title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1237 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model link: https://peerj.com/articles/8192 last-modified: 2019-12-05 description: IntroductionRecent studies highlight the crucial regulatory roles of transposable elements (TEs) on proximal gene expression in distinct biological contexts such as disease and development. However, computational tools extracting potential TE –proximal gene expression associations from RNA-sequencing data are still missing.ImplementationHerein, we developed a novel R package, using a linear regression model, for studying the potential influence of TE species on proximal gene expression from a given RNA-sequencing data set. Our R package, namely TEffectR, makes use of publicly available RepeatMasker TE and Ensembl gene annotations as well as several functions of other R-packages. It calculates total read counts of TEs from sorted and indexed genome aligned BAM files provided by the user, and determines statistically significant relations between TE expression and the transcription of nearby genes under diverse biological conditions.AvailabilityTEffectR is freely available at https://github.com/karakulahg/TEffectR along with a handy tutorial as exemplified by the analysis of RNA-sequencing data including normal and tumour tissue specimens obtained from breast cancer patients. creator: Gökhan Karakülah creator: Nazmiye Arslan creator: Cihangir Yandım creator: Aslı Suner uri: https://doi.org/10.7717/peerj.8192 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Karakülah et al. title: A high latitude Devonian lungfish, from the Famennian of South Africa link: https://peerj.com/articles/8073 last-modified: 2019-12-04 description: New fossil lungfish remains comprising two parasphenoids, tooth plates and scales from the Famennian Witpoort Formation of South Africa are described. From the parasphenoid material, which bears similarity to Oervigia and Sagenodus but is nevertheless unique, a new genus, Isityumzi mlomomde gen. et sp. nov. is erected. Tooth plates and scales from the same locality may be conspecific but are not yet assigned until further material becomes available. The tooth plates closely resemble those of some taxa in the Carboniferous genus Ctenodus. The new taxon is significant as only the second Devonian lungfish described from the African continent, and for hailing from the high-latitude (polar) Waterloo Farm environment situated close to 70° south during the Famennian. creator: Robert W. Gess creator: Alice M. Clement uri: https://doi.org/10.7717/peerj.8073 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gess and Clement title: Rediscovery of Osteocephalus vilarsi (Anura: Hylidae): an overlooked but widespread Amazonian spiny-backed treefrog link: https://peerj.com/articles/8160 last-modified: 2019-12-04 description: Osteocephalus vilarsi (Melin, 1941) is an Amazonian treefrog species known for over 75 years from its holotype only. Due to a lack of published data on its morphological diagnostic characters and their variations, as well as the absence of molecular, acoustic and ecological data supporting its identity, a highly dynamic taxonomic history has led this species to be confused and even synonymised with other Osteocephalus species from distinct species groups. The molecular phylogenetic relationships of O. vilarsi were investigated based on recently collected specimens from eight Northwestern Brazilian localities in the state of Amazonas, leading to its removal from the Osteocephalus taurinus species group and placement in the Osteocephalus planiceps species group. Furthermore, detailed data on morphology and colour variation are provided, as well as advertisement call and tadpole descriptions. Finally, the currently known geographic range of O. vilarsi is considerably extended, first data on the natural history of the species are provided, and the possible ecological preference of O. vilarsi for Amazonian white-sand forests is discussed. creator: Miquéias Ferrão creator: Jiří Moravec creator: Leandro J.C.L. Moraes creator: Vinicius T. de Carvalho creator: Marcelo Gordo creator: Albertina P. Lima uri: https://doi.org/10.7717/peerj.8160 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ferrão et al. title: Management of recurrent ureteral stricture: a retrospectively comparative study with robot-assisted laparoscopic surgery versus open approach link: https://peerj.com/articles/8166 last-modified: 2019-12-04 description: BackgroundManagement of recurrent ureteral stricture is challenging. Consensus on the best surgical choice has not been demonstrated. In this study, we aim to report our experience in treating recurrent ureteral stricture and demonstrate whether robot-assisted procedure for redo ureteral surgery is as effective as open procedure while remaining less invasive.MethodsWe retrospectively assessed 41 patients (22 robot-assisted surgeries and 19 open surgeries) who underwent consecutive robot-assisted and open procedures for redo ureteral surgery from January 2014 to 2018 in our institution. Perioperative outcomes, including demographics, operative time, estimated blood loss, complications, pain scores, success rate and cost, were compared between two groups.ResultsThere was no significant intergroup difference in terms of age, body mass index, gender composition and American Society of Anesthesiologists scores. A total of 31 patients underwent redo pyeloplasty and ten underwent redo uretero-ureterostomy. Compared with open group, robot-assisted group showed shorter operative time (124.55 min vs. 185.11 min, p < 0.0001), less estimated blood loss (100.00 mL vs. 182.60 mL, p = 0.008) and higher cost (61161.77¥ vs. 39470.79¥, p < 0.0001). Complication rate and pain scores were similar between two groups. Median follow-up periods were 30 and 48 months for robot-assisted and open group respectively. Success rate in the robot-assisted (85.71%) and the open group (82.35%) was not significantly different.ConclusionsRobot-assisted surgery for recurrent stricture after previous ureteral reconstruction is as effective as open procedure and is associated with shorter operative time and less estimated blood loss. creator: Qing Wang creator: Yuchao Lu creator: Henglong Hu creator: Jiaqiao Zhang creator: Baolong Qin creator: Jianning Zhu creator: Najib Isse Dirie creator: Zongbiao Zhang creator: Shaogang Wang uri: https://doi.org/10.7717/peerj.8166 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: The response of fine root morphological and physiological traits to added nitrogen in Schrenk’s spruce (Picea schrenkiana) of the Tianshan mountains, China link: https://peerj.com/articles/8194 last-modified: 2019-12-04 description: Fine roots are essential for water and nutrient uptake in plants, but little is known about the variation in fine root traits and the underlying mechanisms that drive it. Understanding the responses of fine root function traits to changing environmental conditions and the role of fine root traits as drivers of forest ecosystem processes are critical for informing physiological and ecological theory as well as ecosystem management. We measured morphological and physiological traits of fine roots from six soil layers and three diameter classes in Schrenk’s spruce (Picea shrenkiana) forests of the Tianshan mountains, China. We found significant effects of nitrogen addition on these morphological and physiological traits, which varied by soil layer and root diameter. Specifically, specific root length (SRL) was higher in medium N addition group (N2) than in control group (N0). Specific root area (SRA) was higher in the control group (N0) than fertilized groups (N1, N2 and N3). Root tissue density (RTD) was higher in low N addition group (N1) than in the other group. Root dry matter content had no significant difference among four treatment groups. SRL, SRA, and RTD of fine roots in different diameter classes were all significantly different between high N addition (N3) and the control (N0) groups. The physiological characteristics of fine roots showed that soluble sugar (SS), fine root vitality (FRV), and tissue water content (TWC) in different soil layers were higher in the control group than in the fertilized groups. While soluble protein (SP), malondialdehyde (MDA) and free proline (FP) were lower in the control group (N0) than in the fertilized groups. In addition, SS, FRV, SP, TWC, FP, and MDA in all N addition treatments groups were significantly different from the control group. Fine root morphological traits were closely related to physiological traits, and added nitrogen inputs change these correlations. Our study confirms that nitrogen addition has specific effects on the morphological and physiological traits of fine roots of Schrenk’s spruce, and the effects of N addition vary according to the amount added. creator: Lu Gong creator: Jingjing Zhao uri: https://doi.org/10.7717/peerj.8194 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Gong and Zhao title: Migraine aura, a predictor of near-death experiences in a crowdsourced study link: https://peerj.com/articles/8202 last-modified: 2019-12-04 description: BackgroundNear-death experiences (NDE) occur with imminent death and in situations of stress and danger but are poorly understood. Evidence suggests that NDE are associated with rapid eye movement (REM) sleep intrusion, a feature of narcolepsy. Previous studies further found REM abnormalities and an increased frequency of dream-enacting behavior in migraine patients, as well as an association between migraine with aura and narcolepsy. We therefore investigated if NDE are more common in people with migraine aura.MethodsWe recruited 1,037 laypeople from 35 countries and five continents, without any filters except for English language and age ≥18 years, via a crowdsourcing platform. Reports were validated using the Greyson NDE Scale.ResultsEighty-one of 1,037 participants had NDE (7.8%; CI [6.3–9.7%]). There were no significant associations between NDE and age (p > 0.6, t-test independent samples) or gender (p > 0.9, Chi-square test). The only significant association was between NDE and migraine aura: 48 (6.1%) of 783 subjects without migraine aura and 33 (13.0%) of 254 subjects with migraine aura had NDE (p < 0.001, odds ratio (OR) = 2.29). In multiple logistic regression analysis, migraine aura remained significant after adjustment for age (p < 0.001, OR = 2.31), gender (p < 0.001, OR = 2.33), or both (p < 0.001, OR = 2.33).ConclusionsIn our sample, migraine aura was a predictor of NDE. This indirectly supports the association between NDE and REM intrusion and might have implications for the understanding of NDE, because a variant of spreading depolarization (SD), terminal SD, occurs in humans at the end of life, while a short-lasting variant of SD is considered the pathophysiological correlate of migraine aura. creator: Daniel Kondziella creator: Markus Harboe Olsen creator: Coline L. Lemale creator: Jens P. Dreier uri: https://doi.org/10.7717/peerj.8202 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Kondziella et al. title: Amino acids and acylcarnitine production by Chlorella vulgaris and Chlorella sorokiniana microalgae from wastewater culture link: https://peerj.com/articles/7977 last-modified: 2019-12-03 description: BackgroundMicroalgae are a widely distributed group of prokaryotic and eukaryotic photosynthetic microorganisms that use a number of substances present in wastewater to produce a variety of biotechnological and nutritional biomolecules.MethodsProduction ofamino acids and acylcarnitine by Chlorella vulgaris and Chlorella sorokiniana was determined after 13 d of culture in wastewater, under various culture conditions. Wastewater was collected from “La Encantada” stream, located in Saltillo, Coahuila, Mexico. Microalgae was cultured at 23°C and natural day light, including the use of the following conditions: (1) extra light (12:12 light:dark cycles, 1,380 lumens), (2) agitation (130 rpm), and (3) both conditions, until exponential phase. Supernatant products were then analyzed by liquid chromatograph coupled to mass spectrometry. In addition, metabolomic profiles related to growing conditions were evaluated.ResultsAmino acids and acylcarnitine production by C. sorokiniana and C. vulgaris resulted in higher Ala and Leu concentrations by C. vulgaris compared with control, where control produced Gly and Pro in higher amounts compared with C. sorokiniana. Tyr, Phe, Val, and Cit were detected in lower amounts under light and shaking culture conditions. High concentrations of C0 acylcarnitines were produced by both microalgae compared with control, where C. sorokiniana production was independent of culture conditions, whereas C. vulgaris one was stimulated by shaking. C4 production was higher by C. sorokiniana compared with control. Furthermore, C4, C6DC, C14:1, C14:2, and C18:1OH production by microalga was low in all culture conditions.ConclusionMicroalgae produced essential amino acids and nutritionally important carnitines from wastewater. In addition, C. sorokiniana biomass has higher potential as animal nutrient supplement, as compared with that of C. vulgaris. creator: Juan M. Ballesteros-Torres creator: Luis Samaniego-Moreno creator: Ricardo Gomez-Flores creator: Reyes S. Tamez-Guerra creator: Cristina Rodríguez-Padilla creator: Patricia Tamez-Guerra uri: https://doi.org/10.7717/peerj.7977 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ballesteros-Torres et al. title: The effect of diet on the structure of gut bacterial community of sympatric pair of whitefishes (Coregonus lavaretus): one story more link: https://peerj.com/articles/8005 last-modified: 2019-12-03 description: In the Coregonus lavaretus complex may be found lacustrine sympatric pairs, which serves as an intriguing model for studying different aspects of fish evolutionary biology. One such sympatric whitefish pair inhabits Teletskoye Lake (West Siberia, Russia) and includes a “large” form (Coregonus lavaretus pidschian (Gmelin, 1789)) and a “small” form (C. l. pravdinellus (Dulkeit, 1949)). C. l. pravdinellus has a narrow trophic specialization and feeds on zooplankton, whereas the diet of C. l. pidschian is based on benthic prey. In the present study we aimed to address the question of how the gut microbial community reflects the divergence in diet of a sympatric pair of whitefish. Studied samples included the mucosa and content were collected for cardiac and pyloric stomach, anterior, middle, and posterior intestine, but only mucosa was collected for the pyloric caeca. In addition, water, sediment, macrophyte (environmental microbiota) and invertebrate (microbiota of prey) samples were collected in the same location. The V3–V4 region of the 16S rRNA genes was chosen for microbiome analysis and the software PICRUSt used to estimate the difference functional roles of the microbiota. The number of OTUs and Chao1 index in mucosa and content of cardiac and pyloric stomach were significantly different between whitefish. Significant differences were observed between whitefish for content from different parts of the intestine in terms of OTU number and Chao1 indices, whereas for mucosa from the same parts of intestine these differences were absent. No significant differences were found for diversity estimates of mucosa and content of different parts of the gut (there were a few exceptions) between whitefish. The form of whitefish and the segment of the digestive system were factors with a significant determinative effect on the structure of the microbiota from gut mucosa and content. The most dominant phyla in mucosa and content of cardiac and pyloric stomach was Proteobacteria (57.0–84.0%) for both whitefish. Throughout the intestine of C. l. pidschian the dominant phyla in mucosa were Proteobacteria (38.8%) and Firmicutes (15.6%), whereas for C. l. pravdinellus–Tenericutes (49.6%) and Proteobacteria (28.1%). For both forms, the phylum Spirochaetes was found in a significant amount (20.0–25.0%) in the mucosa of the posterior intestine. While for the content obtained from anterior, middle and posterior intestines, the dominant bacterial phyla were the same as those described for mucosa from the same parts of the intestine for both whitefish. The bacterial community of the prey and environment was significantly different from bacterial communities found for all parts of the gut mucosa for both whitefish, with the exception of the mucosa of the cardiac stomach. According to PICRUSt the highest level of differences between whitefish at the L3 level were found for the intestinal mucosa (75.3%), whereas the lowest one was registered for stomach content (38.8%). creator: Mikhail M. Solovyev creator: Elena N. Kashinskaya creator: Nickolai A. Bochkarev creator: Karl B. Andree creator: Evgeniy Simonov uri: https://doi.org/10.7717/peerj.8005 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Solovyev et al. title: Phospholipase A2 from krait Bungarus fasciatus venom induces human cancer cell death in vitro link: https://peerj.com/articles/8055 last-modified: 2019-12-03 description: BackgroundSnake venoms are the complex mixtures of different compounds manifesting a wide array of biological activities. The venoms of kraits (genus Bungarus, family Elapidae) induce mainly neurological symptoms; however, these venoms show a cytotoxicity against cancer cells as well. This study was conducted to identify in Bungarus fasciatus venom an active compound(s) exerting cytotoxic effects toward MCF7 human breast cancer cells and A549 human lung cancer cells.MethodsThe crude venom of B. fasciatus was separated by gel-filtration on Superdex HR 75 column and reversed phase HPLC on C18 column. The fractions obtained were screened for cytotoxic effect against MCF7, A549, and HK2 cell lines using colorimetric assay with the tetrazolium dye MTT- 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide. The primary structure of active protein was established by ultra high resolution LC-MS/MS. The molecular mechanism of the isolated protein action on MCF7 cells was elucidated by flow cytometry.ResultsMTT cell viability assays of cancer cells incubated with fractions isolated from B. fasciatus venom revealed a protein with molecular mass of about 13 kDa possessing significant cytotoxicity. This protein manifested the dose and time dependent cytotoxicity for MCF7 and A549 cell lines while showed no toxic effect on human normal kidney HK2 cells. In MCF7, flow cytometry analysis revealed a decrease in the proportion of Ki-67 positive cells. As Ki-67 protein is a cellular marker for proliferation, its decline indicates the reduction in the proliferation of MCF7 cells treated with the protein. Flow cytometry analysis of MCF7 cells stained with propidium iodide and Annexin V conjugated with allophycocyanin showed that a probable mechanism of cell death is apoptosis. Mass spectrometric studies showed that the cytotoxic protein was phospholipase A2. The amino acid sequence of this enzyme earlier was deduced from cloned cDNA, and in this work it was isolated from the venom as a protein for the first time. It is also the first krait phospholipase A2 manifesting the cytotoxicity for cancer cells. creator: Thien V. Tran creator: Andrei E. Siniavin creator: Anh N. Hoang creator: My T.T. Le creator: Chuong D. Pham creator: Trung V. Phung creator: Khoa C. Nguyen creator: Rustam H. Ziganshin creator: Victor I. Tsetlin creator: Ching-Feng Weng creator: Yuri N. Utkin uri: https://doi.org/10.7717/peerj.8055 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tran et al. title: Warm temperatures, cool sponges: the effect of increased temperatures on the Antarctic sponge Isodictya sp. link: https://peerj.com/articles/8088 last-modified: 2019-12-03 description: Although the cellular and molecular responses to exposure to relatively high temperatures (acute thermal stress or heat shock) have been studied previously, only sparse empirical evidence of how it affects cold-water species is available. As climate change becomes more pronounced in areas such as the Western Antarctic Peninsula, both long-term and occasional acute temperature rises will impact species found there, and it has become crucial to understand the capacity of these species to respond to such thermal stress. Here, we use the Antarctic sponge Isodictya sp. to investigate how sessile organisms (particularly Porifera) can adjust to acute short-term heat stress, by exposing this species to 3 and 5 °C for 4 h, corresponding to predicted temperatures under high-end 2080 IPCC-SRES scenarios. Assembling a de novo reference transcriptome (90,188 contigs, >93.7% metazoan BUSCO genes) we have begun to discern the molecular response employed by Isodictya to adjust to heat exposure. Our initial analyses suggest that TGF-β, ubiquitin and hedgehog cascades are involved, alongside other genes. However, the degree and type of response changed little from 3 to 5 °C in the time frame examined, suggesting that even moderate rises in temperature could cause stress at the limits of this organism’s capacity. Given the importance of sponges to Antarctic ecosystems, our findings are vital for discerning the consequences of short-term increases in Antarctic ocean temperature on these and other species. creator: Marcelo González-Aravena creator: Nathan J. Kenny creator: Magdalena Osorio creator: Alejandro Font creator: Ana Riesgo creator: César A. Cárdenas uri: https://doi.org/10.7717/peerj.8088 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 González-Aravena et al.