title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1759 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: FUCHS—towards full circular RNA characterization using RNAseq link: https://peerj.com/articles/2934 last-modified: 2017-02-28 description: Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5′ splice site is linked to an upstream 3′ splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing. Though functional studies have shown that some circRNAs could act as miRNA-sponges, the function of most circRNAs remains unknown. To expand our understanding of possible roles of circular RNAs, we propose a new pipeline that could fully characterizes candidate circRNA structure from RNAseq data—FUCHS: FUll CHaracterization of circular RNA using RNA-Sequencing. Currently, most computational prediction pipelines use back-spliced reads to identify circular RNAs. FUCHS extends this concept by considering all RNA-seq information from long reads (typically >150 bp) to learn more about the exon coverage, the number of double break point fragments, the different circular isoforms arising from one host-gene, and the alternatively spliced exons within the same circRNA boundaries. This new knowledge will enable the user to carry out differential motif enrichment and miRNA seed analysis to determine potential regulators during circRNA biogenesis. FUCHS is an easy-to-use Python based pipeline that contributes a new aspect to the circRNA research. creator: Franziska Metge creator: Lisa F. Czaja-Hasse creator: Richard Reinhardt creator: Chistoph Dieterich uri: https://doi.org/10.7717/peerj.2934 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Metge et al. title: Facilitating permeability of landscapes impacted by roads for protected amphibians: patterns of movement for the great crested newt link: https://peerj.com/articles/2922 last-modified: 2017-02-28 description: Amphibian populations are highly vulnerable to road mortality and habitat fragmentation caused by road networks. Wildlife road tunnels are considered the most promising road mitigation measure for amphibians yet generally remain inadequately monitored, resulting in mixed success rates in the short-term and uncertain conservation benefits in the long-term. We monitored a complex multi-tunnel and fence system over five years and investigated the impact of the scheme on movement patterns of two newt species, including the largest known UK population of the great crested newt (Triturus cristatus), a European Protected Species. We used a stage descriptive approach based on capture positions to quantify newt movement patterns. Newt species successfully used the mitigation but the system constituted a bottleneck to movements from the fences to the tunnels. Crossing rates varied widely among years and were skewed towards autumn dispersal rather than spring breeding migration. There was a substantial negative bias against adult male great crested newts using the system. This study indicates that road tunnels could partially mitigate wider connectivity loss and fragmentation at the landscape scale for newt species. However, the observed bottleneck effects and seasonal bias could have population-level effects which must be better understood, especially for small populations, so that improvements can be made. Current requirements for monitoring mitigation schemes post-implementation are probably too short to assess their effectiveness in maintaining connectivity and to adequately understand their population-level impacts. creator: Cátia Matos creator: Silviu Petrovan creator: Alastair I. Ward creator: Philip Wheeler uri: https://doi.org/10.7717/peerj.2922 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Matos et al. title: Species-specific markers provide molecular genetic evidence for natural introgression of bullhead catfishes in Hungary link: https://peerj.com/articles/2804 last-modified: 2017-02-28 description: Since three bullhead catfish species were introduced to Europe in the late 19th century, they have spread to most European countries. In Hungary, the brown bullhead (Ameiurus nebulosus) was more widespread in the 1970s–1980s, but the black bullhead (Ameiurus melas) has gradually supplanted since their second introduction in 1980. The introgressive hybridization of the two species has been presumed based on morphological examinations, but it has not previously been supported by genetic evidence. In this study, 11 different Hungarian habitats were screened with a new species-specific nuclear genetic, duplex PCR based, marker system to distinguish the introduced catfish species, Ameiurus nebulosus, Ameiurus melas, and Ameiurus natalis, as well as the hybrids of the first two. More than 460 specimens were analyzed using the above markers and additional mitochondrial sequence analyses were also conducted on >25% of the individuals from each habitat sampled. The results showed that only 7.9% of the specimens from two habitats belonged to Ameiurus nebulosus, and 92.1% were classified as Ameiurus melas of all habitats, whereas the presence of Ameiurus natalis was not detected. Two specimens (>0.4%) showed the presence of both nuclear genomes and they were identified as hybrids of Ameiurus melas and Ameiurus nebulosus. An additional two individuals showed contradicting results from the nuclear and mitochondrial assays as a sign of a possible footprint of introgressive hybridization that might have happened two or more generations before. Surprisingly, the level of hybridization was much smaller than expected based on the analyses of the North American continent’s indigenous stock from the hybrid zones. This phenomenon has been observed in several invasive fish species and it is regarded as an added level of complexity in the management of their rapid adaptation. creator: Beatrix Béres creator: Dóra Kánainé Sipos creator: Tamás Müller creator: Ádám Staszny creator: Milán Farkas creator: Katalin Bakos creator: László Orbán creator: Béla Urbányi creator: Balázs Kovács uri: https://doi.org/10.7717/peerj.2804 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Béres et al. title: Effects of shepherds and dogs on livestock depredation by leopards (Panthera pardus) in north-eastern Iran link: https://peerj.com/articles/3049 last-modified: 2017-02-23 description: Human-carnivore conflicts over livestock depredation are increasingly common, yet little is understood about the role of husbandry in conflict mitigation. As shepherds and guarding dogs are most commonly used to curb carnivore attacks on grazing livestock, evaluation and improvement of these practices becomes an important task. We addressed this issue by studying individual leopard (Panthera pardus) attacks on sheep and goats in 34 villages near Golestan National Park, Iran. We obtained and analyzed data on 39 attacks, which included a total loss of 31 sheep and 36 goats in 17 villages. We applied non-parametric testing, Poisson Generalized Linear Modelling (GLM) and model selection to assess how numbers of sheep and goats killed per attack are associated with the presence and absence of shepherds and dogs during attacks, depredation in previous years, villages, seasons, ethnic groups, numbers of sheep and goats kept in villages, and distances from villages to the nearest protected areas. We found that 95.5% of losses were inflicted in forests when sheep and goats were accompanied by shepherds (92.5% of losses) and dogs (77.6%). Leopards tended to kill more sheep and goats per attack (surplus killing) when dogs were absent in villages distant from protected areas, but still inflicted most losses when dogs were present, mainly in villages near protected areas. No other variables affected numbers of sheep and goats killed per attack. These results indicate that local husbandry practices are ineffectual and the mere presence of shepherds and guarding dogs is not enough to secure protection. Shepherds witnessed leopard attacks, but could not deter them while dogs did not exhibit guarding behavior and were sometimes killed by leopards. In an attempt to make practical, low-cost and socially acceptable improvements in local husbandry, we suggest that dogs are raised to create a strong social bond with livestock, shepherds use only best available dogs, small flocks are aggregated into larger ones and available shepherds herd these larger flocks together. Use of deterrents and avoidance of areas close to Golestan and in central, core areas of neighboring protected areas is also essential to keep losses down. creator: Igor Khorozyan creator: Mahmood Soofi creator: Mobin Soufi creator: Amirhossein Khaleghi Hamidi creator: Arash Ghoddousi creator: Matthias Waltert uri: https://doi.org/10.7717/peerj.3049 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Khorozyan et al. title: Development and validation of a 36-gene sequencing assay for hereditary cancer risk assessment link: https://peerj.com/articles/3046 last-modified: 2017-02-23 description: The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen’s high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers. creator: Valentina S. Vysotskaia creator: Gregory J. Hogan creator: Genevieve M. Gould creator: Xin Wang creator: Alex D. Robertson creator: Kevin R. Haas creator: Mark R. Theilmann creator: Lindsay Spurka creator: Peter V. Grauman creator: Henry H. Lai creator: Diana Jeon creator: Genevieve Haliburton creator: Matt Leggett creator: Clement S. Chu creator: Kevin Iori creator: Jared R. Maguire creator: Kaylene Ready creator: Eric A. Evans creator: Hyunseok P. Kang creator: Imran S. Haque uri: https://doi.org/10.7717/peerj.3046 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Vysotskaia et al. title: Effectiveness of removals of the invasive lionfish: how many dives are needed to deplete a reef? link: https://peerj.com/articles/3043 last-modified: 2017-02-23 description: Introduced Indo-Pacific red lionfish (Pterois volitans/miles) have spread throughout the greater Caribbean and are associated with a number of negative impacts on reef ecosystems. Human interventions, in the form of culling activities, are becoming common to reduce their numbers and mitigate the negative effects associated with the invasion. However, marine managers must often decide how to best allocate limited resources. Previous work has identified the population size thresholds needed to limit the negative impacts of lionfish. Here we develop a framework that allows managers to predict the removal effort required to achieve specific targets (represented as the percent of lionfish remaining on the reef). We found an important trade-off between time spent removing and achieving an increasingly smaller lionfish density. The model used in our suggested framework requires relatively little data to parameterize, allowing its use with already existing data, permitting managers to tailor their culling strategy to maximize efficiency and rate of success. creator: Paolo Usseglio creator: Jason D. Selwyn creator: Alan M. Downey-Wall creator: J. Derek Hogan uri: https://doi.org/10.7717/peerj.3043 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Usseglio et al. title: Tartrazine induces structural and functional aberrations and genotoxic effects in vivo link: https://peerj.com/articles/3041 last-modified: 2017-02-23 description: Tartrazine is a synthetic organic azo dye widely used in food and pharmaceutical products. The current study aimed to evaluate the possible adverse effect of this coloring food additive on renal and hepatic structures and functions. Also, the genotoxic potential of tartrazine on white blood cells was investigated using comet assay. Twenty adult male Wistar rats were grouped into two groups of 10 each, control- and tartrazine-treated groups. The control group was administered orally with water alone. The experimental group was administered orally with tartrazine (7.5 mg/kg, b.wt.). Our results showed a marked increase in the levels of ALT, AST, ALP, urea, uric acid, creatinine, MDA and NO, and a decreased level of total antioxidants in the serum of rats dosed with tartrazine compared to controls. On the other hand, administration of tartrazine was associated with severe histopathological and cellular alterations of rat liver and kidney tissues and induced DNA damage in leucocytes as detected by comet assay. Taken together, the results showed that tartrazine intake may lead to adverse health effects. creator: Latifa Khayyat creator: Amina Essawy creator: Jehan Sorour creator: Ahmed Soffar uri: https://doi.org/10.7717/peerj.3041 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Khayyat et al. title: Retrospective observation of drug susceptibility of Candida strains in the years 1999, 2004, and 2015 link: https://peerj.com/articles/3038 last-modified: 2017-02-23 description: IntroductionThere is much literature devoted to the problem of drug resistance and decreased susceptibility of fungi to commonly used antifungals.AimTo analyze drug susceptibility of Candida albicans and non-Candida albicans strains isolated from the hands of people without any symptoms of disease over a 16-year period.Materials and MethodsThe study included a total of 1,274 Candida-type strains isolated from the hands of people without any symptoms of disease, including: in 1999, 432 strains; in 2004, 368; and in 2015, 454 strains. Biological monitoring of hand surface contamination was performed using the Count-TactTM applicator with Count-Tact plates (bioMerieux). Drug susceptibility was evaluated using FUNGITEST®.ResultsIn 1999, the most strains showed resistance to fluconazole (53.2%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (85.8%). Resistance to more than one drug was 35.8% in 1999, 64.7% in 2004, and 92% in 2015. Mean resistance to azole antifungals significantly increased from 98 ± 39.7 strains in 1999 to 118.3 ± 29.6 in 2015 (p < 0.001). In 1999, the most strains showed resistance to fluconazole (50.6%), in 2004 to itraconazole (52.9%), and in 2015 to fluconazole (44.9%). Resistance to more than one drug was 52.9% in 1999, 64.3% in 2004, and 88.1% in 2015. Mean resistance to azole antifungals significantly increased from a mean of 76 ± 9.7 strains in 1999, to 95.3 ± 24.2 in 2004, and to 97.3 ± 16.6 in 2015 (p < 0.001).ConclusionsWe showed increased C. albicans and non-Candida albicans strain resistance to commonly used antifungal chemotherapeutics, mainly imidazole. We found a clear rise in susceptibility of C. albicans and non-Candida albicans strains to several studied antifungals. creator: Cecylia Łukaszuk creator: Elżbieta Krajewska-Kułak creator: Wojciech Kułak uri: https://doi.org/10.7717/peerj.3038 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Łukaszuk et al. title: Inhibition of calcineurin by FK506 stimulates germinal vesicle breakdown of mouse oocytes in hypoxanthine-supplemented medium link: https://peerj.com/articles/3032 last-modified: 2017-02-23 description: Calcineurin (CN) is a serine/threonine phosphatase which plays important roles in meiosis maturation in invertebrate oocytes; however, the role of CN in mouse oocytes is relatively unexplored. In this study, we examined the expression, localization and functional roles of CN in mouse oocytes and granulosa cells. The RT-PCR results showed that the β isoform of calcineurin A subunit (Cn A) expressed significantly higher than α and γ isoforms, and the expression of Cn Aβ mRNA obviously decreased in oocytes in which germinal vesicle breakdown (GVBD) occurred, while only B1 of calcineurin B subunit (Cn B) was detected in oocytes and stably expressed during oocytes maturation. The following fluorescence experiment showed that Cn A was mainly located in the nucleus of germinal vesicle (GV) stage oocytes and gruanlosa cells, and subsequently dispersed into the entire cytoplasm after GVBD. The decline of Cn A in oocytes suggested that it may play an important role in GVBD. To further clarify the role of calcineurin during meiotic maturation, FK506 (a calcineurin inhibitor) was used in the culture medium contained hypoxanthine (HX) which could keep mouse oocytes staying at GV stage. As expected, FK506 could induce a significant elevation of GVBD rate and increase the MPF level of denuded oocytes (DOs). Furthermore, FK506 could also play an induction role of GVBD of oocytes in COCs and follicles, and the process could be counteracted by MAPK kinase inhibitor (U0126). Above all, the results implied that calcineurin might play a crucial role in development of mouse oocytes and MPF and MAPK pathways are involved in this process. creator: Li Wang creator: Yan-Hong Zhen creator: Xiao-Ming Liu creator: Jing Cao creator: Yan-Ling Wang creator: Li-Jun Huo uri: https://doi.org/10.7717/peerj.3032 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Wang et al. title: Eotaria citrica, sp. nov., a new stem otariid from the “Topanga” formation of Southern California link: https://peerj.com/articles/3022 last-modified: 2017-02-23 description: A new taxon of stem otariid, Eotaria citrica sp. nov., is described from the upper Burdigalian to lower Langhian “Topanga” formation of Orange County, California. The new species is described from mandibular and dental remains that show a unique combination of plesiomorphic and derived characters. Specifically, it is characterized by having trenchant and prominent paraconid cusps in p3–m1, lingual cingula of p2–4 with faint crenulations, premolars and molars with vestigial metaconid, bilobed root of m2 and a genial tuberosity located under p3. Furthermore, additional material of the contemporaneous Eotaria crypta is described, providing new information on the morphology of this taxon. Both species of Eotaria represent the earliest stem otariids, reinforcing the hypothesis that the group originated in the north Eastern Pacific Region. At present, the “Topanga” Fm. pinniped fauna includes Eotaria citrica, Eotaria crypta, the desmatophocid Allodesmus sp., the odobenids Neotherium sp., Pelagiarctos sp. and includes the oldest records of crown pinnipeds in California. Overall this pinniped fauna is similar to the nearly contemporaneous Sharktooth Hill bonebed. However, unambiguous records of Eotaria are still missing from Sharktooth Hill. This absence may be due to taphonomic or paleoenvironmental factors. The new “Topanga” record presented here was integrated into an overview of the late Oligocene through early Pleistocene pinniped faunas of Southern California. The results show an overall increase in body size over time until the Pleistocene. Furthermore, desmatophocids were the largest pinnipeds during the middle Miocene, but were extinct by the beginning of the late Miocene. Odobenids diversified and became the dominant pinnipeds in late Miocene through Pleistocene assemblages, usually approaching or exceeding 3 m in body length, while otariids remained as the smallest taxa. This pattern contrasts with modern assemblages, in which the phocid Mirounga angustirostris is the largest pinniped taxon in the region, odobenids are extinct and medium and small size ranges are occupied by otariids or other phocids. creator: Jorge Velez-Juarbe uri: https://doi.org/10.7717/peerj.3022 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Velez-Juarbe