title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1032 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Effects of changes in isotopic baselines on the evaluation of food web structure using isotopic functional indices link: https://peerj.com/articles/9999 last-modified: 2020-10-26 description: BackgroundThis study aimed to assess whether ecological inferences from isotopic functional indices (IFIs) are impacted by changes in isotopic baselines in aquatic food webs. We used sudden CO2-outgassing and associated shifts in DIC-δ13C brought by waterfalls as an excellent natural experimental set-up to quantify impacts of changes in algal isotopic baselines on ecological inferences from IFIs.MethodsCarbon (δ13C) and nitrogen (δ15N) stable isotopic ratios of invertebrate communities sharing similar structure were measured at above- and below-waterfall sampling sites from five rivers and streams in Southern Quebec (Canada). For each sampled invertebrate community, the six Laymans IFIs were then calculated in the δ -space (δ13C vs. δ15N).ResultsAs expected, isotopic functional richness indices, measuring the overall extent of community trophic space, were strongly sensitive to changes in isotopic baselines unlike other IFIs. Indeed, other IFIs were calculated based on the distribution of species within δ-space and were not strongly impacted by changes in the vertical or horizontal distribution of specimens in the δ-space. Our results highlighted that IFIs exhibited different sensitivities to changes in isotopic baselines, leading to potential misinterpretations of IFIs in river studies where isotopic baselines generally show high temporal and spatial variabilities. The identification of isotopic baselines and their associated variability, and the use of independent trophic tracers to identify the actual energy pathways through food webs must be a prerequisite to IFIs-based studies to strengthen the reliability of ecological inferences of food web structural properties. creator: Simon Belle creator: Gilbert Cabana uri: https://doi.org/10.7717/peerj.9999 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Belle and Cabana title: Conservation genomics and pollination biology of an endangered, edaphic-endemic, octoploid herb: El Dorado bedstraw (Galium californicum subsp. sierrae; Rubiaceae) link: https://peerj.com/articles/10042 last-modified: 2020-10-26 description: El Dorado bedstraw (Galium californicum subsp. sierrae) is a federally endangered dioecious, octoploid, perennial herb found only in the Pine Hill region of El Dorado County, CA, USA. Like many species of Galium, El Dorado bedstraw is capable of both sexual and asexual reproduction, spreading via stem-layering as well as seeds. El Dorado bedstraw is also dioecious, and thus dependent on pollinators to transfer pollen from male to female stems. The capacity for asexual reproduction has conservation implications for this plant, due to the potential for populations to become dominated by a small number of clones in the absence of recruitment from seeds. No previous work has examined either the population genetics or pollination biology of this plant. Here, double-digest restriction site-associated DNA sequencing was used to develop a genetic dataset for a sample of El Dorado bedstraw (12 individuals from each of seven locations). Genomic data was used to calculate population genetic statistics and quantify the degree to which clonality affects the sampled populations. Visual observation of insect visitors at every sampling location was used to assess the potential for pollen transfer within and among locations. A total of 23 clonal colonies were detected across 82 successfully sequenced stems, consisting of an average of 2.4 individuals (range: 2–6). Significant isolation by distance among locations was detected using a Mantel test. Insect pollinators were from eleven families, consisting mainly of small species with weak flight. It is recommended that clonality and small-scale population differentiation be taken into account in conservation measures. creator: Dylan Burge uri: https://doi.org/10.7717/peerj.10042 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Burge title: New record of podocopid ostracods from Cretaceous amber link: https://peerj.com/articles/10134 last-modified: 2020-10-26 description: Burmese Cretaceous amber (∼99 Ma, Myanmar) is famous for the preservation of a wide range of fauna and flora, including representatives of marine, freshwater and terrestrial groups. Here, we report on three ostracod specimens, that came visible as syninclusions to an aquatic isopod. The three specimens represent three different taxa, that were found preserved in a single piece of amber. One of the described specimens was studied using µCT scanning data. On the basis of general carapace morphology we assign all three to the group Podocopida, and (tentatively) its ingroup Cypridocopina. A lack of visibility of more particular diagnostic features such as adductor muscle scars and details of the marginal zone precludes a further identification, but we discuss possible affinities with either the marine-brackish group Pontocypridoidea or the non-marine group Cypridoidea. The taphonomy indicates that the studied ostracods had been subject to limited (if any) post-mortem transport, which could be consistent with marginal marine environments. creator: He Wang creator: Mario Schädel creator: Benjamin Sames creator: David J. Horne uri: https://doi.org/10.7717/peerj.10134 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: Spatial modeling could not differentiate early SARS-CoV-2 cases from the distribution of humans on the basis of climate in the United States link: https://peerj.com/articles/10140 last-modified: 2020-10-26 description: The SARS-CoV-2 coronavirus is wreaking havoc globally, yet, as a novel pathogen, knowledge of its biology is still emerging. Climate and seasonality influence the distributions of many diseases, and studies suggest at least some link between SARS-CoV-2 and weather. One such study, building species distribution models (SDMs), predicted SARS-CoV-2 risk may remain concentrated in the Northern Hemisphere, shifting northward in summer months. Others have highlighted issues with SARS-CoV-2 SDMs, notably: the primary niche of the virus is the host it infects, climate may be a weak distributional predictor, global prevalence data have issues, and the virus is not in population equilibrium. While these issues should be considered, we believe climate’s relationship with SARS-CoV-2 is still worth exploring, as it may have some impact on the distribution of cases. To further examine if there is a link to climate, we build model projections with raw SARS-CoV-2 case data and population-scaled case data in the USA. The case data were from across March 2020, before large travel restrictions and public health policies were impacting cases across the country. We show that SDMs built from population-scaled case data cannot be distinguished from control models (built from raw human population data), while SDMs built on raw case data fail to predict the known distribution of cases in the U.S. from March. The population-scaled analyses indicate that climate did not play a central role in early U.S. viral distribution and that human population density was likely the primary driver. We do find slightly more population-scaled viral cases in cooler areas. Ultimately, the temporal and geographic constraints on this study mean that we cannot rule out climate as a partial driver of the SARS-CoV-2 distribution. Climate’s role on SARS-CoV-2 should continue to be cautiously examined, but at this time we should assume that SARS-CoV-2 will continue to spread anywhere in the U.S. where governmental policy does not prevent spread. creator: Robert Harbert creator: Seth W. Cunningham creator: Michael Tessler uri: https://doi.org/10.7717/peerj.10140 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Harbert et al. title: Towards a unified generic framework to define and observe contacts between livestock and wildlife: a systematic review link: https://peerj.com/articles/10221 last-modified: 2020-10-26 description: Wild animals are the source of many pathogens of livestock and humans. Concerns about the potential transmission of economically important and zoonotic diseases from wildlife have led to increased surveillance at the livestock-wildlife interface. Knowledge of the types, frequency and duration of contacts between livestock and wildlife is necessary to identify risk factors for disease transmission and to design possible mitigation strategies. Observing the behaviour of many wildlife species is challenging due to their cryptic nature and avoidance of humans, meaning there are relatively few studies in this area. Further, a consensus on the definition of what constitutes a ‘contact’ between wildlife and livestock is lacking. A systematic review was conducted to investigate which livestock-wildlife contacts have been studied and why, as well as the methods used to observe each species. Over 30,000 publications were screened, of which 122 fulfilled specific criteria for inclusion in the analysis. The majority of studies examined cattle contacts with badgers or with deer; studies involving wild pig contacts with cattle or with domestic pigs were the next most frequent. There was a range of observational methods including motion-activated cameras and global positioning system collars. As a result of the wide variation and lack of consensus in the definitions of direct and indirect contacts, we developed a unified framework to define livestock-wildlife contacts that is sufficiently flexible to be applied to most wildlife and livestock species for non-vector-borne diseases. We hope this framework will help standardise the collection and reporting of contact data; a valuable step towards being able to compare the efficacy of wildlife-livestock observation methods. In doing so, it may aid the development of better disease transmission models and improve the design and effectiveness of interventions to reduce or prevent disease transmission. creator: Sonny A. Bacigalupo creator: Linda K. Dixon creator: Simon Gubbins creator: Adam J. Kucharski creator: Julian A. Drewe uri: https://doi.org/10.7717/peerj.10221 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bacigalupo et al. title: ZFPM2-AS1 promotes the proliferation, migration, and invasion of human non-small cell lung cancer cells involving the JAK-STAT and AKT pathways link: https://peerj.com/articles/10225 last-modified: 2020-10-26 description: PurposeRecent studies have determined that long non-coding RNAs (lncRNAs) are potential prognostic biomarkers for non-small cell lung cancers (NSCLCs). The purpose of this study was to analyze the function and associated pathways of zinc finger protein multitype 2 antisense RNA 1 (ZFPM2-AS1) in NSCLC cells.MethodsWe used qRT-PCR to analyze ZFPM2-AS1’s transcription level. Its proliferation, migration, and invasion capacities were determined using MTT, colony forming, wound healing, and transwell assays. We additionally analyzed the correlation between ZFPM2 and immune infiltration using the Tumor Immune Estimation Resource (TIMER) database, and the protein expression levels using Western blots.ResultsWe found that ZFPM2-AS1 expression in NSCLC specimens and cell lines was elevated compared to the control group. ZFPM2-AS1 is an oncogene and independent prognostic predictor of poor survival in NSCLCs, and its expression had a positive correlation with tumor size and lymph node metastasis in our clinical data. MTT, colony forming, wound healing, and transwell assays showed a positive correlation between ZFPM2-AS1 expression and the proliferation, migration, and invasion of NSCLC cells in the presence and absence of interferon- (IFN-γ). Using the TIMER database, we hypothesized that ZFPM2 was negatively correlated with ZFPM2-AS1 expression, as well as the immune infiltration levels in lung adenocarcinoma (LUAD). Finally, we found that ZFPM2-AS1 negatively regulated ZFPM2 expression, and had a positive correlation with PD-L1 expression through the JAK-STAT and AKT pathways.ConclusionOur study confirmed that ZFPM2-AS1 promotes the proliferation, migration, and invasion of NSCLC cells via the JAK-STAT and AKT pathways. Further research on the ZFPM2-AS1 pathway regulation mechanism is needed. creator: Xiwen Wang creator: Jun Tang creator: Jungang Zhao creator: Bin Lou creator: Li Li uri: https://doi.org/10.7717/peerj.10225 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: CRUNC: a cryopreservation method for unencapsulated gemmae of Marchantia polymorpha link: https://peerj.com/articles/10174 last-modified: 2020-10-23 description: Genetic modifications such as mutation and transformation are powerful tools to study the function of genes and proteins in the model liverwort Marchantia polymorpha, but maintaining the resulting germplasm requires a practical, reliable method. Cryopreservation methods allow researchers to maintain mutant and transgenic lines of M. polymorpha. To date, two methods have been developed for cryopreservation of M. polymorpha gemmae: in the first method, unencapsulated gemmae are stored in liquid nitrogen at −­196 °C, and in the second method, encapsulated gemmae are stored in liquid nitrogen at −­196 °C or a deep freezer at −80 °C. In the present study, we developed a simple method named CRUNC (cr yopreservation of un en c apsulated gemmae), which can be used to store unencapsulated, dried gemmae of wild-type and transgenic M. polymorpha lines in liquid nitrogen and in freezers at −80 °C and −20 °C. Using the CRUNC method, we observed a high recovery rate (as high as 100%) and successful long-term (5 months) storage of the gemmae. Therefore, the CRUNC method is practical for maintaining valuable M. polymorpha germplasm. creator: Hitomi Takahashi creator: Yutaka Kodama uri: https://doi.org/10.7717/peerj.10174 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Takahashi and Kodama title: Involvement of autophagy in realgar quantum dots (RQDs) inhibition of human endometrial cancer JEC cells link: https://peerj.com/articles/9754 last-modified: 2020-10-23 description: Realgar (As4S4) has been used in traditional Chinese medicines for treatment of malignancies. The poor solubility of As4S4 hampered its clinical applications. Realgar quantum dots (RQDs) were developed to overcome these problems. Previous studies revealed that the RQDs were effective against endometrial cancer JEC cells and hepatocarcinoma HepG2 cells via inducing apoptosis.Apoptosis and autophagy are important programmed cell death pathways leading to anticancer effects. This study further examined effects of RQDs on autophagy, focusing on the formation of the autophagosome in JEC cells. CCK8 assay was used to examine cell proliferation. Flow cytometry was used to analyze cell cycle. Transmission electron microscopy (TEM) was used to examine the autophagy, cells were transfected with pEGFP-C3-MAP1LC3B plasmid to examine effects of RQDs on autophagosome via confocal microscope. Autophagy-related proteins were examined by Western blot. RQDs exhibited cytotoxicity in JEC cells in a concentration- and time- dependent manner. RQDs induced G2 and S phase arrest in JEC cells. RQDs significantly induced autophagy, with the double-membrane and autophagosome-like structures by TEM. The diffused distribution of pEGFP-C3-MAP1LC3B green fluorescence were become the punctuate pattern fluorescence after treatment with RQDs in cells transfected with pEGFP-C3-MAP1LC3B plasmid RQDs increased the expression of autophagyregulatory proteins LC3 I/II, Beclin-1, p62 and Atg12 in a concentration-dependent manner, similar to autophagy induced by serum starvation, except for p62, as induction of p62 is a characteristic of arsenic compounds. Taken together, the present study clearly demonstrated that RQDs can induce autophagy in JEC cells as one of mechanisms of anticancer effects, and indicated that RQDs may be developed as an autophagy inducer. creator: Zhengyun Liu creator: Ke Xu creator: Yan Xu creator: Wanling Zhang creator: Nian Jiang creator: Shengyu Wang creator: Guo Luo creator: Jie Liu creator: Jinzhu Wu creator: Huan Wang uri: https://doi.org/10.7717/peerj.9754 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Liu et al. title: Molecular Detection Mapping and Analysis Platform for R (MDMAPR) facilitating the standardization, analysis, visualization, and sharing of qPCR data and metadata link: https://peerj.com/articles/9974 last-modified: 2020-10-23 description: Quantitative polymerase chain reaction (qPCR) has been used as a standard molecular detection tool in many scientific fields. Unfortunately, there is no standard method for managing published qPCR data, and those currently used generally focus on only managing raw fluorescence data. However, associated with qPCR experiments are extensive sample and assay metadata, often under-examined and under-reported. Here, we present the Molecular Detection Mapping and Analysis Platform for R (MDMAPR), an open-source and fully scalable informatics tool for researchers to merge raw qPCR fluorescence data with associated metadata into a standard format, while geospatially visualizing the distribution of the data and relative intensity of the qPCR results. The advance of this approach is in the ability to use MDMAPR to store varied qPCR data. This includes pathogen and environmental qPCR species detection studies ideally suited to geographical visualization. However, it also goes beyond these and can be utilized with other qPCR data including gene expression studies, quantification studies used in identifying health dangers associated with food and water bacteria, and the identification of unknown samples. In addition, MDMAPR’s novel centralized management and geospatial visualization of qPCR data can further enable cross-discipline large-scale qPCR data standardization and accessibility to support research spanning multiple fields of science and qPCR applications. creator: Jiaojia Yu creator: Robert G. Young creator: Lorna E. Deeth creator: Robert H. Hanner uri: https://doi.org/10.7717/peerj.9974 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yu et al. title: Genome-wide identification of Hsp70/110 genes in rainbow trout and their regulated expression in response to heat stress link: https://peerj.com/articles/10022 last-modified: 2020-10-23 description: Heat shock proteins (Hsps) play an important role in many biological processes. However, as a typical cold water fish, the systematic identification of Hsp70/110 gene family of rainbow trout (Oncorhynchus mykiss) has not been reported, and the role of Hsp70/110 gene in the evolution of rainbow trout has not been described systematically. In this study, bioinformatics methods were used to analyze the Hsp70/110 gene family of rainbow trout. A total of 16 hsp70/110 genes were identified and classified into ten subgroups. The 16 Hsp70/110 genes were all distributed on chromosomes 2, 4, 8 and 13. The molecular weight is ranged from 78.93 to 91.39 kD. Gene structure and motif composition are relatively conserved in each subgroup. According to RNA-seq analysis of rainbow trout liver and head kidney, a total of four out of 16 genes were significantly upregulated in liver under heat stress, and a total of seven out of 16 genes were significantly upregulated in head kidney. RT-qPCR was carried out on these gene, and the result were consistent with those of RNA-seq. The significantly regulated expressions of Hsp70/110 genes under heat stress indicats that Hsp70/110 genes are involved in heat stress response in rainbow trout. This systematic analysis provided valuable information about the diverse roles of Hsp70/110 in the evolution of teleost, which will contribute to the functional characterization of Hsp70/110 genes in further research. creator: Fang Ma creator: Lintong Luo uri: https://doi.org/10.7717/peerj.10022 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Ma and Luo