title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1232 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Critical multi-stranded approach for determining the ecological values of diatoms in unique aquatic ecosystems of anthropogenic origin link: https://peerj.com/articles/8117 last-modified: 2019-12-05 description: BackgroundThe ecological state of surface waters is typically assessed by a multi-aspect approach based on a determination of its chemical and physical parameters, by hydromorphology and the use of indicator organisms such as benthic diatoms. By assigning ecological indicator values, it is possible to create diatom indices which serve as the basic tool in assessing the ecological status of surface waters. These ecological indicator values are set according to classification systems, such as the Van Dam, Mertens & Sinkeldam (1994) system, which classifies species of diatoms according to seven different ecological factors. However, recent studies on the autecology of diatoms have shown the need to verify and establish new ecological indicator values. To this end, aquatic ecosystems are good environments to observe the range of tolerance of benthic diatoms to environmental conditions due to their unique physical and chemical parameters. The aim of the present study was to propose the establishment of new, or altered, ecological indicator values, according to the Van Dam, Mertens & Sinkeldam (1994) classification, of species of diatoms characteristic of three post-mining aquatic ecosystems.MethodsIn total, 36 species were identified that were characteristic of three waterbodies: a salt aquatic complex (water outflow, a drainage ditch and a pond), mined iron ore reservoirs and a mined lignite reservoir. Their ecological indicator values were specified using OMNIDIA software, and the environmental conditions prevailing in the studied ecosystems were determined. Of the 36 characteristic species, 16 lacking at least one assigned ecological indicator value were analyzed further. The analysis identified three groups of selected characteristic species which showed a correlation, or lack of such, to the tested physical and chemical parameters.ResultsBased on this multistage study of the autecology of characteristic diatoms, comprising an analysis of environmental conditions, literature analysis and reference ecological indicator values of other species, it is proposed that 32 ecological indicator values be established or adjusted for 16 species, and that Planothidium frequentissimum be excluded from water quality assessments. creator: Rafał M. Olszyński creator: Ewelina Szczepocka creator: Joanna Żelazna-Wieczorek uri: https://doi.org/10.7717/peerj.8117 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Olszyński et al. title: Design and preliminary application of affinity peptide based on the structure of the porcine circovirus type II Capsid (PCV2 Cap) link: https://peerj.com/articles/8132 last-modified: 2019-12-05 description: BackgroundAffinity peptides, as a core part of affinity chromatography, play an important role in the purification of target molecules.MethodsHere we describe the use of molecular docking technology for virtual screening of affinity peptides that specifically recognize the PCV2 Cap protein for the first time. Thirteen candidate peptides with high scores were obtained and then further characterized. Experimentally, the affinity and sensitivity of the peptides studied were identified by ELISA and LSPR, respectively. In order to investigate the purification effect of a selected peptide (L11) for the recombinant PCV2 Cap protein, it was coupled to NHS agarose magnetic beads as an affinity adsorbent (NaMB-L11); and the ligand density of the affinity adsorbent and pH value in the purification of the recombinant PCV2 Cap protein were optimized.ResultsOur data showed that the peptide L11- DYWWQSWE has the smallest KD = 103 nM with higher specificity for PCV2 Cap protein recognition. The NaMB-L11 affinity adsorbent yielded a purified Cap sample with 98% purity at 90% recovery in a single step.ConclusionBased on the structure, we obtained a high affinity peptide L11 binding to the PCV2 Cap protein by molecular docking technology. It not only provides a theoretical basis for the design of PCV2 Cap affinity peptide, but a new method for the purification of the PCV2 Cap protein. creator: Junfang Hao creator: Fangyu Wang creator: Guangxu Xing creator: Yunchao Liu creator: Ruiguang Deng creator: Hao Zhang creator: Anchun Cheng creator: Gaiping Zhang uri: https://doi.org/10.7717/peerj.8132 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hao et al. title: Bleaching and post-bleaching mortality of Acropora corals on a heat-susceptible reef in 2016 link: https://peerj.com/articles/8138 last-modified: 2019-12-05 description: In 2016, global temperatures were the highest on record, and mass coral bleaching occurred world-wide. However, around Sesoko Island, Okinawa, southwestern Japan, the heat stress assessed by degree heating week (DHW) based on local temperature measurements was moderate in 2016; in 1998, DHW was three times higher than in 2016 (10.6 vs. 3.3 in September in respective years). On a reef flat of Sesoko Island where the effect of severe coral bleaching on coral assemblage was monitored in 1998, significant coral bleaching occurred in 2016. Bleaching of the heat stress sensitive Acropora corals began in July 2016 on the reef flat as seawater temperature rose. We observed the bleaching and post-bleaching mortality status of individual colonies of Acropora spp. in 2016 in fixed plots on the reef flat. In total, 123 Acropora colonies were followed for six months after seawater temperature became normal by multiple surveys. At the beginning of September 2016, 99.2% of colonies, were either completely (92.7%) or partially (6.5%) bleached. Of those, the dominant species or species groups were A. gemmifera (Ag), A. digitifera (Ad), and tabular Acropora (tA). For all Acropora colonies, the overall whole and partial mortality was 41.5% and 11.4%, respectively. Whole mortality rate differed significantly among species; 72.5%, 17.9%, and 27.8% in Ag, Ad, and tA, respectively. Mortality rates at the end of the surveys were similar in smaller (≤10 cm in diameter) and larger Ag, but the former suffered mortality earlier than the latter. Higher survival of smaller colonies was observed only in tA (100%), which may be associated with large morphological differences between smaller and larger colonies. Some of the dominant Acropora colonies had survived without partial mortality including 15.0% survival of the most vulnerable Ag at the end of the surveys. These results suggest that moderate heat stress may have a potential for selecting heat-tolerant genotypes. A longer period of mortality lasting for six months, was observed in Ag in addition to immediate whole mortality after bleaching, due to the continuous loss of living tissue by partial mortality. This highlights the need for multiple surveys at least during several months to accurately assess the impact of thermal stress event to corals. In contrast to DHW based on local measurements, DHW obtained from satellite data were similar between 1998 and 2016. Although satellite-based measurement of sea surface temperature is very useful to reveal variations in heat stress at a large spatial scale, temperature should be measured on site when variations at smaller spatial scales are of interest. creator: Kazuhiko Sakai creator: Tanya Singh creator: Akira Iguchi uri: https://doi.org/10.7717/peerj.8138 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sakai et al. 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.