title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1116 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice link: https://peerj.com/articles/9384 last-modified: 2020-06-17 description: Noise induced hearing loss (NIHL) is accompanied by a reduction of cochlear hair cells and spiral ganglion neurons. Different approaches have been applied to prevent noise induced apoptosis / necrosis. Physical intervention is one technique currently under investigation. Specific wavelengths within the near-infrared light (NIR)-spectrum are known to influence cytochrome-c-oxidase activity, which leads in turn to a decrease in apoptotic mechanisms. It has been shown recently that NIR can significantly decrease the cochlear hair cell loss if applied daily for 12 days after a noise exposure. However, it is still unclear if a single NIR-treatment, just before a noise exposure, could induce similar protective effects. Therefore, the present study was conducted to investigate the effect of a single NIR-pre-treatment aimed at preventing or limiting NIHL. The cochleae of adult NMRI-mice were pre-treated with NIR-light (808 nm, 120 mW) for 5, 10, 20, 30 or 40 minutes via the external ear canal. All animals were noised exposed immediately after the pre-treatment by broad band noise (5–20 kHz) for 30 minutes at 115 dB SPL. Frequency specific ABR-recordings to determine auditory threshold shift were carried out before the pre-treatment and two weeks after the noise exposure. The amplitude increase for wave IV and cochlear hair cell loss were determined. A further group of similar mice was noise exposed only and served as a control for the NIR pre-exposed groups. Two weeks after noise exposure, the ABR threshold shifts of NIR-treated animals were significantly lower (p < 0.05) than those of the control animals. The significance was at three frequencies for the 5-minute pre-treatment group and across the entire frequency range for all other treatment groups. Due to NIR light, the amplitude of wave four deteriorates significantly less after noise exposure than in controls. The NIR pre-treatment had no effect on the loss of outer hair cells, which was just as high with or without NIR-light pre-exposure. Relative to the entire number of outer hair cells across the whole cochlea, outer hair cell loss was rather negligible. No inner hair cell loss whatever was detected. Our results suggest that a single NIR pre-treatment induces a very effective protection of cochlear structures from noise exposure. Pre-exposure of 10 min seems to emerge as the optimal dosage for our experimental setup. A saturated effect occurred with higher dosage-treatments. These results are relevant for protection of residual hearing in otoneurosurgery such as cochlear implantation. creator: Dietmar Basta creator: Moritz Gröschel creator: Ira Strübing creator: Patrick Boyle creator: Felix Fröhlich creator: Arne Ernst creator: Rainer Seidl uri: https://doi.org/10.7717/peerj.9384 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Basta et al. title: Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses link: https://peerj.com/articles/9393 last-modified: 2020-06-17 description: Oral squamous cell carcinoma (OSCC) has always been one of the most aggressive and invasive cancers among oral and maxillofacial malignancies. As the morbidity and mortality of the disease have increased year by year, the search for a promising diagnostic and prognostic biomarker for the disease is becoming increasingly urgent. Tumorous and adjacent tissues were collected from three OSCC sufferers and we obtained 229 differentially expressed genes (DEGs) between tumor and normal tissues via high-throughput RNA sequence. Function and pathway enrichment analyses for DEGs were conducted to find a correlation between tumorigenesis status and DEGs. Protein interaction network and molecular complex detection (MCODE) were constructed to detect core modules. Two modules were enriched in MCODE. The diagnostic and prognostic values of the candidate genes were analyzed, which provided evidence for the candidate genes as new tumor markers. Small Proline Rich Protein 3 (SPRR3), a potential tumor marker that may be useful for the diagnosis of OSCC, was screened out. The survival analysis showed that SPRR3 under expression predicted the poor prognosis of OSCC patients. Further experiments have also shown that the expression of SPRR3 decreased as the malignancy of OSCC increased. Therefore, we believe that SPRR3 could be used as a novel diagnostic and prognostic tumor marker. creator: Lu Yu creator: Zongcheng Yang creator: Yingjiao Liu creator: Fen Liu creator: Wenjing Shang creator: Wei Shao creator: Yue Wang creator: Man Xu creator: Ya-nan Wang creator: Yue Fu creator: Xin Xu uri: https://doi.org/10.7717/peerj.9393 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2020 Yu et al. title: CRISPR 2 PCR and high resolution melting profiling for identification and characterization of clinically-relevant Salmonella enterica subsp. enterica link: https://peerj.com/articles/9113 last-modified: 2020-06-16 description: BackgroundNontyphoidal Salmonella spp. constitute a major bacterial cause of food poisoning. Each Salmonella serotype causes distinct virulence to humans.MethodA small cohort study was conducted to characterize several aspects of Salmonella isolates obtained from stool of diarrheal patients (n = 26) admitted to Phayao Ram Hospital, Phayao province, Thailand. A simple CRISPR 2 molecular analysis was developed to rapidly type Salmonella isolates employing both uniplex and high resolution melting (HRM) curve analysis.ResultsCRISPR 2 monoplex PCR generated a single Salmonella serotype-specific amplicon, showing S. 4,[5],12:i:- with highest frequency (42%), S. Enteritidis (15%) and S. Stanley (11%); S. Typhimurium was not detected. CRISPR 2 HRM-PCR allowed further classification of S. 4,[5],12:i:- isolates based on their specific CRISPR 2 signature sequences. The highest prevalence of Salmonella infection was during the summer season (April to August). Additional studies were conducted using standard multiplex HRM-PCR typing, which confirmed CRISPR 2 PCR results and, using a machine-learning algorithm, clustered the majority of Salmonella serotypes into six clades; repetitive element-based (ERIC) PCR, which clustered the serotypes into three clades only; antibiogram profiling, which revealed the majority resistant to ampicillin (69%); and test for extended spectrum β-lactamase production (two isolates) and PCR-based detection of bla alleles.ConclusionCRISPR 2 PCR provided a simple assay for detection and identification of clinically-relevant Salmonella serotypes. In conjunction with antibiogram profiling and rapid assay for β-lactamase producers, this approach should facilitate detection and appropriate treatment of Salmonellosis in a local hospital setting. In addition, CRISPR 2 HRM-PCR profiling enabled clustering of S. 4,[5],12:i:-isolates according to CRISPR 2 locus signature sequences, indicative of their different evolutionary trajectories, thereby providing a powerful tool for future epidemiological studies of virulent Salmonella serotypes. creator: Nuttachat Wisittipanit creator: Chaiwat Pulsrikarn creator: Sudarat Srisong creator: Rungthiwa Srimora creator: Nattinee Kittiwan creator: Kritchai Poonchareon uri: https://doi.org/10.7717/peerj.9113 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wisittipanit et al. title: Quality of life after hip fracture: a 12-month prospective study link: https://peerj.com/articles/9215 last-modified: 2020-06-16 description: BackgroundHip fracture is an important and frequent health problem worldwide. To date, there are still limited studies focused on the analysis of health-related quality of life (HRQOL) after a hip fracture in the Spanish population, especially with long-term follow-up.ObjectiveTo determine the HRQOL at 12 months after hip fracture and to identify potential factors associated with HRQOL.DesignProspective observational study.SettingTraumatology units of two university hospitals in province Cáceres (Spain).ParticipantsA total of 224 patients were admitted to the unit and required immediate surgery due to a hip fracture.MethodsHRQOL was measured with the EuroQol-5D questionnaire (EQ-5D) and the SF-12 Health Survey.ResultsScores from the visual analog scale EQ-5D decreased significantly (p < 0.001) from 72.8 at baseline to 48.3 after 1 month, to 48.2 after 6 months and to 46.1 after 12 months. The EQ-5D index score showed a similar significant reduction (p < 0.001) from 0.6 to 0.1, 0.3 and 0.3, respectively. Values of the physical component summary (PCS-12) significantly decreased (p < 0.001) from 38.6 at baseline to 31.0, 33.1 and 33.5. The mental component summary (MCS-12) decreased from 46.5 to 44.8 after 6 months (p = 0.022) and 44.3 after 12 months (p = 0.005). Factors potentially associated with HRQOL at 12 months after hip fracture were depression status after 12 months (B = 0–1.876; 95% CI [−2.409 to −1.343]; p < 0.001), functional ambulation classification after 12 months (B = −12.133; 95% CI [−17.970 to −6.297]; p < 0.001), EQ-5D VAS at baseline (B = 0.223; 95% CI [0.115–0.330]; p < 0.001), and age (B = −0.323; 95% CI [−0.594 to −0.053; p = 0.015).ConclusionsPatients experience a significant impairment in HRQOL H after a hip fracture, especially in self-care, pain/discomfort, usual activities, mobility and anxiety/depression. The decline in the HRQOL is effective the first month and lasts at least 12 months after the surgical intervention. creator: Francisco Javier Amarilla-Donoso creator: Raul Roncero-Martin creator: Jesus Maria Lavado-Garcia creator: Rosaura Toribio-Felipe creator: Jose Maria Moran-Garcia creator: Fidel Lopez-Espuela uri: https://doi.org/10.7717/peerj.9215 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Amarilla-Donoso et al. title: Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils link: https://peerj.com/articles/9220 last-modified: 2020-06-16 description: BackgroundVulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years.MethodsWe used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression.ResultsWefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program”, which is currently augmenting small, isolated populations. creator: Rebecca M. Gooley creator: Carolyn J. Hogg creator: Samantha Fox creator: David Pemberton creator: Katherine Belov creator: Catherine E. Grueber uri: https://doi.org/10.7717/peerj.9220 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Gooley et al. title: Combination of ferric ammonium citrate with cytokines involved in apoptosis and insulin secretion of human pancreatic beta cells related to diabetes in thalassemia link: https://peerj.com/articles/9298 last-modified: 2020-06-16 description: BackgroundDiabetes mellitus (DM) is a common complication found in β-thalassemia patients. The mechanism of DM in β-thalassemia patients is still unclear, but it could be from an iron overload and increase of some cytokines, such as interleukin1-β (IL-1β) and tumor necrosis factor-α (TNF-α). The objective of this study was to study the effect of interaction between ferric ammonium citrate (FAC) and cytokines, IL-1β and TNF-α, on 1.1B4 human pancreatic β-cell line.MethodsThe effect of the combination of FAC and cytokines on cell viability was studied by MTT assay. Insulin secretion was assessed by the enzyme-linked immunosorbent assay (ELISA). The reactive oxygen species (ROS) and cell apoptosis in normal and high glucose condition were determined by flow cytometer. In addition, gene expression of apoptosis, antioxidant; glutathione peroxidase 1 (GPX1) and superoxide dismutase 2 (SOD2), and insulin secretory function were studied by real-time polymerase chain reaction (Real-time PCR).ResultsThe findings revealed that FAC exposure resulted in the decrease of cell viability and insulin-release, and the induction of ROS and apoptosis in pancreatic cells. Interestingly, a combination of FAC and cytokines had an additive effect on SOD2 antioxidants’ genes expression and endoplasmic reticulum (ER) stress. In addition, it reduced the insulin secretion genes expression; insulin (INS), glucose kinase (GCK), protein convertase 1 (PSCK1), and protein convertase 2 (PSCK2). Moreover, the highest ROS and the lowest insulin secretion were found in FAC combined with IL-1β and TNF-α in the high-glucose condition of human pancreatic beta cell, which could be involved in the mechanism of DM development in β-thalassemia patients. creator: Patchara Rattanaporn creator: Sissades Tongsima creator: Thomas Mandrup-Poulsen creator: Saovaros Svasti creator: Dalina Tanyong uri: https://doi.org/10.7717/peerj.9298 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Rattanaporn et al. title: Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L. link: https://peerj.com/articles/9315 last-modified: 2020-06-16 description: Plastid genomes (plastomes) represent rich sources of information for phylogenomics, from higher-level studies to below the species level. The genus Rhus (sumac) has received a significant amount of study from phylogenetic and biogeographic perspectives, but genomic studies in this genus are lacking. Rhus integrifolia and R. ovata are two shrubby species of high ecological importance in the southwestern USA and Mexico, where they occupy coastal scrub and chaparral habitats. They hybridize frequently, representing a fascinating system in which to investigate the opposing effects of hybridization and divergent selection, yet are poorly characterized from a genomic perspective. In this study, complete plastid genomes were sequenced for one accession of R. integrifolia and one each of R. ovata from California and Arizona. Sequence variation among these three accessions was characterized, and PCR primers potentially useful in phylogeographic studies were designed. Phylogenomic analyses were conducted based on a robustly supported phylogenetic framework based on 52 complete plastomes across the order Sapindales. Repeat content, rather than the size of the inverted repeat, had a stronger relative association with total plastome length across Sapindales when analyzed with phylogenetic least squares regression. Variation at the inverted repeat boundary within Rhus was striking, resulting in major shifts and independent gene losses. Specifically, rps19 was lost independently in the R. integrifolia-ovata complex and in R. chinensis, with a further loss of rps22 and a major contraction of the inverted repeat in two accessions of the latter. Rhus represents a promising novel system to study plastome structural variation of photosynthetic angiosperms at and below the species level. creator: Craig F. Barrett uri: https://doi.org/10.7717/peerj.9315 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Barrett title: Keraphyton gen. nov., a new Late Devonian fern-like plant from Australia link: https://peerj.com/articles/9321 last-modified: 2020-06-16 description: The first plants related to the ferns are represented by several extinct groups that emerged during the Devonian. Among them, the iridopterids are closely allied to the sphenopsids, a group represented today by the genus Equisetum. They have been documented in Middle to early Late Devonian deposits of Laurussia and the Kazakhstan plate. Their Gondwanan record is poor, with occurrences limited to Venezuela and Morocco. Here we describe a new genus from a late Late Devonian locality of New South Wales. It is represented by a single anatomically preserved large stem characterized by a star-shaped vascular system with protoxylem strands located at rib tips, and by a lack of secondary tissues. Within the first fern-like plants, this stem shares the largest number of characters with iridopterid axes but differs by the pattern of its vascular system. Keraphyton mawsoniae gen. et sp. nov. adds a new record of early fern-like plants in eastern Gondwana. It provides new insights into the anatomical diversity within this key group of plants and supports the distinctiveness of the Australian flora in the latest Devonian. creator: Antoine Champreux creator: Brigitte Meyer-Berthaud creator: Anne-Laure Decombeix uri: https://doi.org/10.7717/peerj.9321 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Champreux et al. title: Reversal of glucocorticoid resistance in Acute Lymphoblastic Leukemia cells by miR-145 link: https://peerj.com/articles/9337 last-modified: 2020-06-16 description: ObjectiveTo analyze the expression levels of miR-145 in ALL children and their effects on the prognosis of ALL and to explore the mechanism of miR-145 in reversing the resistance of ALL cells to glucocorticoids.MethodsA GEO database dataset was used to analyze the expression levels of miR-145 in ALL children. The association between miR-145 and childhood prognosis was analyzed by the TARGET database data. The expression levels of miR-145 in the glucocorticoid-resistant ALL cell line CEM-C1 were increased by lipofectamine 2000-mediated transfection. Cell proliferation inhibition experiments were performed to detect the effect of miR-145 on the response of CEM-C1 cell line to glucocorticoids. The expression levels of the apoptotic, autophagic and drug resistance-associated genes and proteins were detected by qPCR and western blot analysis.ResultsThe expression levels of miR-145 were decreased in ALL patients (P < 0.001) and the prognosis of ALL in children with high miR-145 expression was significantly improved (P < 0.001). Increased miR-145 expression can improve the sensitivity of CEM-C1 cells to glucocorticoids. The expression levels of the proapoptotic and the anti-apoptotic genes Bax and Bcl-2 were increased and decreased, respectively, whereas the expression levels of the autophagicgenes Beclin 1 and LC were increased. In addition, the expression levels of the drug resistance gene MDR1 were decreased.ConclusionThe expression levels of miR-145 in ALL children were decreased and they were associated with disease prognosis. The data indicated that miR-145 can reverse cell resistance by regulating apoptosis of CEM-C1 cells and autophagy. creator: Sili Long creator: Danwei Ren creator: Fangfang Zhong creator: Yana Niu creator: Xiang Qin creator: Dan Mu creator: Wenjun Liu uri: https://doi.org/10.7717/peerj.9337 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Long et al. title: Visualization and quantification of mimetic musculature via DiceCT link: https://peerj.com/articles/9343 last-modified: 2020-06-16 description: The muscles of facial expression are of significant interest to studies of communicative behaviors. However, due to their small size and high integration with other facial tissues, the current literature is largely restricted to descriptions of the presence or absence of specific muscles. Using diffusible iodine-based contrast-enhanced computed tomography (DiceCT) to stain and digitally image the mimetic mask of Eulemur flavifrons (the blue-eyed black lemur), we demonstrate—for the first time—the ability to visualize these muscles in three-dimensional space and to measure their relative volumes. Comparing these data to earlier accounts of mimetic organization with the face of lemuroidea, we demonstrate several novel configurations within this taxon, particularly in the superior auriculolabialis and the posterior auricularis. We conclude that DiceCT facilitates the study these muscles in closer detail than has been previously possible, and offers significant potential for future studies of this anatomy. creator: Edwin Dickinson creator: Emily Atkinson creator: Antonio Meza creator: Shruti Kolli creator: Ashley R. Deutsch creator: Anne M. Burrows creator: Adam Hartstone-Rose uri: https://doi.org/10.7717/peerj.9343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Dickinson et al.