PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Wild bees of Grand Staircase-Escalante National Monument: richness, abundance, and spatio-temporal beta-diversity
items: Migration and transformation of dissolved carbon during accumulated cyanobacteria decomposition in shallow eutrophic lakes: a simulated microcosm study
items: Geophysical upheavals and evolutionary diversification of plant species in the Himalaya
items: Along urbanization sprawl, exotic plants distort native bee (Hymenoptera: Apoidea) assemblages in high elevation Andes ecosystem
items: Early identification of recurrence in ovarian cancer: a comparison between the ovarian cancer metastasis index and CA-125 levels
items: Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853)
items: Novel findings on the impact of chytridiomycosis on the cardiac function of anurans: sensitive vs. tolerant species
items: Field evaluation of the potential for avian exposure to clothianidin following the planting of clothianidin-treated corn seed
items: PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence
items: Application of a MALDI-TOF analysis platform (ClinProTools) for rapid and preliminary report of MRSA sequence types in Taiwan

Wild bees of Grand Staircase-Escalante National Monument: richness, abundance, and spatio-temporal beta-diversity
type: item
type: AcademicArticle
description: Interest in bees has grown dramatically in recent years in light of several studies that have reported widespread declines in bees and other pollinators. Investigating declines in wild bees can be difficult, however, due to the lack of faunal surveys that provide baseline data of bee richness and diversity. Protected lands such as national monuments and national parks can provide unique opportunities to learn about and monitor bee populations dynamics in a natural setting because the opportunity for large-scale changes to the landscape are reduced compared to unprotected lands. Here we report on a 4-year study of bees in Grand Staircase-Escalante National Monument (GSENM), found in southern Utah, USA. Using opportunistic collecting and a series of standardized plots, we collected bees throughout the six-month flowering season for four consecutive years. In total, 660 bee species are now known from the area, across 55 genera, and including 49 new species. Two genera not previously known to occur in the state of Utah were discovered, as well as 16 new species records for the state. Bees include ground-nesters, cavity- and twig-nesters, cleptoparasites, narrow specialists, generalists, solitary, and social species. The bee fauna reached peak diversity each spring, but also experienced a second peak in diversity in late summer, following monsoonal rains. The majority of GSENM’s bees are highly localized, occurring in only a few locations throughout the monument, and often in low abundance, but consistently across the four years. Only a few species are widespread and super-abundant. Certain flowering plants appear to be inordinately attractive to the bees in GSENM, including several invasive species. GSENM protects one of the richest bee faunas in the west; the large elevational gradient, incredible number of flowering plants, and the mosaic of habitats are all likely contributors to this rich assemblage of bees.
format: application/pdf
format: text/html
creator: Olivia Messinger Carril
creator: Terry Griswold
creator: James Haefner
creator: Joseph S. Wilson
subject: Biogeography
subject: Conservation Biology
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.5867
publisher: PeerJ Inc.
rights: © 2018
abstract: Interest in bees has grown dramatically in recent years in light of several studies that have reported widespread declines in bees and other pollinators. Investigating declines in wild bees can be difficult, however, due to the lack of faunal surveys that provide baseline data of bee richness and diversity. Protected lands such as national monuments and national parks can provide unique opportunities to learn about and monitor bee populations dynamics in a natural setting because the opportunity for large-scale changes to the landscape are reduced compared to unprotected lands. Here we report on a 4-year study of bees in Grand Staircase-Escalante National Monument (GSENM), found in southern Utah, USA. Using opportunistic collecting and a series of standardized plots, we collected bees throughout the six-month flowering season for four consecutive years. In total, 660 bee species are now known from the area, across 55 genera, and including 49 new species. Two genera not previously known to occur in the state of Utah were discovered, as well as 16 new species records for the state. Bees include ground-nesters, cavity- and twig-nesters, cleptoparasites, narrow specialists, generalists, solitary, and social species. The bee fauna reached peak diversity each spring, but also experienced a second peak in diversity in late summer, following monsoonal rains. The majority of GSENM’s bees are highly localized, occurring in only a few locations throughout the monument, and often in low abundance, but consistently across the four years. Only a few species are widespread and super-abundant. Certain flowering plants appear to be inordinately attractive to the bees in GSENM, including several invasive species. GSENM protects one of the richest bee faunas in the west; the large elevational gradient, incredible number of flowering plants, and the mosaic of habitats are all likely contributors to this rich assemblage of bees.
bibliographic citation: Carril et al. (2018) Wild bees of Grand Staircase-Escalante National Monument: richness, abundance, and spatio-temporal beta-diversity. PeerJ 6:e5867 https://doi.org/10.7717/peerj.5867
date submitted: 2018-03-12
date accepted: 2018-10-03
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/publicdomain/zero/1.0/
author list: Agent
  family name: Carril
  given name: Olivia Messinger
author list: Agent
  family name: Griswold
  given name: Terry
author list: Agent
  family name: Haefner
  given name: James
author list: Agent
  family name: Wilson
  given name: Joseph S.
doi: 10.7717/peerj.5867
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07

Migration and transformation of dissolved carbon during accumulated cyanobacteria decomposition in shallow eutrophic lakes: a simulated microcosm study
type: item
type: AcademicArticle
description: The decomposition processes of accumulated cyanobacteria can release large amounts of organic carbon and affect the carbon cycling in shallow eutrophic lakes. However, the migration and transformation mechanisms of dissolved carbon (DC) require further study and discussion. In this study, a 73-day laboratory microcosm experiment using suction samplers (Rhizon and syringe) was conducted to understand the migration and transformation of DC during the cyanobacteria decomposition. The decomposition of cyanobacteria biomass caused anoxic and reduction conditions, and changed the acid-base environment in the water column. During the early incubation (days 0–18), a large amount of cyanobacteria-derived particulate organic matter (POM) was decomposed into dissolved organic carbon (DOC) in the overlying water, reaching the highest peak value of 1.82 g L−1 in the treatment added the high cyanobacteria biomass (470 g). After 18 days of incubation, the mineralization of increased DOC to dissolved inorganic carbon (DIC) maintained a high DIC level of overlying water in treatments added cyanobacteria biomass. The treatment added the medium cyanobacteria biomass (235 g) presented the lower DOC/total dissolved carbon ratio than the high cyanobacteria biomass associated with the lower mineralization from DOC to DIC. Due to the concentration differences of DIC at water-sediment interface, the main migration of DIC from pore water to overlying water occurred in the treatment without added cyanobacteria biomass. However, the treatments added the cyanobacteria biomass presented the obvious diffusion of DOC and the low migration of DIC at the water-sediment interface. The diffusive fluxes of DOC at the water-sediment interface increased with the cyanobacteria biomass added, reaching the maximum value of 411.01 mg/(m2·d) in the treatment added the high cyanobacteria biomass. In the overlying water, the group added the sediment and medium cyanobacteria biomass presented a faster degradatio…
format: application/pdf
format: text/html
creator: Zhichun Li
creator: Yanping Zhao
creator: Xiaoguang Xu
creator: Ruiming Han
creator: Mingyue Wang
creator: Guoxiang Wang
subject: Ecology
subject: Freshwater Biology
subject: Biogeochemistry
subject: Environmental Impacts
description: doi:10.7717/peerj.5922
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: The decomposition processes of accumulated cyanobacteria can release large amounts of organic carbon and affect the carbon cycling in shallow eutrophic lakes. However, the migration and transformation mechanisms of dissolved carbon (DC) require further study and discussion. In this study, a 73-day laboratory microcosm experiment using suction samplers (Rhizon and syringe) was conducted to understand the migration and transformation of DC during the cyanobacteria decomposition. The decomposition of cyanobacteria biomass caused anoxic and reduction conditions, and changed the acid-base environment in the water column. During the early incubation (days 0–18), a large amount of cyanobacteria-derived particulate organic matter (POM) was decomposed into dissolved organic carbon (DOC) in the overlying water, reaching the highest peak value of 1.82 g L−1 in the treatment added the high cyanobacteria biomass (470 g). After 18 days of incubation, the mineralization of increased DOC to dissolved inorganic carbon (DIC) maintained a high DIC level of overlying water in treatments added cyanobacteria biomass. The treatment added the medium cyanobacteria biomass (235 g) presented the lower DOC/total dissolved carbon ratio than the high cyanobacteria biomass associated with the lower mineralization from DOC to DIC. Due to the concentration differences of DIC at water-sediment interface, the main migration of DIC from pore water to overlying water occurred in the treatment without added cyanobacteria biomass. However, the treatments added the cyanobacteria biomass presented the obvious diffusion of DOC and the low migration of DIC at the water-sediment interface. The diffusive fluxes of DOC at the water-sediment interface increased with the cyanobacteria biomass added, reaching the maximum value of 411.01 mg/(m2·d) in the treatment added the high cyanobacteria biomass. In the overlying water, the group added the sediment and medium cyanobacteria biomass presented a faster degradatio…
bibliographic citation: Li et al. (2018) Migration and transformation of dissolved carbon during accumulated cyanobacteria decomposition in shallow eutrophic lakes: a simulated microcosm study. PeerJ 6:e5922 https://doi.org/10.7717/peerj.5922
date submitted: 2018-06-03
date accepted: 2018-10-11
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Zhichun
author list: Agent
  family name: Zhao
  given name: Yanping
author list: Agent
  family name: Xu
  given name: Xiaoguang
author list: Agent
  family name: Han
  given name: Ruiming
author list: Agent
  family name: Wang
  given name: Mingyue
author list: Agent
  family name: Wang
  given name: Guoxiang
doi: 10.7717/peerj.5922
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: © 2018 Li et al.
attribution name: Li et al.

Geophysical upheavals and evolutionary diversification of plant species in the Himalaya
type: item
type: AcademicArticle
description: The Himalaya is one of the youngest and the loftiest mountain chains of the world; it is also referred to as the water tower of Asia. The Himalayan region harbors nearly 10,000 plant species constituting approximately 2.5% of the global angiosperm diversity of which over 4,000 are endemics. The present-day Himalayan flora consists of an admixture of immigrant taxa and diversified species over the last 40 million years. The interesting questions about the Himalayan flora discussed here are: how did the Himalaya achieve high endemic plant diversity starting with immigrant taxa and what were the main drivers of this diversity? This contribution aims to answer these questions and raise some more. We review and analyze existing information from diverse areas of earth and climate sciences, palaeobiology and phytogeography to evolve a bio-chronological record of plant species divergence and evolution in the Himalaya. From the analysis we infer the effects of major environmental upheavals on plant diversity in the region. The understanding developed in the following discussion is based on the idea that Himalaya experienced at least five phases of major geophysical upheavals, namely: (i) mega-collision between India and Eurasian plates, (ii) tectonic uplift in phases and progressive landform elevation, (iii) onset of southwest (SW) Indian monsoon, (iv) spurring of arid conditions in Central Asia, and (v) cyclic phases of cooling and warming in the Quaternary. The geophysical upheavals that were potentially disrupting for the ecosystem stability had a key role in providing impetus for biological diversification. The upheavals produced new geophysical environments, new ecological niches, imposed physical and physiological isolation barriers, acted as natural selection sieves and led to the formation of new species. This contribution aims to develop a comprehensive understanding of the plant biodiversity profile of the Himalaya in the context of complex, interconnected and dyna…
format: application/pdf
format: text/html
creator: Kumar Manish
creator: Maharaj K. Pandit
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Evolutionary Studies
subject: Plant Science
description: doi:10.7717/peerj.5919
publisher: PeerJ Inc.
rights: © 2018 Manish and Pandit
abstract: The Himalaya is one of the youngest and the loftiest mountain chains of the world; it is also referred to as the water tower of Asia. The Himalayan region harbors nearly 10,000 plant species constituting approximately 2.5% of the global angiosperm diversity of which over 4,000 are endemics. The present-day Himalayan flora consists of an admixture of immigrant taxa and diversified species over the last 40 million years. The interesting questions about the Himalayan flora discussed here are: how did the Himalaya achieve high endemic plant diversity starting with immigrant taxa and what were the main drivers of this diversity? This contribution aims to answer these questions and raise some more. We review and analyze existing information from diverse areas of earth and climate sciences, palaeobiology and phytogeography to evolve a bio-chronological record of plant species divergence and evolution in the Himalaya. From the analysis we infer the effects of major environmental upheavals on plant diversity in the region. The understanding developed in the following discussion is based on the idea that Himalaya experienced at least five phases of major geophysical upheavals, namely: (i) mega-collision between India and Eurasian plates, (ii) tectonic uplift in phases and progressive landform elevation, (iii) onset of southwest (SW) Indian monsoon, (iv) spurring of arid conditions in Central Asia, and (v) cyclic phases of cooling and warming in the Quaternary. The geophysical upheavals that were potentially disrupting for the ecosystem stability had a key role in providing impetus for biological diversification. The upheavals produced new geophysical environments, new ecological niches, imposed physical and physiological isolation barriers, acted as natural selection sieves and led to the formation of new species. This contribution aims to develop a comprehensive understanding of the plant biodiversity profile of the Himalaya in the context of complex, interconnected and dyna…
bibliographic citation: Manish et al. (2018) Geophysical upheavals and evolutionary diversification of plant species in the Himalaya. PeerJ 6:e5919 https://doi.org/10.7717/peerj.5919
date submitted: 2018-03-12
date accepted: 2018-10-11
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Manish
  given name: Kumar
author list: Agent
  family name: Pandit
  given name: Maharaj K.
doi: 10.7717/peerj.5919
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: ©2018 Manish and Pandit
attribution name: Manish and Pandit

Along urbanization sprawl, exotic plants distort native bee (Hymenoptera: Apoidea) assemblages in high elevation Andes ecosystem
type: item
type: AcademicArticle
description: Native bees contribute a considerable portion of pollination services for endemic as well as introduced plant species. Their decline has been attributed to several human-derived influences including global warming as well as the reduction, alteration, and loss of bees’ habitat. With human expansion comes along the introduction of exotic plant species with negative impacts over native ecosystems. Anthropic effects may even have a deeper impact on communities adapted to extreme environments, such as high elevation habitats, where abiotic stressors alone are a natural limitation to biodiversity. Among these effects, the introduction of exotic plants and urbanization may have a greater influence on native communities. In this work, we explored such problems, studying the relationship between the landscape and its effect over richness and abundance of native bees from the subandean belt in the Andes mountain chain. Furthermore, we investigated the effects of exotic plant abundance on this high-altitude bee assemblage. Despite the landscape not showing an effect over bee richness and abundance, exotic plants did have a significant influence over the native bee assemblage. The abundance of exotic plants was associated with a relative increase in the proportion of small and medium bee species. Moreover, Halictidae was the only family that appeared to be favored by an increase in the abundance of exotic plant species. We discuss these results and the urgent need for further research of high-altitude environments due to their vulnerability and high endemicity.
format: application/pdf
format: text/html
creator: Patricia Henríquez-Piskulich
creator: Alejandro Vera
creator: Gino Sandoval
creator: Cristian Villagra
subject: Biodiversity
subject: Conservation Biology
subject: Ecology
subject: Entomology
description: doi:10.7717/peerj.5916
publisher: PeerJ Inc.
rights: © 2018 Henríquez-Piskulich et al.
abstract: Native bees contribute a considerable portion of pollination services for endemic as well as introduced plant species. Their decline has been attributed to several human-derived influences including global warming as well as the reduction, alteration, and loss of bees’ habitat. With human expansion comes along the introduction of exotic plant species with negative impacts over native ecosystems. Anthropic effects may even have a deeper impact on communities adapted to extreme environments, such as high elevation habitats, where abiotic stressors alone are a natural limitation to biodiversity. Among these effects, the introduction of exotic plants and urbanization may have a greater influence on native communities. In this work, we explored such problems, studying the relationship between the landscape and its effect over richness and abundance of native bees from the subandean belt in the Andes mountain chain. Furthermore, we investigated the effects of exotic plant abundance on this high-altitude bee assemblage. Despite the landscape not showing an effect over bee richness and abundance, exotic plants did have a significant influence over the native bee assemblage. The abundance of exotic plants was associated with a relative increase in the proportion of small and medium bee species. Moreover, Halictidae was the only family that appeared to be favored by an increase in the abundance of exotic plant species. We discuss these results and the urgent need for further research of high-altitude environments due to their vulnerability and high endemicity.
bibliographic citation: Henríquez-Piskulich et al. (2018) Along urbanization sprawl, exotic plants distort native bee (Hymenoptera: Apoidea) assemblages in high elevation Andes ecosystem. PeerJ 6:e5916 https://doi.org/10.7717/peerj.5916
date submitted: 2018-08-23
date accepted: 2018-10-11
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Henríquez-Piskulich
  given name: Patricia
author list: Agent
  family name: Vera
  given name: Alejandro
author list: Agent
  family name: Sandoval
  given name: Gino
author list: Agent
  family name: Villagra
  given name: Cristian
doi: 10.7717/peerj.5916
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: © 2018 Henríquez-Piskulich et al.
attribution name: Henríquez-Piskulich et al.

Early identification of recurrence in ovarian cancer: a comparison between the ovarian cancer metastasis index and CA-125 levels
type: item
type: AcademicArticle
description: Ovarian cancer (OC) is the second most common gynecologic malignancy. A clinical observational study was performed to investigate whether indicators that assess the risk of metastasis can identify recurrence earlier in OC patients. By successfully recruiting 41 patients with OC who underwent chemotherapy, we compared cancer antigen-125 (CA-125) and the ovarian cancer metastasis index (OCMI), which was previously developed by us in the clinic for this purpose. Our results showed that patients and their families generally took a sensible attitude toward disease progression and were willing to accept a new way to gain knowledge about the disease. Herein, the new way was the possibility of monitoring recurrence by introducing the OCMI into the clinic. Fifteen patients experienced recurrence during chemotherapy, implying treatment failure. For 53% of these patients, an abnormally high OCMI suggested a strong tendency toward metastasis at least one chemotherapy cycle prior to the pathological examination confirming recurrence. In comparison, the early recognition rate of recurrence using CA-125 levels was merely 13%. Furthermore, we found that the mean values of the OCMI no longer declined after the fourth chemotherapy cycle, implying that excessive chemotherapy brings no benefit to OC patients. In conclusion, our findings provide a novel and feasible approach to monitor the effectiveness of chemotherapy in the treatment of OC by assessing the potential risk of metastasis.
format: application/pdf
format: text/html
creator: Fei Wang
creator: Xuejun Zhao
creator: Wenhua Tan
creator: Wei Liu
creator: Yuxia Jin
creator: Qian Liu
subject: Gynecology and Obstetrics
subject: Oncology
description: doi:10.7717/peerj.5912
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Ovarian cancer (OC) is the second most common gynecologic malignancy. A clinical observational study was performed to investigate whether indicators that assess the risk of metastasis can identify recurrence earlier in OC patients. By successfully recruiting 41 patients with OC who underwent chemotherapy, we compared cancer antigen-125 (CA-125) and the ovarian cancer metastasis index (OCMI), which was previously developed by us in the clinic for this purpose. Our results showed that patients and their families generally took a sensible attitude toward disease progression and were willing to accept a new way to gain knowledge about the disease. Herein, the new way was the possibility of monitoring recurrence by introducing the OCMI into the clinic. Fifteen patients experienced recurrence during chemotherapy, implying treatment failure. For 53% of these patients, an abnormally high OCMI suggested a strong tendency toward metastasis at least one chemotherapy cycle prior to the pathological examination confirming recurrence. In comparison, the early recognition rate of recurrence using CA-125 levels was merely 13%. Furthermore, we found that the mean values of the OCMI no longer declined after the fourth chemotherapy cycle, implying that excessive chemotherapy brings no benefit to OC patients. In conclusion, our findings provide a novel and feasible approach to monitor the effectiveness of chemotherapy in the treatment of OC by assessing the potential risk of metastasis.
bibliographic citation: Wang et al. (2018) Early identification of recurrence in ovarian cancer: a comparison between the ovarian cancer metastasis index and CA-125 levels. PeerJ 6:e5912 https://doi.org/10.7717/peerj.5912
date submitted: 2018-07-30
date accepted: 2018-10-10
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Fei
author list: Agent
  family name: Zhao
  given name: Xuejun
author list: Agent
  family name: Tan
  given name: Wenhua
author list: Agent
  family name: Liu
  given name: Wei
author list: Agent
  family name: Jin
  given name: Yuxia
author list: Agent
  family name: Liu
  given name: Qian
doi: 10.7717/peerj.5912
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: ©2018 Wang et al.
attribution name: Wang et al.

Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853)
type: item
type: AcademicArticle
description: Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism, physiology or health. Experimental studies in fish groups have found an effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The goal of this study was to compare stomach microbiome from cave and surface Astyanax mexicanus, in order to evaluate the potential response of microbiota to contrasting environmental conditions and physiological adaptations of the host. Stomach microbiota was obtained from three different populations: Pachón cave, and two surface rivers (Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9. A high diversity was observed across samples, including 16 phyla, 120 families and 178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaproteobacteria were the most abundant phyla across the samples. Although the relative abundance of the core OTUs at genus level were highly contrasting among populations, we did not recover differences in stomach microbiome between contrasting habitats (cave vs. surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the contrasting conditions of the habitat considered here but is related to water parameters.
format: application/pdf
format: text/html
creator: Patricia Ornelas-García
creator: Silvia Pajares
creator: Víctor M. Sosa-Jiménez
creator: Sylvie Rétaux
creator: Ramsés A. Miranda-Gamboa
subject: Evolutionary Studies
subject: Genomics
subject: Microbiology
subject: Freshwater Biology
description: doi:10.7717/peerj.5906
publisher: PeerJ Inc.
rights: © 2018 Ornelas-García et al.
abstract: Symbiotic relationships between host and microbiome can play a major role in local adaptation. Previous studies with freshwater organisms have shown that microbiome performs numerous important biochemical functions for the host, playing a key role in metabolism, physiology or health. Experimental studies in fish groups have found an effect of enzymatic activity of gut microbiota on a variety of metabolic processes. The goal of this study was to compare stomach microbiome from cave and surface Astyanax mexicanus, in order to evaluate the potential response of microbiota to contrasting environmental conditions and physiological adaptations of the host. Stomach microbiota was obtained from three different populations: Pachón cave, and two surface rivers (Rascón and Micos rivers). The stomach microbiome was analyzed using the Ion 16S Metagenomic kit considering seven variable regions: V2, V3, V4, V6-7, V8 and V9. A high diversity was observed across samples, including 16 phyla, 120 families and 178 genera. Gammaproteobacteria, Firmicutes, Bacteroidetes and Betaproteobacteria were the most abundant phyla across the samples. Although the relative abundance of the core OTUs at genus level were highly contrasting among populations, we did not recover differences in stomach microbiome between contrasting habitats (cave vs. surface rivers). Rather, we observed a consistent association between β-diversity and dissolved oxygen concentration in water. Therefore, and unexpectedly, the microbiota of A. mexicanus is not linked with the contrasting conditions of the habitat considered here but is related to water parameters.
bibliographic citation: Ornelas-García et al. (2018) Microbiome differences between river-dwelling and cave-adapted populations of the fish Astyanax mexicanus (De Filippi, 1853). PeerJ 6:e5906 https://doi.org/10.7717/peerj.5906
date submitted: 2018-07-24
date accepted: 2018-10-09
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ornelas-García
  given name: Patricia
author list: Agent
  family name: Pajares
  given name: Silvia
author list: Agent
  family name: Sosa-Jiménez
  given name: Víctor M.
author list: Agent
  family name: Rétaux
  given name: Sylvie
author list: Agent
  family name: Miranda-Gamboa
  given name: Ramsés A.
doi: 10.7717/peerj.5906
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: ©2018 Ornelas-García et al.
attribution name: Ornelas-García et al.

Novel findings on the impact of chytridiomycosis on the cardiac function of anurans: sensitive vs. tolerant species
type: item
type: AcademicArticle
description: Background Understanding of the physiological effects of chytridiomycosis is crucial to worldwide amphibian conservation. Therefore, we analyzed the cardiac function of two anuran species (Xenopus laevis and Physalaemus albonotatus) with different susceptibilities to infection by the causative agent of chytridiomycosis, Batrachochytrium dendrobatidis (hereafter Bd). Methods We analyzed the in situ heart rate (fH - bpm), relative ventricular mass (RVM -%), and Ca2+ handling in heart of Bd infected animals compared to uninfected controls of both study species. Results Bd infection resulted in a 78% decrease in contraction force values in P. albonotatus when compared to the less susceptible X. laevis. This negative effect was even more evident (82%) for the cardiac pumping capacity. The time to reach peak tension was 125% longer in P. albonotatus than in X. laevis, and cardiac relaxation was 57% longer. Discussion These results indicate a delay in the cardiac cycle of P. albonotatus on a beat-to-beat basis, which was corroborated by the bradycardia observed in situ. In summary, Bd-sensitive species present impaired cardiac function, which could be a factor in mortality risk. The more pronounced effects of Bd in P. albonotatus may not only result from electrolyte imbalance, as previously reported, but also could be an effect of toxins produced by Bd. For X. laevis, the ability to promote cardiac adjustments seems to be an important homeostatic feature that allows greater tolerance to chytridiomycosis. This study provides new physiological mechanisms underlying the tolerance or susceptibility of amphibian species to chytridiomycosis, which determine their adaptability to survive in the affected environments.
format: application/pdf
format: text/html
creator: Raquel F. Salla
creator: Gisele M. Rizzi-Possignolo
creator: Cristiane R. Oliveira
creator: Carolina Lambertini
creator: Lilian Franco-Belussi
creator: Domingos S. Leite
creator: Elaine Cristina M. Silva-Zacarin
creator: Fábio C. Abdalla
creator: Thomas S. Jenkinson
creator: Luís Felipe Toledo
creator: Monica Jones-Costa
subject: Biodiversity
subject: Zoology
description: doi:10.7717/peerj.5891
publisher: PeerJ Inc.
rights: © 2018 Salla et al.
abstract: Background Understanding of the physiological effects of chytridiomycosis is crucial to worldwide amphibian conservation. Therefore, we analyzed the cardiac function of two anuran species (Xenopus laevis and Physalaemus albonotatus) with different susceptibilities to infection by the causative agent of chytridiomycosis, Batrachochytrium dendrobatidis (hereafter Bd). Methods We analyzed the in situ heart rate (fH - bpm), relative ventricular mass (RVM -%), and Ca2+ handling in heart of Bd infected animals compared to uninfected controls of both study species. Results Bd infection resulted in a 78% decrease in contraction force values in P. albonotatus when compared to the less susceptible X. laevis. This negative effect was even more evident (82%) for the cardiac pumping capacity. The time to reach peak tension was 125% longer in P. albonotatus than in X. laevis, and cardiac relaxation was 57% longer. Discussion These results indicate a delay in the cardiac cycle of P. albonotatus on a beat-to-beat basis, which was corroborated by the bradycardia observed in situ. In summary, Bd-sensitive species present impaired cardiac function, which could be a factor in mortality risk. The more pronounced effects of Bd in P. albonotatus may not only result from electrolyte imbalance, as previously reported, but also could be an effect of toxins produced by Bd. For X. laevis, the ability to promote cardiac adjustments seems to be an important homeostatic feature that allows greater tolerance to chytridiomycosis. This study provides new physiological mechanisms underlying the tolerance or susceptibility of amphibian species to chytridiomycosis, which determine their adaptability to survive in the affected environments.
bibliographic citation: Salla et al. (2018) Novel findings on the impact of chytridiomycosis on the cardiac function of anurans: sensitive vs. tolerant species. PeerJ 6:e5891 https://doi.org/10.7717/peerj.5891
date submitted: 2018-03-06
date accepted: 2018-08-29
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Salla
  given name: Raquel F.
author list: Agent
  family name: Rizzi-Possignolo
  given name: Gisele M.
author list: Agent
  family name: Oliveira
  given name: Cristiane R.
author list: Agent
  family name: Lambertini
  given name: Carolina
author list: Agent
  family name: Franco-Belussi
  given name: Lilian
author list: Agent
  family name: Leite
  given name: Domingos S.
author list: Agent
  family name: Silva-Zacarin
  given name: Elaine Cristina M.
author list: Agent
  family name: Abdalla
  given name: Fábio C.
author list: Agent
  family name: Jenkinson
  given name: Thomas S.
author list: Agent
  family name: Toledo
  given name: Luís Felipe
author list: Agent
  family name: Jones-Costa
  given name: Monica
doi: 10.7717/peerj.5891
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: ©2018 Salla et al.
attribution name: Salla et al.

Field evaluation of the potential for avian exposure to clothianidin following the planting of clothianidin-treated corn seed
type: item
type: AcademicArticle
description: The objective of this study was to quantify consumption of clothianidin-treated corn seed by birds following standard planting practices. Based on post-planting seed counts on 21 fields in southwestern Ontario, Canada, between 29 and 813 seeds/ha (mean of 224 ± 167 (SD)) were estimated to remain on the soil surface immediately post planting (i.e., less than one seed per 10 m2). This represents between 0.03 and 1.2% of the total sown seeds. The number of seeds missing on each field on the third day after planting as a result of any process (e.g., removal by foraging birds or mammals or burial as a result of heavy rains) ranged from 0 to 136 seeds/ha (0 to 0.0136 seeds/m2). Behavior monitoring of individual birds and 24 h remote video surveillance were deployed to investigate how much of the treated seed remaining on the soil surface was consumed by birds. Spotting scopes were used to monitor the full duration of the field visits of 596 individual birds during morning hours for three consecutive days after planting on the 21 fields. Two birds were observed consuming treated seeds (one seed each) and three birds consumed seeds for which the treatment status could not be visually confirmed. Additionally, constant (24 h) video surveillance for 2–4 days immediately after planting was deployed at 24 areas where multiple treated seeds were found on the soil surface. Across 1,380 h of collected video footage (including both day and night periods), no birds were observed to consume any treated seeds. This study provides field evidence of two factors that determine exposure of birds to clothianidin-treated corn seeds: (1) standard sowing practices in Ontario are effective at burying treated seeds such that the proportion of sown seeds that remain on the soil surface after planting is low, and (2) birds monitored on these fields consumed very few of the clothianidin-treated corn seeds remaining on the soil surface after planting. As these results are dependent on planting techn…
format: application/pdf
format: text/html
creator: Sean McGee
creator: Melissa Whitfield-Aslund
creator: Daiana Duca
creator: Nicole Kopysh
creator: Tereza Dan
creator: Loren Knopper
creator: Larry Brewer
subject: Agricultural Science
subject: Ecology
subject: Ecotoxicology
description: doi:10.7717/peerj.5880
publisher: PeerJ Inc.
rights: © 2018 McGee et al.
abstract: The objective of this study was to quantify consumption of clothianidin-treated corn seed by birds following standard planting practices. Based on post-planting seed counts on 21 fields in southwestern Ontario, Canada, between 29 and 813 seeds/ha (mean of 224 ± 167 (SD)) were estimated to remain on the soil surface immediately post planting (i.e., less than one seed per 10 m2). This represents between 0.03 and 1.2% of the total sown seeds. The number of seeds missing on each field on the third day after planting as a result of any process (e.g., removal by foraging birds or mammals or burial as a result of heavy rains) ranged from 0 to 136 seeds/ha (0 to 0.0136 seeds/m2). Behavior monitoring of individual birds and 24 h remote video surveillance were deployed to investigate how much of the treated seed remaining on the soil surface was consumed by birds. Spotting scopes were used to monitor the full duration of the field visits of 596 individual birds during morning hours for three consecutive days after planting on the 21 fields. Two birds were observed consuming treated seeds (one seed each) and three birds consumed seeds for which the treatment status could not be visually confirmed. Additionally, constant (24 h) video surveillance for 2–4 days immediately after planting was deployed at 24 areas where multiple treated seeds were found on the soil surface. Across 1,380 h of collected video footage (including both day and night periods), no birds were observed to consume any treated seeds. This study provides field evidence of two factors that determine exposure of birds to clothianidin-treated corn seeds: (1) standard sowing practices in Ontario are effective at burying treated seeds such that the proportion of sown seeds that remain on the soil surface after planting is low, and (2) birds monitored on these fields consumed very few of the clothianidin-treated corn seeds remaining on the soil surface after planting. As these results are dependent on planting techn…
bibliographic citation: McGee et al. (2018) Field evaluation of the potential for avian exposure to clothianidin following the planting of clothianidin-treated corn seed. PeerJ 6:e5880 https://doi.org/10.7717/peerj.5880
date submitted: 2018-06-07
date accepted: 2018-10-04
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: McGee
  given name: Sean
author list: Agent
  family name: Whitfield-Aslund
  given name: Melissa
author list: Agent
  family name: Duca
  given name: Daiana
author list: Agent
  family name: Kopysh
  given name: Nicole
author list: Agent
  family name: Dan
  given name: Tereza
author list: Agent
  family name: Knopper
  given name: Loren
author list: Agent
  family name: Brewer
  given name: Larry
doi: 10.7717/peerj.5880
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: © 2018 McGee et al.
attribution name: McGee et al.

PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence
type: item
type: AcademicArticle
description: We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the −35 and −10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the −35 and −10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the −10 and −35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts −10 and −35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes.
format: application/pdf
format: text/html
creator: Ramit Bharanikumar
creator: Keshav Aditya R. Premkumar
creator: Ashok Palaniappan
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Synthetic Biology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.5862
publisher: PeerJ Inc.
rights: © 2018 Bharanikumar et al.
abstract: We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the −35 and −10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the −35 and −10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the −10 and −35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts −10 and −35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes.
bibliographic citation: Bharanikumar et al. (2018) PromoterPredict: sequence-based modelling of Escherichia coli σ70 promoter strength yields logarithmic dependence between promoter strength and sequence. PeerJ 6:e5862 https://doi.org/10.7717/peerj.5862
date submitted: 2018-04-03
date accepted: 2018-10-03
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bharanikumar
  given name: Ramit
author list: Agent
  family name: Premkumar
  given name: Keshav Aditya R.
author list: Agent
  family name: Palaniappan
  given name: Ashok
doi: 10.7717/peerj.5862
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: © 2018 Bharanikumar et al.
attribution name: Bharanikumar et al.

Application of a MALDI-TOF analysis platform (ClinProTools) for rapid and preliminary report of MRSA sequence types in Taiwan
type: item
type: AcademicArticle
description: Background The accurate and rapid preliminarily identification of the types of methicillin-resistant Staphylococcus aureus (MRSA) is crucial for infection control. Currently, however, expensive, time-consuming, and labor-intensive methods are used for MRSA typing. By contrast, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a potential tool for preliminary lineage typing. The approach has not been standardized, and its performance has not been analyzed in some regions with geographic barriers (e.g., Taiwan Island). Methods The mass spectra of 306 MRSA isolates were obtained from multiple reference hospitals in Taiwan. The multilocus sequence types (MLST) of the isolates were determined. The spectra were analyzed for the selection of characteristic peaks by using the ClinProTools software. Furthermore, various machine learning (ML) algorithms were used to generate binary and multiclass models for classifying the major MLST types (ST5, ST59, and ST239) of MRSA. Results A total of 10 peaks with the highest discriminatory power (m/z range: 2,082–6,594) were identified and evaluated. All the single peaks revealed significant discriminatory power during MLST typing. Moreover, the binary and multiclass ML models achieved sufficient accuracy (82.80–94.40% for binary models and >81.00% for multiclass models) in classifying the major MLST types. Conclusions A combination of MALDI-TOF MS analysis and ML models is a potentially accurate, objective, and efficient tool for infection control and outbreak investigation.
format: application/pdf
format: text/html
creator: Hsin-Yao Wang
creator: Frank Lien
creator: Tsui-Ping Liu
creator: Chun-Hsien Chen
creator: Chao-Jung Chen
creator: Jang-Jih Lu
subject: Microbiology
subject: Infectious Diseases
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.5784
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Background The accurate and rapid preliminarily identification of the types of methicillin-resistant Staphylococcus aureus (MRSA) is crucial for infection control. Currently, however, expensive, time-consuming, and labor-intensive methods are used for MRSA typing. By contrast, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a potential tool for preliminary lineage typing. The approach has not been standardized, and its performance has not been analyzed in some regions with geographic barriers (e.g., Taiwan Island). Methods The mass spectra of 306 MRSA isolates were obtained from multiple reference hospitals in Taiwan. The multilocus sequence types (MLST) of the isolates were determined. The spectra were analyzed for the selection of characteristic peaks by using the ClinProTools software. Furthermore, various machine learning (ML) algorithms were used to generate binary and multiclass models for classifying the major MLST types (ST5, ST59, and ST239) of MRSA. Results A total of 10 peaks with the highest discriminatory power (m/z range: 2,082–6,594) were identified and evaluated. All the single peaks revealed significant discriminatory power during MLST typing. Moreover, the binary and multiclass ML models achieved sufficient accuracy (82.80–94.40% for binary models and >81.00% for multiclass models) in classifying the major MLST types. Conclusions A combination of MALDI-TOF MS analysis and ML models is a potentially accurate, objective, and efficient tool for infection control and outbreak investigation.
bibliographic citation: Wang et al. (2018) Application of a MALDI-TOF analysis platform (ClinProTools) for rapid and preliminary report of MRSA sequence types in Taiwan. PeerJ 6:e5784 https://doi.org/10.7717/peerj.5784
date submitted: 2018-04-24
date accepted: 2018-09-19
issued: 2018-11-07
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Hsin-Yao
author list: Agent
  family name: Lien
  given name: Frank
author list: Agent
  family name: Liu
  given name: Tsui-Ping
author list: Agent
  family name: Chen
  given name: Chun-Hsien
author list: Agent
  family name: Chen
  given name: Chao-Jung
author list: Agent
  family name: Lu
  given name: Jang-Jih
doi: 10.7717/peerj.5784
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-07
copyright: © 2018 Wang et al.
attribution name: Wang et al.

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