title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1414 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Engineering of CHO cells for the production of vertebrate recombinant sialyltransferases link: https://peerj.com/articles/5788 last-modified: 2019-02-11 description: BackgroundSialyltransferases (SIATs) are a family of enzymes that transfer sialic acid (Sia) to glycan chains on glycoproteins, glycolipids, and oligosaccharides. They play key roles in determining cell–cell and cell-matrix interactions and are important in neuronal development, immune regulation, protein stability and clearance. Most fully characterized SIATs are of mammalian origin and these have been used for in vitro and in vivo modification of glycans. Additional versatility could be achieved by the use of animal SIATs from other species that live in much more variable environments. Our aim was to generate a panel of stable CHO cell lines expressing a range of vertebrate SIATs with different physicochemical and functional properties.MethodsThe soluble forms of various animal ST6Gal and ST3Gal enzymes were stably expressed from a Gateway-modified secretion vector in CHO cells. The secreted proteins were IMAC-purified from serum-free media. Functionality of the protein was initially assessed by lectin binding to the host CHO cells. Activity of purified proteins was determined by a number of approaches that included a phosphate-linked sialyltransferase assay, HILIC-HPLC identification of sialyllactose products and enzyme-linked lectin assay (ELLA).ResultsA range of sialyltransferase from mammals, birds and fish were stably expressed in CHO Flp-In cells. The stable cell lines expressing ST6Gal1 modify the glycans on the surface of the CHO cells as detected by fluorescently labelled lectin microscopy. The catalytic domains, as isolated by Ni Sepharose from culture media, have enzymatic activities comparable to commercial enzymes. Sialyllactoses were identified by HILIC-HPLC on incubation of the enzymes from lactose or whey permeate. The enzymes also increased SNA-I labelling of asialofetuin when incubated in a plate format.ConclusionStable cell lines are available that may provide options for the in vivo sialylation of glycoproteins. Proteins are active and should display a variety of biological and physicochemical properties based on the animal source of the enzyme. creator: Benoit Houeix creator: Michael T. Cairns uri: https://doi.org/10.7717/peerj.5788 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Houeix and Cairns title: Potential ecotoxicological effects of antimicrobial surface coatings: a literature survey backed up by analysis of market reports link: https://peerj.com/articles/6315 last-modified: 2019-02-11 description: This review was initiated by the COST action CA15114 AMICI “Anti-Microbial Coating Innovations to prevent infectious diseases,” where one important aspect is to analyze ecotoxicological impacts of antimicrobial coatings (AMCs) to ensure their sustainable use. Scopus database was used to collect scientific literature on the types and uses of AMCs, while market reports were used to collect data on production volumes. Special attention was paid on data obtained for the release of the most prevalent ingredients of AMCs into the aqueous phase that was used as the proxy for their possible ecotoxicological effects. Based on the critical analysis of 2,720 papers, it can be concluded that silver-based AMCs are by far the most studied and used coatings followed by those based on titanium, copper, zinc, chitosan and quaternary ammonium compounds. The literature analysis pointed to biomedicine, followed by marine industry, construction industry (paints), food industry and textiles as the main fields of application of AMCs. The published data on ecotoxicological effects of AMCs was scarce, and also only a small number of the papers provided information on release of antimicrobial ingredients from AMCs. The available release data allowed to conclude that silver, copper and zinc are often released in substantial amounts (up to 100%) from the coatings to the aqueous environment. Chitosan and titanium were mostly not used as active released ingredients in AMCs, but rather as carriers for other release-based antimicrobial ingredients (e.g., conventional antibiotics). While minimizing the prevalence of healthcare-associated infections appeared to be the most prosperous field of AMCs application, the release of environmentally hazardous ingredients of AMCs into hospital wastewaters and thus, also the environmental risks associated with AMCs, comprise currently only a fraction of the release and risks of traditional disinfectants. However, being proactive, while the use of antimicrobial/antifouling coatings could currently pose ecotoxicological effects mainly in marine applications, the broad use of AMCs in other applications like medicine, food packaging and textiles should be postponed until reaching evidences on the (i) profound efficiency of these materials in controlling the spread of pathogenic microbes and (ii) safety of AMCs for the human and ecosystems. creator: Merilin Rosenberg creator: Krunoslav Ilić creator: Katre Juganson creator: Angela Ivask creator: Merja Ahonen creator: Ivana Vinković Vrček creator: Anne Kahru uri: https://doi.org/10.7717/peerj.6315 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Rosenberg et al. title: Integrating gross morphology and bone histology to assess skeletal maturity in early dinosauromorphs: new insights from Dromomeron (Archosauria: Dinosauromorpha) link: https://peerj.com/articles/6331 last-modified: 2019-02-11 description: Understanding growth patterns is central to properly interpreting paleobiological signals in tetrapods, but assessing skeletal maturity in some extinct clades may be difficult when growth patterns are poorly constrained by a lack of ontogenetic series. To overcome this difficulty in assessing the maturity of extinct archosaurian reptiles—crocodylians, birds and their extinct relatives—many studies employ bone histology to observe indicators of the developmental stage reached by a given individual. However, the relationship between gross morphological and histological indicators of maturity has not been examined in most archosaurian groups. In this study, we examined the gross morphology of a hypothesized growth series of Dromomeron romeri femora (96.6–144.4 mm long), the first series of a non-dinosauriform dinosauromorph available for such a study. We also histologically sampled several individuals in this growth series. Previous studies reported that D. romeri lacks well-developed rugose muscle scars that appear during ontogeny in closely related dinosauromorph taxa, so integrating gross morphology and histological signal is needed to determine reliable maturity indicators for early bird-line archosaurs. We found that, although there are small, linear scars indicating muscle attachment sites across the femur, the only rugose muscle scar that appears during ontogeny is the attachment of the M. caudofemoralis longus, and only in the largest-sampled individual. This individual is also the only femur with histological indicators that asymptotic size had been reached, although smaller individuals possess some signal of decreasing growth rates (e.g., decreasing vascular density). The overall femoral bone histology of D. romeri is similar to that of other early bird-line archosaurs (e.g., woven-bone tissue, moderately to well-vascularized, longitudinal vascular canals). All these data indicate that the lack of well-developed femoral scars is autapomorphic for this species, not simply an indication of skeletal immaturity. We found no evidence of the high intraspecific variation present in early dinosaurs and other dinosauriforms, but a limited sample size of other early bird-line archosaur growth series make this tentative. The evolutionary history and phylogenetic signal of gross morphological features must be considered when assessing maturity in extinct archosaurs and their close relatives, and in some groups corroboration with bone histology or with better-known morphological characters is necessary. creator: Christopher T. Griffin creator: Lauren S. Bano creator: Alan H. Turner creator: Nathan D. Smith creator: Randall B. Irmis creator: Sterling J. Nesbitt uri: https://doi.org/10.7717/peerj.6331 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Griffin et al. title: In silico analysis reveals a shared immune signature in CASP8-mutated carcinomas with varying correlations to prognosis link: https://peerj.com/articles/6402 last-modified: 2019-02-11 description: BackgroundSequencing studies across multiple cancers continue to reveal mutations and genes involved in the pathobiology of these cancers. Exome sequencing of oral cancers, a subset of Head and Neck Squamous cell Carcinomas (HNSCs) common among tobacco-chewing populations, revealed that ∼34% of the affected patients harbor mutations in the CASP8 gene. Uterine Corpus Endometrial Carcinoma (UCEC) is another cancer where ∼10% cases harbor CASP8 mutations. Caspase-8, the protease encoded by CASP8 gene, plays a dual role in programmed cell death, which in turn has an important role in tumor cell death and drug resistance. CASP8 is a protease required for the extrinsic pathway of apoptosis and is also a negative regulator of necroptosis. Using multiple tools such as differential gene expression, gene set enrichment, gene ontology, in silico immune cell estimates, and survival analyses to mine data in The Cancer Genome Atlas, we compared the molecular features and survival of these carcinomas with and without CASP8 mutations.ResultsDifferential gene expression followed by gene set enrichment analysis showed that HNSCs with CASP8 mutations displayed a prominent signature of genes involved in immune response and inflammation. Analysis of abundance estimates of immune cells in these tumors further revealed that mutant-CASP8 HNSCs were rich in immune cell infiltrates. However, in contrast to Human Papilloma Virus-positive HNSCs that also exhibit high immune cell infiltration, which in turn is correlated with better overall survival, HNSC patients with mutant-CASP8 tumors did not display any survival advantage. Similar analyses of UCECs revealed that while UCECs with CASP8 mutations also displayed an immune signature, they had better overall survival, in contrast to the HNSC scenario. There was also a significant up-regulation of neutrophils (p-value = 0.0001638) as well as high levels of IL33 mRNA (p-value = 7.63747E−08) in mutant-CASP8 HNSCs, which were not observed in mutant-CASP8 UCECs.ConclusionsThese results suggested that carcinomas with mutant CASP8 have broadly similar immune signatures albeit with different effects on survival. We hypothesize that subtle tissue-dependent differences could influence survival by modifying the micro-environment of mutant-CASP8 carcinomas. High neutrophil numbers, a well-known negative prognosticator in HNSCs, and/or high IL33 levels may be some of the factors affecting survival of mutant-CASP8 cases. creator: Yashoda Ghanekar creator: Subhashini Sadasivam uri: https://doi.org/10.7717/peerj.6402 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Ghanekar and Sadasivam title: The blood parameters and liver function changed inconsistently among children between burns and traumatic injuries link: https://peerj.com/articles/6415 last-modified: 2019-02-11 description: ObjectiveBurn and traumatic injury are two kinds of injury by modality. They cause acute phase response and lead to a series of pathological and physiological changes. In this study, we explored whether there are differences in routine blood parameters and liver enzyme levels between burned and traumatically injured children.MethodsPatients under 18 years old with injuries were recruited. Their demographic and clinical data were recorded. Collected clinical data included routine blood parameters (white blood cell count (WBC), red blood cell count (RBC), platelets (PLT), hemoglobin (HB)), serological enzyme levels (alanine aminotransferase (ALT), aspartate transaminase (AST), glutamyltransferase (GGT), alkaline phosphatase (ALP), cholinesterase (CHE)), and total protein (TP) levels (albumin (ALB), globulin (GLB)). A generalized linear model and multivariate analysis of variance were used to conduct comparisons.ResultsA total of 162 children (109 with burns and 53 with traumatic injuries) with a mean age of 4.36 ± 4.29 years were enrolled in the study. Burned children had higher levels of RBC, HB, WBC, AST and lower levels of TP, CHE, ALB than traumatically injured children (P < 0.05). Moreover, the concentration of WBC and HB was higher in males compared to females (P < 0.001). Conversely, the level of AST and TP in males was lower, AST levels were significantly lower in males (P = 0.005). Age positively correlated with the levels of HB, AST and TP (P < 0.001), and negatively correlated with WBC (P < 0.001). With decreasing body mass index (BMI), the levels of WBC, HB, AST and TP significantly increased in both groups of injured children (P < 0.001). In addition, ISS was positively correlated with WBC and HB levels (P < 0.001), but negatively correlated with AST and TP levels (P < 0.001).ConclusionsChildren with burn injuries suffered a greater acute response and liver damage than traumatically injured children. This may in part underlie clinical observations of differences in children morbidity and mortality in response to different injury types. creator: Chan Nie creator: Tao Wang creator: Huiting Yu creator: Xue Wang creator: Xueqin Zeng creator: Zairong Wei creator: Xiuquan Shi uri: https://doi.org/10.7717/peerj.6415 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nie et al. title: Discordant financial conflicts of interest disclosures between clinical trial conference abstract and subsequent publication link: https://peerj.com/articles/6423 last-modified: 2019-02-11 description: BackgroundFinancial conflicts of interest (FCOI) are known to be prevalent in medicine. Authorship of pivotal trials reap non-financial benefits including publication productivity that can be used for assessment of tenure positions and promotion. The purpose of this investigation was to quantify the prevalence and discordance of academic trial author (authors) FCOI in industry-sponsored drug trials that were initially presented as oral abstracts and subsequently resulted in a peer-reviewed publication.MethodsOral abstracts from the American Society of Clinical Oncology (ASCO) 2017 Annual Meeting that were subsequently published were identified. Studies that were non-industry sponsored, non-adult, or non-therapeutic trials were excluded. Studies that did not have a subsequent peer-reviewed publication or had a publication preceding the ASCO 2017 Annual Meeting were also excluded. FCOI was categorized and impact factor (IF) for the journal at the time of publication was retrieved. FCOI discordance between the oral abstract and publication was calculated based on geographic location and IF.ResultsA total of 22 paired abstract and publications met inclusion criteria for further analysis. A total of 384 authors were identified, of these 280 authors (74.1%) were included in both the oral abstract and subsequent publication. A total of 76% of these 280 authors had FCOI and 66.4% had FCOI discordance. There were statistically significant differences for the sum of FCOI discordance for U.S.-based authors (p = 0.0004) but not for journal IF. When analyzing the sum of absolute differences of FCOI discordance, statistical significance was reached for authors from any of the three geographic regions, as well as, low and high IF journals (all p-values < 0.0001).ConclusionsThis study draws attention to the lack of uniformity and vetting of FCOI reporting in abstracts and journals publishing solid tumor oncology trial results. This is particularly concerning, since FCOI is prevalent globally. creator: Glen J. Weiss creator: Roger B. Davis uri: https://doi.org/10.7717/peerj.6423 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Weiss and Davis title: Elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal link: https://peerj.com/articles/6116 last-modified: 2019-02-08 description: BackgroundGeographical patterns of species diversity are one of the key topics in biogeography and ecology. The effects of biogeographical affinities on the elevational patterns of species diversity have attracted much attention recently, but the factors driving elevational patterns of the percentages of plants with tropical and temperate biogeographical affinities have not been adequately explored.MethodsWe first used univariate least squares regressions to evaluate the effects of each predictor on the elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal. Then, the lowest corrected Akaike information criterion value was used to find the best-fit models for all possible combinations of the aforementioned predictors. We also conducted partial regression analysis to investigate the relative influences of each predictor in the best-fit model of the percentages of plant genera with tropical and temperate affinities.ResultsWith the increase of elevation, the percentage of plant genera with tropical affinity significantly decreased, while that of plant genera with temperate affinity increased. The strongest predictor of the percentages of plant genera with tropical affinity in the examined area was the minimum temperature of the coldest month. For the elevational patterns of the percentages of plant genera with temperate affinity, the strongest predictor was the maximum temperature of the warmest month. Compared with mid-domain effects (MDE), climatic factors explained much more of the elevational variation of the percentages of plant genera with tropical and temperate affinities.DiscussionThe elevational patterns of the percentages of plant genera with tropical affinities and the factors driving them supported the revision of the freezing-tolerance hypothesis. That is, freezing may filter out plant genera with tropical affinity, resulting in the decrease of their percentages, with winter coldness playing a predominant role. Winter coldness may not only exert filtering effects on plant genera with tropical affinity, but may also regulate the interactions between plant genera with tropical and temperate affinities. The elevational patterns of tropical and temperate plant diversities, and those of their percentages, might be controlled by different factors or mechanisms. Freezing-tolerance and the interactions between plant genera with tropical and temperate affinities regulated by climatic factors played stronger roles than MDE in shaping the elevational patterns of the percentages of plant genera with tropical and temperate affinities in Nepal. creator: Yunyun Lai creator: Jianmeng Feng uri: https://doi.org/10.7717/peerj.6116 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lai and Feng title: Invasion genetics of the mummichog (Fundulus heteroclitus): recent anthropogenic introduction in Iberia link: https://peerj.com/articles/6155 last-modified: 2019-02-08 description: Human activities such as trade and transport have increased considerably in the last decades, greatly facilitating the introduction and spread of non-native species at a global level. In the Iberian Peninsula, Fundulus heteroclitus, a small euryhaline coastal fish with short dispersal, was found for the first time in the mid-1970s. Since then, F. heteroclitus has undergone range expansions, colonizing the southern region of Portugal, southwestern coast of Spain and the Ebro Delta in the Mediterranean Sea. Cytochrome b sequences were used to elucidate the species invasion pathway in Iberia. Three Iberian locations (Faro, Cádiz and Ebro Delta) and 13 other locations along the native range of F. heteroclitus in North America were sampled. Results revealed a single haplotype, common to all invasive populations, which can be traced to the northern region of the species’ native range. We posit that the origin of the founder individuals is between New York and Nova Scotia. Additionally, the lack of genetic structure within Iberia is consistent with a recent invasion scenario and a strong founder effect. We suggest the most probable introduction vector is associated with the aquarium trade. We further discuss the hypothesis of a second human-mediated introduction responsible for the establishment of individuals in the Ebro Delta supported by the absence of adequate muddy habitats linking Cádiz and the Ebro Delta. Although the species has a high tolerance to salinity and temperature, ecological niche modelling indicates that benthic habitat constraints prevent along-shore colonisation suggesting that such expansions would need to be aided by human release. creator: Teófilo Morim creator: Grant R. Bigg creator: Pedro M. Madeira creator: Jorge Palma creator: David D. Duvernell creator: Enric Gisbert creator: Regina L. Cunha creator: Rita Castilho uri: https://doi.org/10.7717/peerj.6155 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Morim et al. title: Response of adult honey bees treated in larval stage with prochloraz to infection with Nosema ceranae link: https://peerj.com/articles/6325 last-modified: 2019-02-08 description: Among numerous factors that contribute to honey bee colony losses and problems in beekeeping, pesticides and Nosema ceranae have been often reported. In contrast to insecticides, whose effects on bees have been widely studied, fungicides did not attract considerable attention. Prochloraz, an imidazole fungicide widely used in agriculture, was detected in honey and pollen stored inside hives and has been already proven to alter immune gene expression of honey bees at different developmental stages. The aim of this study was to simulate the realistic conditions of migratory beekeeping, where colonies, both uninfected and infected with N. ceranae, are frequently transported to the vicinity of crop fields treated with prochloraz. We investigated the combined effect of prochloraz and N. ceranae on honey bees that faced fungicide during the larval stage through food consumption and microsporidium infection afterwards. The most pronounced changes in gene expression were observed in newly emerged Nosema-free bees originating from colonies previously contaminated with prochloraz. As exclusively upregulation was registered, prochloraz alone most likely acts as a challenge that induces activation of immune pathways in newly emerged bees. The combination of both stressors (prochloraz and Nosema infection) exerted the greatest effect on six-day-old honey bees. Among ten genes with significantly altered expression, half were upregulated and half downregulated. N. ceranae as a sole stressor had the weakest effects on immune gene expression modulation with only three genes significantly dysregulated. In conclusion, food contaminated with prochloraz consumed in larval stage could present a threat to the development of immunity and detoxification mechanisms in honey bees. creator: Uros Glavinic creator: Tanja Tesovnik creator: Jevrosima Stevanovic creator: Minja Zorc creator: Ivanka Cizelj creator: Zoran Stanimirovic creator: Mojca Narat uri: https://doi.org/10.7717/peerj.6325 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Glavinic et al. title: Membrane potential (Vmem) measurements during mesenchymal stem cell (MSC) proliferation and osteogenic differentiation link: https://peerj.com/articles/6341 last-modified: 2019-02-08 description: BackgroundElectrochemical signals play an important role in cell communication and behavior. Electrically charged ions transported across cell membranes maintain an electrochemical imbalance that gives rise to bioelectric signaling, called membrane potential or Vmem. Vmem plays a key role in numerous inter- and intracellular functions that regulate cell behaviors like proliferation, differentiation and migration, all playing a critical role in embryonic development, healing, and regeneration.MethodsWith the goal of analyzing the changes in Vmem during cell proliferation and differentiation, here we used direct current electrical stimulation (EStim) to promote cell proliferation and differentiation and simultaneously tracked the corresponding changes in Vmem in adipose derived mesenchymal stem cells (AT-MSC).ResultsWe found that EStim caused increased AT-MSC proliferation that corresponded to Vmem depolarization and increased osteogenic differentiation that corresponded to Vmem hyperpolarization. Taken together, this shows that Vmem changes associated with EStim induced cell proliferation and differentiation can be accurately tracked during these important cell functions. Using this tool to monitor Vmem changes associated with these important cell behaviors we hope to learn more about how these electrochemical cues regulate cell function with the ultimate goal of developing new EStim based treatments capable of controlling healing and regeneration. creator: Mit Balvantray Bhavsar creator: Gloria Cato creator: Alexander Hauschild creator: Liudmila Leppik creator: Karla Mychellyne Costa Oliveira creator: Maria José Eischen-Loges creator: John Howard Barker uri: https://doi.org/10.7717/peerj.6341 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bhavsar et al.