title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2013-06 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Non-pneumococcal mitis-group streptococci confound detection of pneumococcal capsular serotype-specific loci in upper respiratory tract link: https://peerj.com/articles/97 last-modified: 2013-06-25 description: We performed culture-based and PCR-based tests for pneumococcal identification and serotyping from carriage specimens collected in rural and urban Kenya. Nasopharyngeal specimens from 237 healthy children <5 years old (C-NPs) and combined nasopharyngeal/oropharyngeal specimens from 158 adults (A-NP/OPs, 118 HIV-positive) were assessed using pneumococcal isolation (following broth culture enrichment) with Quellung-based serotyping, real-time lytA-PCR, and conventional multiplexed PCR-serotyping (cmPCR). Culture-based testing from C-NPs, HIV-positive A-NP/OPs, and HIV-negative A-NP/OPs revealed 85.2%, 40.7%, and 12.5% pneumococcal carriage, respectively. In contrast, cmPCR serotypes were found in 93.2%, 98.3%, and 95.0% of these sets, respectively. Two of 16 lytA-negative C-NPs and 26 of 28 lytA-negative A-NP/OPs were cmPCR-positive for 1–10 serotypes (sts) or serogroups (sgs). A-NP/OPs averaged 5.5 cmPCR serotypes/serogroups (5.2 in HIV-positive, 7.1 in HIV-negative) and C-NPs averaged 1.5 cmPCR serotypes/serogroups. cmPCR serotypes/serogroups from lytA-negative A-NP/OPs included st2, st4, sg7F/7A, sg9N/9L, st10A, sg10F/10C/33C, st13, st17F, sg18C/18A/18B/18F, sg22F/22A, and st39. Nine strains of three non-pneumococcal species (S. oralis, S. mitis, and S. parasanguinis) (7 from A-OP, 1 from both A-NP and A-OP, and 1 from C-NP) were each cmPCR-positive for one of 7 serotypes/serogroups (st5, st13, sg15A/15F, sg10F/10C/33C, sg33F/33A/37, sg18C/18A/18B/18F, sg12F/12A/12B/ 44/46) with amplicons revealing 83.6–99.7% sequence identity to pneumococcal references. In total, 150 cmPCR amplicons from carriage specimens were sequenced, including 25 from lytA-negative specimens. Amplicon sequences derived from specimens yielding a pneumococcal isolate with the corresponding serotype were identical or highly conserved (>98.7%) with the reference cmPCR amplicon for the st, while cmPCR amplicons from lytA-negative specimens were generally more divergent. Separate testing of 56 A-OPs and 56 A-NPs revealed that ∼94% of the positive cmPCR results from A-NP/OPs were from OP microbiota. In contrast, A-NPs yielded >2-fold more pneumococcal isolates than A-OPs. Verified and suspected non-pneumococcal cmPCR serotypes/serogroups appeared to be relatively rare in C-NPs and A-NPs compared to A-OPs. Our findings indicate that non-pneumococcal species can confound serotype-specific PCR and other sequence-based assays due to evolutionarily conserved genes most likely involved in biosynthesis of surface polysaccharide structures. creator: Maria da Gloria Carvalho creator: Fabiana C. Pimenta creator: Iaci Moura creator: Alexis Roundtree creator: Robert E. Gertz creator: Zhongya Li creator: Geofrey Jagero creator: Godfrey Bigogo creator: Muthoni Junghae creator: Laura Conklin creator: Daniel R. Feikin creator: Robert F. Breiman creator: Cynthia G. Whitney creator: Bernard W. Beall uri: https://doi.org/10.7717/peerj.97 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Carvalho et al. title: Wake sorting, selective predation and biogenic mixing: potential reasons for high turbulence in fish schools link: https://peerj.com/articles/96 last-modified: 2013-06-25 description: There has been debate about animals’ contribution to ocean circulation, called biomixing, or biogenic mixing. The energy input of schooling fish is significant but the eddies may be too small; so energy is dissipated as heat before impacting oceanic structure. I suggest that high turbulence caused by some very large aggregations of small animals has an important impact via a more direct ecosystem feedback process than overall ocean circulation. In the model presented here, large schools exhibit cooperative behavior and act like giant sieves grading zooplankton through individual swimmer’s wakes, which focus the best prey in predictable positions. Following schoolers exploit these patterns. Then schools leave, in their wakes, chaotic turbulence enhancing growth of the smaller zooplankton and phytoplankton which has been graded out by the school. The result is a different community structure of plankton than would exist without such biomixing. Changes to plankton abundance and community structure on oceanic scales over the past century are correlated to overfishing and are consistent with this concept. creator: Jay Willis uri: https://doi.org/10.7717/peerj.96 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Willis title: Phylogenetic diversity of plants alters the effect of species richness on invertebrate herbivory link: https://peerj.com/articles/93 last-modified: 2013-06-25 description: Long-standing ecological theory proposes that diverse communities of plants should experience a decrease in herbivory. Yet previous empirical examinations of this hypothesis have revealed that plant species richness increases herbivory in just as many systems as it decreases it. In this study, I ask whether more insight into the role of plant diversity in promoting or suppressing herbivory can be gained by incorporating information about the evolutionary history of species in a community. In an old field system in southern Ontario, I surveyed communities of plants and measured levels of leaf damage on 27 species in 38 plots. I calculated a measure of phylogenetic diversity (PSE) that encapsulates information about the amount of evolutionary history represented in each of the plots and looked for a relationship between levels of herbivory and both species richness and phylogenetic diversity using a generalized linear mixed model (GLMM) that could account for variation in herbivory levels between species. I found that species richness was positively associated with herbivore damage at the plot-level, in keeping with the results from several other recent studies on this question. On the other hand, phylogenetic diversity was associated with decreased herbivory. Importantly, there was also an interaction between species richness and phylogenetic diversity, such that plots with the highest levels of herbivory were plots which had many species but only if those species tended to be closely related to one another. I propose that these results are the consequence of interactions with herbivores whose diets are phylogenetically specialized (for which I introduce the term cladophage), and how phylogenetic diversity may alter their realized host ranges. These results suggest that incorporating a phylogenetic perspective can add valuable additional insight into the role of plant diversity in explaining or predicting levels of herbivory at a whole-community scale. creator: Russell Dinnage uri: https://doi.org/10.7717/peerj.93 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Dinnage title: PTree: pattern-based, stochastic search for maximum parsimony phylogenies link: https://peerj.com/articles/89 last-modified: 2013-06-25 description: Phylogenetic reconstruction is vital to analyzing the evolutionary relationship of genes within and across populations of different species. Nowadays, with next generation sequencing technologies producing sets comprising thousands of sequences, robust identification of the tree topology, which is optimal according to standard criteria such as maximum parsimony, maximum likelihood or posterior probability, with phylogenetic inference methods is a computationally very demanding task. Here, we describe a stochastic search method for a maximum parsimony tree, implemented in a software package we named PTree. Our method is based on a new pattern-based technique that enables us to infer intermediate sequences efficiently where the incorporation of these sequences in the current tree topology yields a phylogenetic tree with a lower cost. Evaluation across multiple datasets showed that our method is comparable to the algorithms implemented in PAUP* or TNT, which are widely used by the bioinformatics community, in terms of topological accuracy and runtime. We show that our method can process large-scale datasets of 1,000–8,000 sequences. We believe that our novel pattern-based method enriches the current set of tools and methods for phylogenetic tree inference. The software is available under: http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/. creator: Ivan Gregor creator: Lars Steinbrück creator: Alice C. McHardy uri: https://doi.org/10.7717/peerj.89 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Gregor et al. title: Qualitative community stability determines parasite establishment and richness in estuarine marshes link: https://peerj.com/articles/92 last-modified: 2013-06-18 description: The establishment of parasites with complex life cycles is generally thought to be regulated by free-living species richness and the stability of local ecological interactions. In this study, we test the prediction that stable host communities are prerequisite for the establishment of complex multi-host parasite life cycles. The colonization of naïve killifish, Fundulus heteroclitus, by parasites was investigated in 4 salt marsh sites that differed in time since major ecological restoration, and which provided a gradient in free-living species richness. The richness of the parasite community, and the rate at which parasite species accumulated in the killifish, were similar between the low diversity unrestored site and the two high diversity (10- and 20-year) restored marsh sites. The parasite community in the newly restored marsh (0 year) included only directly-transmitted parasite species. To explain the paradox of a low diversity, highly invaded salt marsh (unrestored) having the same parasite community as highly diverse restored marsh sites (10 and 20 yrs) we assessed qualitative community stability. We find a significant correlation between system stability and parasite species richness. These data suggest a role for local stability in parasite community assembly, and support the idea that stable trophic relationships are required for the persistence of complex parasite life cycles. creator: Tavis K. Anderson creator: Michael V.K. Sukhdeo uri: https://doi.org/10.7717/peerj.92 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Anderson et al. title: Factors associated with delayed entry into HIV medical care after HIV diagnosis in a resource-limited setting: Data from a cohort study in India link: https://peerj.com/articles/90 last-modified: 2013-06-18 description: Studies from sub-Saharan Africa have shown that a substantial proportion of patients diagnosed with HIV enter into HIV medical care late. However, data from low or middle-income countries outside Africa are scarce. In this study, we investigated risk factors associated with delayed entry into care stratified by gender in a large cohort study in India. 7701 patients were diagnosed with HIV and 5410 entered into care within three months of HIV diagnosis. Nearly 80% entered into care within a year, but most patients who did not enter into care within a year remained lost to follow up or died. Patient with risk factors related to having a low socio-economic status (poverty, being homeless, belonging to a disadvantaged community and illiteracy) were more likely to enter into care late. In addition, male gender and being asymptomatic at the moment of HIV infection were factors associated with delayed entry into care. Substantial gender differences were found. Younger age was found to be associated with delayed entry in men, but not in women. Widows and unmarried men were more likely to enter into care within three months. Women belonging to disadvantaged communities or living far from a town were more likely to enter into care late. The results of this study highlight the need to improve the linkage between HIV diagnosis and HIV treatment in India. HIV programmes should monitor patients diagnosed with HIV until they engage in HIV medical care, especially those at increased risk of attrition. creator: Gerardo Alvarez-Uria uri: https://doi.org/10.7717/peerj.90 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Alvarez-Uria title: Prediction of morbidity and mortality in patients with type 2 diabetes link: https://peerj.com/articles/87 last-modified: 2013-06-11 description: Introduction. The objective of this study was to create a tool that accurately predicts the risk of morbidity and mortality in patients with type 2 diabetes according to an oral hypoglycemic agent.Materials and Methods. The model was based on a cohort of 33,067 patients with type 2 diabetes who were prescribed a single oral hypoglycemic agent at the Cleveland Clinic between 1998 and 2006. Competing risk regression models were created for coronary heart disease (CHD), heart failure, and stroke, while a Cox regression model was created for mortality. Propensity scores were used to account for possible treatment bias. A prediction tool was created and internally validated using tenfold cross-validation. The results were compared to a Framingham model and a model based on the United Kingdom Prospective Diabetes Study (UKPDS) for CHD and stroke, respectively.Results and Discussion. Median follow-up for the mortality outcome was 769 days. The numbers of patients experiencing events were as follows: CHD (3062), heart failure (1408), stroke (1451), and mortality (3661). The prediction tools demonstrated the following concordance indices (c-statistics) for the specific outcomes: CHD (0.730), heart failure (0.753), stroke (0.688), and mortality (0.719). The prediction tool was superior to the Framingham model at predicting CHD and was at least as accurate as the UKPDS model at predicting stroke.Conclusions. We created an accurate tool for predicting the risk of stroke, coronary heart disease, heart failure, and death in patients with type 2 diabetes. The calculator is available online at http://rcalc.ccf.org under the heading “Type 2 Diabetes” and entitled, “Predicting 5-Year Morbidity and Mortality.” This may be a valuable tool to aid the clinician’s choice of an oral hypoglycemic, to better inform patients, and to motivate dialogue between physician and patient. creator: Brian J. Wells creator: Rachel Roth creator: Amy S. Nowacki creator: Susana Arrigain creator: Changhong Yu creator: Wayne A. Rosenkrans creator: Michael W. Kattan uri: https://doi.org/10.7717/peerj.87 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Wells et al. title: Major histocompatibility complex class I evolution in songbirds: universal primers, rapid evolution and base compositional shifts in exon 3 link: https://peerj.com/articles/86 last-modified: 2013-06-11 description: Genes of the Major Histocompatibility Complex (MHC) have become an important marker for the investigation of adaptive genetic variation in vertebrates because of their critical role in pathogen resistance. However, despite significant advances in the last few years the characterization of MHC variation in non-model species still remains a challenging task due to the redundancy and high variation of this gene complex. Here we report the utility of a single pair of primers for the cross-amplification of the third exon of MHC class I genes, which encodes the more polymorphic half of the peptide-binding region (PBR), in oscine passerines (songbirds; Aves: Passeriformes), a group especially challenging for MHC characterization due to the presence of large and complex MHC multigene families. In our survey, although the primers failed to amplify exon 3 from two suboscine passerine birds, they amplified exon 3 of multiple MHC class I genes in all 16 species of oscine songbirds tested, yielding a total of 120 sequences. The 16 songbird species belong to 14 different families, primarily within the Passerida, but also in the Corvida. Using a conservative approach based on the analysis of cloned amplicons (n = 16) from each species, we found between 3 and 10 MHC sequences per individual. Each allele repertoire was highly divergent, with the overall number of polymorphic sites per species ranging from 33 to 108 (out of 264 sites) and the average number of nucleotide differences between alleles ranging from 14.67 to 43.67. Our survey in songbirds allowed us to compare macroevolutionary dynamics of exon 3 between songbirds and non-passerine birds. We found compelling evidence of positive selection acting specifically upon peptide-binding codons across birds, and we estimate the strength of diversifying selection in songbirds to be about twice that in non-passerines. Analysis using comparative methods suggest weaker evidence for a higher GC content in the 3rd codon position of exon 3 in non-passerine birds, a pattern that contrasts with among-clade GC patterns found in other avian studies and may suggests different mutational mechanisms. Our primers represent a useful tool for the characterization of functional and evolutionarily relevant MHC variation across the hyperdiverse songbirds. creator: Miguel Alcaide creator: Mark Liu creator: Scott V. Edwards uri: https://doi.org/10.7717/peerj.86 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Alcaide et al. title: Molecular modeling and pharmacophore elucidation study of the Classical Swine Fever virus helicase as a promising pharmacological target link: https://peerj.com/articles/85 last-modified: 2013-06-11 description: The Classical Swine Fever virus (CSFV) is a major pathogen of livestock and belongs to the flaviviridae viral family. Even though there aren’t any verified zoonosis cases yet, the outcomes of CSFV epidemics have been devastating to local communities. In an effort to shed light to the molecular mechanisms underlying the structural and drug design potential of the viral helicase, the three dimensional structure of CSFV helicase has been modeled using conventional homology modeling techniques and the crystal structure of the Hepatitis C virus (HCV) as a template. The established structure of the CSFV helicase has been in silico evaluated for its viability using a repertoire of in silico tools. The ultimate goal of this study is to introduce the 3D conformation of the CSFV helicase as a reliable structure that may be used as the designing platform for de novo, structure-based drug design experiments. In this direction using the modeled structure of CSVF helicase, a 3D pharmacophore was designed. The pharmacophore comprises of a series of key characteristics that molecular inhibitors must satisfy in order to achieve maximum predicted affinity for the given enzyme. Overall, invaluable insights and conclusions are drawn from this structural study of the CSFV helicase, which may provide the scientific community with the founding plinth in the fight against CSFV infections through the perspective of the CSFV helicase as a potential pharmacological target. Notably, to date no antiviral agent is available against the CSFV nor is expected soon. Subsequently, there is urgent need for new modern and state-of-the-art antiviral strategies to be developed. creator: Dimitrios Vlachakis creator: Sophia Kossida uri: https://doi.org/10.7717/peerj.85 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Vlachakis & Kossida title: Looking after your partner: sentinel behaviour in a socially monogamous bird link: https://peerj.com/articles/83 last-modified: 2013-06-04 description: Natural selection favours those individuals with effective anti-predator defences. The presence of sentinels is known to be an effective form of defence amongst stable groups of individuals within cooperative and polygynous breeding systems. However, the presence of sentinels in the more prevalent socially monogamous breeding systems remains overlooked as an important benefit of such partnerships. Here, we describe a study in which we examined the presence and effectiveness of sentinels in a wild population of the socially monogamous zebra finch (Taeniopygia guttata). We found that when experimentally approached by a human observer during incubation, birds flushed from their nests at significantly greater distances when their reproductive partner was acting as a sentinel than when the partner was absent. The distance at which birds flushed was not influenced by the approach direction of the human observer, the gender of the incubating bird, the presence of conspecifics, the habitat type or the size of the breeding colony. Our results indicate that sentinels are an effective anti-predator defence amongst socially monogamous birds, and may represent a neglected benefit of the formation of stable social partnerships in birds. We suggest that whilst recent work has focused on the sexual conflicts that occur between males and females in socially monogamous pairs, we should not lose sight of the benefits that individuals may gain from their partner. creator: Mark C. Mainwaring creator: Simon C. Griffith uri: https://doi.org/10.7717/peerj.83 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Mainwaring & Griffith title: What is the “normal” fetal heart rate? link: https://peerj.com/articles/82 last-modified: 2013-06-04 description: Aim. There is no consensus about the normal fetal heart rate. Current international guidelines recommend for the normal fetal heart rate (FHR) baseline different ranges of 110 to 150 beats per minute (bpm) or 110 to 160 bpm. We started with a precise definition of “normality” and performed a retrospective computerized analysis of electronically recorded FHR tracings.Methods. We analyzed all recorded cardiotocography tracings of singleton pregnancies in three German medical centers from 2000 to 2007 and identified 78,852 tracings of sufficient quality. For each tracing, the baseline FHR was extracted by eliminating accelerations/decelerations and averaging based on the “delayed moving windows” algorithm. After analyzing 40% of the dataset as “training set” from one hospital generating a hypothetical normal baseline range, evaluation of external validity on the other 60% of the data was performed using data from later years in the same hospital and externally using data from the two other hospitals.Results. Based on the training data set, the “best” FHR range was 115 or 120 to 160 bpm. Validation in all three data sets identified 120 to 160 bpm as the correct symmetric “normal range”. FHR decreases slightly during gestation.Conclusions. Normal ranges for FHR are 120 to 160 bpm. Many international guidelines define ranges of 110 to 160 bpm which seem to be safe in daily practice. However, further studies should confirm that such asymmetric alarm limits are safe, with a particular focus on the lower bound, and should give insights about how to show and further improve the usefulness of the widely used practice of CTG monitoring. creator: Stephanie Pildner von Steinburg creator: Anne-Laure Boulesteix creator: Christian Lederer creator: Stefani Grunow creator: Sven Schiermeier creator: Wolfgang Hatzmann creator: Karl-Theodor M. Schneider creator: Martin Daumer uri: https://doi.org/10.7717/peerj.82 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Pildner von Steinburg et al. title: RRE-deleting self-inactivating and self-activating HIV-1 vectors for improved safety link: https://peerj.com/articles/84 last-modified: 2013-06-04 description: Retroviruses have been shown to efficiently delete sequences between repeats as a consequence of the template switching ability of the viral reverse transcriptase. To evaluate this approach for deriving safety-modified lentiviral vectors, we created HIV-1 vectors engineered to delete the Rev-response element (RRE) during reverse-transcription by sandwiching the RRE between two non-functional hygromycin phosphotransferase sequences. Deletion of the RRE during reverse-transcription lead to the reconstitution of a functional hygromycin phosphotransferase gene in the target cell. The efficiency of functional reconstitution, depending on vector configuration, was between 12% and 23%. Real-time quantitative PCR of genomic DNA of cells transduced with the RRE-deleting vectors that were selected using an independent drug resistance marker, which measured both functional and nonfunctional recombination events, indicated that the overall efficiency of RRE deletion of hygromycin phosphotransferase gene, was between 73.6% and 83.5%. creator: Narasimhachar Srinivasakumar uri: https://doi.org/10.7717/peerj.84 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Srinivasakumar