title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1234 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Effectiveness of water-saving technologies during early stages of restoration of endemic Opuntia cacti in the Galápagos Islands, Ecuador link: https://peerj.com/articles/8156 last-modified: 2019-12-03 description: Restoration of keystone species is a primary strategy used to combat biodiversity loss and recover ecological services. This is particularly true for oceanic islands, which despite their small land mass, host a large fraction of the planet’s imperiled species. The endemic Opuntia spp. cacti are one example and a major focus for restoration in the Galápagos archipelago, Ecuador. These cacti are keystone species that support much of the unique vertebrate animal community in arid zones, yet human activities have substantially reduced Opuntia populations. Extreme aridity poses an obstacle for quickly restoring Opuntia populations though water-saving technologies may provide a solution. The aim of this study was to evaluate current restoration efforts and the utility of two water-saving technologies as tools for the early stages of restoring Opuntia populations in the Galápagos archipelago. We planted 1,425 seedlings between 2013 and 2018, of which 66% had survived by the end of 2018. Compared with no-technology controls, seedlings planted with Groasis Waterboxx® water-saving technology (polypropylene trays with water reservoir and protective refuge for germinants) had a greater rate of survival in their first two-years of growth on one island (Plaza Sur) and greater growth rate on four islands whereas the “Cocoon” water-saving technology (similar technology but made of biodegradable fiber) did not affect growth and actually reduced seedling survival. Survival and growth rate were also influenced by vegetation zone, elevation, and precipitation in ways largely contingent on island. Overall, our findings suggest that water-saving technologies are not always universally applicable but can substantially increase the survival and growth rate of seedlings in certain conditions, providing in some circumstances a useful tool for improving restoration outcomes for rare plants of arid ecosystems. creator: Patricia Isabela Tapia creator: Luka Negoita creator: James P. Gibbs creator: Patricia Jaramillo uri: https://doi.org/10.7717/peerj.8156 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Tapia et al. title: Different distant metastasis patterns based on tumor size could be found in extensive-stage small cell lung cancer patients: a large, population-based SEER study link: https://peerj.com/articles/8163 last-modified: 2019-12-03 description: Background Small-cell lung cancer (SCLC) is a malignant cancer with the ability to metastasize quickly. The relationship between tumor size and the distant metastasis patterns of Extensive-Stage Small Cell Lung Cancer (ES-SCLC) has not been reported.ObjectivesThe aim of this study was to determine the different distant metastasis patterns as they related to tumor size in ES-SCLC.Patients and MethodsWe used Surveillance, Epidemiology, and End Results (SEER) population-based data collected from 2010 through 2013 to identify 11058 ES-SCLC patients with definite evidence of distant metastases. Multivariate logistic regression analysis was used to demonstrate the association between tumor size and distant metastasis patterns including bone, liver, brain, and lung metastases. Age, race, sex, and N stage were also selected in the logistic regression model.ResultsSubtle differences in metastasis patterns were found among patients based on different tumor sizes. Patients with tumors 3–7 cm have a higher risk of bone metastasis compared with those that have tumors ≤3 cm (OR 1.165, 95% CI [1.055–1.287], P = 0.003) and patients with tumors ≥7 cm have a higher risk of lung metastasis (OR 1.183, 95% CI [1.039–1.347], P = 0.011). In addition, patients with tumors ≥7 cm had a lower risk of brain metastasis and liver metastasis than patients with tumors ≤3 cm (OR 0.799, 95% CI [0.709–0.901], P < 0.001; OR 0.747, 95% CI [0.672–0.830], P < 0.001). Interestingly, there was no correlation between a larger tumor and a higher risk of metastasis. However, the tumor metastasis pattern did have some correlation with age, gender, race and N-status.ConclusionThe pattern of distant metastasis of ES-SCLC is related to the tumor size and the tumor size is indicative of the metastatic site. Larger tumor sizes did not correlate with a higher risk of distant metastasis, but the size is related to the pattern of distant metastasis. The study of different distant metastasis patterns based on tumor size and other clinical features (e.g., age, race, sex, and N stage) in ES-SCLC is clinically valuable. creator: Jia Li creator: Feng Liu creator: Haining Yu creator: Chenglong Zhao creator: Zhenxiang Li creator: Haiyong Wang uri: https://doi.org/10.7717/peerj.8163 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Switching between standard coral reef benthic monitoring protocols is complicated: proof of concept link: https://peerj.com/articles/8167 last-modified: 2019-12-03 description: Monitoring the state of coral reefs is necessary to identify drivers of change and assess effectiveness of management actions. There are several widely-used survey methods, each of which is likely to exhibit different biases that should be quantified if the purpose is to combine datasets obtained via different survey methods. The latter is a particularly important consideration when switching methodologies in long-term monitoring programs and is highly relevant to the Caribbean today. This is because of the continuing need for regionally comparable coral reef monitoring datasets and the fact that the Global Coral Reef Monitoring Network (GCRMN)-Caribbean node is now recommending a photoquadrat (PQ) method over the chain intercept transect method widely adopted by the members of the first truly regional monitoring network, Caribbean Coastal Marine Productivity Program (CARICOMP), in the early-1990s. Barbados, a member of the CARICOMP network, has been using a variation of the chain intercept method in its long-term coral reef monitoring program for more than two decades. Now a member of GCRMN-Caribbean, Barbados is considering switching to the PQ method in conformity with other regional members. Since we expect differences between methods, this study seeks to quantify the nature of those differences to inform Barbados and others considering switching methods. In 2017, both methods were concurrently implemented at 21 permanent monitoring plots across three major reef types in Barbados. Differences in % cover estimates for the six major benthic components, that is, hard corals, sponges, gorgonians, macroalgae, turf algae and crustose coralline algae, were examined within and among reef types. Overall, we found a complex pattern of differences between methods that depended on the benthic component, its relative abundance, and the reef type. We conclude that most benthic components would require a different conversion procedure depending on the reef type, and we provide an example of these procedures for Barbados. The factors that likely contribute to the complex pattern of between-method differences are discussed. Overall, our findings highlight that switching methods will be complicated, but not impossible. Finally, our study fills an important gap by underscoring a promising analytical framework to guide the comparison of ecological survey methods on coral reefs. creator: Henri Vallès creator: Hazel A. Oxenford creator: Alex Henderson uri: https://doi.org/10.7717/peerj.8167 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Vallès et al. title: Sentence comprehension in patients with dementia of the Alzheimer’s type link: https://peerj.com/articles/8181 last-modified: 2019-12-03 description: Sentence comprehension is diminished in patients with dementia of the Alzheimer’s type (DAT). However, the underlying reason for such deficits is still not entirely clear. The Syntactic Deficit Hypothesis attributes sentence comprehension deficits in DAT patients to the impairment in syntactic ability, whereas the Processing Resource Deficit Hypothesis proposes that sentence comprehension deficits are the result of working memory deficiency. This study investigated the deficits in sentence comprehension in Chinese-speaking DAT patients with different degrees of severity using sentence-picture matching tasks. The study revealed a significant effect of syntactic complexity in patients and healthy controls, but the effect was stronger in patients than in healthy controls. When working memory demand was minimized, the effect of syntactic complexity was only significant in patients with moderate DAT, but not in healthy controls or those with mild DAT. The findings suggest that in patients with mild DAT, working memory decline was the major source of sentence comprehension difficulty and in patients with moderate DAT, working memory decline and syntactic impairment jointly contributed to the impairments in sentence comprehension. The source of sentence comprehension deficits varied with degree of dementia severity. creator: Xinmiao Liu creator: Wenbin Wang creator: Haiyan Wang creator: Yu Sun uri: https://doi.org/10.7717/peerj.8181 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Liu et al. title: Overexpression of VEGF-C and MMP-9 predicts poor prognosis in Kazakh patients with esophageal squamous cell carcinoma link: https://peerj.com/articles/8182 last-modified: 2019-12-03 description: Vascular endothelial growth factor (VEGF) and Matrix metalloproteinases (MMPs) are believed to participate in infiltration of tumors. High mortality of esophageal squamous cell carcinoma (ESCC) related to its primary infiltration; however, it is not clear whether the expression of VEGF and MMPs is involved in this process. Screening of The Cancer Genome Atlas (TCGA) database showed that among the VEGF family and MMP9, VEGF-A, VEGF-C, and MMP-9 mRNA were overexpression in ESCC. This result was verified using the Oncomine database and in Kazakh patients with ESCC. Overexpression of VEGF-C and MMP-9 and positive association with advanced esophageal cancer and invading ESCC cells (Gene Expression Omnibus (GEO): GSE21293). Immunohistochemical staining revealed that VEGF-C and MMP-9 were overexpressed in Kazakh ESCCs. VEGF-C expression was related to invasive depth, tumor-node-metastasis (TNM) staging, lymphatic, and lymph node metastasis of ESCC. The linear association between them was further confirmed in TCGA database and the specimens from Kazakh patients with ESCC. Patients with both proteins expression had tumors with greater aggressiveness, suffered from poor prognosis compared with patients who did not express either protein or expressed protein alone. Both proteins expression predicted high invasiveness of ESCC, which is related to worse prognosis of Kazakh ESCCs. creator: Jiangfen Li creator: Yufang Xie creator: Xueli Wang creator: Chenhao Jiang creator: Xin Yuan creator: Anzhi Zhang creator: Chunxia Liu creator: Lijuan Pang creator: Feng Li creator: Jianming Hu uri: https://doi.org/10.7717/peerj.8182 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Comparative genomic analysis of the PAL genes in five Rosaceae species and functional identification of Chinese white pear link: https://peerj.com/articles/8064 last-modified: 2019-12-02 description: Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PALs into three categories based on phylogenetic analysis, and all PALs were distributed on 13 chromosomes. We tracked gene duplication events and performed sliding window analysis. These results revealed the evolution of PALs in five Rosaceae plants. We predicted the promoter of the PbPALs by PLANT CARE online software, and found that the promoter region of both PbPAL1 and PbPAL3 have at least one AC element. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stems and roots, while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flowering. Three PbPALs were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 into Arabidopsis thaliana, which resulted in an increase in lignin content and thickening of the cell walls of intervascular fibres and xylem cells. In summary, this research laid a foundation for better understanding the molecular evolution of PALs in five Rosaceae plants. Furthermore, the present study revealed the role of PbPALs in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cells development in pear plants. creator: Guohui Li creator: Han Wang creator: Xi Cheng creator: Xueqiang Su creator: Yu Zhao creator: Taoshan Jiang creator: Qin Jin creator: Yi Lin creator: Yongping Cai uri: https://doi.org/10.7717/peerj.8064 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Li et al. title: Impact of habitat loss on the diversity and structure of ecological networks between oxyurid nematodes and spur-thighed tortoises (Testudo graeca L.) link: https://peerj.com/articles/8076 last-modified: 2019-12-02 description: Habitat loss and fragmentation are recognized as affecting the nature of biotic interactions, although we still know little about such changes for reptilian herbivores and their hindgut nematodes, in which endosymbiont interactions could range from mutualistic to commensal and parasitic. We investigated the potential cost and benefit of endosymbiont interactions between the spur-thighed tortoise (Testudo graeca L.) and adult oxyurid nematodes (Pharyngodonidae order Oxyurida) in scrublands of southern Spain. For this, we assessed the association between richness and abundance of oxyurid species with tortoises’ growth rates and body traits (weight and carapace length) across levels of habitat loss (low, intermediate and high). Furthermore, by using an intrapopulation ecological network approach, we evaluated the structure and diversity of tortoise–oxyurid interactions by focusing on oxyurid species infesting individual tortoises with different body traits and growth rates across habitats. Overall, tortoise body traits were not related to oxyurid infestation across habitats. Oxyurid richness and abundance however, showed contrasting relationships with growth rates across levels of habitat loss. At low habitat loss, oxyurid infestation was positively associated with growth rates (suggesting a mutualistic oxyurid–tortoise relationship), but the association became negative at high habitat loss (suggesting a parasitic relationship). Furthermore, no relationship was observed when habitat loss was intermediate (suggesting a commensal relationship). The network analysis showed that the oxyurid community was not randomly assembled but significantly nested, revealing a structured pattern for all levels of habitat loss. The diversity of interactions was lowest at low habitat loss. The intermediate level, however, showed the greatest specialization, which indicates that individuals were infested by fewer oxyurids in this landscape, whereas at high habitat loss individuals were the most generalized hosts. Related to the latter, connectance was greatest at high habitat loss, reflecting a more uniform spread of interactions among oxyurid species. At an individual level, heavier and larger tortoises tended to show a greater number of oxyurid species interactions. We conclude that there is an association between habitat loss and the tortoise–oxyurid interaction. Although we cannot infer causality in their association, we hypothesize that such oxyurids could have negative, neutral and positive consequences for tortoise growth rates. Ecological network analysis can help in the understanding of the nature of such changes in tortoise–oxyurid interactions by showing how generalized or specialized such interactions are under different environmental conditions and how vulnerable endosymbiont interactions might be to further habitat loss. creator: Julieta Benítez-Malvido creator: Andrés Giménez creator: Eva Graciá creator: Roberto Carlos Rodríguez-Caro creator: Rocío Ruiz De Ybáñez creator: Héctor Hugo Siliceo-Cantero creator: Anna Traveset uri: https://doi.org/10.7717/peerj.8076 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Benítez-Malvido et al. title: Co-expression analysis and ceRNA network reveal eight novel potential lncRNA biomarkers in hepatocellular carcinoma link: https://peerj.com/articles/8101 last-modified: 2019-12-02 description: BackgroundHepatocellular carcinoma (HCC) is the most common primary liver cancer in the world, with a high degree of malignancy and recurrence. The influence of the ceRNA network in tumor on the biological function of liver cancer is very important, It has been reported that many lncRNA play a key role in liver cancer development. In our study, integrated data analysis revealed potential eight novel lncRNA biomarkers in hepatocellular carcinoma.MethodsTranscriptome data and clinical data were downloaded from the The Cancer Genome Atlas (TCGA) data portal. Weighted gene co-expression network analysis was performed to identify the expression pattern of genes in liver cancer. Then, the ceRNA network was constructed using transcriptome data.ResultsThe integrated analysis of miRNA and RNAseq in the database show eight novel lncRNAs that may be involved in important biological pathways, including TNM and disease development in liver cancer. We performed function enrichment analysis of mRNAs affected by these lncRNAs.ConclusionsBy identifying the ceRNA network and the lncRNAs that affect liver cancer, we showed that eight novel lncRNAs play an important role in the development and progress of liver cancer. creator: Ren-chao Zou creator: Zhi-tian Shi creator: Shu-feng Xiao creator: Yang Ke creator: Hao-ran Tang creator: Tian-gen Wu creator: Zhi-tang Guo creator: Fan Ni creator: Sanqi An creator: Lin Wang uri: https://doi.org/10.7717/peerj.8101 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zou et al.