PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships
items: Anti-fouling activity and toxicity of the Mediterranean alien sponge Paraleucilla magna Klautau, Monteiro & Borojevic, 2004 (Porifera, Calcarea)
items: The effect of postoperative oral antibiotic therapy on the incidence of postoperative endophthalmitis after phacoemulsification surgery in dogs: 368 eyes (1997–2010)
items: Mate-guarding duration is mainly influenced by the risk of sperm competition and not by female quality in a golden orb-weaver spider
items: Traumatic surfing injuries in New Zealand: a descriptive epidemiology study
items: Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance
items: Interplay between epigallocatechin-3-gallate and ionic strength during amyloid aggregation
items: Effects of grazing intensity on forage nutritive value of dominant grass species in Borana rangelands of Southern Ethiopia
items: A new vertebrate fauna from the Lower Cretaceous Holly Creek Formation of the Trinity Group, southwest Arkansas, USA
items: Development of a novel embryonic germline gene-related prognostic model of lung adenocarcinoma

Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships
type: item
type: AcademicArticle
description: Bruguiera is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of Bruguiera species are limited. Here, the complete chloroplast sequences of five Bruguiera species were sequenced and assembled using Illumina data. The chloroplast genomes of B. gymnorhiza, B. hainesii, B. cylindrica, B. parviflora and B. sexangula were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, B. gymnorhiza lost a rpl32 gene in the SSC region. In addition, a ndhF gene in B. parviflora straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among Bruguiera species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between B. cylindrica and B. hainesii as well as B. gymnorhiza and B. sexangula indicating close genetic relationships based on maternal inheritance. Notably, B. hainesii, which is considered a hybrid between B. gymnorhiza and B. cylindrica, appears to have inherited the chloroplast from B. cylindrica. Investigating the effects of selection events on shared protein-coding genes showed a positive selection in rps7 and rpl36 genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all Bruguiera species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in Bruguiera and other mangrove species.
format: application/pdf
format: text/html
creator: Panthita Ruang-areerate
creator: Wasitthee Kongkachana
creator: Chaiwat Naktang
creator: Chutima Sonthirod
creator: Nattapol Narong
creator: Nukoon Jomchai
creator: Pasin Maprasop
creator: Chatree Maknual
creator: Nawin Phormsin
creator: Jeremy R. Shearman
creator: Wirulda Pootakham
creator: Sithichoke Tangphatsornruang
subject: Genetics
subject: Genomics
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.12268
publisher: PeerJ Inc.
rights: © 2021 Ruang-areerate et al.
abstract: Bruguiera is a genus of true mangroves that are mostly distributed in the Indo-West Pacific region. However, the number of published whole chloroplast genome sequences of Bruguiera species are limited. Here, the complete chloroplast sequences of five Bruguiera species were sequenced and assembled using Illumina data. The chloroplast genomes of B. gymnorhiza, B. hainesii, B. cylindrica, B. parviflora and B. sexangula were assembled into 161,195, 164,295, 164,297, 163,228 and 164,170 bp, respectively. All chloroplast genomes contain 37 tRNA and eight rRNA genes, with either 84 or 85 protein-coding genes. A comparative analysis of these genomes revealed high similarity in gene structure, gene order and boundary position of the LSC, SSC and two IR regions. Interestingly, B. gymnorhiza lost a rpl32 gene in the SSC region. In addition, a ndhF gene in B. parviflora straddles both the SSC and IRB boundary regions. These genes reveal differences in chloroplast evolution among Bruguiera species. Repeats and SSRs in the chloroplast genome sequences were found to be highly conserved between B. cylindrica and B. hainesii as well as B. gymnorhiza and B. sexangula indicating close genetic relationships based on maternal inheritance. Notably, B. hainesii, which is considered a hybrid between B. gymnorhiza and B. cylindrica, appears to have inherited the chloroplast from B. cylindrica. Investigating the effects of selection events on shared protein-coding genes showed a positive selection in rps7 and rpl36 genes in all species compared to land-plant species. A phylogenetic analysis, based on 59 conserved chloroplast protein-coding genes, showed strong support that all Bruguiera species are in the clade Rhizophoraceae. This study provides valuable genetic information for the study of evolutionary relationships and population genetics in Bruguiera and other mangrove species.
bibliographic citation: Ruang-areerate et al. (2021) Complete chloroplast genome sequences of five Bruguiera species (Rhizophoraceae): comparative analysis and phylogenetic relationships. PeerJ 9:e12268 https://doi.org/10.7717/peerj.12268
date submitted: 2021-04-27
date accepted: 2021-09-16
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ruang-areerate
  given name: Panthita
author list: Agent
  family name: Kongkachana
  given name: Wasitthee
author list: Agent
  family name: Naktang
  given name: Chaiwat
author list: Agent
  family name: Sonthirod
  given name: Chutima
author list: Agent
  family name: Narong
  given name: Nattapol
author list: Agent
  family name: Jomchai
  given name: Nukoon
author list: Agent
  family name: Maprasop
  given name: Pasin
author list: Agent
  family name: Maknual
  given name: Chatree
author list: Agent
  family name: Phormsin
  given name: Nawin
author list: Agent
  family name: Shearman
  given name: Jeremy R.
author list: Agent
  family name: Pootakham
  given name: Wirulda
author list: Agent
  family name: Tangphatsornruang
  given name: Sithichoke
doi: 10.7717/peerj.12268
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: © 2021 Ruang-areerate et al.
attribution name: Ruang-areerate et al.

Anti-fouling activity and toxicity of the Mediterranean alien sponge Paraleucilla magna Klautau, Monteiro & Borojevic, 2004 (Porifera, Calcarea)
type: item
type: AcademicArticle
description: Poriferans, as sessile organisms without rigid external covering, use secondary metabolites for protection from predators and fouling organisms. The present study tested the antifouling activity of ethanolic extract of the Mediterranean alien calcareous sponge Paraleucilla magna towards juvenile mussels Mytilus galloprovincialis. Furthermore, toxicity tests on nauplii of brine shrimp Artemia salina and two microalgae strains, Nannochloropsis sp. and Tetraselmis suecica, were also conducted. A total attachment inhibition of M. galloprovincialis was achieved at a concentration of 400 µg/mL of sponge extract. The 50% mortality of A. salina nauplii was recorded at a concentration of 500 µg/mL of ethanolic extract. The growth inhibitory effect on both marine microalgae strains has been registered at a concentration of 300 µg/mL. Our results suggest promising natural antifouling activity and low toxicity of the ethanolic extract of P. magna that could be used as antifouling compound.
format: application/pdf
format: text/html
creator: Caterina Longo
creator: Roberta Trani
creator: Carlotta Nonnis Marzano
creator: Maria Mercurio
creator: Tamara Lazic
creator: Pietro Cotugno
creator: Erika Santobianchi
creator: Maria Flavia Gravina
subject: Ecology
subject: Marine Biology
subject: Toxicology
subject: Zoology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.12279
publisher: PeerJ Inc.
rights: © 2021 Longo et al.
abstract: Poriferans, as sessile organisms without rigid external covering, use secondary metabolites for protection from predators and fouling organisms. The present study tested the antifouling activity of ethanolic extract of the Mediterranean alien calcareous sponge Paraleucilla magna towards juvenile mussels Mytilus galloprovincialis. Furthermore, toxicity tests on nauplii of brine shrimp Artemia salina and two microalgae strains, Nannochloropsis sp. and Tetraselmis suecica, were also conducted. A total attachment inhibition of M. galloprovincialis was achieved at a concentration of 400 µg/mL of sponge extract. The 50% mortality of A. salina nauplii was recorded at a concentration of 500 µg/mL of ethanolic extract. The growth inhibitory effect on both marine microalgae strains has been registered at a concentration of 300 µg/mL. Our results suggest promising natural antifouling activity and low toxicity of the ethanolic extract of P. magna that could be used as antifouling compound.
bibliographic citation: Longo et al. (2021) Anti-fouling activity and toxicity of the Mediterranean alien sponge Paraleucilla magna Klautau, Monteiro & Borojevic, 2004 (Porifera, Calcarea). PeerJ 9:e12279 https://doi.org/10.7717/peerj.12279
date submitted: 2021-06-08
date accepted: 2021-09-20
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Longo
  given name: Caterina
author list: Agent
  family name: Trani
  given name: Roberta
author list: Agent
  family name: Nonnis Marzano
  given name: Carlotta
author list: Agent
  family name: Mercurio
  given name: Maria
author list: Agent
  family name: Lazic
  given name: Tamara
author list: Agent
  family name: Cotugno
  given name: Pietro
author list: Agent
  family name: Santobianchi
  given name: Erika
author list: Agent
  family name: Gravina
  given name: Maria Flavia
doi: 10.7717/peerj.12279
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: ©2021 Longo et al.
attribution name: Longo et al.

The effect of postoperative oral antibiotic therapy on the incidence of postoperative endophthalmitis after phacoemulsification surgery in dogs: 368 eyes (1997–2010)
type: item
type: AcademicArticle
description: Purpose To assess the effectiveness of postoperative administration of oral antibiotics at reducing the incidence of endophthalmitis following phacoemulsification cataract extraction in dogs. Methods Medical records of the University of Tennessee College of Veterinary Medicine were reviewed for cases having undergone phacoemulsification and divided according to whether or not they had received oral antibiotics postoperatively. Records were then evaluated for a diagnosis of endophthalmitis and incidence rates between the group receiving postoperative oral antibiotics and the group not receiving postoperative oral antibiotics were compared. Results A total of 215 patients (368 eyes) were identified by the search. One-hundred twelve patients (197 eyes) were treated with oral antibiotics postoperatively. One-hundred and three patients (171 eyes) were not treated with oral antibiotics postoperatively. Three cases of endophthalmitis were identified, with one in the antibiotic-treated group and two in the non-antibiotic treated group (P > 0.05, Fisher’s exact test). Conclusions The overall incidence of endophthalmitis at the University of Tennessee from 1997–2010 was 0.82%. The rate of post-phacoemulsification endophthalmitis was unaffected by the postoperative administration of oral antibiotics.
format: application/pdf
format: text/html
creator: Meg D. Sorhus
creator: Amanda Corr
creator: Xiaocun Sun
creator: Daniel A. Ward
subject: Microbiology
subject: Veterinary Medicine
subject: Zoology
subject: Ophthalmology
subject: Surgery and Surgical Specialties
description: doi:10.7717/peerj.12305
publisher: PeerJ Inc.
rights: © 2021 Sorhus et al.
abstract: Purpose To assess the effectiveness of postoperative administration of oral antibiotics at reducing the incidence of endophthalmitis following phacoemulsification cataract extraction in dogs. Methods Medical records of the University of Tennessee College of Veterinary Medicine were reviewed for cases having undergone phacoemulsification and divided according to whether or not they had received oral antibiotics postoperatively. Records were then evaluated for a diagnosis of endophthalmitis and incidence rates between the group receiving postoperative oral antibiotics and the group not receiving postoperative oral antibiotics were compared. Results A total of 215 patients (368 eyes) were identified by the search. One-hundred twelve patients (197 eyes) were treated with oral antibiotics postoperatively. One-hundred and three patients (171 eyes) were not treated with oral antibiotics postoperatively. Three cases of endophthalmitis were identified, with one in the antibiotic-treated group and two in the non-antibiotic treated group (P > 0.05, Fisher’s exact test). Conclusions The overall incidence of endophthalmitis at the University of Tennessee from 1997–2010 was 0.82%. The rate of post-phacoemulsification endophthalmitis was unaffected by the postoperative administration of oral antibiotics.
bibliographic citation: Sorhus et al. (2021) The effect of postoperative oral antibiotic therapy on the incidence of postoperative endophthalmitis after phacoemulsification surgery in dogs: 368 eyes (1997–2010). PeerJ 9:e12305 https://doi.org/10.7717/peerj.12305
date submitted: 2021-05-17
date accepted: 2021-09-22
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sorhus
  given name: Meg D.
author list: Agent
  family name: Corr
  given name: Amanda
author list: Agent
  family name: Sun
  given name: Xiaocun
author list: Agent
  family name: Ward
  given name: Daniel A.
doi: 10.7717/peerj.12305
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: © 2021 Sorhus et al.
attribution name: Sorhus et al.

Mate-guarding duration is mainly influenced by the risk of sperm competition and not by female quality in a golden orb-weaver spider
type: item
type: AcademicArticle
description: Males are expected to mate with as many females as possible, but can maximize their reproductive success through strategic mating decisions. For instance, males can increase their own fitness by mating with high quality females that produce more offspring. Additionally, males can adjust mating effort based on the relative distribution of females and male competitors. To test factors that influence male mate choice, we assessed male mating decisions in the golden silk orb-weaver spider, Trichonephila clavipes (Nephilidae), a species in which females are polyandrous, males guard females before and after copulation occurs and large males are the most successful at guarding mates. We tested the hypothesis that males spend more time guarding high quality females that are spatially isolated, and when the risk of sperm competition is higher. We also hypothesized that this effect increases with male body size. We assessed solitary and aggregated female webs in the field and quantified female quality (i.e., female body condition), male size (i.e., male body size), the risk of sperm competition (i.e., number of males in each female web), and mate-guarding duration (i.e., number of days each male spent in each web). We found that mate-guarding behaviour is largely influenced by the presence of male competitors. In addition, male body size seems to moderately influence male guarding decisions, with larger males guarding for a longer time. Finally, female body condition and type of web (i.e., solitary or aggregated) seem to play small roles in mate-guarding behaviour. As mate-guarding duration increased by 0.718 day per each additional male competitor in the web, and guarding behaviour prevents males from seeking additional mates, it seems that guarding females can be considerably costly. We conclude that failing to guard a sexual partner promotes high costs derived from sperm competition, and a male cannot recover his relative loss in fertilization success by seeking and fertil…
format: application/pdf
format: text/html
creator: Lygia A. Del Matto
creator: Renato C. Macedo-Rego
creator: Eduardo S. A. Santos
subject: Animal Behavior
subject: Ecology
subject: Evolutionary Studies
subject: Zoology
description: doi:10.7717/peerj.12310
publisher: PeerJ Inc.
rights: © 2021 Del Matto et al.
abstract: Males are expected to mate with as many females as possible, but can maximize their reproductive success through strategic mating decisions. For instance, males can increase their own fitness by mating with high quality females that produce more offspring. Additionally, males can adjust mating effort based on the relative distribution of females and male competitors. To test factors that influence male mate choice, we assessed male mating decisions in the golden silk orb-weaver spider, Trichonephila clavipes (Nephilidae), a species in which females are polyandrous, males guard females before and after copulation occurs and large males are the most successful at guarding mates. We tested the hypothesis that males spend more time guarding high quality females that are spatially isolated, and when the risk of sperm competition is higher. We also hypothesized that this effect increases with male body size. We assessed solitary and aggregated female webs in the field and quantified female quality (i.e., female body condition), male size (i.e., male body size), the risk of sperm competition (i.e., number of males in each female web), and mate-guarding duration (i.e., number of days each male spent in each web). We found that mate-guarding behaviour is largely influenced by the presence of male competitors. In addition, male body size seems to moderately influence male guarding decisions, with larger males guarding for a longer time. Finally, female body condition and type of web (i.e., solitary or aggregated) seem to play small roles in mate-guarding behaviour. As mate-guarding duration increased by 0.718 day per each additional male competitor in the web, and guarding behaviour prevents males from seeking additional mates, it seems that guarding females can be considerably costly. We conclude that failing to guard a sexual partner promotes high costs derived from sperm competition, and a male cannot recover his relative loss in fertilization success by seeking and fertil…
bibliographic citation: Del Matto et al. (2021) Mate-guarding duration is mainly influenced by the risk of sperm competition and not by female quality in a golden orb-weaver spider. PeerJ 9:e12310 https://doi.org/10.7717/peerj.12310
date submitted: 2021-01-06
date accepted: 2021-09-23
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Del Matto
  given name: Lygia A.
author list: Agent
  family name: Macedo-Rego
  given name: Renato C.
author list: Agent
  family name: Santos
  given name: Eduardo S. A.
doi: 10.7717/peerj.12310
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: © 2021 Del Matto et al.
attribution name: Del Matto et al.

Traumatic surfing injuries in New Zealand: a descriptive epidemiology study
type: item
type: AcademicArticle
description: Background New Zealand (NZ) has nearly 14,000 km of coastline and a surfing population of approximately 315,000 surfers. Given its popularity, surfing has a high frequency of injury claims, however, there remains a lack of data on traumatic surfing-related injuries from large population studies. The primary purpose of this study was to examine traumatic surfing injuries in NZ specific to injury incidence, duration, location, type, mechanism of injury and associated risk factors. Methods A sample of self-identified surfers currently living in NZ participated in an online retrospective cross-sectional survey between December 2015 and July 2016. Demographic and surfing injury data were collected and analysed. Results The survey yielded 1,473 respondents (18.3% female); a total of 502 surfers reported 702 major traumatic injuries with an overall incidence proportion of 0.34 (95% CI [0.32–0.37]). When comparing the number of injured surfers who sustained an injury at various body locations, a significantly higher proportion of competitive surfers, compared to recreational surfers, had an injury at the neck (6.8% vs 4%, χ2 (1,1473) = 5.84, P = 0.019); shoulder (7.4% vs 4.3%, χ2 (1,1473) = 6.34, P = 0.017), upper back (1% vs 2.4%, χ2 (1,1473) = 4.77, P = 0.043), lower back (7% vs 3.1%, χ2 (1,1473) = 11.98, P = 0.001) and knee (7% vs 3.4%, χ2 (1,1473) = 9.67, P = 0.003). A significantly higher proportion of surfers who performed aerial manoeuvres compared to those who did not reported a higher proportion of knee injuries (9.7% vs 3.9%, χ2 (1,1473) = 13.00, P = 0.001). With respect to injury duration, the shoulder represented the largest proportion of chronic injuries (>3 months) (44.4%), and the head and face represented the largest proportion of acute injuries (≤3 months) (88%). Muscle and tendon injuries were reported most frequently (25.6%) and direct contact injuries accounted for 58.1% of all injury mechanisms. Key risk factors for traumatic injury included: competitiv…
format: application/pdf
format: text/html
creator: James Furness
creator: Katherine McArthur
creator: Debbie Remnant
creator: Darcy Jorgensen
creator: Catherine J. Bacon
creator: Robert W. Moran
creator: Wayne Hing
creator: Mike Climstein
subject: Epidemiology
subject: Sports Injury
subject: Sports Medicine
description: doi:10.7717/peerj.12334
publisher: PeerJ Inc.
rights: © 2021 Furness et al.
abstract: Background New Zealand (NZ) has nearly 14,000 km of coastline and a surfing population of approximately 315,000 surfers. Given its popularity, surfing has a high frequency of injury claims, however, there remains a lack of data on traumatic surfing-related injuries from large population studies. The primary purpose of this study was to examine traumatic surfing injuries in NZ specific to injury incidence, duration, location, type, mechanism of injury and associated risk factors. Methods A sample of self-identified surfers currently living in NZ participated in an online retrospective cross-sectional survey between December 2015 and July 2016. Demographic and surfing injury data were collected and analysed. Results The survey yielded 1,473 respondents (18.3% female); a total of 502 surfers reported 702 major traumatic injuries with an overall incidence proportion of 0.34 (95% CI [0.32–0.37]). When comparing the number of injured surfers who sustained an injury at various body locations, a significantly higher proportion of competitive surfers, compared to recreational surfers, had an injury at the neck (6.8% vs 4%, χ2 (1,1473) = 5.84, P = 0.019); shoulder (7.4% vs 4.3%, χ2 (1,1473) = 6.34, P = 0.017), upper back (1% vs 2.4%, χ2 (1,1473) = 4.77, P = 0.043), lower back (7% vs 3.1%, χ2 (1,1473) = 11.98, P = 0.001) and knee (7% vs 3.4%, χ2 (1,1473) = 9.67, P = 0.003). A significantly higher proportion of surfers who performed aerial manoeuvres compared to those who did not reported a higher proportion of knee injuries (9.7% vs 3.9%, χ2 (1,1473) = 13.00, P = 0.001). With respect to injury duration, the shoulder represented the largest proportion of chronic injuries (>3 months) (44.4%), and the head and face represented the largest proportion of acute injuries (≤3 months) (88%). Muscle and tendon injuries were reported most frequently (25.6%) and direct contact injuries accounted for 58.1% of all injury mechanisms. Key risk factors for traumatic injury included: competitiv…
bibliographic citation: Furness et al. (2021) Traumatic surfing injuries in New Zealand: a descriptive epidemiology study. PeerJ 9:e12334 https://doi.org/10.7717/peerj.12334
date submitted: 2021-07-19
date accepted: 2021-09-27
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Furness
  given name: James
author list: Agent
  family name: McArthur
  given name: Katherine
author list: Agent
  family name: Remnant
  given name: Debbie
author list: Agent
  family name: Jorgensen
  given name: Darcy
author list: Agent
  family name: Bacon
  given name: Catherine J.
author list: Agent
  family name: Moran
  given name: Robert W.
author list: Agent
  family name: Hing
  given name: Wayne
author list: Agent
  family name: Climstein
  given name: Mike
doi: 10.7717/peerj.12334
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: ©2021 Furness et al.
attribution name: Furness et al.

Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance
type: item
type: AcademicArticle
description: Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.
format: application/pdf
format: text/html
creator: Yeelon Yeoh
creator: Teck Yew Low
creator: Nadiah Abu
creator: Pey Yee Lee
subject: Biochemistry
subject: Molecular Biology
subject: Drugs and Devices
subject: Gastroenterology and Hepatology
subject: Oncology
description: doi:10.7717/peerj.12338
publisher: PeerJ Inc.
rights: © 2021 Yeoh et al.
abstract: Resistance to anti-cancer treatments is a critical and widespread health issue that has brought serious impacts on lives, the economy and public policies. Mounting research has suggested that a selected spectrum of patients with advanced colorectal cancer (CRC) tend to respond poorly to both chemotherapeutic and targeted therapeutic regimens. Drug resistance in tumours can occur in an intrinsic or acquired manner, rendering cancer cells insensitive to the treatment of anti-cancer therapies. Multiple factors have been associated with drug resistance. The most well-established factors are the emergence of cancer stem cell-like properties and overexpression of ABC transporters that mediate drug efflux. Besides, there is emerging evidence that signalling pathways that modulate cell survival and drug metabolism play major roles in the maintenance of multidrug resistance in CRC. This article reviews drug resistance in CRC as a result of alterations in the MAPK, PI3K/PKB, Wnt/β-catenin and Notch pathways.
bibliographic citation: Yeoh et al. (2021) Regulation of signal transduction pathways in colorectal cancer: implications for therapeutic resistance. PeerJ 9:e12338 https://doi.org/10.7717/peerj.12338
date submitted: 2021-05-27
date accepted: 2021-09-28
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeoh
  given name: Yeelon
author list: Agent
  family name: Low
  given name: Teck Yew
author list: Agent
  family name: Abu
  given name: Nadiah
author list: Agent
  family name: Lee
  given name: Pey Yee
doi: 10.7717/peerj.12338
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: ©2021 Yeoh et al.
attribution name: Yeoh et al.

Interplay between epigallocatechin-3-gallate and ionic strength during amyloid aggregation
type: item
type: AcademicArticle
description: The formation and accumulation of protein amyloid aggregates is linked with multiple amyloidoses, including neurodegenerative Alzheimer’s or Parkinson’s disease. The mechanism of such fibril formation is impacted by various environmental conditions, which greatly complicates the search for potential anti-amyloid compounds. One of these factors is solution ionic strength, which varies between different aggregation protocols during in vitro drug screenings. In this work, we examine the interplay between ionic strength and a well-known protein aggregation inhibitor—epigallocatechin-3-gallate. We show that changes in solution ionic strength have a major impact on the compound’s inhibitory effect, reflected in both aggregation times and final fibril structure. We also observe that this effect is unique to different amyloid-forming proteins, such as insulin, alpha-synuclein and amyloid-beta.
format: application/pdf
format: text/html
creator: Mantas Ziaunys
creator: Kamile Mikalauskaite
creator: Andrius Sakalauskas
creator: Vytautas Smirnovas
subject: Biochemistry
subject: Biophysics
description: doi:10.7717/peerj.12381
publisher: PeerJ Inc.
rights: © 2021 Ziaunys et al.
abstract: The formation and accumulation of protein amyloid aggregates is linked with multiple amyloidoses, including neurodegenerative Alzheimer’s or Parkinson’s disease. The mechanism of such fibril formation is impacted by various environmental conditions, which greatly complicates the search for potential anti-amyloid compounds. One of these factors is solution ionic strength, which varies between different aggregation protocols during in vitro drug screenings. In this work, we examine the interplay between ionic strength and a well-known protein aggregation inhibitor—epigallocatechin-3-gallate. We show that changes in solution ionic strength have a major impact on the compound’s inhibitory effect, reflected in both aggregation times and final fibril structure. We also observe that this effect is unique to different amyloid-forming proteins, such as insulin, alpha-synuclein and amyloid-beta.
bibliographic citation: Ziaunys et al. (2021) Interplay between epigallocatechin-3-gallate and ionic strength during amyloid aggregation. PeerJ 9:e12381 https://doi.org/10.7717/peerj.12381
date submitted: 2021-07-28
date accepted: 2021-10-04
issued: 2021-10-22
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ziaunys
  given name: Mantas
author list: Agent
  family name: Mikalauskaite
  given name: Kamile
author list: Agent
  family name: Sakalauskas
  given name: Andrius
author list: Agent
  family name: Smirnovas
  given name: Vytautas
doi: 10.7717/peerj.12381
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-22
copyright: © 2021 Ziaunys et al.
attribution name: Ziaunys et al.

Effects of grazing intensity on forage nutritive value of dominant grass species in Borana rangelands of Southern Ethiopia
type: item
type: AcademicArticle
description: Background Forage nutritive value analysis is an essential indicator of rangeland status regarding degradation and livestock nutrient demand. Thus, it is used to maintain healthy and sustainable rangelands that can provide the livestock with sufficient quantity and quality of forage. This study is conducted with the aim of investigating the effects of grazing intensity combined with seasonal variation on the nutritive values of dominant grass species in the Teltele rangeland. Methods The studied area is classified into no-grazed, moderately grazed, and overgrazed plots based on the estimated potential carrying capacity. Sampling data is collected during both rainy and dry seasons. The collected forage samples are analyzed for concentrations of crude protein (CP), acid detergent organic fiber (ADF), neutral detergent fiber (NDF), acid detergent lignin (ADL), ash, dry matter digestibility (DMD), potential dry matter intake (DMI), and relative feed/forage value (RFV). Results The results show significant (P < 0.05) effects of both grazing intensity and season to grazing intensity interactions on all forage nutrient content concentrations across all grass species both within and between treatments. The recorded CP concentrations of all grass species are high in the overgrazed site and low at the no-grazed site, while the fiber concentration is high in NG and low in OG. RFV data also varies greatly, with high value recorded in OG in the rainy season and low value found in NG mainly during the dry season. As a result, it is recommended that moderate grazing should be practiced on the study site to maintain the quality and quantity of forage and to manage it in a sustainable manner.
format: application/pdf
format: text/html
creator: Yeneayehu Fenetahun
creator: Yuan You
creator: Tihunie Fentahun
creator: Xu Xinwen
creator: Wang Yong-dong
subject: Agricultural Science
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Plant Science
description: doi:10.7717/peerj.12204
publisher: PeerJ Inc.
rights: © 2021 Fenetahun et al.
abstract: Background Forage nutritive value analysis is an essential indicator of rangeland status regarding degradation and livestock nutrient demand. Thus, it is used to maintain healthy and sustainable rangelands that can provide the livestock with sufficient quantity and quality of forage. This study is conducted with the aim of investigating the effects of grazing intensity combined with seasonal variation on the nutritive values of dominant grass species in the Teltele rangeland. Methods The studied area is classified into no-grazed, moderately grazed, and overgrazed plots based on the estimated potential carrying capacity. Sampling data is collected during both rainy and dry seasons. The collected forage samples are analyzed for concentrations of crude protein (CP), acid detergent organic fiber (ADF), neutral detergent fiber (NDF), acid detergent lignin (ADL), ash, dry matter digestibility (DMD), potential dry matter intake (DMI), and relative feed/forage value (RFV). Results The results show significant (P < 0.05) effects of both grazing intensity and season to grazing intensity interactions on all forage nutrient content concentrations across all grass species both within and between treatments. The recorded CP concentrations of all grass species are high in the overgrazed site and low at the no-grazed site, while the fiber concentration is high in NG and low in OG. RFV data also varies greatly, with high value recorded in OG in the rainy season and low value found in NG mainly during the dry season. As a result, it is recommended that moderate grazing should be practiced on the study site to maintain the quality and quantity of forage and to manage it in a sustainable manner.
bibliographic citation: Fenetahun et al. (2021) Effects of grazing intensity on forage nutritive value of dominant grass species in Borana rangelands of Southern Ethiopia. PeerJ 9:e12204 https://doi.org/10.7717/peerj.12204
date submitted: 2020-10-20
date accepted: 2021-09-03
issued: 2021-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fenetahun
  given name: Yeneayehu
author list: Agent
  family name: You
  given name: Yuan
author list: Agent
  family name: Fentahun
  given name: Tihunie
author list: Agent
  family name: Xinwen
  given name: Xu
author list: Agent
  family name: Yong-dong
  given name: Wang
doi: 10.7717/peerj.12204
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-21
copyright: ©2021 Fenetahun et al.
attribution name: Fenetahun et al.

A new vertebrate fauna from the Lower Cretaceous Holly Creek Formation of the Trinity Group, southwest Arkansas, USA
type: item
type: AcademicArticle
description: We present a previously discovered but undescribed late Early Cretaceous vertebrate fauna from the Holly Creek Formation of the Trinity Group in Arkansas. The site from the ancient Gulf Coast is dominated by semi-aquatic forms and preserves a diverse aquatic, semi-aquatic, and terrestrial fauna. Fishes include fresh- to brackish-water chondrichthyans and a variety of actinopterygians, including semionotids, an amiid, and a new pycnodontiform, Anomoeodus caddoi sp. nov. Semi-aquatic taxa include lissamphibians, the solemydid turtle Naomichelys, a trionychid turtle, and coelognathosuchian crocodyliforms. Among terrestrial forms are several members of Dinosauria and one or more squamates, one of which, Sciroseps pawhuskai gen. et sp. nov., is described herein. Among Dinosauria, both large and small theropods (Acrocanthosaurus, Deinonychus, and Richardoestesia) and titanosauriform sauropods are represented; herein we also report the first occurrence of a nodosaurid ankylosaur from the Trinity Group. The fauna of the Holly Creek Formation is similar to other, widely scattered late Early Cretaceous assemblages across North America and suggests the presence of a low-diversity, broadly distributed continental ecosystem of the Early Cretaceous following the Late Jurassic faunal turnover. This low-diversity ecosystem contrasts sharply with the highly diverse ecosystem which emerged by the Cenomanian. The contrast underpins the importance of vicariance as an evolutionary driver brought on by Sevier tectonics and climatic changes, such as rising sea level and formation of the Western Interior Seaway, impacting the early Late Cretaceous ecosystem.
format: application/pdf
format: text/html
creator: Celina A. Suarez
creator: Joseph Frederickson
creator: Richard L. Cifelli
creator: Jeffrey G. Pittman
creator: Randall L. Nydam
creator: ReBecca K. Hunt-Foster
creator: Kirsty Morgan
subject: Biodiversity
subject: Biogeography
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.12242
publisher: PeerJ Inc.
rights: © 2021 Suarez et al.
abstract: We present a previously discovered but undescribed late Early Cretaceous vertebrate fauna from the Holly Creek Formation of the Trinity Group in Arkansas. The site from the ancient Gulf Coast is dominated by semi-aquatic forms and preserves a diverse aquatic, semi-aquatic, and terrestrial fauna. Fishes include fresh- to brackish-water chondrichthyans and a variety of actinopterygians, including semionotids, an amiid, and a new pycnodontiform, Anomoeodus caddoi sp. nov. Semi-aquatic taxa include lissamphibians, the solemydid turtle Naomichelys, a trionychid turtle, and coelognathosuchian crocodyliforms. Among terrestrial forms are several members of Dinosauria and one or more squamates, one of which, Sciroseps pawhuskai gen. et sp. nov., is described herein. Among Dinosauria, both large and small theropods (Acrocanthosaurus, Deinonychus, and Richardoestesia) and titanosauriform sauropods are represented; herein we also report the first occurrence of a nodosaurid ankylosaur from the Trinity Group. The fauna of the Holly Creek Formation is similar to other, widely scattered late Early Cretaceous assemblages across North America and suggests the presence of a low-diversity, broadly distributed continental ecosystem of the Early Cretaceous following the Late Jurassic faunal turnover. This low-diversity ecosystem contrasts sharply with the highly diverse ecosystem which emerged by the Cenomanian. The contrast underpins the importance of vicariance as an evolutionary driver brought on by Sevier tectonics and climatic changes, such as rising sea level and formation of the Western Interior Seaway, impacting the early Late Cretaceous ecosystem.
bibliographic citation: Suarez et al. (2021) A new vertebrate fauna from the Lower Cretaceous Holly Creek Formation of the Trinity Group, southwest Arkansas, USA. PeerJ 9:e12242 https://doi.org/10.7717/peerj.12242
date submitted: 2021-03-16
date accepted: 2021-09-12
issued: 2021-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Suarez
  given name: Celina A.
author list: Agent
  family name: Frederickson
  given name: Joseph
author list: Agent
  family name: Cifelli
  given name: Richard L.
author list: Agent
  family name: Pittman
  given name: Jeffrey G.
author list: Agent
  family name: Nydam
  given name: Randall L.
author list: Agent
  family name: Hunt-Foster
  given name: ReBecca K.
author list: Agent
  family name: Morgan
  given name: Kirsty
doi: 10.7717/peerj.12242
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-21
copyright: © 2021 Suarez et al.
attribution name: Suarez et al.

Development of a novel embryonic germline gene-related prognostic model of lung adenocarcinoma
type: item
type: AcademicArticle
description: Background Emerging evidence implicates the correlation of embryonic germline genes with the tumor progress and patient’s outcome. However, the prognostic value of these genes in lung adenocarcinoma (LUAD) has not been fully studied. Here we systematically evaluated this issue, and constructed a novel signature and a nomogram associated with embryonic germline genes for predicting the outcomes of lung adenocarcinoma. Methods The LUAD cohorts retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were used as training set and testing set, respectively. The embryonic germline genes were downloaded from the website https://venn.lodder.dev. Then, the differentially expressed embryonic germline genes (DEGGs) between the tumor and normal samples were identified by limma package. The functional enrichment and pathway analyses were also performed by clusterProfiler package. The prognostic model was constructed by the least absolute shrinkage and selection operator (LASSO)-Cox regression method. Survival and Receiver Operating Characteristic (ROC) analyses were performed to validate the model using training set and four testing GEO datasets. Finally, a prognostic nomogram based on the signature genes was constructed using multivariate regression method. Results Among the identified 269 DEGGs, 249 were up-regulated and 20 were down-regulated. GO and KEGG analyses revealed that these DEGGs were mainly enriched in the process of cell proliferation and DNA damage repair. Then, 103 DEGGs with prognostic value were identified by univariate Cox regression and further filtered by LASSO method. The resulting sixteen DEGGs were included in step multivariate Cox regression and an eleven embryonic germline gene related signature (EGRS) was constructed. The model could robustly stratify the LUAD patients into high-risk and low-risk groups in both training and testing sets, and low-risk patients had much better outcomes. The multi-ROC analysis also showed…
format: application/pdf
format: text/html
creator: Linjun Liu
creator: Ke Xu
creator: Yubai Zhou
subject: Bioinformatics
subject: Oncology
subject: Respiratory Medicine
subject: Medical Genetics
description: doi:10.7717/peerj.12257
publisher: PeerJ Inc.
rights: © 2021 Liu et al.
abstract: Background Emerging evidence implicates the correlation of embryonic germline genes with the tumor progress and patient’s outcome. However, the prognostic value of these genes in lung adenocarcinoma (LUAD) has not been fully studied. Here we systematically evaluated this issue, and constructed a novel signature and a nomogram associated with embryonic germline genes for predicting the outcomes of lung adenocarcinoma. Methods The LUAD cohorts retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database were used as training set and testing set, respectively. The embryonic germline genes were downloaded from the website https://venn.lodder.dev. Then, the differentially expressed embryonic germline genes (DEGGs) between the tumor and normal samples were identified by limma package. The functional enrichment and pathway analyses were also performed by clusterProfiler package. The prognostic model was constructed by the least absolute shrinkage and selection operator (LASSO)-Cox regression method. Survival and Receiver Operating Characteristic (ROC) analyses were performed to validate the model using training set and four testing GEO datasets. Finally, a prognostic nomogram based on the signature genes was constructed using multivariate regression method. Results Among the identified 269 DEGGs, 249 were up-regulated and 20 were down-regulated. GO and KEGG analyses revealed that these DEGGs were mainly enriched in the process of cell proliferation and DNA damage repair. Then, 103 DEGGs with prognostic value were identified by univariate Cox regression and further filtered by LASSO method. The resulting sixteen DEGGs were included in step multivariate Cox regression and an eleven embryonic germline gene related signature (EGRS) was constructed. The model could robustly stratify the LUAD patients into high-risk and low-risk groups in both training and testing sets, and low-risk patients had much better outcomes. The multi-ROC analysis also showed…
bibliographic citation: Liu et al. (2021) Development of a novel embryonic germline gene-related prognostic model of lung adenocarcinoma. PeerJ 9:e12257 https://doi.org/10.7717/peerj.12257
date submitted: 2021-06-04
date accepted: 2021-09-15
issued: 2021-10-21
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liu
  given name: Linjun
author list: Agent
  family name: Xu
  given name: Ke
author list: Agent
  family name: Zhou
  given name: Yubai
doi: 10.7717/peerj.12257
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-10-21
copyright: ©2021 Liu et al.
attribution name: Liu et al.

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