title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1270 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Physiological and gene transcription assays to assess responses of mussels to environmental changes link: https://peerj.com/articles/7800 last-modified: 2019-10-04 description: Coastal regions worldwide face increasing management concerns due to natural and anthropogenic forces that have the potential to significantly degrade nearshore marine resources. The goal of our study was to develop and test a monitoring strategy for nearshore marine ecosystems in remote areas that are not readily accessible for sampling. Mussel species have been used extensively to assess ecosystem vulnerability to multiple, interacting stressors. We sampled bay mussels (Mytilus trossulus) in 2015 and 2016 from six intertidal sites in Lake Clark and Katmai National Parks and Preserves, in south-central Alaska. Reference ranges for physiological assays and gene transcription were determined for use in future assessment efforts. Both techniques identified differences among sites, suggesting influences of both large-scale and local environmental factors and underscoring the value of this combined approach to ecosystem health monitoring. creator: Katrina L. Counihan creator: Lizabeth Bowen creator: Brenda Ballachey creator: Heather Coletti creator: Tuula Hollmen creator: Benjamin Pister creator: Tammy L. Wilson uri: https://doi.org/10.7717/peerj.7800 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: The cuticle inward barrier in Drosophila melanogaster is shaped by mitochondrial and nuclear genotypes and a sex-specific effect of diet link: https://peerj.com/articles/7802 last-modified: 2019-10-04 description: An important role of the insect cuticle is to prevent wetting (i.e., permeation of water) and also to prevent penetration of potentially harmful substances. This barrier function mainly depends on the hydrophobic cuticle surface composed of lipids including cuticular hydrocarbons (CHCs). We investigated to what extent the cuticle inward barrier function depends on the genotype, comprising mitochondrial and nuclear genes in the fruit fly Drosophila melanogaster, and investigated the contribution of interactions between mitochondrial and nuclear genotypes (mito-nuclear interactions) on this function. In addition, we assessed the effects of nutrition and sex on the cuticle barrier function. Based on a dye penetration assay, we find that cuticle barrier function varies across three fly lines that were captured from geographically separated regions in three continents. Testing different combinations of mito-nuclear genotypes, we show that the inward barrier efficiency is modulated by the nuclear and mitochondrial genomes independently. We also find an interaction between diet and sex. Our findings provide new insights into the regulation of cuticle inward barrier function in nature. creator: Wei Dong creator: Ralph Dobler creator: Damian K. Dowling creator: Bernard Moussian uri: https://doi.org/10.7717/peerj.7802 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dong et al. title: HIF inhibitor topotecan has a neuroprotective effect in a murine retinal ischemia-reperfusion model link: https://peerj.com/articles/7849 last-modified: 2019-10-04 description: PurposeThe therapeutic approach for retinal ganglion cell (RGC) degeneration has not been fully established. Recently, it has been reported that hypoxia-inducible factor (HIF) may be involved with retinal neurodegeneration. In this study, we investigated neuroprotective effects of a HIF inhibitor against RGC degeneration induced in a murine model of retinal ischemia-reperfusion (I/R).MethodsEight-weeks-old male C57/BL6J mice were treated with intraperitoneal injection of a HIF inhibitor topotecan (1.25 mg/kg) for 14 days followed by a retinal I/R procedure. Seven days after the I/R injury, the therapeutic effect was evaluated histologically and electrophysiologically.ResultsThe increase of HIF-1α expression and the decrease of retinal thickness and RGC number in I/R were significantly suppressed by administration of topotecan. Impaired visual function in I/R was improved by topotecan evaluated with electroretinogram and visual evoked potentials.ConclusionsTopotecan administration suppressed HIF-1a expression and improved RGC survival resulting in a functional protection against retinal I/R. These data indicated that the HIF inhibitor topotecan may have therapeutic potentials for RGC degeneration induced with retinal ischemia or high intraocular pressure. creator: Hiromitsu Kunimi creator: Yukihiro Miwa creator: Yusaku Katada creator: Kazuo Tsubota creator: Toshihide Kurihara uri: https://doi.org/10.7717/peerj.7849 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kunimi et al. title: The association between serum lipids and risk of premature mortality in Latin America: a systematic review of population-based prospective cohort studies link: https://peerj.com/articles/7856 last-modified: 2019-10-04 description: ObjectiveTo synthetize the scientific evidence on the association between serum lipids and premature mortality in Latin America (LA).MethodsFive data bases were searched from inception without language restrictions: Embase, Medline, Global Health, Scopus and LILACS. Population-based studies following random sampling methods were identified. The exposure variable was lipid biomarkers (e.g., total, LDL- or HDL- cholesterol). The outcome was all-cause and cause-specific mortality. The risk of bias was assessed following the Newcastle-Ottawa criteria. Results were summarized qualitatively.ResultsThe initial search resulted in 264 abstracts, five (N = 27,903) were included for the synthesis. Three papers reported on the same study from Puerto Rico (baseline in 1965), one was from Brazil (1996) and one from Peru (2007). All reports analysed different exposure variables and used different risk estimates (relative risks, hazard ratios or odds ratios). None of the reviewed reports showed strong association between individual lipid biomarkers and all-cause or cardiovascular mortality.ConclusionThe available evidence is outdated, inconsistently reported on several lipid biomarker definitions and used different methods to study the long-term mortality risk. These findings strongly support the need to better ascertain the mortality risk associated with lipid biomarkers in LA. creator: Rodrigo M. Carrillo-Larco creator: Leonardo Albitres-Flores creator: Noël C. Barengo creator: Antonio Bernabe-Ortiz uri: https://doi.org/10.7717/peerj.7856 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Carrillo-Larco et al. title: Identification of potential biomarkers and pivotal biological pathways for prostate cancer using bioinformatics analysis methods link: https://peerj.com/articles/7872 last-modified: 2019-10-04 description: BackgroundProstate cancer (PCa) is a common urinary malignancy, whose molecular mechanism has not been fully elucidated. We aimed to screen for key genes and biological pathways related to PCa using bioinformatics method.MethodsDifferentially expressed genes (DEGs) were filtered out from the GSE103512 dataset and subjected to the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The protein–protein interactions (PPI) network was constructed, following by the identification of hub genes. The results of former studies were compared with ours. The relative expression levels of hub genes were examined in The Cancer Genome Atlas (TCGA) and Oncomine public databases. The University of California Santa Cruz Xena online tools were used to study whether the expression of hub genes was correlated with the survival of PCa patients from TCGA cohorts.ResultsTotally, 252 (186 upregulated and 66 downregulated) DEGs were identified. GO analysis enriched mainly in “oxidation-reduction process” and “positive regulation of transcription from RNA polymerase II promoter”; KEGG pathway analysis enriched mostly in “metabolic pathways” and “protein digestion and absorption.” Kallikrein-related peptidase 3, cadherin 1 (CDH1), Kallikrein-related peptidase 2 (KLK2), forkhead box A1 (FOXA1), and epithelial cell adhesion molecule (EPCAM) were identified as hub genes from the PPI network. CDH1, FOXA1, and EPCAM were validated by other relevant gene expression omnibus datasets. All hub genes were validated by both TCGA and Oncomine except KLK2. Two additional top DEGs (ABCC4 and SLPI) were found to be associated with the prognosis of PCa patients.ConclusionsThis study excavated the key genes and pathways in PCa, which might be biomarkers for diagnosis, prognosis, and potential therapeutic targets. creator: Zihao He creator: Xiaolu Duan creator: Guohua Zeng uri: https://doi.org/10.7717/peerj.7872 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 He et al. title: Structural, functional and molecular dynamics analysis of cathepsin B gene SNPs associated with tropical calcific pancreatitis, a rare disease of tropics link: https://peerj.com/articles/7425 last-modified: 2019-10-03 description: Tropical Calcific Pancreatitis (TCP) is a neglected juvenile form of chronic non-alcoholic pancreatitis. Cathepsin B (CTSB), a lysosomal protease involved in the cellular degradation process, has recently been studied as a potential candidate gene in the pathogenesis of TCP. According to the Cathepsin B hypothesis, mutated CTSB can lead to premature intracellular activation of trypsinogen, a key regulatory mechanism in pancreatitis. So far, CTSB mutations have been studied in pancreatitis and neurodegenerative disorders, but little is known about the structural and functional effect of variants in CTSB. In this study, we investigated the effect of single nucleotide variants (SNVs) specifically associated with TCP, using molecular dynamics and simulation algorithms. There were two non-synonymous variants (L26V and S53G) of CTSB, located in the propeptide region. We tried to predict the effect of these variants on structure and function using multiple algorithms: SIFT, Polyphen2, PANTHER, SDM sever, i-Mutant2.0 suite, mCSM algorithm, and Vadar. Further, using databases like miRdbSNP, PolymiRTS, and miRNASNP, two SNPs in the 3′UTR region were predicted to affect the miRNA binding sites. Structural mutated models of nsSNP mutants (L26V and S53G) were prepared by MODELLER v9.15 and evaluated using TM-Align, Verify 3D, ProSA and Ramachandran plot. The 3D mutated structures were simulated using GROMACS 5.0 to predict the impact of these SNPs on protein stability. The results from in silico analysis and molecular dynamics simulations suggested that these variants in the propeptide region of Cathepsin B could lead to structural and functional changes in the protein and thus could be pathogenic. Hence, the structural and functional analysis results have given interim conclusions that these variants can have a deleterious effect in TCP pathogenesis, either uniquely or in combination with other mutations. Thus, it could be extrapolated that Cathepsin B gene can be screened in samples from all TCP patients in future, to decipher the distribution of variants in patients. creator: Garima Singh creator: Sri Krishna jayadev Magani creator: Rinku Sharma creator: Basharat Bhat creator: Ashish Shrivastava creator: Madhusudhan Chinthakindi creator: Ashutosh Singh uri: https://doi.org/10.7717/peerj.7425 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Singh et al. title: An application of PCR-RFLP species identification assay for environmental DNA detection link: https://peerj.com/articles/7597 last-modified: 2019-10-03 description: Recent advancement of environmental DNA (eDNA) methods for surveying species in aquatic ecosystems has been used for various organisms and contributed to monitoring and conservation of species and environments. Amphibians are one of the promising taxa which could be monitored efficiently by applying quantitative PCR (qPCR) or next generation sequencing to eDNA. However, the cost of eDNA detection using these approaches can be quite high and requires instruments that are not usually installed in ecology laboratories. For aiding researchers in starting eDNA studies of amphibians, especially those not specialized in molecular biology, we developed a cost efficient protocol using PCR-RFLP method. We attempted to detect eDNA of three Japanese Rana species (Rana japonica, Rana ornativentris, and Rana tagoi tagoi) in various spatial scales including an area close to the Fukushima nuclear power plant where the environment is recovering after the disaster in 2011. Our PCR-RFLP protocol was successful in detecting Rana species in static water in both laboratory and field; however, it could not detect Rana species in non-static water samples from the field. Even a more sensitive detection method (standard qPCR) was unable to detect frogs in all non-static water samples. We speculate that our new protocol is effective for frogs living in lentic habitats, but not for lotic habitats which may still require the gold standard of field observation for detection approach. creator: Takeshi Igawa creator: Teruhiko Takahara creator: Quintin Lau creator: Shohei Komaki uri: https://doi.org/10.7717/peerj.7597 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Igawa et al. title: Effects of trapping effort and trap placement on estimating abundance of Humboldt’s flying squirrels link: https://peerj.com/articles/7783 last-modified: 2019-10-03 description: Live trapping is a common tool used to assess demography of small mammals. However, live-trapping is often expensive and stressful to captured individuals. Thus, assessing the relative tradeoffs among study goals, project expenses, and animal well-being is necessary. Here, we evaluated how apparent bias and precision of estimates for apparent annual survival, abundance, capture probability, and recapture probability of Humboldt’s flying squirrels (Glaucomys oregonensis) varied with the number of secondary trapping occasions. We used data from forested sites trapped on 12 consecutive occasions annually in the HJ Andrews Experimental Forest (9 sites, 6 years) and the Siuslaw National Forest (seven sites, three years) in Oregon. We used Huggins robust design models to estimate parameters of interest for the first 4, 8, and 12 trapping occasions. We also estimated the effect of attaching Tomahawk traps to tree boles on site- and year-specific flying squirrel capture frequencies. Our estimates with 12 occasions were similar to those from previous studies. Abundances and capture probabilities were variable among years on both sites; however, variation was much lower on the Siuslaw sites. Reducing the length of primary trapping occasions from 12 to 8 nights had very little impact on parameter estimates, but further reducing the length of primary trapping occasions to four nights caused substantial apparent bias in parameter estimates and decreased precision. We found that attaching Tomahawk traps to tree boles increased the site- and year-specific capture frequency of flying squirrels. Our results suggest that live-trapping studies targeting Humboldt’s flying squirrels in the Pacific Northwest of the United States could reduce per-site costs and stress to captured individuals without biasing estimates by reducing the length of primary trapping occasions to 8 nights. We encourage similar analyses for other commonly-trapped species in these and other ecosystems. creator: Matthew J. Weldy creator: Todd M. Wilson creator: Damon B. Lesmeister creator: Clinton W. Epps uri: https://doi.org/10.7717/peerj.7783 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Establishment of an in vitro model of cultured viable human, porcine and canine skin and comparison of different media supplements link: https://peerj.com/articles/7811 last-modified: 2019-10-03 description: Transdermal drug delivery provides several advantages over conventional drug administration, such as the avoidance of first-pass metabolism and better patient compliance. In vitro research can abbreviate and facilitate the pharmaceutical development considerably compared to in vivo research as drug screening and clinical studies can be reduced. These advantages led to the development of corresponding skin models. Viable skin models are more useful than non-viable ones, due to the influence of skin metabolism on the results. While most in vitro studies concentrate on evaluating human-based models, the current study is designed for the investigation of both human and animal diseases. So far, there is little information available in the literature about viable animal skin cultures which are in fact intended for application in the veterinary and not the human field. Hence, the current study aims to fill the gap. For the in vitro viable skin model, specimens of human, porcine and canine skin were cultured over two weeks under serum-free conditions. To evaluate the influence of medium supplementation on skin viability, two different supplement mixtures were compared with basic medium. The skin specimens were maintained at a viability-level >50% until the end of the study. From the tested supplements, the addition of bovine pituitary extract and epidermal growth factor increased skin viability whereas hydrocortisone and insulin induced a decrease. This in vitro viable skin model may be a useful tool for the investigation of skin diseases, especially for the veterinary field. creator: Isa Bauhammer creator: Manuel Sacha creator: Eleonore Haltner uri: https://doi.org/10.7717/peerj.7811 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Bauhammer et al. title: Expression of leptin and leptin receptors in colorectal cancer—an immunohistochemical study link: https://peerj.com/articles/7624 last-modified: 2019-10-02 description: Obesity is demonstrated to be a risk factor in the development of cancers of various organs, such as colon, prostate, pancreas and so on. Leptine (LEP) is the most renowned of the adipokines. As a hormone, it mediates its effect through leptin receptor (LEPR), which is widely expressed in various tissues including colon mucosa. In this study, we have investigated the degree of expression of LEP and LEPR in colorectal cancer (CRC). We collected 44 surgically resected colon cancer tissues along with normal adjacent colon tissue (NACT) from a sample of CRC patients from the Malaysian population and looked for leptin and leptin receptors using immunohistochemistry (IHC). All the samples showed low presence of both LEP and LEPR in NACT, while both LEP and LEPR were present at high intensity in the cancerous tissues with 100% and 97.7% prevalence, respectively. Both were sparsed in the cytoplasm and were concentrated beneath the cell membrane. However, we did not find any significant correlation between their expression and pathological parameters like grade, tumor size, and lymph node involvement. Our study further emphasizes the possible causal role of LEP and LEPR with CRC, and also the prospect of using LEPR as a possible therapeutic target. creator: Saad M. Al-Shibli creator: Norra Harun creator: Abdelkader E. Ashour creator: Mohd Hanif B. Mohd Kasmuri creator: Shaikh Mizan uri: https://doi.org/10.7717/peerj.7624 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Al-Shibli et al.