title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1283 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Identification and evaluation of Lonicera japonica flos introduced to the Hailuogou area based on ITS sequences and active compounds link: https://peerj.com/articles/7636 last-modified: 2019-09-03 description: Lonicera japonica flos (LJF), the dried flower buds of L. japonica Thunb., have been used in traditional Chinese herbal medicine for thousands of years. Recent studies have reported that LJF has many medicinal properties because of its antioxidative, hypoglycemic, hypolipidemic, anti-allergic, anti-inflammatory, and antibacterial effects. LJF is widely used in China in foods and healthcare products, and is contained in more than 30% of current traditional Chinese medicine prescriptions. Because of this, many Chinese villages cultivate LJF instead of traditional crops due to its high commercial value in the herbal medicine market. Since 2005, the flower buds of L. japonica are the only original LJF parts considered according to the Chinese Pharmacopoeia of the People’s Republic of China. However, for historical and commercial reasons, some closely related species of Lonicera Linn. continue to be mislabeled and used as LJF. Currently, there are hundreds of commercial varieties of LJF on the market and it is difficult to choose fine LJF varieties to cultivate. In this study, a total of 21 varieties labeled as LJF on the market were planted in the Hailuogou area. In order to choose the optimum variety, internal transcribed spacer (ITS) sequence alignment analysis was used to test whether the 21 varieties were genuine LJF or not. Cluster analysis of active components based on the content of chlorogenic acid and luteoloside in flower buds, stems and leaves was used to evaluate the quality of the varieties. Results demonstrated that four of the varieties were L. macranthoides Hand.-Mazz., while the other 17 varieties were L. japonica, and genuine LJF. The ITS sequence analysis was proven to be highly effective in identifying LJF and Lonicerae flos. Among the 17 L. japonica varieties, the amounts of chlorogenic acid and luteoloside in flower buds, stems and leaves were significantly different. Based on the cluster analysis method, the variety H11 was observed to have the highest level of active components, and is therefore recommended for large-scale planting in the Hailuogou area. creator: Haiyan He creator: Dan Zhang creator: Jianing Gao creator: Theis Raaschou Andersen creator: Zishen Mou uri: https://doi.org/10.7717/peerj.7636 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 He et al. title: Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791) link: https://peerj.com/articles/7644 last-modified: 2019-09-03 description: Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together. creator: Zhansheng Guo creator: Leng Han creator: Zhenlin Liang creator: Xuguang Hou uri: https://doi.org/10.7717/peerj.7644 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al. title: Identification of Aloperine as an anti-apoptotic Bcl2 protein inhibitor in glioma cells link: https://peerj.com/articles/7652 last-modified: 2019-09-03 description: ObjectiveAloperine (ALO), an alkaloid isolated from the leaves of Sophora alopecuroides, has been suggested to exhibit anti-inflammatory and anti-tumor properties and is traditionally used to treat various human diseases, including cancer. However, limited information is available about the mechanisms that determine the anti-tumor activities of ALO.MethodsHerein, through comprehensive bioinformatics methods and in vitro functional analyses, we evaluated the detailed anti-tumor mechanisms of ALO.ResultsUsing the databases Bioinformatics analysis tool for molecular mechanism of traditional Chinese medicine and PubChem Project, we identified the potential targets of ALO. A protein–protein interaction network was constructed to determine the relationship among these probable targets. Functional enrichment analysis revealed that ALO is potentially involved in the induction of apoptosis. In addition, molecular docking demonstrated that ALO expectedly docks into the active pocket of the Bcl2 protein, suggesting Bcl2 as a direct target of ALO. Moreover, western blot and qPCR analysis showed that ALO downregulated Bcl2 expression in human glioma cell lines, SK-N-AS and U118. Using flow cytometry methods, we further confirmed that ALO significantly promotes apoptosis in SK-N-AS and U118 cell lines, similar to the effect induced by ABT-737, a well-known Bcl2 inhibitor. In addition, Bcl-2 overexpression could rescue ALO-induced Bcl-2 inhibition and suppress pro-apoptotic effects in glioma cells.ConclusionTaken together, these findings suggest that the natural agent ALO effectively enhances apoptosis by acting as a potential Bcl2 inhibitor in human glioma cells. creator: Zhijie Xu creator: Xiang Wang creator: Xi Chen creator: Shuangshuang Zeng creator: Long Qian creator: Jie Wei creator: Zhicheng Gong creator: Yuanliang Yan uri: https://doi.org/10.7717/peerj.7652 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xu et al. title: Effects of mechanical and chemical control on invasive Spartina alterniflora in the Yellow River Delta, China link: https://peerj.com/articles/7655 last-modified: 2019-09-03 description: Spartina alterniflora is one of the most noxious invasive plants in China and many other regions. Exploring environmentally friendly, economic and effective techniques for controlling Spartina alterniflora is of great significance for the management of coastal wetlands. In the present study, different approaches, including mowing and waterlogging, mowing and tilling and herbicide application, were used to control Spartina alterniflora. The results suggest that the integrated approach of mowing and waterlogging could eradicate Spartina alterniflora, the herbicide haloxyfop-r-methyl could kill almost all the Spartina alterniflora, and the integrated approach of mowing and tilling at the end of the growing season was a perfect way to inhibit the germination of Spartina alterniflora in the following year. However, no matter which control approach is adopted, secondary invasion of Spartina alterniflora must be avoided. Otherwise, all the efforts will be wasted in a few years. creator: Baohua Xie creator: Guangxuan Han creator: Peiyang Qiao creator: Baoling Mei creator: Qing Wang creator: Yingfeng Zhou creator: Anfeng Zhang creator: Weimin Song creator: Bo Guan uri: https://doi.org/10.7717/peerj.7655 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Xie et al. title: Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae link: https://peerj.com/articles/6904 last-modified: 2019-09-02 description: BackgroundEnterobacter cloacae (EC) is a Gram-negative bacterium that has been utilized extensively in biotechnological and environmental science applications, possibly because of its high capability for adapting itself and surviving in hazardous conditions. A search for the EC from agricultural and industrial areas that possesses high capability to tolerate and/or accumulate cadmium ions has been conducted in this study. Plausible mechanisms of cellular adaptations in the presence of toxic cadmium have also been proposed.MethodsNine strains of EC were isolated and subsequently identified by biochemical characterization and MALDI-Biotyper. Minimum inhibitory concentrations (MICs) against cadmium, zinc and copper ions were determined by agar dilution method. Growth tolerance against cadmium ions was spectrophotometrically monitored at 600 nm. Cadmium accumulation at both cellular and protein levels was investigated using atomic absorption spectrophotometer. Proteomics analysis by 2D-DIGE in conjunction with protein identification by QTOF-LC-MS/MS was used to study differentially expressed proteins between the tolerant and intolerant strains as consequences of cadmium exposure. Expression of such proteins was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatics tools were applied to propose the functional roles of cadmium-binding protein and its association in cadmium tolerance mechanisms.ResultsThe cadmium-tolerant strain (EC01) and intolerant strain (EC07) with the MICs of 1.6 and 0.4 mM, respectively, were isolated. The whole cell lysate of EC01 exhibited approximately two-fold higher in cadmium binding capability than those of the EC07 and ATCC 13047, possibly by the expression of Cd-binding proteins. Our proteomics analysis revealed the higher expression of DUF326-like domain (a high cysteine-rich protein) of up to 220 fold in the EC01 than that of the EC07. Confirmation of the transcription level of this gene by qRT-PCR revealed a 14-fold induction in the EC01. Regulation of the DUF326-like domain in EC01 was more pronounced to mediate rapid cadmium accumulation (in 6 h) and tolerance than the other resistance mechanisms found in the ATCC 13047 and the EC07 strains. The only one major responsive protein against toxic cadmium found in these three strains belonged to an antioxidative enzyme, namely catalase. The unique proteins found in the ATCC 13047 and EC07 were identified as two groups: (i) ATP synthase subunit alpha, putative hydrolase and superoxide dismutase and (ii) OmpX, protein YciF, OmpC porin, DNA protection during starvation protein, and TrpR binding protein WrbA, respectively.ConclusionAll these findings gain insights not only into the molecular mechanisms of cadmium tolerance in EC but also open up a high feasibility to apply the newly discovered DUF326-like domain as cadmium biosorbents for environmental remediation in the future. creator: Kitipong Chuanboon creator: Piyada Na Nakorn creator: Supitcha Pannengpetch creator: Vishuda Laengsri creator: Pornlada Nuchnoi creator: Chartchalerm Isarankura-Na-Ayudhya creator: Patcharee Isarankura-Na-Ayudhya uri: https://doi.org/10.7717/peerj.6904 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chuanboon et al. title: Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus) link: https://peerj.com/articles/7453 last-modified: 2019-09-02 description: BackgroundThe Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India.ResultsWe tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID(unbiased) and PID(sibs) value of 4.7 × 10−10 and 1.5 × 10−4, respectively, indicating a high statistical power in individual discrimination from poor quality samples.ConclusionOur results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore. creator: Shrushti Modi creator: Bilal Habib creator: Pallavi Ghaskadbi creator: Parag Nigam creator: Samrat Mondol uri: https://doi.org/10.7717/peerj.7453 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Modi et al. title: The pre-Pleistocene fossil thylacinids (Dasyuromorphia: Thylacinidae) and the evolutionary context of the modern thylacine link: https://peerj.com/articles/7457 last-modified: 2019-09-02 description: The thylacine is popularly used as a classic example of convergent evolution between placental and marsupial mammals. Despite having a fossil history spanning over 20 million years and known since the 1960s, the thylacine is often presented in both scientific literature and popular culture as an evolutionary singleton unique in its morphological and ecological adaptations within the Australian ecosystem. Here, we synthesise and critically evaluate the current state of published knowledge regarding the known fossil record of Thylacinidae prior to the appearance of the modern species. We also present phylogenetic analyses and body mass estimates of the thylacinids to reveal trends in the evolution of hypercarnivory and ecological shifts within the family. We find support that Mutpuracinus archibaldi occupies an uncertain position outside of Thylacinidae, and consider Nimbacinus richi to likely be synonymous with N. dicksoni. The Thylacinidae were small-bodied (< ~8 kg) unspecialised faunivores until after the ~15–14 Ma middle Miocene climatic transition (MMCT). After the MMCT they dramatically increase in size and develop adaptations to a hypercarnivorous diet, potentially in response to the aridification of the Australian environment and the concomitant radiation of dasyurids. This fossil history of the thylacinids provides a foundation for understanding the ecology of the modern thylacine. It provides a framework for future studies of the evolution of hypercarnivory, cursoriality, morphological and ecological disparity, and convergence within mammalian carnivores. creator: Douglass S. Rovinsky creator: Alistair R. Evans creator: Justin W. Adams uri: https://doi.org/10.7717/peerj.7457 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rovinsky et al. title: lnc-SAMD14-4 can regulate expression of the COL1A1 and COL1A2 in human chondrocytes link: https://peerj.com/articles/7491 last-modified: 2019-09-02 description: Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or < − 2.0-fold change; p < 0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. QPCR was used to validate chip results. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, the gain/loss of function experiments of lnc-SAMD14-4 was implemented in IL-1β-treated human chondrocytes. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA. creator: Haibin Zhang creator: Cheng Chen creator: Yinghong Cui creator: Yuqing Li creator: Zhaojun Wang creator: Xinzhan Mao creator: Pengcheng Dou creator: Yihan Li creator: Chi Ma uri: https://doi.org/10.7717/peerj.7491 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Zhang et al. title: Type I-like behavior of the type II α7 nicotinic acetylcholine receptor positive allosteric modulator A-867744 link: https://peerj.com/articles/7542 last-modified: 2019-09-02 description: Cognitive impairment often involves the decreased expression or hypofunction of alpha 7-type nicotinic acetylcholine receptors (α7 nAChRs). Agonists or positive allosteric modulators (PAMs) of α7 nAChRs are known to be potential treatments for dementias, different neurodegenerative disorders, pain syndromes and conditions involving inflammation. In some of these conditions, it is desirable to maintain the temporal precision of fast cholinergic events, while in others, this temporal precision is unnecessary. For this reason, the optimal therapeutic effect for distinct indications may require PAMs with different mechanisms of action. The two major mechanisms are called “type I”, which are compounds that augment α7 nAChR-mediated currents but maintain their characteristic fast kinetics; and “type II”, which are compounds that produce augmented and prolonged currents. In this study, we performed a kinetic analysis of two type II PAMs of the α7 nAChR: PNU-120596 and A-867744, using a fast perfusion method that allowed high temporal resolution. We characterized the type of modulation produced by the two compounds, the state-dependence of the modulatory action, and the interaction between the two compounds. We found fundamental differences between the modulation mechanisms by PNU-120596 and A-867744. Most importantly, during brief agonist pulses, A-867744 caused a strikingly type I-like modulation, while PNU-120596 caused a type II-like prolonged activation. Our results demonstrate that specific compounds, even though all labeled as type II PAMs, can behave in completely different ways, including their onset and offset kinetics, state preference, and single channel open time. Our results emphasize that subtle details of the mechanism of action may be significant in assessing the therapeutic applicability of α7 nAChR PAM compounds. creator: Krisztina Pesti creator: Peter Lukacs creator: Arpad Mike uri: https://doi.org/10.7717/peerj.7542 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pesti et al. title: Revealing biases in the sampling of ecological interaction networks link: https://peerj.com/articles/7566 last-modified: 2019-09-02 description: The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. These ecological and statistical issues directly affect ecologists’ abilities to accurately construct ecological networks. However, statistical biases introduced by sampling are difficult to quantify in the absence of full knowledge of the underlying ecological network’s structure. To explore properties of large-scale ecological networks, we developed the software EcoNetGen, which constructs and samples networks with predetermined topologies. These networks may represent a wide variety of communities that vary in size and types of ecological interactions. We sampled these networks with different mathematical sampling designs that correspond to methods used in field observations. The observed networks generated by each sampling process were then analyzed with respect to the number of components, size of components and other network metrics. We show that the sampling effort needed to estimate underlying network properties depends strongly both on the sampling design and on the underlying network topology. In particular, networks with random or scale-free modules require more complete sampling to reveal their structure, compared to networks whose modules are nested or bipartite. Overall, modules with nested structure were the easiest to detect, regardless of the sampling design used. Sampling a network starting with any species that had a high degree (e.g., abundant generalist species) was consistently found to be the most accurate strategy to estimate network structure. Because high-degree species tend to be generalists, abundant in natural communities relative to specialists, and connected to each other, sampling by degree may therefore be common but unintentional in empirical sampling of networks. Conversely, sampling according to module (representing different interaction types or taxa) results in a rather complete view of certain modules, but fails to provide a complete picture of the underlying network. To reduce biases introduced by sampling methods, we recommend that these findings be incorporated into field design considerations for projects aiming to characterize large species interaction networks. creator: Marcus A.M. de Aguiar creator: Erica A. Newman creator: Mathias M. Pires creator: Justin D. Yeakel creator: Carl Boettiger creator: Laura A. Burkle creator: Dominique Gravel creator: Paulo R. Guimarães creator: James L. O’Donnell creator: Timothée Poisot creator: Marie-Josée Fortin creator: David H. Hembry uri: https://doi.org/10.7717/peerj.7566 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 de Aguiar et al.