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

title: Onset of human preterm and term birth is related to unique inflammatory transcriptome profiles at the maternal fetal interface
link: https://peerj.com/articles/3685
last-modified: 2017-09-01
description: BackgroundPreterm birth is a main determinant of neonatal mortality and morbidity and a major contributor to the overall mortality and burden of disease. However, research of the preterm birth is hindered by the imprecise definition of the clinical phenotype and complexity of the molecular phenotype due to multiple pregnancy tissue types and molecular processes that may contribute to the preterm birth. Here we comprehensively evaluate the mRNA transcriptome that characterizes preterm and term labor in tissues comprising the pregnancy using precisely phenotyped samples. The four complementary phenotypes together provide comprehensive insight into preterm and term parturition.MethodsSamples of maternal blood, chorion, amnion, placenta, decidua, fetal blood, and myometrium from the uterine fundus and lower segment (n = 183) were obtained during cesarean delivery from women with four complementary phenotypes: delivering preterm with (PL) and without labor (PNL), term with (TL) and without labor (TNL). Enrolled were 35 pregnant women with four precisely and prospectively defined phenotypes: PL (n = 8), PNL (n = 10), TL (n = 7) and TNL (n = 10). Gene expression data were analyzed using shrunken centroid analysis to identify a minimal set of genes that uniquely characterizes each of the four phenotypes. Expression profiles of 73 genes and non-coding RNA sequences uniquely identified each of the four phenotypes. The shrunken centroid analysis and 10 times 10-fold cross-validation was also used to minimize false positive finings and overfitting. Identified were the pathways and molecular processes associated with and the cis-regulatory elements in gene’s 5′ promoter or 3′-UTR regions of the set of genes which expression uniquely characterized the four phenotypes.ResultsThe largest differences in gene expression among the four groups occurred at maternal fetal interface in decidua, chorion and amnion. The gene expression profiles showed suppression of chemokines expression in TNL, withdrawal of this suppression in TL, activation of multiple pathways of inflammation in PL, and an immune rejection profile in PNL. The genes constituting expression signatures showed over-representation of three putative regulatory elements in their 5′and 3′ UTR regions.ConclusionsThe results suggest that pregnancy is maintained by downregulation of chemokines at the maternal-fetal interface. Withdrawal of this downregulation results in the term birth and its overriding by the activation of multiple pathways of the immune system in the preterm birth. Complications of the pregnancy associated with impairment of placental function, which necessitated premature delivery of the fetus in the absence of labor, show gene expression patterns associated with immune rejection.
creator: Radek Bukowski
creator: Yoel Sadovsky
creator: Hani Goodarzi
creator: Heping Zhang
creator: Joseph R. Biggio
creator: Michael Varner
creator: Samuel Parry
creator: Feifei Xiao
creator: Sean M. Esplin
creator: William Andrews
creator: George R. Saade
creator: John V. Ilekis
creator: Uma M. Reddy
creator: Donald A. Baldwin
uri: https://doi.org/10.7717/peerj.3685
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Bukowski et al.

title: Measuring coral calcification under ocean acidification: methodological considerations for the 45Ca-uptake and total alkalinity anomaly technique
link: https://peerj.com/articles/3749
last-modified: 2017-09-01
description: As the oceans become less alkaline due to rising CO2 levels, deleterious consequences are expected for calcifying corals. Predicting how coral calcification will be affected by on-going ocean acidification (OA) requires an accurate assessment of CaCO3 deposition and an understanding of the relative importance that decreasing calcification and/or increasing dissolution play for the overall calcification budget of individual corals. Here, we assessed the compatibility of the 45Ca-uptake and total alkalinity (TA) anomaly techniques as measures of gross and net calcification (GC, NC), respectively, to determine coral calcification at pHT 8.1 and 7.5. Considering the differing buffering capacity of seawater at both pH values, we were also interested in how strongly coral calcification alters the seawater carbonate chemistry under prolonged incubation in sealed chambers, potentially interfering with physiological functioning. Our data indicate that NC estimates by TA are erroneously ∼5% and ∼21% higher than GC estimates from 45Ca for ambient and reduced pH, respectively. Considering also previous data, we show that the consistent discrepancy between both techniques across studies is not constant, but largely depends on the absolute value of CaCO3 deposition. Deriving rates of coral dissolution from the difference between NC and GC was not possible and we advocate a more direct approach for the future by simultaneously measuring skeletal calcium influx and efflux. Substantial changes in carbonate system parameters for incubation times beyond two hours in our experiment demonstrate the necessity to test and optimize experimental incubation setups when measuring coral calcification in closed systems, especially under OA conditions.
creator: Stephanie Cohen
creator: Thomas Krueger
creator: Maoz Fine
uri: https://doi.org/10.7717/peerj.3749
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Cohen et al.

title: The influence of fundamental frequency on perceived duration in spectrally comparable sounds
link: https://peerj.com/articles/3734
last-modified: 2017-09-01
description: The perceived duration of a sound is affected by its fundamental frequency and intensity: higher sounds are judged to be longer, as are sounds with greater intensity. Since increasing intensity lengthens the perceived duration of the auditory object, and increasing the fundamental frequency increases the sound’s perceived loudness (up to ca. 3 kHz), frequency modulation of duration could be potentially explained by a confounding effect where the primary cause of the modulation would be variations in intensity. Here, a series of experiments are described that were designed to disentangle the contributions of fundamental frequency, intensity, and duration to perceived loudness and duration. In two forced-choice tasks, participants judged duration and intensity differences between two sounds varying simultaneously in intensity, fundamental frequency, fundamental frequency gliding range, and duration. The results suggest that fundamental frequency and intensity each have an impact on duration judgments, while frequency gliding range did not influence the present results. We also demonstrate that the modulation of perceived duration by sound fundamental frequency cannot be fully explained by the confounding relationship between frequency and intensity.
creator: Caitlin Dawson
creator: Daniel Aalto
creator: Juraj Simko
creator: Martti Vainio
uri: https://doi.org/10.7717/peerj.3734
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Dawson et al.

title: A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes
link: https://peerj.com/articles/3703
last-modified: 2017-09-01
description: BackgroundHeterocyclic aromatic amines (HAA) are environmental and food contaminants that are potentially carcinogenic for humans. 2-Amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx) is one of the most abundant HAA formed in cooked meat. MeIQx is metabolized by cytochrome P450 1A2 in the human liver into detoxificated and bioactivated products. Once bioactivated, MeIQx metabolites can lead to DNA adduct formation responsible for further genome instability.MethodsUsing a computational approach, we developed a numerical model for MeIQx metabolism in the liver that predicts the MeIQx biotransformation into detoxification or bioactivation pathways according to the concentration of MeIQx.ResultsOur results demonstrate that (1) the detoxification pathway predominates, (2) the ratio between detoxification and bioactivation pathways is not linear and shows a maximum at 10 µM of MeIQx in hepatocyte cell models, and (3) CYP1A2 is a key enzyme in the system that regulates the balance between bioactivation and detoxification. Our analysis suggests that such a ratio could be considered as an indicator of MeIQx genotoxicity at a low concentration of MeIQx.ConclusionsOur model permits the investigation of the balance between bioactivation (i.e., DNA adduct formation pathway through the prediction of potential genotoxic compounds) and detoxification of MeIQx in order to predict the behaviour of this environmental contaminant in the human liver. It highlights the importance of complex regulations of enzyme competitions that should be taken into account in any further multi-organ models.
creator: Victorien Delannée
creator: Sophie Langouët
creator: Nathalie Théret
creator: Anne Siegel
uri: https://doi.org/10.7717/peerj.3703
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Delannée et al.

title: A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog
link: https://peerj.com/articles/3702
last-modified: 2017-09-01
description: Whole genome sequencing (WGS) is a very valuable resource to understand the evolutionary history of poorly known species. However, in organisms with large genomes, as most amphibians, WGS is still excessively challenging and transcriptome sequencing (RNA-seq) represents a cost-effective tool to explore genome-wide variability. Non-model organisms do not usually have a reference genome and the transcriptome must be assembled de-novo. We used RNA-seq to obtain the transcriptomic profile for Oreobates cruralis, a poorly known South American direct-developing frog. In total, 550,871 transcripts were assembled, corresponding to 422,999 putative genes. Of those, we identified 23,500, 37,349, 38,120 and 45,885 genes present in the Pfam, EggNOG, KEGG and GO databases, respectively. Interestingly, our results suggested that genes related to immune system and defense mechanisms are abundant in the transcriptome of O. cruralis. We also present a pipeline to assist with pre-processing, assembling, evaluating and functionally annotating a de-novo transcriptome from RNA-seq data of non-model organisms. Our pipeline guides the inexperienced user in an intuitive way through all the necessary steps to build de-novo transcriptome assemblies using readily available software and is freely available at: https://github.com/biomendi/TRANSCRIPTOME-ASSEMBLY-PIPELINE/wiki.
creator: Santiago Montero-Mendieta
creator: Manfred Grabherr
creator: Henrik Lantz
creator: Ignacio De la Riva
creator: Jennifer A. Leonard
creator: Matthew T. Webster
creator: Carles Vilà
uri: https://doi.org/10.7717/peerj.3702
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Montero-Mendieta et al.

title: Tracing hepatitis B virus (HBV) genotype B5 (formerly B6) evolutionary history in the circumpolar Arctic through phylogeographic modelling
link: https://peerj.com/articles/3757
last-modified: 2017-08-31
description: BackgroundIndigenous populations of the circumpolar Arctic are considered to be endemically infected (>2% prevalence) with hepatitis B virus (HBV), with subgenotype B5 (formerly B6) unique to these populations. The distinctive properties of HBV/B5, including high nucleotide diversity yet no significant liver disease, suggest virus adaptation through long-term host-pathogen association.MethodsTo investigate the origin and evolutionary spread of HBV/B5 into the circumpolar Arctic, fifty-seven partial and full genome sequences from Alaska, Canada and Greenland, having known location and sampling dates spanning 40 years, were phylogeographically investigated by Bayesian analysis (BEAST 2) using a reversible-jump-based substitution model and a clock rate estimated at 4.1 × 10−5 substitutions/site/year.ResultsFollowing an initial divergence from an Asian viral ancestor approximately 1954 years before present (YBP; 95% highest probability density interval [1188, 2901]), HBV/B5 coalescence occurred almost 1000 years later. Surprisingly, the HBV/B5 ancestor appears to locate first to Greenland in a rapid coastal route progression based on the landscape aware geographic model, with subsequent B5 evolution and spread westward. Bayesian skyline plot analysis demonstrated an HBV/B5 population expansion occurring approximately 400 YBP, coinciding with the disruption of the Neo-Eskimo Thule culture into more heterogeneous and regionally distinct Inuit populations throughout the North American Arctic.DiscussionHBV/B5 origin and spread appears to occur coincident with the movement of Neo-Eskimo (Inuit) populations within the past 1000 years, further supporting the hypothesis of HBV/host co-expansion, and illustrating the concept of host-pathogen adaptation and balance.
creator: Remco Bouckaert
creator: Brenna C. Simons
creator: Henrik Krarup
creator: T. Max Friesen
creator: Carla Osiowy
uri: https://doi.org/10.7717/peerj.3757
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Bouckaert et al.

title: Remote sensing and spatial statistical techniques for modelling Ommatissus lybicus (Hemiptera: Tropiduchidae) habitat and population densities
link: https://peerj.com/articles/3752
last-modified: 2017-08-31
description: In order to understand the distribution and prevalence of Ommatissus lybicus (Hemiptera: Tropiduchidae) as well as analyse their current biographical patterns and predict their future spread, comprehensive and detailed information on the environmental, climatic, and agricultural practices are essential. The spatial analytical techniques such as Remote Sensing and Spatial Statistics Tools, can help detect and model spatial links and correlations between the presence, absence and density of O. lybicus in response to climatic, environmental, and human factors. The main objective of this paper is to review remote sensing and relevant analytical techniques that can be applied in mapping and modelling the habitat and population density of O. lybicus. An exhaustive search of related literature revealed that there are very limited studies linking location-based infestation levels of pests like the O. lybicus with climatic, environmental, and human practice related variables. This review also highlights the accumulated knowledge and addresses the gaps in this area of research. Furthermore, it makes recommendations for future studies, and gives suggestions on monitoring and surveillance methods in designing both local and regional level integrated pest management strategies of palm tree and other affected cultivated crops.
creator: Khalifa M. Al-Kindi
creator: Paul Kwan
creator: Nigel R. Andrew
creator: Mitchell Welch
uri: https://doi.org/10.7717/peerj.3752
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Al-Kindi et al.

title: Intraclutch eggshell colour variation in birds: are females able to identify their eggs individually?
link: https://peerj.com/articles/3707
last-modified: 2017-08-31
description: BackgroundOne possibility suggested regarding female post-mating strategies is differential allocation into offspring investment. Female birds produce not only the largest, but also most colourful eggs of all oviparous taxa. Larger eggs provide space for bigger embryos, or more nutrition for their development, but the question why eggs are more colourful and why there is variation in eggshell colouration remains. In this context, the focus of interest has been to explain inter-clutch variation but in many bird species, eggshell colouration also varies within a clutch. Surprisingly, less attention has been paid to this phenomenon. Therefore, we propose the “female egg recognition” hypothesis, suggesting that mothers use colour characteristics to interpret egg attributes and allocate further investment into each egg accordingly. To evaluate the feasibility of the hypothesis, we tested several underlying predictions and examined their suitability using a dataset from our tree sparrow (Passer montanus) study. We predict (i) substantial within-clutch variation in eggshell colouration which, (ii) should be related to laying sequence, (iii) reflect egg quality and, (iv) should stimulate a female response.MethodsEggshell coloration data were obtained via digital photography under standardized conditions, taken after clutch completion. Lightness (L*), representing the achromatic properties of an egg has been chosen as the most important predictor in dark cavities and was related to egg quality and position in the nest.ResultsIn our tree sparrows, first and mainly last eggs were less pigmented, providing information about laying order. Egg volume, which predicts chick quality, positively correlates with eggshell coloration. Finally, we could show that female tree sparrows placed darker, but not bigger, eggs into more central incubation positions.DiscussionAll basic prerequisites for the “female egg recognition” hypothesis are fulfilled. In this context practicability and feasibility of the hypothesis and alternative explanations are discussed. However future work is necessary to determine a direct effect on offspring condition.
creator: Miroslav Poláček
creator: Michaela Bartíková
creator: Herbert Hoi
uri: https://doi.org/10.7717/peerj.3707
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Poláček et al.

title: Fourteen new species of Oecetis McLachlan, 1877 (Trichoptera: Leptoceridae) from the Neotropical region
link: https://peerj.com/articles/3753
last-modified: 2017-08-30
description: BackgroundThe caddisfly genus Oecetis currently contains 534 valid species. Its larval stages are found in freshwaters around the world. The adults can be distinguished from other Leptoceridae by the unbranched forewing M vein and the exceptionally long maxillary palps. In the Neotropical region, 55 species of Oecetis have been recorded and most of them can be placed in one of the six species groups known from this biogeographical region: the avara-, falicia-, inconspicua-, punctata-, punctipennis-, and testacea-groups. More than 50% of the known diversity of Neotropical Oecetis has been described in the past 40 years. Here, we describe an additional 14 new species of Oecetis to further document the diversity of this genus in the Neotropical region.MethodsThe descriptions and illustrations presented here are based on male specimens. Specimens were collected with Malaise traps or ultraviolet light traps. They were preserved in alcohol or pinned as stated in material examined section. Specimens had their genitalia prepared in 85% lactic acid to better observe internal characters and illustrations were aided by the use of a microscope with drawing tube attached.Results and DiscussionThis study raises the number of species of Oecetis in the Neotropics from 55 to 69. Eight of the new species presented here could not be reliably placed in one of the known species groups (Oecetis acuticlasper n. sp., Oecetis flinti n. sp., Oecetis carinata n. sp., Oecetis cassicoleata n. sp., Oecetis blahniki n. sp., Oecetis gibbosa n. sp., Oecetis licina n. sp., and Oecetis pertica n. sp.). The others are placed in the punctata-group (Oecetis bidigitata n. sp., Oecetis quasipunctata n. sp.), testacea-group (Oecetis plenuspinosa n. sp.), and falicia-group (Oecetis calori n. sp., Oecetis hastapulla n. sp., Oecetis machaera n. sp.). Most of the diagnostic characters rely on structures of the inferior appendages and phallic apparatus, and the shape of tergum X.
creator: Fabio B. Quinteiro
creator: Ralph W. Holzenthal
uri: https://doi.org/10.7717/peerj.3753
license: http://creativecommons.org/licenses/by/4.0/
rights: © 2017 Quinteiro and Holzenthal

title: The jaw is a second-class lever in Pedetes capensis (Rodentia: Pedetidae)
link: https://peerj.com/articles/3741
last-modified: 2017-08-30
description: The mammalian jaw is often modelled as a third-class lever for the purposes of biomechanical analyses, owing to the position of the resultant muscle force between the jaw joint and the teeth. However, it has been proposed that in some rodents the jaws operate as a second-class lever during distal molar bites, owing to the rostral position of the masticatory musculature. In particular, the infraorbital portion of the zygomatico-mandibularis (IOZM) has been suggested to be of major importance in converting the masticatory system from a third-class to a second-class lever. The presence of the IOZM is diagnostic of the hystricomorph rodents, and is particularly well-developed in Pedetes capensis, the South African springhare. In this study, finite element analysis (FEA) was used to assess the lever mechanics of the springhare masticatory system, and to determine the function of the IOZM. An FE model of the skull of P. capensis was constructed and loaded with all masticatory muscles, and then solved for biting at each tooth in turn. Further load cases were created in which each masticatory muscle was removed in turn. The analyses showed that the mechanical advantage of the springhare jaws was above one at all molar bites and very close to one during the premolar bite. Removing the IOZM or masseter caused a drop in mechanical advantage at all bites, but affected strain patterns and cranial deformation very little. Removing the ZM had only a small effect on mechanical advantage, but produced a substantial reduction in strain and deformation across the skull. It was concluded that the masticatory system of P. capensis acts as a second class lever during bites along almost the entire cheek tooth row. The IOZM is clearly a major contributor to this effect, but the masseter also has a part to play. The benefit of the IOZM is that it adds force without substantially contributing to strain or deformation of the skull. This may help explain why the hystricomorphous morphology has evolved multiple times independently within Rodentia.
creator: Philip G. Cox
uri: https://doi.org/10.7717/peerj.3741
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2017 Cox