PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery
items: Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153
items: A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides
items: Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas
items: Bird-window collisions: Mitigation efficacy and risk factors across two years
items: Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli
items: Distribution and abundance of the land snail Pollicaria elephas (Gastropoda: Pupinidae) in limestone habitats in Perak, Malaysia
items: Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum)
items: A new HSI denoising method via interpolated block matching 3D and guided filter
items: Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication

Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery
type: item
type: AcademicArticle
description: Marine life has provided mankind with unique and extraordinary chemical structures and scaffolds with potent biological activities. Many organisms and secondary metabolites derived from fungi and symbionts are found to be more environmentally friendly to study than the marine corals per se. Marine symbionts such as Aspergillus sp., a fungus, which can be isolated and grown in the lab would be a potential and continuous source of bioactive natural compounds without affecting the marine environment. The Red Sea is known for its biodiversity and is well-studied in terms of its marine-derived bioactive metabolites. The harsh environmental conditions lead to the development of unique metabolic pathways. This, in turn, results in enhanced synthesis and release of toxic and bioactive chemicals. Interestingly, the Persian Gulf and the Gulf of Oman carry a variety of environmental stresses, some of which are similar to the Red Sea. When compared to the Red Sea, the Persian Gulf has been shown to be rich in marine fungi as well, and is, therefore, expected to contain elaborate and interesting bioactive compounds. Such compounds may or may not be similar to the ones isolated from the Red Sea environment. Astoundingly, there are a very limited number of studies on the bioactive portfolio of marine-derived metabolites from the Persian Gulf and the Gulf of Oman. In this perspective, we are looking at the Red Sea as a comparator marine environment and bioactive materials repertoire to provide a futuristic perspective on the potential of the understudied and possibly overlooked bioactive metabolites derived from the marine life of the Persian Gulf and the Gulf of Oman despite its proven biodiversity and harsher environmental stress.
format: application/pdf
format: text/html
creator: Reham K. Abuhijjleh
creator: Samiullah Shabbir
creator: Ahmed M. Al-Abd
creator: Nada H. Jiaan
creator: Shahad Alshamil
creator: Eman M. El-labbad
creator: Sherief I. Khalifa
subject: Biochemistry
subject: Ecology
subject: Marine Biology
subject: Natural Resource Management
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.11778
publisher: PeerJ Inc.
rights: © 2021 Abuhijjleh et al.
abstract: Marine life has provided mankind with unique and extraordinary chemical structures and scaffolds with potent biological activities. Many organisms and secondary metabolites derived from fungi and symbionts are found to be more environmentally friendly to study than the marine corals per se. Marine symbionts such as Aspergillus sp., a fungus, which can be isolated and grown in the lab would be a potential and continuous source of bioactive natural compounds without affecting the marine environment. The Red Sea is known for its biodiversity and is well-studied in terms of its marine-derived bioactive metabolites. The harsh environmental conditions lead to the development of unique metabolic pathways. This, in turn, results in enhanced synthesis and release of toxic and bioactive chemicals. Interestingly, the Persian Gulf and the Gulf of Oman carry a variety of environmental stresses, some of which are similar to the Red Sea. When compared to the Red Sea, the Persian Gulf has been shown to be rich in marine fungi as well, and is, therefore, expected to contain elaborate and interesting bioactive compounds. Such compounds may or may not be similar to the ones isolated from the Red Sea environment. Astoundingly, there are a very limited number of studies on the bioactive portfolio of marine-derived metabolites from the Persian Gulf and the Gulf of Oman. In this perspective, we are looking at the Red Sea as a comparator marine environment and bioactive materials repertoire to provide a futuristic perspective on the potential of the understudied and possibly overlooked bioactive metabolites derived from the marine life of the Persian Gulf and the Gulf of Oman despite its proven biodiversity and harsher environmental stress.
bibliographic citation: Abuhijjleh et al. (2021) Bioactive marine metabolites derived from the Persian Gulf compared to the Red Sea: similar environments and wide gap in drug discovery. PeerJ 9:e11778 https://doi.org/10.7717/peerj.11778
date submitted: 2021-03-08
date accepted: 2021-06-24
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Abuhijjleh
  given name: Reham K.
author list: Agent
  family name: Shabbir
  given name: Samiullah
author list: Agent
  family name: Al-Abd
  given name: Ahmed M.
author list: Agent
  family name: Jiaan
  given name: Nada H.
author list: Agent
  family name: Alshamil
  given name: Shahad
author list: Agent
  family name: El-labbad
  given name: Eman M.
author list: Agent
  family name: Khalifa
  given name: Sherief I.
doi: 10.7717/peerj.11778
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: © 2021 Abuhijjleh et al.
attribution name: Abuhijjleh et al.

Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153
type: item
type: AcademicArticle
description: Background Polychlorinated biphenyls (PCBs) are persistent pollutants with carcinogenesis and mutagenesis effects which have been closely associated with PCBs-induced DNA damage. However, the detailed DNA damage events and corresponding pathway alterations under PCBs poisoning is still not well understood. Methods Whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were used to explore genome wide variations and related pathway changes in HEK293T cells that challenged by 15 µM PCB153 for 96 h in vitro. Double strand breaks (DSBs) were measured by 53BP1 foci detection, altered pathways were confirmed by quantitative real-time PCR (qPCR). Results The results indicated that abundant copy number variations (CNVs), including four duplications and 30 deletions, occurred in PCB153-exposed HEK293T cells. Multiple large fragment deletions (>1 Mb) involving up to 245 Mb regions on many chromosomes. Missense mutations were found in six tumor susceptibility genes, two of which are key members participating in homologous recombination (HR) repair response, BRCA1 and BRCA2. RNA-seq data showed that PCB153 poisoning apparently suppressedHR repairing genes. Besides, 15 µM PCB153 exposure significantly increased 53BP1 foci formation and effectively reduced BRCA1, RAD51B and RAD51C expression, indicating an elevated DSBs and impaired HR repairing. Conclusion This study firstly reported multiple large chromosomal deletions and impaired HR repairing in PCB153-exposed HEK293T cells, which provided a new insight into the understanding of early response and the mechanism underlying PCB153 genotoxicity. The chromosomal instabilities might be related to the impaired HR repairing that induced by PCB153; however, further investigations, especially on actual toxic effects of human body, are needed to confirm such speculation.
format: application/pdf
format: text/html
creator: Jiaci Li
creator: Yaqing Jing
creator: Yi Liu
creator: Yawei Ru
creator: Mingyan Ju
creator: Yuxia Zhao
creator: Guang Li
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Environmental Impacts
description: doi:10.7717/peerj.11816
publisher: PeerJ Inc.
rights: © 2021 Li et al.
abstract: Background Polychlorinated biphenyls (PCBs) are persistent pollutants with carcinogenesis and mutagenesis effects which have been closely associated with PCBs-induced DNA damage. However, the detailed DNA damage events and corresponding pathway alterations under PCBs poisoning is still not well understood. Methods Whole-genome sequencing (WGS) and RNA sequencing (RNA-seq) were used to explore genome wide variations and related pathway changes in HEK293T cells that challenged by 15 µM PCB153 for 96 h in vitro. Double strand breaks (DSBs) were measured by 53BP1 foci detection, altered pathways were confirmed by quantitative real-time PCR (qPCR). Results The results indicated that abundant copy number variations (CNVs), including four duplications and 30 deletions, occurred in PCB153-exposed HEK293T cells. Multiple large fragment deletions (>1 Mb) involving up to 245 Mb regions on many chromosomes. Missense mutations were found in six tumor susceptibility genes, two of which are key members participating in homologous recombination (HR) repair response, BRCA1 and BRCA2. RNA-seq data showed that PCB153 poisoning apparently suppressedHR repairing genes. Besides, 15 µM PCB153 exposure significantly increased 53BP1 foci formation and effectively reduced BRCA1, RAD51B and RAD51C expression, indicating an elevated DSBs and impaired HR repairing. Conclusion This study firstly reported multiple large chromosomal deletions and impaired HR repairing in PCB153-exposed HEK293T cells, which provided a new insight into the understanding of early response and the mechanism underlying PCB153 genotoxicity. The chromosomal instabilities might be related to the impaired HR repairing that induced by PCB153; however, further investigations, especially on actual toxic effects of human body, are needed to confirm such speculation.
bibliographic citation: Li et al. (2021) Large chromosomal deletions and impaired homologous recombination repairing in HEK293T cells exposed to polychlorinated biphenyl 153. PeerJ 9:e11816 https://doi.org/10.7717/peerj.11816
date submitted: 2021-04-01
date accepted: 2021-06-29
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jiaci
author list: Agent
  family name: Jing
  given name: Yaqing
author list: Agent
  family name: Liu
  given name: Yi
author list: Agent
  family name: Ru
  given name: Yawei
author list: Agent
  family name: Ju
  given name: Mingyan
author list: Agent
  family name: Zhao
  given name: Yuxia
author list: Agent
  family name: Li
  given name: Guang
doi: 10.7717/peerj.11816
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Li et al.
attribution name: Li et al.

A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides
type: item
type: AcademicArticle
description: Background Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date. Methods The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities. Results Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in…
format: application/pdf
format: text/html
creator: Nguyen Thi-Hanh Vu
creator: Tung Ngoc Quach
creator: Xuan Thi-Thanh Dao
creator: Ha Thanh Le
creator: Chi Phuong Le
creator: Lam Tung Nguyen
creator: Lam Tung Le
creator: Cuong Cao Ngo
creator: Ha Hoang
creator: Ha Hoang Chu
creator: Quyet-Tien Phi
subject: Biochemistry
subject: Biotechnology
subject: Genomics
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.11839
publisher: PeerJ Inc.
rights: © 2021 Vu et al.
abstract: Background Lignocellulose is a renewable and enormous biomass resource, which can be degraded efficiently by a range of cocktails of carbohydrate-active enzymes secreted by termite gut symbiotic bacteria. There is an urgent need to find enzymes with novel characteristics for improving the conversion processes in the production of lignocellulosic-based products. Although various studies dedicated to the genus Cellulosimicrobium as gut symbiont, genetic potential related to plant biomass-acting enzymes and exopolysaccharides production has been fully untapped to date. Methods The cellulolytic bacterial strain MP1 was isolated from termite guts and identified to the species level by phenotypic, phylogenetic, and genomic analysis. To further explore genes related to cellulose and hemicellulose degradation, the draft genome of strain MP1 was obtained by using whole-genome sequencing, assembly, and annotation through the Illumina platform. Lignocellulose degrading enzymes and levan production in the liquid medium were also examined to shed light on bacterial activities. Results Among 65 isolates obtained, the strain MP1 was the most efficient cellulase producer with cellulase activity of 0.65 ± 0.02 IU/ml. The whole genome analysis depicted that strain MP1 consists of a circular chromosome that contained 4,580,223 bp with an average GC content of 73.9%. The genome comprises 23 contigs including 67 rRNA genes, three tRNA genes, a single tmRNA gene, and 4,046 protein-coding sequences. In support of the phenotypic identification, the 16S rRNA gene sequence, average nucleotide identity, and whole-genome-based taxonomic analysis demonstrated that the strain MP1 belongs to the species Cellulosimicrobium cellulans. A total of 30 genes related to the degradation of cellulases and hemicellulases were identified in the C. cellulans MP1 genome. Of note, the presence of sacC1-levB-sacC2-ls operon responsible for levan and levan-type fructooligosaccharides biosynthesis was detected in…
bibliographic citation: Vu et al. (2021) A genomic perspective on the potential of termite-associated Cellulosimicrobium cellulans MP1 as producer of plant biomass-acting enzymes and exopolysaccharides. PeerJ 9:e11839 https://doi.org/10.7717/peerj.11839
date submitted: 2021-03-11
date accepted: 2021-07-01
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vu
  given name: Nguyen Thi-Hanh
author list: Agent
  family name: Quach
  given name: Tung Ngoc
author list: Agent
  family name: Dao
  given name: Xuan Thi-Thanh
author list: Agent
  family name: Le
  given name: Ha Thanh
author list: Agent
  family name: Le
  given name: Chi Phuong
author list: Agent
  family name: Nguyen
  given name: Lam Tung
author list: Agent
  family name: Le
  given name: Lam Tung
author list: Agent
  family name: Ngo
  given name: Cuong Cao
author list: Agent
  family name: Hoang
  given name: Ha
author list: Agent
  family name: Chu
  given name: Ha Hoang
author list: Agent
  family name: Phi
  given name: Quyet-Tien
doi: 10.7717/peerj.11839
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Vu et al.
attribution name: Vu et al.

Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas
type: item
type: AcademicArticle
description: The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of a…
format: application/pdf
format: text/html
creator: Ruben U. Tovar
creator: Valentin Cantu
creator: Brian Fremaux
creator: Pedro Gonzalez Jr
creator: Amanda Spikes
creator: Dana M. García
subject: Developmental Biology
subject: Evolutionary Studies
description: doi:10.7717/peerj.11840
publisher: PeerJ Inc.
rights: © 2021 Tovar et al.
abstract: The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes—the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of a…
bibliographic citation: Tovar et al. (2021) Comparative development and ocular histology between epigean and subterranean salamanders (Eurycea) from central Texas. PeerJ 9:e11840 https://doi.org/10.7717/peerj.11840
date submitted: 2018-10-20
date accepted: 2021-07-01
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Tovar
  given name: Ruben U.
author list: Agent
  family name: Cantu
  given name: Valentin
author list: Agent
  family name: Fremaux
  given name: Brian
author list: Agent
  family name: Gonzalez Jr
  given name: Pedro
author list: Agent
  family name: Spikes
  given name: Amanda
author list: Agent
  family name: García
  given name: Dana M.
doi: 10.7717/peerj.11840
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Tovar et al.
attribution name: Tovar et al.

Bird-window collisions: Mitigation efficacy and risk factors across two years
type: item
type: AcademicArticle
description: Background Research on bird-window collision mitigation is needed to prevent up to a billion bird fatalities yearly in the U.S. At the University of Utah campus (Salt Lake City, Utah, USA), past research documented collisions, especially for Cedar Waxwings (Bombycilla cedrorum) drawn to fruiting ornamental pears in winter. Mirrored windows, which have a metallic coating that turns window exteriors into mirrors, had frequent collisions, which were mitigated when Feather Friendly®bird deterrent markers were applied. Bird-friendly windows–ORNILUX®ultraviolet (UV) and fritted windows–also reduced collisions when data were collected across fall and winter. Extending this prior research, we evaluated additional mitigation and tested the replicability of effects for pear trees, mirrored windows, and bird-friendly windows across two years. Methods Using published data from eight buildings monitored for collisions in year 1 (Fall and Winter, 2019–2020), we added another year of monitoring, Fall and Winter, 2020–2021. Between years, Feather Friendly®mitigation markers were added to collision-prone areas of two buildings, including both mirrored and transparent windows. Results The two buildings that received new Feather Friendly®mitigation had significantly fewer collisions post-mitigation. Control areas also had nonsignificant decline in collisions. The interaction of area (mitigation vs. control) by time (year 1 vs. 2) was significant, based on generalized estimating equations (GEE). The total yearly collisions across all eight buildings declined from 39 to 23. A second GEE analysis of all 8 buildings showed that mirrored windows, pear trees, and bird-friendly windows were each significant when analyzed separately. The best-fit model showed more collisions for mirrored windows and fewer collisions for bird-friendly windows. We found pear tree proximity to be related to more collisions in winter than fall. In addition, pear trees showed reduced collisions from year 1 to 2, c…
format: application/pdf
format: text/html
creator: Barbara B. Brown
creator: Sabrina Santos
creator: Natalia Ocampo-Peñuela
subject: Animal Behavior
subject: Conservation Biology
subject: Ecology
subject: Zoology
subject: Environmental Impacts
description: doi:10.7717/peerj.11867
publisher: PeerJ Inc.
rights: © 2021 Brown et al.
abstract: Background Research on bird-window collision mitigation is needed to prevent up to a billion bird fatalities yearly in the U.S. At the University of Utah campus (Salt Lake City, Utah, USA), past research documented collisions, especially for Cedar Waxwings (Bombycilla cedrorum) drawn to fruiting ornamental pears in winter. Mirrored windows, which have a metallic coating that turns window exteriors into mirrors, had frequent collisions, which were mitigated when Feather Friendly®bird deterrent markers were applied. Bird-friendly windows–ORNILUX®ultraviolet (UV) and fritted windows–also reduced collisions when data were collected across fall and winter. Extending this prior research, we evaluated additional mitigation and tested the replicability of effects for pear trees, mirrored windows, and bird-friendly windows across two years. Methods Using published data from eight buildings monitored for collisions in year 1 (Fall and Winter, 2019–2020), we added another year of monitoring, Fall and Winter, 2020–2021. Between years, Feather Friendly®mitigation markers were added to collision-prone areas of two buildings, including both mirrored and transparent windows. Results The two buildings that received new Feather Friendly®mitigation had significantly fewer collisions post-mitigation. Control areas also had nonsignificant decline in collisions. The interaction of area (mitigation vs. control) by time (year 1 vs. 2) was significant, based on generalized estimating equations (GEE). The total yearly collisions across all eight buildings declined from 39 to 23. A second GEE analysis of all 8 buildings showed that mirrored windows, pear trees, and bird-friendly windows were each significant when analyzed separately. The best-fit model showed more collisions for mirrored windows and fewer collisions for bird-friendly windows. We found pear tree proximity to be related to more collisions in winter than fall. In addition, pear trees showed reduced collisions from year 1 to 2, c…
bibliographic citation: Brown et al. (2021) Bird-window collisions: Mitigation efficacy and risk factors across two years. PeerJ 9:e11867 https://doi.org/10.7717/peerj.11867
date submitted: 2021-05-10
date accepted: 2021-07-05
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Brown
  given name: Barbara B.
author list: Agent
  family name: Santos
  given name: Sabrina
author list: Agent
  family name: Ocampo-Peñuela
  given name: Natalia
doi: 10.7717/peerj.11867
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Brown et al.
attribution name: Brown et al.

Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli
type: item
type: AcademicArticle
description: Shiga toxin-producing Escherichia coli (STEC) is a major intestinal pathogen and causes serious gastrointestinal illness, which includes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome. The major virulence factors of STEC are Shiga toxins (Stx1 and Stx2), which belong to the AB-type toxin family. Among several subtypes of Stx1 and Stx2, the production of Stx2a is thought to be a risk factor for severe STEC infections, but Stx2a production levels vary markedly between STEC strains, even strains with the same serotype. Therefore, quantitative analyses of Stx2 production by STEC strains are important to understand the virulence potential of specific lineages or sublineages. In this study, we developed a novel Stx2 quantification method by utilizing homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technology. To determine suitable “sandwich” assay conditions, we tested 6 combinations of fluorescence-labeled monoclonal antibodies (mAbs) specific to Stx2 and compared the HTRF signal intensities obtained at various incubation times. Through this analysis, we selected the most suitable mAb pair, one recognizing the A subunit and the other recognizing the B subunit, thus together detecting Stx holotoxins. The optimal incubation time was also determined (18 h). Then, we optimized the concentrations of the two mAbs based on the range for linearity. The established HTRF assay detected 0.5 ng/ml of the highly purified recombinant Stx2a and Stx2e proteins and the working range was 1–64 ng/ml for both Stx2a and Stx2e. Through the quantification analysis of Stx proteins in STEC cell lysates, we confirmed that other Stx2 subtypes (Stx2b, Stx2c, Stx2d and Stx2g) can also be quantified at a certain level of accuracy, while this assay system does not detect Stx2f, which is highly divergent in sequence from other Stx2 subtypes, and Stx1. As the HTRF protocol we established is simple, this assay system should prove useful for the quant…
format: application/pdf
format: text/html
creator: Keiji Nakamura
creator: Chikashi Tokuda
creator: Hideyuki Arimitsu
creator: Yoshiki Etoh
creator: Mitsuhiro Hamasaki
creator: Yuichiro Deguchi
creator: Itsuki Taniguchi
creator: Yasuhiro Gotoh
creator: Yoshitoshi Ogura
creator: Tetsuya Hayashi
subject: Biochemistry
subject: Microbiology
description: doi:10.7717/peerj.11871
publisher: PeerJ Inc.
rights: © 2021 Nakamura et al.
abstract: Shiga toxin-producing Escherichia coli (STEC) is a major intestinal pathogen and causes serious gastrointestinal illness, which includes diarrhea, hemorrhagic colitis, and life-threatening hemolytic uremic syndrome. The major virulence factors of STEC are Shiga toxins (Stx1 and Stx2), which belong to the AB-type toxin family. Among several subtypes of Stx1 and Stx2, the production of Stx2a is thought to be a risk factor for severe STEC infections, but Stx2a production levels vary markedly between STEC strains, even strains with the same serotype. Therefore, quantitative analyses of Stx2 production by STEC strains are important to understand the virulence potential of specific lineages or sublineages. In this study, we developed a novel Stx2 quantification method by utilizing homogeneous time-resolved fluorescence resonance energy transfer (HTRF) technology. To determine suitable “sandwich” assay conditions, we tested 6 combinations of fluorescence-labeled monoclonal antibodies (mAbs) specific to Stx2 and compared the HTRF signal intensities obtained at various incubation times. Through this analysis, we selected the most suitable mAb pair, one recognizing the A subunit and the other recognizing the B subunit, thus together detecting Stx holotoxins. The optimal incubation time was also determined (18 h). Then, we optimized the concentrations of the two mAbs based on the range for linearity. The established HTRF assay detected 0.5 ng/ml of the highly purified recombinant Stx2a and Stx2e proteins and the working range was 1–64 ng/ml for both Stx2a and Stx2e. Through the quantification analysis of Stx proteins in STEC cell lysates, we confirmed that other Stx2 subtypes (Stx2b, Stx2c, Stx2d and Stx2g) can also be quantified at a certain level of accuracy, while this assay system does not detect Stx2f, which is highly divergent in sequence from other Stx2 subtypes, and Stx1. As the HTRF protocol we established is simple, this assay system should prove useful for the quant…
bibliographic citation: Nakamura et al. (2021) Development of a homogeneous time-resolved FRET (HTRF) assay for the quantification of Shiga toxin 2 produced by E. coli. PeerJ 9:e11871 https://doi.org/10.7717/peerj.11871
date submitted: 2021-04-20
date accepted: 2021-07-06
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nakamura
  given name: Keiji
author list: Agent
  family name: Tokuda
  given name: Chikashi
author list: Agent
  family name: Arimitsu
  given name: Hideyuki
author list: Agent
  family name: Etoh
  given name: Yoshiki
author list: Agent
  family name: Hamasaki
  given name: Mitsuhiro
author list: Agent
  family name: Deguchi
  given name: Yuichiro
author list: Agent
  family name: Taniguchi
  given name: Itsuki
author list: Agent
  family name: Gotoh
  given name: Yasuhiro
author list: Agent
  family name: Ogura
  given name: Yoshitoshi
author list: Agent
  family name: Hayashi
  given name: Tetsuya
doi: 10.7717/peerj.11871
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: © 2021 Nakamura et al.
attribution name: Nakamura et al.

Distribution and abundance of the land snail Pollicaria elephas (Gastropoda: Pupinidae) in limestone habitats in Perak, Malaysia
type: item
type: AcademicArticle
description: This study aimed to reveal the habitat variables that determine the distribution and abundance of the land snail Pollicaria elephas in limestone habitats in Perak, Malaysia. Seventeen plots were selected on a limestone hill to determine the effect of environmental variables on the abundance of this land snail. The environmental variables we considered included habitat (canopy cover and leaf litter thickness), topography (elevation, aspect, ruggedness, and slope), microclimate (soil temperature, air temperature, and humidity), and vegetation (abundance of respective vascular plant species). The correlation analyses suggested that the snails’ abundance was positively correlated with the abundance of the four vascular plant species: Diospyros toposia var. toposoides, Croton cascarilloides, Kibatalia laurifolia, and Mallotus peltatus. Plots with lower soil temperatures had more snails than plots with higher soil temperatures. Our results show that plots in the southern part of the limestone hill, in which P. elephas were absent, were similar in habitat, topography, microclimate, and vegetation to the plots in the northern part of the limestone hill, where specimens were mostly present. The absence of this species in suitable habitats may be due to their low dispersal ability rather than adverse environmental conditions.
format: application/pdf
format: text/html
creator: Thor-Seng Liew
creator: Chee-Chean Phung
creator: Mohamad Afandi Mat Said
creator: Pui Kiat Hoo
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.11886
publisher: PeerJ Inc.
rights: © 2021 Liew et al.
abstract: This study aimed to reveal the habitat variables that determine the distribution and abundance of the land snail Pollicaria elephas in limestone habitats in Perak, Malaysia. Seventeen plots were selected on a limestone hill to determine the effect of environmental variables on the abundance of this land snail. The environmental variables we considered included habitat (canopy cover and leaf litter thickness), topography (elevation, aspect, ruggedness, and slope), microclimate (soil temperature, air temperature, and humidity), and vegetation (abundance of respective vascular plant species). The correlation analyses suggested that the snails’ abundance was positively correlated with the abundance of the four vascular plant species: Diospyros toposia var. toposoides, Croton cascarilloides, Kibatalia laurifolia, and Mallotus peltatus. Plots with lower soil temperatures had more snails than plots with higher soil temperatures. Our results show that plots in the southern part of the limestone hill, in which P. elephas were absent, were similar in habitat, topography, microclimate, and vegetation to the plots in the northern part of the limestone hill, where specimens were mostly present. The absence of this species in suitable habitats may be due to their low dispersal ability rather than adverse environmental conditions.
bibliographic citation: Liew et al. (2021) Distribution and abundance of the land snail Pollicaria elephas (Gastropoda: Pupinidae) in limestone habitats in Perak, Malaysia. PeerJ 9:e11886 https://doi.org/10.7717/peerj.11886
date submitted: 2020-09-28
date accepted: 2021-07-09
issued: 2021-07-28
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liew
  given name: Thor-Seng
author list: Agent
  family name: Phung
  given name: Chee-Chean
author list: Agent
  family name: Mat Said
  given name: Mohamad Afandi
author list: Agent
  family name: Hoo
  given name: Pui Kiat
doi: 10.7717/peerj.11886
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-28
copyright: ©2021 Liew et al.
attribution name: Liew et al.

Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum)
type: item
type: AcademicArticle
description: Many pollination studies with honey bees have examined the effect of colony density on crop yield and yet overlook the effect of variation in the population size of these colonies. High colony density in northern highbush blueberry has been met with concerns from beekeepers who feel higher densities will intensify outbreaks of European foulbrood (EFB, Melissococcus plutonius, Truper and dé Clari), a honey bee brood disease. The purpose of this study was to confirm the prevalence of EFB in colonies pollinating blueberries and to determine whether field-level variation in the population of adult workers in colonies explained variation in blueberry fruit set and/or yield. We addressed these objectives over the course of two production seasons at 13 commercial blueberry fields in Oregon, USA, stocked with identical densities of 10 colonies/ha. We confirmed that all colonies had negligible symptoms of EFB at the start of blueberry pollination, but 53% of colonies in 2019 and 41% in 2020 had symptoms immediately following the pollination season. We also validated a method for rapidly assessing adult honey bee colony populations, namely by counting the rate of foragers returning to colonies, and it was found to be strongly correlated to true internal adult bee population independent of year and ambient temperature at the time of evaluation. Using returning forager counts, we determined there was considerable variation in the average population of colonies at each field, ranging from an estimated 10,300 to 30,700 adult worker bees per colony. While average colony strength did not predict variation in fruit set, it was related to variation in yield, independent of year. Our linear model of flight count (as a proxy for colony strength) predicts estimated yield increases of up to 25,000 kg/ha of blueberries could be achieved by colonies stronger than the recommended six frame minimum, suggesting that higher pollination benefits could be achieved without increasing hive density…
format: application/pdf
format: text/html
creator: Kennedy Judith Grant
creator: Lisa DeVetter
creator: Andony Melathopoulos
subject: Agricultural Science
subject: Ecology
subject: Ecosystem Science
subject: Entomology
subject: Plant Science
description: doi:10.7717/peerj.11634
publisher: PeerJ Inc.
rights: © 2021 Grant et al.
abstract: Many pollination studies with honey bees have examined the effect of colony density on crop yield and yet overlook the effect of variation in the population size of these colonies. High colony density in northern highbush blueberry has been met with concerns from beekeepers who feel higher densities will intensify outbreaks of European foulbrood (EFB, Melissococcus plutonius, Truper and dé Clari), a honey bee brood disease. The purpose of this study was to confirm the prevalence of EFB in colonies pollinating blueberries and to determine whether field-level variation in the population of adult workers in colonies explained variation in blueberry fruit set and/or yield. We addressed these objectives over the course of two production seasons at 13 commercial blueberry fields in Oregon, USA, stocked with identical densities of 10 colonies/ha. We confirmed that all colonies had negligible symptoms of EFB at the start of blueberry pollination, but 53% of colonies in 2019 and 41% in 2020 had symptoms immediately following the pollination season. We also validated a method for rapidly assessing adult honey bee colony populations, namely by counting the rate of foragers returning to colonies, and it was found to be strongly correlated to true internal adult bee population independent of year and ambient temperature at the time of evaluation. Using returning forager counts, we determined there was considerable variation in the average population of colonies at each field, ranging from an estimated 10,300 to 30,700 adult worker bees per colony. While average colony strength did not predict variation in fruit set, it was related to variation in yield, independent of year. Our linear model of flight count (as a proxy for colony strength) predicts estimated yield increases of up to 25,000 kg/ha of blueberries could be achieved by colonies stronger than the recommended six frame minimum, suggesting that higher pollination benefits could be achieved without increasing hive density…
bibliographic citation: Grant et al. (2021) Honey bee (Apis mellifera) colony strength and its effects on pollination and yield in highbush blueberries (Vaccinium corymbosum). PeerJ 9:e11634 https://doi.org/10.7717/peerj.11634
date submitted: 2021-02-11
date accepted: 2021-05-27
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Grant
  given name: Kennedy Judith
author list: Agent
  family name: DeVetter
  given name: Lisa
author list: Agent
  family name: Melathopoulos
  given name: Andony
doi: 10.7717/peerj.11634
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Grant et al.
attribution name: Grant et al.

A new HSI denoising method via interpolated block matching 3D and guided filter
type: item
type: AcademicArticle
description: A new hyperspectral images (HSIs) denoising method via Interpolated Block-Matching and 3D filtering and Guided Filtering (IBM3DGF) denoising method is proposed. First, inter-spectral correlation analysis is used to obtain inter-spectral correlation coefficients and divide the HSIs into several adjacent groups. Second, high-resolution HSIs are produced by using adjacent three images to interpolate. Third, Block-Matching and 3D filtering (BM3D) is conducted to reduce the noise level of each group; Fourth, the guided image filtering is utilized to denoise HSI of each group. Finally, the inverse interpolation is applied to retrieve HSI. Experimental results of synthetic and real HSIs showed that, comparing with other state-of-the-art denoising methods, the proposed IBM3DGF method shows superior performance according to spatial and spectral domain noise assessment. Therefore, the proposed method has a potential to effectively remove the spatial/spectral noise for HSIs.
format: application/pdf
format: text/html
creator: Ping Xu
creator: Bingqiang Chen
creator: Jingcheng Zhang
creator: Lingyun Xue
creator: Lei Zhu
subject: Computational Science
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.11642
publisher: PeerJ Inc.
rights: © 2021 Xu et al.
abstract: A new hyperspectral images (HSIs) denoising method via Interpolated Block-Matching and 3D filtering and Guided Filtering (IBM3DGF) denoising method is proposed. First, inter-spectral correlation analysis is used to obtain inter-spectral correlation coefficients and divide the HSIs into several adjacent groups. Second, high-resolution HSIs are produced by using adjacent three images to interpolate. Third, Block-Matching and 3D filtering (BM3D) is conducted to reduce the noise level of each group; Fourth, the guided image filtering is utilized to denoise HSI of each group. Finally, the inverse interpolation is applied to retrieve HSI. Experimental results of synthetic and real HSIs showed that, comparing with other state-of-the-art denoising methods, the proposed IBM3DGF method shows superior performance according to spatial and spectral domain noise assessment. Therefore, the proposed method has a potential to effectively remove the spatial/spectral noise for HSIs.
bibliographic citation: Xu et al. (2021) A new HSI denoising method via interpolated block matching 3D and guided filter. PeerJ 9:e11642 https://doi.org/10.7717/peerj.11642
date submitted: 2019-01-17
date accepted: 2021-05-28
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Ping
author list: Agent
  family name: Chen
  given name: Bingqiang
author list: Agent
  family name: Zhang
  given name: Jingcheng
author list: Agent
  family name: Xue
  given name: Lingyun
author list: Agent
  family name: Zhu
  given name: Lei
doi: 10.7717/peerj.11642
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Xu et al.
attribution name: Xu et al.

Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication
type: item
type: AcademicArticle
description: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming.
format: application/pdf
format: text/html
creator: Susana Marcela Simancas-Giraldo
creator: Nan Xiang
creator: Meghan Moger Kennedy
creator: Rassil Nafeh
creator: Edoardo Zelli
creator: Christian Wild
subject: Marine Biology
subject: Climate Change Biology
subject: Aquatic and Marine Chemistry
description: doi:10.7717/peerj.11663
publisher: PeerJ Inc.
rights: © 2021 Simancas-Giraldo et al.
abstract: Eutrophication with dissolved organic carbon (DOC) as a far under-investigated stressor, and ocean warming, can strongly affect coral reefs and hard corals as major reefs ecosystem engineers. However, no previous studies have investigated the metabolic responses of soft corals to DOC eutrophication, or its interaction with ocean warming. Thus, we investigated respiration and photosynthesis response of Xenia umbellata, a common mixotrophic soft coral from the Indo-pacific, to (1) three levels of DOC eutrophication simulated by glucose addition over the first 21 days of experiment and (2) ocean warming scenarios where the temperature was gradually increased from 26 °C (control condition) to 32 °C over another 24 days in an aquarium experiment. We found no significant difference in response to DOC treatments and all corals survived regardless of the DOC concentrations, whilst subsequent exposure to simulated ocean warming significantly decreased gross photosynthesis by approximately 50% at 30 °C, and 65% at 32 °C, net photosynthesis by 75% at 30 °C and 79% at 32 °C, and respiration by a maximum of 75% at 30 °C; with a slight increase at 32 °C of 25%. The ratio between gross photosynthesis and respiration decreased by the end of the warming period but remained similar between controls and colonies previously exposed to DOC. Our findings suggest that soft corals may be more resistant than hard corals to DOC eutrophication and in consequence, may potentially experiment in less magnitude the negative effects of increased temperature or subsequently both stressors. The results of this study may contribute to explain the successful role of soft corals in phase shifts as reported from many coral reefs. Where predicted declines in reef ecosystems health due to increased eutrophication levels can be exacerbated by future warming.
bibliographic citation: Simancas-Giraldo et al. (2021) Photosynthesis and respiration of the soft coral Xenia umbellata respond to warming but not to organic carbon eutrophication. PeerJ 9:e11663 https://doi.org/10.7717/peerj.11663
date submitted: 2020-12-09
date accepted: 2021-06-01
issued: 2021-07-27
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simancas-Giraldo
  given name: Susana Marcela
author list: Agent
  family name: Xiang
  given name: Nan
author list: Agent
  family name: Kennedy
  given name: Meghan Moger
author list: Agent
  family name: Nafeh
  given name: Rassil
author list: Agent
  family name: Zelli
  given name: Edoardo
author list: Agent
  family name: Wild
  given name: Christian
doi: 10.7717/peerj.11663
volume: 9
issn: 2167-8359
publication name: PeerJ
publication date: 2021-07-27
copyright: ©2021 Simancas-Giraldo et al.
attribution name: Simancas-Giraldo et al.

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