PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
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
items: The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae)
items: Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies
items: Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides
items: Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.
items: Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus
items: Otolith microchemistry and diadromy in Patagonian river fishes
items: Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe

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.

The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae)
type: item
type: AcademicArticle
description: The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansi…
format: application/pdf
format: text/html
creator: Angela M. Mendoza
creator: Wilmar Bolívar-García
creator: Ella Vázquez-Domínguez
creator: Roberto Ibáñez
creator: Gabriela Parra Olea
subject: Biogeography
subject: Zoology
description: doi:10.7717/peerj.6115
publisher: PeerJ Inc.
rights: © 2019 Mendoza et al.
abstract: The complex geological history of Central America has been useful for understanding the processes influencing the distribution and diversity of multiple groups of organisms. Anurans are an excellent choice for such studies because they typically exhibit site fidelity and reduced movement. The objective of this work was to identify the impact of recognized geographic barriers on the genetic structure, phylogeographic patterns and divergence times of a wide-ranging amphibian species, Hyalinobatrachium fleischmanni. We amplified three mitochondrial regions, two coding (COI and ND1) and one ribosomal (16S), in samples collected from the coasts of Veracruz and Guerrero in Mexico to the humid forests of Chocó in Ecuador. We examined the biogeographic history of the species through spatial clustering analyses (Geneland and sPCA), Bayesian and maximum likelihood reconstructions, and spatiotemporal diffusion analysis. Our data suggest a Central American origin of H. fleischmanni and two posterior independent dispersals towards North and South American regions. The first clade comprises individuals from Colombia, Ecuador, Panama and the sister species Hyalinobatrachium tatayoi; this clade shows little structure, despite the presence of the Andes mountain range and the long distances between sampling sites. The second clade consists of individuals from Costa Rica, Nicaragua, and eastern Honduras with no apparent structure. The third clade includes individuals from western Honduras, Guatemala, and Mexico and displays deep population structure. Herein, we synthesize the impact of known geographic areas that act as barriers to glassfrog dispersal and demonstrated their effect of differentiating H. fleischmanni into three markedly isolated clades. The observed genetic structure is associated with an initial dispersal event from Central America followed by vicariance that likely occurred during the Pliocene. The southern samples are characterized by a very recent population expansi…
bibliographic citation: Mendoza et al. (2019) The role of Central American barriers in shaping the evolutionary history of the northernmost glassfrog, Hyalinobatrachium fleischmanni (Anura: Centrolenidae). PeerJ 7:e6115 https://doi.org/10.7717/peerj.6115
date submitted: 2018-07-31
date accepted: 2018-11-15
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mendoza
  given name: Angela M.
author list: Agent
  family name: Bolívar-García
  given name: Wilmar
author list: Agent
  family name: Vázquez-Domínguez
  given name: Ella
author list: Agent
  family name: Ibáñez
  given name: Roberto
author list: Agent
  family name: Parra Olea
  given name: Gabriela
doi: 10.7717/peerj.6115
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Mendoza et al.
attribution name: Mendoza et al.

Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies
type: item
type: AcademicArticle
description: Background New reagents have emerged allowing researchers to assess a growing number of vaccine-associated immune parameters. Multiplex immunoassay(s) are emerging as efficient high-throughput assays in malaria serology. Currently, commercial vendors market several bead reagents for cytometric bead assays (CBA) but relative performances are not well published. We have compared two types of bead-based multiplex assays to measure relative antibody levels to malarial antigens. Methods Assays for the measurement of antibodies to five Plasmodium falciparum vaccine candidates using non-magnetic and magnetic fluorescent microspheres were compared for their performances with a Bio-Plex200 instrument. Mean fluorescence intensity (MFI) was determined from individuals from western Kenya and compared to known positive and negative control plasma samples. Results P. falciparum recombinant antigens were successfully coupled to both non-magnetic and magnetic beads in multiplex assays. MFIs between the two bead types were comparable for all antigens tested. Bead recovery was superior with magnetic beads for all antigens. MFI values of stored non-magnetic coupled beads did not differ from freshly coupled beads, though they showed higher levels of bead aggregation. Discussion Magnetic and non-magnetic beads performed similarly in P. falciparum antibody assays. Magnetic beads were more expensive, but had higher bead recovery, were more convenient to use, and provided rapid and easy protocol manipulation. Magnetic beads are a suitable alternative to non-magnetic beads in malarial antibody serology.
format: application/pdf
format: text/html
creator: Bartholomew N. Ondigo
creator: Gregory S. Park
creator: Cyrus Ayieko
creator: Donald D. Nyangahu
creator: Ronald Wasswa
creator: Chandy C. John
subject: Global Health
subject: Immunology
subject: Infectious Diseases
subject: Translational Medicine
description: doi:10.7717/peerj.6120
publisher: PeerJ Inc.
rights: © 2019 Ondigo et al.
abstract: Background New reagents have emerged allowing researchers to assess a growing number of vaccine-associated immune parameters. Multiplex immunoassay(s) are emerging as efficient high-throughput assays in malaria serology. Currently, commercial vendors market several bead reagents for cytometric bead assays (CBA) but relative performances are not well published. We have compared two types of bead-based multiplex assays to measure relative antibody levels to malarial antigens. Methods Assays for the measurement of antibodies to five Plasmodium falciparum vaccine candidates using non-magnetic and magnetic fluorescent microspheres were compared for their performances with a Bio-Plex200 instrument. Mean fluorescence intensity (MFI) was determined from individuals from western Kenya and compared to known positive and negative control plasma samples. Results P. falciparum recombinant antigens were successfully coupled to both non-magnetic and magnetic beads in multiplex assays. MFIs between the two bead types were comparable for all antigens tested. Bead recovery was superior with magnetic beads for all antigens. MFI values of stored non-magnetic coupled beads did not differ from freshly coupled beads, though they showed higher levels of bead aggregation. Discussion Magnetic and non-magnetic beads performed similarly in P. falciparum antibody assays. Magnetic beads were more expensive, but had higher bead recovery, were more convenient to use, and provided rapid and easy protocol manipulation. Magnetic beads are a suitable alternative to non-magnetic beads in malarial antibody serology.
bibliographic citation: Ondigo et al. (2019) Comparison of non-magnetic and magnetic beads multiplex assay for assessment of Plasmodium falciparum antibodies. PeerJ 7:e6120 https://doi.org/10.7717/peerj.6120
date submitted: 2018-04-26
date accepted: 2018-11-16
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ondigo
  given name: Bartholomew N.
author list: Agent
  family name: Park
  given name: Gregory S.
author list: Agent
  family name: Ayieko
  given name: Cyrus
author list: Agent
  family name: Nyangahu
  given name: Donald D.
author list: Agent
  family name: Wasswa
  given name: Ronald
author list: Agent
  family name: John
  given name: Chandy C.
doi: 10.7717/peerj.6120
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Ondigo et al.
attribution name: Ondigo et al.

Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides
type: item
type: AcademicArticle
description: Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
format: application/pdf
format: text/html
creator: Liang-Yu Chen
creator: Hao-Tian Cui
creator: Chun Su
creator: Feng-Wu Bai
creator: Xin-Qing Zhao
subject: Biochemistry
subject: Genomics
subject: Microbiology
description: doi:10.7717/peerj.6122
publisher: PeerJ Inc.
rights: © 2019 Chen et al.
abstract: Genome sequences of marine streptomycetes are valuable for the discovery of useful enzymes and bioactive compounds by genome mining. However, publicly available complete genome sequences of marine streptomycetes are still limited. Here, we present the complete genome sequence of a marine streptomycete Streptomyces sp. S063 CGMCC 14582. Species delineation based on the pairwise digital DNA-DNA hybridization and genome comparison ANI (average nucleotide identity) value showed that Streptomyces sp. S063 CGMCC 14582 possesses a unique genome that is clearly different from all of the other available genomes. Bioactivity tests showed that Streptomyces sp. S063 CGMCC 14582 produces metabolites with anti-complement activities, which are useful for treatment of numerous diseases that arise from inappropriate activation of the human complement system. Analysis of the genome reveals no biosynthetic gene cluster (BGC) which shows even low similarity to that of the known anti-complement agents was detected in the genome, indicating that Streptomyces sp. S063 CGMCC 14582 may produce novel anti-complement agents of microbial origin. Four BGCs which are potentially involved in biosynthesis of non-ribosomal peptides were disrupted, but no decrease of anti-complement activities was observed, suggesting that these four BGCs are not involved in biosynthesis of the anti-complement agents. In addition, LC-MS/MS analysis and subsequent alignment through the Global Natural Products Social Molecular Networking (GNPS) platform led to the detection of novel peptides produced by the strain. Streptomyces sp. S063 CGMCC 14582 grows rapidly and is salt tolerant, which benefits efficient secondary metabolite production via seawater-based fermentation. Our results indicate that Streptomyces sp. S063 has great potential to produce novel bioactive compounds, and also is a good host for heterologous production of useful secondary metabolites for drug discovery.
bibliographic citation: Chen et al. (2019) Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PeerJ 7:e6122 https://doi.org/10.7717/peerj.6122
date submitted: 2018-08-07
date accepted: 2018-11-12
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Chen
  given name: Liang-Yu
author list: Agent
  family name: Cui
  given name: Hao-Tian
author list: Agent
  family name: Su
  given name: Chun
author list: Agent
  family name: Bai
  given name: Feng-Wu
author list: Agent
  family name: Zhao
  given name: Xin-Qing
doi: 10.7717/peerj.6122
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Chen et al.
attribution name: Chen et al.

Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.
type: item
type: AcademicArticle
description: The potential of environmental release enhances with increased commercial applications of the nanomaterials. In this work, a simple and efficient test to estimate the acute toxicity of nanoparticles is carried out on Artemia species and their hatching rates. We have tested six different engineered nanoparticles (silver, gold, copper oxide, zinc oxide, TiO2 and SiO2 nanoparticles) and three soluble salts (CuSO4, ZnSO4 and AgNO3) on Artemia sp. The physicochemical properties of the nanoparticles involved in this study were analyzed in normal water and marine water. Hydrated and bleached Artemia cysts were allowed to hatch in continuously aerated, filtered sterile salt water containing nanoparticles; hatching of viable nauplii and total hatchlings have been recorded. In parallel, standard Artemia toxicity test was conducted on the nauplii monitoring the viability. In hatching experiments, a reduction in hatching rate was observed along with mortality of newly hatched nauplii. The results of the hatching experiment and of the standard Artemia test showed a good correlation. The toxicity of the nanoparticles was compared and the order of toxicity was estimated as Ag>CuO>ZnO>Au>TiO2>SiO2. The study thus suggests that the hatching test itself is a reliable assay for determining the toxicity of nanomaterials.
format: application/pdf
format: text/html
creator: Rohit Rekulapally
creator: Lakshmi Narsimha Murthy Chavali
creator: Mohammed M. Idris
creator: Shashi Singh
subject: Toxicology
subject: Ecotoxicology
description: doi:10.7717/peerj.6138
publisher: PeerJ Inc.
rights: © 2019 Rekulapally et al.
abstract: The potential of environmental release enhances with increased commercial applications of the nanomaterials. In this work, a simple and efficient test to estimate the acute toxicity of nanoparticles is carried out on Artemia species and their hatching rates. We have tested six different engineered nanoparticles (silver, gold, copper oxide, zinc oxide, TiO2 and SiO2 nanoparticles) and three soluble salts (CuSO4, ZnSO4 and AgNO3) on Artemia sp. The physicochemical properties of the nanoparticles involved in this study were analyzed in normal water and marine water. Hydrated and bleached Artemia cysts were allowed to hatch in continuously aerated, filtered sterile salt water containing nanoparticles; hatching of viable nauplii and total hatchlings have been recorded. In parallel, standard Artemia toxicity test was conducted on the nauplii monitoring the viability. In hatching experiments, a reduction in hatching rate was observed along with mortality of newly hatched nauplii. The results of the hatching experiment and of the standard Artemia test showed a good correlation. The toxicity of the nanoparticles was compared and the order of toxicity was estimated as Ag>CuO>ZnO>Au>TiO2>SiO2. The study thus suggests that the hatching test itself is a reliable assay for determining the toxicity of nanomaterials.
bibliographic citation: Rekulapally et al. (2019) Toxicity of TiO2, SiO2, ZnO, CuO, Au and Ag engineered nanoparticles on hatching and early nauplii of Artemia sp.. PeerJ 6:e6138 https://doi.org/10.7717/peerj.6138
date submitted: 2018-07-18
date accepted: 2018-11-20
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rekulapally
  given name: Rohit
author list: Agent
  family name: Murthy Chavali
  given name: Lakshmi Narsimha
author list: Agent
  family name: Idris
  given name: Mohammed M.
author list: Agent
  family name: Singh
  given name: Shashi
doi: 10.7717/peerj.6138
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: © 2019 Rekulapally et al.
attribution name: Rekulapally et al.

Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus
type: item
type: AcademicArticle
description: Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to res…
format: application/pdf
format: text/html
creator: Therese A. Catanach
creator: Andrew D. Sweet
creator: Nam-phuong D. Nguyen
creator: Rhiannon M. Peery
creator: Andrew H. Debevec
creator: Andrea K. Thomer
creator: Amanda C. Owings
creator: Bret M. Boyd
creator: Aron D. Katz
creator: Felipe N. Soto-Adames
creator: Julie M. Allen
subject: Bioinformatics
subject: Computational Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6142
publisher: PeerJ Inc.
rights: © 2019 Catanach et al.
abstract: Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to res…
bibliographic citation: Catanach et al. (2019) Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 7:e6142 https://doi.org/10.7717/peerj.6142
date submitted: 2018-02-07
date accepted: 2018-11-14
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Catanach
  given name: Therese A.
author list: Agent
  family name: Sweet
  given name: Andrew D.
author list: Agent
  family name: Nguyen
  given name: Nam-phuong D.
author list: Agent
  family name: Peery
  given name: Rhiannon M.
author list: Agent
  family name: Debevec
  given name: Andrew H.
author list: Agent
  family name: Thomer
  given name: Andrea K.
author list: Agent
  family name: Owings
  given name: Amanda C.
author list: Agent
  family name: Boyd
  given name: Bret M.
author list: Agent
  family name: Katz
  given name: Aron D.
author list: Agent
  family name: Soto-Adames
  given name: Felipe N.
author list: Agent
  family name: Allen
  given name: Julie M.
doi: 10.7717/peerj.6142
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Catanach et al.
attribution name: Catanach et al.

Otolith microchemistry and diadromy in Patagonian river fishes
type: item
type: AcademicArticle
description: Coastal habitats in Chile are hypothesized to support a number of diadromous fish species. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39–48°S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was suggested for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited patterns consistent with anadromy, whereas the screened population of O. mykiss appeared restricted to freshwater. Salmo trutta exhibited variable patterns suggesting freshwater residency and possibly anadromy in one case. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.
format: application/pdf
format: text/html
creator: Dominique Alò
creator: Cristian Correa
creator: Horacio Samaniego
creator: Corey A. Krabbenhoft
creator: Thomas F. Turner
subject: Aquaculture, Fisheries and Fish Science
subject: Ecology
subject: Freshwater Biology
description: doi:10.7717/peerj.6149
publisher: PeerJ Inc.
rights: © 2019 Alò et al.
abstract: Coastal habitats in Chile are hypothesized to support a number of diadromous fish species. The objective of this study was to document migratory life histories of native galaxiids and introduced salmonids from a wide latitudinal range in Chilean Patagonia (39–48°S). Otolith microchemistry data were analysed using a recursive partitioning approach to test for diadromy. Based on annular analysis of Sr:Ca ratios, a diadromous life history was suggested for populations of native Aplochiton taeniatus, A. marinus, and Galaxias maculatus. Lifetime residency in freshwater was suggested for populations of A. zebra and G. platei. Among introduced salmonids, populations of Oncorhynchus tshawytscha and O. kisutch exhibited patterns consistent with anadromy, whereas the screened population of O. mykiss appeared restricted to freshwater. Salmo trutta exhibited variable patterns suggesting freshwater residency and possibly anadromy in one case. The capacity and geographic scope of hydropower development is increasing and may disrupt migratory routes of diadromous fishes. Identification of diadromous species is a critical first step for preventing their loss due to hydropower development.
bibliographic citation: Alò et al. (2019) Otolith microchemistry and diadromy in Patagonian river fishes. PeerJ 7:e6149 https://doi.org/10.7717/peerj.6149
date submitted: 2018-06-01
date accepted: 2018-11-21
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Alò
  given name: Dominique
author list: Agent
  family name: Correa
  given name: Cristian
author list: Agent
  family name: Samaniego
  given name: Horacio
author list: Agent
  family name: Krabbenhoft
  given name: Corey A.
author list: Agent
  family name: Turner
  given name: Thomas F.
doi: 10.7717/peerj.6149
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Alò et al.
attribution name: Alò et al.

Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe
type: item
type: AcademicArticle
description: Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
format: application/pdf
format: text/html
creator: Beatriz Roncero-Ramos
creator: M. Ángeles Muñoz-Martín
creator: Sonia Chamizo
creator: Lara Fernández-Valbuena
creator: Diego Mendoza
creator: Elvira Perona
creator: Yolanda Cantón
creator: Pilar Mateo
subject: Biodiversity
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.6169
publisher: PeerJ Inc.
rights: © 2019 Roncero-Ramos et al.
abstract: Cyanobacteria are key microbes in topsoil communities that have important roles in preventing soil erosion, carbon and nitrogen fixation, and influencing soil hydrology. However, little is known regarding the identity and distribution of the microbial components in the photosynthetic assemblages that form a cohesive biological soil crust (biocrust) in drylands of Europe. In this study, we investigated the cyanobacterial species colonizing biocrusts in three representative dryland ecosystems from the most arid region in Europe (SE Spain) that are characterized by different soil conditions. Isolated cyanobacterial cultures were identified by a polyphasic approach, including 16S rRNA gene sequencing, phylogenetic relationship determination, and morphological and ecological habitat assessments. Three well-differentiated groups were identified: heterocystous-cyanobacteria (Nostoc commune, Nostoc calcicola, Tolypothrix distorta and Scytonema hyalinum), which play an important role in N and C cycling in soil; nonheterocystous bundle-forming cyanobacteria (Microcoleus steenstrupii, Trichocoleus desertorum, and Schizothrix cf. calcicola); and narrow filamentous cyanobacteria (Leptolyngbya frigida and Oculatella kazantipica), all of which are essential genera for initial biocrust formation. The results of this study contribute to our understanding of cyanobacterial species composition in biocrusts from important and understudied European habitats, such as the Mediterranean Basin, a hotspot of biodiversity, where these species are keystone pioneer organisms.
bibliographic citation: Roncero-Ramos et al. (2019) Polyphasic evaluation of key cyanobacteria in biocrusts from the most arid region in Europe. PeerJ 7:e6169 https://doi.org/10.7717/peerj.6169
date submitted: 2018-07-11
date accepted: 2018-11-27
issued: 2019-01-03
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Roncero-Ramos
  given name: Beatriz
author list: Agent
  family name: Muñoz-Martín
  given name: M. Ángeles
author list: Agent
  family name: Chamizo
  given name: Sonia
author list: Agent
  family name: Fernández-Valbuena
  given name: Lara
author list: Agent
  family name: Mendoza
  given name: Diego
author list: Agent
  family name: Perona
  given name: Elvira
author list: Agent
  family name: Cantón
  given name: Yolanda
author list: Agent
  family name: Mateo
  given name: Pilar
doi: 10.7717/peerj.6169
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-01-03
copyright: ©2019 Roncero-Ramos et al.
attribution name: Roncero-Ramos et al.

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