PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Antioxidant nutrition in Atlantic salmon (Salmo salar) parr and post-smolt, fed diets with high inclusion of plant ingredients and graded levels of micronutrients and selected amino acids
items: Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
items: Cranial bone histology of Metoposaurus krasiejowensis (Amphibia, Temnospondyli) from the Late Triassic of Poland
items: Comparisons of forecasting for hepatitis in Guangxi Province, China by using three neural networks models
items: RGFA: powerful and convenient handling of assembly graphs
items: Community assembly and functional leaf traits mediate precipitation use efficiency of alpine grasslands along environmental gradients on the Tibetan Plateau
items: Cloning, expression and characterization of a cold-adapted endo-1, 4-β-glucanase from Citrobacter farmeri A1, a symbiotic bacterium of Reticulitermes labralis
items: Planning horizon affects prophylactic decision-making and epidemic dynamics
items: Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)
items: Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study

Antioxidant nutrition in Atlantic salmon (Salmo salar) parr and post-smolt, fed diets with high inclusion of plant ingredients and graded levels of micronutrients and selected amino acids
type: item
type: AcademicArticle
description: The shift from marine to plant-based ingredients in fish feeds affects the dietary concentrations and bioavailability of micronutrients, amino acids and lipids and consequently warrants a re-evaluation of dietary nutrient recommendations. In the present study, an Atlantic salmon diet high in plant ingredients was supplemented with graded levels of nutrient premix (NP), containing selected amino acids, taurine, cholesterol, vitamins and minerals. This article presents the results on the antioxidant nutrients vitamin C, E and selenium (Se), and effects on tissue redox status. The feed ingredients appeared to contain sufficient levels of vitamin E and Se to cover the requirements to prevent clinical deficiency symptoms. The body levels of α-tocopherol (TOH) in parr and that of Se in parr and post-smolt showed a linear relationship with dietary concentration, while α-TOH in post-smolt seemed to be saturable with a breakpoint near 140 mg kg−1. Ascorbic acid (Asc) concentration in the basal feed was below the expected minimum requirement, but the experimental period was probably too short for the fish to develop visible deficiency symptoms. Asc was saturable in both parr and post-smolt whole body at dietary concentrations of 190 and 63–89 mg kg−1, respectively. Maximum whole body Asc concentration was approximately 40 mg kg−1 in parr and 14 mg kg−1 in post-smolt. Retention ranged from 41 to 10% in parr and from −206 to 12% in post-smolt with increasing NP supplementation. This indicates that the post-smolts had an extraordinarily high consumption of Asc. Analyses of glutathione (GSH) and glutathione disulphide (GSSG) concentrations and the calculated GSH based redox potentials in liver and muscle tissue, indicated only minor effects of diets on redox regulation. However, the post-smolt were more oxidized than the parr. This was supported by the high consumption of Asc and high expression of gpx1 and gpx3 in liver. Based on the present trials, the recommendations for suppl…
format: application/pdf
format: text/html
creator: Kristin Hamre
creator: Nini H. Sissener
creator: Erik-Jan Lock
creator: Pål A. Olsvik
creator: Marit Espe
creator: Bente E. Torstensen
creator: Joana Silva
creator: Johan Johansen
creator: Rune Waagbø
creator: Gro-Ingunn Hemre
subject: Agricultural Science
subject: Aquaculture, Fisheries and Fish Science
subject: Veterinary Medicine
description: doi:10.7717/peerj.2688
publisher: PeerJ Inc.
rights: © 2016 Hamre et al.
abstract: The shift from marine to plant-based ingredients in fish feeds affects the dietary concentrations and bioavailability of micronutrients, amino acids and lipids and consequently warrants a re-evaluation of dietary nutrient recommendations. In the present study, an Atlantic salmon diet high in plant ingredients was supplemented with graded levels of nutrient premix (NP), containing selected amino acids, taurine, cholesterol, vitamins and minerals. This article presents the results on the antioxidant nutrients vitamin C, E and selenium (Se), and effects on tissue redox status. The feed ingredients appeared to contain sufficient levels of vitamin E and Se to cover the requirements to prevent clinical deficiency symptoms. The body levels of α-tocopherol (TOH) in parr and that of Se in parr and post-smolt showed a linear relationship with dietary concentration, while α-TOH in post-smolt seemed to be saturable with a breakpoint near 140 mg kg−1. Ascorbic acid (Asc) concentration in the basal feed was below the expected minimum requirement, but the experimental period was probably too short for the fish to develop visible deficiency symptoms. Asc was saturable in both parr and post-smolt whole body at dietary concentrations of 190 and 63–89 mg kg−1, respectively. Maximum whole body Asc concentration was approximately 40 mg kg−1 in parr and 14 mg kg−1 in post-smolt. Retention ranged from 41 to 10% in parr and from −206 to 12% in post-smolt with increasing NP supplementation. This indicates that the post-smolts had an extraordinarily high consumption of Asc. Analyses of glutathione (GSH) and glutathione disulphide (GSSG) concentrations and the calculated GSH based redox potentials in liver and muscle tissue, indicated only minor effects of diets on redox regulation. However, the post-smolt were more oxidized than the parr. This was supported by the high consumption of Asc and high expression of gpx1 and gpx3 in liver. Based on the present trials, the recommendations for suppl…
bibliographic citation: Hamre et al. (2016) Antioxidant nutrition in Atlantic salmon (Salmo salar) parr and post-smolt, fed diets with high inclusion of plant ingredients and graded levels of micronutrients and selected amino acids. PeerJ 4:e2688 https://doi.org/10.7717/peerj.2688
date submitted: 2016-05-17
date accepted: 2016-10-14
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hamre
  given name: Kristin
author list: Agent
  family name: Sissener
  given name: Nini H.
author list: Agent
  family name: Lock
  given name: Erik-Jan
author list: Agent
  family name: Olsvik
  given name: Pål A.
author list: Agent
  family name: Espe
  given name: Marit
author list: Agent
  family name: Torstensen
  given name: Bente E.
author list: Agent
  family name: Silva
  given name: Joana
author list: Agent
  family name: Johansen
  given name: Johan
author list: Agent
  family name: Waagbø
  given name: Rune
author list: Agent
  family name: Hemre
  given name: Gro-Ingunn
doi: 10.7717/peerj.2688
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: © 2016 Hamre et al.
attribution name: Hamre et al.

Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone
type: item
type: AcademicArticle
description: Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously litt…
format: application/pdf
format: text/html
creator: Cristina N. Butterfield
creator: Zhou Li
creator: Peter F. Andeer
creator: Susan Spaulding
creator: Brian C. Thomas
creator: Andrea Singh
creator: Robert L. Hettich
creator: Kenwyn B. Suttle
creator: Alexander J. Probst
creator: Susannah G. Tringe
creator: Trent Northen
creator: Chongle Pan
creator: Jillian F. Banfield
subject: Bioinformatics
subject: Environmental Sciences
subject: Genomics
subject: Microbiology
subject: Soil Science
description: doi:10.7717/peerj.2687
publisher: PeerJ Inc.
rights: © 2016 Butterfield et al.
abstract: Annually, half of all plant-derived carbon is added to soil where it is microbially respired to CO2. However, understanding of the microbiology of this process is limited because most culture-independent methods cannot link metabolic processes to the organisms present, and this link to causative agents is necessary to predict the results of perturbations on the system. We collected soil samples at two sub-root depths (10–20 cm and 30–40 cm) before and after a rainfall-driven nutrient perturbation event in a Northern California grassland that experiences a Mediterranean climate. From ten samples, we reconstructed 198 metagenome-assembled genomes that represent all major phylotypes. We also quantified 6,835 proteins and 175 metabolites and showed that after the rain event the concentrations of many sugars and amino acids approach zero at the base of the soil profile. Unexpectedly, the genomes of novel members of the Gemmatimonadetes and Candidate Phylum Rokubacteria phyla encode pathways for methylotrophy. We infer that these abundant organisms contribute substantially to carbon turnover in the soil, given that methylotrophy proteins were among the most abundant proteins in the proteome. Previously undescribed Bathyarchaeota and Thermoplasmatales archaea are abundant in deeper soil horizons and are inferred to contribute appreciably to aromatic amino acid degradation. Many of the other bacteria appear to breakdown other components of plant biomass, as evidenced by the prevalence of various sugar and amino acid transporters and corresponding hydrolyzing machinery in the proteome. Overall, our work provides organism-resolved insight into the spatial distribution of bacteria and archaea whose activities combine to degrade plant-derived organics, limiting the transport of methanol, amino acids and sugars into underlying weathered rock. The new insights into the soil carbon cycle during an intense period of carbon turnover, including biogeochemical roles to previously litt…
bibliographic citation: Butterfield et al. (2016) Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PeerJ 4:e2687 https://doi.org/10.7717/peerj.2687
date submitted: 2016-08-10
date accepted: 2016-10-14
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Butterfield
  given name: Cristina N.
author list: Agent
  family name: Li
  given name: Zhou
author list: Agent
  family name: Andeer
  given name: Peter F.
author list: Agent
  family name: Spaulding
  given name: Susan
author list: Agent
  family name: Thomas
  given name: Brian C.
author list: Agent
  family name: Singh
  given name: Andrea
author list: Agent
  family name: Hettich
  given name: Robert L.
author list: Agent
  family name: Suttle
  given name: Kenwyn B.
author list: Agent
  family name: Probst
  given name: Alexander J.
author list: Agent
  family name: Tringe
  given name: Susannah G.
author list: Agent
  family name: Northen
  given name: Trent
author list: Agent
  family name: Pan
  given name: Chongle
author list: Agent
  family name: Banfield
  given name: Jillian F.
doi: 10.7717/peerj.2687
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: ©2016 Butterfield et al.
attribution name: Butterfield et al.

Cranial bone histology of Metoposaurus krasiejowensis (Amphibia, Temnospondyli) from the Late Triassic of Poland
type: item
type: AcademicArticle
description: In this study, 21 skull bones of Metoposaurus krasiejowensis from the Late Triassic of Poland were investigated histologically. Dermal bones show a diploë structure, with an ornamented external surface. The ridges consist of mostly well vascularized parallel-fibered bone; the valleys are built of an avascular layer of lamellar bone. The thick middle region consists of cancellous bone, with varying porosity. The thin and less vascularized internal cortex consists of parallel-fibered bone. The numerous Sharpey’s fibers and ISF are present in all bones. The cyclicity of growth is manifested as an alternation of thick, avascular annuli and high vascularized zones as well as a sequence of resting lines. The detailed histological framework of dermal bones varies even within a single bone; this seems to be related to the local biomechanical loading of the particular part of the skull. The dynamic processes observed during the ornamentation creation indicate that the positions of the ridges and grooves change during growth and could be a specific adaptation to changing biomechanical conditions and stress distribution during bone development. In the supratemporal, the cementing lines show that the remodeling process could be involved in the creations of sculpture. The common occurrence of ISF suggests that metaplastic ossification plays an important role during cranial development. Endochondral bones preserved the numerous remains of calcified cartilage. This indicates that ossification follows a pattern known for stereospondyl intercentra, with relatively slow ossification of the trabecular part and late development of the periosteal cortex. The large accumulation of Sharpey’s fibers in the occipital condyles indicates the presence of strong muscles and ligaments connecting the skull to the vertebral column.
format: application/pdf
format: text/html
creator: Kamil Gruntmejer
creator: Dorota Konietzko-Meier
creator: Adam Bodzioch
subject: Paleontology
subject: Histology
description: doi:10.7717/peerj.2685
publisher: PeerJ Inc.
rights: © 2016 Gruntmejer et al.
abstract: In this study, 21 skull bones of Metoposaurus krasiejowensis from the Late Triassic of Poland were investigated histologically. Dermal bones show a diploë structure, with an ornamented external surface. The ridges consist of mostly well vascularized parallel-fibered bone; the valleys are built of an avascular layer of lamellar bone. The thick middle region consists of cancellous bone, with varying porosity. The thin and less vascularized internal cortex consists of parallel-fibered bone. The numerous Sharpey’s fibers and ISF are present in all bones. The cyclicity of growth is manifested as an alternation of thick, avascular annuli and high vascularized zones as well as a sequence of resting lines. The detailed histological framework of dermal bones varies even within a single bone; this seems to be related to the local biomechanical loading of the particular part of the skull. The dynamic processes observed during the ornamentation creation indicate that the positions of the ridges and grooves change during growth and could be a specific adaptation to changing biomechanical conditions and stress distribution during bone development. In the supratemporal, the cementing lines show that the remodeling process could be involved in the creations of sculpture. The common occurrence of ISF suggests that metaplastic ossification plays an important role during cranial development. Endochondral bones preserved the numerous remains of calcified cartilage. This indicates that ossification follows a pattern known for stereospondyl intercentra, with relatively slow ossification of the trabecular part and late development of the periosteal cortex. The large accumulation of Sharpey’s fibers in the occipital condyles indicates the presence of strong muscles and ligaments connecting the skull to the vertebral column.
bibliographic citation: Gruntmejer et al. (2016) Cranial bone histology of Metoposaurus krasiejowensis (Amphibia, Temnospondyli) from the Late Triassic of Poland. PeerJ 4:e2685 https://doi.org/10.7717/peerj.2685
date submitted: 2016-04-07
date accepted: 2016-10-13
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gruntmejer
  given name: Kamil
author list: Agent
  family name: Konietzko-Meier
  given name: Dorota
author list: Agent
  family name: Bodzioch
  given name: Adam
doi: 10.7717/peerj.2685
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: ©2016 Gruntmejer et al.
attribution name: Gruntmejer et al.

Comparisons of forecasting for hepatitis in Guangxi Province, China by using three neural networks models
type: item
type: AcademicArticle
description: This study compares and evaluates the prediction of hepatitis in Guangxi Province, China by using back propagation neural networks based genetic algorithm (BPNN-GA), generalized regression neural networks (GRNN), and wavelet neural networks (WNN). In order to compare the results of forecasting, the data obtained from 2004 to 2013 and 2014 were used as modeling and forecasting samples, respectively. The results show that when the small data set of hepatitis has seasonal fluctuation, the prediction result by BPNN-GA will be better than the two other methods. The WNN method is suitable for predicting the large data set of hepatitis that has seasonal fluctuation and the same for the GRNN method when the data increases steadily.
format: application/pdf
format: text/html
creator: Ruijing Gan
creator: Ni Chen
creator: Daizheng Huang
subject: Epidemiology
subject: Hematology
subject: Infectious Diseases
subject: Computational Science
description: doi:10.7717/peerj.2684
publisher: PeerJ Inc.
rights: © 2016 Gan et al.
abstract: This study compares and evaluates the prediction of hepatitis in Guangxi Province, China by using back propagation neural networks based genetic algorithm (BPNN-GA), generalized regression neural networks (GRNN), and wavelet neural networks (WNN). In order to compare the results of forecasting, the data obtained from 2004 to 2013 and 2014 were used as modeling and forecasting samples, respectively. The results show that when the small data set of hepatitis has seasonal fluctuation, the prediction result by BPNN-GA will be better than the two other methods. The WNN method is suitable for predicting the large data set of hepatitis that has seasonal fluctuation and the same for the GRNN method when the data increases steadily.
bibliographic citation: Gan et al. (2016) Comparisons of forecasting for hepatitis in Guangxi Province, China by using three neural networks models. PeerJ 4:e2684 https://doi.org/10.7717/peerj.2684
date submitted: 2016-05-24
date accepted: 2016-10-13
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gan
  given name: Ruijing
author list: Agent
  family name: Chen
  given name: Ni
author list: Agent
  family name: Huang
  given name: Daizheng
doi: 10.7717/peerj.2684
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: © 2016 Gan et al.
attribution name: Gan et al.

RGFA: powerful and convenient handling of assembly graphs
type: item
type: AcademicArticle
description: The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA can be employed to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g., to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs.
format: application/pdf
format: text/html
creator: Giorgio Gonnella
creator: Stefan Kurtz
subject: Bioinformatics
subject: Genomics
description: doi:10.7717/peerj.2681
publisher: PeerJ Inc.
rights: © 2016 Gonnella and Kurtz
abstract: The “Graphical Fragment Assembly” (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph- and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA can be employed to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g., to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs.
bibliographic citation: Gonnella et al. (2016) RGFA: powerful and convenient handling of assembly graphs. PeerJ 4:e2681 https://doi.org/10.7717/peerj.2681
date submitted: 2016-09-23
date accepted: 2016-10-13
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gonnella
  given name: Giorgio
author list: Agent
  family name: Kurtz
  given name: Stefan
doi: 10.7717/peerj.2681
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: ©2016 Gonnella and Kurtz
attribution name: Gonnella and Kurtz

Community assembly and functional leaf traits mediate precipitation use efficiency of alpine grasslands along environmental gradients on the Tibetan Plateau
type: item
type: AcademicArticle
description: The alpine grasslands on the Tibetan Plateau are sensitive and vulnerable to climate change. However, it is still unknown how precipitation use efficiency (PUE), the ratio of aboveground net primary productivity (ANPP) to precipitation, is related to community assembly of plant species, functional groups or traits for the Tibetan alpine grasslands along actual environmental gradients. We conducted a multi-site field survey at grazing-excluded pastures across meadow, steppe and desert-steppe to measure aboveground biomass (AGB) in August, 2010. We used species richness (SR), the Shannon diversity index, and cover-weighted functional group composition (FGC) of 1-xerophytes, 2-mesophytes, and 3-hygrophytes to describe community assembly at the species level; and chose community-level leaf area index (LAIc), specific leaf area (SLAc), and species-mixed foliar δ13C to quantify community assembly at the functional trait level. Our results showed that PUE decreased with increasing accumulated active temperatures (AccT) when daily temperature average is higher than 5 °C, but increased with increasing climatic moisture index (CMI), which was demined as the ratio of growing season precipitation (GSP) to AccT. We also found that PUE increased with increasing SR, the Shannon diversity index, FGC and LAIc, decreased with increasing foliar δ13C, and had no relation with SLAc at the regional scale. Neither soil total nitrogen (STN) nor organic carbon has no influence on PUE at the regional scale. The community assembly of the Shannon index, LAIc and SLAc together accounted for 46.3% of variance in PUE, whilst CMI accounted for 47.9% of variance in PUE at the regional scale. This implies that community structural properties and plant functional traits can mediate the sensitivity of alpine grassland productivity in response to climate change. Thus, a long-term observation on community structural and functional changes is recommended for better understanding the response of alpine ec…
format: application/pdf
format: text/html
creator: Shaowei Li
creator: Jianshuang Wu
subject: Agricultural Science
subject: Biodiversity
subject: Biogeography
subject: Ecology
subject: Environmental Sciences
description: doi:10.7717/peerj.2680
publisher: PeerJ Inc.
rights: © 2016 Li and Wu
abstract: The alpine grasslands on the Tibetan Plateau are sensitive and vulnerable to climate change. However, it is still unknown how precipitation use efficiency (PUE), the ratio of aboveground net primary productivity (ANPP) to precipitation, is related to community assembly of plant species, functional groups or traits for the Tibetan alpine grasslands along actual environmental gradients. We conducted a multi-site field survey at grazing-excluded pastures across meadow, steppe and desert-steppe to measure aboveground biomass (AGB) in August, 2010. We used species richness (SR), the Shannon diversity index, and cover-weighted functional group composition (FGC) of 1-xerophytes, 2-mesophytes, and 3-hygrophytes to describe community assembly at the species level; and chose community-level leaf area index (LAIc), specific leaf area (SLAc), and species-mixed foliar δ13C to quantify community assembly at the functional trait level. Our results showed that PUE decreased with increasing accumulated active temperatures (AccT) when daily temperature average is higher than 5 °C, but increased with increasing climatic moisture index (CMI), which was demined as the ratio of growing season precipitation (GSP) to AccT. We also found that PUE increased with increasing SR, the Shannon diversity index, FGC and LAIc, decreased with increasing foliar δ13C, and had no relation with SLAc at the regional scale. Neither soil total nitrogen (STN) nor organic carbon has no influence on PUE at the regional scale. The community assembly of the Shannon index, LAIc and SLAc together accounted for 46.3% of variance in PUE, whilst CMI accounted for 47.9% of variance in PUE at the regional scale. This implies that community structural properties and plant functional traits can mediate the sensitivity of alpine grassland productivity in response to climate change. Thus, a long-term observation on community structural and functional changes is recommended for better understanding the response of alpine ec…
bibliographic citation: Li et al. (2016) Community assembly and functional leaf traits mediate precipitation use efficiency of alpine grasslands along environmental gradients on the Tibetan Plateau. PeerJ 4:e2680 https://doi.org/10.7717/peerj.2680
date submitted: 2016-03-16
date accepted: 2016-10-13
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Shaowei
author list: Agent
  family name: Wu
  given name: Jianshuang
doi: 10.7717/peerj.2680
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: © 2016 Li and Wu
attribution name: Li and Wu

Cloning, expression and characterization of a cold-adapted endo-1, 4-β-glucanase from Citrobacter farmeri A1, a symbiotic bacterium of Reticulitermes labralis
type: item
type: AcademicArticle
description: Background Many biotechnological and industrial applications can benefit from cold-adapted EglCs through increased efficiency of catalytic processes at low temperature. In our previous study, Citrobacter farmeri A1 which was isolated from a wood-inhabiting termite Reticulitermes labralis could secrete a cold-adapted EglC. However, its EglC was difficult to purify for enzymatic properties detection because of its low activity (0.8 U/ml). The objective of the present study was to clone and express the C. farmeri EglC gene in Escherichia coli to improve production level and determine the enzymatic properties of the recombinant enzyme. Methods The EglC gene was cloned from C. farmeri A1 by thermal asymmetric interlaced PCR. EglC was transformed into vector pET22b and functionally expressed in E. coli. The recombination protein EglC22b was purified for properties detection. Results SDS-PAGE revealed that the molecular mass of the recombinant endoglucanase was approximately 42 kDa. The activity of the E. coli pET22b-EglC crude extract was 9.5 U/ml. Additionally, it was active at pH 6.5–8.0 with an optimum pH of 7.0. The recombinant enzyme had an optimal temperature of 30–40 °C and exhibited >50% relative activity even at 5 °C, whereas it lost approximately 90% of its activity after incubation at 60 °C for 30 min. Its activity was enhanced by Co2+ and Fe3+, but inhibited by Cd2+, Zn2+, Li+, Triton X-100, DMSO, acetonitrile, Tween 80, SDS, and EDTA. Conclusion These biochemical properties indicate that the recombinant enzyme is a cold-adapted endoglucanase that can be used for various industrial applications.
format: application/pdf
format: text/html
creator: Xi Bai
creator: Xianjun Yuan
creator: Aiyou Wen
creator: Junfeng Li
creator: Yunfeng Bai
creator: Tao Shao
subject: Biotechnology
description: doi:10.7717/peerj.2679
publisher: PeerJ Inc.
rights: © 2016 Bai et al.
abstract: Background Many biotechnological and industrial applications can benefit from cold-adapted EglCs through increased efficiency of catalytic processes at low temperature. In our previous study, Citrobacter farmeri A1 which was isolated from a wood-inhabiting termite Reticulitermes labralis could secrete a cold-adapted EglC. However, its EglC was difficult to purify for enzymatic properties detection because of its low activity (0.8 U/ml). The objective of the present study was to clone and express the C. farmeri EglC gene in Escherichia coli to improve production level and determine the enzymatic properties of the recombinant enzyme. Methods The EglC gene was cloned from C. farmeri A1 by thermal asymmetric interlaced PCR. EglC was transformed into vector pET22b and functionally expressed in E. coli. The recombination protein EglC22b was purified for properties detection. Results SDS-PAGE revealed that the molecular mass of the recombinant endoglucanase was approximately 42 kDa. The activity of the E. coli pET22b-EglC crude extract was 9.5 U/ml. Additionally, it was active at pH 6.5–8.0 with an optimum pH of 7.0. The recombinant enzyme had an optimal temperature of 30–40 °C and exhibited >50% relative activity even at 5 °C, whereas it lost approximately 90% of its activity after incubation at 60 °C for 30 min. Its activity was enhanced by Co2+ and Fe3+, but inhibited by Cd2+, Zn2+, Li+, Triton X-100, DMSO, acetonitrile, Tween 80, SDS, and EDTA. Conclusion These biochemical properties indicate that the recombinant enzyme is a cold-adapted endoglucanase that can be used for various industrial applications.
bibliographic citation: Bai et al. (2016) Cloning, expression and characterization of a cold-adapted endo-1, 4-β-glucanase from Citrobacter farmeri A1, a symbiotic bacterium of Reticulitermes labralis. PeerJ 4:e2679 https://doi.org/10.7717/peerj.2679
date submitted: 2016-06-22
date accepted: 2016-10-12
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bai
  given name: Xi
author list: Agent
  family name: Yuan
  given name: Xianjun
author list: Agent
  family name: Wen
  given name: Aiyou
author list: Agent
  family name: Li
  given name: Junfeng
author list: Agent
  family name: Bai
  given name: Yunfeng
author list: Agent
  family name: Shao
  given name: Tao
doi: 10.7717/peerj.2679
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: ©2016 Bai et al.
attribution name: Bai et al.

Planning horizon affects prophylactic decision-making and epidemic dynamics
type: item
type: AcademicArticle
description: The spread of infectious diseases can be impacted by human behavior, and behavioral decisions often depend implicitly on a planning horizon—the time in the future over which options are weighed. We investigate the effects of planning horizons on epidemic dynamics. We developed an epidemiological agent-based model (along with an ODE analog) to explore the decision-making of self-interested individuals on adopting prophylactic behavior. The decision-making process incorporates prophylaxis efficacy and disease prevalence with the individuals’ payoffs and planning horizon. Our results show that for short and long planning horizons individuals do not consider engaging in prophylactic behavior. In contrast, individuals adopt prophylactic behavior when considering intermediate planning horizons. Such adoption, however, is not always monotonically associated with the prevalence of the disease, depending on the perceived protection efficacy and the disease parameters. Adoption of prophylactic behavior reduces the epidemic peak size while prolonging the epidemic and potentially generates secondary waves of infection. These effects can be made stronger by increasing the behavioral decision frequency or distorting an individual’s perceived risk of infection.
format: application/pdf
format: text/html
creator: Luis G. Nardin
creator: Craig R. Miller
creator: Benjamin J. Ridenhour
creator: Stephen M. Krone
creator: Paul Joyce
creator: Bert O. Baumgaertner
subject: Mathematical Biology
subject: Epidemiology
subject: Infectious Diseases
subject: Public Health
subject: Computational Science
description: doi:10.7717/peerj.2678
publisher: PeerJ Inc.
rights: © 2016 Nardin et al.
abstract: The spread of infectious diseases can be impacted by human behavior, and behavioral decisions often depend implicitly on a planning horizon—the time in the future over which options are weighed. We investigate the effects of planning horizons on epidemic dynamics. We developed an epidemiological agent-based model (along with an ODE analog) to explore the decision-making of self-interested individuals on adopting prophylactic behavior. The decision-making process incorporates prophylaxis efficacy and disease prevalence with the individuals’ payoffs and planning horizon. Our results show that for short and long planning horizons individuals do not consider engaging in prophylactic behavior. In contrast, individuals adopt prophylactic behavior when considering intermediate planning horizons. Such adoption, however, is not always monotonically associated with the prevalence of the disease, depending on the perceived protection efficacy and the disease parameters. Adoption of prophylactic behavior reduces the epidemic peak size while prolonging the epidemic and potentially generates secondary waves of infection. These effects can be made stronger by increasing the behavioral decision frequency or distorting an individual’s perceived risk of infection.
bibliographic citation: Nardin et al. (2016) Planning horizon affects prophylactic decision-making and epidemic dynamics. PeerJ 4:e2678 https://doi.org/10.7717/peerj.2678
date submitted: 2016-08-22
date accepted: 2016-10-12
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Nardin
  given name: Luis G.
author list: Agent
  family name: Miller
  given name: Craig R.
author list: Agent
  family name: Ridenhour
  given name: Benjamin J.
author list: Agent
  family name: Krone
  given name: Stephen M.
author list: Agent
  family name: Joyce
  given name: Paul
author list: Agent
  family name: Baumgaertner
  given name: Bert O.
doi: 10.7717/peerj.2678
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: ©2016 Nardin et al.
attribution name: Nardin et al.

Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)
type: item
type: AcademicArticle
description: Background Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised. Methods We developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure. Results When all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance. Discussion Previously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further algorithm development.
format: application/pdf
format: text/html
creator: Matthew Z. DeMaere
creator: Aaron E. Darling
subject: Bioinformatics
subject: Computational Biology
subject: Genomics
subject: Microbiology
subject: Computational Science
description: doi:10.7717/peerj.2676
publisher: PeerJ Inc.
rights: © 2016 DeMaere and Darling
abstract: Background Chromosome conformation capture, coupled with high throughput DNA sequencing in protocols like Hi-C and 3C-seq, has been proposed as a viable means of generating data to resolve the genomes of microorganisms living in naturally occuring environments. Metagenomic Hi-C and 3C-seq datasets have begun to emerge, but the feasibility of resolving genomes when closely related organisms (strain-level diversity) are present in the sample has not yet been systematically characterised. Methods We developed a computational simulation pipeline for metagenomic 3C and Hi-C sequencing to evaluate the accuracy of genomic reconstructions at, above, and below an operationally defined species boundary. We simulated datasets and measured accuracy over a wide range of parameters. Five clustering algorithms were evaluated (2 hard, 3 soft) using an adaptation of the extended B-cubed validation measure. Results When all genomes in a sample are below 95% sequence identity, all of the tested clustering algorithms performed well. When sequence data contains genomes above 95% identity (our operational definition of strain-level diversity), a naive soft-clustering extension of the Louvain method achieves the highest performance. Discussion Previously, only hard-clustering algorithms have been applied to metagenomic 3C and Hi-C data, yet none of these perform well when strain-level diversity exists in a metagenomic sample. Our simple extension of the Louvain method performed the best in these scenarios, however, accuracy remained well below the levels observed for samples without strain-level diversity. Strain resolution is also highly dependent on the amount of available 3C sequence data, suggesting that depth of sequencing must be carefully considered during experimental design. Finally, there appears to be great scope to improve the accuracy of strain resolution through further algorithm development.
bibliographic citation: DeMaere et al. (2016) Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C). PeerJ 4:e2676 https://doi.org/10.7717/peerj.2676
date submitted: 2016-05-05
date accepted: 2016-10-11
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: DeMaere
  given name: Matthew Z.
author list: Agent
  family name: Darling
  given name: Aaron E.
doi: 10.7717/peerj.2676
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: ©2016 DeMaere and Darling
attribution name: DeMaere and Darling

Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study
type: item
type: AcademicArticle
description: Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.
format: application/pdf
format: text/html
creator: Zhonglou Sun
creator: Tao Pan
creator: Hui Wang
creator: Mujia Pang
creator: Baowei Zhang
subject: Biogeography
subject: Conservation Biology
subject: Zoology
description: doi:10.7717/peerj.2654
publisher: PeerJ Inc.
rights: © 2016 Sun et al.
abstract: Great rivers were generally looked at as the geographical barrier to gene flow for many taxonomic groups. The Yangtze River is the third largest river in the world, and flows across South China and into the East China Sea. Up until now, few studies have been carried out to evaluate its effect as a geographical barrier. In this study, we attempted to determine the barrier effect of the Yangtze River on the tufted deer (Elaphodus cephalophus) using the molecular ecology approach. Using mitochondrial DNA control region (CR) sequences and 13 nuclear microsatellite loci, we explored the genetic structure and gene flow in two adjacent tufted deer populations (Dabashan and Wulingshan populations), which are separated by the Yangtze River. Results indicated that there are high genetic diversity levels in the two populations, but no distinguishable haplotype group or potential genetic cluster was detected which corresponded to specific geographical population. At the same time, high gene flow was observed between Wulingshan and Dabashan populations. The tufted deer populations experienced population decrease from 0.3 to 0.09 Ma BP, then followed by a distinct population increase. A strong signal of recent population decline (T = 4,396 years) was detected in the Wulingshan population by a Markov-Switching Vector Autoregressions(MSVAR) process population demography analysis. The results indicated that the Yangtze River may not act as an effective barrier to gene flow in the tufted deer. Finally, we surmised that the population demography of the tufted deer was likely affected by Pleistocene climate fluctuations and ancient human activities.
bibliographic citation: Sun et al. (2016) Yangtze River, an insignificant genetic boundary in tufted deer (Elaphodus cephalophus): the evidence from a first population genetics study. PeerJ 4:e2654 https://doi.org/10.7717/peerj.2654
date submitted: 2016-02-05
date accepted: 2016-10-04
issued: 2016-11-08
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Sun
  given name: Zhonglou
author list: Agent
  family name: Pan
  given name: Tao
author list: Agent
  family name: Wang
  given name: Hui
author list: Agent
  family name: Pang
  given name: Mujia
author list: Agent
  family name: Zhang
  given name: Baowei
doi: 10.7717/peerj.2654
volume: 4
issn: 2167-8359
publication name: PeerJ
publication date: 2016-11-08
copyright: © 2016 Sun et al.
attribution name: Sun et al.

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