title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=1813
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Temporal dynamics of the developing lung transcriptome in three common inbred strains of laboratory mice reveals multiple stages of postnatal alveolar development
link: https://peerj.com/articles/2318
last-modified: 2016-08-09
description: To characterize temporal patterns of transcriptional activity during normal lung development, we generated genome wide gene expression data for 26 pre- and post-natal time points in three common inbred strains of laboratory mice (C57BL/6J, A/J, and C3H/HeJ). Using Principal Component Analysis and least squares regression modeling, we identified both strain-independent and strain-dependent patterns of gene expression. The 4,683 genes contributing to the strain-independent expression patterns were used to define a murine Developing Lung Characteristic Subtranscriptome (mDLCS). Regression modeling of the Principal Components supported the four canonical stages of mammalian embryonic lung development (embryonic, pseudoglandular, canalicular, saccular) defined previously by morphology and histology. For postnatal alveolar development, the regression model was consistent with four stages of alveolarization characterized by episodic transcriptional activity of genes related to pulmonary vascularization. Genes expressed in a strain-dependent manner were enriched for annotations related to neurogenesis, extracellular matrix organization, and Wnt signaling. Finally, a comparison of mouse and human transcriptomics from pre-natal stages of lung development revealed conservation of pathways associated with cell cycle, axon guidance, immune function, and metabolism as well as organism-specific expression of genes associated with extracellular matrix organization and protein modification. The mouse lung development transcriptome data generated for this study serves as a unique reference set to identify genes and pathways essential for normal mammalian lung development and for investigations into the developmental origins of respiratory disease and cancer. The gene expression data are available from the Gene Expression Omnibus (GEO) archive (GSE74243). Temporal expression patterns of mouse genes can be investigated using a study specific web resource (http://lungdevelopment.jax.org).
creator: Kyle J. Beauchemin
creator: Julie M. Wells
creator: Alvin T. Kho
creator: Vivek M. Philip
creator: Daniela Kamir
creator: Isaac S. Kohane
creator: Joel H. Graber
creator: Carol J. Bult
uri: https://doi.org/10.7717/peerj.2318
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Beauchemin et al.

title: An optimized approach to germ-free rearing in the jewel wasp Nasonia
link: https://peerj.com/articles/2316
last-modified: 2016-08-09
description: Development of a Nasonia in vitrogerm-free rearing system in 2012 enabled investigation of Nasonia-microbiota interactions and real-time visualization of parasitoid metamorphosis. However, the use of antibiotics, bleach, and fetal bovine serum introduced artifacts relative to conventional rearing of Nasonia. Here, we optimize the germ-free rearing procedure by using filter sterilization in lieu of antibiotics and by removing residual bleach and fetal bovine serum. Comparison of these methods reveals no influence on larval survival or growth, and a 52% improvement in adult production. Additionally, adult males produced in the new germ-free system are similar in size to conventionally reared males. Experimental implications of these changes are discussed.
creator: J. Dylan Shropshire
creator: Edward J. van Opstal
creator: Seth R. Bordenstein
uri: https://doi.org/10.7717/peerj.2316
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Shropshire et al.

title: An investigation into the bilateral functional differences of the lower limb muscles in standing and walking
link: https://peerj.com/articles/2315
last-modified: 2016-08-09
description: To date, most studies use surface electromyographic (sEMG) signals as the control source on active rehabilitation robots, and unilateral data are collected based on the gait symmetry hypothesis, which has caused much controversy. The purpose of this study is to quantitatively evaluate the sEMG activity asymmetry of bilateral muscles in lower extremities during functional tasks. Nine participants were instructed to perform static and dynamic steady state tests. sEMG signals from the tibialis anterior, soleus, medial gastrocnemius and lateral gastrocnemius muscles of bilateral lower extremities were recorded in the experiments. Muscle activities are quantified in terms of sEMG amplitude. We investigated whether characteristics of left limb and the one of the right limb have the same statistical characteristics during functional tasks using The Wilcoxon rank-sum test, and studied dynamic signal irregularity degree for sEMG activities via sample entropy. The total of muscle activities showed significant differences between left limb and right limb during the static steady state (p = 0.000). For dynamic steady states, there were significant differences for most muscle activities between left limb and right limb at different speeds (p = 0.000). Nevertheless, there was no difference between the lateral gastrocnemius for bilateral limb at 2.0 kilometers per hour (p = 0.060). For medial gastrocnemius, differences were not found between left limb and right limb at 1.0 and 3.0 kilometers per hours (p = 0.390 and p = 0.085, respectively). Similarly, there was no difference for soleus at 3.0 kilometers per hour (p = 0.115). The importance of the differences in muscle activities between left limb and right limb were found. These results can potentially be used for evaluating lower limb extremity function of special populations (elderly people or stroke patients) in an objective and simple method.
creator: Shengyun Liang
creator: Jiali Xu
creator: Lei wang
creator: Guoru Zhao
uri: https://doi.org/10.7717/peerj.2315
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Liang et al.

title: The core clock gene Per1 phases molecular and electrical circadian rhythms in SCN neurons
link: https://peerj.com/articles/2297
last-modified: 2016-08-09
description: The brain’s biological clock, the suprachiasmatic nucleus (SCN), exhibits endogenous 24-hour rhythms in gene expression and spontaneous firing rate; however, the functional relationship between these neuronal rhythms is not fully understood. Here, we used a Per1::GFP transgenic mouse line that allows for the simultaneous quantification of molecular clock state and firing rate in SCN neurons to examine the relationship between these key components of the circadian clock. We find that there is a stable, phased relationship between E-box-driven clock gene expression and spontaneous firing rate in SCN neurons and that these relationships are independent of light input onto the system or of GABAA receptor-mediated synaptic activity. Importantly, the concordant phasing of gene and neural rhythms is disrupted in the absence of the homologous clock gene Per1, but persists in the absence of the core clock gene Per2. These results suggest that Per1 plays a unique, non-redundant role in phasing gene expression and firing rate rhythms in SCN neurons to increase the robustness of cellular timekeeping.
creator: Jeff R. Jones
creator: Douglas G. McMahon
uri: https://doi.org/10.7717/peerj.2297
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Jones and McMahon

title: A comparison of blood gases, biochemistry, and hematology to ecomorphology in a health assessment of pinfish (Lagodon rhomboides)
link: https://peerj.com/articles/2262
last-modified: 2016-08-09
description: Despite the promise of hematological parameters and blood chemistry in monitoring the health of marine fishes, baseline data is often lacking for small fishes that comprise central roles in marine food webs. This study establishes blood chemistry and hematological baseline parameters for the pinfish Lagodon rhomboides, a small marine teleost that is among the most dominant members of near-shore estuarine communities of the Atlantic Ocean and Gulf of Mexico. Given their prominence, pinfishes are an ideal candidate species to use as a model for monitoring changes across a wide range of near-shore marine communities. However, pinfishes exhibit substantial morphological differences associated with a preference for feeding in primarily sea-grass or sand dominated habitats, suggesting that differences in the foraging ecology of individuals could confound health assessments. Here we collect baseline data on the blood physiology of pinfish while assessing the relationship between blood parameters and measured aspects of feeding morphology using data collected from 37 individual fish. Our findings provide new baseline health data for this important near shore fish species and find no evidence for a strong linkage between blood physiology and either sex or measured aspects of feeding morphology. Comparing our hematological and biochemical data to published results from other marine teleost species suggests that analyses of trends in blood value variation correlated with major evolutionary transitions in ecology will shed new light on the physiological changes that underlie the successful diversification of fishes.
creator: Sara Collins
creator: Alex Dornburg
creator: Joseph M. Flores
creator: Daniel S. Dombrowski
creator: Gregory A. Lewbart
uri: https://doi.org/10.7717/peerj.2262
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Collins et al.

title: Systematic relationships of five newly sequenced cervid species
link: https://peerj.com/articles/2307
last-modified: 2016-08-04
description: Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.
creator: Nicola S. Heckeberg
creator: Dirk Erpenbeck
creator: Gert Wörheide
creator: Gertrud E. Rössner
uri: https://doi.org/10.7717/peerj.2307
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Heckeberg et al.

title: Short-term exposure to predation affects body elemental composition, climbing speed and survival ability in Drosophila melanogaster
link: https://peerj.com/articles/2314
last-modified: 2016-08-04
description: Factors such as temperature, habitat, larval density, food availability and food quality substantially affect organismal development. In addition, risk of predation has a complex impact on the behavioural and morphological life history responses of prey. Responses to predation risk seem to be mediated by physiological stress, which is an adaptation for maintaining homeostasis and improving survivorship during life-threatening situations. We tested whether predator exposure during the larval phase of development has any influence on body elemental composition, energy reserves, body size, climbing speed and survival ability of adult Drosophila melanogaster. Fruit fly larvae were exposed to predation by jumping spiders (Phidippus apacheanus), and the percentage of carbon (C) and nitrogen (N) content, extracted lipids, escape response and survival were measured from predator-exposed and control adult flies. The results revealed predation as an important determinant of adult phenotype formation and survival ability. D. melanogaster reared together with spiders had a higher concentration of body N (but equal body C), a lower body mass and lipid reserves, a higher climbing speed and improved adult survival ability. The results suggest that the potential of predators to affect the development and the adult phenotype of D. melanogaster is high enough to use predators as a more natural stimulus in laboratory experiments when testing, for example, fruit fly memory and learning ability, or when comparing natural populations living under different predation pressures.
creator: Indrikis Krams
creator: Sarah Eichler Inwood
creator: Giedrius Trakimas
creator: Ronalds Krams
creator: Gordon M. Burghardt
creator: David M. Butler
creator: Severi Luoto
creator: Tatjana Krama
uri: https://doi.org/10.7717/peerj.2314
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Krams et al.

title: Familiar face + novel face = familiar face? Representational bias in the perception of morphed faces in chimpanzees
link: https://peerj.com/articles/2304
last-modified: 2016-08-04
description: Highly social animals possess a well-developed ability to distinguish the faces of familiar from novel conspecifics to induce distinct behaviors for maintaining society. However, the behaviors of animals when they encounter ambiguous faces of familiar yet novel conspecifics, e.g., strangers with faces resembling known individuals, have not been well characterised. Using a morphing technique and preferential-looking paradigm, we address this question via the chimpanzee’s facial–recognition abilities. We presented eight subjects with three types of stimuli: (1) familiar faces, (2) novel faces and (3) intermediate morphed faces that were 50% familiar and 50% novel faces of conspecifics. We found that chimpanzees spent more time looking at novel faces and scanned novel faces more extensively than familiar or intermediate faces. Interestingly, chimpanzees looked at intermediate faces in a manner similar to familiar faces with regards to the fixation duration, fixation count, and saccade length for facial scanning, even though the participant was encountering the intermediate faces for the first time. We excluded the possibility that subjects merely detected and avoided traces of morphing in the intermediate faces. These findings suggest a bias for a feeling-of-familiarity that chimpanzees perceive familiarity with an intermediate face by detecting traces of a known individual, as 50% alternation is sufficient to perceive familiarity.
creator: Yoshi-Taka Matsuda
creator: Masako Myowa-Yamakoshi
creator: Satoshi Hirata
uri: https://doi.org/10.7717/peerj.2304
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Matsuda et al.

title: Novel fermented chickpea milk with enhanced level of γ-aminobutyric acid and neuroprotective effect on PC12 cells
link: https://peerj.com/articles/2292
last-modified: 2016-08-04
description: In this study, novel fermented chickpea milk with high γ -aminobutyric acid (GABA) content and potential neuroprotective activity was developed. Fermentation starter that can produce GABA was selected from 377 strains of lactic acid bacteria isolated from traditional Chinese fermented foods. Among the screened strains, strain M-6 showed the highest GABA-producing capacity in De Man–Rogosa and Sharp (MRS) broth and chickpea milk. M-6 was identified as Lactobacillus plantarum based on Gram staining, API carbohydrate fermentation pattern testing, and 16s rDNA sequencing. The complete gene encoding glutamate decarboxylase was cloned to confirm the presence of the gene in L. plantarum M-6. The fermentation condition was optimized by response surface methodology. Results demonstrated that L. plantarum M-6 produced the highest GABA content of 537.23 mg/L. The optimal condition included an inoculum concentration of 7%, presence of 0.2% (m/v) monosodium glutamate and 55 µ M pyridoxal-5-phosphate, incubation temperature of 39 °C and fermentation time of 48 h . GABA-enriched chickpea milk exerted protective effects on PC12 cells against MnCl2 -induced injury. GABA-enriched chickpea milk improved cell viability and markedly attenuated the release of lactate dehydrogenase compared with the impaired cells.
creator: Wen Li
creator: Mingming Wei
creator: Junjun Wu
creator: Xin Rui
creator: Mingsheng Dong
uri: https://doi.org/10.7717/peerj.2292
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Li et al.

title: Use of the melting curve assay as a means for high-throughput quantification of Illumina sequencing libraries
link: https://peerj.com/articles/2281
last-modified: 2016-08-04
description: Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to issues of cost and/or processing time.Methods. An inexpensive and high-throughput library quantification method has been developed, based on an adaptation of the melting curve assay. Sequencing libraries were subjected to the assay using the Bio-Rad Laboratories CFX ConnectTM Real-Time PCR Detection System. The library quantity was calculated through summation of reduction of relative fluorescence units between 86 and 95 °C.Results.PCR-enriched sequencing libraries are suitable for this quantification without pre-purification of DNA. Short DNA molecules, which ideally should be eliminated from the library for subsequent processing, were differentiated from the target DNA in a mixture on the basis of differences in melting temperature. Quantification results for long sequences targeted using the melting curve assay were correlated with those from existing methods (R2 > 0.77), and that observed from MiSeq sequencing (R2 = 0.82).Discussion.The results of multiplexed sequencing suggested that the normalisation performance of the described method is equivalent to that of another recently reported high-throughput bead-based method, BeNUS. However, costs for the melting curve assay are considerably lower and processing times shorter than those of other existing methods, suggesting greater suitability for highly multiplexed sequencing applications.
creator: Hiroshi Shinozuka
creator: John W. Forster
uri: https://doi.org/10.7717/peerj.2281
license: http://creativecommons.org/licenses/by/4.0/
rights: ©2016 Shinozuka and Forster