PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America
items: Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains
items: Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study
items: Associated bacteria of Botryococcus braunii (Chlorophyta)
items: Evaluating the effects of a temporary fostering program on shelter dog welfare
items: Pixel: a content management platform for quantitative omics data
items: Biodegradation of thiocyanate by a native groundwater microbial consortium
items: Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
items: Proteomics alterations in chicken jejunum caused by 24 h fasting
items: Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)

Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America
type: item
type: AcademicArticle
description: A new species of mastodon from the Pleistocene of western North America, Mammut pacificus sp. nov. is herein recognized, with specimens identified throughout California and from two localities in southern Idaho. This new taxon differs from the contemporaneous M. americanum in having narrower teeth, most prominently in M3/m3, as well as six sacral vertebrae, femur with a proportionally greater mid-shaft diameter, and no mandibular tusks at any growth stage. All known Pleistocene Mammut remains from California are consistent with our diagnosis of M. pacificus, which indicates that M. americanum was not present in California.
format: application/pdf
format: text/html
creator: Alton C. Dooley
creator: Eric Scott
creator: Jeremy Green
creator: Kathleen B. Springer
creator: Brett S. Dooley
creator: Gregory James Smith
subject: Paleontology
subject: Taxonomy
description: doi:10.7717/peerj.6614
publisher: PeerJ Inc.
rights: © 2019 Dooley et al.
abstract: A new species of mastodon from the Pleistocene of western North America, Mammut pacificus sp. nov. is herein recognized, with specimens identified throughout California and from two localities in southern Idaho. This new taxon differs from the contemporaneous M. americanum in having narrower teeth, most prominently in M3/m3, as well as six sacral vertebrae, femur with a proportionally greater mid-shaft diameter, and no mandibular tusks at any growth stage. All known Pleistocene Mammut remains from California are consistent with our diagnosis of M. pacificus, which indicates that M. americanum was not present in California.
bibliographic citation: Dooley et al. (2019) Mammut pacificus sp. nov., a newly recognized species of mastodon from the Pleistocene of western North America. PeerJ 7:e6614 https://doi.org/10.7717/peerj.6614
date submitted: 2018-10-16
date accepted: 2019-02-12
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Dooley
  given name: Alton C.
author list: Agent
  family name: Scott
  given name: Eric
author list: Agent
  family name: Green
  given name: Jeremy
author list: Agent
  family name: Springer
  given name: Kathleen B.
author list: Agent
  family name: Dooley
  given name: Brett S.
author list: Agent
  family name: Smith
  given name: Gregory James
doi: 10.7717/peerj.6614
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Dooley et al.
attribution name: Dooley et al.

Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains
type: item
type: AcademicArticle
description: Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence …
format: application/pdf
format: text/html
creator: Marta Maria Ciucani
creator: Davide Palumbo
creator: Marco Galaverni
creator: Patrizia Serventi
creator: Elena Fabbri
creator: Gloria Ravegnini
creator: Sabrina Angelini
creator: Elena Maini
creator: Davide Persico
creator: Romolo Caniglia
creator: Elisabetta Cilli
subject: Biodiversity
subject: Conservation Biology
subject: Evolutionary Studies
subject: Genetics
subject: Paleontology
description: doi:10.7717/peerj.6424
publisher: PeerJ Inc.
rights: © 2019 Ciucani et al.
abstract: Background The contemporary Italian wolf (Canis lupus italicus) represents a case of morphological and genetic uniqueness. Today, Italian wolves are also the only documented population to fall exclusively within the mitochondrial haplogroup 2, which was the most diffused across Eurasian and North American wolves during the Late Pleistocene. However, the dynamics leading to such distinctiveness are still debated. Methods In order to shed light on the ancient genetic variability of this wolf population and on the origin of its current diversity, we collected 19 Late Pleistocene-Holocene samples from northern Italy, which we analyzed at a short portion of the hypervariable region 1 of the mitochondrial DNA, highly informative for wolf and dog phylogenetic analyses. Results Four out of the six detected haplotypes matched the ones found in ancient wolves from northern Europe and Beringia, or in modern European and Chinese wolves, and appeared closely related to the two haplotypes currently found in Italian wolves. The haplotype of two Late Pleistocene samples matched with primitive and contemporary dog sequences from the canine mitochondrial clade A. All these haplotypes belonged to haplogroup 2. The only exception was a Holocene sample dated 3,250 years ago, affiliated to haplogroup 1. Discussion In this study we describe the genetic variability of the most ancient wolf specimens from Italy analyzed so far, providing a preliminary overview of the genetic make-up of the population that inhabited this area from the last glacial maximum to the Middle Age period. Our results endorsed that the genetic diversity carried by the Pleistocene wolves here analyzed showed a strong continuity with other northern Eurasian wolf specimens from the same chronological period. Contrarily, the Holocene samples showed a greater similarity only with modern sequences from Europe and Asia, and the occurrence of an haplogroup 1 haplotype allowed to date back previous finding about its presence …
bibliographic citation: Ciucani et al. (2019) Old wild wolves: ancient DNA survey unveils population dynamics in Late Pleistocene and Holocene Italian remains. PeerJ 7:e6424 https://doi.org/10.7717/peerj.6424
date submitted: 2018-03-26
date accepted: 2019-01-07
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Ciucani
  given name: Marta Maria
author list: Agent
  family name: Palumbo
  given name: Davide
author list: Agent
  family name: Galaverni
  given name: Marco
author list: Agent
  family name: Serventi
  given name: Patrizia
author list: Agent
  family name: Fabbri
  given name: Elena
author list: Agent
  family name: Ravegnini
  given name: Gloria
author list: Agent
  family name: Angelini
  given name: Sabrina
author list: Agent
  family name: Maini
  given name: Elena
author list: Agent
  family name: Persico
  given name: Davide
author list: Agent
  family name: Caniglia
  given name: Romolo
author list: Agent
  family name: Cilli
  given name: Elisabetta
doi: 10.7717/peerj.6424
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Ciucani et al.
attribution name: Ciucani et al.

Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study
type: item
type: AcademicArticle
description: Background This study was designed to investigate the clinicopathological characteristics, treatment and survival of patients with pulmonary large cell neuroendocrine carcinoma (LCNEC). Methods The Surveillance, Epidemiology and End Results database was utilized to identify patients diagnosed with pulmonary LCNEC between 2004 and 2013. Kaplan–Meier analysis was conducted to determine the overall survival (OS) and cancer-specific survival (CSS) rate. Univariate survival analysis along with log-rank test, and Cox proportional hazards model were employed to detect independent prognostic factors. Results Pulmonary LCNEC accounted for 0.58% (2972/510607) of the total number of lung and bronchus carcinoma. And a total of 1,530 eligible cases were identified, with the median follow-up time of 11 months. To be specific, the 3-, 5-year OS and CSS rates were 22.8%, 16.8% and 26.5%, 20.8% respectively. Generally, pulmonary LCNEC was commonly detected in the elderly (72.2%), males (55.9%), the upper lobe (62.0%) and advanced AJCC stage (65.5%). Multivariate analysis revealed that elderly [(≥60 and <80 years) HR:1.203, 95% CI [1.053–1.375], P = 0.007; (≥80 years) HR:1.530, 95% CI [1.238–1.891], P < 0.001] and advanced AJCC stage [(stage III) HR:2.606, 95% CI [2.083–3.260], P < 0.001; (stage IV) HR:4.881, 95% CI [3.923–6.072], P < 0.001] were independent unfavorable prognostic factors, and that female (HR:0.845, 95% CI [0.754–0.947], P = 0.004)), surgery [(Segmentectomy/wedge resection) HR:0.526, 95% CI [0.413–0.669], P < 0.001; (Lobectomy/Bilobectomy) HR:0.357, 95% CI [0.290–0.440], P < 0.001;(Pneumonectomy) HR:0.491, 95% CI [0.355–0.679], P < 0.001] , chemotherapy (HR:0.442, 95% CI [0.389–0.503], P < 0.001) and radiation (HR:0.837, 95% CI [0.738–0.949], P = 0.005) were independent favorable prognostic factors. Conclusion To sum up, age at diagnosis, sex, AJCC 8th edition stage, surgery, chemotherapy and radiation were significantly associated with OS of patients with pulmonary …
format: application/pdf
format: text/html
creator: Ling Cao
creator: Zhi-wen Li
creator: Min Wang
creator: Ting-ting Zhang
creator: Bo Bao
creator: Yun-peng Liu
subject: Epidemiology
subject: Oncology
subject: Public Health
description: doi:10.7717/peerj.6539
publisher: PeerJ Inc.
rights: © 2019 Cao et al.
abstract: Background This study was designed to investigate the clinicopathological characteristics, treatment and survival of patients with pulmonary large cell neuroendocrine carcinoma (LCNEC). Methods The Surveillance, Epidemiology and End Results database was utilized to identify patients diagnosed with pulmonary LCNEC between 2004 and 2013. Kaplan–Meier analysis was conducted to determine the overall survival (OS) and cancer-specific survival (CSS) rate. Univariate survival analysis along with log-rank test, and Cox proportional hazards model were employed to detect independent prognostic factors. Results Pulmonary LCNEC accounted for 0.58% (2972/510607) of the total number of lung and bronchus carcinoma. And a total of 1,530 eligible cases were identified, with the median follow-up time of 11 months. To be specific, the 3-, 5-year OS and CSS rates were 22.8%, 16.8% and 26.5%, 20.8% respectively. Generally, pulmonary LCNEC was commonly detected in the elderly (72.2%), males (55.9%), the upper lobe (62.0%) and advanced AJCC stage (65.5%). Multivariate analysis revealed that elderly [(≥60 and <80 years) HR:1.203, 95% CI [1.053–1.375], P = 0.007; (≥80 years) HR:1.530, 95% CI [1.238–1.891], P < 0.001] and advanced AJCC stage [(stage III) HR:2.606, 95% CI [2.083–3.260], P < 0.001; (stage IV) HR:4.881, 95% CI [3.923–6.072], P < 0.001] were independent unfavorable prognostic factors, and that female (HR:0.845, 95% CI [0.754–0.947], P = 0.004)), surgery [(Segmentectomy/wedge resection) HR:0.526, 95% CI [0.413–0.669], P < 0.001; (Lobectomy/Bilobectomy) HR:0.357, 95% CI [0.290–0.440], P < 0.001;(Pneumonectomy) HR:0.491, 95% CI [0.355–0.679], P < 0.001] , chemotherapy (HR:0.442, 95% CI [0.389–0.503], P < 0.001) and radiation (HR:0.837, 95% CI [0.738–0.949], P = 0.005) were independent favorable prognostic factors. Conclusion To sum up, age at diagnosis, sex, AJCC 8th edition stage, surgery, chemotherapy and radiation were significantly associated with OS of patients with pulmonary …
bibliographic citation: Cao et al. (2019) Clinicopathological characteristics, treatment and survival of pulmonary large cell neuroendocrine carcinoma: a SEER population-based study. PeerJ 7:e6539 https://doi.org/10.7717/peerj.6539
date submitted: 2018-09-13
date accepted: 2019-01-30
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cao
  given name: Ling
author list: Agent
  family name: Li
  given name: Zhi-wen
author list: Agent
  family name: Wang
  given name: Min
author list: Agent
  family name: Zhang
  given name: Ting-ting
author list: Agent
  family name: Bao
  given name: Bo
author list: Agent
  family name: Liu
  given name: Yun-peng
doi: 10.7717/peerj.6539
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Cao et al.
attribution name: Cao et al.

Associated bacteria of Botryococcus braunii (Chlorophyta)
type: item
type: AcademicArticle
description: Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.
format: application/pdf
format: text/html
creator: Joao D. Gouveia
creator: Jie Lian
creator: Georg Steinert
creator: Hauke Smidt
creator: Detmer Sipkema
creator: Rene H. Wijffels
creator: Maria J. Barbosa
subject: Microbiology
subject: Taxonomy
description: doi:10.7717/peerj.6610
publisher: PeerJ Inc.
rights: © 2019 Gouveia et al.
abstract: Botryococcus braunii (Chlorophyta) is a green microalga known for producing hydrocarbons and exopolysaccharides (EPS). Improving the biomass productivity of B. braunii and hence, the productivity of the hydrocarbons and of the EPS, will make B. braunii more attractive for industries. Microalgae usually cohabit with bacteria which leads to the formation of species-specific communities with environmental and biological advantages. Bacteria have been found and identified with a few B. braunii strains, but little is known about the bacterial community across the different strains. A better knowledge of the bacterial community of B. braunii will help to optimize the biomass productivity, hydrocarbons, and EPS accumulation. To better understand the bacterial community diversity of B. braunii, we screened 12 strains from culture collections. Using 16S rRNA gene analysis by MiSeq we described the bacterial diversity across 12 B. braunii strains and identified possible shared communities. We found three bacterial families common to all strains: Rhizobiaceae, Bradyrhizobiaceae, and Comamonadaceae. Additionally, the results also suggest that each strain has its own specific bacteria that may be the result of long-term isolated culture.
bibliographic citation: Gouveia et al. (2019) Associated bacteria of Botryococcus braunii (Chlorophyta). PeerJ 7:e6610 https://doi.org/10.7717/peerj.6610
date submitted: 2018-10-16
date accepted: 2019-02-12
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gouveia
  given name: Joao D.
author list: Agent
  family name: Lian
  given name: Jie
author list: Agent
  family name: Steinert
  given name: Georg
author list: Agent
  family name: Smidt
  given name: Hauke
author list: Agent
  family name: Sipkema
  given name: Detmer
author list: Agent
  family name: Wijffels
  given name: Rene H.
author list: Agent
  family name: Barbosa
  given name: Maria J.
doi: 10.7717/peerj.6610
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: © 2019 Gouveia et al.
attribution name: Gouveia et al.

Evaluating the effects of a temporary fostering program on shelter dog welfare
type: item
type: AcademicArticle
description: One of the greatest stressors for dogs living in animal shelters is social isolation. Many studies have demonstrated that human interaction reduces cortisol in shelter dogs, with the possibility that longer periods of interaction may yield greater effects. These types of interventions are contingent upon removing the dog from the kennel and any such reductions in cortisol are often lost when the dog returns to the kennel. More recently, animal shelters are utilizing short-term fostering programs to provide relief from the perceived stresses of kennel life; however the effects of these programs are not well understood. This study assessed the impacts of one- and two-night fostering programs on the urinary cortisol levels, resting pulse rates, longest bout of uninterrupted rest, and proportion of time spent resting of dogs awaiting adoption. Five animal shelters, open and limited-admission facilities, from across the United States participated in the study. During the study, dogs’ urine was collected in the morning before, during, and after fostering stays for cortisol: creatinine analysis. Non-invasive health monitors were worn by the dogs, which collected heart rates and activity levels, in the shelter and in foster homes. In total, 207 dogs participated in the study, and 1,076 cortisol values were used in our analysis. Across all shelters, we found that dogs’ cortisol: creatinine ratios dropped significantly during their fostering stay, but returned to baseline levels after return to the shelter. However, the observed reduction in cortisol varied in magnitude across shelters. We found that dogs of greater weight, age, and average resting pulse rate had higher cortisol levels; and dogs with longer bouts of uninterrupted rest had lower cortisol levels. Dogs had their longest bouts of rest during sleepovers, followed by in the shelter after their sleepovers. Lastly, significant differences were found when comparing in-shelter cortisol values at our five shelters, diff…
format: application/pdf
format: text/html
creator: Lisa M. Gunter
creator: Erica N. Feuerbacher
creator: Rachel J. Gilchrist
creator: Clive D.L. Wynne
subject: Animal Behavior
subject: Neuroscience
subject: Veterinary Medicine
description: doi:10.7717/peerj.6620
publisher: PeerJ Inc.
rights: © 2019 Gunter et al.
abstract: One of the greatest stressors for dogs living in animal shelters is social isolation. Many studies have demonstrated that human interaction reduces cortisol in shelter dogs, with the possibility that longer periods of interaction may yield greater effects. These types of interventions are contingent upon removing the dog from the kennel and any such reductions in cortisol are often lost when the dog returns to the kennel. More recently, animal shelters are utilizing short-term fostering programs to provide relief from the perceived stresses of kennel life; however the effects of these programs are not well understood. This study assessed the impacts of one- and two-night fostering programs on the urinary cortisol levels, resting pulse rates, longest bout of uninterrupted rest, and proportion of time spent resting of dogs awaiting adoption. Five animal shelters, open and limited-admission facilities, from across the United States participated in the study. During the study, dogs’ urine was collected in the morning before, during, and after fostering stays for cortisol: creatinine analysis. Non-invasive health monitors were worn by the dogs, which collected heart rates and activity levels, in the shelter and in foster homes. In total, 207 dogs participated in the study, and 1,076 cortisol values were used in our analysis. Across all shelters, we found that dogs’ cortisol: creatinine ratios dropped significantly during their fostering stay, but returned to baseline levels after return to the shelter. However, the observed reduction in cortisol varied in magnitude across shelters. We found that dogs of greater weight, age, and average resting pulse rate had higher cortisol levels; and dogs with longer bouts of uninterrupted rest had lower cortisol levels. Dogs had their longest bouts of rest during sleepovers, followed by in the shelter after their sleepovers. Lastly, significant differences were found when comparing in-shelter cortisol values at our five shelters, diff…
bibliographic citation: Gunter et al. (2019) Evaluating the effects of a temporary fostering program on shelter dog welfare. PeerJ 7:e6620 https://doi.org/10.7717/peerj.6620
date submitted: 2018-10-10
date accepted: 2019-02-14
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Gunter
  given name: Lisa M.
author list: Agent
  family name: Feuerbacher
  given name: Erica N.
author list: Agent
  family name: Gilchrist
  given name: Rachel J.
author list: Agent
  family name: Wynne
  given name: Clive D.L.
doi: 10.7717/peerj.6620
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: ©2019 Gunter et al.
attribution name: Gunter et al.

Pixel: a content management platform for quantitative omics data
type: item
type: AcademicArticle
description: Background In biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
format: application/pdf
format: text/html
creator: Thomas Denecker
creator: William Durand
creator: Julien Maupetit
creator: Charles Hébert
creator: Jean-Michel Camadro
creator: Pierre Poulain
creator: Gaëlle Lelandais
subject: Computational Biology
subject: Genomics
subject: Data Science
description: doi:10.7717/peerj.6623
publisher: PeerJ Inc.
rights: © 2019 Denecker et al.
abstract: Background In biology, high-throughput experimental technologies, also referred as “omics” technologies, are increasingly used in research laboratories. Several thousands of gene expression measurements can be obtained in a single experiment. Researchers are routinely facing the challenge to annotate, store, explore and mine all the biological information they have at their disposal. We present here the Pixel web application (Pixel Web App), an original content management platform to help people involved in a multi-omics biological project. Methods The Pixel Web App is built with open source technologies and hosted on the collaborative development platform GitHub (https://github.com/Candihub/pixel). It is written in Python using the Django framework and stores all the data in a PostgreSQL database. It is developed in the open and licensed under the BSD 3-clause license. The Pixel Web App is also heavily tested with both unit and functional tests, a strong code coverage and continuous integration provided by CircleCI. To ease the development and the deployment of the Pixel Web App, Docker and Docker Compose are used to bundle the application as well as its dependencies. Results The Pixel Web App offers researchers an intuitive way to annotate, store, explore and mine their multi-omics results. It can be installed on a personal computer or on a server to fit the needs of many users. In addition, anyone can enhance the application to better suit their needs, either by contributing directly on GitHub (encouraged) or by extending Pixel on their own. The Pixel Web App does not provide any computational programs to analyze the data. Still, it helps to rapidly explore and mine existing results and holds a strategic position in the management of research data.
bibliographic citation: Denecker et al. (2019) Pixel: a content management platform for quantitative omics data. PeerJ 7:e6623 https://doi.org/10.7717/peerj.6623
date submitted: 2018-10-05
date accepted: 2019-02-14
issued: 2019-03-27
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Denecker
  given name: Thomas
author list: Agent
  family name: Durand
  given name: William
author list: Agent
  family name: Maupetit
  given name: Julien
author list: Agent
  family name: Hébert
  given name: Charles
author list: Agent
  family name: Camadro
  given name: Jean-Michel
author list: Agent
  family name: Poulain
  given name: Pierre
author list: Agent
  family name: Lelandais
  given name: Gaëlle
doi: 10.7717/peerj.6623
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-27
copyright: ©2019 Denecker et al.
attribution name: Denecker et al.

Biodegradation of thiocyanate by a native groundwater microbial consortium
type: item
type: AcademicArticle
description: Gold ore processing typically generates large amounts of thiocyanate (SCN−)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN−-contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN−-degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L−1 SCN−, was collected from an aquifer below an unlined tailings dam. An SCN−-degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN−-degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN−-degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN− degradation in groundwater by native aquifer microorganisms.
format: application/pdf
format: text/html
creator: Liam P. Spurr
creator: Mathew P. Watts
creator: Han M. Gan
creator: John W. Moreau
subject: Bioengineering
subject: Microbiology
subject: Environmental Contamination and Remediation
description: doi:10.7717/peerj.6498
publisher: PeerJ Inc.
rights: © 2019 Spurr et al.
abstract: Gold ore processing typically generates large amounts of thiocyanate (SCN−)-contaminated effluent. When this effluent is stored in unlined tailings dams, contamination of the underlying aquifer can occur. The potential for bioremediation of SCN−-contaminated groundwater, either in situ or ex situ, remains largely unexplored. This study aimed to enrich and characterise SCN−-degrading microorganisms from mining-contaminated groundwater under a range of culturing conditions. Mildly acidic and suboxic groundwater, containing ∼135 mg L−1 SCN−, was collected from an aquifer below an unlined tailings dam. An SCN−-degrading consortium was enriched from contaminated groundwater using combinatory amendments of air, glucose and phosphate. Biodegradation occurred in all oxic cultures, except with the sole addition of glucose, but was inhibited by NH4+ and did not occur under anoxic conditions. The SCN−-degrading consortium was characterised using 16S and 18S rRNA gene sequencing, identifying a variety of heterotrophic taxa in addition to sulphur-oxidising bacteria. Interestingly, few recognised SCN−-degrading taxa were identified in significant abundance. These results provide both proof-of-concept and the required conditions for biostimulation of SCN− degradation in groundwater by native aquifer microorganisms.
bibliographic citation: Spurr et al. (2019) Biodegradation of thiocyanate by a native groundwater microbial consortium. PeerJ 7:e6498 https://doi.org/10.7717/peerj.6498
date submitted: 2017-12-30
date accepted: 2019-01-20
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Spurr
  given name: Liam P.
author list: Agent
  family name: Watts
  given name: Mathew P.
author list: Agent
  family name: Gan
  given name: Han M.
author list: Agent
  family name: Moreau
  given name: John W.
doi: 10.7717/peerj.6498
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Spurr et al.
attribution name: Spurr et al.

Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia)
type: item
type: AcademicArticle
description: Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.
format: application/pdf
format: text/html
creator: Shuheng Shen
creator: Xutian Chai
creator: Qiang Zhou
creator: Dong Luo
creator: Yanrong Wang
creator: Zhipeng Liu
subject: Agricultural Science
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.6542
publisher: PeerJ Inc.
rights: © 2019 Shen et al.
abstract: Background Sainfoin (Onobrychis viciifolia) is a highly nutritious, tannin-containing, and tetraploid forage legume. Due to the lack of detailed transcriptomic and genomic information on this species, genetic and breeding projects for sainfoin improvement have been significantly hindered. Methods In this study, a total of 24,630,711 clean reads were generated from 14 different sainfoin tissues using Illumina paired-end sequencing technology and deposited in the NCBI SRA database (SRX3763386). From these clean reads, 77,764 unigene sequences were obtained and 6,752 EST-SSRs were identified using de novo assembly. A total of 2,469 primer pairs were designed, and 200 primer pairs were randomly selected to analyze the polymorphism in five sainfoin wild accessions. Results Further analysis of 40 sainfoin individuals from the five wild populations using 61 EST-SSR loci showed that the number of alleles per locus ranged from 4 to 15, and the expected heterozygosity varied from 0.55 to 0.91. Additionally, by counting the EST-SSR band number and sequencing the three or four bands in one sainfoin individual, sainfoin was confirmed to be autotetraploid. This finding provides a high level of information about this plant. Discussion Through this study, 61 EST-SSR markers were successfully developed and shown to be useful for genetic studies and investigations of population genetic structures and variabilities among different sainfoin accessions.
bibliographic citation: Shen et al. (2019) Development of polymorphic EST-SSR markers and characterization of the autotetraploid genome of sainfoin (Onobrychis viciifolia). PeerJ 7:e6542 https://doi.org/10.7717/peerj.6542
date submitted: 2018-10-10
date accepted: 2019-01-30
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Shen
  given name: Shuheng
author list: Agent
  family name: Chai
  given name: Xutian
author list: Agent
  family name: Zhou
  given name: Qiang
author list: Agent
  family name: Luo
  given name: Dong
author list: Agent
  family name: Wang
  given name: Yanrong
author list: Agent
  family name: Liu
  given name: Zhipeng
doi: 10.7717/peerj.6542
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 Shen et al.
attribution name: Shen et al.

Proteomics alterations in chicken jejunum caused by 24 h fasting
type: item
type: AcademicArticle
description: The small intestine is the longest part of the chicken (Gallus gallus) gastrointestinal system that is specialized for nutrient absorption. It is known that decrease in intestinal villi area or height in early age can cause a reduction in essential nutrient intake, which may lead to delayed growth and consequently poorer performance of broiler chickens. The small intestinal absorptive surface is known to be affected by various factors, among others things the nutritional state. In our experiment, we aimed to investigate the possible protein expression alterations that lie behind the villus area and height decrease caused by feed deprivation. A total of 24 chickens were divided into three groups, namely ad libitum fed, fasted for 24 h, fasted for 24 h then refed for 2 h. The morphometric parameters were also measured in the duodenum, jejunum and ileum tissue sections using image analysis. Differential proteome analyses from jejunum samples were performed using two-dimensional difference gel electrophoresis followed by tryptic digestion and protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Overall 541 protein spots were detected after 2D. Among them, eleven showed 1.5-fold or higher significant difference in expression and were successfully identified. In response to 24 h fasting, the expression of nine proteins was higher and that of two proteins was lower compared to the ad libitum fed group. The functions of the differentially expressed proteins indicate that the 24 h fasting mainly affects the expression of structural proteins, and proteins involved in lipid transport, general stress response, and intestinal defense.
format: application/pdf
format: text/html
creator: Ádám Simon
creator: Gabriella Gulyás
creator: Zoltán Mészár
creator: Mangesh Bhide
creator: János Oláh
creator: Péter Bai
creator: Éva Csősz
creator: András Jávor
creator: István Komlósi
creator: Judit Remenyik
creator: Levente Czeglédi
subject: Agricultural Science
subject: Genetics
subject: Molecular Biology
subject: Veterinary Medicine
subject: Zoology
description: doi:10.7717/peerj.6588
publisher: PeerJ Inc.
rights: © 2019 Simon et al.
abstract: The small intestine is the longest part of the chicken (Gallus gallus) gastrointestinal system that is specialized for nutrient absorption. It is known that decrease in intestinal villi area or height in early age can cause a reduction in essential nutrient intake, which may lead to delayed growth and consequently poorer performance of broiler chickens. The small intestinal absorptive surface is known to be affected by various factors, among others things the nutritional state. In our experiment, we aimed to investigate the possible protein expression alterations that lie behind the villus area and height decrease caused by feed deprivation. A total of 24 chickens were divided into three groups, namely ad libitum fed, fasted for 24 h, fasted for 24 h then refed for 2 h. The morphometric parameters were also measured in the duodenum, jejunum and ileum tissue sections using image analysis. Differential proteome analyses from jejunum samples were performed using two-dimensional difference gel electrophoresis followed by tryptic digestion and protein identification by matrix-assisted laser desorption/ionization mass spectrometry. Overall 541 protein spots were detected after 2D. Among them, eleven showed 1.5-fold or higher significant difference in expression and were successfully identified. In response to 24 h fasting, the expression of nine proteins was higher and that of two proteins was lower compared to the ad libitum fed group. The functions of the differentially expressed proteins indicate that the 24 h fasting mainly affects the expression of structural proteins, and proteins involved in lipid transport, general stress response, and intestinal defense.
bibliographic citation: Simon et al. (2019) Proteomics alterations in chicken jejunum caused by 24 h fasting. PeerJ 7:e6588 https://doi.org/10.7717/peerj.6588
date submitted: 2018-10-01
date accepted: 2019-02-09
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Simon
  given name: Ádám
author list: Agent
  family name: Gulyás
  given name: Gabriella
author list: Agent
  family name: Mészár
  given name: Zoltán
author list: Agent
  family name: Bhide
  given name: Mangesh
author list: Agent
  family name: Oláh
  given name: János
author list: Agent
  family name: Bai
  given name: Péter
author list: Agent
  family name: Csősz
  given name: Éva
author list: Agent
  family name: Jávor
  given name: András
author list: Agent
  family name: Komlósi
  given name: István
author list: Agent
  family name: Remenyik
  given name: Judit
author list: Agent
  family name: Czeglédi
  given name: Levente
doi: 10.7717/peerj.6588
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Simon et al.
attribution name: Simon et al.

Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri)
type: item
type: AcademicArticle
description: The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD g…
format: application/pdf
format: text/html
creator: Xueqiang Su
creator: Tiankai Meng
creator: Yu Zhao
creator: Guohui Li
creator: Xi Cheng
creator: Muhammad Abdullah
creator: Xu Sun
creator: Yongping Cai
creator: Yi Lin
subject: Agricultural Science
subject: Bioinformatics
subject: Genetics
subject: Genomics
description: doi:10.7717/peerj.6628
publisher: PeerJ Inc.
rights: © 2019 Su et al.
abstract: The INDETERMINATE DOMAIN (IDD) gene family encodes hybrid transcription factors with distinct zinc finger motifs and appears to be found in all higher plant genomes. IDD genes have been identified throughout the genomes of the model plants Arabidopsis thaliana and Oryza sativa, and the functions of many members of this gene family have been studied. However, few studies have investigated the IDD gene family in Rosaceae species (among these species, a genome-wide identification of the IDD gene family has only been completed in Malus domestica). This study focuses on a comparative genomic analysis of the IDD gene family in five Rosaceae species (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Rubus occidentalis and Prunus avium). We identified a total of 68 IDD genes: 16 genes in Chinese white pear, 14 genes in F. vesca, 13 genes in Prunus mume, 14 genes in R. occidentalis and 11 genes in Prunus avium. The evolution of the IDD genes in these five Rosaceae species was revealed by constructing a phylogenetic tree, tracking gene duplication events, and performing a sliding window analysis and a conserved microsynteny analysis. The expression analysis of different organs showed that most of the pear IDD genes are found at a very high transcription level in fruits, flowers and buds. Based on our results with those obtained in previous research, we speculated that PbIDD2 and PbIDD8 might participate in flowering induction in pear. A temporal expression analysis showed that the expression patterns of PbIDD3 and PbIDD5 were completely opposite to the accumulation pattern of fruit lignin and the stone cell content. The results of the composite phylogenetic tree and expression pattern analysis indicated that PbIDD3 and PbIDD5 might be involved in the metabolism of lignin and secondary cell wall (SCW) formation. In summary, we provide basic information about the IDD genes in five Rosaceae species and thereby provide a theoretical basis for studying the function of these IDD g…
bibliographic citation: Su et al. (2019) Comparative genomic analysis of the IDD genes in five Rosaceae species and expression analysis in Chinese white pear (Pyrus bretschneideri). PeerJ 7:e6628 https://doi.org/10.7717/peerj.6628
date submitted: 2018-10-04
date accepted: 2019-02-15
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Su
  given name: Xueqiang
author list: Agent
  family name: Meng
  given name: Tiankai
author list: Agent
  family name: Zhao
  given name: Yu
author list: Agent
  family name: Li
  given name: Guohui
author list: Agent
  family name: Cheng
  given name: Xi
author list: Agent
  family name: Abdullah
  given name: Muhammad
author list: Agent
  family name: Sun
  given name: Xu
author list: Agent
  family name: Cai
  given name: Yongping
author list: Agent
  family name: Lin
  given name: Yi
doi: 10.7717/peerj.6628
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Su et al.
attribution name: Su et al.

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