title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1386 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Noblella thiuni sp. n., a new (singleton) species of minute terrestrial-breeding frog (Amphibia, Anura, Strabomantidae) from the montane forest of the Amazonian Andes of Puno, Peru link: https://peerj.com/articles/6780 last-modified: 2019-04-23 description: We describe a new species of minute, terrestrial-breeding frog in the genus Noblella. We collected a single specimen in the leaf litter of primary montane forest (2,225 m a.s.l.) near Thiuni, in the Provice of Carabaya, Department of Puno, in the upper watershed of a tributary of the Inambari River of southern Peru, the same locality where we found the types of Psychrophrynella glauca Catenazzi & Ttito 2018. We placed the new species within Noblella on the basis of molecular data, minute size, and overall morphological resemblance with the type species N. peruviana and other species of Noblella, including having three phalanges on finger IV (as in N. coloma, N. heyeri, N. lynchi, N. madreselva, N. peruviana, and N. pygmaea), and terminal phalanges T-shaped and pointed. Noblella thiuni sp. n. is distinguished from all other species of Noblella by having ventral surfaces of legs bright red, and chest and belly copper reddish with a profusion of silvery spots. The new species further differs from known Peruvian species of Noblella by the combination of the following characters: tympanic membrane absent, eyelids lacking tubercles, dorsal skin finely shagreen, tarsal tubercles or folds absent, three phalanges on Finger IV, tips of digits not expanded, no circumferential grooves on digits, inguinal spots present. The new species has a snout–vent length of 11.0 mm in one adult or subadult male. Our new finding confirms the high levels of endemism and beta diversity of small, terrestrial-breeding frogs inhabiting the moss layers and leaf litter in the montane forests of the Amazonian slopes of the Andes and adjacent moist puna grasslands, and suggests much work remains to be done to properly document this diversity. creator: Alessandro Catenazzi creator: Alex Ttito uri: https://doi.org/10.7717/peerj.6780 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Catenazzi and Ttito title: A network approach to identify bioregions in the distribution of Mediterranean amphipods associated with Posidonia oceanica meadows link: https://peerj.com/articles/6786 last-modified: 2019-04-23 description: Although amphipods are key components of the macro-fauna associated with Posidonia oceanica meadows, to date no studies focused on the structure and diversity of their assemblages across the whole Mediterranean Sea. Here, we applied a network approach based on modularity on a dataset mined from literature to identify biogeographic modules and to assess the biogeographic roles of associated localities. We also correlated the patterns evidenced with the biogeographic distribution of amphipod groups by means of a multivariate analysis. Modularity analysis highlighted four biogeographic modules bounded by the main Mediterranean biogeographic divides and evidenced a decrease in species diversity along a NW-SE gradient. Assemblages associated with Central-Western Mediterranean and, to a lesser extent, Tunisian modules showed the highest species richness and were identified as hubs, characterized by species with regional distributions that behave as source in a biogeographic context. The paleogeographic history of the host seagrass and the ecology of associated amphipods, both suggest the joint effect of species persistence and post-Last Glacial Maximum expansion in explaining the pattern of amphipod distribution in the Mediterranean Sea. creator: Bruno Bellisario creator: Federica Camisa creator: Chiara Abbattista creator: Roberta Cimmaruta uri: https://doi.org/10.7717/peerj.6786 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bellisario et al. title: Gastrocnemius fascicles are shorter and more pennate throughout the first month following acute Achilles tendon rupture link: https://peerj.com/articles/6788 last-modified: 2019-04-23 description: The purpose of this study was to characterize the short-term effects of Achilles tendon ruptures on medial gastrocnemius. We hypothesized that the fascicles of the medial gastrocnemius muscle of the injured Achilles tendon would be shorter and more pennate immediately following the injury and would persist throughout 4 weeks post-injury. B-mode longitudinal ultrasound images of the medial gastrocnemius were acquired in 10 adults who suffered acute Achilles tendon ruptures and were treated non-operatively. Ultrasound images were acquired during the initial clinical visit following injury as well as 2 and 4 weeks following this initial clinical visit. Resting muscle structure was characterized by measuring fascicle length, pennation angle, muscle thickness, and muscle echo intensity in both the injured and contralateral (control) limbs. Fascicle length was 15% shorter (P < 0.001) and pennation angle was 21% greater (P < 0.001) in the injured muscle compared to the uninjured (control) muscle at the presentation of injury (week 0). These differences in fascicle length persisted through 4 weeks after injury (P < 0.002) and pennation angle returned to pre-injury levels. Muscle thickness changes were not detected at any of the post-injury visits (difference < 4%, P > 0.026). Echo intensity of the injured limb was 8% lower at the presentation of the injury but was not different compared to the contralateral muscle at 2 and 4 weeks post-injury. Our results suggest that Achilles tendon ruptures elicit rapid changes in the configuration of the medial gastrocnemius, which may explain long-term functional deficits. creator: Todd J. Hullfish creator: Kathryn M. O’Connor creator: Josh R. Baxter uri: https://doi.org/10.7717/peerj.6788 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hullfish et al. title: The effect of pharmacological inhibition of Serine Proteases on neuronal networks in vitro link: https://peerj.com/articles/6796 last-modified: 2019-04-23 description: Neurons are embedded in an extracellular matrix (ECM), which functions both as a scaffold and as a regulator of neuronal function. The ECM is in turn dynamically altered through the action of serine proteases, which break down its constituents. This pathway has been implicated in the regulation of synaptic plasticity and of neuronal intrinsic excitability. In this study, we determined the short-term effects of interfering with proteolytic processes in the ECM, with a newly developed serine protease inhibitor. We monitored the spontaneous electrophysiological activity of in vitro primary rat cortical cultures, using microelectrode arrays. While pharmacological inhibition at a low dosage had no significant effect, at elevated concentrations it altered significantly network synchronization and functional connectivity but left unaltered single-cell electrical properties. These results suggest that serine protease inhibition affects synaptic properties, likely through its actions on the ECM. creator: Sebastiaan Van De Vijver creator: Stephan Missault creator: Jeroen Van Soom creator: Pieter Van Der Veken creator: Koen Augustyns creator: Jurgen Joossens creator: Stefanie Dedeurwaerdere creator: Michele Giugliano uri: https://doi.org/10.7717/peerj.6796 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Van De Vijver et al. title: CYP2C11 played a significant role in down-regulating rat blood pressure under the challenge of a high-salt diet link: https://peerj.com/articles/6807 last-modified: 2019-04-23 description: BackgroundArachidonic acid (AA) is oxidized by cytochrome P450s (CYPs) to form epoxyeicosatrienoic acids (EETs), compounds that modulate ion transport, gene expression, and vasorelaxation. Both CYP2Cs and CYP2Js are involved in kidney EET epoxidation.MethodsIn this study, we used a CYP2C11-null rat model to explore the in vivo effects of CYP2C11 on vasorelaxation. For 2 months, CYP2C11-null and wild-type (WT) Sprague-Dawley rats were either fed normal lab (0.3% (w/w) sodium chloride) or high-salt (8% (w/w) sodium chloride) diets. Subsequently, an invasive method was used to determine blood pressure. Next, western blots, quantitative PCR, and immunohistochemistry were used to determine renal expression of CYPs involved in AA metabolism.ResultsAmong CYP2C11-null rats, a high-salt diet (females: 156.79 ± 15.89 mm Hg, males: 130.25 ± 16.76 mm Hg, n = 10) resulted in significantly higher blood pressure than a normal diet (females: 118.05 ± 8.43 mm Hg, P < 0.01; males: 115.15 ± 11.45 mm Hg, P < 0.05, n = 10). Compared with WT rats under the high-salt diet, western blots showed that CYP2C11-null rats had higher renal expression of CYP2J2 and CYP4A. This was consistent with the results of immunohistochemistry and the qPCR, respectively. The two rat strains did not differ in the renal expression of CYP2C23 or CYP2C24.ConclusionOur findings suggested that CYP2C11 plays an important role in lowering blood pressure under the challenge of a high-salt diet. creator: Wei Liu creator: Danjuan Sui creator: Huanying Ye creator: Zhen Ouyang creator: Yuan Wei uri: https://doi.org/10.7717/peerj.6807 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Identification of a putative competitive endogenous RNA network for lung adenocarcinoma using TCGA datasets link: https://peerj.com/articles/6809 last-modified: 2019-04-23 description: The mechanisms underlying the oncogenesis and progression of lung adenocarcinoma (LUAD) are currently unclear. The discovery of competitive endogenous RNA (ceRNA) regulatory networks has provided a new direction for the treatment and prognosis of patients with LUAD. However, the mechanism of action of ceRNA in LUAD remains elusive. In the present study, differentially expressed mRNAs, microRNAs (miRs) and long non-coding RNAs from the cancer genome atlas database were screened. CeRNAs for LUAD were then identified using online prediction software. Among the ceRNAs identified, family with sequence similarity 83 member A (FAM83A), miR-34c-5p, KCNQ1OT1 and FLJ26245 were observed to be significantly associated with the overall survival of patients with LUAD. Of note, FAM83A has potential significance in drug resistance, and may present a candidate biomarker for the prognosis and treatment of patients with LUAD. creator: Yuanyong Wang creator: Tong Lu creator: Yang Wo creator: Xiao Sun creator: Shicheng Li creator: Shuncheng Miao creator: Yanting Dong creator: Xiaoliang Leng creator: Wenjie Jiao uri: https://doi.org/10.7717/peerj.6809 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Identification of optimal endogenous reference RNAs for RT-qPCR normalization in hindgut of rat models with anorectal malformations link: https://peerj.com/articles/6829 last-modified: 2019-04-23 description: BackgroundQuantitative real-time polymerase chain reaction (RT-qPCR) is a sensitive method for quantifying mRNA abundance. With relative expression analysis, however, reliable data output is dependent on stably expressed reference genes across the samples being studied. In anorectal malformations (ARMs), there is limited data on the selection of appropriate reference genes.PurposeThis study was aimed to investigate the optimal reference genes for PCR in ARM rat models.MethodsWe selected 15 commonly used reference genes (Rps18, Actb, B2m, Gapdh, Ppia, Hprt1, Pgk1, Ywhaz, Tbp, Ubc, Rps16, Rpl13a, Rplp1, Sdha, and Hmbs) as candidate reference genes and detected their mRNA expression in ARM samples by RT-qPCR. The expression stability and variability of these transcripts were subsequently evaluated using four methods (geNorm, NormFinder, comparative ΔCt, and BestKeeper).ResultsThe abundance of the candidate reference genes was qualified by RT-qPCR and the cycle threshold (Ct) values ranged between 14.07 (Rplp1) and 21.89 (Sdha). In the overall candidate genes, different variations existed across the different algorithms. A comprehensive analysis revealed that Rpl13a ranked first among the relatively stable genes, followed by Ywhaz, Rps18, Sdha, and Hmbs.ConclusionsThe most stable reference genes for RT-qPCR were Rpl13a, Ywhaz, and Rps18 in ETU-induced ARMs in rat fetus. This study provided a foundation for reference gene selection for future gene expression analyses. creator: Caiyun Long creator: Yunxia Xiao creator: Siying Li creator: Xiaobing Tang creator: Zhengwei Yuan creator: Yuzuo Bai uri: https://doi.org/10.7717/peerj.6829 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Long et al. title: Next-generation sequencing of BRCA1 and BRCA2 genes for rapid detection of germline mutations in hereditary breast/ovarian cancer link: https://peerj.com/articles/6661 last-modified: 2019-04-22 description: BackgroundConventional methods used to identify BRCA1 and BRCA2 germline mutations in hereditary cancers, such as Sanger sequencing/multiplex ligation-dependent probe amplification (MLPA), are time-consuming and expensive, due to the large size of the genes. The recent introduction of next-generation sequencing (NGS) benchtop platforms offered a powerful alternative for mutation detection, dramatically improving the speed and the efficiency of DNA testing. Here we tested the performance of the Ion Torrent PGM platform with the Ion AmpliSeq BRCA1 and BRCA2 Panel in our clinical routine of breast/ovarian hereditary cancer syndrome assessment.MethodsWe first tested the NGS approach in a cohort of 11 patients (training set) who had previously undergone genetic diagnosis in our laboratory by conventional methods. Then, we applied the optimized pipeline to the consecutive cohort of 136 uncharacterized probands (validation set).ResultsBy minimal adjustments in the analytical pipeline of Torrent Suite Software we obtained a 100% concordance with Sanger results regarding the identification of single nucleotide alterations, insertions, and deletions with the exception of three large genomic rearrangements (LGRs) contained in the training set. The optimized pipeline applied to the validation set (VS), identified pathogenic and polymorphic variants, including a novel BRCA2 pathogenic variant at exon 3, 100% of which were confirmed by Sanger in their correct zygosity status. To identify LGRs, all negative samples of the VS were subjected to MLPA analysis.DiscussionOur experience strongly supports that the Ion Torrent PGM technology in BRCA1 and BRCA2 germline variant identification, combined with MLPA analysis, is highly sensitive, easy to use, faster, and cheaper than traditional (Sanger sequencing/MLPA) approaches. creator: Arianna Nicolussi creator: Francesca Belardinilli creator: Yasaman Mahdavian creator: Valeria Colicchia creator: Sonia D’Inzeo creator: Marialaura Petroni creator: Massimo Zani creator: Sergio Ferraro creator: Virginia Valentini creator: Laura Ottini creator: Giuseppe Giannini creator: Carlo Capalbo creator: Anna Coppa uri: https://doi.org/10.7717/peerj.6661 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Nicolussi et al. title: MicroRNA profiling of mouse liver in response to DENV-1 infection by deep sequencing link: https://peerj.com/articles/6697 last-modified: 2019-04-22 description: BackgroundDengue caused by dengue virus (DENV) serotypes −1 to −4 is the most important mosquito-borne viral disease in the tropical and sub-tropical countries worldwide. Yet many of the pathophysiological mechanisms of host responses during DENV infection remain largely unknown and incompletely understood.MethodsUsing a mouse model, the miRNA expressions in liver during DENV-1 infection was investigated using high throughput miRNA sequencing. The differential expressions of miRNAs were then validated by qPCR, followed by target genes prediction. The identified miRNA targets were subjected to gene ontology (GO) annotation and pathway enrichment analysis to elucidate the potential biological pathways and molecular mechanisms associated with DENV-1 infection.ResultsA total of 224 and 372 miRNAs out of 433 known mouse miRNAs were detected in the livers of DENV-1-infected and uninfected mice, respectively; of these, 207 miRNAs were present in both libraries. The miR-148a-3p and miR-122-5p were the two most abundant miRNAs in both groups. Thirty-one miRNAs were found to have at least 2-fold change in upregulation or downregulation, in which seven miRNAs were upregulated and 24 miRNAs were downregulated in the DENV-1-infected mouse livers. The miR-1a-3p was found to be the most downregulated miRNA in the DENV-1-infected mouse livers, with a significant fold change of 0.10. To validate the miRNA sequencing result, the expression pattern of 12 miRNAs, which were highly differentially expressed or most abundant, were assessed by qPCR and nine of them correlated positively with the one observed in deep sequencing. In silico functional analysis revealed that the adaptive immune responses involving TGF-beta, MAPK, PI3K-Akt, Rap1, Wnt and Ras signalling pathways were modulated collectively by 23 highly differentially expressed miRNAs during DENV-1 infection.ConclusionThis study provides the first insight into the global miRNA expressions of mouse livers in response to DENV-1 infection in vivo and the possible roles of miRNAs in modulating the adaptive immune responses during DENV-1 infection. creator: Lian Yih Pong creator: Sinikka Parkkinen creator: Amreeta Dhanoa creator: Han Ming Gan creator: Indeevari Abisheka Chiharu Wickremesinghe creator: Sharifah Syed Hassan uri: https://doi.org/10.7717/peerj.6697 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pong et al. title: Integrated analysis of two-lncRNA signature as a potential prognostic biomarker in cervical cancer: a study based on public database link: https://peerj.com/articles/6761 last-modified: 2019-04-22 description: BackgroundCervical cancer (CC) is a common gynecological malignancy in women worldwide. Evidence suggests that long non-coding RNAs (lncRNAs) can be used as biomarkers in patients with CC. However, prognostic biomarkers for CC are still lacking. The aim of our study was to find lncRNA biomarkers which are able to predict prognosis in CC based on the data from The Cancer Genome Atlas (TCGA).MethodsThe patients were divided into three groups according to FIGO stage. Differentially expressed lncRNAs were identified in CC tissue compared to adjacent normal tissues based on a fold change >2 and <0.5 at P < 0.05 for up- and downregulated lncRNA, respectively. The relationship between survival outcome and lncRNA expression was assessed with univariate and multivariate Cox proportional hazards regression analysis. We constructed a risk score as a method to evaluate prognosis. We used receiver operating characteristic (ROC) curve and the area under curve (AUC) analyses to assess the diagnostic value of a two-lncRNA signature. We detected the expression levels of the two lncRNAs in 31 pairs of newly diagnosed CC specimens and paired adjacent non-cancerous tissue specimens, and also in CC cell lines. Finally, the results were statistically compared using t-tests.ResultsIn total, 289 RNA sequencing profiles and accompanying clinical data were obtained. We identified 49 differentially expressed lncRNAs, of which two related to overall survival (OS) in CC patients. These two lncRNAs (ILF3-AS1 and RASA4CP) were found together as a single prognostic signature. Meanwhile, the prognosis of patients with low-risk CC was better and positively correlated with OS (P < 0.001). Further analysis showed that the combined two-lncRNA expression signature could be used as an independent biomarker to evaluate the prognosis in CC. qRT-PCR results were consistent with TCGA, confirming downregulated expression of both lncRNAs. Furthermore, upon ROC curve analysis, the AUC of the combined lncRNAs was greater than that of the single lncRNAs alone (0.723 vs 0.704 and 0.685), respectively; P < 0.05.ConclusionsOur study showed that the two-lncRNA signature of ILF3-AS1 and RASA4CP can be used as an independent biomarker for the prognosis of CC, based on bioinformatic analysis. creator: Wenjuan Wu creator: Jing Sui creator: Tong Liu creator: Sheng Yang creator: Siyi Xu creator: Man Zhang creator: Shaoping Huang creator: Lihong Yin creator: Yuepu Pu creator: Geyu Liang uri: https://doi.org/10.7717/peerj.6761 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wu et al.