microbial communities across distinct vegetation types, we opted to utilize sample plots representing four specific vegetation types. These included a woodland with the dominant tree species Drypetes perreticulata, a woodland with the dominant tree species Horsfieldia hainanensis, a Zea mays farmland and a Citrus reticulata fields. Through the application of high-throughput sequencing, the 16S V3_V4 region of soil bacteria and the ITS region of fungi were sequenced in this experiment. Subsequently, a comparative analysis was conducted to explore and assess the structure and dissimilarities of soil bacterial and fungal communities of the four vegetation types were analyzed comparatively. Results Our findings indicated that woodland soil exhibit a higher richness of microbial diversity compared to farmland soils. There were significant differences between woodland and farmland soil microbial community composition. However, all four dominant phyla of soil fungi were Ascomycota across the four vegetation types, but the bacterial dominant phyla were different in the two-farmland soil microbial communities with the highest similarity. Furthermore, we established a significant correlation between the nutrient content of differ…
format: application/pdf
format: text/html
creator: Yong Jiang
creator: Wenxu Zhu
creator: Keye Zhu
creator: Yang Ge
creator: Wuzheng Li
creator: Nanyan Liao
subject: Microbiology
subject: Molecular Biology
subject: Soil Science
subject: Forestry
description: doi:10.7717/peerj.16260
publisher: PeerJ Inc.
rights: © 2023 Jiang et al.
abstract: Background Soil microbial community diversity serves as a highly sensitive indicator for assessing the response of terrestrial ecosystems to various changes, and it holds significant ecological relevance in terms of indicating ecological alterations. At the global scale, vegetation type acts as a major driving force behind the diversity of soil microbial communities, encompassing both bacterial and fungal components. Modifications in vegetation type not only induce transformations in the visual appearance of land, but also influence the soil ecosystem’s material cycle and energy flow, resulting in substantial impacts on the composition and performance of soil microbes. Methods In order to examine the disparities in the structure and diversity of soil microbial communities across distinct vegetation types, we opted to utilize sample plots representing four specific vegetation types. These included a woodland with the dominant tree species Drypetes perreticulata, a woodland with the dominant tree species Horsfieldia hainanensis, a Zea mays farmland and a Citrus reticulata fields. Through the application of high-throughput sequencing, the 16S V3_V4 region of soil bacteria and the ITS region of fungi were sequenced in this experiment. Subsequently, a comparative analysis was conducted to explore and assess the structure and dissimilarities of soil bacterial and fungal communities of the four vegetation types were analyzed comparatively. Results Our findings indicated that woodland soil exhibit a higher richness of microbial diversity compared to farmland soils. There were significant differences between woodland and farmland soil microbial community composition. However, all four dominant phyla of soil fungi were Ascomycota across the four vegetation types, but the bacterial dominant phyla were different in the two-farmland soil microbial communities with the highest similarity. Furthermore, we established a significant correlation between the nutrient content of differ…
bibliographic citation: Jiang et al. (2023) Similarities and differences in the microbial structure of surface soils of different vegetation types. PeerJ 11:e16260 https://doi.org/10.7717/peerj.16260
date submitted: 2023-06-21
date accepted: 2023-09-18
issued: 2023-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jiang
  given name: Yong
author list: Agent
  family name: Zhu
  given name: Wenxu
author list: Agent
  family name: Zhu
  given name: Keye
author list: Agent
  family name: Ge
  given name: Yang
author list: Agent
  family name: Li
  given name: Wuzheng
author list: Agent
  family name: Liao
  given name: Nanyan
doi: 10.7717/peerj.16260
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-19
copyright: ©2023 Jiang et al.
attribution name: Jiang et al.

Association between sports expertise and visual attention in male and female soccer players
type: item
type: AcademicArticle
description: Background Visual attention plays a crucial role in daily living and in sports, affecting an athlete’s performance and thus, potentially, the outcome of a match. However, studies assessing the association between the level of sports expertise and visual attention have yielded mixed results. This study was conducted to examine whether visual attention could be developed with increased sports expertise, and whether visual attention differed between male athletes and female athletes. Methods A total of 128 participants were included in this study: 64 first-level national soccer athletes recruited from college soccer teams (considered elite athletes; 32 men and 32 women with similar soccer performance requirements and training experience), and 64 physical education college students with limited soccer experience (considered novice athletes; 32 men and 32 women with matched soccer experience). To assess visual attention, we used a multiple object tracking (MOT) task with four targets among a total of 10 objects moving at a fixed speed of 10°/s in random directions across a computer monitor screen. Tracking accuracy on the MOT task was calculated for each participant as the proportion of correctly selected targets. A univariate analysis of variance was performed, with group (expert, novice) and sex (male, female) as independent variables, and tracking accuracy on the MOT task as the dependent variable to assess whether sports expertise or sex influenced visual attention. Simple effects tests followed by comparisons with Bonferroni corrections were used, and effect size calculations were performed using Cohen’s f statistic. Results Tracking accuracy on the MOT task was significantly affected by sports expertise (F(1,124) = 91.732, p < 0.001, ηP2 = 0.425), with accuracy among expert soccer athletes superior to that among novice soccer athletes. Moreover, a statistically significant interaction between sports expertise and sex was detected (F(1,124) = 7.046, p = 0.009, η P2=…
format: application/pdf
format: text/html
creator: Peng Jin
creator: Zheqi Ji
creator: Tianyi Wang
creator: Xiaomin Zhu
subject: Psychiatry and Psychology
description: doi:10.7717/peerj.16286
publisher: PeerJ Inc.
rights: © 2023 Jin et al.
abstract: Background Visual attention plays a crucial role in daily living and in sports, affecting an athlete’s performance and thus, potentially, the outcome of a match. However, studies assessing the association between the level of sports expertise and visual attention have yielded mixed results. This study was conducted to examine whether visual attention could be developed with increased sports expertise, and whether visual attention differed between male athletes and female athletes. Methods A total of 128 participants were included in this study: 64 first-level national soccer athletes recruited from college soccer teams (considered elite athletes; 32 men and 32 women with similar soccer performance requirements and training experience), and 64 physical education college students with limited soccer experience (considered novice athletes; 32 men and 32 women with matched soccer experience). To assess visual attention, we used a multiple object tracking (MOT) task with four targets among a total of 10 objects moving at a fixed speed of 10°/s in random directions across a computer monitor screen. Tracking accuracy on the MOT task was calculated for each participant as the proportion of correctly selected targets. A univariate analysis of variance was performed, with group (expert, novice) and sex (male, female) as independent variables, and tracking accuracy on the MOT task as the dependent variable to assess whether sports expertise or sex influenced visual attention. Simple effects tests followed by comparisons with Bonferroni corrections were used, and effect size calculations were performed using Cohen’s f statistic. Results Tracking accuracy on the MOT task was significantly affected by sports expertise (F(1,124) = 91.732, p < 0.001, ηP2 = 0.425), with accuracy among expert soccer athletes superior to that among novice soccer athletes. Moreover, a statistically significant interaction between sports expertise and sex was detected (F(1,124) = 7.046, p = 0.009, η P2=…
bibliographic citation: Jin et al. (2023) Association between sports expertise and visual attention in male and female soccer players. PeerJ 11:e16286 https://doi.org/10.7717/peerj.16286
date submitted: 2023-08-02
date accepted: 2023-09-21
issued: 2023-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jin
  given name: Peng
author list: Agent
  family name: Ji
  given name: Zheqi
author list: Agent
  family name: Wang
  given name: Tianyi
author list: Agent
  family name: Zhu
  given name: Xiaomin
doi: 10.7717/peerj.16286
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-19
copyright: ©2023 Jin et al.
attribution name: Jin et al.

Tissue-specific expression of senescence biomarkers in spontaneously hypertensive rats: evidence of premature aging in hypertension
type: item
type: AcademicArticle
description: Background Cellular senescence is an age-related physiological process that contributes to tissue dysfunction and accelerated onset of chronic metabolic diseases including hypertension. Indeed, elevation of blood pressure in hypertension coincides with premature vascular aging and dysfunction. In addition, onsets of metabolic disturbance and osteopenia in patients with hypertension have also been reported. It is possible that hypertension enhances premature aging and causes progressive loss of function in multiple organs. However, the landscape of cellular senescence in critical tissues affected by hypertension remains elusive. Materials and Methods Heart, liver, bone, hypothalamus, and kidney were collected from spontaneously hypertensive rats (SHR) and age- and sex-matched normotensive Wistar rats (WT) at 6, 12, 24 and 36 weeks of age (n = 10 animals/group). Changes in mRNA levels of senescence biomarkers namely cyclin-dependent kinase (CDK) inhibitors (CDKIs), i.e., Cdkn2a (encoding p16Ink4a) and Cdkn1a (encoding p21cip1) as well as senescence-associated secretory phenotypes (SASPs), i.e., Timp1, Mmp12, Il6 and Cxcl1, were determined. Additionally, bone collagen alignment and hydroxy apatite crystal dimensions were determined by synchrotron radiation small- and wide-angle X-ray scattering (SAXS/WAXS) techniques. Results Real-time PCR revealed that transcript levels of genes encoding CDKIs and SASPs in the heart and liver were upregulated in SHR from 6 to 36 weeks of age. Expression of Timp1 and Cxcl1 was increased in bone tissues isolated from 36-week-old SHR. In contrast, we found that expression levels of Timp1 and Il6 mRNA were decreased in hypothalamus and kidney of SHR in all age groups. Simultaneous SAXS/WAXS analysis also revealed misalignment of bone collagen fibers in SHR as compared to WT. Conclusion Premature aging was identified in an organ directly affected by high blood pressure (i.e., heart) and those with known functional defects in SHR (i.e., liv…
format: application/pdf
format: text/html
creator: Ratthapon Somsura
creator: Kanokwan Kamkajon
creator: Khuanjit Chaimongkolnukul
creator: Surachai Chantip
creator: Jarinthorn Teerapornpuntakit
creator: Kannikar Wongdee
creator: Nuntaporn Kamonsutthipaijit
creator: Suwimol Tangtrongsup
creator: Nattapon Panupinthu
creator: Wacharaporn Tiyasatkulkovit
creator: Narattaphol Charoenphandhu
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Cardiology
subject: Metabolic Sciences
description: doi:10.7717/peerj.16300
publisher: PeerJ Inc.
rights: © 2023 Somsura et al.
abstract: Background Cellular senescence is an age-related physiological process that contributes to tissue dysfunction and accelerated onset of chronic metabolic diseases including hypertension. Indeed, elevation of blood pressure in hypertension coincides with premature vascular aging and dysfunction. In addition, onsets of metabolic disturbance and osteopenia in patients with hypertension have also been reported. It is possible that hypertension enhances premature aging and causes progressive loss of function in multiple organs. However, the landscape of cellular senescence in critical tissues affected by hypertension remains elusive. Materials and Methods Heart, liver, bone, hypothalamus, and kidney were collected from spontaneously hypertensive rats (SHR) and age- and sex-matched normotensive Wistar rats (WT) at 6, 12, 24 and 36 weeks of age (n = 10 animals/group). Changes in mRNA levels of senescence biomarkers namely cyclin-dependent kinase (CDK) inhibitors (CDKIs), i.e., Cdkn2a (encoding p16Ink4a) and Cdkn1a (encoding p21cip1) as well as senescence-associated secretory phenotypes (SASPs), i.e., Timp1, Mmp12, Il6 and Cxcl1, were determined. Additionally, bone collagen alignment and hydroxy apatite crystal dimensions were determined by synchrotron radiation small- and wide-angle X-ray scattering (SAXS/WAXS) techniques. Results Real-time PCR revealed that transcript levels of genes encoding CDKIs and SASPs in the heart and liver were upregulated in SHR from 6 to 36 weeks of age. Expression of Timp1 and Cxcl1 was increased in bone tissues isolated from 36-week-old SHR. In contrast, we found that expression levels of Timp1 and Il6 mRNA were decreased in hypothalamus and kidney of SHR in all age groups. Simultaneous SAXS/WAXS analysis also revealed misalignment of bone collagen fibers in SHR as compared to WT. Conclusion Premature aging was identified in an organ directly affected by high blood pressure (i.e., heart) and those with known functional defects in SHR (i.e., liv…
bibliographic citation: Somsura et al. (2023) Tissue-specific expression of senescence biomarkers in spontaneously hypertensive rats: evidence of premature aging in hypertension. PeerJ 11:e16300 https://doi.org/10.7717/peerj.16300
date submitted: 2023-06-27
date accepted: 2023-09-25
issued: 2023-10-19
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Somsura
  given name: Ratthapon
author list: Agent
  family name: Kamkajon
  given name: Kanokwan
author list: Agent
  family name: Chaimongkolnukul
  given name: Khuanjit
author list: Agent
  family name: Chantip
  given name: Surachai
author list: Agent
  family name: Teerapornpuntakit
  given name: Jarinthorn
author list: Agent
  family name: Wongdee
  given name: Kannikar
author list: Agent
  family name: Kamonsutthipaijit
  given name: Nuntaporn
author list: Agent
  family name: Tangtrongsup
  given name: Suwimol
author list: Agent
  family name: Panupinthu
  given name: Nattapon
author list: Agent
  family name: Tiyasatkulkovit
  given name: Wacharaporn
author list: Agent
  family name: Charoenphandhu
  given name: Narattaphol
doi: 10.7717/peerj.16300
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-19
copyright: © 2023 Somsura et al.
attribution name: Somsura et al.

A systematic review on physical mutagens in rice breeding in Southeast Asia
type: item
type: AcademicArticle
description: In the 1920s, Lewis Stadler initiated the introduction of permanent improvements to the genetic makeup of irradiated plants. Since then, studies related to breeding mutations have grown, as efforts have been made to expand and improve crop productivity and quality. Stadler’s discovery began with x-rays on corn and barley and later extended to the use of gamma-rays, thermal, and fast neutrons in crops. Radiation has since been shown to be an effective and unique method for increasing the genetic variability of species, including rice. Numerous systematic reviews have been conducted on the impact of physical mutagens on the production and grain quality of rice in Southeast Asia. However, the existing literature still lacks information on the type of radiation used, the rice planting materials used, the dosage of physical mutagens, and the differences in mutated characteristics. Therefore, this article aims to review existing literature on the use of physical mutagens in rice crops in Southeast Asian countries. Guided by the PRISMA Statement review method, 28 primary studies were identified through a systematic review of the Scopus, Science Direct, Emerald Insight, Multidisciplinary Digital Publishing, and MDPI journal databases published between 2016 and 2020. The results show that 96% of the articles used seeds as planting materials, and 80% of the articles focused on gamma-rays as a source of physical mutagens. The optimal dosage of gamma-rays applied was around 100 to 250 Gy to improve plant development, abiotic stress, biochemical properties, and nutritional and industrial quality of rice.
format: application/pdf
format: text/html
creator: Rosina Baadu
creator: Khim Phin Chong
creator: Jualang Azlan Gansau
creator: Muhammad Rawi Mohamed Zin
creator: Jedol Dayou
subject: Agricultural Science
subject: Biophysics
subject: Biotechnology
subject: Plant Science
description: doi:10.7717/peerj.15682
publisher: PeerJ Inc.
rights: © 2023 Baadu et al.
abstract: In the 1920s, Lewis Stadler initiated the introduction of permanent improvements to the genetic makeup of irradiated plants. Since then, studies related to breeding mutations have grown, as efforts have been made to expand and improve crop productivity and quality. Stadler’s discovery began with x-rays on corn and barley and later extended to the use of gamma-rays, thermal, and fast neutrons in crops. Radiation has since been shown to be an effective and unique method for increasing the genetic variability of species, including rice. Numerous systematic reviews have been conducted on the impact of physical mutagens on the production and grain quality of rice in Southeast Asia. However, the existing literature still lacks information on the type of radiation used, the rice planting materials used, the dosage of physical mutagens, and the differences in mutated characteristics. Therefore, this article aims to review existing literature on the use of physical mutagens in rice crops in Southeast Asian countries. Guided by the PRISMA Statement review method, 28 primary studies were identified through a systematic review of the Scopus, Science Direct, Emerald Insight, Multidisciplinary Digital Publishing, and MDPI journal databases published between 2016 and 2020. The results show that 96% of the articles used seeds as planting materials, and 80% of the articles focused on gamma-rays as a source of physical mutagens. The optimal dosage of gamma-rays applied was around 100 to 250 Gy to improve plant development, abiotic stress, biochemical properties, and nutritional and industrial quality of rice.
bibliographic citation: Baadu et al. (2023) A systematic review on physical mutagens in rice breeding in Southeast Asia. PeerJ 11:e15682 https://doi.org/10.7717/peerj.15682
date submitted: 2022-09-07
date accepted: 2023-06-14
issued: 2023-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baadu
  given name: Rosina
author list: Agent
  family name: Chong
  given name: Khim Phin
author list: Agent
  family name: Gansau
  given name: Jualang Azlan
author list: Agent
  family name: Mohamed Zin
  given name: Muhammad Rawi
author list: Agent
  family name: Dayou
  given name: Jedol
doi: 10.7717/peerj.15682
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-18
copyright: © 2023 Baadu et al.
attribution name: Baadu et al.

Contact-independent exposure to Rhodococcus rhodochrous DAP96253 volatiles does not improve the survival rate of Myotis lucifugus (little brown bats) affected by White-nose Syndrome
type: item
type: AcademicArticle
description: Since the emergence of White-nose Syndrome, a fungal disease in bats, caused by Pseudogymnoascus destructans, hibernating populations of little brown bats (Myotis lucifugus) have declined by 70–90% within P. destructans positive hibernacula. To reduce the impact of White-nose Syndrome to North American little brown bat populations we evaluated if exposure to volatile organic compounds produced by induced cells from Rhodococcus rhodochrous strain DAP96253 could improve the overwinter survival of bats infected by P. destructans. Two simultaneous field treatment trials were conducted at natural hibernacula located in Rockcastle and Breckinridge counties, Kentucky, USA. A combined total of 120 little brown bats were randomly divided into control groups (n = 60) which were not exposed to volatile organic compounds and treatment groups (n = 60) which were exposed to volatile organic compounds produced by non-growth, fermented cell paste composed of R. rhodochrous strain DAP96253 cells. Cox proportional hazard models revealed a significant decreased survival at the Rockcastle field trial site but not the Breckinridge field site. At the Breckinridge hibernacula, overwinter survival for both treatment and control groups were 60%. At the Rockcastle hibernacula, Kaplan-Meier survival curves indicated significantly increased overwinter survival of bats in the control group (43% survived) compared to the treatment group (20% survived). Although complete inhibition of P. destructans by volatile organic compounds produced by induced R. rhodochrous strain DAP96253 cells was observed in vitro studies, our results suggest that these volatile organic compounds do not inhibit P. destructans in situ and may promote P. destructans growth.
format: application/pdf
format: text/html
creator: Sarah Hooper
creator: Sybill Amelon
subject: Conservation Biology
subject: Microbiology
subject: Mycology
subject: Veterinary Medicine
description: doi:10.7717/peerj.15782
publisher: PeerJ Inc.
rights: © 2023
abstract: Since the emergence of White-nose Syndrome, a fungal disease in bats, caused by Pseudogymnoascus destructans, hibernating populations of little brown bats (Myotis lucifugus) have declined by 70–90% within P. destructans positive hibernacula. To reduce the impact of White-nose Syndrome to North American little brown bat populations we evaluated if exposure to volatile organic compounds produced by induced cells from Rhodococcus rhodochrous strain DAP96253 could improve the overwinter survival of bats infected by P. destructans. Two simultaneous field treatment trials were conducted at natural hibernacula located in Rockcastle and Breckinridge counties, Kentucky, USA. A combined total of 120 little brown bats were randomly divided into control groups (n = 60) which were not exposed to volatile organic compounds and treatment groups (n = 60) which were exposed to volatile organic compounds produced by non-growth, fermented cell paste composed of R. rhodochrous strain DAP96253 cells. Cox proportional hazard models revealed a significant decreased survival at the Rockcastle field trial site but not the Breckinridge field site. At the Breckinridge hibernacula, overwinter survival for both treatment and control groups were 60%. At the Rockcastle hibernacula, Kaplan-Meier survival curves indicated significantly increased overwinter survival of bats in the control group (43% survived) compared to the treatment group (20% survived). Although complete inhibition of P. destructans by volatile organic compounds produced by induced R. rhodochrous strain DAP96253 cells was observed in vitro studies, our results suggest that these volatile organic compounds do not inhibit P. destructans in situ and may promote P. destructans growth.
bibliographic citation: Hooper et al. (2023) Contact-independent exposure to Rhodococcus rhodochrous DAP96253 volatiles does not improve the survival rate of Myotis lucifugus (little brown bats) affected by White-nose Syndrome. PeerJ 11:e15782 https://doi.org/10.7717/peerj.15782
date submitted: 2023-01-11
date accepted: 2023-07-03
issued: 2023-10-18
is part of: PeerJ
license: https://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Hooper
  given name: Sarah
author list: Agent
  family name: Amelon
  given name: Sybill
doi: 10.7717/peerj.15782
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-18

Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding
type: item
type: AcademicArticle
description: The 534 protein kinases encoded in the human genome constitute a large druggable class of proteins that include both well-studied and understudied “dark” members. Accurate prediction of dark kinase functions is a major bioinformatics challenge. Here, we employ a graph mining approach that uses the evolutionary and functional context encoded in knowledge graphs (KGs) to predict protein and pathway associations for understudied kinases. We propose a new scalable graph embedding approach, RegPattern2Vec, which employs regular pattern constrained random walks to sample diverse aspects of node context within a KG flexibly. RegPattern2Vec learns functional representations of kinases, interacting partners, post-translational modifications, pathways, cellular localization, and chemical interactions from a kinase-centric KG that integrates and conceptualizes data from curated heterogeneous data resources. By contextualizing information relevant to prediction, RegPattern2Vec improves accuracy and efficiency in comparison to other random walk-based graph embedding approaches. We show that the predictions produced by our model overlap with pathway enrichment data produced using experimentally validated Protein-Protein Interaction (PPI) data from both publicly available databases and experimental datasets not used in training. Our model also has the advantage of using the collected random walks as biological context to interpret the predicted protein-pathway associations. We provide high-confidence pathway predictions for 34 dark kinases and present three case studies in which analysis of meta-paths associated with the prediction enables biological interpretation. Overall, RegPattern2Vec efficiently samples multiple node types for link prediction on biological knowledge graphs and the predicted associations between understudied kinases, pseudokinases, and known pathways serve as a conceptual starting point for hypothesis generation and testing.
format: application/pdf
format: text/html
creator: Mariah V. Salcedo
creator: Nathan Gravel
creator: Abbas Keshavarzi
creator: Liang-Chin Huang
creator: Krzysztof J. Kochut
creator: Natarajan Kannan
subject: Biochemistry
subject: Bioinformatics
subject: Computational Science
subject: Data Mining and Machine Learning
subject: Data Science
description: doi:10.7717/peerj.15815
publisher: PeerJ Inc.
rights: © 2023 Salcedo et al.
abstract: The 534 protein kinases encoded in the human genome constitute a large druggable class of proteins that include both well-studied and understudied “dark” members. Accurate prediction of dark kinase functions is a major bioinformatics challenge. Here, we employ a graph mining approach that uses the evolutionary and functional context encoded in knowledge graphs (KGs) to predict protein and pathway associations for understudied kinases. We propose a new scalable graph embedding approach, RegPattern2Vec, which employs regular pattern constrained random walks to sample diverse aspects of node context within a KG flexibly. RegPattern2Vec learns functional representations of kinases, interacting partners, post-translational modifications, pathways, cellular localization, and chemical interactions from a kinase-centric KG that integrates and conceptualizes data from curated heterogeneous data resources. By contextualizing information relevant to prediction, RegPattern2Vec improves accuracy and efficiency in comparison to other random walk-based graph embedding approaches. We show that the predictions produced by our model overlap with pathway enrichment data produced using experimentally validated Protein-Protein Interaction (PPI) data from both publicly available databases and experimental datasets not used in training. Our model also has the advantage of using the collected random walks as biological context to interpret the predicted protein-pathway associations. We provide high-confidence pathway predictions for 34 dark kinases and present three case studies in which analysis of meta-paths associated with the prediction enables biological interpretation. Overall, RegPattern2Vec efficiently samples multiple node types for link prediction on biological knowledge graphs and the predicted associations between understudied kinases, pseudokinases, and known pathways serve as a conceptual starting point for hypothesis generation and testing.
bibliographic citation: Salcedo et al. (2023) Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding. PeerJ 11:e15815 https://doi.org/10.7717/peerj.15815
date submitted: 2023-01-24
date accepted: 2023-07-10
issued: 2023-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salcedo
  given name: Mariah V.
author list: Agent
  family name: Gravel
  given name: Nathan
author list: Agent
  family name: Keshavarzi
  given name: Abbas
author list: Agent
  family name: Huang
  given name: Liang-Chin
author list: Agent
  family name: Kochut
  given name: Krzysztof J.
author list: Agent
  family name: Kannan
  given name: Natarajan
doi: 10.7717/peerj.15815
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-18
copyright: ©2023 Salcedo et al.
attribution name: Salcedo et al.

Delineating the calling pattern of Oecanthus indicus from native and non-native plant species
type: item
type: AcademicArticle
description: The study attempted to understand the effect of the host plants on the call parameters of native tree cricket, Oecanthus indicus (Order: Orthoptera, Sub-order: Ensifera, Family: Gryllidae) while calling from native (Justicia adhatoda) and non-native host plant species (Lantana camara and Hyptis suaveolens). The study was conducted at four locations across India. Calls of O. indicus were recorded on these host plants in the field and spectral and temporal parameters of calls were analysed. The results suggested that the peak frequency varied among the two non-native plant species while the difference in temporal pattern between the native and non-native host plants was observed only in the syllable period. The study also quantified the choice of calling positions of insects from the three-host species. The native O. indicus chose non-native H. suaveolens leaves extensively as a preferable site to baffle (37%). Differences in the call parameters and choice of the host plant by insects may ultimately affect the preference and performance of insects on invasive plants. The study would aid in exploring the underlying evolutionary and ecological processes of adaptive success of insects on non-native plants.
format: application/pdf
format: text/html
creator: Anupam Sunny
creator: Purnima Singh
creator: Swati Diwakar
creator: Gyan Prakash Sharma
subject: Animal Behavior
subject: Ecology
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.16153
publisher: PeerJ Inc.
rights: © 2023 Sunny et al.
abstract: The study attempted to understand the effect of the host plants on the call parameters of native tree cricket, Oecanthus indicus (Order: Orthoptera, Sub-order: Ensifera, Family: Gryllidae) while calling from native (Justicia adhatoda) and non-native host plant species (Lantana camara and Hyptis suaveolens). The study was conducted at four locations across India. Calls of O. indicus were recorded on these host plants in the field and spectral and temporal parameters of calls were analysed. The results suggested that the peak frequency varied among the two non-native plant species while the difference in temporal pattern between the native and non-native host plants was observed only in the syllable period. The study also quantified the choice of calling positions of insects from the three-host species. The native O. indicus chose non-native H. suaveolens leaves extensively as a preferable site to baffle (37%). Differences in the call parameters and choice of the host plant by insects may ultimately affect the preference and performance of insects on invasive plants. The study would aid in exploring the underlying evolutionary and ecological processes of adaptive success of insects on non-native plants.
bibliographic citation: Sunny et al. (2023) Delineating the calling pattern of Oecanthus indicus from native and non-native plant species. PeerJ 11:e16153 https://doi.org/10.7717/peerj.16153
date submitted: 2023-03-14
date accepted: 2023-08-31
issued: 2023-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sunny
  given name: Anupam
author list: Agent
  family name: Singh
  given name: Purnima
author list: Agent
  family name: Diwakar
  given name: Swati
author list: Agent
  family name: Sharma
  given name: Gyan Prakash
doi: 10.7717/peerj.16153
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-18
copyright: © 2023 Sunny et al.
attribution name: Sunny et al.

The effects of anthropogenic disturbance and seasonality on the ant communities of Lang Tengah Island
type: item
type: AcademicArticle
description: Anthropogenic disturbances and seasonal changes significantly impact diversity and community composition of ants, but their effects are often intertwined. We investigated these drivers on Lang Tengah Island, a location with a pronounced monsoon season and three resorts that close during this period. We surveyed four sites, two disturbed and two undisturbed, before and after the monsoon season, using pitfall traps to sample epigaeic ant communities. Undisturbed habitats had higher species diversity, but both habitats (undisturbed and disturbed sites) have a high proportion of ants with characteristics of being encroached by generalist and invasive/tramp ant species. Post-monsoon sampling yielded an increase in species richness and diversity. Seasonal changes, such as monsoonal rains, can temporarily alter ant interactions and resource distribution, potentially maintaining diversity. Future studies should validate these findings for ant communities under similar pressures, using ant composition and functional roles for conservation and management purposes.
format: application/pdf
format: text/html
creator: Sze Huei Yek
creator: Taneswarry Sethu Pathy
creator: Deniece Yin Chia Yeo
creator: Jason Yew Seng Gan
subject: Biodiversity
subject: Conservation Biology
subject: Entomology
subject: Natural Resource Management
subject: Environmental Impacts
description: doi:10.7717/peerj.16157
publisher: PeerJ Inc.
rights: © 2023 Yek et al.
abstract: Anthropogenic disturbances and seasonal changes significantly impact diversity and community composition of ants, but their effects are often intertwined. We investigated these drivers on Lang Tengah Island, a location with a pronounced monsoon season and three resorts that close during this period. We surveyed four sites, two disturbed and two undisturbed, before and after the monsoon season, using pitfall traps to sample epigaeic ant communities. Undisturbed habitats had higher species diversity, but both habitats (undisturbed and disturbed sites) have a high proportion of ants with characteristics of being encroached by generalist and invasive/tramp ant species. Post-monsoon sampling yielded an increase in species richness and diversity. Seasonal changes, such as monsoonal rains, can temporarily alter ant interactions and resource distribution, potentially maintaining diversity. Future studies should validate these findings for ant communities under similar pressures, using ant composition and functional roles for conservation and management purposes.
bibliographic citation: Yek et al. (2023) The effects of anthropogenic disturbance and seasonality on the ant communities of Lang Tengah Island. PeerJ 11:e16157 https://doi.org/10.7717/peerj.16157
date submitted: 2023-03-10
date accepted: 2023-08-31
issued: 2023-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yek
  given name: Sze Huei
author list: Agent
  family name: Sethu Pathy
  given name: Taneswarry
author list: Agent
  family name: Yeo
  given name: Deniece Yin Chia
author list: Agent
  family name: Gan
  given name: Jason Yew Seng
doi: 10.7717/peerj.16157
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-18
copyright: ©2023 Yek et al.
attribution name: Yek et al.

Effects of nanoscale zinc oxide treatment on growth, rhizosphere microbiota, and metabolism of Aconitum carmichaelii
type: item
type: AcademicArticle
description: Trace elements play a crucial role in the growth and bioactive substance content of medicinal plants, but their utilization efficiency in soil is often low. In this study, soil and Aconitum carmichaelii samples were collected and measured from 22 different locations, followed by an analysis of the relationship between trace elements and the yield and alkaloid content of the plants. The results indicated a significant positive correlation between zinc, trace elements in the soil, and the yield and alkaloid content of A. carmichaelii. Subsequent treatment of A. carmichaelii with both bulk zinc oxide (ZnO) and zinc oxide nanoparticles (ZnO NPs) demonstrated that the use of ZnO NPs significantly enhanced plant growth and monoester-type alkaloid content. To elucidate the underlying mechanisms responsible for these effects, metabolomic analysis was performed, resulting in the identification of 38 differentially expressed metabolites in eight metabolic pathways between the two treatments. Additionally, significant differences were observed in the rhizosphere bacterial communities, with Bacteroidota and Actinobacteriota identified as valuable biomarkers for ZnO NP treatment. Covariation analysis further revealed significant correlations between specific microbial communities and metabolite expression levels. These findings provide compelling evidence that nanoscale zinc exhibits much higher utilization efficiency compared to traditional zinc fertilizer.
format: application/pdf
format: text/html
creator: Cun Chen
creator: Yu-yang Zhao
creator: Duo Wang
creator: Ying-hong Ren
creator: Hong-ling Liu
creator: Ye Tian
creator: Yue-fei Geng
creator: Ying-rui Tang
creator: Xing-fu Chen
subject: Agricultural Science
subject: Microbiology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.16177
publisher: PeerJ Inc.
rights: © 2023 Chen et al.
abstract: Trace elements play a crucial role in the growth and bioactive substance content of medicinal plants, but their utilization efficiency in soil is often low. In this study, soil and Aconitum carmichaelii samples were collected and measured from 22 different locations, followed by an analysis of the relationship between trace elements and the yield and alkaloid content of the plants. The results indicated a significant positive correlation between zinc, trace elements in the soil, and the yield and alkaloid content of A. carmichaelii. Subsequent treatment of A. carmichaelii with both bulk zinc oxide (ZnO) and zinc oxide nanoparticles (ZnO NPs) demonstrated that the use of ZnO NPs significantly enhanced plant growth and monoester-type alkaloid content. To elucidate the underlying mechanisms responsible for these effects, metabolomic analysis was performed, resulting in the identification of 38 differentially expressed metabolites in eight metabolic pathways between the two treatments. Additionally, significant differences were observed in the rhizosphere bacterial communities, with Bacteroidota and Actinobacteriota identified as valuable biomarkers for ZnO NP treatment. Covariation analysis further revealed significant correlations between specific microbial communities and metabolite expression levels. These findings provide compelling evidence that nanoscale zinc exhibits much higher utilization efficiency compared to traditional zinc fertilizer.
bibliographic citation: Chen et al. (2023) Effects of nanoscale zinc oxide treatment on growth, rhizosphere microbiota, and metabolism of Aconitum carmichaelii. PeerJ 11:e16177 https://doi.org/10.7717/peerj.16177
date submitted: 2023-07-10
date accepted: 2023-09-04
issued: 2023-10-18
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Cun
author list: Agent
  family name: Zhao
  given name: Yu-yang
author list: Agent
  family name: Wang
  given name: Duo
author list: Agent
  family name: Ren
  given name: Ying-hong
author list: Agent
  family name: Liu
  given name: Hong-ling
author list: Agent
  family name: Tian
  given name: Ye
author list: Agent
  family name: Geng
  given name: Yue-fei
author list: Agent
  family name: Tang
  given name: Ying-rui
author list: Agent
  family name: Chen
  given name: Xing-fu
doi: 10.7717/peerj.16177
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-10-18
copyright: ©2023 Chen et al.
attribution name: Chen et al.

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