PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Evolution of African barbs from the Lake Victoria drainage system, Kenya
items: Spatial analyses of threats to ecosystem service hotspots in Greater Durban, South Africa
items: Inhibitory effect of microalgae and cyanobacteria extracts on influenza virus replication and neuraminidase activity
items: Impact of organic and inorganic fertilizers on the yield and quality of silage corn intercropped with soybean
items: Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia
items: Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding
items: Recent advances and challenges on application of tissue engineering for treatment of congenital heart disease
items: Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan
items: Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
items: Infection and coinfection by human papillomavirus, Epstein–Barr virus and Merkel cell polyomavirus in patients with squamous cell carcinoma of the larynx: a retrospective study

Evolution of African barbs from the Lake Victoria drainage system, Kenya
type: item
type: AcademicArticle
description: The Lake Victoria drainage basin (LVD) in Kenya is home to ten nominal species of small barbs (Enteromius) and one of large barbs (Labeobarbus altianalis). A recent molecular study genetically characterized small barbs in this region and found evidence of introgression between certain species, complicating the taxonomy and species identification of these fishes. This study aimed to extend our understanding on the evolution of these fishes by: (1) determining whether putatively pure individuals of Enteromius cercops are found in the Kenyan LVD, as the previous study only found hybrid individuals of this species in this region; (2) testing the sister relationship between Enteromius profundus, endemic to Lake Victoria, and Enteromius radiatus, also found in Lake Victoria, which had been previously synonymized; (3) examining the phylogenetic relationships of small barbs of the Kenyan LVD with those reported from other ichthyological provinces of Africa; and (4) examining the phylogenetic relationships of Labeobarbus altianalis with other Labeobarbus species. To this end, we obtained mitochondrial Cytochrome b and nuclear Growth Hormone (GH) intron 2 gene sequences of nine Enteromius species from the LVD in Kenya, as well as cytochrome b sequences for L. altianalis. We conducted Maximum likelihood and Bayesian phylogenetic analyses to establish their evolutionary relationships in relation to many other barbs specimens from Africa. Phylogenetic analyses did not reveal instances of hybridization/introgression among the individuals sequenced by us. A sister relationship between E. profundus and E. radiatus was not found. This latter species shows instead a sister relationship with a lineage comprised of two species from West Africa. Other sister relationships between taxa from the East coast and other ecoregions from Africa are observed, suggesting that past drainage connections and vicariant events contributed to the diversification of Enteromius. Finally, only a single ha…
format: application/pdf
format: text/html
creator: Violet M. Ndeda
creator: Mariana Mateos
creator: Luis A. Hurtado
subject: Biodiversity
subject: Evolutionary Studies
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.5762
publisher: PeerJ Inc.
rights: © 2018 Ndeda et al.
abstract: The Lake Victoria drainage basin (LVD) in Kenya is home to ten nominal species of small barbs (Enteromius) and one of large barbs (Labeobarbus altianalis). A recent molecular study genetically characterized small barbs in this region and found evidence of introgression between certain species, complicating the taxonomy and species identification of these fishes. This study aimed to extend our understanding on the evolution of these fishes by: (1) determining whether putatively pure individuals of Enteromius cercops are found in the Kenyan LVD, as the previous study only found hybrid individuals of this species in this region; (2) testing the sister relationship between Enteromius profundus, endemic to Lake Victoria, and Enteromius radiatus, also found in Lake Victoria, which had been previously synonymized; (3) examining the phylogenetic relationships of small barbs of the Kenyan LVD with those reported from other ichthyological provinces of Africa; and (4) examining the phylogenetic relationships of Labeobarbus altianalis with other Labeobarbus species. To this end, we obtained mitochondrial Cytochrome b and nuclear Growth Hormone (GH) intron 2 gene sequences of nine Enteromius species from the LVD in Kenya, as well as cytochrome b sequences for L. altianalis. We conducted Maximum likelihood and Bayesian phylogenetic analyses to establish their evolutionary relationships in relation to many other barbs specimens from Africa. Phylogenetic analyses did not reveal instances of hybridization/introgression among the individuals sequenced by us. A sister relationship between E. profundus and E. radiatus was not found. This latter species shows instead a sister relationship with a lineage comprised of two species from West Africa. Other sister relationships between taxa from the East coast and other ecoregions from Africa are observed, suggesting that past drainage connections and vicariant events contributed to the diversification of Enteromius. Finally, only a single ha…
bibliographic citation: Ndeda et al. (2018) Evolution of African barbs from the Lake Victoria drainage system, Kenya. PeerJ 6:e5762 https://doi.org/10.7717/peerj.5762
date submitted: 2018-06-26
date accepted: 2018-09-16
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ndeda
  given name: Violet M.
author list: Agent
  family name: Mateos
  given name: Mariana
author list: Agent
  family name: Hurtado
  given name: Luis A.
doi: 10.7717/peerj.5762
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Ndeda et al.
attribution name: Ndeda et al.

Spatial analyses of threats to ecosystem service hotspots in Greater Durban, South Africa
type: item
type: AcademicArticle
description: Background Population growth at all scales and rapid rates of urbanization, particularly in the global South, are placing increasing pressure on ecosystems and their ability to provide services essential for human well-being. The spatial consideration of threats to ecosystem services related to changes in land use is necessary in order to avoid undue impacts on society due to the loss or reduced supply of ecosystem services. This study assesses the potential threats of land use change from strategic and local development proposals to ecosystem services in the city of Durban. Methods We analysed the spatial relationship between five categories of ecosystem service hotspots (carbon storage, water yield, sediment retention, nutrient retention and flood attenuation) and urban land use change related to selected strategic planning proposals, development proposals and sand-mining applications in Durban, South Africa (eThekwini Municipality) with a view to determining the consequences for progress towards a more sustainable development path in the city. We identified the potential levels of threat related to habitat destruction or transformation for the five categories of ecosystem services and a subset of 13 ecosystem service hotspots, using GIS spatial analysis tools. Results The results show that on average, should Durban’s strategic development plans be realised, approximately 42% loss of ecosystem service hotspots is expected in the two municipal town-planning regions assessed. With respect to development applications between 2009 and 2012, approximately 36% of all environmental impact assessments and 84% of sand mining applications occurred within ecosystem service hotspots within Durban. Discussion The findings highlight the tension between short-term development pressures and longer-term sustainability goals and confirm that current planning and development proposals pose a threat to ecosystems and their ability to deliver services that support human well-being in …
format: application/pdf
format: text/html
creator: Rashieda Davids
creator: Mathieu Rouget
creator: Richard Boon
creator: Debra Roberts
subject: Ecosystem Science
subject: Coupled Natural and Human Systems
subject: Natural Resource Management
subject: Environmental Impacts
subject: Spatial and Geographic Information Science
description: doi:10.7717/peerj.5723
publisher: PeerJ Inc.
rights: © 2018 Davids et al.
abstract: Background Population growth at all scales and rapid rates of urbanization, particularly in the global South, are placing increasing pressure on ecosystems and their ability to provide services essential for human well-being. The spatial consideration of threats to ecosystem services related to changes in land use is necessary in order to avoid undue impacts on society due to the loss or reduced supply of ecosystem services. This study assesses the potential threats of land use change from strategic and local development proposals to ecosystem services in the city of Durban. Methods We analysed the spatial relationship between five categories of ecosystem service hotspots (carbon storage, water yield, sediment retention, nutrient retention and flood attenuation) and urban land use change related to selected strategic planning proposals, development proposals and sand-mining applications in Durban, South Africa (eThekwini Municipality) with a view to determining the consequences for progress towards a more sustainable development path in the city. We identified the potential levels of threat related to habitat destruction or transformation for the five categories of ecosystem services and a subset of 13 ecosystem service hotspots, using GIS spatial analysis tools. Results The results show that on average, should Durban’s strategic development plans be realised, approximately 42% loss of ecosystem service hotspots is expected in the two municipal town-planning regions assessed. With respect to development applications between 2009 and 2012, approximately 36% of all environmental impact assessments and 84% of sand mining applications occurred within ecosystem service hotspots within Durban. Discussion The findings highlight the tension between short-term development pressures and longer-term sustainability goals and confirm that current planning and development proposals pose a threat to ecosystems and their ability to deliver services that support human well-being in …
bibliographic citation: Davids et al. (2018) Spatial analyses of threats to ecosystem service hotspots in Greater Durban, South Africa. PeerJ 6:e5723 https://doi.org/10.7717/peerj.5723
date submitted: 2018-02-12
date accepted: 2018-09-11
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Davids
  given name: Rashieda
author list: Agent
  family name: Rouget
  given name: Mathieu
author list: Agent
  family name: Boon
  given name: Richard
author list: Agent
  family name: Roberts
  given name: Debra
doi: 10.7717/peerj.5723
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Davids et al.
attribution name: Davids et al.

Inhibitory effect of microalgae and cyanobacteria extracts on influenza virus replication and neuraminidase activity
type: item
type: AcademicArticle
description: Background The influenza virus can cause seasonal infections with mild to severe symptoms, circulating worldwide, and it can affect people in any age group. Therefore, this infection is a serious public health problem that causes severe illness and death in high-risk populations. Every year, 0.5% of the world’s population is infected by this pathogen. This percentage can increase up to ten times during pandemics. Influenza vaccination is the most effective way to prevent disease. In addition, anti-influenza drugs are essential for prophylactic and therapeutic interventions. The oseltamivir (OST, a neuraminidase inhibitor) is the primary antiviral used in clinics during outbreaks. However, OST resistant viruses may emerge naturally or due to antiviral pressure, with a prevalence of 1–2% worldwide. Thus, the search for new anti-influenza drugs is extremely important. Currently, several groups have been developing studies describing the biotechnological potential of microalgae and cyanobacteria, including antiviral activity of their extracts. In Brazil, this potential is poorly known and explored. Methods With the aim of increasing the knowledge on this topic, 38 extracts from microalgae and cyanobacteria isolated from marine and freshwater biomes in Brazil were tested against: cellular toxicity; OST-sensitive and resistant influenza replications; and neuraminidase activity. Results For this purpose, Madin-Darby Canine Kidney (MDCK)-infected cells were treated with 200 μg/mL of each extract. A total of 17 extracts (45%) inhibited influenza A replication, with seven of them resulting in more than 80% inhibition. Moreover, functional assays performed with viral neuraminidase revealed two extracts (from Leptolyngbya sp. and Chlorellaceae) with IC50 mean < 210 μg/mL for influenza A and B, and also OST-sensitive and resistant strains. Furthermore, MDCK cells exposed to 1 mg/mL of all the extracts showed viability higher than 80%. Discussion Our results suggest that extracts…
format: application/pdf
format: text/html
creator: Thauane Silva
creator: Paulo S. Salomon
creator: Lidilhone Hamerski
creator: Juline Walter
creator: Rafael B. Menezes
creator: José Edson Siqueira
creator: Aline Santos
creator: Jéssica Aparecida Morais Santos
creator: Natália Ferme
creator: Thaise Guimarães
creator: Giovana O. Fistarol
creator: Paulo I. Hargreaves
creator: Cristiane Thompson
creator: Fabiano Thompson
creator: Thiago Moreno Souza
creator: Marilda Siqueira
creator: Milene Miranda
subject: Marine Biology
subject: Virology
subject: Freshwater Biology
description: doi:10.7717/peerj.5716
publisher: PeerJ Inc.
rights: © 2018 Silva et al.
abstract: Background The influenza virus can cause seasonal infections with mild to severe symptoms, circulating worldwide, and it can affect people in any age group. Therefore, this infection is a serious public health problem that causes severe illness and death in high-risk populations. Every year, 0.5% of the world’s population is infected by this pathogen. This percentage can increase up to ten times during pandemics. Influenza vaccination is the most effective way to prevent disease. In addition, anti-influenza drugs are essential for prophylactic and therapeutic interventions. The oseltamivir (OST, a neuraminidase inhibitor) is the primary antiviral used in clinics during outbreaks. However, OST resistant viruses may emerge naturally or due to antiviral pressure, with a prevalence of 1–2% worldwide. Thus, the search for new anti-influenza drugs is extremely important. Currently, several groups have been developing studies describing the biotechnological potential of microalgae and cyanobacteria, including antiviral activity of their extracts. In Brazil, this potential is poorly known and explored. Methods With the aim of increasing the knowledge on this topic, 38 extracts from microalgae and cyanobacteria isolated from marine and freshwater biomes in Brazil were tested against: cellular toxicity; OST-sensitive and resistant influenza replications; and neuraminidase activity. Results For this purpose, Madin-Darby Canine Kidney (MDCK)-infected cells were treated with 200 μg/mL of each extract. A total of 17 extracts (45%) inhibited influenza A replication, with seven of them resulting in more than 80% inhibition. Moreover, functional assays performed with viral neuraminidase revealed two extracts (from Leptolyngbya sp. and Chlorellaceae) with IC50 mean < 210 μg/mL for influenza A and B, and also OST-sensitive and resistant strains. Furthermore, MDCK cells exposed to 1 mg/mL of all the extracts showed viability higher than 80%. Discussion Our results suggest that extracts…
bibliographic citation: Silva et al. (2018) Inhibitory effect of microalgae and cyanobacteria extracts on influenza virus replication and neuraminidase activity. PeerJ 6:e5716 https://doi.org/10.7717/peerj.5716
date submitted: 2018-04-23
date accepted: 2018-09-10
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Silva
  given name: Thauane
author list: Agent
  family name: S. Salomon
  given name: Paulo
author list: Agent
  family name: Hamerski
  given name: Lidilhone
author list: Agent
  family name: Walter
  given name: Juline
author list: Agent
  family name: B. Menezes
  given name: Rafael
author list: Agent
  family name: Siqueira
  given name: José Edson
author list: Agent
  family name: Santos
  given name: Aline
author list: Agent
  family name: Santos
  given name: Jéssica Aparecida Morais
author list: Agent
  family name: Ferme
  given name: Natália
author list: Agent
  family name: Guimarães
  given name: Thaise
author list: Agent
  family name: O. Fistarol
  given name: Giovana
author list: Agent
  family name: I. Hargreaves
  given name: Paulo
author list: Agent
  family name: Thompson
  given name: Cristiane
author list: Agent
  family name: Thompson
  given name: Fabiano
author list: Agent
  family name: Souza
  given name: Thiago Moreno
author list: Agent
  family name: Siqueira
  given name: Marilda
author list: Agent
  family name: Miranda
  given name: Milene
doi: 10.7717/peerj.5716
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Silva et al.
attribution name: Silva et al.

Impact of organic and inorganic fertilizers on the yield and quality of silage corn intercropped with soybean
type: item
type: AcademicArticle
description: Background Corn silage is an important feed for intense ruminant production, but the growth of corn relies heavily on the use of chemical fertilizers. Sustainable crop production requires careful management of all nutrient sources available on a farm, particularly in corn-based cropping systems. Methods Experiments were conducted to determine the appropriate technique of corn-legume intercropping in conjunction with the supplemental use of chemical fertilizers, organic manure, and biofertilizers (BFs). Acetylene reduction assays (ARAs) were also performed on corn and soybean roots. Results Combining chemical fertilizers with chicken manure (CM) in a 50:50 ratio and applying 50% NPK+50% CM+BF produced fresh forage and dry matter (DM) yields that were similar to those produced in the 100% nitrogen (N), phosphorus (P), potassium (K) treatment. Among the lone fertilizer treatments, the inorganic fertilizer (100% NPK) treatment produced the highest DM yield (13.86 t/ha) of forage and outyielded the 100% CM (9.74 t/ha) treatment. However, when CM was combined with NPK, the resulting DM yield of forage (13.86 t/ha) was the same as that resulting from 100% NPK (13.68 t/ha). Compared with CM applications alone, combinations of NPK and CM applications resulted in increased plant height, crop growth rates (CGRs) and leaf area index (LAI), but the values of these parameters were similar to those resulting from 100% NPK application. Fertilizers in which the ratio was 50% CM+50% NPK or 50% CM+50% NPK+BF resulted in protein yields that were similar to those resulting from conventional fertilizers. Similarly, the CP content did not significantly differ between applications of the 100% NPK and 50% CM+50% NPK fertilizers. The use of BFs had no significant impact on improving either the yield or quality of forage fertilized with inorganic or organic fertilizer. Lactic acid responded differently to different fertilizer applications and was significantly higher in the fertilized plots t…
format: application/pdf
format: text/html
creator: Ali Baghdadi
creator: Ridzwan A. Halim
creator: Ali Ghasemzadeh
creator: Mohd Fauzi Ramlan
creator: Siti Zaharah Sakimin
subject: Agricultural Science
subject: Ecology
subject: Plant Science
subject: Soil Science
description: doi:10.7717/peerj.5280
publisher: PeerJ Inc.
rights: © 2018 Baghdadi et al.
abstract: Background Corn silage is an important feed for intense ruminant production, but the growth of corn relies heavily on the use of chemical fertilizers. Sustainable crop production requires careful management of all nutrient sources available on a farm, particularly in corn-based cropping systems. Methods Experiments were conducted to determine the appropriate technique of corn-legume intercropping in conjunction with the supplemental use of chemical fertilizers, organic manure, and biofertilizers (BFs). Acetylene reduction assays (ARAs) were also performed on corn and soybean roots. Results Combining chemical fertilizers with chicken manure (CM) in a 50:50 ratio and applying 50% NPK+50% CM+BF produced fresh forage and dry matter (DM) yields that were similar to those produced in the 100% nitrogen (N), phosphorus (P), potassium (K) treatment. Among the lone fertilizer treatments, the inorganic fertilizer (100% NPK) treatment produced the highest DM yield (13.86 t/ha) of forage and outyielded the 100% CM (9.74 t/ha) treatment. However, when CM was combined with NPK, the resulting DM yield of forage (13.86 t/ha) was the same as that resulting from 100% NPK (13.68 t/ha). Compared with CM applications alone, combinations of NPK and CM applications resulted in increased plant height, crop growth rates (CGRs) and leaf area index (LAI), but the values of these parameters were similar to those resulting from 100% NPK application. Fertilizers in which the ratio was 50% CM+50% NPK or 50% CM+50% NPK+BF resulted in protein yields that were similar to those resulting from conventional fertilizers. Similarly, the CP content did not significantly differ between applications of the 100% NPK and 50% CM+50% NPK fertilizers. The use of BFs had no significant impact on improving either the yield or quality of forage fertilized with inorganic or organic fertilizer. Lactic acid responded differently to different fertilizer applications and was significantly higher in the fertilized plots t…
bibliographic citation: Baghdadi et al. (2018) Impact of organic and inorganic fertilizers on the yield and quality of silage corn intercropped with soybean. PeerJ 6:e5280 https://doi.org/10.7717/peerj.5280
date submitted: 2018-04-26
date accepted: 2018-07-02
issued: 2018-10-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Baghdadi
  given name: Ali
author list: Agent
  family name: Halim
  given name: Ridzwan A.
author list: Agent
  family name: Ghasemzadeh
  given name: Ali
author list: Agent
  family name: Ramlan
  given name: Mohd Fauzi
author list: Agent
  family name: Sakimin
  given name: Siti Zaharah
doi: 10.7717/peerj.5280
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-26
copyright: ©2018 Baghdadi et al.
attribution name: Baghdadi et al.

Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia
type: item
type: AcademicArticle
description: Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Actinobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against bacteria and fungi. It was shown that representatives of the genera Nocardia and Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic properties. However, despite the lack of antimicrobial and fungicidal activity of Nocardia extracts, those strains are specific in terms of their fatty acid spectrum. When assessing fatty acid profile, we found that polyunsaturated fatty acids were quantitatively dominant in extracts of Nocardia sp. and Streptomyces sp. grown in different media. Saturated fatty acids were the second most abundant type in the fatty acid profile. It was due to palmitic acid. Also, a few monounsaturated fatty acids were detected. The obtained materials can become a basis for development of approaches to use bacteria isolated from caves as a biological sources of bioactive compounds to create medical and veterinary drugs.
format: application/pdf
format: text/html
creator: Irina V. Voytsekhovskaya
creator: Denis V. Axenov-Gribanov
creator: Svetlana A. Murzina
creator: Svetlana N. Pekkoeva
creator: Eugeniy S. Protasov
creator: Stanislav V. Gamaiunov
creator: Maxim A. Timofeyev
subject: Agricultural Science
subject: Biodiversity
subject: Ecology
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.5832
publisher: PeerJ Inc.
rights: © 2018 Voytsekhovskaya et al.
abstract: Extreme and unusual ecosystems such as isolated ancient caves are considered as potential tools for the discovery of novel natural products with biological activities. Actinobacteria that inhabit these unusual ecosystems are examined as a promising source for the development of new drugs. In this study we focused on the preliminary estimation of fatty acid composition and antibacterial properties of culturable actinobacteria isolated from water surface of underground lakes located in Badzheyskaya and Okhotnichya caves in Siberia. Here we present isolation of 17 strains of actinobacteria that belong to the Streptomyces, Nocardia and Nocardiopsis genera. Using assays for antibacterial and antifungal activities, we found that a number of strains belonging to the genus Streptomyces isolated from Badzheyskaya cave demonstrated inhibition activity against bacteria and fungi. It was shown that representatives of the genera Nocardia and Nocardiopsis isolated from Okhotnichya cave did not demonstrate any tested antibiotic properties. However, despite the lack of antimicrobial and fungicidal activity of Nocardia extracts, those strains are specific in terms of their fatty acid spectrum. When assessing fatty acid profile, we found that polyunsaturated fatty acids were quantitatively dominant in extracts of Nocardia sp. and Streptomyces sp. grown in different media. Saturated fatty acids were the second most abundant type in the fatty acid profile. It was due to palmitic acid. Also, a few monounsaturated fatty acids were detected. The obtained materials can become a basis for development of approaches to use bacteria isolated from caves as a biological sources of bioactive compounds to create medical and veterinary drugs.
bibliographic citation: Voytsekhovskaya et al. (2018) Estimation of antimicrobial activities and fatty acid composition of actinobacteria isolated from water surface of underground lakes from Badzheyskaya and Okhotnichya caves in Siberia. PeerJ 6:e5832 https://doi.org/10.7717/peerj.5832
date submitted: 2018-05-23
date accepted: 2018-09-24
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Voytsekhovskaya
  given name: Irina V.
author list: Agent
  family name: Axenov-Gribanov
  given name: Denis V.
author list: Agent
  family name: Murzina
  given name: Svetlana A.
author list: Agent
  family name: Pekkoeva
  given name: Svetlana N.
author list: Agent
  family name: Protasov
  given name: Eugeniy S.
author list: Agent
  family name: Gamaiunov
  given name: Stanislav V.
author list: Agent
  family name: Timofeyev
  given name: Maxim A.
doi: 10.7717/peerj.5832
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: ©2018 Voytsekhovskaya et al.
attribution name: Voytsekhovskaya et al.

Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding
type: item
type: AcademicArticle
description: Sabah is a province of Malaysia located on the northern part of the island of Borneo. Most of the leaf beetle fauna studies from this region conducted over the past 15 years have focussed on the mainland habitats while the leaf beetle fauna from island habitats (ca. 500 islands) have largely been overlooked. This study looks into the leaf beetle fauna of 13 small satellite islands off the west coast of Sabah. All specimens were first sorted into morpho-species operational taxonomic unit (OTU) before being identified to species rank where possible based on morphological characters and species names assigned when the specimens fitted the description of species in the literature. We collected 75 OTUs from 35 genera and five subfamilies according to morphology, 12 of which were identifiable to species level. In addition, the DNA barcode for each OTU was cross checked with records in GenBank and Barcoding of Life Data system (BOLD) to verify their identity. The number of species recorded was reduced from 12 species and 63 OTUs (total 75 OTUs) to 12 species and 56 OTUs (total 68 OTUs) after removal of the colour polymorphic species based on DNA barcode analyses. Pulau Gaya has the highest species richness and Pulau Sulug has the lowest species richness. A total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from the 12 leaf beetle species and 48 OTUs. Based on the DNA barcode analyses, it was possible to confirm several polymorphic OTUs and cryptic species. The mean intraspecific and interspecific genetic divergence were determined as 0.77% and 16.11%, respectively. DNA barcodes of this study show a low similarity with records in GenBank and BOLD, highlighting the lack of representation and the urgency of studying leaf beetles from this region. The study provides the first documentation of leaf beetle fauna from island habitats of Sabah and the first DNA barcoding data for leaf beetles from this part of the world, with the next steps being larger…
format: application/pdf
format: text/html
creator: Kam-Cheng Yeong
creator: Haruo Takizawa
creator: Thor-Seng Liew
subject: Biodiversity
subject: Biogeography
subject: Entomology
subject: Molecular Biology
description: doi:10.7717/peerj.5811
publisher: PeerJ Inc.
rights: © 2018 Yeong et al.
abstract: Sabah is a province of Malaysia located on the northern part of the island of Borneo. Most of the leaf beetle fauna studies from this region conducted over the past 15 years have focussed on the mainland habitats while the leaf beetle fauna from island habitats (ca. 500 islands) have largely been overlooked. This study looks into the leaf beetle fauna of 13 small satellite islands off the west coast of Sabah. All specimens were first sorted into morpho-species operational taxonomic unit (OTU) before being identified to species rank where possible based on morphological characters and species names assigned when the specimens fitted the description of species in the literature. We collected 75 OTUs from 35 genera and five subfamilies according to morphology, 12 of which were identifiable to species level. In addition, the DNA barcode for each OTU was cross checked with records in GenBank and Barcoding of Life Data system (BOLD) to verify their identity. The number of species recorded was reduced from 12 species and 63 OTUs (total 75 OTUs) to 12 species and 56 OTUs (total 68 OTUs) after removal of the colour polymorphic species based on DNA barcode analyses. Pulau Gaya has the highest species richness and Pulau Sulug has the lowest species richness. A total of 64 Barcode Index Numbers consisting of 101 DNA barcodes were obtained from the 12 leaf beetle species and 48 OTUs. Based on the DNA barcode analyses, it was possible to confirm several polymorphic OTUs and cryptic species. The mean intraspecific and interspecific genetic divergence were determined as 0.77% and 16.11%, respectively. DNA barcodes of this study show a low similarity with records in GenBank and BOLD, highlighting the lack of representation and the urgency of studying leaf beetles from this region. The study provides the first documentation of leaf beetle fauna from island habitats of Sabah and the first DNA barcoding data for leaf beetles from this part of the world, with the next steps being larger…
bibliographic citation: Yeong et al. (2018) Investigating leaf beetles (Coleoptera, Chrysomelidae) on the west coast islands of Sabah via checklist-taking and DNA barcoding. PeerJ 6:e5811 https://doi.org/10.7717/peerj.5811
date submitted: 2018-03-29
date accepted: 2018-09-23
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yeong
  given name: Kam-Cheng
author list: Agent
  family name: Takizawa
  given name: Haruo
author list: Agent
  family name: Liew
  given name: Thor-Seng
doi: 10.7717/peerj.5811
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: © 2018 Yeong et al.
attribution name: Yeong et al.

Recent advances and challenges on application of tissue engineering for treatment of congenital heart disease
type: item
type: AcademicArticle
description: Congenital heart disease (CHD) affects a considerable number of children and adults worldwide. This implicates not only developmental disorders, high mortality, and reduced quality of life but also, high costs for the healthcare systems. CHD refers to a variety of heart and vascular malformations which could be very challenging to reconstruct the malformed region surgically, especially when the patient is an infant or a child. Advanced technology and research have offered a better mechanistic insight on the impact of CHD in the heart and vascular system of infants, children, and adults and identified potential therapeutic solutions. Many artificial materials and devices have been used for cardiovascular surgery. Surgeons and the medical industry created and evolved the ball valves to the carbon-based leaflet valves and introduced bioprosthesis as an alternative. However, with research further progressing, contracting tissue has been developed in laboratories and tissue engineering (TE) could represent a revolutionary answer for CHD surgery. Development of engineered tissue for cardiac and aortic reconstruction for developing bodies of infants and children can be very challenging. Nevertheless, using acellular scaffolds, allograft, xenografts, and autografts is already very common. Seeding of cells on surface and within scaffold is a key challenging factor for use of the above. The use of different types of stem cells has been investigated and proven to be suitable for tissue engineering. They are the most promising source of cells for heart reconstruction in a developing body, even for adults. Some stem cell types are more effective than others, with some disadvantages which may be eliminated in the future.
format: application/pdf
format: text/html
creator: Antonia Mantakaki
creator: Adegbenro Omotuyi John Fakoya
creator: Fatemeh Sharifpanah
subject: Cell Biology
subject: Developmental Biology
subject: Anatomy and Physiology
subject: Cardiology
subject: Pathology
description: doi:10.7717/peerj.5805
publisher: PeerJ Inc.
rights: © 2018 Mantakaki et al.
abstract: Congenital heart disease (CHD) affects a considerable number of children and adults worldwide. This implicates not only developmental disorders, high mortality, and reduced quality of life but also, high costs for the healthcare systems. CHD refers to a variety of heart and vascular malformations which could be very challenging to reconstruct the malformed region surgically, especially when the patient is an infant or a child. Advanced technology and research have offered a better mechanistic insight on the impact of CHD in the heart and vascular system of infants, children, and adults and identified potential therapeutic solutions. Many artificial materials and devices have been used for cardiovascular surgery. Surgeons and the medical industry created and evolved the ball valves to the carbon-based leaflet valves and introduced bioprosthesis as an alternative. However, with research further progressing, contracting tissue has been developed in laboratories and tissue engineering (TE) could represent a revolutionary answer for CHD surgery. Development of engineered tissue for cardiac and aortic reconstruction for developing bodies of infants and children can be very challenging. Nevertheless, using acellular scaffolds, allograft, xenografts, and autografts is already very common. Seeding of cells on surface and within scaffold is a key challenging factor for use of the above. The use of different types of stem cells has been investigated and proven to be suitable for tissue engineering. They are the most promising source of cells for heart reconstruction in a developing body, even for adults. Some stem cell types are more effective than others, with some disadvantages which may be eliminated in the future.
bibliographic citation: Mantakaki et al. (2018) Recent advances and challenges on application of tissue engineering for treatment of congenital heart disease. PeerJ 6:e5805 https://doi.org/10.7717/peerj.5805
date submitted: 2018-03-13
date accepted: 2018-09-21
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Mantakaki
  given name: Antonia
author list: Agent
  family name: Fakoya
  given name: Adegbenro Omotuyi John
author list: Agent
  family name: Sharifpanah
  given name: Fatemeh
doi: 10.7717/peerj.5805
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: ©2018 Mantakaki et al.
attribution name: Mantakaki et al.

Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan
type: item
type: AcademicArticle
description: It can be challenging to identify scleractinian corals from the genus Pocillopora Lamarck 1816 in the field because of their large range of inter- and intra-specific morphological variation that co-occur with changes in the physical environment. This task is made more arduous in the context of a depth gradient, where light and water current could greatly affect the morphology of the corallum. Pocillopora verrucosa (Ellis & Solander 1786) in Taiwan was previously reported exclusively from shallow waters (<10 m in depth), but a recent observation of this species in the mesophotic zone (>40 m in depth) questions this bathymetric distribution. We used the mitochondrial open reading frame and the histone 3 molecular markers to investigate the vertical and horizontal spatial distribution of P. verrucosa around Ludao (Green Island), Taiwan. We genotyped 101 P. verrucosa-like colonies collected from four depth zones, ranging from 7 to 45 m, at three sites around the island. Of the 101 colonies sampled, 85 were genotyped as P. verrucosa, 15 as P. meandrina, and one specimen as an undescribed Pocillopora species. P. verrucosa was found at all depths, while P. meandrina and the undescribed Pocillopora specimen were limited to 15 m depth. P. verrucosa has a large bathymetric distribution around Ludao and could benefit from the refuge that the mesophotic zone offers. This study illustrates the difficulty of identifying Pocillopora corals in the field and emphasizes the relevance of molecular taxonomy as an important and complementary tool to traditional taxonomy for clarifying vertical and horizontal species distribution. Our results also illustrate the need in conservation biology to target species genetic diversity rather than just species diversity.
format: application/pdf
format: text/html
creator: Stéphane De Palmas
creator: Derek Soto
creator: Vianney Denis
creator: Ming-Jay Ho
creator: Chaolun Allen Chen
subject: Biodiversity
subject: Genetics
subject: Marine Biology
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.5797
publisher: PeerJ Inc.
rights: © 2018 De Palmas et al.
abstract: It can be challenging to identify scleractinian corals from the genus Pocillopora Lamarck 1816 in the field because of their large range of inter- and intra-specific morphological variation that co-occur with changes in the physical environment. This task is made more arduous in the context of a depth gradient, where light and water current could greatly affect the morphology of the corallum. Pocillopora verrucosa (Ellis & Solander 1786) in Taiwan was previously reported exclusively from shallow waters (<10 m in depth), but a recent observation of this species in the mesophotic zone (>40 m in depth) questions this bathymetric distribution. We used the mitochondrial open reading frame and the histone 3 molecular markers to investigate the vertical and horizontal spatial distribution of P. verrucosa around Ludao (Green Island), Taiwan. We genotyped 101 P. verrucosa-like colonies collected from four depth zones, ranging from 7 to 45 m, at three sites around the island. Of the 101 colonies sampled, 85 were genotyped as P. verrucosa, 15 as P. meandrina, and one specimen as an undescribed Pocillopora species. P. verrucosa was found at all depths, while P. meandrina and the undescribed Pocillopora specimen were limited to 15 m depth. P. verrucosa has a large bathymetric distribution around Ludao and could benefit from the refuge that the mesophotic zone offers. This study illustrates the difficulty of identifying Pocillopora corals in the field and emphasizes the relevance of molecular taxonomy as an important and complementary tool to traditional taxonomy for clarifying vertical and horizontal species distribution. Our results also illustrate the need in conservation biology to target species genetic diversity rather than just species diversity.
bibliographic citation: De Palmas et al. (2018) Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan. PeerJ 6:e5797 https://doi.org/10.7717/peerj.5797
date submitted: 2018-08-07
date accepted: 2018-09-20
issued: 2018-10-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: De Palmas
  given name: Stéphane
author list: Agent
  family name: Soto
  given name: Derek
author list: Agent
  family name: Denis
  given name: Vianney
author list: Agent
  family name: Ho
  given name: Ming-Jay
author list: Agent
  family name: Chen
  given name: Chaolun Allen
doi: 10.7717/peerj.5797
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-25
copyright: © 2018 De Palmas et al.
attribution name: De Palmas et al.

Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus
type: item
type: AcademicArticle
description: Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylogeny of the species within the genus Staphylococcus; with the idea that those who cannot afford whole genome sequencing can use these loci to carry out species assignation confidently. We retrieved 177 orthologous groups (OGs) by using a genome-based phylogeny and an average nucleotide identity analysis. The top 26 OGs showed topologies similar to the species tree and the concatenation of them yielded a topology almost identical to that of the species tree. Furthermore, a phylogeny of just the top seven OGs could be used for species assignment. We sequenced four staphylococcus isolates to test the 26 OGs and found that these OGs were far superior to commonly used markers for this genus. On the whole, our procedure allowed identification of the most adequate markers for inferring the phylogeny within the genus Staphylococcus. We anticipate that this approach will be employed for the identification of the most suitable markers for other bacterial genera and can be very helpful to sort out poorly classified genera.
format: application/pdf
format: text/html
creator: Lucia Graña-Miraglia
creator: César Arreguín-Pérez
creator: Gamaliel López-Leal
creator: Alan Muñoz
creator: Angeles Pérez-Oseguera
creator: Estefan Miranda-Miranda
creator: Raquel Cossío-Bayúgar
creator: Santiago Castillo-Ramírez
subject: Ecology
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.5839
publisher: PeerJ Inc.
rights: © 2018 Graña-Miraglia et al.
abstract: Although genome sequencing has become a very promising approach to conduct microbial taxonomy, few labs have the resources to afford this especially when dealing with data sets of hundreds to thousands of isolates. The goal of this study was to identify the most adequate loci for inferring the phylogeny of the species within the genus Staphylococcus; with the idea that those who cannot afford whole genome sequencing can use these loci to carry out species assignation confidently. We retrieved 177 orthologous groups (OGs) by using a genome-based phylogeny and an average nucleotide identity analysis. The top 26 OGs showed topologies similar to the species tree and the concatenation of them yielded a topology almost identical to that of the species tree. Furthermore, a phylogeny of just the top seven OGs could be used for species assignment. We sequenced four staphylococcus isolates to test the 26 OGs and found that these OGs were far superior to commonly used markers for this genus. On the whole, our procedure allowed identification of the most adequate markers for inferring the phylogeny within the genus Staphylococcus. We anticipate that this approach will be employed for the identification of the most suitable markers for other bacterial genera and can be very helpful to sort out poorly classified genera.
bibliographic citation: Graña-Miraglia et al. (2018) Phylogenomics picks out the par excellence markers for species phylogeny in the genus Staphylococcus. PeerJ 6:e5839 https://doi.org/10.7717/peerj.5839
date submitted: 2018-06-04
date accepted: 2018-09-28
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Graña-Miraglia
  given name: Lucia
author list: Agent
  family name: Arreguín-Pérez
  given name: César
author list: Agent
  family name: López-Leal
  given name: Gamaliel
author list: Agent
  family name: Muñoz
  given name: Alan
author list: Agent
  family name: Pérez-Oseguera
  given name: Angeles
author list: Agent
  family name: Miranda-Miranda
  given name: Estefan
author list: Agent
  family name: Cossío-Bayúgar
  given name: Raquel
author list: Agent
  family name: Castillo-Ramírez
  given name: Santiago
doi: 10.7717/peerj.5839
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Graña-Miraglia et al.
attribution name: Graña-Miraglia et al.

Infection and coinfection by human papillomavirus, Epstein–Barr virus and Merkel cell polyomavirus in patients with squamous cell carcinoma of the larynx: a retrospective study
type: item
type: AcademicArticle
description: Background Human papillomavirus (HPV) is recognized as an important risk factor for laryngeal carcinogenesis. Although HPV-16 and 18 have been strongly implicated, the presence of other high-risk HPV (HR-HPV) genotypes or the coinfection with Epstein-Barr virus (EBV) or Merkel cell polyomavirus (MCPV) may increase the risk, but their etiological association has not been definitively established. Methods We characterized the genotype-specific HPV and the frequency of EBV and MCPV infections through the detection of their DNA in 195 laryngeal specimens of squamous cell carcinoma (SCC) histologically confirmed. Results HPV DNA was detected in 93 (47.7%) specimens. HPV-11 was the most frequent with 68 cases (73.1%), and HPV-52 was the most frequently HR-HPV found with 51 cases, which corresponds to 54.8% of all HPV-positive specimens. EBV DNA was detected in 54 (27.7%) tumor tissue specimens of which 25 (46.3%) were in coinfection with HPV. MCPV DNA was detected only in 11 (5.6%) cases of which 5 (45.4%) were in coinfection with an HR-HPV. No association between the presence of DNA of the three examined viruses and the patient smoking habits, alcohol consumption, age, the keratinization status, differentiation grade, or localization of the tumor in the larynx were found. Discussion HPV-52 was the most prevalent HR-HPV, which may suggest that this and other genotypes in addition to HPV-16 and 18 could be considered for prophylaxis. However, further studies including non-cancer larynx cases and the evaluation of other molecular markers and viral co-infection mechanisms are needed to determine the role of the different HR-HPV genotypes, EBV, and MCPV in the etiology of SCC of the larynx.
format: application/pdf
format: text/html
creator: Jose Manuel Vazquez-Guillen
creator: Gerardo C. Palacios-Saucedo
creator: Lydia Guadalupe Rivera-Morales
creator: Monica Valeria Alonzo-Morado
creator: Saira Berenice Burciaga-Bernal
creator: Maribel Montufar-Martinez
creator: Rocio Ortiz-Lopez
creator: Vianey Gonzalez-Villasana
creator: Ana Carolina Martinez-Torres
creator: Julio Cesar Serna-Hernandez
creator: Silvia Judith Hernandez-Martinez
creator: Edmundo Erbey Castelan-Maldonado
creator: Angel Zavala-Pompa
creator: Martha Socorro Montalvo-Bañuelos
creator: Ricardo Garcia-Cabello
creator: Ethel Corinthia Sanchez-Fresno
creator: Cristina Rodriguez-Padilla
subject: Virology
subject: Oncology
subject: Otorhinolaryngology
subject: Respiratory Medicine
description: doi:10.7717/peerj.5834
publisher: PeerJ Inc.
rights: © 2018 Vazquez-Guillen et al.
abstract: Background Human papillomavirus (HPV) is recognized as an important risk factor for laryngeal carcinogenesis. Although HPV-16 and 18 have been strongly implicated, the presence of other high-risk HPV (HR-HPV) genotypes or the coinfection with Epstein-Barr virus (EBV) or Merkel cell polyomavirus (MCPV) may increase the risk, but their etiological association has not been definitively established. Methods We characterized the genotype-specific HPV and the frequency of EBV and MCPV infections through the detection of their DNA in 195 laryngeal specimens of squamous cell carcinoma (SCC) histologically confirmed. Results HPV DNA was detected in 93 (47.7%) specimens. HPV-11 was the most frequent with 68 cases (73.1%), and HPV-52 was the most frequently HR-HPV found with 51 cases, which corresponds to 54.8% of all HPV-positive specimens. EBV DNA was detected in 54 (27.7%) tumor tissue specimens of which 25 (46.3%) were in coinfection with HPV. MCPV DNA was detected only in 11 (5.6%) cases of which 5 (45.4%) were in coinfection with an HR-HPV. No association between the presence of DNA of the three examined viruses and the patient smoking habits, alcohol consumption, age, the keratinization status, differentiation grade, or localization of the tumor in the larynx were found. Discussion HPV-52 was the most prevalent HR-HPV, which may suggest that this and other genotypes in addition to HPV-16 and 18 could be considered for prophylaxis. However, further studies including non-cancer larynx cases and the evaluation of other molecular markers and viral co-infection mechanisms are needed to determine the role of the different HR-HPV genotypes, EBV, and MCPV in the etiology of SCC of the larynx.
bibliographic citation: Vazquez-Guillen et al. (2018) Infection and coinfection by human papillomavirus, Epstein–Barr virus and Merkel cell polyomavirus in patients with squamous cell carcinoma of the larynx: a retrospective study. PeerJ 6:e5834 https://doi.org/10.7717/peerj.5834
date submitted: 2018-03-21
date accepted: 2018-09-27
issued: 2018-10-24
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Vazquez-Guillen
  given name: Jose Manuel
author list: Agent
  family name: Palacios-Saucedo
  given name: Gerardo C.
author list: Agent
  family name: Rivera-Morales
  given name: Lydia Guadalupe
author list: Agent
  family name: Alonzo-Morado
  given name: Monica Valeria
author list: Agent
  family name: Burciaga-Bernal
  given name: Saira Berenice
author list: Agent
  family name: Montufar-Martinez
  given name: Maribel
author list: Agent
  family name: Ortiz-Lopez
  given name: Rocio
author list: Agent
  family name: Gonzalez-Villasana
  given name: Vianey
author list: Agent
  family name: Martinez-Torres
  given name: Ana Carolina
author list: Agent
  family name: Serna-Hernandez
  given name: Julio Cesar
author list: Agent
  family name: Hernandez-Martinez
  given name: Silvia Judith
author list: Agent
  family name: Castelan-Maldonado
  given name: Edmundo Erbey
author list: Agent
  family name: Zavala-Pompa
  given name: Angel
author list: Agent
  family name: Montalvo-Bañuelos
  given name: Martha Socorro
author list: Agent
  family name: Garcia-Cabello
  given name: Ricardo
author list: Agent
  family name: Sanchez-Fresno
  given name: Ethel Corinthia
author list: Agent
  family name: Rodriguez-Padilla
  given name: Cristina
doi: 10.7717/peerj.5834
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-24
copyright: ©2018 Vazquez-Guillen et al.
attribution name: Vazquez-Guillen et al.

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