PeerJ
type: channel
link: https://peerj.com/articles/
description: Articles published in PeerJ
publisher: PeerJ Inc.
publication name: PeerJ
issn: 2167-8359
items: Effect of seasonality on chemical profile and antifungal activity of essential oil isolated from leaves Psidium salutare (Kunth) O. Berg
items: A large-scale survey on finger counting routines, their temporal stability and flexibility in educated adults
items: Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria
items: High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue
items: Iberian pig adaptation to acorn consumption: I. Net portal appearance of metabolites
items: SLiMEnrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions
items: Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae)
items: BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
items: Do subterranean mammals use the Earth’s magnetic field as a heading indicator to dig straight tunnels?
items: Cancellous bone and theropod dinosaur locomotion. Part I—an examination of cancellous bone architecture in the hindlimb bones of theropods

Effect of seasonality on chemical profile and antifungal activity of essential oil isolated from leaves Psidium salutare (Kunth) O. Berg
type: item
type: AcademicArticle
description: Medicinal plants play a crucial role in the search for components that are capable of neutralizing the multiple mechanisms of fungal resistance. Psidium salutare (Kunth) O. Berg is a plant native to Brazil used as both food and traditional medicine to treat diseases and symptoms such as stomach ache and diarrhea, whose symptoms could be related to fungal infections from the genus Candida. The objective of this study was to investigate the influence of seasonal variability on the chemical composition of the Psidium salutare essential oil, its antifungal potential and its effect on the Candida albicans morphogenesis. The essential oils were collected in three different seasonal collection periods and isolated by the hydrodistillation process in a modified Clevenger apparatus with identification of the chemical composition determined by gas chromatography coupled to mass spectrometry (GC/MS). The antifungal assays were performed against Candida strains through the broth microdilution method to determine the minimum fungicidal concentration (MFC). Fungal growth was assessed by optical density reading and the Candida albicans dimorphic effect was evaluated by optical microscopy in microculture chambers. The chemical profile of the essential oils identified 40 substances in the different collection periods with γ-terpinene being the predominant constituent. The antifungal activity revealed an action against the C. albicans, C. krusei and C. tropicalis strains with an IC50 ranging from 345.5 to 2,754.2 µg/mL and a MFC higher than 1,024 µg/mL. When combined with essential oils at sub-inhibitory concentrations (MIC/16), fluconazole had its potentiated effect, i.e. a synergistic effect was observed in the combination of fluconazole with P.salutare oil against all Candida strains; however, for C. albicans, its effect was reinforced by the natural product in all the collection periods. The results show that the Psidium salutare oil affected the dimorphic transition capacity, si…
format: application/pdf
format: text/html
creator: Delmacia G. de Macêdo
creator: Marta Maria A. Souza
creator: Maria Flaviana B. Morais-Braga
creator: Henrique Douglas M. Coutinho
creator: Antonia Thassya L. dos Santos
creator: Rafael P. da Cruz
creator: José Galberto M. da Costa
creator: Fábio Fernandes G. Rodrigues
creator: Lucindo J. Quintans-junior
creator: Jackson Roberto G. da Silva Almeida
creator: Irwin Rose A. de Menezes
subject: Microbiology
subject: Infectious Diseases
subject: Pharmacology
description: doi:10.7717/peerj.5476
publisher: PeerJ Inc.
rights: © 2018 de Macêdo et al.
abstract: Medicinal plants play a crucial role in the search for components that are capable of neutralizing the multiple mechanisms of fungal resistance. Psidium salutare (Kunth) O. Berg is a plant native to Brazil used as both food and traditional medicine to treat diseases and symptoms such as stomach ache and diarrhea, whose symptoms could be related to fungal infections from the genus Candida. The objective of this study was to investigate the influence of seasonal variability on the chemical composition of the Psidium salutare essential oil, its antifungal potential and its effect on the Candida albicans morphogenesis. The essential oils were collected in three different seasonal collection periods and isolated by the hydrodistillation process in a modified Clevenger apparatus with identification of the chemical composition determined by gas chromatography coupled to mass spectrometry (GC/MS). The antifungal assays were performed against Candida strains through the broth microdilution method to determine the minimum fungicidal concentration (MFC). Fungal growth was assessed by optical density reading and the Candida albicans dimorphic effect was evaluated by optical microscopy in microculture chambers. The chemical profile of the essential oils identified 40 substances in the different collection periods with γ-terpinene being the predominant constituent. The antifungal activity revealed an action against the C. albicans, C. krusei and C. tropicalis strains with an IC50 ranging from 345.5 to 2,754.2 µg/mL and a MFC higher than 1,024 µg/mL. When combined with essential oils at sub-inhibitory concentrations (MIC/16), fluconazole had its potentiated effect, i.e. a synergistic effect was observed in the combination of fluconazole with P.salutare oil against all Candida strains; however, for C. albicans, its effect was reinforced by the natural product in all the collection periods. The results show that the Psidium salutare oil affected the dimorphic transition capacity, si…
bibliographic citation: de Macêdo et al. (2018) Effect of seasonality on chemical profile and antifungal activity of essential oil isolated from leaves Psidium salutare (Kunth) O. Berg. PeerJ 6:e5476 https://doi.org/10.7717/peerj.5476
date submitted: 2018-03-08
date accepted: 2018-07-30
issued: 2018-11-01
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: de Macêdo
  given name: Delmacia G.
author list: Agent
  family name: Souza
  given name: Marta Maria A.
author list: Agent
  family name: Morais-Braga
  given name: Maria Flaviana B.
author list: Agent
  family name: Coutinho
  given name: Henrique Douglas M.
author list: Agent
  family name: dos Santos
  given name: Antonia Thassya L.
author list: Agent
  family name: da Cruz
  given name: Rafael P.
author list: Agent
  family name: da Costa
  given name: José Galberto M.
author list: Agent
  family name: Rodrigues
  given name: Fábio Fernandes G.
author list: Agent
  family name: Quintans-junior
  given name: Lucindo J.
author list: Agent
  family name: da Silva Almeida
  given name: Jackson Roberto G.
author list: Agent
  family name: de Menezes
  given name: Irwin Rose A.
doi: 10.7717/peerj.5476
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-11-01
copyright: ©2018 de Macêdo et al.
attribution name: de Macêdo et al.

A large-scale survey on finger counting routines, their temporal stability and flexibility in educated adults
type: item
type: AcademicArticle
description: A strong link between bodily activity and number processing has been established in recent years. Although numerous observations indicate that adults use finger counting (FC) in various contexts of everyday life for different purposes, existing knowledge of FC routines and their use is still limited. In particular, it remains unknown how stable the (default) FC habits are over time and how flexible they can be. To investigate these questions, 380 Polish participants completed a questionnaire on their FC routines, the stability of these routines, and the context of FC usage, preceded by the request to count on their fingers from 1 to 10. Next, the test–retest stability of FC habits was examined in 84 participants 2 months following the first session. To the best of our knowledge, such a study design has been adopted for the first time. The results indicate that default FC routines of the majority of participants (75%) are relatively stable over time. At the same time, FC routines can flexibly adapt according to the situation (e.g., when holding an object). As regards prevalence, almost all participants, in line with previous findings on Western individuals, declared starting from the closed palm and extending consecutive fingers. Furthermore, we observed relations between FC preferences and handedness (more left-handers start from the left hand) and that actual finger use is still widespread in healthy adults for a variety of activities (the most prevalent uses of FC are listing elements, presenting arguments and plans, and calendar calculations). In sum, the results show the practical relevance of FC in adulthood, the relative stability of preferences over time along with flexible adaptation to a current situation, as well as an association of FC routines with handedness. Taken together our results suggest that FC is the phenomenon, which is moderated or mediated by multiple embodied factors.
format: application/pdf
format: text/html
creator: Mateusz Hohol
creator: Kinga Wołoszyn
creator: Hans-Christoph Nuerk
creator: Krzysztof Cipora
subject: Psychiatry
subject: Psychology
description: doi:10.7717/peerj.5878
publisher: PeerJ Inc.
rights: © 2018 Hohol et al.
abstract: A strong link between bodily activity and number processing has been established in recent years. Although numerous observations indicate that adults use finger counting (FC) in various contexts of everyday life for different purposes, existing knowledge of FC routines and their use is still limited. In particular, it remains unknown how stable the (default) FC habits are over time and how flexible they can be. To investigate these questions, 380 Polish participants completed a questionnaire on their FC routines, the stability of these routines, and the context of FC usage, preceded by the request to count on their fingers from 1 to 10. Next, the test–retest stability of FC habits was examined in 84 participants 2 months following the first session. To the best of our knowledge, such a study design has been adopted for the first time. The results indicate that default FC routines of the majority of participants (75%) are relatively stable over time. At the same time, FC routines can flexibly adapt according to the situation (e.g., when holding an object). As regards prevalence, almost all participants, in line with previous findings on Western individuals, declared starting from the closed palm and extending consecutive fingers. Furthermore, we observed relations between FC preferences and handedness (more left-handers start from the left hand) and that actual finger use is still widespread in healthy adults for a variety of activities (the most prevalent uses of FC are listing elements, presenting arguments and plans, and calendar calculations). In sum, the results show the practical relevance of FC in adulthood, the relative stability of preferences over time along with flexible adaptation to a current situation, as well as an association of FC routines with handedness. Taken together our results suggest that FC is the phenomenon, which is moderated or mediated by multiple embodied factors.
bibliographic citation: Hohol et al. (2018) A large-scale survey on finger counting routines, their temporal stability and flexibility in educated adults. PeerJ 6:e5878 https://doi.org/10.7717/peerj.5878
date submitted: 2018-06-28
date accepted: 2018-10-05
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Hohol
  given name: Mateusz
author list: Agent
  family name: Wołoszyn
  given name: Kinga
author list: Agent
  family name: Nuerk
  given name: Hans-Christoph
author list: Agent
  family name: Cipora
  given name: Krzysztof
doi: 10.7717/peerj.5878
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: © 2018 Hohol et al.
attribution name: Hohol et al.

Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria
type: item
type: AcademicArticle
description: Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as SoGloI was identified from sugarcane. SoGloI had a size of 1,091 bp with one open reading frame (ORF) of 885 bp encoding a protein of 294 amino acids. SoGloI was predicted as a Ni2+-dependent GLOI protein with two typical glyoxalase domains at positions 28–149 and 159–283, respectively. SoGloI was cloned into an expression plasmid vector, and the Trx-His-S-tag SoGloI protein produced in Escherichia coli was about 51 kDa. The recombinant E. coli cells expressing SoGloI compared to the control grew faster and tolerated higher concentrations of NaCl, CuCl2, CdCl2, or ZnSO4. SoGloI ubiquitously expressed in various sugarcane tissues. The expression was up-regulated under the treatments of NaCl, CuCl2, CdCl2, ZnSO4 and abscisic acid (ABA), or under simulated biotic stress conditions upon exposure to salicylic acid (SA) and methyl jasmonate (MeJA). SoGloI activity steadily increased when sugarcane was subjected to NaCl, CuCl2, CdCl2, or ZnSO4 treatments. Sub-cellular observations indicated that the SoGloI protein was located in both cytosol and nucleus. These results suggest that the SoGloI gene may play an important role in sugarcane’s response to various biotic and abiotic stresses.
format: application/pdf
format: text/html
creator: Qibin Wu
creator: Shiwu Gao
creator: Yong-Bao Pan
creator: Yachun Su
creator: Michael P. Grisham
creator: Jinlong Guo
creator: Liping Xu
creator: Youxiong Que
subject: Agricultural Science
subject: Biotechnology
subject: Molecular Biology
subject: Plant Science
description: doi:10.7717/peerj.5873
publisher: PeerJ Inc.
rights: © 2018 Wu et al.
abstract: Glyoxalase I belongs to the glyoxalase system that detoxifies methylglyoxal (MG), a cytotoxic by-product produced mainly from triose phosphates. The concentration of MG increases rapidly under stress conditions. In this study, a novel glyoxalase I gene, designated as SoGloI was identified from sugarcane. SoGloI had a size of 1,091 bp with one open reading frame (ORF) of 885 bp encoding a protein of 294 amino acids. SoGloI was predicted as a Ni2+-dependent GLOI protein with two typical glyoxalase domains at positions 28–149 and 159–283, respectively. SoGloI was cloned into an expression plasmid vector, and the Trx-His-S-tag SoGloI protein produced in Escherichia coli was about 51 kDa. The recombinant E. coli cells expressing SoGloI compared to the control grew faster and tolerated higher concentrations of NaCl, CuCl2, CdCl2, or ZnSO4. SoGloI ubiquitously expressed in various sugarcane tissues. The expression was up-regulated under the treatments of NaCl, CuCl2, CdCl2, ZnSO4 and abscisic acid (ABA), or under simulated biotic stress conditions upon exposure to salicylic acid (SA) and methyl jasmonate (MeJA). SoGloI activity steadily increased when sugarcane was subjected to NaCl, CuCl2, CdCl2, or ZnSO4 treatments. Sub-cellular observations indicated that the SoGloI protein was located in both cytosol and nucleus. These results suggest that the SoGloI gene may play an important role in sugarcane’s response to various biotic and abiotic stresses.
bibliographic citation: Wu et al. (2018) Heterologous expression of a Glyoxalase I gene from sugarcane confers tolerance to several environmental stresses in bacteria. PeerJ 6:e5873 https://doi.org/10.7717/peerj.5873
date submitted: 2017-06-23
date accepted: 2018-10-01
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wu
  given name: Qibin
author list: Agent
  family name: Gao
  given name: Shiwu
author list: Agent
  family name: Pan
  given name: Yong-Bao
author list: Agent
  family name: Su
  given name: Yachun
author list: Agent
  family name: Grisham
  given name: Michael P.
author list: Agent
  family name: Guo
  given name: Jinlong
author list: Agent
  family name: Xu
  given name: Liping
author list: Agent
  family name: Que
  given name: Youxiong
doi: 10.7717/peerj.5873
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: ©2018 Wu et al.
attribution name: Wu et al.

High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue
type: item
type: AcademicArticle
description: Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn2+ ion. Kinetic analysis with Ala-Pro as the substrate showed that the Km and kcat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s−1, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess.
format: application/pdf
format: text/html
creator: Tzu-Fan Wang
creator: Meng-Chun Chi
creator: Kuan-Ling Lai
creator: Min-Guan Lin
creator: Yi-Yu Chen
creator: Huei-Fen Lo
creator: Long-Liu Lin
subject: Biochemistry
subject: Biotechnology
subject: Microbiology
description: doi:10.7717/peerj.5863
publisher: PeerJ Inc.
rights: © 2018 Wang et al.
abstract: Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn2+ ion. Kinetic analysis with Ala-Pro as the substrate showed that the Km and kcat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s−1, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess.
bibliographic citation: Wang et al. (2018) High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue. PeerJ 6:e5863 https://doi.org/10.7717/peerj.5863
date submitted: 2018-08-22
date accepted: 2018-10-03
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Wang
  given name: Tzu-Fan
author list: Agent
  family name: Chi
  given name: Meng-Chun
author list: Agent
  family name: Lai
  given name: Kuan-Ling
author list: Agent
  family name: Lin
  given name: Min-Guan
author list: Agent
  family name: Chen
  given name: Yi-Yu
author list: Agent
  family name: Lo
  given name: Huei-Fen
author list: Agent
  family name: Lin
  given name: Long-Liu
doi: 10.7717/peerj.5863
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: © 2018 Wang et al.
attribution name: Wang et al.

Iberian pig adaptation to acorn consumption: I. Net portal appearance of metabolites
type: item
type: AcademicArticle
description: Most valuable cured products from Iberian pigs come from pure bred animals raised for a final grazing-fattening period where pigs eat mainly acorns, a low protein energy rich fruit. This is a nutritional challenge for animals fed equilibrated diets from weaning. The aim of the study was to determine net portal appearance (NPA) of metabolites in gilts fed acorns and evaluate adaptational changes after one week of feeding. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for para-aminohippuric acid (PAH) infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two portions, at 09:00 (0.25) and 15:00 h (the remaining 0.75). On the day prior to the first sampling period, pigs were fed 2.4 kg of oak acorns. After feeding 0.25 of ration a 6 h serial blood collection was initiated. Following an identical protocol, a second sampling session was performed 1 week later. Adaptation to acorn consumption decreased NPA of ammonia (47%, P < 0.001). Although there was a transfer of urea from the gastrointestinal tract to the circulation in both sampling periods, no differences in NPA of urea was found (P > 0.05). NPA of glucose was not influenced by sampling period (P > 0.05), but NPA of lactate was greatly increased (231%, P < 0.001). There was a negative NPA of albumin although adaptation to acorn feeding did not alter it. Although NPA of triglycerides and cholesterol were unchanged, a subtle increase in arterial and portal cholesterol was noticed (9.6%, P < 0.01). Pigs fed a protein deficient diet for one week adapted decreasing NPA of ammonia for saving metabolic energy as less ammonia would become available for conversion to urea.
format: application/pdf
format: text/html
creator: Ignacio Fernández-Fígares
creator: Jose Miguel Rodríguez-López
creator: Lucrecia González-Valero
creator: Manuel Lachica
subject: Agricultural Science
subject: Anthropology
subject: Nutrition
subject: Natural Resource Management
description: doi:10.7717/peerj.5861
publisher: PeerJ Inc.
rights: © 2018 Fernández-Fígares et al.
abstract: Most valuable cured products from Iberian pigs come from pure bred animals raised for a final grazing-fattening period where pigs eat mainly acorns, a low protein energy rich fruit. This is a nutritional challenge for animals fed equilibrated diets from weaning. The aim of the study was to determine net portal appearance (NPA) of metabolites in gilts fed acorns and evaluate adaptational changes after one week of feeding. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for para-aminohippuric acid (PAH) infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two portions, at 09:00 (0.25) and 15:00 h (the remaining 0.75). On the day prior to the first sampling period, pigs were fed 2.4 kg of oak acorns. After feeding 0.25 of ration a 6 h serial blood collection was initiated. Following an identical protocol, a second sampling session was performed 1 week later. Adaptation to acorn consumption decreased NPA of ammonia (47%, P < 0.001). Although there was a transfer of urea from the gastrointestinal tract to the circulation in both sampling periods, no differences in NPA of urea was found (P > 0.05). NPA of glucose was not influenced by sampling period (P > 0.05), but NPA of lactate was greatly increased (231%, P < 0.001). There was a negative NPA of albumin although adaptation to acorn feeding did not alter it. Although NPA of triglycerides and cholesterol were unchanged, a subtle increase in arterial and portal cholesterol was noticed (9.6%, P < 0.01). Pigs fed a protein deficient diet for one week adapted decreasing NPA of ammonia for saving metabolic energy as less ammonia would become available for conversion to urea.
bibliographic citation: Fernández-Fígares et al. (2018) Iberian pig adaptation to acorn consumption: I. Net portal appearance of metabolites. PeerJ 6:e5861 https://doi.org/10.7717/peerj.5861
date submitted: 2018-02-27
date accepted: 2018-10-02
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Fernández-Fígares
  given name: Ignacio
author list: Agent
  family name: Rodríguez-López
  given name: Jose Miguel
author list: Agent
  family name: González-Valero
  given name: Lucrecia
author list: Agent
  family name: Lachica
  given name: Manuel
doi: 10.7717/peerj.5861
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: ©2018 Fernández-Fígares et al.
attribution name: Fernández-Fígares et al.

SLiMEnrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions
type: item
type: AcademicArticle
description: Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (SLiMEnrich) to assess how well a given source of PPI data captures DMIs and thus, by inference, how useful that data should be for SLiM discovery. SLiMEnrich interrogates a PPI network for pairs of interacting proteins in which the first protein is known or predicted to interact with the second protein via a DMI. Permutation tests compare the number of known/predicted DMIs to the expected distribution if the two sets of proteins are randomly associated. This provides an estimate of DMI enrichment within the data and the false positive rate for individual DMIs. As a case study, we detect significant DMI enrichment in a high-throughput Y2H human PPI study. SLiMEnrich analysis supports Y2H data as a source of DMIs and highlights the high false positive rates associated with naïve DMI prediction. SLiMEnrich is available as an R Shiny app. The code is open source and available via a GNU GPL v3 license at: https://github.com/slimsuite/SLiMEnrich. A web server is available at: http://shiny.slimsuite.unsw.edu.au/SLiMEnrich/.
format: application/pdf
format: text/html
creator: Sobia Idrees
creator: Åsa Pérez-Bercoff
creator: Richard J. Edwards
subject: Bioinformatics
subject: Computational Biology
subject: Molecular Biology
description: doi:10.7717/peerj.5858
publisher: PeerJ Inc.
rights: © 2018 Idrees et al.
abstract: Many important cellular processes involve protein–protein interactions (PPIs) mediated by a Short Linear Motif (SLiM) in one protein interacting with a globular domain in another. Despite their significance, these domain-motif interactions (DMIs) are typically low affinity, which makes them challenging to identify by classical experimental approaches, such as affinity pulldown mass spectrometry (AP-MS) and yeast two-hybrid (Y2H). DMIs are generally underrepresented in PPI networks as a result. A number of computational methods now exist to predict SLiMs and/or DMIs from experimental interaction data but it is yet to be established how effective different PPI detection methods are for capturing these low affinity SLiM-mediated interactions. Here, we introduce a new computational pipeline (SLiMEnrich) to assess how well a given source of PPI data captures DMIs and thus, by inference, how useful that data should be for SLiM discovery. SLiMEnrich interrogates a PPI network for pairs of interacting proteins in which the first protein is known or predicted to interact with the second protein via a DMI. Permutation tests compare the number of known/predicted DMIs to the expected distribution if the two sets of proteins are randomly associated. This provides an estimate of DMI enrichment within the data and the false positive rate for individual DMIs. As a case study, we detect significant DMI enrichment in a high-throughput Y2H human PPI study. SLiMEnrich analysis supports Y2H data as a source of DMIs and highlights the high false positive rates associated with naïve DMI prediction. SLiMEnrich is available as an R Shiny app. The code is open source and available via a GNU GPL v3 license at: https://github.com/slimsuite/SLiMEnrich. A web server is available at: http://shiny.slimsuite.unsw.edu.au/SLiMEnrich/.
bibliographic citation: Idrees et al. (2018) SLiMEnrich: computational assessment of protein–protein interaction data as a source of domain-motif interactions. PeerJ 6:e5858 https://doi.org/10.7717/peerj.5858
date submitted: 2018-03-13
date accepted: 2018-10-02
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Idrees
  given name: Sobia
author list: Agent
  family name: Pérez-Bercoff
  given name: Åsa
author list: Agent
  family name: Edwards
  given name: Richard J.
doi: 10.7717/peerj.5858
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: ©2018 Idrees et al.
attribution name: Idrees et al.

Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae)
type: item
type: AcademicArticle
description: The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.
format: application/pdf
format: text/html
creator: Luis Amador
creator: Andrés Parada
creator: Guillermo D’Elía
creator: Juan M. Guayasamin
subject: Biodiversity
subject: Evolutionary Studies
subject: Genetics
subject: Taxonomy
subject: Zoology
description: doi:10.7717/peerj.5856
publisher: PeerJ Inc.
rights: © 2018 Amador et al.
abstract: The glassfrog Centrolene buckleyi has been recognized as a species complex. Herein, using coalescence-based species delimitation methods, we evaluate the specific diversity within this taxon. Four coalescence approaches (generalized mixed Yule coalescents, Bayesian general mixed Yule-coalescent, Poisson tree processes, and Bayesian Poisson tree processes) were consistent with the delimitation results, identifying four lineages within what is currently recognized as C. buckleyi. We propose three new candidate species that should be tested with nuclear markers, morphological, and behavioral data. In the meantime, for conservation purposes, candidate species should be considered evolutionary significant units, in light of observed population crashes in the C. buckleyi species complex. Finally, our results support the validity of C. venezuelense, formerly considered as a subspecies of C. buckleyi.
bibliographic citation: Amador et al. (2018) Uncovering hidden specific diversity of Andean glassfrogs of the Centrolene buckleyi species complex (Anura: Centrolenidae). PeerJ 6:e5856 https://doi.org/10.7717/peerj.5856
date submitted: 2018-03-16
date accepted: 2018-10-02
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Amador
  given name: Luis
author list: Agent
  family name: Parada
  given name: Andrés
author list: Agent
  family name: D’Elía
  given name: Guillermo
author list: Agent
  family name: Guayasamin
  given name: Juan M.
doi: 10.7717/peerj.5856
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: © 2018 Amador et al.
attribution name: Amador et al.

BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
type: item
type: AcademicArticle
description: The increase in bioinformatics resources such as tools/scripts and databases poses a great challenge for users seeking to construct interactive and reproducible biological data analysis applications. Here, we propose an open-source, comprehensive, flexible R package named BioInstaller that consists of the R functions, Shiny application, the HTTP representational state transfer application programming interfaces, and a docker image. BioInstaller can be used to collect, manage and share various types of bioinformatics resources and perform interactive and reproducible data analyses based on the extendible Shiny application with Tom’s Obvious, Minimal Language and SQLite format databases. The source code of BioInstaller is freely available at our lab website, http://bioinfo.rjh.com.cn/labs/jhuang/tools/bioinstaller, the popular package host GitHub, https://github.com/JhuangLab/BioInstaller, and the Comprehensive R Archive Network, https://CRAN.R-project.org/package=BioInstaller. In addition, a docker image can be downloaded from DockerHub (https://hub.docker.com/r/bioinstaller/bioinstaller).
format: application/pdf
format: text/html
creator: Jianfeng Li
creator: Bowen Cui
creator: Yuting Dai
creator: Ling Bai
creator: Jinyan Huang
subject: Bioinformatics
subject: Statistics
description: doi:10.7717/peerj.5853
publisher: PeerJ Inc.
rights: © 2018 Li et al.
abstract: The increase in bioinformatics resources such as tools/scripts and databases poses a great challenge for users seeking to construct interactive and reproducible biological data analysis applications. Here, we propose an open-source, comprehensive, flexible R package named BioInstaller that consists of the R functions, Shiny application, the HTTP representational state transfer application programming interfaces, and a docker image. BioInstaller can be used to collect, manage and share various types of bioinformatics resources and perform interactive and reproducible data analyses based on the extendible Shiny application with Tom’s Obvious, Minimal Language and SQLite format databases. The source code of BioInstaller is freely available at our lab website, http://bioinfo.rjh.com.cn/labs/jhuang/tools/bioinstaller, the popular package host GitHub, https://github.com/JhuangLab/BioInstaller, and the Comprehensive R Archive Network, https://CRAN.R-project.org/package=BioInstaller. In addition, a docker image can be downloaded from DockerHub (https://hub.docker.com/r/bioinstaller/bioinstaller).
bibliographic citation: Li et al. (2018) BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform. PeerJ 6:e5853 https://doi.org/10.7717/peerj.5853
date submitted: 2018-08-17
date accepted: 2018-09-27
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Li
  given name: Jianfeng
author list: Agent
  family name: Cui
  given name: Bowen
author list: Agent
  family name: Dai
  given name: Yuting
author list: Agent
  family name: Bai
  given name: Ling
author list: Agent
  family name: Huang
  given name: Jinyan
doi: 10.7717/peerj.5853
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: © 2018 Li et al.
attribution name: Li et al.

Do subterranean mammals use the Earth’s magnetic field as a heading indicator to dig straight tunnels?
type: item
type: AcademicArticle
description: Subterranean rodents are able to dig long straight tunnels. Keeping the course of such “runways” is important in the context of optimal foraging strategies and natal or mating dispersal. These tunnels are built in the course of a long time, and in social species, by several animals. Although the ability to keep the course of digging has already been described in the 1950s, its proximate mechanism could still not be satisfactorily explained. Here, we analyzed the directional orientation of 68 burrow systems in five subterranean rodent species (Fukomys anselli, F. mechowii, Heliophobius argenteocinereus, Spalax galili, and Ctenomys talarum) on the base of detailed maps of burrow systems charted within the framework of other studies and provided to us. The directional orientation of the vast majority of all evaluated burrow systems on the individual level (94%) showed a significant deviation from a random distribution. The second order statistics (averaging mean vectors of all the studied burrow systems of a respective species) revealed significant deviations from random distribution with a prevalence of north–south (H. argenteocinereus), NNW–SSE (C. talarum), and NE–SW (Fukomys mole-rats) oriented tunnels. Burrow systems of S. galili were randomly oriented. We suggest that the Earth’s magnetic field acts as a common heading indicator, facilitating to keep the course of digging. This study provides a field test and further evidence for magnetoreception and its biological meaning in subterranean mammals. Furthermore, it lays the foundation for future field experiments.
format: application/pdf
format: text/html
creator: Sandra Malewski
creator: Sabine Begall
creator: Cristian E. Schleich
creator: C. Daniel Antenucci
creator: Hynek Burda
subject: Animal Behavior
subject: Biodiversity
subject: Ecology
subject: Zoology
description: doi:10.7717/peerj.5819
publisher: PeerJ Inc.
rights: © 2018 Malewski et al.
abstract: Subterranean rodents are able to dig long straight tunnels. Keeping the course of such “runways” is important in the context of optimal foraging strategies and natal or mating dispersal. These tunnels are built in the course of a long time, and in social species, by several animals. Although the ability to keep the course of digging has already been described in the 1950s, its proximate mechanism could still not be satisfactorily explained. Here, we analyzed the directional orientation of 68 burrow systems in five subterranean rodent species (Fukomys anselli, F. mechowii, Heliophobius argenteocinereus, Spalax galili, and Ctenomys talarum) on the base of detailed maps of burrow systems charted within the framework of other studies and provided to us. The directional orientation of the vast majority of all evaluated burrow systems on the individual level (94%) showed a significant deviation from a random distribution. The second order statistics (averaging mean vectors of all the studied burrow systems of a respective species) revealed significant deviations from random distribution with a prevalence of north–south (H. argenteocinereus), NNW–SSE (C. talarum), and NE–SW (Fukomys mole-rats) oriented tunnels. Burrow systems of S. galili were randomly oriented. We suggest that the Earth’s magnetic field acts as a common heading indicator, facilitating to keep the course of digging. This study provides a field test and further evidence for magnetoreception and its biological meaning in subterranean mammals. Furthermore, it lays the foundation for future field experiments.
bibliographic citation: Malewski et al. (2018) Do subterranean mammals use the Earth’s magnetic field as a heading indicator to dig straight tunnels?. PeerJ 6:e5819 https://doi.org/10.7717/peerj.5819
date submitted: 2018-03-27
date accepted: 2018-09-23
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Malewski
  given name: Sandra
author list: Agent
  family name: Begall
  given name: Sabine
author list: Agent
  family name: Schleich
  given name: Cristian E.
author list: Agent
  family name: Antenucci
  given name: C. Daniel
author list: Agent
  family name: Burda
  given name: Hynek
doi: 10.7717/peerj.5819
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: © 2018 Malewski et al.
attribution name: Malewski et al.

Cancellous bone and theropod dinosaur locomotion. Part I—an examination of cancellous bone architecture in the hindlimb bones of theropods
type: item
type: AcademicArticle
description: This paper is the first of a three-part series that investigates the architecture of cancellous (‘spongy’) bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is widely known to be highly sensitive to its mechanical environment, and has previously been used to infer locomotor biomechanics in extinct tetrapod vertebrates, especially primates. Despite great promise, cancellous bone architecture has remained little utilized for investigating locomotion in many other extinct vertebrate groups, such as dinosaurs. Documentation and quantification of architectural patterns across a whole bone, and across multiple bones, can provide much information on cancellous bone architectural patterns and variation across species. Additionally, this also lends itself to analysis of the musculoskeletal biomechanical factors involved in a direct, mechanistic fashion. On this premise, computed tomographic and image analysis techniques were used to describe and analyse the three-dimensional architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs for the first time. A comprehensive survey across many extant and extinct species is produced, identifying several patterns of similarity and contrast between groups. For instance, more stemward non-avian theropods (e.g. ceratosaurs and tyrannosaurids) exhibit cancellous bone architectures more comparable to that present in humans, whereas species more closely related to birds (e.g. paravians) exhibit architectural patterns bearing greater similarity to those of extant birds. Many of the observed patterns may be linked to particular aspects of locomotor biomechanics, such as the degree of hip or knee flexion during stance and gait. A further important observation is the abundance of markedly oblique trabeculae in the diaphyses of the femur and tibia of birds, which in large species produces spira…
format: application/pdf
format: text/html
creator: Peter J. Bishop
creator: Scott A. Hocknull
creator: Christofer J. Clemente
creator: John R. Hutchinson
creator: Andrew A. Farke
creator: Belinda R. Beck
creator: Rod S. Barrett
creator: David G. Lloyd
subject: Evolutionary Studies
subject: Paleontology
subject: Zoology
description: doi:10.7717/peerj.5778
publisher: PeerJ Inc.
rights: © 2018 Bishop et al.
abstract: This paper is the first of a three-part series that investigates the architecture of cancellous (‘spongy’) bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is widely known to be highly sensitive to its mechanical environment, and has previously been used to infer locomotor biomechanics in extinct tetrapod vertebrates, especially primates. Despite great promise, cancellous bone architecture has remained little utilized for investigating locomotion in many other extinct vertebrate groups, such as dinosaurs. Documentation and quantification of architectural patterns across a whole bone, and across multiple bones, can provide much information on cancellous bone architectural patterns and variation across species. Additionally, this also lends itself to analysis of the musculoskeletal biomechanical factors involved in a direct, mechanistic fashion. On this premise, computed tomographic and image analysis techniques were used to describe and analyse the three-dimensional architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs for the first time. A comprehensive survey across many extant and extinct species is produced, identifying several patterns of similarity and contrast between groups. For instance, more stemward non-avian theropods (e.g. ceratosaurs and tyrannosaurids) exhibit cancellous bone architectures more comparable to that present in humans, whereas species more closely related to birds (e.g. paravians) exhibit architectural patterns bearing greater similarity to those of extant birds. Many of the observed patterns may be linked to particular aspects of locomotor biomechanics, such as the degree of hip or knee flexion during stance and gait. A further important observation is the abundance of markedly oblique trabeculae in the diaphyses of the femur and tibia of birds, which in large species produces spira…
bibliographic citation: Bishop et al. (2018) Cancellous bone and theropod dinosaur locomotion. Part I—an examination of cancellous bone architecture in the hindlimb bones of theropods. PeerJ 6:e5778 https://doi.org/10.7717/peerj.5778
date submitted: 2018-01-08
date accepted: 2018-09-18
issued: 2018-10-31
is part of: PeerJ
license: http://creativecommons.org/licenses/by/4.0/
author list: Agent
  family name: Bishop
  given name: Peter J.
author list: Agent
  family name: Hocknull
  given name: Scott A.
author list: Agent
  family name: Clemente
  given name: Christofer J.
author list: Agent
  family name: Hutchinson
  given name: John R.
author list: Agent
  family name: Farke
  given name: Andrew A.
author list: Agent
  family name: Beck
  given name: Belinda R.
author list: Agent
  family name: Barrett
  given name: Rod S.
author list: Agent
  family name: Lloyd
  given name: David G.
doi: 10.7717/peerj.5778
volume: 6
issn: 2167-8359
publication name: PeerJ
publication date: 2018-10-31
copyright: © 2018 Bishop et al.
attribution name: Bishop et al.

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