title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=904 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Dynamic residue interaction network analysis of the oseltamivir binding site of N1 neuraminidase and its H274Y mutation site conferring drug resistance in influenza A virus link: https://peerj.com/articles/11552 last-modified: 2021-06-02 description: BackgroundOseltamivir (OTV)-resistant influenza virus exhibits His-to-Tyr mutation at residue 274 (H274Y) in N1 neuraminidase (NA). However, the molecular mechanisms by which the H274Y mutation in NA reduces its binding affinity to OTV have not been fully elucidated.MethodsIn this study, we used dynamic residue interaction network (dRIN) analysis based on molecular dynamics simulation to investigate the correlation between the OTV binding site of NA and its H274Y mutation site.ResultsdRIN analysis revealed that the OTV binding site and H274Y mutation site of NA interact via the three interface residues connecting them. H274Y mutation significantly enhanced the interaction between residue 274 and the three interface residues in NA, thereby significantly decreasing the interaction between OTV and its surrounding loop 150 residues. Thus, we concluded that such changes in residue interactions could reduce the binding affinity of OTV to NA, resulting in drug resistant influenza viruses. Using dRIN analysis, we succeeded in understanding the characteristic changes in residue interactions due to H274Y mutation, which can elucidate the molecular mechanism of reduction in OTV binding affinity to influenza NA. Finally, the dRIN analysis used in this study can be widely applied to various systems such as individual proteins, protein-ligand complexes, and protein-protein complexes, to characterize the dynamic aspects of the interactions. creator: Mohini Yadav creator: Manabu Igarashi creator: Norifumi Yamamoto uri: https://doi.org/10.7717/peerj.11552 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yadav et al. title: Alien plants of Europe: introduction pathways, gateways and time trends link: https://peerj.com/articles/11270 last-modified: 2021-06-01 description: The Convention on Biological Diversity (CBD) pathways classification framework used in the implementation of the European Union’s (EU) Regulation 1143/2014 on invasive alien species (IAS Regulation) has recently been adopted by the European Alien Species Information Network (EASIN), the official information system supporting the implementation of the IAS Regulation. In the current paper, the result of an alignment of the primary introduction pathways of all alien plants in Europe included in the EASIN catalogue is presented, based on the CBD framework. In total, 6,250 alien plant taxa (marine plants excluded), both alien to Europe (native range outside Europe) and alien in Europe (native range partially in Europe) are reported. Altogether 5,175 plant taxa had their primary introduction pathway aligned based on the CBD framework, while for the rest the pathway remains unknown. In addition, the taxonomy, year and country of its first record in the wild are provided for each taxon. Our analyses reveal that the main primary introduction pathways of alien plants into Europe are linked to accidental escapes from ornamental and horticultural activities. Northwestern European countries seem to act as the main gateway areas of alien plants into Europe. Recent first observations of new alien taxa growing spontaneously exhibit a contemporary accelerating trend for plants alien to Europe, particularly linked to ornamental and horticultural activities. On the other hand, the number of new plants alien in Europe seems to have stabilized over the last few decades. The present work can assist in the prioritization of introduction pathways control, with the target of slowing down the rate of alien plants introductions into Europe, following also the requirements of the IAS Regulation. creator: Margarita Arianoutsou creator: Ioannis Bazos creator: Anastasia Christopoulou creator: Yannis Kokkoris creator: Andreas Zikos creator: Sevasti Zervou creator: Pinelopi Delipetrou creator: Ana Cristina Cardoso creator: Ivan Deriu creator: Eugenio Gervasini creator: Konstantinos Tsiamis uri: https://doi.org/10.7717/peerj.11270 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Arianoutsou et al. title: A new pterosaur tracksite from the Lower Cretaceous of Wuerho, Junggar Basin, China: inferring the first putative pterosaur trackmaker link: https://peerj.com/articles/11361 last-modified: 2021-06-01 description: We report the discovery of 114 small pterosaur footprints preserved in a greyish-green fine sandstone slab comprising 57 manus imprints and 57 pes imprints. Due to the chaotic distribution of footprints, the trackways are difficult to recognize. The pes imprints are sub-triangular and enlongate, the metatarsal part is roughly subequal to the digital part. The manus imprints are asymmetrical, longer than wide, and the lengths of digits I–III gradually increase. According to the diagnostic features of the Wuerho small pterosaur tracks, the present set was classified as Pteraichnus and is different from the nine reported valid ichnospecies of Pteraichnus. We therefore propose a new ichnospecies, Pteraichnus wuerhoensis isp. nov. The description is based on the anatomical characteristics (lengths of digits I–IV, length of digital part, length of metatarsal part) extracted from the pes imprints and comparisons with the pes bone fossils of Noripterus complicidens. We infer that the footprints were probably left by N. complicidens and the total width of the wings was presumably 2–2.3 m. In addition, the high density (365 per square meter) and varied sizes of the Wuerho small pterosaur tracks suggest that many pterosaurs of different ages lived in Huangyangquan Reservoir tracksite 1 area. Thus the trackmakers may have had gregarious behavior. creator: Yang Li creator: Xiaolin Wang creator: Shunxing Jiang uri: https://doi.org/10.7717/peerj.11361 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Early maternal separation is not associated with changes in telomere length in domestic kittens (Felis catus) link: https://peerj.com/articles/11394 last-modified: 2021-06-01 description: ObjectiveStudies of multiple species have found that adverse early life experiences, including childhood trauma and maternal separation, can result in accelerated telomere shortening. The objective of this study was to determine if premature separation from the mother affected telomere length in domestic kittens (Felis catus). Subjects were 42 orphaned kittens and 10 mother-reared kittens from local animal rescue groups and shelters. DNA was extracted from whole blood collected from kittens at approximately 1 week and 2 months of age. Telomere length was assessed by qPCR (quantitative polymerase chain reaction) from a total of 86 samples and expressed as a ratio of telomere PCR relative to a single copy gene PCR (T/S).ResultsA generalized linear mixed model found there were no detectable differences in telomere length based on survival (F1, 76.2 = 3.35, p = 0.07), orphan status (F1, 56.5 = 0.44, p = 0.51), time point (F1, 43.5 = 0.19, p = 0.67), or the interaction between orphan status and time (F1, 43.5 = 0.86, p = 0.36). Although in other species telomere shortening is commonly associated with aging, even early in life, we did not find evidence for telomere shortening by two months of age. Our results suggest that the experience of early maternal separation in domestic cats who are subsequently hand-reared by humans does not accelerate telomere shortening compared to mother-reared kittens, at least in the first few months of life. creator: Mikel Delgado creator: C.A. Tony Buffington creator: Melissa Bain creator: Dana L. Smith creator: Karen Vernau uri: https://doi.org/10.7717/peerj.11394 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Delgado et al. title: Guiclupea superstes, gen. et sp. nov., the youngest ellimmichthyiform (clupeomorph) fish to date from the Oligocene of South China link: https://peerj.com/articles/11418 last-modified: 2021-06-01 description: A new ellimmichthyiform, Guiclupea superstes, gen. et sp. nov., from the Oligocene Ningming Formation of Ningming Basin, Guangxi Zhuang Autonomous Region, South China is described herein. With relatively large body size, parietals meeting at the midline, anterior ceratohyal with a beryciform foramen in the center, a complete predorsal scutes series of very high number and about equally-size scutes with radiating ridges on dorsal surface, first preural centrum unfused with first uroneural but fused with the parhypural, and first ural centrum of roughly the same size as the preural centrum, Guiclupea superstes cannot be assigned to the order Clupeiformes. The phylogenetic analyses using parsimony and Bayesian inference methods with Chanos/Elops as outgroup respectively suggests that the new form is closer to ellimmichthyiform genus Diplomystus than to any other fishes, although there are some discrepancies between the two criteria and different outgroups used. It shares with Diplomystus the high supraoccipital crest, pelvic-fin insertion in advance of dorsal fin origin, and the number of predorsal scutes more than 20. The new form represents the youngest ellimmichthyiform fish record in the world. Its discovery indicates that the members of the Ellimmichthyiformes had a wider distribution range and a longer evolutional history than previously known. creator: Gengjiao Chen creator: Mee-mann Chang creator: Feixiang Wu creator: Xiaowen Liao uri: https://doi.org/10.7717/peerj.11418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data link: https://peerj.com/articles/11425 last-modified: 2021-06-01 description: Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation. creator: Sofia G. Seabra creator: Ana S.B. Rodrigues creator: Sara E. Silva creator: Ana Carina Neto creator: Francisco Pina-Martins creator: Eduardo Marabuto creator: Vinton Thompson creator: Michael R. Wilson creator: Selçuk Yurtsever creator: Antti Halkka creator: Maria Teresa Rebelo creator: Paulo A.V. Borges creator: José A. Quartau creator: Chris D. Jiggins creator: Octávio S. Paulo uri: https://doi.org/10.7717/peerj.11425 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Seabra et al. title: Development of landscape conservation value map of Jeju island, Korea for integrative landscape management and planning using conservation value of landscape typology link: https://peerj.com/articles/11449 last-modified: 2021-06-01 description: Understanding landscape as a socio-ecological system where systematic interactions occur among diverse ecosystems and human society is necessary for a sustainable landscape and resource management. However, many countries with rapid economic growth, including South Korea, depend on conventional planning and policy decisions to meet increasing demands for the use of specific natural resources. Such resource-oriented planning and policy which neglect considerations for the surrounding landscape can result in conflicts of interest and regulation. We designed a landscape conservation value (LCV) map of Jeju Island, Korea to overcome rising managerial and policy issues with the provision of systematic perspectives of landscape. With a consideration for natural and human-modified characteristics of the landscape, we used landform and land cover data to create fundamental landscape types. Then, the LCV was assigned to each type by a board of landscape experts. Within a study region, we observed relatively high values in registered protected areas and unique landscapes, and areas where high and low values are aligned. The resultant LCV map can identify areas that potentially require an integrated approach to prevent adverse effects caused by a conventional approach. creator: Baysok Jun creator: Ilkwon Kim creator: Jihoon Shin creator: Hyuksoo Kwon uri: https://doi.org/10.7717/peerj.11449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Jun et al. title: Oyster farms are the main spawning grounds of the black sea bream Acanthopagrus schlegelii in Hiroshima Bay, Japan link: https://peerj.com/articles/11475 last-modified: 2021-06-01 description: Understanding the anthropogenic impact of oyster farms is essential for the management and conservation of marine fishes. In Japan, Hiroshima Bay is the region with the most intense oyster farming and thus suitable to study the impact of these farms. Here, we surveyed spherical planktonic eggs of the black sea bream Acanthopagrus schlegelii, one of the most abundant fish in the Bay. Our survey was performed at fourteen stations which included places with oyster farms and historical spawning grounds. We found the highest egg densities in four stations, one with historical spawning aggregations and three with major oyster farms. Besides, surveys at the innermost part of Hiroshima Bay, where two major rivers discharge, showed a low density of eggs indicating that black sea bream avoids spawning in low salinity areas. Our study suggests that oyster farms benefit spawners of black sea bream by providing more food sources than historical spawning grounds for efficient spawning. Yet, whether oyster farms represent a full advantage for the species remains unclear, particularly because they are known to host jellyfishes that prey on eggs and limit water flow that can influence the survival of fish eggs. creator: Kentaro Kawai creator: Hiroki Fujita creator: Gustavo Sanchez creator: Tetsuya Umino uri: https://doi.org/10.7717/peerj.11475 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kawai et al. title: Myocardial contrast echocardiography assessment of mouse myocardial infarction: comparison of kinetic parameters with conventional methods link: https://peerj.com/articles/11500 last-modified: 2021-06-01 description: This study explores the use of a minimally invasive assessment of myocardial infarction (MI) in mice using myocardial contrast echocardiography (MCE). The technique uses existing equipment and software readily available to the average researcher. C57/BL6 mice were randomized to either MI or sham surgery and evaluated using MCE at 1- or 2-weeks post-surgery. Size-isolated microbubbles were injected via retro-orbital catheter where their non-linear characteristics were utilized to produce the two-dimensional parameters of Wash-in-Rate and the Peak Enhancement, indicative of relative myocardial perfusion and blood volume, respectively. Three-dimensional cardiac reconstructions allowed the calculation of the Percent Agent, interpreted as the vascularity of the entire myocardium. These MCE parameters were compared to conventional assessments including M-Mode, strain analysis, and 2,3,5-Triphenyltetrazolium chloride (TTC) staining. Except for the Wash-in-Rate 2-week cohort, all MCE parameters were able to differentiate sham-operated versus MI animals and correlated with TTC staining (P < 0.05). MCE parameters were also able to identify MI group animals which failed to develop infarctions as determined by TTC staining. This study provides basic validation of these MCE parameters to detect MI in mice complementary to conventional methods while providing additional hemodynamic information in vivo. creator: Nicholas T. Thielen creator: Adison A. Kleinsasser creator: Jessica L. Freeling uri: https://doi.org/10.7717/peerj.11500 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Thielen et al. title: Neuromedin U and neurotensin may promote the development of the tumour microenvironment in neuroblastoma link: https://peerj.com/articles/11512 last-modified: 2021-06-01 description: Stage 4S neuroblastoma, as defined by the International Neuroblastoma Staging System committee (INSS), is known to regress spontaneously and have a more favourable outcome compared with stage 4 tumours. Comparing the molecular differences between these two stages may provide insights into the progression of neuroblastoma. Our study aimed to explore the molecular differences in the tumour microenvironment (TME) between INSS stage 4S and stage 4 tumours to provide an insight into the mechanisms underlying the biological processes of neuroblastoma. We downloaded the datasets GSE120572 and GSE73517 from the GEO database and pre-processed them using the limma package. CIBERSORT deconvolution agorithm was applied to analyse the differences in 22 infiltrating immune leukocyte subsets between the two stages. We used gene ontology (GO) enrichment analysis to determine the biological process (BP) annotation of differentially expressed genes (DEGs) using the online WebGestalt tool. Hub genes were determined in the STRING database and Cytoscape, and the expression of these genes was verified in the Oncomine database. Then these critical genes were performed survival analysis in TARGET database. We further validated the hub genes using a transwell assay and wound healing assay to detect the function of the genes in the neuroblastoma cell line SK-N-BE(2). GO analysis revealed that the 216 DEGs between stage 4S and stage 4 were enriched in aggressive biological processes. Neuromedin U (NMU) and neurotensin (NTS), which were significantly associated with patients’ overall survival rate, were verified to be elevated in stage 4, and to promote the proliferation and invasion of the SK-N-BE(2) cell. Tumour infiltrating leukocyte analysis showed a high infiltration of regulatory T cells and type 2 tumour-associated macrophages in stage 4 but not in stage 4S. Results of gene co-expression correlation, and the results of previous studies, suggest that NMU and NTS may play certain roles in modulating TME, thus facilitating the progression of neuroblastoma. creator: Daheng Yang creator: Xianwei Zhang creator: Zheqian Li creator: Fei Xu creator: Chenjie Tang creator: Hongbing Chen uri: https://doi.org/10.7717/peerj.11512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yang et al.