PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A novel gene signature related to oxidative stress predicts the prognosis in clear cell renal cell carcinoma
items: Feeding ecology of the Terciopelo pit viper snake (Bothrops asper) in Ecuador
items: Occurrence of microplastics in freshwater gastropods from a tropical river U-Taphao, southern Thailand
items: Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves (Camellia sinensis) post-harvest
items: Heat stress does not induce wasting symptoms in the giant California sea cucumber (Apostichopus californicus)
items: Non-avian theropod phalanges from the marine Fox Hills Formation (Maastrichtian), western South Dakota, USA
items: Bioinformatic prediction of the molecular links between Alzheimer’s disease and diabetes mellitus
items: Effect of sulfur on pollen germination of Clemenules mandarin and Nova tangelo
items: Genomic relatedness and dissemination of blaNDM-5 among Acinetobacter baumannii isolated from hospital environments and clinical specimens in Thailand
items: Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data

A novel gene signature related to oxidative stress predicts the prognosis in clear cell renal cell carcinoma
type: item
type: AcademicArticle
description: Clear cell renal cell carcinoma (ccRCC) is considered to be related to the worse prognosis, which might in part be attributed to the early recurrence and metastasis, compared with other type of kidney cancer. Oxidative stress refers to an imbalance between production of oxidants and antioxidant defense. Accumulative studies have indicated that oxidative stress genes contribute to the tumor invasion, metastasis and drug sensitivity. However, the biological functions of oxidative stress genes in ccRCC remain largely unknown. In this study, we identified 1,399 oxidative stress genes from GeneCards with a relevance score ≥7. Data for analysis were accessed from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) database, and were utilized as training set and validation set respectively. Univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox were employed to construct a prognostic signature in ccRCC. Finally, a prognostic signature including four different oxidative stress genes was constructed from 1,399 genes, and its predictive performance was verified through Kaplan-Meier survival analysis and the receiver operating characteristic (ROC) curve. Interestingly, we found that there was significant correlation between the expression of oxidative stress genes and the immune infiltration and the sensitivity of tumor cells to chemotherapeutics. Moreover, the highest hazard ratio gene urocortin (UCN) was chosen for further study; some necessary vitro experiments proved that the UCN could promote the ability of ccRCC proliferation and migration and contribute to the degree of oxidative stress. In conclusion, it was promising to predict the prognosis of ccRCC through the four oxidative stress genes signature. UCN played oncogenic roles in ccRCC by influencing proliferation and oxidative stress pathway, which was expected to be the novel therapeutic target for ccRCC.
format: application/pdf
format: text/html
creator: Sheng Ma
creator: Yue Ge
creator: Zezhong Xiong
creator: Yanan Wang
creator: Le Li
creator: Zheng Chao
creator: Beining Li
creator: Junbiao Zhang
creator: Siquan Ma
creator: Jun Xiao
creator: Bo Liu
creator: Zhihua Wang
subject: Bioinformatics
subject: Cell Biology
subject: Oncology
subject: Urology
subject: Medical Genetics
description: doi:10.7717/peerj.14784
publisher: PeerJ Inc.
rights: © 2023 Ma et al.
abstract: Clear cell renal cell carcinoma (ccRCC) is considered to be related to the worse prognosis, which might in part be attributed to the early recurrence and metastasis, compared with other type of kidney cancer. Oxidative stress refers to an imbalance between production of oxidants and antioxidant defense. Accumulative studies have indicated that oxidative stress genes contribute to the tumor invasion, metastasis and drug sensitivity. However, the biological functions of oxidative stress genes in ccRCC remain largely unknown. In this study, we identified 1,399 oxidative stress genes from GeneCards with a relevance score ≥7. Data for analysis were accessed from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) database, and were utilized as training set and validation set respectively. Univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox were employed to construct a prognostic signature in ccRCC. Finally, a prognostic signature including four different oxidative stress genes was constructed from 1,399 genes, and its predictive performance was verified through Kaplan-Meier survival analysis and the receiver operating characteristic (ROC) curve. Interestingly, we found that there was significant correlation between the expression of oxidative stress genes and the immune infiltration and the sensitivity of tumor cells to chemotherapeutics. Moreover, the highest hazard ratio gene urocortin (UCN) was chosen for further study; some necessary vitro experiments proved that the UCN could promote the ability of ccRCC proliferation and migration and contribute to the degree of oxidative stress. In conclusion, it was promising to predict the prognosis of ccRCC through the four oxidative stress genes signature. UCN played oncogenic roles in ccRCC by influencing proliferation and oxidative stress pathway, which was expected to be the novel therapeutic target for ccRCC.
bibliographic citation: Ma et al. (2023) A novel gene signature related to oxidative stress predicts the prognosis in clear cell renal cell carcinoma. PeerJ 11:e14784 https://doi.org/10.7717/peerj.14784
date submitted: 2022-10-20
date accepted: 2023-01-03
issued: 2023-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ma
  given name: Sheng
author list: Agent
  family name: Ge
  given name: Yue
author list: Agent
  family name: Xiong
  given name: Zezhong
author list: Agent
  family name: Wang
  given name: Yanan
author list: Agent
  family name: Li
  given name: Le
author list: Agent
  family name: Chao
  given name: Zheng
author list: Agent
  family name: Li
  given name: Beining
author list: Agent
  family name: Zhang
  given name: Junbiao
author list: Agent
  family name: Ma
  given name: Siquan
author list: Agent
  family name: Xiao
  given name: Jun
author list: Agent
  family name: Liu
  given name: Bo
author list: Agent
  family name: Wang
  given name: Zhihua
doi: 10.7717/peerj.14784
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-08
copyright: ©2023 Ma et al.
attribution name: Ma et al.

Feeding ecology of the Terciopelo pit viper snake (Bothrops asper) in Ecuador
type: item
type: AcademicArticle
description: Thoroughly documenting prey items and diet composition is crucial for understanding a predator’s role in the ecosystem. In gape restricted predators, such as snakes, documenting and analyzing the type and size of the prey is important to interpret their ecological role. We describe the diet patterns of a species of venomous snake, the Terciopelo pit viper (Bothrops asper), from its Ecuadorian populations. Examining the gastrointestinal contents of museum specimens collected over an extensive area of the Pacific lowlands of Ecuador, we encountered 69 identifiable prey items from four major taxonomic groups (amphibians, centipedes, mammals, and reptiles). We evaluated the observed composition of prey to check for differences between sexes and size-classes. To complement our observations of the Terciopelo species complex throughout their distribution, we carried out a systematic literature review. Our data show an ontogenetic shift in diet, with a transition from more diverse diet in juveniles towards a mammal-specialized diet in adults, and distinct proportion of prey taxa between the sexes in the juvenile size class.
format: application/pdf
format: text/html
creator: Amaru Loaiza-Lange
creator: Diana Székely
creator: Omar Torres-Carvajal
creator: Nicolás Tinoco
creator: David Salazar-Valenzuela
creator: Paul Székely
subject: Animal Behavior
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.14817
publisher: PeerJ Inc.
rights: © 2023 Loaiza-Lange et al.
abstract: Thoroughly documenting prey items and diet composition is crucial for understanding a predator’s role in the ecosystem. In gape restricted predators, such as snakes, documenting and analyzing the type and size of the prey is important to interpret their ecological role. We describe the diet patterns of a species of venomous snake, the Terciopelo pit viper (Bothrops asper), from its Ecuadorian populations. Examining the gastrointestinal contents of museum specimens collected over an extensive area of the Pacific lowlands of Ecuador, we encountered 69 identifiable prey items from four major taxonomic groups (amphibians, centipedes, mammals, and reptiles). We evaluated the observed composition of prey to check for differences between sexes and size-classes. To complement our observations of the Terciopelo species complex throughout their distribution, we carried out a systematic literature review. Our data show an ontogenetic shift in diet, with a transition from more diverse diet in juveniles towards a mammal-specialized diet in adults, and distinct proportion of prey taxa between the sexes in the juvenile size class.
bibliographic citation: Loaiza-Lange et al. (2023) Feeding ecology of the Terciopelo pit viper snake (Bothrops asper) in Ecuador. PeerJ 11:e14817 https://doi.org/10.7717/peerj.14817
date submitted: 2022-06-14
date accepted: 2023-01-06
issued: 2023-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Loaiza-Lange
  given name: Amaru
author list: Agent
  family name: Székely
  given name: Diana
author list: Agent
  family name: Torres-Carvajal
  given name: Omar
author list: Agent
  family name: Tinoco
  given name: Nicolás
author list: Agent
  family name: Salazar-Valenzuela
  given name: David
author list: Agent
  family name: Székely
  given name: Paul
doi: 10.7717/peerj.14817
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-08
copyright: © 2023 Loaiza-Lange et al.
attribution name: Loaiza-Lange et al.

Occurrence of microplastics in freshwater gastropods from a tropical river U-Taphao, southern Thailand
type: item
type: AcademicArticle
description: Background Microplastics (MPs) are pollutants in rivers and marine environments. Rivers can be sources and sinks of MPs that enter the biota. Previous studies focusing on freshwater species are quite limited, especially for gastropods. Freshwater gastropods are essential to aquatic ecosystems because they are food to other aquatic animals, such as fish, shrimp, and crabs. They are a crucial link in the food chain between water resources and human food. Therefore, this study aimed to investigate MP accumulation in freshwater gastropods, commonly known as snails (Filopaludina sumatrensis speciosa and Pomacea canaliculata), in a river flowing into a shallow coastal lagoon. Method In this study, snail tissue samples were digested with 30% hydrogen peroxide. The mixture was heated at 60 °C for 24 h. MP particles were identified, counted, and characterized (shape, size, and color) by visual identification under a stereomicroscope. Furthermore, polymer-type identification was performed using Fourier transform infrared spectroscopy (FTIR). Analysis of variance (ANOVA) was applied for the statistical analysis. Results The MPs found were as follows: 4.76 particles/individual were found in F. sumatrensis speciosa upstream, 5.20 particles/individual were found in F. sumatrensis speciosa downstream, 7.28 particles/individual were found in P. canaliculata upstream, and 4.00 particles/individual were found in P. canaliculata downstream. It was found in the two-way ANOVA that the accumulation of MPs in gastropods was affected by species and study sites (upstream and downstream). There was a significant difference in the amount of MPs in P. canaliculata between upstream and downstream sites (p = 0.003). Fibers were the most common MPs in both species. Moreover, P. canaliculata upstream had the most significant amount of MPs. The smallest amount of MPs was recorded for P. canaliculata downstream, but there was great diversity in shape, size, and polymer type. MPs sized 500 μm–1 mm we…
format: application/pdf
format: text/html
creator: Preyanuch Jitkaew
creator: Siriporn Pradit
creator: Prakrit Noppradit
creator: Karnda Sengloyluan
creator: Mathinee Yucharoen
creator: Suvit Suwanno
creator: Varaporn Tanrattanakul
creator: Kittiwara Sornplang
creator: Thongchai Nitiratsuwan
subject: Ecology
subject: Zoology
subject: Freshwater Biology
subject: Aquatic and Marine Chemistry
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.14861
publisher: PeerJ Inc.
rights: © 2023 Jitkaew et al.
abstract: Background Microplastics (MPs) are pollutants in rivers and marine environments. Rivers can be sources and sinks of MPs that enter the biota. Previous studies focusing on freshwater species are quite limited, especially for gastropods. Freshwater gastropods are essential to aquatic ecosystems because they are food to other aquatic animals, such as fish, shrimp, and crabs. They are a crucial link in the food chain between water resources and human food. Therefore, this study aimed to investigate MP accumulation in freshwater gastropods, commonly known as snails (Filopaludina sumatrensis speciosa and Pomacea canaliculata), in a river flowing into a shallow coastal lagoon. Method In this study, snail tissue samples were digested with 30% hydrogen peroxide. The mixture was heated at 60 °C for 24 h. MP particles were identified, counted, and characterized (shape, size, and color) by visual identification under a stereomicroscope. Furthermore, polymer-type identification was performed using Fourier transform infrared spectroscopy (FTIR). Analysis of variance (ANOVA) was applied for the statistical analysis. Results The MPs found were as follows: 4.76 particles/individual were found in F. sumatrensis speciosa upstream, 5.20 particles/individual were found in F. sumatrensis speciosa downstream, 7.28 particles/individual were found in P. canaliculata upstream, and 4.00 particles/individual were found in P. canaliculata downstream. It was found in the two-way ANOVA that the accumulation of MPs in gastropods was affected by species and study sites (upstream and downstream). There was a significant difference in the amount of MPs in P. canaliculata between upstream and downstream sites (p = 0.003). Fibers were the most common MPs in both species. Moreover, P. canaliculata upstream had the most significant amount of MPs. The smallest amount of MPs was recorded for P. canaliculata downstream, but there was great diversity in shape, size, and polymer type. MPs sized 500 μm–1 mm we…
bibliographic citation: Jitkaew et al. (2023) Occurrence of microplastics in freshwater gastropods from a tropical river U-Taphao, southern Thailand. PeerJ 11:e14861 https://doi.org/10.7717/peerj.14861
date submitted: 2022-10-26
date accepted: 2023-01-17
issued: 2023-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Jitkaew
  given name: Preyanuch
author list: Agent
  family name: Pradit
  given name: Siriporn
author list: Agent
  family name: Noppradit
  given name: Prakrit
author list: Agent
  family name: Sengloyluan
  given name: Karnda
author list: Agent
  family name: Yucharoen
  given name: Mathinee
author list: Agent
  family name: Suwanno
  given name: Suvit
author list: Agent
  family name: Tanrattanakul
  given name: Varaporn
author list: Agent
  family name: Sornplang
  given name: Kittiwara
author list: Agent
  family name: Nitiratsuwan
  given name: Thongchai
doi: 10.7717/peerj.14861
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-08
copyright: © 2023 Jitkaew et al.
attribution name: Jitkaew et al.

Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves (Camellia sinensis) post-harvest
type: item
type: AcademicArticle
description: Sugar metabolites not only act as the key compounds in tea plant response to stress but are also critical for tea quality formation during the post-harvest processing of tea leaves. However, the mechanisms by which sugar metabolites in post-harvest tea leaves respond to mechanical stress are unclear. In this study, we aimed to investigate the effects of mechanical stress on saccharide metabolites and related post-harvest tea genes. Withered (C15) and mechanically-stressed (V15) for 15 min Oolong tea leaves were used for metabolome and transcriptome sequencing analyses. We identified a total of 19 sugar metabolites, most of which increased in C15 and V15. A total of 69 genes related to sugar metabolism were identified using transcriptome analysis, most of which were down-regulated in C15 and V15. To further understand the relationship between the down-regulated genes and sugar metabolites, we analyzed the sucrose and starch, galactose, and glycolysis metabolic pathways, and found that several key genes of invertase (INV), α-amylase (AMY), β-amylase (BMY), aldose 1-epimerase (AEP), and α-galactosidase (AGAL) were down-regulated. This inhibited the hydrolysis of sugars and might have contributed to the enrichment of galactose and D-mannose in V15. Additionally, galactinol synthase (Gols), raffinose synthase (RS), hexokinase (HXK), 6-phosphofructokinase 1 (PFK-1), and pyruvate kinase (PK) genes were significantly upregulated in V15, promoting the accumulation of D-fructose-6-phosphate (D-Fru-6P), D-glucose-6-phosphate (D-glu-6P), and D-glucose. Transcriptome and metabolome association analysis showed that the glycolysis pathway was enhanced and the hydrolysis rate of sugars related to hemicellulose synthesis slowed in response to mechanical stress. In this study, we explored the role of sugar in the response of post-harvest tea leaves to mechanical stress by analyzing differences in the expression of sugar metabolites and related genes. Our results improve the understan…
format: application/pdf
format: text/html
creator: Zhilong Hao
creator: Yanping Tan
creator: Jiao Feng
creator: Hongzheng Lin
creator: Zhilin Sun
creator: Jia Yun Zhuang
creator: Qianlian Chen
creator: Xinyi Jin
creator: Yun Sun
subject: Agricultural Science
subject: Food Science and Technology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.14869
publisher: PeerJ Inc.
rights: © 2023 Hao et al.
abstract: Sugar metabolites not only act as the key compounds in tea plant response to stress but are also critical for tea quality formation during the post-harvest processing of tea leaves. However, the mechanisms by which sugar metabolites in post-harvest tea leaves respond to mechanical stress are unclear. In this study, we aimed to investigate the effects of mechanical stress on saccharide metabolites and related post-harvest tea genes. Withered (C15) and mechanically-stressed (V15) for 15 min Oolong tea leaves were used for metabolome and transcriptome sequencing analyses. We identified a total of 19 sugar metabolites, most of which increased in C15 and V15. A total of 69 genes related to sugar metabolism were identified using transcriptome analysis, most of which were down-regulated in C15 and V15. To further understand the relationship between the down-regulated genes and sugar metabolites, we analyzed the sucrose and starch, galactose, and glycolysis metabolic pathways, and found that several key genes of invertase (INV), α-amylase (AMY), β-amylase (BMY), aldose 1-epimerase (AEP), and α-galactosidase (AGAL) were down-regulated. This inhibited the hydrolysis of sugars and might have contributed to the enrichment of galactose and D-mannose in V15. Additionally, galactinol synthase (Gols), raffinose synthase (RS), hexokinase (HXK), 6-phosphofructokinase 1 (PFK-1), and pyruvate kinase (PK) genes were significantly upregulated in V15, promoting the accumulation of D-fructose-6-phosphate (D-Fru-6P), D-glucose-6-phosphate (D-glu-6P), and D-glucose. Transcriptome and metabolome association analysis showed that the glycolysis pathway was enhanced and the hydrolysis rate of sugars related to hemicellulose synthesis slowed in response to mechanical stress. In this study, we explored the role of sugar in the response of post-harvest tea leaves to mechanical stress by analyzing differences in the expression of sugar metabolites and related genes. Our results improve the understan…
bibliographic citation: Hao et al. (2023) Integrated metabolomic and transcriptomic analysis reveal the effect of mechanical stress on sugar metabolism in tea leaves (Camellia sinensis) post-harvest. PeerJ 11:e14869 https://doi.org/10.7717/peerj.14869
date submitted: 2022-08-15
date accepted: 2023-01-18
issued: 2023-02-08
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hao
  given name: Zhilong
author list: Agent
  family name: Tan
  given name: Yanping
author list: Agent
  family name: Feng
  given name: Jiao
author list: Agent
  family name: Lin
  given name: Hongzheng
author list: Agent
  family name: Sun
  given name: Zhilin
author list: Agent
  family name: Zhuang
  given name: Jia Yun
author list: Agent
  family name: Chen
  given name: Qianlian
author list: Agent
  family name: Jin
  given name: Xinyi
author list: Agent
  family name: Sun
  given name: Yun
doi: 10.7717/peerj.14869
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-08
copyright: © 2023 Hao et al.
attribution name: Hao et al.

Heat stress does not induce wasting symptoms in the giant California sea cucumber (Apostichopus californicus)
type: item
type: AcademicArticle
description: Oceanic heatwaves have significant impacts on disease dynamics in marine ecosystems. Following an extreme heatwave in Nanoose Bay, British Columbia, Canada, a severe sea cucumber wasting event occurred that resulted in the mass mortality of Apostichopus californicus. Here, we sought to determine if heat stress in isolation could trigger wasting symptoms in A. californicus. We exposed sea cucumbers to (i) a simulated marine heatwave (22 °C), (ii) an elevated temperature treatment (17 °C), or (iii) control conditions (12 °C). We measured the presence of skin lesions, mortality, posture maintenance, antipredator defences, spawning, and organ evisceration during the 79-hour thermal exposure, as well as 7-days post-exposure. Both the 22 °C and 17 °C treatments elicited stress responses where individuals exhibited a reduced ability to maintain posture and an increase in stress spawning. The 22 °C heatwave was particularly stressful, as it was the only treatment where mortality was observed. However, none of the treatments induced wasting symptoms as observed in the Nanoose Bay event. This study provides evidence that sea cucumber wasting may not be triggered by heat stress in isolation, leaving the cause of the mass mortality event observed in Nanoose unknown.
format: application/pdf
format: text/html
creator: Declan Dawson Taylor
creator: Jonathan J. Farr
creator: Em G. Lim
creator: Jenna L. Fleet
creator: Sara J. Smith
creator: Daniel M. Wuitchik
subject: Ecology
subject: Marine Biology
subject: Zoology
description: doi:10.7717/peerj.14548
publisher: PeerJ Inc.
rights: © 2022 Dawson Taylor et al.
abstract: Oceanic heatwaves have significant impacts on disease dynamics in marine ecosystems. Following an extreme heatwave in Nanoose Bay, British Columbia, Canada, a severe sea cucumber wasting event occurred that resulted in the mass mortality of Apostichopus californicus. Here, we sought to determine if heat stress in isolation could trigger wasting symptoms in A. californicus. We exposed sea cucumbers to (i) a simulated marine heatwave (22 °C), (ii) an elevated temperature treatment (17 °C), or (iii) control conditions (12 °C). We measured the presence of skin lesions, mortality, posture maintenance, antipredator defences, spawning, and organ evisceration during the 79-hour thermal exposure, as well as 7-days post-exposure. Both the 22 °C and 17 °C treatments elicited stress responses where individuals exhibited a reduced ability to maintain posture and an increase in stress spawning. The 22 °C heatwave was particularly stressful, as it was the only treatment where mortality was observed. However, none of the treatments induced wasting symptoms as observed in the Nanoose Bay event. This study provides evidence that sea cucumber wasting may not be triggered by heat stress in isolation, leaving the cause of the mass mortality event observed in Nanoose unknown.
bibliographic citation: Dawson Taylor et al. (2023) Heat stress does not induce wasting symptoms in the giant California sea cucumber (Apostichopus californicus). PeerJ 11:e14548 https://doi.org/10.7717/peerj.14548
date submitted: 2022-06-10
date accepted: 2022-11-20
issued: 2023-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dawson Taylor
  given name: Declan
author list: Agent
  family name: Farr
  given name: Jonathan J.
author list: Agent
  family name: Lim
  given name: Em G.
author list: Agent
  family name: Fleet
  given name: Jenna L.
author list: Agent
  family name: Smith
  given name: Sara J.
author list: Agent
  family name: Wuitchik
  given name: Daniel M.
doi: 10.7717/peerj.14548
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-07
copyright: ©2022 Dawson Taylor et al.
attribution name: Dawson Taylor et al.

Non-avian theropod phalanges from the marine Fox Hills Formation (Maastrichtian), western South Dakota, USA
type: item
type: AcademicArticle
description: We report here the first dinosaur skeletal material described from the marine Fox Hills Formation (Maastrichtian) of western South Dakota. The find consists of two theropod pedal phalanges: one recovered from the middle part of the Fairpoint Member in Meade County, South Dakota; and the other from the Iron Lightning Member in Ziebach County, South Dakota. Comparison with pedal phalanges of other theropods suggests strongly that the Fairpoint specimen is a right pedal phalanx, possibly III-2, from a large ornithomimid. The Iron Lightning specimen we cautiously identify as an ornithomimid left pedal phalanx II-2. The Fairpoint bone comes from thinly bedded and cross-bedded marine sandstones containing large hematitic concretions and concretionary horizons. Associated fossils include osteichthyan teeth, fin spines and otoliths, and abundant teeth of common Cretaceous nearshore and pelagic chondrichthyans. Leaf impressions and other plant debris, blocks of fossilized wood, and Ophiomorpha burrows are also common. The Iron Lightning bone comes from a channel deposit composed of fine to coarse sandstone beds, some of which contain bivalves, and a disseminated assemblage of mammal teeth, chondrichthyan teeth, and fragmentary dinosaur teeth and claws. We interpret the depositional environment of the two specimens as marginal marine. The Fairpoint bone derives from a nearshore foreset setting, above wave base subject to tidal flux and storm activity. The Iron Lightning specimen comes from a topset channel infill probably related to deposition on a tidal flat or associated coastal setting. The taphonomic history and ages of the two bones differ. Orthogonal cracks in the cortical bone of the Fairpoint specimen suggest post-mortem desiccation in a dryland coastal setting prior to transport and preservation in the nearby nearshore setting described above. The pristine surface of the Iron Lightning specimen indicates little transport before incorporation into the channel deposit …
format: application/pdf
format: text/html
creator: John A. Chamberlain, Jr
creator: Katja Knoll
creator: Joseph J. W. Sertich
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.14665
publisher: PeerJ Inc.
rights: © 2023 Chamberlain, Jr et al.
abstract: We report here the first dinosaur skeletal material described from the marine Fox Hills Formation (Maastrichtian) of western South Dakota. The find consists of two theropod pedal phalanges: one recovered from the middle part of the Fairpoint Member in Meade County, South Dakota; and the other from the Iron Lightning Member in Ziebach County, South Dakota. Comparison with pedal phalanges of other theropods suggests strongly that the Fairpoint specimen is a right pedal phalanx, possibly III-2, from a large ornithomimid. The Iron Lightning specimen we cautiously identify as an ornithomimid left pedal phalanx II-2. The Fairpoint bone comes from thinly bedded and cross-bedded marine sandstones containing large hematitic concretions and concretionary horizons. Associated fossils include osteichthyan teeth, fin spines and otoliths, and abundant teeth of common Cretaceous nearshore and pelagic chondrichthyans. Leaf impressions and other plant debris, blocks of fossilized wood, and Ophiomorpha burrows are also common. The Iron Lightning bone comes from a channel deposit composed of fine to coarse sandstone beds, some of which contain bivalves, and a disseminated assemblage of mammal teeth, chondrichthyan teeth, and fragmentary dinosaur teeth and claws. We interpret the depositional environment of the two specimens as marginal marine. The Fairpoint bone derives from a nearshore foreset setting, above wave base subject to tidal flux and storm activity. The Iron Lightning specimen comes from a topset channel infill probably related to deposition on a tidal flat or associated coastal setting. The taphonomic history and ages of the two bones differ. Orthogonal cracks in the cortical bone of the Fairpoint specimen suggest post-mortem desiccation in a dryland coastal setting prior to transport and preservation in the nearby nearshore setting described above. The pristine surface of the Iron Lightning specimen indicates little transport before incorporation into the channel deposit …
bibliographic citation: Chamberlain, Jr et al. (2023) Non-avian theropod phalanges from the marine Fox Hills Formation (Maastrichtian), western South Dakota, USA. PeerJ 11:e14665 https://doi.org/10.7717/peerj.14665
date submitted: 2022-04-11
date accepted: 2022-12-09
issued: 2023-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chamberlain, Jr
  given name: John A.
author list: Agent
  family name: Knoll
  given name: Katja
author list: Agent
  family name: J. W. Sertich
  given name: Joseph
doi: 10.7717/peerj.14665
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-07
copyright: © 2023 Chamberlain, Jr et al.
attribution name: Chamberlain, Jr et al.

Bioinformatic prediction of the molecular links between Alzheimer’s disease and diabetes mellitus
type: item
type: AcademicArticle
description: Background Alzheimer’s disease (AD) and type 2 diabetes mellitus (DM2) are chronic degenerative diseases with complex molecular processes that are potentially interconnected. The aim of this work was to predict the potential molecular links between AD and DM2 from different sources of biological information. Materials and Methods In this work, data mining of nine databases (DisGeNET, Ensembl, OMIM, Protein Data Bank, The Human Protein Atlas, UniProt, Gene Expression Omnibus, Human Cell Atlas, and PubMed) was performed to identify gene and protein information that was shared in AD and DM2. Next, the information was mapped to human protein-protein interaction (PPI) networks based on experimental data using the STRING web platform. Then, gene ontology biological process (GOBP) and pathway analyses with EnrichR showed its specific and shared biological process and pathway deregulations. Finally, potential biomarkers and drug targets were predicted with the Metascape platform. Results A total of 1,551 genes shared in AD and DM2 were identified. The highest average degree of nodes within the PPI was for DM2 (average = 2.97), followed by AD (average degree = 2.35). GOBP for AD was related to specific transcriptional and translation genetic terms occurring in neurons cells. The GOBP and pathway information for the association AD-DM2 were linked mainly to bioenergetics and cytokine signaling. Within the AD-DM2 association, 10 hub proteins were identified, seven of which were predicted to be present in plasma and exhibit pharmacological interaction with monoclonal antibodies in use, anticancer drugs, and flavonoid derivatives. Conclusion Our data mining and analysis strategy showed that there are a plenty of biological information based on experiments that links AD and DM2, which could provide a rational guide to design further diagnosis and treatment for AD and DM2.
format: application/pdf
format: text/html
creator: Ricardo Castillo-Velázquez
creator: Flavio Martínez-Morales
creator: Julio E. Castañeda-Delgado
creator: Mariana H. García-Hernández
creator: Verónica Herrera-Mayorga
creator: Francisco A. Paredes-Sánchez
creator: Gildardo Rivera
creator: Bruno Rivas-Santiago
creator: Edgar E. Lara-Ramírez
subject: Bioinformatics
subject: Cognitive Disorders
subject: Diabetes and Endocrinology
subject: Neurology
subject: Metabolic Sciences
description: doi:10.7717/peerj.14738
publisher: PeerJ Inc.
rights: © 2023 Castillo-Velázquez et al.
abstract: Background Alzheimer’s disease (AD) and type 2 diabetes mellitus (DM2) are chronic degenerative diseases with complex molecular processes that are potentially interconnected. The aim of this work was to predict the potential molecular links between AD and DM2 from different sources of biological information. Materials and Methods In this work, data mining of nine databases (DisGeNET, Ensembl, OMIM, Protein Data Bank, The Human Protein Atlas, UniProt, Gene Expression Omnibus, Human Cell Atlas, and PubMed) was performed to identify gene and protein information that was shared in AD and DM2. Next, the information was mapped to human protein-protein interaction (PPI) networks based on experimental data using the STRING web platform. Then, gene ontology biological process (GOBP) and pathway analyses with EnrichR showed its specific and shared biological process and pathway deregulations. Finally, potential biomarkers and drug targets were predicted with the Metascape platform. Results A total of 1,551 genes shared in AD and DM2 were identified. The highest average degree of nodes within the PPI was for DM2 (average = 2.97), followed by AD (average degree = 2.35). GOBP for AD was related to specific transcriptional and translation genetic terms occurring in neurons cells. The GOBP and pathway information for the association AD-DM2 were linked mainly to bioenergetics and cytokine signaling. Within the AD-DM2 association, 10 hub proteins were identified, seven of which were predicted to be present in plasma and exhibit pharmacological interaction with monoclonal antibodies in use, anticancer drugs, and flavonoid derivatives. Conclusion Our data mining and analysis strategy showed that there are a plenty of biological information based on experiments that links AD and DM2, which could provide a rational guide to design further diagnosis and treatment for AD and DM2.
bibliographic citation: Castillo-Velázquez et al. (2023) Bioinformatic prediction of the molecular links between Alzheimer’s disease and diabetes mellitus. PeerJ 11:e14738 https://doi.org/10.7717/peerj.14738
date submitted: 2022-10-20
date accepted: 2022-12-22
issued: 2023-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Castillo-Velázquez
  given name: Ricardo
author list: Agent
  family name: Martínez-Morales
  given name: Flavio
author list: Agent
  family name: Castañeda-Delgado
  given name: Julio E.
author list: Agent
  family name: García-Hernández
  given name: Mariana H.
author list: Agent
  family name: Herrera-Mayorga
  given name: Verónica
author list: Agent
  family name: Paredes-Sánchez
  given name: Francisco A.
author list: Agent
  family name: Rivera
  given name: Gildardo
author list: Agent
  family name: Rivas-Santiago
  given name: Bruno
author list: Agent
  family name: Lara-Ramírez
  given name: Edgar E.
doi: 10.7717/peerj.14738
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-07
copyright: ©2023 Castillo-Velázquez et al.
attribution name: Castillo-Velázquez et al.

Effect of sulfur on pollen germination of Clemenules mandarin and Nova tangelo
type: item
type: AcademicArticle
description: This study aims to elucidate whether sulfur can inhibit citrus pollination by affecting pollen grains. For this, four sulfur-based products (inorganic sulfur, water dispersible granular sulfur, ammonium sulfate, copper sulfate) were tested to evaluate their effect on pollen germination and pollen tube growth of two citrus varieties: Clemenules mandarin (Citrus clementina) and Nova tangelo (Citrus clementina x [Citrus paradisi x Citrus reticulata]). Pollen grains were extracted from the flowers of these two varieties and subsequently placed in Petri dishes with modified BK (boron and potassium) germination medium with six concentrations of the sulfur-based products (0.2, 2, 20, 200, 2,000, 20,000 mg l−1). All the dishes were incubated and the pollen germination rate was calculated. All the sulfur products showed progressive pollen germination inhibition with a rising sulfur concentration. CTC50 (50% cytotoxicity inhibition) was around 20 mg l−1, with significant differences among treatments. Total pollen germination inhibition took place at 20,000 mg l−1. These results demonstrate that sulfur application can affect citrus pollination.
format: application/pdf
format: text/html
creator: Roberto Beltrán
creator: Nuria Cebrián
creator: Carlos Zornoza
creator: Francisco García Breijo
creator: José Reig Armiñana
creator: Alfonso Garmendia
creator: Hugo Merle
subject: Agricultural Science
subject: Plant Science
description: doi:10.7717/peerj.14775
publisher: PeerJ Inc.
rights: © 2023 Beltrán et al.
abstract: This study aims to elucidate whether sulfur can inhibit citrus pollination by affecting pollen grains. For this, four sulfur-based products (inorganic sulfur, water dispersible granular sulfur, ammonium sulfate, copper sulfate) were tested to evaluate their effect on pollen germination and pollen tube growth of two citrus varieties: Clemenules mandarin (Citrus clementina) and Nova tangelo (Citrus clementina x [Citrus paradisi x Citrus reticulata]). Pollen grains were extracted from the flowers of these two varieties and subsequently placed in Petri dishes with modified BK (boron and potassium) germination medium with six concentrations of the sulfur-based products (0.2, 2, 20, 200, 2,000, 20,000 mg l−1). All the dishes were incubated and the pollen germination rate was calculated. All the sulfur products showed progressive pollen germination inhibition with a rising sulfur concentration. CTC50 (50% cytotoxicity inhibition) was around 20 mg l−1, with significant differences among treatments. Total pollen germination inhibition took place at 20,000 mg l−1. These results demonstrate that sulfur application can affect citrus pollination.
bibliographic citation: Beltrán et al. (2023) Effect of sulfur on pollen germination of Clemenules mandarin and Nova tangelo. PeerJ 11:e14775 https://doi.org/10.7717/peerj.14775
date submitted: 2022-09-28
date accepted: 2023-01-03
issued: 2023-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Beltrán
  given name: Roberto
author list: Agent
  family name: Cebrián
  given name: Nuria
author list: Agent
  family name: Zornoza
  given name: Carlos
author list: Agent
  family name: García Breijo
  given name: Francisco
author list: Agent
  family name: Reig Armiñana
  given name: José
author list: Agent
  family name: Garmendia
  given name: Alfonso
author list: Agent
  family name: Merle
  given name: Hugo
doi: 10.7717/peerj.14775
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-07
copyright: © 2023 Beltrán et al.
attribution name: Beltrán et al.

Genomic relatedness and dissemination of blaNDM-5 among Acinetobacter baumannii isolated from hospital environments and clinical specimens in Thailand
type: item
type: AcademicArticle
description: Background Acinetobacter baumannii (A. baumannii) is an important cause of nosocomial infection, especially in intensive care units (ICUs). It has the propensity to tolerate various environments and multiple classes of antibiotics. Our study aimed to characterize the comparative genomes of A. baumannii from hospital environments and clinical isolates. Methods Clinical and environmental A. baumannii isolates were collected from a university hospital. Antibiotic susceptibility testing was performed, antibiotic resistance genes (ARGs) were characterized, and repetitive element palindromic-PCR (rep-PCR) typing was performed. Eight representative A. baumannii isolated from environmental and clinical samples from the same wards were selected for whole-genome sequencing (WGS) using the Illumina platform. Results A total of 106 A. baumannii isolates were obtained from 312 hospital environmental samples. A high percentage of samples with A. baumannii colonization were detected from AMBU bags (77.9%), followed by bedrails (66.7%) and suction tubes (66.7%). We found that 93.4% of the environmental isolates were multidrug-resistant A. baumannii (MDRAB), and 44.7% were extremely drug-resistant A. baumannii (XDRAB). blaOXA-23 blaNDM, and blaOXA-58 were present in 80.2%, 78.3%, and 0.9% of all isolates, respectively. Sixty-one A. baumannii isolates were collected from patient specimens in the same ward. Among all A. baumannii clinical isolates, MDRAB and XDRAB accounted for 82% and 55.7%, respectively. The most dominant ARGs identified was blaOXA-23 (80.3%), followed by blaNDM (55.7%). The genetic diversity of all isolates using rep-PCR could be divided into 33 genotypes. The genome size of eight A. baumannii ranged from 3.78–4.01 Mb. We found six of eight strains to be blaNDM-5-harboring A. baumannii. Mobile genetic elements (MGEs), such as integron1 (intl1), located upstream of blaNDM-5 were observed. The phylogenomic relationship of the core and pan genomes as well as the singl…
format: application/pdf
format: text/html
creator: Thawatchai Kitti
creator: Suphattra Manrueang
creator: Udomluk Leungtongkam
creator: Supat Khongfak
creator: Rapee Thummeepak
creator: Surat Wannalerdsakun
creator: Thanyasiri Jindayok
creator: Sutthirat Sitthisak
subject: Genomics
subject: Microbiology
subject: Epidemiology
subject: Infectious Diseases
description: doi:10.7717/peerj.14831
publisher: PeerJ Inc.
rights: © 2023 Kitti et al.
abstract: Background Acinetobacter baumannii (A. baumannii) is an important cause of nosocomial infection, especially in intensive care units (ICUs). It has the propensity to tolerate various environments and multiple classes of antibiotics. Our study aimed to characterize the comparative genomes of A. baumannii from hospital environments and clinical isolates. Methods Clinical and environmental A. baumannii isolates were collected from a university hospital. Antibiotic susceptibility testing was performed, antibiotic resistance genes (ARGs) were characterized, and repetitive element palindromic-PCR (rep-PCR) typing was performed. Eight representative A. baumannii isolated from environmental and clinical samples from the same wards were selected for whole-genome sequencing (WGS) using the Illumina platform. Results A total of 106 A. baumannii isolates were obtained from 312 hospital environmental samples. A high percentage of samples with A. baumannii colonization were detected from AMBU bags (77.9%), followed by bedrails (66.7%) and suction tubes (66.7%). We found that 93.4% of the environmental isolates were multidrug-resistant A. baumannii (MDRAB), and 44.7% were extremely drug-resistant A. baumannii (XDRAB). blaOXA-23 blaNDM, and blaOXA-58 were present in 80.2%, 78.3%, and 0.9% of all isolates, respectively. Sixty-one A. baumannii isolates were collected from patient specimens in the same ward. Among all A. baumannii clinical isolates, MDRAB and XDRAB accounted for 82% and 55.7%, respectively. The most dominant ARGs identified was blaOXA-23 (80.3%), followed by blaNDM (55.7%). The genetic diversity of all isolates using rep-PCR could be divided into 33 genotypes. The genome size of eight A. baumannii ranged from 3.78–4.01 Mb. We found six of eight strains to be blaNDM-5-harboring A. baumannii. Mobile genetic elements (MGEs), such as integron1 (intl1), located upstream of blaNDM-5 were observed. The phylogenomic relationship of the core and pan genomes as well as the singl…
bibliographic citation: Kitti et al. (2023) Genomic relatedness and dissemination of blaNDM-5 among Acinetobacter baumannii isolated from hospital environments and clinical specimens in Thailand. PeerJ 11:e14831 https://doi.org/10.7717/peerj.14831
date submitted: 2022-10-06
date accepted: 2023-01-09
issued: 2023-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kitti
  given name: Thawatchai
author list: Agent
  family name: Manrueang
  given name: Suphattra
author list: Agent
  family name: Leungtongkam
  given name: Udomluk
author list: Agent
  family name: Khongfak
  given name: Supat
author list: Agent
  family name: Thummeepak
  given name: Rapee
author list: Agent
  family name: Wannalerdsakun
  given name: Surat
author list: Agent
  family name: Jindayok
  given name: Thanyasiri
author list: Agent
  family name: Sitthisak
  given name: Sutthirat
doi: 10.7717/peerj.14831
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-07
copyright: © 2023 Kitti et al.
attribution name: Kitti et al.

Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data
type: item
type: AcademicArticle
description: Optimal control simulations of musculoskeletal models can be used to reconstruct motions measured with optical motion capture to estimate joint and muscle kinematics and kinetics. These simulations are mutually and dynamically consistent, in contrast to traditional inverse methods. Commonly, optimal control simulations are generated by tracking generalized coordinates in combination with ground reaction forces. The generalized coordinates are estimated from marker positions using, for example, inverse kinematics. Hence, inaccuracies in the estimated coordinates are tracked in the simulation. We developed an approach to reconstruct arbitrary motions, such as change of direction motions, using optimal control simulations of 3D full-body musculoskeletal models by directly tracking marker and ground reaction force data. For evaluation, we recorded three trials each of straight running, curved running, and a v-cut for 10 participants. We reconstructed the recordings with marker tracking simulations, coordinate tracking simulations, and inverse kinematics and dynamics. First, we analyzed the convergence of the simulations and found that the wall time increased three to four times when using marker tracking compared to coordinate tracking. Then, we compared the marker trajectories, ground reaction forces, pelvis translations, joint angles, and joint moments between the three reconstruction methods. Root mean squared deviations between measured and estimated marker positions were smallest for inverse kinematics (e.g., 7.6 ± 5.1 mm for v-cut). However, measurement noise and soft tissue artifacts are likely also tracked in inverse kinematics, meaning that this approach does not reflect a gold standard. Marker tracking simulations resulted in slightly higher root mean squared marker deviations (e.g., 9.5 ± 6.2 mm for v-cut) than inverse kinematics. In contrast, coordinate tracking resulted in deviations that were nearly twice as high (e.g., 16.8 ± 10.5 mm for v-cut). Joint ang…
format: application/pdf
format: text/html
creator: Marlies Nitschke
creator: Robert Marzilger
creator: Sigrid Leyendecker
creator: Bjoern M. Eskofier
creator: Anne D. Koelewijn
subject: Computational Biology
subject: Kinesiology
subject: Radiology and Medical Imaging
subject: Computational Science
subject: Biomechanics
description: doi:10.7717/peerj.14852
publisher: PeerJ Inc.
rights: © 2023 Nitschke et al.
abstract: Optimal control simulations of musculoskeletal models can be used to reconstruct motions measured with optical motion capture to estimate joint and muscle kinematics and kinetics. These simulations are mutually and dynamically consistent, in contrast to traditional inverse methods. Commonly, optimal control simulations are generated by tracking generalized coordinates in combination with ground reaction forces. The generalized coordinates are estimated from marker positions using, for example, inverse kinematics. Hence, inaccuracies in the estimated coordinates are tracked in the simulation. We developed an approach to reconstruct arbitrary motions, such as change of direction motions, using optimal control simulations of 3D full-body musculoskeletal models by directly tracking marker and ground reaction force data. For evaluation, we recorded three trials each of straight running, curved running, and a v-cut for 10 participants. We reconstructed the recordings with marker tracking simulations, coordinate tracking simulations, and inverse kinematics and dynamics. First, we analyzed the convergence of the simulations and found that the wall time increased three to four times when using marker tracking compared to coordinate tracking. Then, we compared the marker trajectories, ground reaction forces, pelvis translations, joint angles, and joint moments between the three reconstruction methods. Root mean squared deviations between measured and estimated marker positions were smallest for inverse kinematics (e.g., 7.6 ± 5.1 mm for v-cut). However, measurement noise and soft tissue artifacts are likely also tracked in inverse kinematics, meaning that this approach does not reflect a gold standard. Marker tracking simulations resulted in slightly higher root mean squared marker deviations (e.g., 9.5 ± 6.2 mm for v-cut) than inverse kinematics. In contrast, coordinate tracking resulted in deviations that were nearly twice as high (e.g., 16.8 ± 10.5 mm for v-cut). Joint ang…
bibliographic citation: Nitschke et al. (2023) Change the direction: 3D optimal control simulation by directly tracking marker and ground reaction force data. PeerJ 11:e14852 https://doi.org/10.7717/peerj.14852
date submitted: 2022-08-01
date accepted: 2023-01-13
issued: 2023-02-07
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nitschke
  given name: Marlies
author list: Agent
  family name: Marzilger
  given name: Robert
author list: Agent
  family name: Leyendecker
  given name: Sigrid
author list: Agent
  family name: Eskofier
  given name: Bjoern M.
author list: Agent
  family name: Koelewijn
  given name: Anne D.
doi: 10.7717/peerj.14852
volume: 11
issn: 2167-8359
publication name: PeerJ
publication date: 2023-02-07
copyright: © 2023 Nitschke et al.
attribution name: Nitschke et al.

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