PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration
items: Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX)
items: Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis
items: Underwater sound production varies within not between species in sympatric newts
items: Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing
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

Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration
type: item
type: AcademicArticle
description: Objectives Grb2-associated binder 1 (Gab1), a scaffolding adaptor protein, plays an important role in transmitting key signals that control cell growth, migration, and function from multiple tyrosine kinase receptors. This study was designed to investigate the influence of upregulation of Gab1 in endothelial progenitor cells (EPCs) stimulated with hepatocyte growth factor (HGF), and the underlying molecular mechanisms. Materials and Methods Endothelial progenitor cells isolated from human umbilical cord blood were identified and divided into four groups. EPCs in the Control group were cultured normally; those in the Control+HGF group were treated with HGF stimulation; those in the AD-Gab1 group were transfected with adenovirus containing the Gab1 gene but not treated with HGF stimulation; and, those in the AD-Gab1+HGF group were treated with both HGF stimulation and transfection with adenovirus containing the Gab1 gene. Subsequently, Gab1 expression and proliferation and migration ability were compared for EPCs grown under different conditions. Furthermore, we measured phosphorylation levels of three key proteins Gab1, SHP2, and ERK1/2. Results The AD-Gab1+HGF group had the highest expression of Gab1 and higher proliferation and migration than the other three groups. Conclusions Upregulation of Gab1 promoted HGF-induced EPC proliferation and migration. Mechanistically, HGF stimulated Gab1 tyrosine phosphorylation in EPCs, thus leading to activation of extracellular regulated MAP kinase 1/2, which is involved in proliferation and migration signaling.
format: application/pdf
format: text/html
creator: Qing Fan
creator: Liyu Zhang
creator: Wenjie Zhu
creator: Sheng Xue
creator: Yisheng Song
creator: Qing Chang
subject: Cell Biology
subject: Molecular Biology
description: doi:10.7717/peerj.6675
publisher: PeerJ Inc.
rights: © 2019 Fan et al.
abstract: Objectives Grb2-associated binder 1 (Gab1), a scaffolding adaptor protein, plays an important role in transmitting key signals that control cell growth, migration, and function from multiple tyrosine kinase receptors. This study was designed to investigate the influence of upregulation of Gab1 in endothelial progenitor cells (EPCs) stimulated with hepatocyte growth factor (HGF), and the underlying molecular mechanisms. Materials and Methods Endothelial progenitor cells isolated from human umbilical cord blood were identified and divided into four groups. EPCs in the Control group were cultured normally; those in the Control+HGF group were treated with HGF stimulation; those in the AD-Gab1 group were transfected with adenovirus containing the Gab1 gene but not treated with HGF stimulation; and, those in the AD-Gab1+HGF group were treated with both HGF stimulation and transfection with adenovirus containing the Gab1 gene. Subsequently, Gab1 expression and proliferation and migration ability were compared for EPCs grown under different conditions. Furthermore, we measured phosphorylation levels of three key proteins Gab1, SHP2, and ERK1/2. Results The AD-Gab1+HGF group had the highest expression of Gab1 and higher proliferation and migration than the other three groups. Conclusions Upregulation of Gab1 promoted HGF-induced EPC proliferation and migration. Mechanistically, HGF stimulated Gab1 tyrosine phosphorylation in EPCs, thus leading to activation of extracellular regulated MAP kinase 1/2, which is involved in proliferation and migration signaling.
bibliographic citation: Fan et al. (2019) Up-regulation of Grb2-associated binder 1 promotes hepatocyte growth factor-induced endothelial progenitor cell proliferation and migration. PeerJ 7:e6675 https://doi.org/10.7717/peerj.6675
date submitted: 2018-11-21
date accepted: 2019-02-25
issued: 2019-03-29
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fan
  given name: Qing
author list: Agent
  family name: Zhang
  given name: Liyu
author list: Agent
  family name: Zhu
  given name: Wenjie
author list: Agent
  family name: Xue
  given name: Sheng
author list: Agent
  family name: Song
  given name: Yisheng
author list: Agent
  family name: Chang
  given name: Qing
doi: 10.7717/peerj.6675
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-29
copyright: © 2019 Fan et al.
attribution name: Fan et al.

Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX)
type: item
type: AcademicArticle
description: In this study, we investigated the impact of initial tumor volume, rate of tumor growth, cohort size, study duration, and data analysis method on chemotherapy treatment response classifications in patient-derived xenografts (PDXs). The analyses were conducted on cisplatin treatment response data for 70 PDX models representing ten cancer types with up to 28-day study duration and cohort sizes of 3–10 tumor-bearing mice. The results demonstrated that a 21-day dosing study using a cohort size of eight was necessary to reliably detect responsive models (i.e., tumor volume ratio of treated animals to control between 0.1 and 0.42)—independent of analysis method. A cohort of three tumor-bearing animals led to a reliable classification of models that were both highly responsive and highly nonresponsive to cisplatin (i.e., tumor volume ratio of treated animals to control animals less than 0.10). In our set of PDXs, we found that tumor growth rate in the control group impacted treatment response classification more than initial tumor volume. We repeated the study design factors using docetaxel treated PDXs with consistent results. Our results highlight the importance of defining endpoints for PDX dosing studies when deciding the size of cohorts to use in dosing studies and illustrate that response classifications for a study do not differ significantly across the commonly used analysis methods that are based on tumor volume changes in treatment versus control groups.
format: application/pdf
format: text/html
creator: Joan E. Malcolm
creator: Timothy M. Stearns
creator: Susan D. Airhart
creator: Joel H. Graber
creator: Carol J. Bult
subject: Bioengineering
subject: Drugs and Devices
subject: Oncology
subject: Translational Medicine
description: doi:10.7717/peerj.6586
publisher: PeerJ Inc.
rights: © 2019 Malcolm et al.
abstract: In this study, we investigated the impact of initial tumor volume, rate of tumor growth, cohort size, study duration, and data analysis method on chemotherapy treatment response classifications in patient-derived xenografts (PDXs). The analyses were conducted on cisplatin treatment response data for 70 PDX models representing ten cancer types with up to 28-day study duration and cohort sizes of 3–10 tumor-bearing mice. The results demonstrated that a 21-day dosing study using a cohort size of eight was necessary to reliably detect responsive models (i.e., tumor volume ratio of treated animals to control between 0.1 and 0.42)—independent of analysis method. A cohort of three tumor-bearing animals led to a reliable classification of models that were both highly responsive and highly nonresponsive to cisplatin (i.e., tumor volume ratio of treated animals to control animals less than 0.10). In our set of PDXs, we found that tumor growth rate in the control group impacted treatment response classification more than initial tumor volume. We repeated the study design factors using docetaxel treated PDXs with consistent results. Our results highlight the importance of defining endpoints for PDX dosing studies when deciding the size of cohorts to use in dosing studies and illustrate that response classifications for a study do not differ significantly across the commonly used analysis methods that are based on tumor volume changes in treatment versus control groups.
bibliographic citation: Malcolm et al. (2019) Factors that influence response classifications in chemotherapy treated patient-derived xenografts (PDX). PeerJ 7:e6586 https://doi.org/10.7717/peerj.6586
date submitted: 2018-09-12
date accepted: 2019-02-08
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malcolm
  given name: Joan E.
author list: Agent
  family name: Stearns
  given name: Timothy M.
author list: Agent
  family name: Airhart
  given name: Susan D.
author list: Agent
  family name: Graber
  given name: Joel H.
author list: Agent
  family name: Bult
  given name: Carol J.
doi: 10.7717/peerj.6586
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: ©2019 Malcolm et al.
attribution name: Malcolm et al.

Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis
type: item
type: AcademicArticle
description: Background Necrotic enteritis (NE) is caused by type A strains of the bacterium Clostridium perfringens. Total global economic losses to the poultry industry due to NE is estimated to be over two billion dollars annually. Traditionally, NE has been effectively controlled by inclusion of antibiotics in the diet of poultry. However, recent concerns regarding the impact of this practice on increasing antibiotic resistance in human pathogens have led us to consider alternative approaches, such as vaccination, for controlling this disease. NE strains of C. perfringens produce two major toxins, a-toxin and NetB. Immune responses against either toxin can provide partial protection against NE. Methods We have developed a fusion protein combining a non-toxic carboxyl-terminal domain of a-toxin (PlcC) and an attenuated, mutant form of NetB (NetB-W262A) for use as a vaccine antigen to immunize poultry against NE. We utilized a DNA sequence that was codon-optimized for Nicotiana benthamiana to enable high levels of expression. The 6-His tagged PlcC-NetB fusion protein was synthesized in N. benthamiana using a geminiviral replicon transient expression system, purified by metal affinity chromatography, and used to immunize broiler birds. Results Immunized birds produced a strong serum IgY response against both the plant produced PlcC-NetB protein and against bacterially produced His-PlcC and His-NetB. Immunized birds were significantly protected against a subsequent in-feed challenge with virulent C. perfringens when treated with the fusion protein. These results indicate that a plant-produced PlcC-NetB toxoid is a promising vaccine candidate for controlling NE in poultry.
format: application/pdf
format: text/html
creator: Joseph G.L. Hunter
creator: Shyra Wilde
creator: Amanda M. Tafoya
creator: Jamie Horsman
creator: Miranda Yousif
creator: Andrew G. Diamos
creator: Kenneth L. Roland
creator: Hugh S. Mason
subject: Agricultural Science
subject: Biotechnology
subject: Microbiology
subject: Veterinary Medicine
description: doi:10.7717/peerj.6600
publisher: PeerJ Inc.
rights: © 2019 Hunter et al.
abstract: Background Necrotic enteritis (NE) is caused by type A strains of the bacterium Clostridium perfringens. Total global economic losses to the poultry industry due to NE is estimated to be over two billion dollars annually. Traditionally, NE has been effectively controlled by inclusion of antibiotics in the diet of poultry. However, recent concerns regarding the impact of this practice on increasing antibiotic resistance in human pathogens have led us to consider alternative approaches, such as vaccination, for controlling this disease. NE strains of C. perfringens produce two major toxins, a-toxin and NetB. Immune responses against either toxin can provide partial protection against NE. Methods We have developed a fusion protein combining a non-toxic carboxyl-terminal domain of a-toxin (PlcC) and an attenuated, mutant form of NetB (NetB-W262A) for use as a vaccine antigen to immunize poultry against NE. We utilized a DNA sequence that was codon-optimized for Nicotiana benthamiana to enable high levels of expression. The 6-His tagged PlcC-NetB fusion protein was synthesized in N. benthamiana using a geminiviral replicon transient expression system, purified by metal affinity chromatography, and used to immunize broiler birds. Results Immunized birds produced a strong serum IgY response against both the plant produced PlcC-NetB protein and against bacterially produced His-PlcC and His-NetB. Immunized birds were significantly protected against a subsequent in-feed challenge with virulent C. perfringens when treated with the fusion protein. These results indicate that a plant-produced PlcC-NetB toxoid is a promising vaccine candidate for controlling NE in poultry.
bibliographic citation: Hunter et al. (2019) Evaluation of a toxoid fusion protein vaccine produced in plants to protect poultry against necrotic enteritis. PeerJ 7:e6600 https://doi.org/10.7717/peerj.6600
date submitted: 2018-11-21
date accepted: 2019-02-08
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hunter
  given name: Joseph G.L.
author list: Agent
  family name: Wilde
  given name: Shyra
author list: Agent
  family name: Tafoya
  given name: Amanda M.
author list: Agent
  family name: Horsman
  given name: Jamie
author list: Agent
  family name: Yousif
  given name: Miranda
author list: Agent
  family name: Diamos
  given name: Andrew G.
author list: Agent
  family name: Roland
  given name: Kenneth L.
author list: Agent
  family name: Mason
  given name: Hugh S.
doi: 10.7717/peerj.6600
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: © 2019 Hunter et al.
attribution name: Hunter et al.

Underwater sound production varies within not between species in sympatric newts
type: item
type: AcademicArticle
description: Sound production is a widespread phenomenon among animals. Effective sound use for mate or species recognition requires some acoustic differentiation at an individual or species level. Several species of caudate amphibians produce underwater sounds, but information about intra- and interspecific variation in their acoustic production is missing. We examined individual, sex, and species variation in underwater sound production in adults of two sympatric newt taxa, Ichthyosaura alpestris and Lissotriton vulgaris. Individual newts produced simple low- (peak frequency = 7–8 kHz) and mid-high frequency (14–17 kHz) clicks, which greatly overlap between sexes and species. Individual differences explained about 40–50% of total variation in sound parameters. These results provide foundations for further studies on the mechanisms and eco-evolutionary consequences of underwater acoustics in newts.
format: application/pdf
format: text/html
creator: Jiří Hubáček
creator: Monika Šugerková
creator: Lumír Gvoždík
subject: Animal Behavior
subject: Zoology
subject: Freshwater Biology
description: doi:10.7717/peerj.6649
publisher: PeerJ Inc.
rights: © 2019 Hubáček et al.
abstract: Sound production is a widespread phenomenon among animals. Effective sound use for mate or species recognition requires some acoustic differentiation at an individual or species level. Several species of caudate amphibians produce underwater sounds, but information about intra- and interspecific variation in their acoustic production is missing. We examined individual, sex, and species variation in underwater sound production in adults of two sympatric newt taxa, Ichthyosaura alpestris and Lissotriton vulgaris. Individual newts produced simple low- (peak frequency = 7–8 kHz) and mid-high frequency (14–17 kHz) clicks, which greatly overlap between sexes and species. Individual differences explained about 40–50% of total variation in sound parameters. These results provide foundations for further studies on the mechanisms and eco-evolutionary consequences of underwater acoustics in newts.
bibliographic citation: Hubáček et al. (2019) Underwater sound production varies within not between species in sympatric newts. PeerJ 7:e6649 https://doi.org/10.7717/peerj.6649
date submitted: 2018-10-29
date accepted: 2019-02-20
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hubáček
  given name: Jiří
author list: Agent
  family name: Šugerková
  given name: Monika
author list: Agent
  family name: Gvoždík
  given name: Lumír
doi: 10.7717/peerj.6649
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: ©2019 Hubáček et al.
attribution name: Hubáček et al.

Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing
type: item
type: AcademicArticle
description: The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.
format: application/pdf
format: text/html
creator: Siyu Han
creator: Yu Guan
creator: Hailong Dou
creator: Haitao Yang
creator: Meng Yao
creator: Jianping Ge
creator: Limin Feng
subject: Ecology
subject: Microbiology
subject: Molecular Biology
subject: Zoology
description: doi:10.7717/peerj.6684
publisher: PeerJ Inc.
rights: © 2019 Han et al.
abstract: The analysis of gut microbiota using fecal samples provides a non-invasive approach to understand the complex interactions between host species and their intestinal bacterial community. However, information on gut microbiota for wild endangered carnivores is scarce. The goal of this study was to describe the gut microbiota of two leopard subspecies, the Amur leopard (Panthera pardus orientalis) and North Chinese leopard (Panthera pardus japonensis). Fecal samples from the Amur leopard (n = 8) and North Chinese leopard (n = 13) were collected in Northeast Tiger and Leopard National Park and Shanxi Tieqiaoshan Provincial Nature Reserve in China, respectively. The gut microbiota of leopards was analyzed via high-throughput sequencing of the V3–V4 region of bacterial 16S rRNA gene using the Life Ion S5™ XL platform. A total of 1,413,825 clean reads representing 4,203 operational taxonomic units (OTUs) were detected. For Amur leopard samples, Firmicutes (78.4%) was the dominant phylum, followed by Proteobacteria (9.6%) and Actinobacteria (7.6%). And for the North Chinese leopard, Firmicutes (68.6%), Actinobacteria (11.6%) and Fusobacteria (6.4%) were the most predominant phyla. Clostridiales was the most diverse bacterial order with 37.9% for Amur leopard and 45.7% for North Chinese leopard. Based on the beta-diversity analysis, no significant difference was found in the bacterial community composition between the Amur leopard and North Chinese leopard samples. The current study provides the initial data about the composition and structure of the gut microbiota for wild Amur leopards and North Chinese leopards, and has laid the foundation for further investigations of the health, dietary preferences and physiological regulation of leopards.
bibliographic citation: Han et al. (2019) Comparison of the fecal microbiota of two free-ranging Chinese subspecies of the leopard (Panthera pardus) using high-throughput sequencing. PeerJ 7:e6684 https://doi.org/10.7717/peerj.6684
date submitted: 2018-08-14
date accepted: 2019-02-26
issued: 2019-03-28
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Han
  given name: Siyu
author list: Agent
  family name: Guan
  given name: Yu
author list: Agent
  family name: Dou
  given name: Hailong
author list: Agent
  family name: Yang
  given name: Haitao
author list: Agent
  family name: Yao
  given name: Meng
author list: Agent
  family name: Ge
  given name: Jianping
author list: Agent
  family name: Feng
  given name: Limin
doi: 10.7717/peerj.6684
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-28
copyright: ©2019 Han et al.
attribution name: Han et al.

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.

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