title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1809
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Anxiolytic effects of fluoxetine and nicotine exposure on exploratory behavior in zebrafish
link: https://peerj.com/articles/2352
last-modified: 2016-08-24
description: Zebrafish (Danio rerio) have emerged as a popular model for studying the pharmacology and behavior of anxiety. While there have been numerous studies documenting the anxiolytic and anxiogenic effects of common drugs in zebrafish, many do not report or test for behavioral differences between the sexes. Previous studies have indicated that males and females differ in their baseline level of anxiety. In this study, we test for a sex interaction with fluoxetine and nicotine. We exposed fish to system water (control), 10 mg/L fluoxetine, or 1 mg/L nicotine for three minutes prior to being subjected to four minutes in an open-field drop test. Video recordings were tracked using ProAnalyst. Fish from both drug treatments reduced swimming speed, increased vertical position, and increased use of the top half of the open field when compared with the control, though fluoxetine had a larger effect on depth related behaviors while nicotine mostly affected swimming speed. A significant sex effect was observed where females swam at a slower and more constant speed than males, however neither drug produced a sex-dependent response.
creator: Matthew L. Singer
creator: Kris Oreschak
creator: Zachariah Rhinehart
creator: Barrie D. Robison
uri: https://doi.org/10.7717/peerj.2352
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Singer et al.

title: Identification of biomarkers for periodontal disease using the immunoproteomics approach
link: https://peerj.com/articles/2327
last-modified: 2016-08-24
description: BackgroundPeriodontitis is one of the most common oral diseases associated with the host’s immune response against periodontopathogenic infection. Failure to accurately diagnose the stage of periodontitis has limited the ability to predict disease status. Therefore, we aimed to look for reliable diagnostic markers for detection or differentiation of early stage periodontitis using the immunoprotemic approach.MethodIn the present study, patient serum samples from four distinct stages of periodontitis (i.e., mild chronic, moderate chronic, severe chronic, and aggressive) and healthy controls were subjected to two-dimensional gel electrophoresis (2-DE), followed by silver staining. Notably, we consistently identified 14 protein clusters in the sera of patients and normal controls.ResultsOverall, we found that protein levels were comparable between patients and controls, with the exception of the clusters corresponding to A1AT, HP, IGKC and KNG1 (p < 0.05). In addition, the immunogenicity of these proteins was analysed via immunoblotting, which revealed differential profiles for periodontal disease and controls. For this reason, IgM obtained from severe chronic periodontitis (CP) sera could be employed as a suitable autoantibody for the detection of periodontitis.DiscussionTaken together, the present study suggests that differentially expressed host immune response proteins could be used as potential biomarkers for screening periodontitis. Future studies exploring the diagnostic potential of such factors are warranted.
creator: Jesinda P. Kerishnan
creator: Sani Mohammad
creator: Muhamad Shaifunizam Alias
creator: Alan Kang-Wai Mu
creator: Rathna Devi Vaithilingam
creator: Nor Adinar Baharuddin
creator: Syarida H. Safii
creator: Zainal Ariff Abdul Rahman
creator: Yu Nieng Chen
creator: Yeng Chen
uri: https://doi.org/10.7717/peerj.2327
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2016 Kerishnan et al.

title: Analysis of genotype diversity and evolution of Dengue virus serotype 2 using complete genomes
link: https://peerj.com/articles/2326
last-modified: 2016-08-24
description: BackgroundDengue is one of the most common arboviral diseases prevalent worldwide and is caused by Dengue viruses (genus Flavivirus, family Flaviviridae). There are four serotypes of Dengue Virus (DENV-1 to DENV-4), each of which is further subdivided into distinct genotypes. DENV-2 is frequently associated with severe dengue infections and epidemics. DENV-2 consists of six genotypes such as Asian/American, Asian I, Asian II, Cosmopolitan, American and sylvatic. Comparative genomic study was carried out to infer population structure of DENV-2 and to analyze the role of evolutionary and spatiotemporal factors in emergence of diversifying lineages.MethodsComplete genome sequences of 990 strains of DENV-2 were analyzed using Bayesian-based population genetics and phylogenetic approaches to infer genetically distinct lineages. The role of spatiotemporal factors, genetic recombination and selection pressure in the evolution of DENV-2 is examined using the sequence-based bioinformatics approaches.ResultsDENV-2 genetic structure is complex and consists of fifteen subpopulations/lineages. The Asian/American genotype is observed to be diversified into seven lineages. The Asian I, Cosmopolitan and sylvatic genotypes were found to be subdivided into two lineages, each. The populations of American and Asian II genotypes were observed to be homogeneous. Significant evidence of episodic positive selection was observed in all the genes, except NS4A. Positive selection operational on a few codons in envelope gene confers antigenic and lineage diversity in the American strains of Asian/American genotype. Selection on codons of non-structural genes was observed to impact diversification of lineages in Asian I, cosmopolitan and sylvatic genotypes. Evidence of intra/inter-genotype recombination was obtained and the uncertainty in classification of recombinant strains was resolved using the population genetics approach.DiscussionComplete genome-based analysis revealed that the worldwide population of DENV-2 strains is subdivided into fifteen lineages. The population structure of DENV-2 is spatiotemporal and is shaped by episodic positive selection and recombination. Intra-genotype diversity was observed in four genotypes (Asian/American, Asian I, cosmopolitan and sylvatic). Episodic positive selection on envelope and non-structural genes translates into antigenic diversity and appears to be responsible for emergence of strains/lineages in DENV-2 genotypes. Understanding of the genotype diversity and emerging lineages will be useful to design strategies for epidemiological surveillance and vaccine design.
creator: Vaishali P. Waman
creator: Pandurang Kolekar
creator: Mukund R. Ramtirthkar
creator: Mohan M. Kale
creator: Urmila Kulkarni-Kale
uri: https://doi.org/10.7717/peerj.2326
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Waman et al.

title: Investigation of the mechanisms of action behind Electromotive Drug Administration (EMDA)
link: https://peerj.com/articles/2309
last-modified: 2016-08-24
description: ObjectiveBladder cancer is a cause of considerable morbidity worldwide. Electromotive Drug Administration is a method that combines intravesical chemotherapy with local electric field application. Electroporation has been suggested among other mechanisms as having a possible role in the therapy, so the goal of the present study was to investigate the electric fields present in the bladder wall during the treatment to determine which mechanisms might be involved.Material and MethodsElectromotive Drug Administration involves applying intravesical mitomycin C with direct current of 20 mA delivered through a catheter electrode for 30 min. For numerical electric field computation we built a 3-D nonhomogeneous patient specific model based on CT images and used finite element method simulations to determine the electric fields in the whole body.ResultsResults indicate that highest electric field in the bladder wall was 37.7 V/m. The mean electric field magnitude in the bladder wall was 3.03 V/m. The mean magnitude of the current density in the bladder wall was 0.61 A/m2.ConclusionsThe present study shows that electroporation is not the mechanism of action in EMDA. A more likely explanation of the mechanism of action is iontophoretic forces increasing the mitomycin C concentration in the bladder wall.
creator: Bor Kos
creator: Juan Luis Vásquez
creator: Damijan Miklavčič
creator: Gregers G.G. Hermann
creator: Julie Gehl
uri: https://doi.org/10.7717/peerj.2309
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Kos et al.

title: I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation
link: https://peerj.com/articles/2350
last-modified: 2016-08-23
description: In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization.
creator: Evelyn L. Jensen
creator: Arne Ø. Mooers
creator: Adalgisa Caccone
creator: Michael A. Russello
uri: https://doi.org/10.7717/peerj.2350
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Jensen et al.

title: Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci
link: https://peerj.com/articles/2366
last-modified: 2016-08-23
description: BackgroundVestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp. could be amplified in the GoM seep tubeworm, Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation of S. jonesi.MethodsSeventy-seven S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed for Escarpia laminata (18 loci) and Escarpia southwardae (30 loci) were tested to determine if they were homologous and polymorphic in S. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring in S. jonesi.ResultsMicrosatellite pre-screening identified 13 (27%) of the Escarpia loci were homologous and polymorphic in S. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongst S. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci on S. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents.DiscussionThe ability to develop “universal” microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.
creator: Chunya Huang
creator: Stephen W. Schaeffer
creator: Charles R. Fisher
creator: Dominique A. Cowart
uri: https://doi.org/10.7717/peerj.2366
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Huang et al.

title: SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees
link: https://peerj.com/articles/2359
last-modified: 2016-08-23
description: We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.
creator: Dan F. DeBlasio
creator: Jennifer H. Wisecaver
uri: https://doi.org/10.7717/peerj.2359
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 DeBlasio and Wisecaver

title: Reliability and validity of an iPhone® application for the measurement of lumbar spine flexion and extension range of motion
link: https://peerj.com/articles/2355
last-modified: 2016-08-23
description: BackgroundMeasurement of lumbar spine range of motion (ROM) is often considered to be an essential component of lumbar spine physiotherapy and orthopedic assessment. The measurement can be carried out through various instruments such as inclinometers, goniometers, and etc. Recent smartphones have been equipped with accelerometers and magnetometers, which, through specific software applications (apps) can be used for inclinometric functions.PurposeThe main purpose was to investigate the reliability and validity of an iPhone® app (TiltMeter© -advanced level and inclinometer) for measuring standing lumbar spine flexion–extension ROM in asymptomatic subjects.DesignA cross-sectional study was carried out.SettingThis study was conducted in a physiotherapy clinic located at School of Rehabilitation Sciences, Iran University of Medical Science and Health Services, Tehran, Iran.SubjectsA convenience sample of 30 asymptomatic adults (15 males; 15 females; age range = 18–55 years) was recruited between August 2015 and December 2015.MethodsFollowing a 2–minute warm-up, the subjects were asked to stand in a relaxed position and their skin was marked at the T12–L1 and S1–S2 spinal levels. From this position, they were asked to perform maximum lumbar flexion followed by maximum lumbar extension with their knees straight. Two blinded raters each used an inclinometer and the iPhone ® app to measure lumbar spine flexion–extension ROM. A third rater read the measured angles. To calculate total lumbar spine flexion–extension ROM, the measurement from S1–S2 was subtracted from T12–L1. The second (2 hours later) and third (48 hours later) sessions were carried out in the same manner as the first session. All of the measurements were conducted 3 times and the mean value of 3 repetitions for each measurement was used for analysis. Intraclass correlation coefficient (ICC) models (3, k) and (2, k) were used to determine the intra-rater and inter-rater reliability, respectively. The Pearson correlation coefficients were used to establish concurrent validity of the iPhone® app. Furthermore, minimum detectable change at the 95% confidence level (MDC95) was computed as 1.96 × standard error of measurement × $\sqrt{2}$2.ResultsGood to excellent intra-rater and inter-rater reliability were demonstrated for both the gravity-based inclinometer with ICC values of ≥0.84 and ≥0.77 and the iPhone® app with ICC values of ≥0.85 and ≥0.85, respectively. The MDC95 ranged from 5.82°to 8.18°for the intra-rater analysis and from 7.38°to 8.66° for the inter-rater analysis. The concurrent validity for flexion and extension between the 2 instruments was 0.85 and 0.91, respectively.ConclusionsThe iPhone®app possesses good to excellent intra-rater and inter-rater reliability and concurrent validity. It seems that the iPhone® app can be used for the measurement of lumbar spine flexion–extension ROM.Level of evidenceIIb.
creator: Mohammad Reza Pourahmadi
creator: Morteza Taghipour
creator: Elham Jannati
creator: Mohammad Ali Mohseni-Bandpei
creator: Ismail Ebrahimi Takamjani
creator: Fatemeh Rajabzadeh
uri: https://doi.org/10.7717/peerj.2355
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Pourahmadi et al.

title: Effects of cattle grazing on small mammal communities in the Hulunber meadow steppe
link: https://peerj.com/articles/2349
last-modified: 2016-08-23
description: Small mammals play important roles in many ecosystems, and understanding their response to disturbances such as cattle grazing is fundamental for developing sustainable land use strategies. However, how small mammals respond to cattle grazing remains controversial. A potential cause is that most of previous studies adopt rather simple experimental designs based solely on the presence/absence of grazing, and are thus unable to detect any complex relationships between diversity and grazing intensity. In this study, we conducted manipulated experiments in the Hulunber meadow steppe to survey small mammal community structures under four levels of grazing intensities. We found dramatic changes in species composition in native small mammal communities when grazing intensity reached intermediate levels (0.46 animal unit/ha). As grazing intensity increased, Spermophilus dauricus gradually became the single dominant species. Species richness and diversity of small mammals in ungrazed and lightly grazed (0.23 animal unit/ha) area were much higher than in intermediately and heavily grazed area. We did not detect a humped relationship between small mammal diversity and disturbance levels predicted by the intermediate disturbance hypothesis (IDH). Our study highlighted the necessity of conducting manipulated experiments under multiple grazing intensities.
creator: Chan Cao
creator: Ling-Ying Shuai
creator: Xiao-Ping Xin
creator: Zhi-Tao Liu
creator: Yan-Ling Song
creator: Zhi-Gao Zeng
uri: https://doi.org/10.7717/peerj.2349
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2016 Cao et al.

title: CardioTF, a database of deconstructing transcriptional circuits in the heart system
link: https://peerj.com/articles/2339
last-modified: 2016-08-23
description: Background: Information on cardiovascular gene transcription is fragmented and far behind the present requirements of the systems biology field. To create a comprehensive source of data for cardiovascular gene regulation and to facilitate a deeper understanding of genomic data, the CardioTF database was constructed. The purpose of this database is to collate information on cardiovascular transcription factors (TFs), position weight matrices (PWMs), and enhancer sequences discovered using the ChIP-seq method.Methods: The Naïve-Bayes algorithm was used to classify literature and identify all PubMed abstracts on cardiovascular development. The natural language learning tool GNAT was then used to identify corresponding gene names embedded within these abstracts. Local Perl scripts were used to integrate and dump data from public databases into the MariaDB management system (MySQL). In-house R scripts were written to analyze and visualize the results.Results: Known cardiovascular TFs from humans and human homologs from fly, Ciona, zebrafish, frog, chicken, and mouse were identified and deposited in the database. PWMs from Jaspar, hPDI, and UniPROBE databases were deposited in the database and can be retrieved using their corresponding TF names. Gene enhancer regions from various sources of ChIP-seq data were deposited into the database and were able to be visualized by graphical output. Besides biocuration, mouse homologs of the 81 core cardiac TFs were selected using a Naïve-Bayes approach and then by intersecting four independent data sources: RNA profiling, expert annotation, PubMed abstracts and phenotype.Discussion: The CardioTF database can be used as a portal to construct transcriptional network of cardiac development.Availability and Implementation: Database URL: http://www.cardiosignal.org/database/cardiotf.html.
creator: Yisong Zhen
uri: https://doi.org/10.7717/peerj.2339
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2016 Zhen