PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America
items: Remote sensing inversion and spatial variation of land surface temperature over mining areas of Jixi, Heilongjiang, China
items: Pro-inflammatory response ensured by LPS and Pam3CSK4 in RAW 264.7 cells did not improve a fungistatic effect on Cryptococcus gattii infection
items: Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect
items: Three new deep-sea species of Thyasiridae (Mollusca: Bivalvia) from the abyssal plain of the northwestern Pacific Ocean and hadal depths of the Kuril-Kamchatka Trench
items: Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results
items: Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli
items: miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2
items: The Italian record of the Cretaceous shark, Ptychodus latissimus Agassiz, 1835 (Chondrichthyes; Elasmobranchii)
items: Hissing of geese: caller identity encoded in a non-vocal acoustic signal

A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America
type: item
type: AcademicArticle
description: Background Studies with integrative approaches (based on different lines of evidence) are fundamental for understanding the diversity of organisms. Different data sources can improve the understanding of the taxonomy and evolution of snakes. We used this integrative approach to verify the taxonomic status of Hydrodynastes gigas (Duméril, Bibron & Duméril, 1854), given its wide distribution throughout South America, including the validity of the recently described Hydrodynastes melanogigas Franco, Fernandes & Bentim, 2007. Methods We performed a phylogenetic analysis of Bayesian Inference with mtDNA 16S and Cytb, and nuDNA Cmos and NT3 concatenated (1,902 bp). In addition, we performed traditional morphometric analyses, meristic, hemipenis morphology and coloration pattern of H. gigas and H. melanogigas. Results According to molecular and morphological characters, H. gigas is widely distributed throughout South America. We found no evidence to support that H. gigas and H. melanogigas species are distinct lineages, therefore, H. melanogigas is a junior synonym of H. gigas. Thus, the melanic pattern of H. melanogigas is the result of a polymorphism of H. gigas. Melanic populations of H. gigas can be found in the Tocantins-Araguaia basin.
format: application/pdf
format: text/html
creator: Priscila S. Carvalho
creator: Hussam Zaher
creator: Nelson J. da Silva Jr
creator: Diego J. Santana
subject: Biodiversity
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10073
publisher: PeerJ Inc.
rights: © 2020 Carvalho et al.
abstract: Background Studies with integrative approaches (based on different lines of evidence) are fundamental for understanding the diversity of organisms. Different data sources can improve the understanding of the taxonomy and evolution of snakes. We used this integrative approach to verify the taxonomic status of Hydrodynastes gigas (Duméril, Bibron & Duméril, 1854), given its wide distribution throughout South America, including the validity of the recently described Hydrodynastes melanogigas Franco, Fernandes & Bentim, 2007. Methods We performed a phylogenetic analysis of Bayesian Inference with mtDNA 16S and Cytb, and nuDNA Cmos and NT3 concatenated (1,902 bp). In addition, we performed traditional morphometric analyses, meristic, hemipenis morphology and coloration pattern of H. gigas and H. melanogigas. Results According to molecular and morphological characters, H. gigas is widely distributed throughout South America. We found no evidence to support that H. gigas and H. melanogigas species are distinct lineages, therefore, H. melanogigas is a junior synonym of H. gigas. Thus, the melanic pattern of H. melanogigas is the result of a polymorphism of H. gigas. Melanic populations of H. gigas can be found in the Tocantins-Araguaia basin.
bibliographic citation: Carvalho et al. (2020) A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America. PeerJ 8:e10073 https://doi.org/10.7717/peerj.10073
date submitted: 2020-05-19
date accepted: 2020-09-09
issued: 2020-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Carvalho
  given name: Priscila S.
author list: Agent
  family name: Zaher
  given name: Hussam
author list: Agent
  family name: da Silva Jr
  given name: Nelson J.
author list: Agent
  family name: Santana
  given name: Diego J.
doi: 10.7717/peerj.10073
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-25
copyright: ©2020 Carvalho et al.
attribution name: Carvalho et al.

Remote sensing inversion and spatial variation of land surface temperature over mining areas of Jixi, Heilongjiang, China
type: item
type: AcademicArticle
description: Background Jixi is a typical mining city in China that has undergone dramatic changes in its land-use pattern of mining areas over the development of its coal resources. The impacts of coal mining activities have greatly affected the regional land surface temperature and ecological system. Methods The Landsat 8 Operational Land Imager (OLI) data from 2015 and 2019 were used from the Jiguan, Didao, and Chengzihe District of Jixi in Heilongjiang, China as the study area. The calculations to determine the land-use classification, vegetation coverage, and land surface temperature (LST) were performed using ArcGIS10.5 and ENVI 5.3 software packages. A correlation analysis revealed the impact of land-use type, vegetation coverage, and coal mining activities on LSTs. Results The results show significant spatial differentiation in the LSTs of Jixi City. The LSTs for various land-use types were ranked from high to low as follows: mining land > construction land > grassland > cultivated land > forest land > water area. The LST was lower in areas with high vegetation coverage than in other areas. For every 0.1 increase in vegetation coverage, the LST is expected to drop by approximately 0.75 °C. An analysis of mining land patches indicates that the patch area of mining lands has a significant positive correlation with both the average and maximum patch temperatures. The average patch temperature shows a logarithmic increase with the growth of the patch area, and within 200,000 m2, the average patch temperature increases significantly. The maximum patch temperature shows a linear increase with the patch area growth, and for every 100,000 m2 increase in the patch area of mining lands, the maximum patch temperature increases by approximately 0.81 °C. The higher the average patch temperature of mining land, the higher the temperature in its buffer zone, and the greater its influence scope. This study provides a useful reference for exploring the warming effects caused by coal mini…
format: application/pdf
format: text/html
creator: Jia-shuo Cao
creator: Zheng-yu Deng
creator: Wen Li
creator: Yuan-dong Hu
subject: Coupled Natural and Human Systems
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.10257
publisher: PeerJ Inc.
rights: © 2020 Cao et al.
abstract: Background Jixi is a typical mining city in China that has undergone dramatic changes in its land-use pattern of mining areas over the development of its coal resources. The impacts of coal mining activities have greatly affected the regional land surface temperature and ecological system. Methods The Landsat 8 Operational Land Imager (OLI) data from 2015 and 2019 were used from the Jiguan, Didao, and Chengzihe District of Jixi in Heilongjiang, China as the study area. The calculations to determine the land-use classification, vegetation coverage, and land surface temperature (LST) were performed using ArcGIS10.5 and ENVI 5.3 software packages. A correlation analysis revealed the impact of land-use type, vegetation coverage, and coal mining activities on LSTs. Results The results show significant spatial differentiation in the LSTs of Jixi City. The LSTs for various land-use types were ranked from high to low as follows: mining land > construction land > grassland > cultivated land > forest land > water area. The LST was lower in areas with high vegetation coverage than in other areas. For every 0.1 increase in vegetation coverage, the LST is expected to drop by approximately 0.75 °C. An analysis of mining land patches indicates that the patch area of mining lands has a significant positive correlation with both the average and maximum patch temperatures. The average patch temperature shows a logarithmic increase with the growth of the patch area, and within 200,000 m2, the average patch temperature increases significantly. The maximum patch temperature shows a linear increase with the patch area growth, and for every 100,000 m2 increase in the patch area of mining lands, the maximum patch temperature increases by approximately 0.81 °C. The higher the average patch temperature of mining land, the higher the temperature in its buffer zone, and the greater its influence scope. This study provides a useful reference for exploring the warming effects caused by coal mini…
bibliographic citation: Cao et al. (2020) Remote sensing inversion and spatial variation of land surface temperature over mining areas of Jixi, Heilongjiang, China. PeerJ 8:e10257 https://doi.org/10.7717/peerj.10257
date submitted: 2020-04-20
date accepted: 2020-10-06
issued: 2020-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Jia-shuo
author list: Agent
  family name: Deng
  given name: Zheng-yu
author list: Agent
  family name: Li
  given name: Wen
author list: Agent
  family name: Hu
  given name: Yuan-dong
doi: 10.7717/peerj.10257
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-25
copyright: ©2020 Cao et al.
attribution name: Cao et al.

Pro-inflammatory response ensured by LPS and Pam3CSK4 in RAW 264.7 cells did not improve a fungistatic effect on Cryptococcus gattii infection
type: item
type: AcademicArticle
description: Background The macrophage lineage is characterized by plasticity due to the acquisition of distinct functional phenotypes, and two major subsets are evaluated; classical M1 activation (strong microbicidal activity) and alternative M2 activation (immunoregulatory functions). The M1 subset expresses inducible nitric oxide synthase (iNOS), which is a primary marker to identify these cells, whereas M2 macrophages are characterized by expression of Arginase-1, found in inflammatory zone 1 (Fizz1), chitinase-like molecule (Ym-1), and CD206. The micro-environmental stimuli and signals in tissues are critical in the macrophage polarization. Toll-like receptors (TLR) ligands, such as lipopolysaccharide (LPS), palmitoyl-3-cysteine-serine-lysine-4 (Pam3CSK4), and ArtinM (mannose-binding lectin) are inductors of M1 subset. The impact of TLR2 and TLR4 signals to fight against Cryptococcus gattii infection is unknown, which is a fungal pathogen that preferentially infects the lung of immunocompetent individuals. The macrophages initiate an immune response to combat the C. gattii, then we evaluated in RAW 264.7 cell the effect of TLR2 and TLR4 agonists on the macrophage polarization dynamic and the impact on the growth of C. gattii. Methods and Results We demonstrated that P3C4, LPS, and ArtinM induced an increase in the levels of iNOS transcripts in RAW 264.7 cells, whereas the relative expression of arginase-1, Ym-1, and Fizz1 was significantly increased in the presence of IL-4 alone. The effects of TLR2 and TLR4 agonists on repolarization from the M2 to M1 subset was evaluated, and the first stimulus was composed of IL-4 and, after 24 h of incubation, the cells were submitted to a second stimulus of P3C4, LPS, ArtinM, or Medium. These TLR agonists induced the production of TNF-α in polarized RAW 264.7 cells to the M2 subset, moreover the measurement of M1/M2 markers using qRT-PCR demonstrated that a second stimulus with LPS for 24 h induced a significant augmentation of levels …
format: application/pdf
format: text/html
creator: Gabriela Yamazaki de Campos
creator: Raquel Amorim Oliveira
creator: Patrícia Kellen Martins Oliveira-Brito
creator: Maria Cristina Roque-Barreira
creator: Thiago Aparecido da Silva
subject: Cell Biology
subject: Mycology
subject: Immunology
subject: Infectious Diseases
description: doi:10.7717/peerj.10295
publisher: PeerJ Inc.
rights: © 2020 de Campos et al.
abstract: Background The macrophage lineage is characterized by plasticity due to the acquisition of distinct functional phenotypes, and two major subsets are evaluated; classical M1 activation (strong microbicidal activity) and alternative M2 activation (immunoregulatory functions). The M1 subset expresses inducible nitric oxide synthase (iNOS), which is a primary marker to identify these cells, whereas M2 macrophages are characterized by expression of Arginase-1, found in inflammatory zone 1 (Fizz1), chitinase-like molecule (Ym-1), and CD206. The micro-environmental stimuli and signals in tissues are critical in the macrophage polarization. Toll-like receptors (TLR) ligands, such as lipopolysaccharide (LPS), palmitoyl-3-cysteine-serine-lysine-4 (Pam3CSK4), and ArtinM (mannose-binding lectin) are inductors of M1 subset. The impact of TLR2 and TLR4 signals to fight against Cryptococcus gattii infection is unknown, which is a fungal pathogen that preferentially infects the lung of immunocompetent individuals. The macrophages initiate an immune response to combat the C. gattii, then we evaluated in RAW 264.7 cell the effect of TLR2 and TLR4 agonists on the macrophage polarization dynamic and the impact on the growth of C. gattii. Methods and Results We demonstrated that P3C4, LPS, and ArtinM induced an increase in the levels of iNOS transcripts in RAW 264.7 cells, whereas the relative expression of arginase-1, Ym-1, and Fizz1 was significantly increased in the presence of IL-4 alone. The effects of TLR2 and TLR4 agonists on repolarization from the M2 to M1 subset was evaluated, and the first stimulus was composed of IL-4 and, after 24 h of incubation, the cells were submitted to a second stimulus of P3C4, LPS, ArtinM, or Medium. These TLR agonists induced the production of TNF-α in polarized RAW 264.7 cells to the M2 subset, moreover the measurement of M1/M2 markers using qRT-PCR demonstrated that a second stimulus with LPS for 24 h induced a significant augmentation of levels …
bibliographic citation: de Campos et al. (2020) Pro-inflammatory response ensured by LPS and Pam3CSK4 in RAW 264.7 cells did not improve a fungistatic effect on Cryptococcus gattii infection. PeerJ 8:e10295 https://doi.org/10.7717/peerj.10295
date submitted: 2020-06-09
date accepted: 2020-10-13
issued: 2020-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Campos
  given name: Gabriela Yamazaki
author list: Agent
  family name: Oliveira
  given name: Raquel Amorim
author list: Agent
  family name: Oliveira-Brito
  given name: Patrícia Kellen Martins
author list: Agent
  family name: Roque-Barreira
  given name: Maria Cristina
author list: Agent
  family name: da Silva
  given name: Thiago Aparecido
doi: 10.7717/peerj.10295
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-25
copyright: ©2020 de Campos et al.
attribution name: de Campos et al.

Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect
type: item
type: AcademicArticle
description: Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a “CAU” anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.
format: application/pdf
format: text/html
creator: Ting-Ting Zhang
creator: Yi-Kun Hou
creator: Ting Yang
creator: Shu-Ya Zhang
creator: Ming Yue
creator: Jianni Liu
creator: Zhonghu Li
subject: Evolutionary Studies
subject: Genomics
subject: Plant Science
description: doi:10.7717/peerj.10312
publisher: PeerJ Inc.
rights: © 2020 Zhang et al.
abstract: Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a “CAU” anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.
bibliographic citation: Zhang et al. (2020) Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect. PeerJ 8:e10312 https://doi.org/10.7717/peerj.10312
date submitted: 2019-11-27
date accepted: 2020-10-15
issued: 2020-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhang
  given name: Ting-Ting
author list: Agent
  family name: Hou
  given name: Yi-Kun
author list: Agent
  family name: Yang
  given name: Ting
author list: Agent
  family name: Zhang
  given name: Shu-Ya
author list: Agent
  family name: Yue
  given name: Ming
author list: Agent
  family name: Liu
  given name: Jianni
author list: Agent
  family name: Li
  given name: Zhonghu
doi: 10.7717/peerj.10312
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-25
copyright: ©2020 Zhang et al.
attribution name: Zhang et al.

Three new deep-sea species of Thyasiridae (Mollusca: Bivalvia) from the abyssal plain of the northwestern Pacific Ocean and hadal depths of the Kuril-Kamchatka Trench
type: item
type: AcademicArticle
description: The Thyasiridae is the most species-rich family of bivalves in the abyssal and hadal zones of the northwestern Pacific Ocean. In recent years, with at least 14 thyasirid species found in that region at depths exceeding 3,000 m. Some of them are the numerically dominant species in bottom communities. However, all members in that family have not yet been identified to the species level. Based on the material collected from 1953 to 2016 by five deep-sea expeditions, three new species of Thyasiridae (Mollusca: Bivalvia) are described from the abyssal and hadal zones of the northwestern Pacific. “Axinulus” roseus sp. nov. was found in the Kuril-Kamchatka Trench at 9,000–9,583 m depth. This species has a large rhomboidal shell with strong commarginal sculpture, a well defined, long and deep lunule and escutcheon without an auricle, a ctenidium consisting of a single demibranch, extensively lobed lateral pouches, and a large prodissoconch with specific sculpture. It is one of the dominant species in terms of abundance in macrobenthic communities in the deepest basin of the Kuril-Kamchatka Trench with a population density of up to 396 ind. m−2. The species has a shell length of up to 9.0 mm and it is the largest thyasirid with a single demibranch. “Axinulus” oliveri sp. nov. was found in a vast region of the northwestern Pacific on the abyssal plain adjacent to the Kuril-Kamchatka Trench, on the abyssal slope of the Kuril Islands, and in the Kuril-Kamchatka Trench at 4,648–6,168 m depth. This species is characterized by its ovate-rhomboidal shell, a well defined, deep and long escutcheon with a distinct auricle, a ctenidium with a single demibranch, and extensively lobed lateral pouches. It is widespread in the northwestern Pacific and forms populations with a density of up to 36 ind. m−2. Scanning electron microscopic observation of the gills of “A.” roseus sp. nov. and “A.” oliveri sp. nov. revealed that these species are not chemosymbiotic. “Axinulus” roseus sp. nov. and…
format: application/pdf
format: text/html
creator: Gennady M. Kamenev
subject: Biodiversity
subject: Ecology
subject: Marine Biology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10405
publisher: PeerJ Inc.
rights: © 2020 Kamenev
abstract: The Thyasiridae is the most species-rich family of bivalves in the abyssal and hadal zones of the northwestern Pacific Ocean. In recent years, with at least 14 thyasirid species found in that region at depths exceeding 3,000 m. Some of them are the numerically dominant species in bottom communities. However, all members in that family have not yet been identified to the species level. Based on the material collected from 1953 to 2016 by five deep-sea expeditions, three new species of Thyasiridae (Mollusca: Bivalvia) are described from the abyssal and hadal zones of the northwestern Pacific. “Axinulus” roseus sp. nov. was found in the Kuril-Kamchatka Trench at 9,000–9,583 m depth. This species has a large rhomboidal shell with strong commarginal sculpture, a well defined, long and deep lunule and escutcheon without an auricle, a ctenidium consisting of a single demibranch, extensively lobed lateral pouches, and a large prodissoconch with specific sculpture. It is one of the dominant species in terms of abundance in macrobenthic communities in the deepest basin of the Kuril-Kamchatka Trench with a population density of up to 396 ind. m−2. The species has a shell length of up to 9.0 mm and it is the largest thyasirid with a single demibranch. “Axinulus” oliveri sp. nov. was found in a vast region of the northwestern Pacific on the abyssal plain adjacent to the Kuril-Kamchatka Trench, on the abyssal slope of the Kuril Islands, and in the Kuril-Kamchatka Trench at 4,648–6,168 m depth. This species is characterized by its ovate-rhomboidal shell, a well defined, deep and long escutcheon with a distinct auricle, a ctenidium with a single demibranch, and extensively lobed lateral pouches. It is widespread in the northwestern Pacific and forms populations with a density of up to 36 ind. m−2. Scanning electron microscopic observation of the gills of “A.” roseus sp. nov. and “A.” oliveri sp. nov. revealed that these species are not chemosymbiotic. “Axinulus” roseus sp. nov. and…
bibliographic citation: Kamenev (2020) Three new deep-sea species of Thyasiridae (Mollusca: Bivalvia) from the abyssal plain of the northwestern Pacific Ocean and hadal depths of the Kuril-Kamchatka Trench. PeerJ 8:e10405 https://doi.org/10.7717/peerj.10405
date submitted: 2020-09-04
date accepted: 2020-10-31
issued: 2020-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Kamenev
  given name: Gennady M.
doi: 10.7717/peerj.10405
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-25
copyright: © 2020 Kamenev
attribution name: Kamenev

Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results
type: item
type: AcademicArticle
description: Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovi sp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis.
format: application/pdf
format: text/html
creator: Petr G. Garibian
creator: Anna N. Neretina
creator: Derek J. Taylor
creator: Alexey A. Kotov
subject: Molecular Biology
subject: Taxonomy
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.10410
publisher: PeerJ Inc.
rights: © 2020 Garibian et al.
abstract: Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovi sp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis.
bibliographic citation: Garibian et al. (2020) Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results. PeerJ 8:e10410 https://doi.org/10.7717/peerj.10410
date submitted: 2020-07-13
date accepted: 2020-11-02
issued: 2020-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Garibian
  given name: Petr G.
author list: Agent
  family name: Neretina
  given name: Anna N.
author list: Agent
  family name: Taylor
  given name: Derek J.
author list: Agent
  family name: Kotov
  given name: Alexey A.
doi: 10.7717/peerj.10410
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-25
copyright: © 2020 Garibian et al.
attribution name: Garibian et al.

Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli
type: item
type: AcademicArticle
description: Background The global problem of antibiotic resistance requires the search for and development of new methods of treatment. One of the promising strategies is the use of low doses of antimicrobial peptides, in particular, human defensins HNP-1, hBD-1, and hBD-3, in combination with antibacterial drugs already used in clinical practice. This approach may be used to increase the effectiveness of conventional antibiotics. However, this requires thorough study of the effectiveness of defensins in combination with antibiotics against a large number of bacterial strains with known phenotypes of antibiotic resistance. The aim of this work was to study the antibacterial effect of HNP-1, hBD-1 and hBD-3 in combination with rifampicin or amikacin against clinical isolates of Staphylococcus aureus (n = 27) and Escherichia coli (n = 24) collected from hospitalized patients. Methods The standard checkerboard assay was used to determine minimum inhibitory concentrations (MICs) of antimicrobials. The combined microbicidal effects of two substances (defensin + conventional antibiotic) were assessed by the fractional inhibitory concentration index (FICI). Results The highest anti-staphylococcal activity (including methicillin-resistant strains) among defensins was demonstrated by hBD-3 that had MIC of 1 (0.5–4) mg/L (hereinafter, MIC values are presented as median and interquartile range). The MIC of HNP-1 against S. aureus was 4 (2–8) mg/L; the MIC of hBD-1 was 8 (4–8) mg/L. Against E. coli, the most effective was also found to be hBD-3 that had MIC of 4 (4–8) mg/L; the MIC of HNP-1 was 12 (4–32) mg/L. The combinations of HNP-1 + rifampicin and hBD-3 + rifampicin demonstrated synergistic effects against S. aureus. Against E. coli, combinations of HNP-1 + amikacin and hBD-3 + amikacin also showed synergy of action.
format: application/pdf
format: text/html
creator: Albert Bolatchiev
subject: Microbiology
subject: Infectious Diseases
subject: Pharmacology
description: doi:10.7717/peerj.10455
publisher: PeerJ Inc.
rights: © 2020 Bolatchiev
abstract: Background The global problem of antibiotic resistance requires the search for and development of new methods of treatment. One of the promising strategies is the use of low doses of antimicrobial peptides, in particular, human defensins HNP-1, hBD-1, and hBD-3, in combination with antibacterial drugs already used in clinical practice. This approach may be used to increase the effectiveness of conventional antibiotics. However, this requires thorough study of the effectiveness of defensins in combination with antibiotics against a large number of bacterial strains with known phenotypes of antibiotic resistance. The aim of this work was to study the antibacterial effect of HNP-1, hBD-1 and hBD-3 in combination with rifampicin or amikacin against clinical isolates of Staphylococcus aureus (n = 27) and Escherichia coli (n = 24) collected from hospitalized patients. Methods The standard checkerboard assay was used to determine minimum inhibitory concentrations (MICs) of antimicrobials. The combined microbicidal effects of two substances (defensin + conventional antibiotic) were assessed by the fractional inhibitory concentration index (FICI). Results The highest anti-staphylococcal activity (including methicillin-resistant strains) among defensins was demonstrated by hBD-3 that had MIC of 1 (0.5–4) mg/L (hereinafter, MIC values are presented as median and interquartile range). The MIC of HNP-1 against S. aureus was 4 (2–8) mg/L; the MIC of hBD-1 was 8 (4–8) mg/L. Against E. coli, the most effective was also found to be hBD-3 that had MIC of 4 (4–8) mg/L; the MIC of HNP-1 was 12 (4–32) mg/L. The combinations of HNP-1 + rifampicin and hBD-3 + rifampicin demonstrated synergistic effects against S. aureus. Against E. coli, combinations of HNP-1 + amikacin and hBD-3 + amikacin also showed synergy of action.
bibliographic citation: Bolatchiev (2020) Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli. PeerJ 8:e10455 https://doi.org/10.7717/peerj.10455
date submitted: 2020-09-15
date accepted: 2020-11-09
issued: 2020-11-25
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bolatchiev
  given name: Albert
doi: 10.7717/peerj.10455
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-25
copyright: © 2020 Bolatchiev
attribution name: Bolatchiev

miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2
type: item
type: AcademicArticle
description: Background The present study is to screen lymph node metastasis-related microRNAs (miRNAs) in lung adenocarcinoma (LUAD) and uncover their underlying mechanisms. Methods The miRNA microarray dataset was collected from the Gene Expression Omnibus database under accession number GSE64859. The differentially expressed miRNAs (DEMs) were identified using a t-test. Target genes of DEMs were predicted through the miRWalk2.0 database. The function of these target genes was annotated with the clusterProfiler and the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools. Protein-protein interaction network was established using the STRING database to extract hub target genes. The expressions and associations with survival and lymph node metastasis of miRNAs and target genes were validated by analysis of The Cancer Genome Atlas (TCGA) dataset. Results Eight DEMs were identified between lymph node metastasis and non-metastasis samples of GSE64859 dataset. miRNA-target gene pairs were predicted between six DEMs and 251 target genes (i.e. hsa-miR-224-PRPF4B, hsa-miR-147b-WDR82 and hsa-miR-31-NR3C2). The clusterProfiler analysis showed WDR82 was involved in the mRNA surveillance pathway, while the GO enrichment analysis using the DAVID database indicated PRPF4B participated in the protein phosphorylation and NR3C2 was related with the transcription, DNA-templated. WDR82 and PRPF4B may be hub genes because they could interact with others. Two DEMs (miR-31-5p and miR-31-3p) and 45 target genes (including PRPF4B and NR3C2) were significantly associated with overall survival. The expressions of miR-224 and miR-147b were validated to be upregulated, while WDR82, PRPF4B and NR3C2 were downregulated in lymph node metastasis samples of TCGA datasets compared with non-metastasis samples. Also, there were significantly negative expression correlations between miR-147b and WDR82, between miR-224 and PRPF4B, as well as between miR-31 and NR3C2 in LUAD samples. Conclus…
format: application/pdf
format: text/html
creator: Yan Wang
creator: Shengtao Shang
creator: Kun Yu
creator: Hongbin Sun
creator: Wenduan Ma
creator: Wei Zhao
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.9704
publisher: PeerJ Inc.
rights: © 2020 Wang et al.
abstract: Background The present study is to screen lymph node metastasis-related microRNAs (miRNAs) in lung adenocarcinoma (LUAD) and uncover their underlying mechanisms. Methods The miRNA microarray dataset was collected from the Gene Expression Omnibus database under accession number GSE64859. The differentially expressed miRNAs (DEMs) were identified using a t-test. Target genes of DEMs were predicted through the miRWalk2.0 database. The function of these target genes was annotated with the clusterProfiler and the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools. Protein-protein interaction network was established using the STRING database to extract hub target genes. The expressions and associations with survival and lymph node metastasis of miRNAs and target genes were validated by analysis of The Cancer Genome Atlas (TCGA) dataset. Results Eight DEMs were identified between lymph node metastasis and non-metastasis samples of GSE64859 dataset. miRNA-target gene pairs were predicted between six DEMs and 251 target genes (i.e. hsa-miR-224-PRPF4B, hsa-miR-147b-WDR82 and hsa-miR-31-NR3C2). The clusterProfiler analysis showed WDR82 was involved in the mRNA surveillance pathway, while the GO enrichment analysis using the DAVID database indicated PRPF4B participated in the protein phosphorylation and NR3C2 was related with the transcription, DNA-templated. WDR82 and PRPF4B may be hub genes because they could interact with others. Two DEMs (miR-31-5p and miR-31-3p) and 45 target genes (including PRPF4B and NR3C2) were significantly associated with overall survival. The expressions of miR-224 and miR-147b were validated to be upregulated, while WDR82, PRPF4B and NR3C2 were downregulated in lymph node metastasis samples of TCGA datasets compared with non-metastasis samples. Also, there were significantly negative expression correlations between miR-147b and WDR82, between miR-224 and PRPF4B, as well as between miR-31 and NR3C2 in LUAD samples. Conclus…
bibliographic citation: Wang et al. (2020) miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2. PeerJ 8:e9704 https://doi.org/10.7717/peerj.9704
date submitted: 2019-05-30
date accepted: 2020-07-22
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Yan
author list: Agent
  family name: Shang
  given name: Shengtao
author list: Agent
  family name: Yu
  given name: Kun
author list: Agent
  family name: Sun
  given name: Hongbin
author list: Agent
  family name: Ma
  given name: Wenduan
author list: Agent
  family name: Zhao
  given name: Wei
doi: 10.7717/peerj.9704
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Wang et al.
attribution name: Wang et al.

The Italian record of the Cretaceous shark, Ptychodus latissimus Agassiz, 1835 (Chondrichthyes; Elasmobranchii)
type: item
type: AcademicArticle
description: Associated and isolated teeth of the extinct elasmobranch Ptychodus latissimus Agassiz, 1835 from the Upper Cretaceous Scaglia Rossa pelagic limestone of northern Italy are described and discussed here in detail for the first time. The dentition of this widely distributed species consists of low-crowned molariform teeth that exhibit marked and strong occlusal ornamentations suitable for crushing hard-shelled prey. The associated tooth sets and isolated teeth analyzed here are heterogeneous in size and crown outline, but unambiguously belong to a single species. Re-examination of this Italian material consisting of ca. 30 specimens mostly coming from historical collections allows for a rigorous assessment of the intraspecific variability of P. latissimus, including the identification of three different tooth “morphotypes” based on their positions within the jaws. The relatively flat crowns and occlusal sharp and thick ridges indicate a high adaptation for crushing hard-shelled prey in P. latissimus indicating that the durophagous adaptations of this species were certainly more pronounced than in all other species of Ptychodus. We hypothesize that P. latissimus was a third-level predator occupying habitats with abundant thick-shelled prey, such as inoceramid bivalves and ammonites.
format: application/pdf
format: text/html
creator: Manuel Amadori
creator: Jacopo Amalfitano
creator: Luca Giusberti
creator: Eliana Fornaciari
creator: Giorgio Carnevale
creator: Juergen Kriwet
subject: Biodiversity
subject: Evolutionary Studies
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.10167
publisher: PeerJ Inc.
rights: © 2020 Amadori et al.
abstract: Associated and isolated teeth of the extinct elasmobranch Ptychodus latissimus Agassiz, 1835 from the Upper Cretaceous Scaglia Rossa pelagic limestone of northern Italy are described and discussed here in detail for the first time. The dentition of this widely distributed species consists of low-crowned molariform teeth that exhibit marked and strong occlusal ornamentations suitable for crushing hard-shelled prey. The associated tooth sets and isolated teeth analyzed here are heterogeneous in size and crown outline, but unambiguously belong to a single species. Re-examination of this Italian material consisting of ca. 30 specimens mostly coming from historical collections allows for a rigorous assessment of the intraspecific variability of P. latissimus, including the identification of three different tooth “morphotypes” based on their positions within the jaws. The relatively flat crowns and occlusal sharp and thick ridges indicate a high adaptation for crushing hard-shelled prey in P. latissimus indicating that the durophagous adaptations of this species were certainly more pronounced than in all other species of Ptychodus. We hypothesize that P. latissimus was a third-level predator occupying habitats with abundant thick-shelled prey, such as inoceramid bivalves and ammonites.
bibliographic citation: Amadori et al. (2020) The Italian record of the Cretaceous shark, Ptychodus latissimus Agassiz, 1835 (Chondrichthyes; Elasmobranchii). PeerJ 8:e10167 https://doi.org/10.7717/peerj.10167
date submitted: 2020-07-03
date accepted: 2020-09-22
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amadori
  given name: Manuel
author list: Agent
  family name: Amalfitano
  given name: Jacopo
author list: Agent
  family name: Giusberti
  given name: Luca
author list: Agent
  family name: Fornaciari
  given name: Eliana
author list: Agent
  family name: Carnevale
  given name: Giorgio
author list: Agent
  family name: Kriwet
  given name: Juergen
doi: 10.7717/peerj.10167
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: © 2020 Amadori et al.
attribution name: Amadori et al.

Hissing of geese: caller identity encoded in a non-vocal acoustic signal
type: item
type: AcademicArticle
description: Non-vocal, or unvoiced, signals surprisingly have received very little attention until recently especially when compared to other acoustic signals. Some sounds made by terrestrial vertebrates are produced not only by the larynx but also by the syrinx. Furthermore, some birds are known to produce several types of non-syrinx sounds. Besides mechanical sounds produced by feathers, bills and/or wings, sounds can be also produced by constriction, anywhere along the pathway from the lungs to the lips or nostrils (in mammals), or to the bill (in birds), resulting in turbulent, aerodynamic sounds. These noises often emulate whispering, snorting or hissing. Even though hissing sounds have been studied in mammals and reptiles, only a few studies have analyzed hissing sounds in birds. Presently, only the hissing of small, nesting passerines as a defense against their respective predators have been studied. We studied hissing in domestic goose. This bird represents a ground nesting non-passerine bird which frequently produces hissing out of the nest in comparison to passerines producing hissing during nesting in holes e.g., parids. Compared to vocally produced alarm calls, almost nothing is known about how non-vocal hissing sounds potentially encode information about a caller’s identity. Therefore, we aimed to test whether non-vocal air expirations can encode an individual’s identity similar to those sounds generated by the syrinx or the larynx. We analyzed 217 hissing sounds from 22 individual geese. We calculated the Potential for Individual Coding (PIC) comparing the coefficient of variation both within and among individuals. In addition, we conducted a series of 15 a stepwise discriminant function analysis (DFA) models. All 16 acoustic variables showed a higher coefficient of variation among individuals. Twelve DFA models revealed 51.2–54.4% classification result (cross-validated output) and all 15 models showed 60.8–68.2% classification output based on conventional DFA in …
format: application/pdf
format: text/html
creator: Richard Policht
creator: Artur Kowalczyk
creator: Ewa Łukaszewicz
creator: Vlastimil Hart
subject: Agricultural Science
subject: Animal Behavior
subject: Zoology
description: doi:10.7717/peerj.10197
publisher: PeerJ Inc.
rights: © 2020 Policht et al.
abstract: Non-vocal, or unvoiced, signals surprisingly have received very little attention until recently especially when compared to other acoustic signals. Some sounds made by terrestrial vertebrates are produced not only by the larynx but also by the syrinx. Furthermore, some birds are known to produce several types of non-syrinx sounds. Besides mechanical sounds produced by feathers, bills and/or wings, sounds can be also produced by constriction, anywhere along the pathway from the lungs to the lips or nostrils (in mammals), or to the bill (in birds), resulting in turbulent, aerodynamic sounds. These noises often emulate whispering, snorting or hissing. Even though hissing sounds have been studied in mammals and reptiles, only a few studies have analyzed hissing sounds in birds. Presently, only the hissing of small, nesting passerines as a defense against their respective predators have been studied. We studied hissing in domestic goose. This bird represents a ground nesting non-passerine bird which frequently produces hissing out of the nest in comparison to passerines producing hissing during nesting in holes e.g., parids. Compared to vocally produced alarm calls, almost nothing is known about how non-vocal hissing sounds potentially encode information about a caller’s identity. Therefore, we aimed to test whether non-vocal air expirations can encode an individual’s identity similar to those sounds generated by the syrinx or the larynx. We analyzed 217 hissing sounds from 22 individual geese. We calculated the Potential for Individual Coding (PIC) comparing the coefficient of variation both within and among individuals. In addition, we conducted a series of 15 a stepwise discriminant function analysis (DFA) models. All 16 acoustic variables showed a higher coefficient of variation among individuals. Twelve DFA models revealed 51.2–54.4% classification result (cross-validated output) and all 15 models showed 60.8–68.2% classification output based on conventional DFA in …
bibliographic citation: Policht et al. (2020) Hissing of geese: caller identity encoded in a non-vocal acoustic signal. PeerJ 8:e10197 https://doi.org/10.7717/peerj.10197
date submitted: 2019-09-16
date accepted: 2020-09-26
issued: 2020-11-24
is part of: PeerJ
license: https://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Policht
  given name: Richard
author list: Agent
  family name: Kowalczyk
  given name: Artur
author list: Agent
  family name: Łukaszewicz
  given name: Ewa
author list: Agent
  family name: Hart
  given name: Vlastimil
doi: 10.7717/peerj.10197
volume: 8
issn: 2167-8359
publication name: PeerJ
publication date: 2020-11-24
copyright: ©2020 Policht et al.
attribution name: Policht et al.

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