title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1354 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: P5CR1 protein expression and the effect of gene-silencing on lung adenocarcinoma link: https://peerj.com/articles/6934 last-modified: 2019-05-14 description: The present study aimed to investigate the expression of pyrroline-5-carboxylate reductase 1 (P5CR1) protein in lung adenocarcinoma and paracancerous tissues and to explore the effect of silencing the encoding gene PYCR1 on the proliferation, migration, invasion, and cisplatin sensitivity in lung adenocarcinoma cells, thereby providing a novel therapeutic target for the treatment of the disease. Immunohistochemistry staining was used to detect the P5CR1 protein expression in lung adenocarcinoma and paracancerous tissues, and statistical analysis evaluated the correlation between P5CR1 protein expression and gender, age, tissue part, or pathological grade. The CCK8 assay was performed to detect the proliferation and cisplatin sensitivity, while the effect of PYCR1 on the migration and invasion of lung adenocarcinoma cells was detected by scratch test and transwell chamber assay. The findings demonstrated that the P5CR1 protein expression was significantly elevated in lung adenocarcinoma tissues and correlated with the pathological grade, whereas no significant correlation was established between the protein expression and gender, age, or tissue part. Furthermore, after PYCR1 gene silencing, the proliferation and invasion were significantly suppressed, while the sensitivity to cisplatin was significantly enhanced. Therefore, it can be speculated that the PYCR1 gene affects the biological behavior of lung adenocarcinoma and cisplatin resistance, serving as a potential therapeutic target for lung adenocarcinoma. creator: Yang She creator: Aiyou Mao creator: Feng Li creator: Xiaobin Wei uri: https://doi.org/10.7717/peerj.6934 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 She et al. title: Association between iscR-based phylogeny, serovars and potential virulence markers of Haemophilus parasuis link: https://peerj.com/articles/6950 last-modified: 2019-05-14 description: Haemophilus parasuis is an economically important bacterial pathogen of swine. Extensive genetic and phenotypic heterogeneity among H. parasuis strains have been observed, which hinders the deciphering of the population structure and its association with clinical virulence. In this study, two highly divergent clades were defined according to iron–sulphur cluster regulator (iscR)-based phylogeny analysis of 148 isolates. Clear separation of serovars and potential virulence markers (PVMs) were observed between the two clades, which are indicative of independent evolution of the two lineages. Previously suggested virulence factors showed no correlation with clinical virulence, and were probably clade or serovar specific genes emerged during different stage of evolution. PVMs profiles varied widely among isolates in the same serovar. Higher strain diversity in respect of PVMs was found for isolates from multi-strain infected farms than those from single strain infected ones, which indicates that multi-strain infection in one farm may increase the frequency of gene transfer in H. parasuis. Systemic isolates were more frequently found in serovar 13 and serovar 12, while no correlation between clinical virulence and iscR-based phylogeny was observed. It shows that iscR is a reliable marker for studying population structure of H. parasuis, while other factors should be included to avoid the interference of gene exchange of iscR between isolates. The two lineages of H. parasuis may have undergone independent evolution, but show no difference in clinical virulence. Wide distribution of systemic isolates across the entire population poses new challenge for development of vaccine with better cross-protection. Our study provides new information for better deciphering the population structure of H. parasuis, which helps understanding the extreme diversity within this pathogenic bacterium. creator: Junxing Li creator: Lihua Xu creator: Fei Su creator: Bin Yu creator: Xiufang Yuan uri: https://doi.org/10.7717/peerj.6950 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Li et al. title: Alternative bait trials in the Barents Sea snow crab fishery link: https://peerj.com/articles/6874 last-modified: 2019-05-13 description: Commercial harvesting of snow crab (Chionoecetes opilio) in the Barents Sea started in 2012 by Norwegian fishing vessels. This new fishery has significant bait requirements, representing an emerging conservation challenge. In this study, we evaluate the performance of five alternative (natural) baits manufactured from the waste stream of existing and sustainably managed harp seal (Pagophilus groenlandicus) and minke whale (Balaenoptera acutorostrata) capture. Five different types of new bait were evaluated, including seal fat (SF), seal fat with skin (SFS), seal meat with bone (SMB), whale fat with skin (WFS), and whale meat with fat (WMF). A comparative fishing experiment was conducted onboard a commercial snow crab fishing vessel in the Barents Sea (May–June, 2016) to evaluate the performance of traditional bait (squid, Illexs spp.) and alternative baits at catching snow crabs. Performance of the different baits were compared on the basis of the number of commercial crab caught per trap haul catch per unit effort (CPUE) and carapace width (CW). Our results showed that SF and SFS performed equally well to traditional bait, with no statistical difference in CPUE (p-value = 0.325 and 0.069, respectively). All of the other experimental baits significantly decreased CPUE, when compared to squid. No significant effect of bait treatment on CW was detected and the cumulative distribution of CW was the same between control traps and each of the bait treatments. Overall the results indicated that SF and SFS represent a viable alternative to replace traditional bait, addressing a key conservation challenge in this bait intensive snow crab fishery. creator: Tomas Araya-Schmidt creator: Leonore Olsen creator: Lasse Rindahl creator: Roger B. Larsen creator: Paul D. Winger uri: https://doi.org/10.7717/peerj.6874 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Araya-Schmidt et al. title: The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast link: https://peerj.com/articles/6883 last-modified: 2019-05-13 description: The clinging jellyfish Gonionemus sp. is a small hydromedusa species known historically from the Swedish west coast but not reported in recent times. This species is thought to be native to the northwest Pacific where it is notorious for causing severe stings in humans and is considered invasive or cryptogenic elsewhere. This year, unlike in the past, severe stings in swimmers making contact with Gonionemus sp. medusae occurred in Swedish waters from a sheltered eelgrass bed in the inner Skagerrak archipelago. To the best of our knowledge, this is only the second sting record of Gonionemus sp. from the Northeast Atlantic—with the first record occurring off the Belgian coast in the 1970s. Stinging Gonionemus sp. medusae have also been recently reported from the northwestern Atlantic coast, where, like on the Swedish coast, stings were not reported in the past. We analyzed sea surface temperature data from the past 30 years and show that 2018 had an exceptionally cold spring followed by an exceptionally hot summer. It is suggested that the 2018 temperature anomalies contributed to the Swedish outbreak. An analysis of mitochondrial COI sequences showed that Swedish medusae belong to the same clade as those from toxic populations in the Sea of Japan and northwest Atlantic. Gonionemus sp. is particularly prone to human-mediated dispersal and we suggest that it is possible that this year’s outbreak is the result of anthropogenic factors either through a climate-driven northward range shift or an introduction via shipping activity. We examined medusa growth rates and details of medusa morphology including nematocysts. Two types of penetrating nematocysts: euryteles and b-mastigophores were observed, suggesting that Gonionemus sp. medusae are able to feed on hard-bodied organisms like copepods and cladocerans. Given the now-regular occurrence and regional spread of Gonionemus sp. in the northwest Atlantic, it seems likely that outbreaks in Sweden will continue. More information on its life cycle, dispersal mechanisms, and ecology are thus desirable. creator: Annette F. Govindarajan creator: Björn Källström creator: Erik Selander creator: Carina Östman creator: Thomas G. Dahlgren uri: https://doi.org/10.7717/peerj.6883 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Govindarajan et al. title: Towards an in-depth characterization of Symbiodiniaceae in tropical giant clams via metabarcoding of pooled multi-gene amplicons link: https://peerj.com/articles/6898 last-modified: 2019-05-13 description: High-throughput sequencing is revolutionizing our ability to comprehensively characterize free-living and symbiotic Symbiodiniaceae, a diverse dinoflagellate group that plays a critical role in coral reef ecosystems. Most studies however, focus on a single marker for metabarcoding Symbiodiniaceae, potentially missing important ecological traits that a combination of markers may capture. In this proof-of-concept study, we used a small set of symbiotic giant clam (Tridacna maxima) samples obtained from nine French Polynesian locations and tested a dual-index sequence library preparation method that pools and simultaneously sequences multiple Symbiodiniaceae gene amplicons per sample for in-depth biodiversity assessments. The rationale for this approach was to allow the metabarcoding of multiple genes without extra costs associated with additional single amplicon dual indexing and library preparations. Our results showed that the technique effectively recovered very similar proportions of sequence reads and dominant Symbiodiniaceae clades among the three pooled gene amplicons investigated per sample, and captured varying levels of phylogenetic resolution enabling a more comprehensive assessment of the diversity present. The pooled Symbiodiniaceae multi-gene metabarcoding approach described here is readily scalable, offering considerable analytical cost savings while providing sufficient phylogenetic information and sequence coverage. creator: Xavier Pochon creator: Patricia Wecker creator: Michael Stat creator: Véronique Berteaux-Lecellier creator: Gaël Lecellier uri: https://doi.org/10.7717/peerj.6898 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Pochon et al. title: The interactive effect of herbivory, nutrient enrichment and mucilage on shallow rocky macroalgal communities link: https://peerj.com/articles/6908 last-modified: 2019-05-13 description: This paper focuses on the interactive short and long-term effect of three different stressors on a macroalgal assemblage. Three stressors are considered: herbivory, nutrients and mucilage. The experiment was conducted in Tavolara Punta Coda Cavallo Marine Protected Area (Mediterranean Sea) during a bloom of the benthic mucilage-producing microalga Chrysophaeum taylorii (Pelagophyceae); this microalga is recently spreading in the Mediterranean Sea. On a rocky substratum, 36 plots 20 × 20 cm in size were prepared. Factorial combinations of three experimental treatments were applied in triplicate, including three grazing levels crossed with two nutrient enrichment and two mucilage removal treatments. Significant differences were observed among treatments 8 weeks later, at the end of summer. In particular, dark filamentous algae were more abundant in all enriched plots, especially where mucilage and macroalgae had been removed; a higher percent cover of crustose coralline algae was instead observed where nutrients had been increased and no grazing pressure acted. Furthermore, the abundance of Dictyota spp. and Laurencia spp. was significantly higher in enriched mucilage-free plots where the grazing pressure was null or low. However, the effects of the treatments on the overall assemblage of the macroalgal community were not long persistent (36 weeks later). These results illustrate the capacity of a shallow-water macroalgal community to quickly recover from the simultaneous impacts of herbivory, nutrient enrichment, and mucilage. creator: Sarah Caronni creator: Chiara Calabretti creator: Sandra Citterio creator: Maria Anna Delaria creator: Rodolfo Gentili creator: Giovanni Macri creator: Chiara Montagnani creator: Augusto Navone creator: Pieraugusto Panzalis creator: Giulia Piazza creator: Giulia Ceccherelli uri: https://doi.org/10.7717/peerj.6908 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Caronni et al. title: Using GIS to examine biogeographic and macroevolutionary patterns in some late Paleozoic cephalopods from the North American Midcontinent Sea link: https://peerj.com/articles/6910 last-modified: 2019-05-13 description: Geographic range is an important macroevolutionary parameter frequently considered in paleontological studies as species’ distributions and range sizes are determined by a variety of biotic and abiotic factors well known to affect the differential birth and death of species. Thus, considering how distributions and range sizes fluctuate over time can provide important insight into evolutionary dynamics. This study uses Geographic Information Systems (GIS) and analyses of evolutionary rates to examine how in some species within the Cephalopoda, an important pelagic clade, geographic range size and rates of speciation and extinction changed throughout the Pennsylvanian and early Permian in the North American Midcontinent Sea. This period is particularly interesting for biogeographic and evolutionary studies because it is characterized by repetitive interglacial-glacial cycles, a global transition from an icehouse to a greenhouse climate during the Late Paleozoic Ice Age, and decelerated macroevolutionary dynamics, i.e. low speciation and extinction rates. The analyses presented herein indicate that cephalopod species diversity was not completely static and actually fluctuated throughout the Pennsylvanian and early Permian, matching findings from other studies. However, contrary to some other studies, the mean geographic ranges of cephalopod species did not change significantly through time, despite numerous climate oscillations; further, geographic range size did not correlate with rates of speciation and extinction. These results suggest that pelagic organisms may have responded differently to late Paleozoic climate changes than benthic organisms, although additional consideration of this issue is needed. Finally, these results indicate that, at least in the case of cephalopods, macroevolution during the late Paleozoic was more dynamic than previously characterized, and patterns may have varied across different clades during this interval. creator: Kayla M. Kolis creator: Bruce S. Lieberman uri: https://doi.org/10.7717/peerj.6910 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Kolis and Lieberman title: Conspecific coprophagy stimulates normal development in a germ-free model invertebrate link: https://peerj.com/articles/6914 last-modified: 2019-05-13 description: Microbial assemblages residing within and on animal gastric tissues contribute to various host beneficial processes that include diet accessibility and nutrient provisioning, and we sought to examine the degree to which intergenerational and community-acquired gut bacteria impact development in a tractable germ-free (GF) invertebrate model system. Coprophagy is a common behavior in cockroaches and termites that provides access to both nutrients and the primary means by which juveniles are inoculated with beneficial gut bacteria. This hypothesis was tested in the American cockroach (Periplaneta americana) by interfering with this means of acquiring gut bacteria, which resulted in GF insects that exhibited prolonged growth rates and gut tissue dysmorphias relative to wild-type (WT) P. americana. Conventionalization of GF P. americana via consumption of frass (feces) from conspecifics and siblings reared under non-sterile conditions resulted in colonization of P. americana gut tissues by a diverse microbial community and a significant (p < 0.05) recovery of WT level growth and hindgut tissue development phenotypes. These data suggest that coprophagy is essential for normal gut tissue and organismal development by introducing beneficial gut bacteria to P. americana, and that the GF P. americana model system is a useful system for examining how gut bacteria impact host outcomes. creator: Benjamin C. Jahnes creator: Madeline Herrmann creator: Zakee L. Sabree uri: https://doi.org/10.7717/peerj.6914 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jahnes et al. title: Plant diversity is closely related to the density of zokor mounds in three alpine rangelands on the Tibetan Plateau link: https://peerj.com/articles/6921 last-modified: 2019-05-13 description: BackgroundPlateau zokor (Myospalax baileyi) is a subterranean rodent endemic to the Tibetan Plateau. This species has been generally viewed as a pest in China due to the competition for food with livestock and also causing soil erosion. As a result, plateau zokor has been the target of widespread poisoning or trapping campaigns designed to control or eliminate it since 1970s. But there is little research on the effect of plateau zokor on plant diversity in alpine rangelands. Therefore, objectively evaluating the positive effects of the plateau zokors disturbance on their living environment and plant communities is of great significance to understand the function of plateau zokor in alpine ecosystem.MethodsHere, we selected three rangelands (alpine meadow, alpine steppe and alpine shrub meadow) in which plateau zokors are typically distributed on the Tibetan Plateau, and five zokor mound density gradients were selected in each rangeland type to study the effects of the mounds on soil moisture and temperature related to plant species diversity.ResultsThe results showed that, with the mound density increasing, the soil temperature decreased significantly in all three rangeland types, and the soil moisture significantly increased in all three rangeland types. In the alpine meadow, both the plant diversity and cumulative species richness increased significantly with increasing mound density. The increase in broad-leaved forbs is the main reason for the increase of plant diversity in the alpine meadow disturbed by zokor mounds. In the alpine steppe, the plant diversity decreased significantly with increasing mound density, while the cumulative species richness initially decreased and then increased. In the alpine shrub meadow, the plant diversity first increased and then decreased with increasing mound density as did the cumulative species richness. In conclusion, plateau zokor mounds dominated the distribution of soil moisture and temperature and significantly affected plant diversity in these three rangelands on Tibetan Plateau; the results further deepen our understanding toward a co-evolved process. creator: Yujie Niu creator: Jianwei Zhou creator: Siwei Yang creator: Bin Chu creator: Huimin Zhu creator: Bo Zhang creator: Qiangen Fang creator: Zhuangsheng Tang creator: Limin Hua uri: https://doi.org/10.7717/peerj.6921 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Niu et al. title: Automated pupillometry to detect command following in neurological patients: a proof-of-concept study link: https://peerj.com/articles/6929 last-modified: 2019-05-13 description: BackgroundLevels of consciousness in patients with acute and chronic brain injury are notoriously underestimated. Paradigms based on electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) may detect covert consciousness in clinically unresponsive patients but are subject to logistical challenges and the need for advanced statistical analysis.MethodsTo assess the feasibility of automated pupillometry for the detection of command following, we enrolled 20 healthy volunteers and 48 patients with a wide range of neurological disorders, including seven patients in the intensive care unit (ICU), who were asked to engage in mental arithmetic.ResultsFourteen of 20 (70%) healthy volunteers and 17 of 43 (39.5%) neurological patients, including 1 in the ICU, fulfilled prespecified criteria for command following by showing pupillary dilations during ≥4 of five arithmetic tasks. None of the five sedated and unconscious ICU patients passed this threshold.ConclusionsAutomated pupillometry combined with mental arithmetic appears to be a promising paradigm for the detection of covert consciousness in people with brain injury. We plan to build on this study by focusing on non-communicating ICU patients in whom the level of consciousness is unknown. If some of these patients show reproducible pupillary dilation during mental arithmetic, this would suggest that the present paradigm can reveal covert consciousness in unresponsive patients in whom standard investigations have failed to detect signs of consciousness. creator: Alexandra Vassilieva creator: Markus Harboe Olsen creator: Costanza Peinkhofer creator: Gitte Moos Knudsen creator: Daniel Kondziella uri: https://doi.org/10.7717/peerj.6929 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Vassilieva et al.