PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Isolation of cancer stem cells by selection for miR-302 expressing cells
items: Robust and automatic definition of microbiome states
items: Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization
items: Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS
items: The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender
items: Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile
items: Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging
items: Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil
items: Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer)
items: Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)

Isolation of cancer stem cells by selection for miR-302 expressing cells
type: item
type: AcademicArticle
description: Background Cancer stem cells are believed to be a major reason for long-term therapy failure because they are multi-drug resistant and able to rest mitotically inactive in the hypoxic center of tumors. Due to their variable number and their often low proliferation rate, cancer stem cells are difficult to purify in decent quantities and to grow in cell culture systems, where they are easily outcompeted by faster growing more ‘differentiated’, i.e., less stem cell-like tumor cells. Methods Here we present a proof of principle study based on the idea to select cancer stem cells by means of the expression of a stem cell-specific gene. A selectable egfp-neo coding sequence was inserted in the last exon of the non-coding murine miR-302 host gene. As a stem cell specific regulatory element, 2.1 kb of the genomic region immediately upstream of the miR-302 host gene transcription start site was used. Stable transgenic CJ7 embryonic stem cells were used to induce teratomas. Results After three weeks, tumors were removed for analysis and primary cultures were established. Stem cell-like cells were selected from these culture based on G418 selection. When the selection was removed, stem cell morphology and miR-302 expression were rapidly lost, indicating that it was not the original ES cells that had been isolated. Conclusions We show the possibility to use drug resistance expressed from a regulatory sequence of a stem cell-specific marker, to isolate and propagate cancer stem cells that otherwise might be hidden in the majority of tumor cells.
format: application/pdf
format: text/html
creator: Karim Rahimi
creator: Annette C. Füchtbauer
creator: Fardin Fathi
creator: Seyed J. Mowla
creator: Ernst-Martin Füchtbauer
subject: Cell Biology
subject: Developmental Biology
subject: Genetics
subject: Molecular Biology
subject: Oncology
description: doi:10.7717/peerj.6635
publisher: PeerJ Inc.
rights: © 2019 Rahimi et al.
abstract: Background Cancer stem cells are believed to be a major reason for long-term therapy failure because they are multi-drug resistant and able to rest mitotically inactive in the hypoxic center of tumors. Due to their variable number and their often low proliferation rate, cancer stem cells are difficult to purify in decent quantities and to grow in cell culture systems, where they are easily outcompeted by faster growing more ‘differentiated’, i.e., less stem cell-like tumor cells. Methods Here we present a proof of principle study based on the idea to select cancer stem cells by means of the expression of a stem cell-specific gene. A selectable egfp-neo coding sequence was inserted in the last exon of the non-coding murine miR-302 host gene. As a stem cell specific regulatory element, 2.1 kb of the genomic region immediately upstream of the miR-302 host gene transcription start site was used. Stable transgenic CJ7 embryonic stem cells were used to induce teratomas. Results After three weeks, tumors were removed for analysis and primary cultures were established. Stem cell-like cells were selected from these culture based on G418 selection. When the selection was removed, stem cell morphology and miR-302 expression were rapidly lost, indicating that it was not the original ES cells that had been isolated. Conclusions We show the possibility to use drug resistance expressed from a regulatory sequence of a stem cell-specific marker, to isolate and propagate cancer stem cells that otherwise might be hidden in the majority of tumor cells.
bibliographic citation: Rahimi et al. (2019) Isolation of cancer stem cells by selection for miR-302 expressing cells. PeerJ 7:e6635 https://doi.org/10.7717/peerj.6635
date submitted: 2018-10-10
date accepted: 2019-02-18
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Rahimi
  given name: Karim
author list: Agent
  family name: Füchtbauer
  given name: Annette C.
author list: Agent
  family name: Fathi
  given name: Fardin
author list: Agent
  family name: Mowla
  given name: Seyed J.
author list: Agent
  family name: Füchtbauer
  given name: Ernst-Martin
doi: 10.7717/peerj.6635
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 Rahimi et al.
attribution name: Rahimi et al.

Robust and automatic definition of microbiome states
type: item
type: AcademicArticle
description: Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.
format: application/pdf
format: text/html
creator: Beatriz García-Jiménez
creator: Mark D. Wilkinson
subject: Bioinformatics
subject: Computational Biology
subject: Microbiology
subject: Data Mining and Machine Learning
description: doi:10.7717/peerj.6657
publisher: PeerJ Inc.
rights: © 2019 García-Jiménez and Wilkinson
abstract: Analysis of microbiome dynamics would allow elucidation of patterns within microbial community evolution under a variety of biologically or economically important circumstances; however, this is currently hampered in part by the lack of rigorous, formal, yet generally-applicable approaches to discerning distinct configurations of complex microbial populations. Clustering approaches to define microbiome “community state-types” at a population-scale are widely used, though not yet standardized. Similarly, distinct variations within a state-type are well documented, but there is no rigorous approach to discriminating these more subtle variations in community structure. Finally, intra-individual variations with even fewer differences will likely be found in, for example, longitudinal data, and will correlate with important features such as sickness versus health. We propose an automated, generic, objective, domain-independent, and internally-validating procedure to define statistically distinct microbiome states within datasets containing any degree of phylotypic diversity. Robustness of state identification is objectively established by a combination of diverse techniques for stable cluster verification. To demonstrate the efficacy of our approach in detecting discreet states even in datasets containing highly similar bacterial communities, and to demonstrate the broad applicability of our method, we reuse eight distinct longitudinal microbiome datasets from a variety of ecological niches and species. We also demonstrate our algorithm’s flexibility by providing it distinct taxa subsets as clustering input, demonstrating that it operates on filtered or unfiltered data, and at a range of different taxonomic levels. The final output is a set of robustly defined states which can then be used as general biomarkers for a wide variety of downstream purposes such as association with disease, monitoring response to intervention, or identifying optimally performant populations.
bibliographic citation: García-Jiménez et al. (2019) Robust and automatic definition of microbiome states. PeerJ 7:e6657 https://doi.org/10.7717/peerj.6657
date submitted: 2018-03-09
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: García-Jiménez
  given name: Beatriz
author list: Agent
  family name: Wilkinson
  given name: Mark D.
doi: 10.7717/peerj.6657
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 García-Jiménez and Wilkinson
attribution name: García-Jiménez and Wilkinson

Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization
type: item
type: AcademicArticle
description: In the present study, the complete mitochondrial genomes (mitogenomes) of five Achilidae (Hemiptera: Fulgoroidea), Betatropis formosana, two new species (Magadhaideus luodiana sp. nov and Peltatavertexalis horizontalis sp. nov), Plectoderini sp. and Paracatonidia sp., were sequenced for the first time through next-generation sequencing. The five mitogenomes ranged from 15,214 to 16,216 bp in length, with the typical gene content and arrangement usually observed in Hexapods. The motif “ATGATAA” between atp8 and atp6 was found in all the analyzed species. An overlap “AAGCTTA” between trnW and trnC was observed in the mitogenomes of most Fulgoroidea. The structural and compositional analyses of 26 Fulgoroidea mitogenomes, including the gene rearrangement of five tRNAs (trnW, trnC and trnY; trnT and trnP), the A + T content and AT-skew of the whole mitogenomes, and the nuclear acid and amino acid compositions of the protein-coding genes (PCGs), revealed family-level differences between Delphacidae and other families (Achilidae, Flatidae, Fulgoridae, Issidae and Ricaniidae). Phylogenetic analyses of 13 protein-coding genes from 26 Fulgoroidea species by maximum likelihood and Bayesian Inference were consistent and well supported the basal position of Delphacidae, a close affinity among the families Flatidae, Issidae and Ricaniidae, and a close relationship between Achilidae and Fulgoridae.
format: application/pdf
format: text/html
creator: Shi-Yan Xu
creator: Jian-Kun Long
creator: Xiang-Sheng Chen
subject: Entomology
subject: Genomics
subject: Molecular Biology
subject: Taxonomy
description: doi:10.7717/peerj.6659
publisher: PeerJ Inc.
rights: © 2019 Xuet al.
abstract: In the present study, the complete mitochondrial genomes (mitogenomes) of five Achilidae (Hemiptera: Fulgoroidea), Betatropis formosana, two new species (Magadhaideus luodiana sp. nov and Peltatavertexalis horizontalis sp. nov), Plectoderini sp. and Paracatonidia sp., were sequenced for the first time through next-generation sequencing. The five mitogenomes ranged from 15,214 to 16,216 bp in length, with the typical gene content and arrangement usually observed in Hexapods. The motif “ATGATAA” between atp8 and atp6 was found in all the analyzed species. An overlap “AAGCTTA” between trnW and trnC was observed in the mitogenomes of most Fulgoroidea. The structural and compositional analyses of 26 Fulgoroidea mitogenomes, including the gene rearrangement of five tRNAs (trnW, trnC and trnY; trnT and trnP), the A + T content and AT-skew of the whole mitogenomes, and the nuclear acid and amino acid compositions of the protein-coding genes (PCGs), revealed family-level differences between Delphacidae and other families (Achilidae, Flatidae, Fulgoridae, Issidae and Ricaniidae). Phylogenetic analyses of 13 protein-coding genes from 26 Fulgoroidea species by maximum likelihood and Bayesian Inference were consistent and well supported the basal position of Delphacidae, a close affinity among the families Flatidae, Issidae and Ricaniidae, and a close relationship between Achilidae and Fulgoridae.
bibliographic citation: Xu et al. (2019) Comparative analysis of the complete mitochondrial genomes of five Achilidae species (Hemiptera: Fulgoroidea) and other Fulgoroidea reveals conserved mitochondrial genome organization. PeerJ 7:e6659 https://doi.org/10.7717/peerj.6659
date submitted: 2018-10-25
date accepted: 2019-02-19
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Xu
  given name: Shi-Yan
author list: Agent
  family name: Long
  given name: Jian-Kun
author list: Agent
  family name: Chen
  given name: Xiang-Sheng
doi: 10.7717/peerj.6659
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Xu et al.
attribution name: Xuet al.

Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS
type: item
type: AcademicArticle
description: Background Quercetin (Qr), isoquercitrin (IQ), and quercetin-3-O-β-D-glucuronide (QG) are powerful phytochemicals that have been shown to exhibit disease prevention and health promotion properties. However, there may exist transformations between Qr, IQ, and QG in vivo. And the pharmacokinetic profiles of Qr, IQ, and QG have not been systematically compared. The pharmacokinetics study would be helpful to better understand the pharmacological actions of them. Methods Herein, we developed a reliable HPLC-MS method to compare the pharmacokinetics of Qr, IQ, and QG after separate (50 mg/kg) oral administration of them in rats, using puerarin as internal standard. The detection was performed using negative selected ion monitoring. This method was validated in terms of selectivity, linearity, precision, accuracy, extraction recovery, matrix effect, and stability; and shows reliabilities in monitoring the pharmacokinetic behaviors of these three compounds. Results Our results showed that after separate oral administration of Qr, IQ, and QG, all of the compounds could be detected in plasma. In addition, QG could be detected in the Qr group; Qr and QG could be measured in the IQ group; and Qr could be found in rat plasma after 1.5 h of QG administration. Moreover, the AUC0−t of Qr in the; Qr group (2,590.5 ± 987.9 mg/L*min), IQ group (2,212.7 ± 914.1 mg/L*min), and QG group (3,505.7 ± 1,565.0 mg/L*min) was larger than the AUC0−t of QG in the; Qr group (1,550.0 ± 454.2 mg/L*min), IQ group (669.3 ± 188.3 mg/L*min), and QG group (962.7 ± 602.3 mg/L*min). The AUC0−t of IQ was the lowest among all groups. Discussion Quercetin, IQ, and QG can all be absorbed into plasma. A mutual transformation exists between Qr and QG, and IQ can be metabolized into Qr and QG in SD rats. These results would provide a meaningful basis for understanding the pharmacological actions of these three compounds.
format: application/pdf
format: text/html
creator: Hongli Yin
creator: Ji Ma
creator: Jichun Han
creator: Maoru Li
creator: Jing Shang
subject: Plant Science
subject: Drugs and Devices
subject: Pharmacology
subject: Metabolic Sciences
description: doi:10.7717/peerj.6665
publisher: PeerJ Inc.
rights: © 2019 Yin et al.
abstract: Background Quercetin (Qr), isoquercitrin (IQ), and quercetin-3-O-β-D-glucuronide (QG) are powerful phytochemicals that have been shown to exhibit disease prevention and health promotion properties. However, there may exist transformations between Qr, IQ, and QG in vivo. And the pharmacokinetic profiles of Qr, IQ, and QG have not been systematically compared. The pharmacokinetics study would be helpful to better understand the pharmacological actions of them. Methods Herein, we developed a reliable HPLC-MS method to compare the pharmacokinetics of Qr, IQ, and QG after separate (50 mg/kg) oral administration of them in rats, using puerarin as internal standard. The detection was performed using negative selected ion monitoring. This method was validated in terms of selectivity, linearity, precision, accuracy, extraction recovery, matrix effect, and stability; and shows reliabilities in monitoring the pharmacokinetic behaviors of these three compounds. Results Our results showed that after separate oral administration of Qr, IQ, and QG, all of the compounds could be detected in plasma. In addition, QG could be detected in the Qr group; Qr and QG could be measured in the IQ group; and Qr could be found in rat plasma after 1.5 h of QG administration. Moreover, the AUC0−t of Qr in the; Qr group (2,590.5 ± 987.9 mg/L*min), IQ group (2,212.7 ± 914.1 mg/L*min), and QG group (3,505.7 ± 1,565.0 mg/L*min) was larger than the AUC0−t of QG in the; Qr group (1,550.0 ± 454.2 mg/L*min), IQ group (669.3 ± 188.3 mg/L*min), and QG group (962.7 ± 602.3 mg/L*min). The AUC0−t of IQ was the lowest among all groups. Discussion Quercetin, IQ, and QG can all be absorbed into plasma. A mutual transformation exists between Qr and QG, and IQ can be metabolized into Qr and QG in SD rats. These results would provide a meaningful basis for understanding the pharmacological actions of these three compounds.
bibliographic citation: Yin et al. (2019) Pharmacokinetic comparison of quercetin, isoquercitrin, and quercetin-3-O-β-D-glucuronide in rats by HPLC-MS. PeerJ 7:e6665 https://doi.org/10.7717/peerj.6665
date submitted: 2018-10-29
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Yin
  given name: Hongli
author list: Agent
  family name: Ma
  given name: Ji
author list: Agent
  family name: Han
  given name: Jichun
author list: Agent
  family name: Li
  given name: Maoru
author list: Agent
  family name: Shang
  given name: Jing
doi: 10.7717/peerj.6665
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Yin et al.
attribution name: Yin et al.

The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender
type: item
type: AcademicArticle
description: Background Elevated serum uric acid (SUA) has a positive correlation with insulin secretion and insulin resistance indexes. However, whether weight- and gender-specific differences regarding the relationship between SUA within the normal range and β-cell function and insulin resistance exist is unknown in type 2 diabetes mellitus (T2DM) patients. Methods A total of 380 patients with type 2 diabetes were divided into two groups as overweight/obesity (n = 268) and normal weight (n = 112). Each group were again divided into low (LSUA) and high normal SUA (HSUA). The HbA1c, C-peptide, SUA, creatinine, and lipids profiles were measured. HOMA2IR and HOMA%2B were estimated using fasting glucose and C-peptide by homeostasis model assessment (HOMA). Pearson’s correlations and multiple linear regression analyses were conducted to assess the associations between SUA levels and islet function indexes. Results In overweight/obesity subgroup, the levels of body mass index, fasting C-peptide (FCP), P2hCP, fasting CPI (FCPI), postprandial CPI (PPCPI), ΔC-peptide, HOMA2%B, and HOMA2IR were higher in HSUA group than in LSUA group. In contrast, the HbA1c, FBS, and P2hBS were lower in HSUA than in LSUA. In normal weight subgroup, there were no differences between the HSUA than LSUA group in terms of clinical characteristics. Pearson’s correlations indicated that there were no significant correlations between SUA and insulin secretory capacity in normal weight group, but in overweight/obesity group, SUA had positive significant correlations with P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. In the female group, there were no significant correlations between SUA and insulin secretory capacity. However, in the male group, SUA had positive significant correlations with insulin secretory capacity include P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. Multiple linear regression showed that SUA was significantly associated with HOMA2%B, but not with HOMA2IR in overweight/obesity and male group. …
format: application/pdf
format: text/html
creator: Xing Zhong
creator: Deyuan Zhang
creator: Lina Yang
creator: Yijun Du
creator: Tianrong Pan
subject: Diabetes and Endocrinology
description: doi:10.7717/peerj.6666
publisher: PeerJ Inc.
rights: © 2019 Zhong et al.
abstract: Background Elevated serum uric acid (SUA) has a positive correlation with insulin secretion and insulin resistance indexes. However, whether weight- and gender-specific differences regarding the relationship between SUA within the normal range and β-cell function and insulin resistance exist is unknown in type 2 diabetes mellitus (T2DM) patients. Methods A total of 380 patients with type 2 diabetes were divided into two groups as overweight/obesity (n = 268) and normal weight (n = 112). Each group were again divided into low (LSUA) and high normal SUA (HSUA). The HbA1c, C-peptide, SUA, creatinine, and lipids profiles were measured. HOMA2IR and HOMA%2B were estimated using fasting glucose and C-peptide by homeostasis model assessment (HOMA). Pearson’s correlations and multiple linear regression analyses were conducted to assess the associations between SUA levels and islet function indexes. Results In overweight/obesity subgroup, the levels of body mass index, fasting C-peptide (FCP), P2hCP, fasting CPI (FCPI), postprandial CPI (PPCPI), ΔC-peptide, HOMA2%B, and HOMA2IR were higher in HSUA group than in LSUA group. In contrast, the HbA1c, FBS, and P2hBS were lower in HSUA than in LSUA. In normal weight subgroup, there were no differences between the HSUA than LSUA group in terms of clinical characteristics. Pearson’s correlations indicated that there were no significant correlations between SUA and insulin secretory capacity in normal weight group, but in overweight/obesity group, SUA had positive significant correlations with P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. In the female group, there were no significant correlations between SUA and insulin secretory capacity. However, in the male group, SUA had positive significant correlations with insulin secretory capacity include P2hCP, FCPI, PPCPI, ΔC-peptide, and HOMA2%B. Multiple linear regression showed that SUA was significantly associated with HOMA2%B, but not with HOMA2IR in overweight/obesity and male group. …
bibliographic citation: Zhong et al. (2019) The relationship between serum uric acid within the normal range and β-cell function in Chinese patients with type 2 diabetes: differences by body mass index and gender. PeerJ 7:e6666 https://doi.org/10.7717/peerj.6666
date submitted: 2018-11-21
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Zhong
  given name: Xing
author list: Agent
  family name: Zhang
  given name: Deyuan
author list: Agent
  family name: Yang
  given name: Lina
author list: Agent
  family name: Du
  given name: Yijun
author list: Agent
  family name: Pan
  given name: Tianrong
doi: 10.7717/peerj.6666
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: © 2019 Zhong et al.
attribution name: Zhong et al.

Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile
type: item
type: AcademicArticle
description: This contribution describes the skull remains of a swordfish (Perciformes, Xiphioidei), recovered from Middle Eocene beds of central Chile. Comparison with known fossil and extant xiphioids reveals derived traits only present in the Neogene swordfish Xiphias gladius (Xiphiidae, Xiphiinae), these being a elongated rostrum composed of premaxillaries and possible prenasals, a dorsoventrally high and slender hyomandibular-metapterygoid complex, and a rounded, convex operculum. Also, strong ridges and sulci are present in the dorsal part of the rostrum, a feature only present in the billfish genera Aglyptorhynchus and Xiphiorhynchus, and in the swordfish genus Blochius. In addition, the specimen also has villiform teeth in the rostrum and lower jaw, a feature previously documented only in the Paleocene genus Hemingwaya. Such a unique combination of characters in the specimen allows classifying it as a new genus and species, Loancorhynchus catrillancai. Phylogenetic analyses obtained Xiphiorhynchus outside the Xiphiidae, suggesting instead narrow relationships to the Paleocene-Eocene genera Hemingwaya + Palaeorhynchus + Homorhynchus. Loancorhynchus is obtained as an intermediate form between Xiphias and Blochius. The specimen represents the first Paleogene swordfish described in the southeastern Pacific.
format: application/pdf
format: text/html
creator: Rodrigo A. Otero
subject: Paleontology
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.6671
publisher: PeerJ Inc.
rights: © 2019 Otero
abstract: This contribution describes the skull remains of a swordfish (Perciformes, Xiphioidei), recovered from Middle Eocene beds of central Chile. Comparison with known fossil and extant xiphioids reveals derived traits only present in the Neogene swordfish Xiphias gladius (Xiphiidae, Xiphiinae), these being a elongated rostrum composed of premaxillaries and possible prenasals, a dorsoventrally high and slender hyomandibular-metapterygoid complex, and a rounded, convex operculum. Also, strong ridges and sulci are present in the dorsal part of the rostrum, a feature only present in the billfish genera Aglyptorhynchus and Xiphiorhynchus, and in the swordfish genus Blochius. In addition, the specimen also has villiform teeth in the rostrum and lower jaw, a feature previously documented only in the Paleocene genus Hemingwaya. Such a unique combination of characters in the specimen allows classifying it as a new genus and species, Loancorhynchus catrillancai. Phylogenetic analyses obtained Xiphiorhynchus outside the Xiphiidae, suggesting instead narrow relationships to the Paleocene-Eocene genera Hemingwaya + Palaeorhynchus + Homorhynchus. Loancorhynchus is obtained as an intermediate form between Xiphias and Blochius. The specimen represents the first Paleogene swordfish described in the southeastern Pacific.
bibliographic citation: Otero (2019) Loancorhynchus catrillancai gen. et sp. nov., a new swordfish (Xiphioidei, Blochiidae) from the Middle Eocene of central Chile. PeerJ 7:e6671 https://doi.org/10.7717/peerj.6671
date submitted: 2018-12-07
date accepted: 2019-02-22
issued: 2019-03-26
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Otero
  given name: Rodrigo A.
doi: 10.7717/peerj.6671
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-26
copyright: ©2019 Otero
attribution name: Otero

Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging
type: item
type: AcademicArticle
description: The amount of information acquired with functional neuroimaging techniques, particularly fNIRS and fMRI, is rapidly growing and has enormous potential for studying human brain functioning. Therefore, many scientists focus on solving computational neuroimaging and Big Data issues to advance the discipline. However, the main obstacle—the accurate translation of the hemodynamic response (HR) by the investigation of a physiological phenomenon called neurovascular coupling—is still not fully overcome and, more importantly, often overlooked in this context. This article provides a brief and critical overview of significant findings from cellular biology and in vivo brain physiology with a focus on advancing existing HR modelling paradigms. A brief historical timeline of these disciplines of neuroscience is presented for readers to grasp the concept better, and some possible solutions for further scientific discussion are provided.
format: application/pdf
format: text/html
creator: Sigita Cinciute
subject: Biophysics
subject: Cell Biology
subject: Molecular Biology
subject: Neuroscience
description: doi:10.7717/peerj.6621
publisher: PeerJ Inc.
rights: © 2019 Cinciute
abstract: The amount of information acquired with functional neuroimaging techniques, particularly fNIRS and fMRI, is rapidly growing and has enormous potential for studying human brain functioning. Therefore, many scientists focus on solving computational neuroimaging and Big Data issues to advance the discipline. However, the main obstacle—the accurate translation of the hemodynamic response (HR) by the investigation of a physiological phenomenon called neurovascular coupling—is still not fully overcome and, more importantly, often overlooked in this context. This article provides a brief and critical overview of significant findings from cellular biology and in vivo brain physiology with a focus on advancing existing HR modelling paradigms. A brief historical timeline of these disciplines of neuroscience is presented for readers to grasp the concept better, and some possible solutions for further scientific discussion are provided.
bibliographic citation: Cinciute (2019) Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging. PeerJ 7:e6621 https://doi.org/10.7717/peerj.6621
date submitted: 2018-10-11
date accepted: 2019-02-14
issued: 2019-03-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Cinciute
  given name: Sigita
doi: 10.7717/peerj.6621
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-25
copyright: © 2019 Cinciute
attribution name: Cinciute

Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil
type: item
type: AcademicArticle
description: Biochar was widely developed for the soil amendment and remediation of heavy metal contaminated soil. The Cd hyperaccumulator, Solanum nigrum L., has been paid much more attention with the wide application of phytoremediation. The effects of biochar on the growth and accumulation capacity of Solanum nigrum L. in Cd contaminated soil have not been explored so far. The objectives of this study were to explore the dual effects of biochar addition on available Cd in the soil and hyperaccumulation of Cd in Solanum nigrum L. under different Cd contaminated levels. The correlations of soil physicochemical and biochemical properties and Cd absorption of Solanum nigrum L. were analyzed after a 60-day pot experiment under three biochar doses (0%, 1% and 5%) and four Cd concentrations (0, 25, 50 and 100 mg kg−1). The availability of Cd obtained by DTPA extraction significantly decreased after biochar application (P = 0.003, P = 0.0001, P = 0.0001 under 1% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, P = 0.0001, P = 0.0001, P = 0.0001 under 5% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, n ≥ 3). The 1% biochar dose significantly increased leaf dry weight (P = 0.039, P = 0.002 for the Cd concentrations of 50 and 100 mg kg−1, n ≥ 3) compared with the control in higher Cd concentrations (50 and 100 100 mg kg−1). In the presence of biochar, the bioconcentration factor (BCF) increased under the Cd concentrations of 50 and 100 mg kg−1. The translocation factors (TF) decreased with the biochar doses under the Cd concentration of 100 mg kg−1. The dose of 5% biochar significantly increased the urease activity by 41.18% compared to the 1% biochar addition in the Cd contaminated soil of 50 mg kg−1 concentration. The activities of acid phosphatase were inhibited by 1% biochar dose in all the Cd contaminated soils. The dry weight of the root of Solanum nigrum L. was significantly negatively correlated with acid phosphatase activity and BCF, respectively…
format: application/pdf
format: text/html
creator: Kang Li
creator: Baoshan Yang
creator: Hui Wang
creator: Xiaohan Xu
creator: Yongchao Gao
creator: Yidan Zhu
subject: Environmental Contamination and Remediation
subject: Environmental Impacts
description: doi:10.7717/peerj.6631
publisher: PeerJ Inc.
rights: © 2019 Li et al.
abstract: Biochar was widely developed for the soil amendment and remediation of heavy metal contaminated soil. The Cd hyperaccumulator, Solanum nigrum L., has been paid much more attention with the wide application of phytoremediation. The effects of biochar on the growth and accumulation capacity of Solanum nigrum L. in Cd contaminated soil have not been explored so far. The objectives of this study were to explore the dual effects of biochar addition on available Cd in the soil and hyperaccumulation of Cd in Solanum nigrum L. under different Cd contaminated levels. The correlations of soil physicochemical and biochemical properties and Cd absorption of Solanum nigrum L. were analyzed after a 60-day pot experiment under three biochar doses (0%, 1% and 5%) and four Cd concentrations (0, 25, 50 and 100 mg kg−1). The availability of Cd obtained by DTPA extraction significantly decreased after biochar application (P = 0.003, P = 0.0001, P = 0.0001 under 1% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, P = 0.0001, P = 0.0001, P = 0.0001 under 5% biochar addition for 25, 50, and 100 mg kg−1 Cd concentrations, n ≥ 3). The 1% biochar dose significantly increased leaf dry weight (P = 0.039, P = 0.002 for the Cd concentrations of 50 and 100 mg kg−1, n ≥ 3) compared with the control in higher Cd concentrations (50 and 100 100 mg kg−1). In the presence of biochar, the bioconcentration factor (BCF) increased under the Cd concentrations of 50 and 100 mg kg−1. The translocation factors (TF) decreased with the biochar doses under the Cd concentration of 100 mg kg−1. The dose of 5% biochar significantly increased the urease activity by 41.18% compared to the 1% biochar addition in the Cd contaminated soil of 50 mg kg−1 concentration. The activities of acid phosphatase were inhibited by 1% biochar dose in all the Cd contaminated soils. The dry weight of the root of Solanum nigrum L. was significantly negatively correlated with acid phosphatase activity and BCF, respectively…
bibliographic citation: Li et al. (2019) Dual effects of biochar and hyperaccumulator Solanum nigrum L. on the remediation of Cd-contaminated soil. PeerJ 7:e6631 https://doi.org/10.7717/peerj.6631
date submitted: 2018-10-11
date accepted: 2019-02-17
issued: 2019-03-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Kang
author list: Agent
  family name: Yang
  given name: Baoshan
author list: Agent
  family name: Wang
  given name: Hui
author list: Agent
  family name: Xu
  given name: Xiaohan
author list: Agent
  family name: Gao
  given name: Yongchao
author list: Agent
  family name: Zhu
  given name: Yidan
doi: 10.7717/peerj.6631
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-25
copyright: ©2019 Li et al.
attribution name: Li et al.

Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer)
type: item
type: AcademicArticle
description: Butterflies can directly absorb heat from the sun via their wings to facilitate autonomous flight. However, how is the heat absorbed by the butterfly from sunlight stored and transmitted in the wing? The answer to this scientific question remains unclear. The butterfly Tirumala limniace (Cramer) is a typical heat absorption insect, and its wing surface color is only composed of light and dark colors. Thus, in this study, we measured a number of wing traits relevant for heat absorption including the thoracic temperature at different light intensities and wing opening angles, the thoracic temperature of butterflies with only one right fore wing or one right hind wing; In addition, the spectral reflectance of the wing surfaces, the thoracic temperature of butterflies with the scales removed or present in light or dark areas, and the real-time changes in heat absorption by the wing surfaces with temperature were also measured. We found that high intensity light (600–60,000 lx) allowed the butterflies to absorb more heat and 60−90° was the optimal angle for heat absorption. The heat absorption capacity was stronger in the fore wings than the hind wings. Dark areas on the wing surfaces were heat absorption areas. The dark areas in the lower region of the fore wing surface and the inside region of the hind wing surface were heat storage areas. Heat was transferred from the heat storage areas to the wing base through the veins near the heat storage areas of the fore and hind wings.
format: application/pdf
format: text/html
creator: Huaijian Liao
creator: Ting Du
creator: Yuqi Zhang
creator: Lei Shi
creator: Xiyu Huai
creator: Chengli Zhou
creator: Jiang Deng
subject: Animal Behavior
subject: Biophysics
subject: Entomology
description: doi:10.7717/peerj.6648
publisher: PeerJ Inc.
rights: © 2019 Liao et al.
abstract: Butterflies can directly absorb heat from the sun via their wings to facilitate autonomous flight. However, how is the heat absorbed by the butterfly from sunlight stored and transmitted in the wing? The answer to this scientific question remains unclear. The butterfly Tirumala limniace (Cramer) is a typical heat absorption insect, and its wing surface color is only composed of light and dark colors. Thus, in this study, we measured a number of wing traits relevant for heat absorption including the thoracic temperature at different light intensities and wing opening angles, the thoracic temperature of butterflies with only one right fore wing or one right hind wing; In addition, the spectral reflectance of the wing surfaces, the thoracic temperature of butterflies with the scales removed or present in light or dark areas, and the real-time changes in heat absorption by the wing surfaces with temperature were also measured. We found that high intensity light (600–60,000 lx) allowed the butterflies to absorb more heat and 60−90° was the optimal angle for heat absorption. The heat absorption capacity was stronger in the fore wings than the hind wings. Dark areas on the wing surfaces were heat absorption areas. The dark areas in the lower region of the fore wing surface and the inside region of the hind wing surface were heat storage areas. Heat was transferred from the heat storage areas to the wing base through the veins near the heat storage areas of the fore and hind wings.
bibliographic citation: Liao et al. (2019) Capacity for heat absorption by the wings of the butterfly Tirumala limniace (Cramer). PeerJ 7:e6648 https://doi.org/10.7717/peerj.6648
date submitted: 2018-08-28
date accepted: 2019-02-20
issued: 2019-03-25
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Liao
  given name: Huaijian
author list: Agent
  family name: Du
  given name: Ting
author list: Agent
  family name: Zhang
  given name: Yuqi
author list: Agent
  family name: Shi
  given name: Lei
author list: Agent
  family name: Huai
  given name: Xiyu
author list: Agent
  family name: Zhou
  given name: Chengli
author list: Agent
  family name: Deng
  given name: Jiang
doi: 10.7717/peerj.6648
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-25
copyright: © 2019 Liao et al.
attribution name: Liao et al.

Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae)
type: item
type: AcademicArticle
description: Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
format: application/pdf
format: text/html
creator: Pedro Senna Bittencourt
creator: Zilca Campos
creator: Fábio de Lima Muniz
creator: Boris Marioni
creator: Bruno Campos Souza
creator: Ronis Da Silveira
creator: Benoit de Thoisy
creator: Tomas Hrbek
creator: Izeni Pires Farias
subject: Biodiversity
subject: Biogeography
subject: Evolutionary Studies
subject: Genetics
subject: Population Biology
description: doi:10.7717/peerj.6580
publisher: PeerJ Inc.
rights: © 2019 Bittencourt et al.
abstract: Schneider’s dwarf caiman Paleosuchus trigonatus is one of the smallest living crocodilians. Due to its broad distribution, cryptic behavior, and small home range, the species is well suited for the study of phylogeographic patterns on a continental scale. Additionally, this species is under threat due to habitat loss, trade and harvest, but is considered at low conservation risk by the IUCN. In the present study we test the hypothesis that P. trigonatus is comprised of geographically structured lineages. Phylogenetic reconstructions of the mitochondrial cytochrome b gene and single locus species discovery methods revealed the existence of two well-supported lineages within P. trigonatus—an Amazonian and Guianan lineage. Fossil calibrated divergence of these lineages was estimated to have occurred in the Late Miocene (7.5 Ma). The hypothesis that the Atlantic coast drainages might have been colonized from the southeast or central Amazon is supported by demographic metrics and relatively low genetic diversity of the Coastal and upper Branco populations when compared to the Amazon basin populations. The Amazon basin lineage is structured along an east-west gradient, with a sharp transition in haplotype frequencies to the east and west of the Negro and Madeira rivers. These lineages are already under anthropogenic threat and, therefore, are conservation dependent. Recognition of these lineages will foster discussion of conservation future of P. trigonatus and these lineages.
bibliographic citation: Bittencourt et al. (2019) Evidence of cryptic lineages within a small South American crocodilian: the Schneider’s dwarf caiman Paleosuchus trigonatus (Alligatoridae: Caimaninae). PeerJ 7:e6580 https://doi.org/10.7717/peerj.6580
date submitted: 2018-03-21
date accepted: 2019-02-01
issued: 2019-03-22
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bittencourt
  given name: Pedro Senna
author list: Agent
  family name: Campos
  given name: Zilca
author list: Agent
  family name: Muniz
  given name: Fábio de Lima
author list: Agent
  family name: Marioni
  given name: Boris
author list: Agent
  family name: Souza
  given name: Bruno Campos
author list: Agent
  family name: Da Silveira
  given name: Ronis
author list: Agent
  family name: de Thoisy
  given name: Benoit
author list: Agent
  family name: Hrbek
  given name: Tomas
author list: Agent
  family name: Farias
  given name: Izeni Pires
doi: 10.7717/peerj.6580
volume: 7
issn: 2167-8359
publication name: PeerJ
publication date: 2019-03-22
copyright: ©2019 Bittencourt et al.
attribution name: Bittencourt et al.

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