title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1657 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region link: https://peerj.com/articles/3901 last-modified: 2017-10-10 description: We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes. creator: Zachary R. Hanna creator: James B. Henderson creator: Anna B. Sellas creator: Jérôme Fuchs creator: Rauri C.K. Bowie creator: John P. Dumbacher uri: https://doi.org/10.7717/peerj.3901 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hanna et al. title: Infection of army ant pupae by two new parasitoid mites (Mesostigmata: Uropodina) link: https://peerj.com/articles/3870 last-modified: 2017-10-10 description: A great variety of parasites and parasitoids exploit ant societies. Among them are the Mesostigmata mites, a particularly common and diverse group of ant-associated arthropods. While parasitism is ubiquitous in Mesostigmata, parasitoidism has only been described in the genus Macrodinychus. Yet information about the basic biology of most Macrodinychus species is lacking. Out of 24 formally described species, information about basic life-history traits is only available for three species. Here we formally describe two new Macrodinychus species, i.e. Macrodinychus hilpertae and Macrodinychus derbyensis. In both species, immature stages developed as ecto-parasitoids on ant pupae of the South-East Asian army ant Leptogenys distinguenda. By piercing the developing ant with their chelicera, the mites apparently suck ant hemolymph, ultimately killing host individuals. We compare infection rates among all studied Macrodinychus species and discuss possible host countermeasures against parasitoidism. The cryptic lifestyle of living inside ant nests has certainly hampered the scientific discovery of Macrodinychus mites and we expect that many more macrodinychid species await scientific discovery and description. creator: Adrian Brückner creator: Hans Klompen creator: Andrew Iain Bruce creator: Rosli Hashim creator: Christoph von Beeren uri: https://doi.org/10.7717/peerj.3870 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Brückner et al. title: Extending SEQenv: a taxa-centric approach to environmental annotations of 16S rDNA sequences link: https://peerj.com/articles/3827 last-modified: 2017-10-10 description: Understanding how the environment selects a given taxon and the diversity patterns that emerge as a result of environmental filtering can dramatically improve our ability to analyse any environment in depth as well as advancing our knowledge on how the response of different taxa can impact each other and ecosystem functions. Most of the work investigating microbial biogeography has been site-specific, and logical environmental factors, rather than geographical location, may be more influential on microbial diversity. SEQenv, a novel pipeline aiming to provide environmental annotations of sequences emerged to provide a consistent description of the environmental niches using the ENVO ontology. While the pipeline provides a list of environmental terms on the basis of sample datasets and, therefore, the annotations obtained are at the dataset level, it lacks a taxa centric approach to environmental annotation. The work here describes an extension developed to enhance the SEQenv pipeline, which provided the means to directly generate environmental annotations for taxa under different contexts. 16S rDNA amplicon datasets belonging to distinct biomes were selected to illustrate the applicability of the extended SEQenv pipeline. A literature survey of the results demonstrates the immense importance of sequence level environmental annotations by illustrating the distribution of both taxa across environments as well as the various environmental sources of a specific taxon. Significantly enhancing the SEQenv pipeline in the process, this information would be valuable to any biologist seeking to understand the various taxa present in the habitat and the environment they originated from, enabling a more thorough analysis of which lineages are abundant in certain habitats and the recovery of patterns in taxon distribution across different habitats and environmental gradients. creator: Ali Z. Ijaz creator: Thomas C. Jeffries creator: Umer Z. Ijaz creator: Kelly Hamonts creator: Brajesh K. Singh uri: https://doi.org/10.7717/peerj.3827 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Ijaz et al. title: Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders link: https://peerj.com/articles/3823 last-modified: 2017-10-10 description: BackgroundParkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobacteria that can cause human diseases like nocardiosis. This illness can lead to lung infection or central nervous system (CNS) invasion in both immunocompromised and immunocompetent individuals. The main species involved in CNS are N. farcinica, N. nova, N. brasiliensis and N. cyriacigeorgica. Some studies have highlighted the ability of N. cyriacigeorgica to induce Parkinson’s disease-like symptoms in animals. Actinobacteria are known to produce a large variety of secondary metabolites, some of which can be neurotoxic. We hypothesized that neurotoxic secondary metabolite production and the onset of PD-like symptoms in animals could be linked.MethodsHere we used a method to screen bacteria that could induce dopaminergic neurodegeneration before performing mouse experiments.ResultsThe nematode Caenorhabditis elegans allowed us to demonstrate that Nocardia strains belonging to N. cyriacigeorgica and N. farcinica species can induce dopaminergic neurodegeneration. Strains of interest involved with the nematodes in neurodegenerative disorders were then injected in mice. Infected mice had behavioral disorders that may be related to neuronal damage, thus confirming the ability of Nocardia strains to induce neurodegeneration. These behavioral disorders were induced by N. cyriacigeorgica species (N. cyriacigeorgica GUH-2 and N. cyriacigeorgica 44484) and N. farcinica 10152.DiscussionWe conclude that C. elegans is a good model for detecting Nocardia strains involved in neurodegeneration. This model allowed us to detect bacteria with high neurodegenerative effects and which should be studied in mice to characterize the induced behavioral disorders and bacterial dissemination. creator: Claire Bernardin Souibgui creator: Anthony Zoropogui creator: Jeremy Voisin creator: Sebastien Ribun creator: Valentin Vasselon creator: Petar Pujic creator: Veronica Rodriguez-Nava creator: Patrick Belly creator: Benoit Cournoyer creator: Didier Blaha uri: https://doi.org/10.7717/peerj.3823 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bernardin Souibgui et al. title: Clinical outcomes of residual or recurrent nasopharyngeal carcinoma treated with endoscopic nasopharyngectomy plus chemoradiotherapy or with chemoradiotherapy alone: a retrospective study link: https://peerj.com/articles/3912 last-modified: 2017-10-09 description: BackgroundLocal residual and recurrent nasopharyngeal carcinoma (NPC) generally shows treatment failure after standard radiotherapy with or without concurrent chemotherapy. Whether endoscopic nasopharyngectomy might provide an additional therapeutic advantage remains controversial. Therefore, we retrospectively compared the clinical prognoses of patients with residual or recurrent NPC treated with endoscopic nasopharyngectomy combined with chemoradiotherapy (CRT) with those of patients treated with CRT alone.Methods and MaterialsA total of sixty-two patients with local residual or recurrent NPC were studied retrospectively: 36 patients received endoscopic nasopharyngectomy combined with CRT, whereas 26 patients who refused the surgery or had surgical contraindications received CRT alone. Serum Epstein-Barr virus (EBV) DNA levels were measured pre- and post-treatment. The differences in prognosis between the two treatment regimens and the pre- and post-treatment changes in EBV-DNA levels were analyzed.ResultsThe median follow-up time was 31 months, with a 3-year overall survival (OS) of 51.40% and a 3-year disease-free survival (DFS) of 46.86%. The surgery + CRT group had a better OS than the CRT alone group did (χ2 = 4.054, P = 0.044). The pretreatment EBV-DNA levels showed a positive correlation with the clinical staging of recurrent NPC (χ2 = 11.674, P = 0.009). Patients with negative pretreatment serum EBV-DNA levels showed a superior OS to those of patients who tested positive for EBV-DNA (>0 copy/mL) (χ2 = 9.833, P = 0.002). The post-treatment EBV-DNA levels, compared with the pretreatment levels, decreased significantly in the surgery + CRT group (Z =  − 3.484, P = 0.000). In contrast, the EBV-DNA levels after CRT alone did not decrease significantly (Z =  − 1.956, P = 0.051). Multivariate analysis indicated that local staging, pretreatment EBV-DNA load, and the treatment method were independent risk factors for OS. Subgroup analysis indicated that the patients who tested negative for EBV-DNA before the treatment and those who received surgery + CRT showed a better OS than those who received CRT alone.ConclusionsThe pretreatment serum EBV-DNA level was associated with disease prognosis. The combination therapy preceded by surgery can effectively decrease the copy number of EBV-DNA. Patients with local intermediate- and late-stage NPC, especially those negative for EBV-DNA, may consider opting for surgery followed by post-operative adjuvant radiotherapy or chemotherapy. creator: Jingjin Weng creator: Jiazhang Wei creator: Jinyuan Si creator: Yangda Qin creator: Min Li creator: Fei Liu creator: Yongfeng Si creator: Jiping Su uri: https://doi.org/10.7717/peerj.3912 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Weng et al. title: Comparison of human papillomavirus (HPV) detection in urine and cervical swab samples using the HPV GenoArray Diagnostic assay link: https://peerj.com/articles/3910 last-modified: 2017-10-09 description: Human papillomavirus (HPV) is the leading cause of cervical cancer. Urine-based HPV testing offers a simple and non-invasive method because of its increasing acceptance. A total of 164 pairs of cervical swab and urine samples from Thai women who underwent cervical cancer screening were used for HPV testing with HPV GenoArray Diagnostic Kits. The overall concordance percentage for HPV detection in the cervical swab and urine samples was 65.2%. The HPV genotypes most commonly detected were HPV16 and HPV18. An analysis of the urine samples and a second analysis of the cervical swab samples showed that the differences in the overall HPV detection rate between women with normal and abnormal cytology were not significant (p > 0.05). Urine samples processed with the GenoArray assay is an alternative for women who decline to undergo Pap smear even though it is not ideal as the first-line screening option. creator: Pornjarim Nilyanimit creator: Jira Chansaenroj creator: Anant Karalak creator: Piyawat Laowahutanont creator: Pairoj Junyangdikul creator: Yong Poovorawan uri: https://doi.org/10.7717/peerj.3910 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Nilyanimit et al. title: Histamine-2 receptor antagonist famotidine modulates cardiac stem cell characteristics in hypertensive heart disease link: https://peerj.com/articles/3882 last-modified: 2017-10-09 description: BackgroundCardiac stem cells (CSCs) play a vital role in cardiac homeostasis. A decrease in the efficiency of cardiac stem cells is speculated in various cardiac abnormalities. The maintenance of a healthy stem cell population is essential for the prevention of adverse cardiac remodeling leading to cardiac failure. Famotidine, a histamine-2 receptor antagonist, is currently used to treat ulcers of the stomach and intestines. In repurposing the use of the drug, reduction of cardiac hypertrophy and improvement in cardiac function of spontaneously hypertensive rats (SHR) was reported by our group. Given that stem cells are affected in cardiac pathologies, the effect of histamine-2 receptor antagonism on CSC characteristics was investigated.MethodsTo examine whether famotidine has a positive effect on CSCs, spontaneously hypertensive rats (SHR) treated with the drug were sacrificed; and CSCs isolated from atrial appendages was evaluated. Six-month-old male SHRs were treated with famotidine (30 mg/kg/day) for two months. The effect of famotidine treatment on migration, proliferation and survival of CSCs was compared with untreated SHRs and normotensive Wistar rats.ResultsFunctional efficiency of CSCs from SHR was compromised relative to that in Wistar rat. Famotidine increased the migration and proliferation potential, along with retention of stemness of CSCs in treated SHRs. Cellular senescence and oxidative stress were also reduced. The expression of H2R was unaffected by the treatment.DiscussionAs anticipated, CSCs from SHRs were functionally impaired. Stem cell attributes of famotidine-treated SHRs was comparable to that of Wistar rats. Therefore, in addition to being cardioprotective, the histamine 2 receptor antagonist modulated cardiac stem cells characteristics. Restoration of stem cell efficiency by famotidine is possibly mediated by reduction of oxidative stress as the expression of H2R was unaffected by the treatment. Maintenance of healthy stem cell population is suggested as a possible mechanism underlying the cardioprotective effect of famotidine. creator: Sherin Saheera creator: Ajay G. Potnuri creator: Renuka Nair uri: https://doi.org/10.7717/peerj.3882 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Saheera et al. title: Influence of exercise duration on cardiorespiratory responses, energy cost and tissue oxygenation within a 6 hour treadmill run link: https://peerj.com/articles/3694 last-modified: 2017-10-09 description: PurposeThe physiological mechanisms for alterations in oxygen utilization ($\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2) and the energy cost of running (Cr) during prolonged running are not completely understood, and could be linked with alterations in muscle and cerebral tissue oxygenation.MethodsEight trained ultramarathon runners (three women; mean ± SD; age 37 ± 7 yr; maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2 60 ± 15 mL min−1 kg−1) completed a 6 hr treadmill run (6TR), which consisted of four modules, including periods of moderate (3 min at 10 km h−1, 10-CR) and heavy exercise intensities (6 min at 70% of maximum $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2, HILL), separated by three, 100 min periods of self-paced running (SP). We measured $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2, minute ventilation (${\dot {\mathrm{V }}}_{\mathrm{E}}$V ̇E), ventilatory efficiency (${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇E:V ̇O2), respiratory exchange ratio (RER), Cr, muscle and cerebral tissue saturation index (TSI) during the modules, and heart rate (HR) and perceived exertion (RPE) during the modules and SP.ResultsParticipants ran 58.3 ± 10.5 km during 6TR. Speed decreased and HR and RPE increased during SP. Across the modules, HR and $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2 increased (10-CR), and RER decreased (10-CR and HILL). There were no significant changes in ${\dot {\mathrm{V }}}_{\mathrm{E}}$V ̇E, ${\dot {\mathrm{V }}}_{\mathrm{E}}:\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇E:V ̇O2, Cr, TSI and RPE across the modules.ConclusionsIn the context of positive pacing (decreasing speed), increased cardiac drift and perceived exertion over the 6TR, we observed increased RER and increased HR at moderate and heavy exercise intensity, increased $\dot {\mathrm{V }}{\mathrm{O}}_{2}$V ̇O2 at moderate intensity, and no effect of exercise duration on ventilatory efficiency, energy cost of running and tissue oxygenation. creator: Hugo A. Kerhervé creator: Scott McLean creator: Karen Birkenhead creator: David Parr creator: Colin Solomon uri: https://doi.org/10.7717/peerj.3694 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Kerhervé et al. title: Independent evolution of tetraloop in enterovirus oriL replicative element and its putative binding partners in virus protein 3C link: https://peerj.com/articles/3896 last-modified: 2017-10-06 description: BackgroundEnteroviruses are small non-enveloped viruses with a (+) ssRNA genome with one open reading frame. Enterovirus protein 3C (or 3CD for some species) binds the replicative element oriL to initiate replication. The replication of enteroviruses features a low-fidelity process, which allows the virus to adapt to the changing environment on the one hand, and requires additional mechanisms to maintain the genome stability on the other. Structural disturbances in the apical region of oriL domain d can be compensated by amino acid substitutions in positions 154 or 156 of 3C (amino acid numeration corresponds to poliovirus 3C), thus suggesting the co-evolution of these interacting sequences in nature. The aim of this work was to understand co-evolution patterns of two interacting replication machinery elements in enteroviruses, the apical region of oriL domain d and its putative binding partners in the 3C protein.MethodsTo evaluate the variability of the domain d loop sequence we retrieved all available full enterovirus sequences (>6, 400 nucleotides), which were present in the NCBI database on February 2017 and analysed the variety and abundance of sequences in domain d of the replicative element oriL and in the protein 3C.ResultsA total of 2,842 full genome sequences was analysed. The majority of domain d apical loops were tetraloops, which belonged to consensus YNHG (Y = U/C, N = any nucleotide, H = A/C/U). The putative RNA-binding tripeptide 154–156 (Enterovirus C 3C protein numeration) was less diverse than the apical domain d loop region and, in contrast to it, was species-specific.DiscussionDespite the suggestion that the RNA-binding tripeptide interacts with the apical region of domain d, they evolve independently in nature. Together, our data indicate the plastic evolution of both interplayers of 3C-oriL recognition. creator: Maria A. Prostova creator: Andrei A. Deviatkin creator: Irina O. Tcelykh creator: Alexander N. Lukashev creator: Anatoly P. Gmyl uri: https://doi.org/10.7717/peerj.3896 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Prostova et al. title: Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods link: https://peerj.com/articles/3894 last-modified: 2017-10-06 description: Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently. creator: Carlos A. Santamaria creator: Joanna K. Bluemel creator: Nancy Bunbury creator: Melinda Curran uri: https://doi.org/10.7717/peerj.3894 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Santamaria et al.