title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1016 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results link: https://peerj.com/articles/10410 last-modified: 2020-11-25 description: Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovisp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis. creator: Petr G. Garibian creator: Anna N. Neretina creator: Derek J. Taylor creator: Alexey A. Kotov uri: https://doi.org/10.7717/peerj.10410 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Garibian et al. title: Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli link: https://peerj.com/articles/10455 last-modified: 2020-11-25 description: BackgroundThe global problem of antibiotic resistance requires the search for and development of new methods of treatment. One of the promising strategies is the use of low doses of antimicrobial peptides, in particular, human defensins HNP-1, hBD-1, and hBD-3, in combination with antibacterial drugs already used in clinical practice. This approach may be used to increase the effectiveness of conventional antibiotics. However, this requires thorough study of the effectiveness of defensins in combination with antibiotics against a large number of bacterial strains with known phenotypes of antibiotic resistance. The aim of this work was to study the antibacterial effect of HNP-1, hBD-1 and hBD-3 in combination with rifampicin or amikacin against clinical isolates of Staphylococcus aureus (n = 27) and Escherichia coli (n = 24) collected from hospitalized patients.MethodsThe standard checkerboard assay was used to determine minimum inhibitory concentrations (MICs) of antimicrobials. The combined microbicidal effects of two substances (defensin + conventional antibiotic) were assessed by the fractional inhibitory concentration index (FICI).ResultsThe highest anti-staphylococcal activity (including methicillin-resistant strains) among defensins was demonstrated by hBD-3 that had MIC of 1 (0.5–4) mg/L (hereinafter, MIC values are presented as median and interquartile range). The MIC of HNP-1 against S. aureus was 4 (2–8) mg/L; the MIC of hBD-1 was 8 (4–8) mg/L. Against E. coli, the most effective was also found to be hBD-3 that had MIC of 4 (4–8) mg/L; the MIC of HNP-1 was 12 (4–32) mg/L. The combinations of HNP-1 + rifampicin and hBD-3 + rifampicin demonstrated synergistic effects against S. aureus. Against E. coli, combinations of HNP-1 + amikacin and hBD-3 + amikacin also showed synergy of action. creator: Albert Bolatchiev uri: https://doi.org/10.7717/peerj.10455 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bolatchiev title: miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2 link: https://peerj.com/articles/9704 last-modified: 2020-11-24 description: BackgroundThe present study is to screen lymph node metastasis-related microRNAs (miRNAs) in lung adenocarcinoma (LUAD) and uncover their underlying mechanisms.MethodsThe miRNA microarray dataset was collected from the Gene Expression Omnibus database under accession number GSE64859. The differentially expressed miRNAs (DEMs) were identified using a t-test. Target genes of DEMs were predicted through the miRWalk2.0 database. The function of these target genes was annotated with the clusterProfiler and the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools. Protein-protein interaction network was established using the STRING database to extract hub target genes. The expressions and associations with survival and lymph node metastasis of miRNAs and target genes were validated by analysis of The Cancer Genome Atlas (TCGA) dataset.ResultsEight DEMs were identified between lymph node metastasis and non-metastasis samples of GSE64859 dataset. miRNA-target gene pairs were predicted between six DEMs and 251 target genes (i.e. hsa-miR-224-PRPF4B, hsa-miR-147b-WDR82 and hsa-miR-31-NR3C2). The clusterProfiler analysis showed WDR82 was involved in the mRNA surveillance pathway, while the GO enrichment analysis using the DAVID database indicated PRPF4B participated in the protein phosphorylation and NR3C2 was related with the transcription, DNA-templated. WDR82 and PRPF4B may be hub genes because they could interact with others. Two DEMs (miR-31-5p and miR-31-3p) and 45 target genes (including PRPF4B and NR3C2) were significantly associated with overall survival. The expressions of miR-224 and miR-147b were validated to be upregulated, while WDR82, PRPF4B and NR3C2 were downregulated in lymph node metastasis samples of TCGA datasets compared with non-metastasis samples. Also, there were significantly negative expression correlations between miR-147b and WDR82, between miR-224 and PRPF4B, as well as between miR-31 and NR3C2 in LUAD samples.ConclusionsThe present study identified several crucial miRNA-mRNA interaction pairs, which may provide novel explanations for the lymph node metastasis and poor prognosis for LUAD patients. creator: Yan Wang creator: Shengtao Shang creator: Kun Yu creator: Hongbin Sun creator: Wenduan Ma creator: Wei Zhao uri: https://doi.org/10.7717/peerj.9704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Wang et al. title: The Italian record of the Cretaceous shark, Ptychodus latissimus Agassiz, 1835 (Chondrichthyes; Elasmobranchii) link: https://peerj.com/articles/10167 last-modified: 2020-11-24 description: Associated and isolated teeth of the extinct elasmobranch Ptychodus latissimusAgassiz, 1835 from the Upper Cretaceous Scaglia Rossa pelagic limestone of northern Italy are described and discussed here in detail for the first time. The dentition of this widely distributed species consists of low-crowned molariform teeth that exhibit marked and strong occlusal ornamentations suitable for crushing hard-shelled prey. The associated tooth sets and isolated teeth analyzed here are heterogeneous in size and crown outline, but unambiguously belong to a single species. Re-examination of this Italian material consisting of ca. 30 specimens mostly coming from historical collections allows for a rigorous assessment of the intraspecific variability of P. latissimus, including the identification of three different tooth “morphotypes” based on their positions within the jaws. The relatively flat crowns and occlusal sharp and thick ridges indicate a high adaptation for crushing hard-shelled prey in P. latissimus indicating that the durophagous adaptations of this species were certainly more pronounced than in all other species of Ptychodus. We hypothesize that P. latissimus was a third-level predator occupying habitats with abundant thick-shelled prey, such as inoceramid bivalves and ammonites. creator: Manuel Amadori creator: Jacopo Amalfitano creator: Luca Giusberti creator: Eliana Fornaciari creator: Giorgio Carnevale creator: Juergen Kriwet uri: https://doi.org/10.7717/peerj.10167 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Amadori et al. title: Hissing of geese: caller identity encoded in a non-vocal acoustic signal link: https://peerj.com/articles/10197 last-modified: 2020-11-24 description: Non-vocal, or unvoiced, signals surprisingly have received very little attention until recently especially when compared to other acoustic signals. Some sounds made by terrestrial vertebrates are produced not only by the larynx but also by the syrinx. Furthermore, some birds are known to produce several types of non-syrinx sounds. Besides mechanical sounds produced by feathers, bills and/or wings, sounds can be also produced by constriction, anywhere along the pathway from the lungs to the lips or nostrils (in mammals), or to the bill (in birds), resulting in turbulent, aerodynamic sounds. These noises often emulate whispering, snorting or hissing. Even though hissing sounds have been studied in mammals and reptiles, only a few studies have analyzed hissing sounds in birds. Presently, only the hissing of small, nesting passerines as a defense against their respective predators have been studied. We studied hissing in domestic goose. This bird represents a ground nesting non-passerine bird which frequently produces hissing out of the nest in comparison to passerines producing hissing during nesting in holes e.g., parids. Compared to vocally produced alarm calls, almost nothing is known about how non-vocal hissing sounds potentially encode information about a caller’s identity. Therefore, we aimed to test whether non-vocal air expirations can encode an individual’s identity similar to those sounds generated by the syrinx or the larynx. We analyzed 217 hissing sounds from 22 individual geese. We calculated the Potential for Individual Coding (PIC) comparing the coefficient of variation both within and among individuals. In addition, we conducted a series of 15 a stepwise discriminant function analysis (DFA) models. All 16 acoustic variables showed a higher coefficient of variation among individuals. Twelve DFA models revealed 51.2–54.4% classification result (cross-validated output) and all 15 models showed 60.8–68.2% classification output based on conventional DFA in comparison to a 4.5% success rate when classification by chance. This indicates the stability of the DFA results even when using different combinations of variables. Our findings showed that an individual’s identity could be encoded with respect to the energy distribution at the beginning of a signal and the lowest frequencies. Body weight did not influence an individual’s sound expression. Recognition of hissing mates in dangerous situations could increase the probability of their surviving via a more efficient anti-predator response. creator: Richard Policht creator: Artur Kowalczyk creator: Ewa Łukaszewicz creator: Vlastimil Hart uri: https://doi.org/10.7717/peerj.10197 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Policht et al. title: Habitat conditions strongly affect macro- and microelement concentrations in Taraxacum microspecies growing on coastal meadows along a soil salinity gradient link: https://peerj.com/articles/10233 last-modified: 2020-11-24 description: Wild greens can contribute to the human diet as an important source of essential nutrients and drugs. Since environmental factors, including soil properties, may affect the chemical composition of plants, it is necessary among others to assess various habitats in terms of their usefulness for wild plant harvesting and to study impact of environmental factors on the qualitative and quantitative chemical composition of plants. This study was aimed at (1) examining the mineral composition of leaves of three dandelion microspecies, (2) determining the variability of macro- and microelement concentrations in dandelion leaves from populations growing on salty, brackish and non-saline coastal meadows, and (3) assessing the effects of different habitat conditions on the mineral composition of dandelion leaves. It was hypothesized that dandelion microspecies would differ significantly in the mineral composition of leaves. It was also expected that soil conditions would significantly affect nutrient concentrations in dandelion leaves, with soil salinity being the most important factor that differentiated studied populations. Leaves of three dandelion microspecies (Taraxacum balticum, T. nordstedtii, T. haematicum) were harvested in Baltic costal grasslands, along the soil salinity gradient, to determine macro- and microelement concentrations. Soil samples collected in the closest vicinity of the harvested plants showed the study sites to differ significantly in their soil properties. Moderately saline and organic soils, rich in potassium (K), magnesium (Mg), and calcium (Ca), supported T. balticum. Moderately or weakly saline and non-saline, organic or mineral soils, with lower median values of K, Mg, and Ca, were typical of T. nordstedtii sites, while the lowest median values of all the soil properties studied were found for T. haematicum sites. Our results proved that dandelion microspecies differ significantly in the mineral composition of their leaves. The between-microspecies differences were significant for all the macroelements except magnesium and all the microelements except molybdenum. Most of the macro- and microelements in leaves of the dandelion microspecies correlated positively and significantly with the soil properties, the strongest correlations being found for soil salinity and the leaf Na, Mn, Ca, Fe, K and Zn contents, followed by soil pH and the leaf Na, Mn, Fe, K, Ca, Zn and Mg. Moreover, the impact of soil properties on the mineral contents in leaves of the dandelions we examined seems to be stronger than the genetic differences between dandelion microspecies. Results of our studies on mineral composition of dandelion leaves lend support to the contention that wild greens provide essential mineral nutrients to the diet. Coastal meadows, fed by the brackish water of the Baltic Sea and free of anthropogenic pollution, are a good habitat to collect wild greens from. creator: Beata Bosiacka creator: Monika Myśliwy creator: Mateusz Bosiacki uri: https://doi.org/10.7717/peerj.10233 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bosiacka et al. title: Spatially resolved dendritic integration: towards a functional classification of neurons link: https://peerj.com/articles/10250 last-modified: 2020-11-24 description: The vast tree-like dendritic structure of neurons allows them to receive and integrate input from many neurons. A wide variety of neuronal morphologies exist, however, their role in dendritic integration, and how it shapes the response of the neuron, is not yet fully understood. Here, we study the evolution and interactions of dendritic spikes in excitable neurons with complex real branch structures. We focus on dozens of digitally reconstructed illustrative neurons from the online repository NeuroMorpho.org, which contains over 130,000 neurons. Yet, our methods can be promptly extended to any other neuron. This approach allows us to estimate and map specific and heterogeneous patterns of activity observed across extensive dendritic trees with thousands of compartments. We propose a classification of neurons based on the location of the soma (centrality) and the number of branches connected to the soma. These are key topological factors in determining the neuron’s energy consumption, firing rate, and the dynamic range, which quantifies the range in synaptic input rate that can be reliably encoded by the neuron’s firing rate. Moreover, we find that bifurcations, the structural building blocks of complex dendrites, play a major role in increasing the dynamic range of neurons. Our results provide a better understanding of the effects of neuronal morphology in the diversity of neuronal dynamics and function. creator: Christoph Kirch creator: Leonardo L. Gollo uri: https://doi.org/10.7717/peerj.10250 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Kirch and Gollo title: DPM1 expression as a potential prognostic tumor marker in hepatocellular carcinoma link: https://peerj.com/articles/10307 last-modified: 2020-11-24 description: BackgroundAltered glycosylation of proteins contributes to tumor progression. Dolichol phosphate mannose synthase (DPMS), an essential mannosyltransferase, plays a central role in post-translational modification of proteins, including N-linked glycoproteins, O-mannosylation, C-mannosylation and glycosylphosphatidylinositol anchors synthesis. Little is known about the function of DPMS in liver cancer.MethodsThe study explored the roles of DPMS in the prognosis of hepatocellular carcinoma using UALCAN, Human Protein Atlas, GEPIA, cBioPortal and Metascape databases. The mRNA expressions of DPM1/2/3 also were detected by quantitative real-time PCR experiments in vitro.ResultsThe transcriptional and proteinic expressions of DPM1/2/3 were both over-expressed in patients with hepatocellular carcinoma. Over-expressions of DPMS were discovered to be dramatically associated with clinical cancer stages and pathological tumor grades in hepatocellular carcinoma patients. In addition, higher mRNA expressions of DPM1/2/3 were found to be significantly related to shorter overall survival in liver cancer patients. Futhermore, high genetic alteration rate of DPMS (41%) was also observed in patients with liver cancer, and genetic alteration in DPMS was associated with shorter overall survival in hepatocellular carcinoma patients. We also performed quantitative real-time PCR experiments in human normal hepatocytes and hepatoma cells to verify the expressions of DPM1/2/3 and results showed that the expression of DPM1 was significantly increased in hepatoma cells SMMC-7721 and HepG2.ConclusionsTaken together, these results suggested that DPM1 could be a potential prognostic biomarker for survivals of hepatocellular carcinoma patients. creator: Ming Li creator: Shengli Xia creator: Ping Shi uri: https://doi.org/10.7717/peerj.10307 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: HIV-1 promoter is gradually silenced when integrated into BACH2 in Jurkat T-cells link: https://peerj.com/articles/10321 last-modified: 2020-11-24 description: BackgroundThe persistence of the latent HIV-1 reservoir is a major obstacle to curing HIV-1 infection. HIV-1 integrates into the cellular genome and some targeted genomic loci are frequently detected in clonally expanded latently HIV-1 infected cells, for instance, the gene BTB domain and CNC homology 2 (BACH2).MethodsWe investigated HIV-1 promoter activity after integration into specific sites in BACH2 in Jurkat T-cells. The HIV-1-based vector LTatCL[M] contains two fluorophores: (1) Cerulean, which reports the activity of the HIV-1 promoter and (2) mCherry driven by a constitutive promotor and flanked by genetic insulators. This vector was inserted into introns 2 and 5 of BACH2 of Jurkat T-cells via CRISPR/Cas9 technology in the same and convergent transcriptional orientation of BACH2, and into the genomic safe harbour AAVS1. Single cell clones representing active (Cerulean+/mCherry+) and inactive (Cerulean–/mCherry+) HIV-1 promoters were characterised.ResultsUpon targeted integration of the 5.3 kb vector LTatCL[M] into BACH2, the HIV-1 promoter was gradually silenced as reflected by the decrease in Cerulean expression over a period of 162 days. Silenced HIV-1 promoters could be reactivated by TNF-α and Romidepsin. This observation was independent of the targeted intron and the transcriptional orientation. BACH2 mRNA and protein expression was not impaired by mono-allelic integration of LTatCL[M].ConclusionSuccessful targeted integration of the HIV-1-based vector LTatCL[M] allows longitudinal analyses of HIV-1 promoter activity. creator: Anne Inderbitzin creator: Yik Lim Kok creator: Lisa Jörimann creator: Audrey Kelley creator: Kathrin Neumann creator: Daniel Heinzer creator: Toni Cathomen creator: Karin J. Metzner uri: https://doi.org/10.7717/peerj.10321 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Inderbitzin et al. title: Wnt16 signaling promotes osteoblast differentiation of periosteal derived cells in vitro and in vivo link: https://peerj.com/articles/10374 last-modified: 2020-11-24 description: BackgroundPeriosteum plays critical roles in de novo bone formation and fracture repair. Wnt16 has been regarded as a key regulator in periosteum bone formation. However, the role of Wnt16 in periosteum derived cells (PDCs) osteogenic differentiation remains unclear. The study goal is to uncover whether and how Wnt16 acts on the osteogenesis of PDCs.MethodsWe detected the variation of Wnt16 mRNA expression in PDCs, which were isolated from mouse femur and identified by flow cytometry, cultured in osteogenic medium for 14 days, then knocked down and over-expressed Wnt16 in PDCs to analysis its effects in osteogenesis. Further, we seeded PDCs (Wnt16 over-expressed/vector) in β-tricalcium phosphate cubes, and transplanted this complex into a critical size calvarial defect. Lastly, we used immunofluorescence, Topflash and NFAT luciferase reporter assay to study the possible downstream signaling pathway of Wnt16.ResultsWnt16 mRNA expression showed an increasing trend in PDCs under osteogenic induction for 14 days. Wnt16 shRNA reduced mRNA expression of Runx2, collage type I (Col-1) and osteocalcin (OCN) after 7 days of osteogenic induction, as well as alizarin red staining intensity after 21days. Wnt16 also increased the mRNA expression of Runx2 and OCN and the protein production of Runx2 and Col-1 after 2 days of osteogenic stimulation. In the orthotopic transplantation assay, more bone volume, trabecula number and less trabecula space were found in Wnt16 over-expressed group. Besides, in the newly formed tissue Brdu positive area was smaller and Col-1 was larger in Wnt16 over-expressed group compared to the control group. Finally, Wnt16 upregulated CTNNB1/β-catenin expression and its nuclear translocation in PDCs, also increased Topflash reporter luciferase activity. By contrast, Wnt16 failed to increase NFAT reporter luciferase activity.ConclusionTogether, Wnt16 plays a positive role in regulating PDCs osteogenesis, and Wnt16 may have a potential use in improving bone regeneration. creator: Ying Jin creator: Xiaoyan Sun creator: Fang Pei creator: Zhihe Zhao creator: Jeremy Mao uri: https://doi.org/10.7717/peerj.10374 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Jin et al.