PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis
items: Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles
items: Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China
items: Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
items: Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system
items: Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern
items: A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context
items: Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis
items: The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas
items: Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity

Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis
type: item
type: AcademicArticle
description: In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes.
format: application/pdf
format: text/html
creator: Daniel Doherty-Weason
creator: Fernanda X. Oyarzun
creator: Luciano Vera
creator: Miguel Bascur
creator: Fabián Guzmán
creator: Francisco Silva
creator: Ángel Urzúa
creator: Antonio Brante
subject: Evolutionary Studies
subject: Marine Biology
description: doi:10.7717/peerj.6151
publisher: PeerJ Inc.
rights: © 2019 Doherty-Weason et al.
abstract: In marine invertebrates, the modes of development at early stages are related to the type and capacity of larval feeding to achieve growth. Therefore, studying the factors that determine larval feeding strategies can help to understand the diversity of life histories and evolution of marine invertebrates. The polychaete Boccardia wellingtonensis is a poecilogonous species that encapsulates and incubates its offspring. This species produces two types of larvae: (1) larvae that do not feed within the capsule and hatch as planktotrophic larvae (indirect development), and (2) adelphophagic larvae that feed on nurse eggs and other larvae inside the capsule to hatch as advanced larvae or juveniles (direct development). Otherwise, the larval types are indistinguishable at the same stage of development. The non-apparent morphological differences between both types of larvae suggest that other factors are influencing their feeding behavior. This work studied the potential role of the activity of 19 digestive enzymes on the different feeding capacities of planktotrophic and adelphophagic larvae of B. wellingtonensis. Also, differences in larval feeding structures and the larval capacity to feed from intracapsular fluid were evaluated by electron and fluorescence microscopy. Results showed that both types of larvae present similar feeding structures and had the capacity to ingest intracapsular fluid protein. Adelphophagic larvae showed overall the highest activities of digestive enzymes. Significant differences between larval types were observed in nine enzymes related to the use of internal and external nutritional sources. Given that larval feeding is closely related to larval development in species with encapsulation, this work supports that the study of the digestive enzymatic machinery of larvae may contribute to understanding the evolution of developmental modes.
bibliographic citation: Doherty-Weason et al. (2019) Role of the larval feeding morphology and digestive enzyme activity in the early development of the polychaete Boccardia wellingtonensis. PeerJ 7:e6151 https://doi.org/10.7717/peerj.6151
date submitted: 2018-08-13
date accepted: 2018-11-22
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Doherty-Weason
  given name: Daniel
author list: Agent
  family name: Oyarzun
  given name: Fernanda X.
author list: Agent
  family name: Vera
  given name: Luciano
author list: Agent
  family name: Bascur
  given name: Miguel
author list: Agent
  family name: Guzmán
  given name: Fabián
author list: Agent
  family name: Silva
  given name: Francisco
author list: Agent
  family name: Urzúa
  given name: Ángel
author list: Agent
  family name: Brante
  given name: Antonio
doi: 10.7717/peerj.6151
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Doherty-Weason et al.
attribution name: Doherty-Weason et al.

Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles
type: item
type: AcademicArticle
description: Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders.
format: application/pdf
format: text/html
creator: Haiying Guo
creator: Yizhan Xing
creator: Fang Deng
creator: Ke Yang
creator: Yuhong Li
subject: Cell Biology
subject: Dermatology
description: doi:10.7717/peerj.6153
publisher: PeerJ Inc.
rights: © 2019 Guo et al.
abstract: Secreted Frizzled-related Protein 4 (sFRP4) belongs to Wnt inhibitors. Previously, we reported that sFRP4 inhibited the differentiation of melanocyte. Here, by using of immunostaining, we showed that sFRP4 is expressed in both human and mouse hair follicles, especially in the outer root sheath and inner root sheath. To reveal the role of sFRP4 in hair follicle growth and hair cycle, we induced synchronized hair cycle in the dorsal skin of mice by depilation, and injected sFRP4 intradermally into the skin. By hematoxylin and eosin staining, we found that the regeneration of hair follicles was inhibited by sFRP4. However, the structure of hair follicles remained complete. Compared with phosphate buffer saline-treated hair follicles, the sFRP4-treated hair follicles still had the same expression pattern of keratins. Our findings reveal that sFRP4 inhibits but not blocks the regeneration of hair follicles, and supply a potential therapeutic application to treat hair follicle regeneration disorders.
bibliographic citation: Guo et al. (2019) Secreted Frizzled-related protein 4 inhibits the regeneration of hair follicles. PeerJ 6:e6153 https://doi.org/10.7717/peerj.6153
date submitted: 2018-08-28
date accepted: 2018-11-24
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Guo
  given name: Haiying
author list: Agent
  family name: Xing
  given name: Yizhan
author list: Agent
  family name: Deng
  given name: Fang
author list: Agent
  family name: Yang
  given name: Ke
author list: Agent
  family name: Li
  given name: Yuhong
doi: 10.7717/peerj.6153
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Guo et al.
attribution name: Guo et al.

Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China
type: item
type: AcademicArticle
description: A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus.
format: application/pdf
format: text/html
creator: Xin Hong
creator: Jeremy Keene
creator: Zhi-Jing Qiu
creator: Fang Wen
subject: Plant Science
subject: Taxonomy
description: doi:10.7717/peerj.6157
publisher: PeerJ Inc.
rights: © 2019 Hong et al.
abstract: A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogenetic relationships and generic placement of this species, not only morphological anatomical features but also chromosome and DNA sequence data were examined and analysed here. Two samples from different populations identified as Primulina anisocymosa are monophyletic and were nested in a monophyletic clade within Primulina with high branch support. The somatic chromosome number of the new species is also reported (2n = 36), supporting its placement in the genus.
bibliographic citation: Hong et al. (2019) Primulina anisocymosa (Gesneriaceae), a new species with a unique inflorescence structure from Guangdong, China. PeerJ 7:e6157 https://doi.org/10.7717/peerj.6157
date submitted: 2018-08-01
date accepted: 2018-11-25
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hong
  given name: Xin
author list: Agent
  family name: Keene
  given name: Jeremy
author list: Agent
  family name: Qiu
  given name: Zhi-Jing
author list: Agent
  family name: Wen
  given name: Fang
doi: 10.7717/peerj.6157
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Hong et al.
attribution name: Hong et al.

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
type: item
type: AcademicArticle
description: Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
format: application/pdf
format: text/html
creator: Paul P. Gardner
creator: Renee J. Watson
creator: Xochitl C. Morgan
creator: Jenny L. Draper
creator: Robert D. Finn
creator: Sergio E. Morales
creator: Matthew B. Stott
subject: Bioinformatics
subject: Computational Biology
description: doi:10.7717/peerj.6160
publisher: PeerJ Inc.
rights: © 2019 Gardner et al.
abstract: Metagenomic and meta-barcode DNA sequencing has rapidly become a widely-used technique for investigating a range of questions, particularly related to health and environmental monitoring. There has also been a proliferation of bioinformatic tools for analysing metagenomic and amplicon datasets, which makes selecting adequate tools a significant challenge. A number of benchmark studies have been undertaken; however, these can present conflicting results. In order to address this issue we have applied a robust Z-score ranking procedure and a network meta-analysis method to identify software tools that are consistently accurate for mapping DNA sequences to taxonomic hierarchies. Based upon these results we have identified some tools and computational strategies that produce robust predictions.
bibliographic citation: Gardner et al. (2019) Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies. PeerJ 7:e6160 https://doi.org/10.7717/peerj.6160
date submitted: 2017-11-08
date accepted: 2018-11-14
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gardner
  given name: Paul P.
author list: Agent
  family name: Watson
  given name: Renee J.
author list: Agent
  family name: Morgan
  given name: Xochitl C.
author list: Agent
  family name: Draper
  given name: Jenny L.
author list: Agent
  family name: Finn
  given name: Robert D.
author list: Agent
  family name: Morales
  given name: Sergio E.
author list: Agent
  family name: Stott
  given name: Matthew B.
doi: 10.7717/peerj.6160
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: ©2019 Gardner et al.
attribution name: Gardner et al.

Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system
type: item
type: AcademicArticle
description: Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregate…
format: application/pdf
format: text/html
creator: Naling Bai
creator: Hanlin Zhang
creator: Shuangxi Li
creator: Xianqing Zheng
creator: Juanqin Zhang
creator: Haiyun Zhang
creator: Sheng Zhou
creator: Huifeng Sun
creator: Weiguang Lv
subject: Ecology
subject: Microbiology
description: doi:10.7717/peerj.6171
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregate…
bibliographic citation: Bai et al. (2019) Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system. PeerJ 6:e6171 https://doi.org/10.7717/peerj.6171
date submitted: 2018-10-14
date accepted: 2018-11-27
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Naling
author list: Agent
  family name: Zhang
  given name: Hanlin
author list: Agent
  family name: Li
  given name: Shuangxi
author list: Agent
  family name: Zheng
  given name: Xianqing
author list: Agent
  family name: Zhang
  given name: Juanqin
author list: Agent
  family name: Zhang
  given name: Haiyun
author list: Agent
  family name: Zhou
  given name: Sheng
author list: Agent
  family name: Sun
  given name: Huifeng
author list: Agent
  family name: Lv
  given name: Weiguang
doi: 10.7717/peerj.6171
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bai et al.
attribution name: Bai et al.

Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern
type: item
type: AcademicArticle
description: Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exp…
format: application/pdf
format: text/html
creator: Wei Bai
creator: Changgui Kou
creator: Lili Zhang
creator: Yueyue You
creator: Weiying Yu
creator: Wanqing Hua
creator: Yuanyuan Li
creator: Yaqin Yu
creator: Tiancheng Zhao
creator: Yanhua Wu
subject: Biochemistry
subject: Genetics
subject: Epidemiology
subject: Public Health
description: doi:10.7717/peerj.6175
publisher: PeerJ Inc.
rights: © 2019 Bai et al.
abstract: Background Dyslipidemia contributes to the risk of many diseases, including stroke, cardiovascular disease and metabolic-related diseases. Previous studies have indicated that single nucleotide polymorphisms (SNPs) are associated with different levels of serum lipid. Therefore, this study explored the relationship between the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms and dyslipidemia in the total sample population and stratified by genders in a northeast Chinese population. Methods A total of 3,850 participants from Jilin Province, China, were enrolled in our study, and their serum lipid levels were measured. Six functional SNPs (APOA1 rs5072, APOC3 rs5128, APOA4 rs5104, APOA5 rs651821, ZPR1 rs2075294 and BUD13 rs10488698) were genotyped using polymerase chain reaction and MALDI-TOF-MS. Logistic regression analysis was performed to explore the relationship of APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster gene polymorphisms with dyslipidemia. Linkage disequilibrium and haplotype analyses were performed with the SNPStats program and Haploview software. Results All SNPs conformed to Hardy–Weinberg equilibrium. Logistic regression analysis revealed that rs5072, rs5128 and rs651821 were associated with hypertriglyceridemia, rs5104 and rs651821 were associated with low-HDL cholesterolemia in overall group. rs651821 was associated with hypertriglyceridemia and low-HDL cholesterolemia in both the male and female group. However, among females, rs5072 was observed to be associated with hypertriglyceridemia. Haplotype analysis showed that haplotypes TGCCGC and CAGCGC were associated with dyslipidemia in the overall, male and female groups. Conclusion SNPs in the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster were associated with dyslipidemia. Furthermore, the association of APOA1 rs5072 in this gene cluster with dyslipidemia differed between genders; thus, additional studies are needed to confirm this conclusion, and the mechanisms underlying these results warrant further exp…
bibliographic citation: Bai et al. (2019) Functional polymorphisms of the APOA1/C3/A4/A5-ZPR1-BUD13 gene cluster are associated with dyslipidemia in a sex-specific pattern. PeerJ 6:e6175 https://doi.org/10.7717/peerj.6175
date submitted: 2018-05-29
date accepted: 2018-11-26
issued: 2019-01-04
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Wei
author list: Agent
  family name: Kou
  given name: Changgui
author list: Agent
  family name: Zhang
  given name: Lili
author list: Agent
  family name: You
  given name: Yueyue
author list: Agent
  family name: Yu
  given name: Weiying
author list: Agent
  family name: Hua
  given name: Wanqing
author list: Agent
  family name: Li
  given name: Yuanyuan
author list: Agent
  family name: Yu
  given name: Yaqin
author list: Agent
  family name: Zhao
  given name: Tiancheng
author list: Agent
  family name: Wu
  given name: Yanhua
doi: 10.7717/peerj.6175
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-04
copyright: © 2019 Bai et al.
attribution name: Bai et al.

A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context
type: item
type: AcademicArticle
description: A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.
format: application/pdf
format: text/html
creator: Jennifer A. Clack
creator: Carys E. Bennett
creator: Sarah J. Davies
creator: Andrew C. Scott
creator: Janet E. Sherwin
creator: Timothy R. Smithson
subject: Evolutionary Studies
subject: Paleontology
description: doi:10.7717/peerj.5972
publisher: PeerJ Inc.
rights: © 2019 Clack et al.
abstract: A conglomerate bed from the Tournaisian Ballagan Formation of Scotland preserves a rich array of vertebrate and other nonmarine fossils providing an insight into the wider ecosystem and paleoenvironment that existed during this pivotal stage of Earth history. It challenges hypotheses of a long-lasting post-extinction trough following the end-Devonian extinction event. The fauna recovered includes a wide size range of tetrapods, rhizodonts, and dipnoans, from tiny juveniles or small-bodied taxa up to large adults, and more than one taxon of each group is likely. Some fauna, such as actinopterygians and chondrichthyans, are rare as macrofauna but are better represented in the microfossil assemblage. The fauna provides evidence of the largest Carboniferous lungfish ever found. The specimens are preserved in a localized, poorly-sorted conglomerate which was deposited in the deepest part of a river channel, the youngest of a group of channels. In addition to the fossils (micro- and macro-), the conglomerate includes locally-derived clasts of paleosols and other distinctive elements of the surrounding floodplains. Charcoal fragments represent small woody axes and possible larger trunk tissue from arborescent pteridosperms. Preservation of the fossils indicates some aerial exposure prior to transport, with abrasion from rolling. The findings presented here contrast with other published trends in vertebrate size that are used to interpret a reduction in maximum sizes during the Tournaisian. The richness of the fauna runs counter to the assumption of a depauperate nonmarine fauna following the end-Devonian Hangenberg event, and charcoal content highlights the occurrence of fire, with the requisite levels of atmospheric oxygen during that stage.
bibliographic citation: Clack et al. (2019) A Tournaisian (earliest Carboniferous) conglomerate-preserved non-marine faunal assemblage and its environmental and sedimentological context. PeerJ 6:e5972 https://doi.org/10.7717/peerj.5972
date submitted: 2018-08-06
date accepted: 2018-10-19
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Clack
  given name: Jennifer A.
author list: Agent
  family name: Bennett
  given name: Carys E.
author list: Agent
  family name: Davies
  given name: Sarah J.
author list: Agent
  family name: Scott
  given name: Andrew C.
author list: Agent
  family name: Sherwin
  given name: Janet E.
author list: Agent
  family name: Smithson
  given name: Timothy R.
doi: 10.7717/peerj.5972
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: © 2019 Clack et al.
attribution name: Clack et al.

Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis
type: item
type: AcademicArticle
description: Background Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins from S. nigrum were screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking. Methods Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA). Results Docking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and…
format: application/pdf
format: text/html
creator: Rumana Ahmad
subject: Biochemistry
subject: Bioinformatics
subject: Cell Biology
subject: Computational Biology
subject: Plant Science
description: doi:10.7717/peerj.6012
publisher: PeerJ Inc.
rights: © 2019 Ahmad
abstract: Background Solanum nigrum (black nightshade; S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins from S. nigrum were screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking. Methods Bioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA). Results Docking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and…
bibliographic citation: Ahmad (2019) Steroidal glycoalkaloids from Solanum nigrum target cytoskeletal proteins: an in silico analysis. PeerJ 7:e6012 https://doi.org/10.7717/peerj.6012
date submitted: 2018-03-05
date accepted: 2018-10-26
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ahmad
  given name: Rumana
doi: 10.7717/peerj.6012
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Ahmad
attribution name: Ahmad

The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas
type: item
type: AcademicArticle
description: The evolution of distinct ecologies and correlated morphologies (“ecomorphs,” in combination) among similar species allows sympatric occupation of diverse microhabitats. Particular ecomorphs may evolve repeatedly, that is, convergently, as separate lineages arrive at similar solutions. Caribbean Anolis lizards (anoles) are a classic ecomorph system, particularly well-studied for the diverse morphotypes resulting from adaptive radiations. But few studies have analyzed the equally species-diverse mainland Anolis. Here, we use clustering analyses of nine traits for 336 species of Anolis to objectively identify morphological groups (morphotypes). We analyze the presence of recovered morphotypes on mainland and islands in general and relative to the composition of 76 mainland and 91 island anole assemblages. We test for evolutionary convergence of morphotypes within and between mainland and island environments by mapping our recovered morphotypes onto recent phylogenetic estimates and by analyzing four of our measured traits using program SURFACE. We find that particular morphotypes tend to be restricted to either mainland or island environments. Morphotype diversity and convergence are not concentrated within either island or mainland environments. Morphotype content of assemblages differs between mainland and island areas, with island assemblages displaying greater numbers of morphotypes than mainland assemblages. Taken with recent research, these results suggest a restructuring of one of the classic adaptive radiation stories and a reconsideration of research concerning island–mainland faunal differences. Island radiations of anoles are unexceptional relative to mainland radiations with regard to species count, rates of speciation and phenotypic evolution, morphotype diversity, and rates of convergence. But local island assemblage appear to be more diverse than mainland assemblages. The explanation for this assemblage disparity may reside in one of the classic hypothe…
format: application/pdf
format: text/html
creator: Steven Poe
creator: Christopher G. Anderson
subject: Biodiversity
subject: Ecology
subject: Evolutionary Studies
description: doi:10.7717/peerj.6040
publisher: PeerJ Inc.
rights: © 2019 Poe and Anderson
abstract: The evolution of distinct ecologies and correlated morphologies (“ecomorphs,” in combination) among similar species allows sympatric occupation of diverse microhabitats. Particular ecomorphs may evolve repeatedly, that is, convergently, as separate lineages arrive at similar solutions. Caribbean Anolis lizards (anoles) are a classic ecomorph system, particularly well-studied for the diverse morphotypes resulting from adaptive radiations. But few studies have analyzed the equally species-diverse mainland Anolis. Here, we use clustering analyses of nine traits for 336 species of Anolis to objectively identify morphological groups (morphotypes). We analyze the presence of recovered morphotypes on mainland and islands in general and relative to the composition of 76 mainland and 91 island anole assemblages. We test for evolutionary convergence of morphotypes within and between mainland and island environments by mapping our recovered morphotypes onto recent phylogenetic estimates and by analyzing four of our measured traits using program SURFACE. We find that particular morphotypes tend to be restricted to either mainland or island environments. Morphotype diversity and convergence are not concentrated within either island or mainland environments. Morphotype content of assemblages differs between mainland and island areas, with island assemblages displaying greater numbers of morphotypes than mainland assemblages. Taken with recent research, these results suggest a restructuring of one of the classic adaptive radiation stories and a reconsideration of research concerning island–mainland faunal differences. Island radiations of anoles are unexceptional relative to mainland radiations with regard to species count, rates of speciation and phenotypic evolution, morphotype diversity, and rates of convergence. But local island assemblage appear to be more diverse than mainland assemblages. The explanation for this assemblage disparity may reside in one of the classic hypothe…
bibliographic citation: Poe et al. (2019) The existence and evolution of morphotypes in Anolis lizards: coexistence patterns, not adaptive radiations, distinguish mainland and island faunas. PeerJ 6:e6040 https://doi.org/10.7717/peerj.6040
date submitted: 2017-11-21
date accepted: 2018-10-30
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Poe
  given name: Steven
author list: Agent
  family name: Anderson
  given name: Christopher G.
doi: 10.7717/peerj.6040
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: © 2019 Poe and Anderson
attribution name: Poe and Anderson

Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity
type: item
type: AcademicArticle
description: Chitin is the second most abundant organic compound in nature and represents a rich carbon and nitrogen source that is primarily transformed by bacterial communities. Bacteria capable of gradually hydrolyzing chitin into N-acetylglucosamine monomers can have applications in the transformation of residues from shrimp and other crustaceans. The objective of the present study was to isolate, characterize and identify microorganisms with high chitinolytic activity. These microorganisms were isolated and characterized based on macro- and microscopic morphological traits. Strains were selected on colloidal chitin agar medium primarily based on a hydrolysis halo larger than 2 mm and a growing phase no longer than 6 days. Secondary selection consisted of semi-quantitative evaluation of chitinolytic activity with a drop dilution assay. From the above, ten strains were selected. Then, strain-specific activity was evaluated. The B4 strain showed the highest specific activity, which was 6,677.07 U/mg protein. Molecular identification indicated that the isolated strains belong to the species Stenotrophomonas maltophilia.
format: application/pdf
format: text/html
creator: Roger Salas-Ovilla
creator: Didiana Gálvez-López
creator: Alfredo Vázquez-Ovando
creator: Miguel Salvador-Figueroa
creator: Raymundo Rosas-Quijano
subject: Microbiology
subject: Molecular Biology
description: doi:10.7717/peerj.6102
publisher: PeerJ Inc.
rights: © 2019 Salas-Ovilla et al.
abstract: Chitin is the second most abundant organic compound in nature and represents a rich carbon and nitrogen source that is primarily transformed by bacterial communities. Bacteria capable of gradually hydrolyzing chitin into N-acetylglucosamine monomers can have applications in the transformation of residues from shrimp and other crustaceans. The objective of the present study was to isolate, characterize and identify microorganisms with high chitinolytic activity. These microorganisms were isolated and characterized based on macro- and microscopic morphological traits. Strains were selected on colloidal chitin agar medium primarily based on a hydrolysis halo larger than 2 mm and a growing phase no longer than 6 days. Secondary selection consisted of semi-quantitative evaluation of chitinolytic activity with a drop dilution assay. From the above, ten strains were selected. Then, strain-specific activity was evaluated. The B4 strain showed the highest specific activity, which was 6,677.07 U/mg protein. Molecular identification indicated that the isolated strains belong to the species Stenotrophomonas maltophilia.
bibliographic citation: Salas-Ovilla et al. (2019) Isolation and identification of marine strains of Stenotrophomona maltophilia with high chitinolytic activity. PeerJ 7:e6102 https://doi.org/10.7717/peerj.6102
date submitted: 2018-08-27
date accepted: 2018-11-06
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salas-Ovilla
  given name: Roger
author list: Agent
  family name: Gálvez-López
  given name: Didiana
author list: Agent
  family name: Vázquez-Ovando
  given name: Alfredo
author list: Agent
  family name: Salvador-Figueroa
  given name: Miguel
author list: Agent
  family name: Rosas-Quijano
  given name: Raymundo
doi: 10.7717/peerj.6102
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Salas-Ovilla et al.
attribution name: Salas-Ovilla et al.

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