Molecular typing and profiling of topoisomerase mutations causing resistance to ciprofloxacin and levofloxacin in Elizabethkingia species
Objectives Several Elizabethkingia species often exhibit extensive antibiotic resistance, causing infections associated with severe morbidity and high mortality rates worldwide. In this study, we determined fluoroquinolone susceptibility profiles of clinical Elizabethkingia spp. isolates and investigated the resistance mechanisms. Methods In 2017–2018, 131 Elizabethkingia spp. isolates were recovered from specimens collected at tertiary care centers in northern Taiwan. Initial species identification using the Vitek MS system and subsequent verification by 16S rRNA sequencing confirmed the presence of Elizabethkingia anophelis (n = 111), E. miricola (n = 11), and E. meningoseptica (n = 9). Fluoroquinolone susceptibility was determined using the microbroth dilution method, and fluoroquinolone resistance genes were analyzed by sequencing. Results Among Elizabethkingia spp. isolates, 91% and 77% were resistant to ciprofloxacin and levofloxacin, respectively. The most prevalent alterations were two single mutations in GyrA, Ser83Ile, and Ser83Arg, detected in 76% of the isolates exhibiting fluoroquinolone MIC between 8 and 128 μg/ml. Another GyrA single mutation, Asp87Asn, was identified in two quinolone-resistant E. miricola strains. None of the isolates had alterations in GyrB, ParC, or ParE. We developed a high-resolution melting assay for rapid identification of the prevalent gyrA gene mutations. The genetic relationship between the isolates was evaluated by random amplified polymorphic DNA PCR that yielded diverse pulsotypes, indicating the absence of any temporal or spatial overlap among the patients during hospitalization. Conclusion Our analysis of fluoroquinolone-resistant Elizabethkingia spp. isolates provides information for further research on the variations of the resistance mechanism and potential clinical guidance for infection management.
Jian et al. (2018) Molecular typing and profiling of topoisomerase mutations causing resistance to ciprofloxacin and levofloxacin in Elizabethkingia species. PeerJ 6:e5608 https://doi.org/10.7717/peerj.5608
Explanation of observational data engenders a causal belief about smoking and cancer
Most researchers do not deliberately claim causal results in an observational study. But do we lead our readers to draw a causal conclusion unintentionally by explaining why significant correlations and relationships may exist? Here we perform a randomized controlled experiment in a massive open online course run in 2013 that teaches data analysis concepts to test the hypothesis that explaining an analysis will lead readers to interpret an inferential analysis as causal. We test this hypothesis with a single example of an observational study on the relationship between smoking and cancer. We show that adding an explanation to the description of an inferential analysis leads to a 15.2% increase in readers interpreting the analysis as causal (95% confidence interval for difference in two proportions: 12.8%–17.5%). We then replicate this finding in a second large scale massive open online course. Nearly every scientific study, regardless of the study design, includes an explanation for observed effects. Our results suggest that these explanations may be misleading to the audience of these data analyses and that qualification of explanations could be a useful avenue of exploration in future research to counteract the problem. Our results invite many opportunities for further research to broaden the scope of these findings beyond the single smoking-cancer example examined here.
Myint et al. (2018) Explanation of observational data engenders a causal belief about smoking and cancer. PeerJ 6:e5597 https://doi.org/10.7717/peerj.5597
A close relative of the Amazon river dolphin in marine deposits: a new Iniidae from the late Miocene of Angola
Background A few odontocetes (echolocating toothed cetaceans) have been able to independently colonize freshwater ecosystems. Although some extant species of delphinids (true dolphins) and phocoenids (porpoises) at least occasionally migrate upstream of large river systems, they have close relatives in fully marine regions. This contrasts with the three odontocete families only containing extant species with a strictly freshwater habitat (Iniidae in South America, the recently extinct Lipotidae in China, and Platanistidae in southeast Asia). Among those, the fossil record of Iniidae includes taxa from freshwater deposits of South America, partly overlapping geographically with the extant Amazon river dolphin Inia geoffrensis, whereas a few marine species from the Americas were only tentatively referred to the family, leaving the transition from a marine to freshwater environment poorly understood. Methods Based on a partial odontocete skeleton including the cranium, discovered in late Miocene (Tortonian-Messinian) marine deposits near the estuary of the Cuanza River, Angola, we describe a new large iniid genus and species. The new taxon is compared to other extinct and extant iniids, and its phylogenetic relationships with the latter are investigated through cladistic analysis. Results and Discussion The new genus and species Kwanzacetus khoisani shares a series of morphological features with Inia geoffrensis, including the combination of a frontal boss with nasals being lower on the anterior wall of the vertex, the laterally directed postorbital process of the frontal, the anteroposterior thickening of the nuchal crest, and robust teeth with wrinkled enamel. As confirmed (although with a low support) with the phylogenetic analysis, this makes the new taxon the closest relative of I. geoffrensis found in marine deposits. The geographic provenance of K. khoisani, on the eastern coast of South Atlantic, suggests that the transition from the marine environment to a freshwater, Amazonian habitat may have occurred on the Atlantic side of South America. This new record further increases the inioid diversity during the late Miocene, a time interval confirmed here as the heyday for this superfamily. Finally, this first description of a Neogene cetacean from inland deposits of western sub-Saharan Africa reveals the potential of this large coastal area for deciphering key steps of the evolutionary history of modern cetaceans in the South Atlantic.
Lambert et al. (2018) A close relative of the Amazon river dolphin in marine deposits: a new Iniidae from the late Miocene of Angola. PeerJ 6:e5556 https://doi.org/10.7717/peerj.5556
Children are not like other loads: a cross-cultural perspective on the influence of burdens and companionship on human walking
A major portion of humans’ activity-based energy expenditure is taken up by locomotion, particularly walking. Walking behaviors have energetic outcomes and as such can be important windows into how populations and groups adjust to different environmental and task constraints. While sex differences in the speed of paired walkers have been established by others, the dynamics of how walkers adjust their speed in more varied groups and in groups containing children remains unexplored. Furthermore, little ecological data exists to illustrate the relationships between walking speed and child-carrying. Here, we aim to determine how culture impacts the effects of group composition and infant-carrying on walking speed. Because the determinants of group dynamics and parental investment are partially cultural, we examine walking behavior in the Northwestern United States and in Central Uganda. Using an observational method, we recorded the speed, load carriage, and group composition of pedestrians in a single naturalistic urban environment within each country. Our data suggest that children are treated fundamentally differently than other loads or the presence of walking partners, and that major speed adjustments are child-dependent. Our data furthermore indicate that Ugandans walk more slowly in groups than when alone, while Americans walk more quickly in groups. Clear distinctions between the groups make large generalizations about walking behavior difficult, and highlight the importance of culturally specific contexts.
Bouterse et al. (2018) Children are not like other loads: a cross-cultural perspective on the influence of burdens and companionship on human walking. PeerJ 6:e5547 https://doi.org/10.7717/peerj.5547
Interaction of guidance types and the Need for Cognitive Closure in wiki-based learning
One purpose of wikis is the collaborative generation of content. During creation processes, controversies between authors emerge that they discuss on the article’s talk page. Research suggests that controversies based on opposing points of view and contradictory evidence can be fruitful to trigger individual elaboration processes. However, previous research also showed that many wikis are not necessarily suited to identify relevant discussion contents and thus users need additional support as guidance. In an experimental laboratory study (N = 181) on wiki talk pages, we investigated two guidance measures in conjunction with the need for cognitive closure: (1) visual markers to highlight controversy status (implicit guidance) and (2) a collaboration script that directs users towards discussions (explicit guidance). Effects on wiki processes and learning outcomes were analysed. The results show that both guidance types can affect user behaviours, but in interaction with the individual Need for Cognitive Closure there were no meaningful effects. With respect to learning outcomes, we found an anticipated pattern for the interaction of the Need for Cognitive Closure with both guidance principles. The data provides support for differences in the learning success depending on the provided guidance type and the individual Need for Cognitive Closure.
Heimbuch et al. (2018) Interaction of guidance types and the Need for Cognitive Closure in wiki-based learning. PeerJ 6:e5541 https://doi.org/10.7717/peerj.5541
Effects of macroalgae loss in an Antarctic marine food web: applying extinction thresholds to food web studies
Antarctica is seriously affected by climate change, particularly at the Western Antarctic Peninsula (WAP) where a rapid regional warming is observed. Potter Cove is a WAP fjord at Shetland Islands that constitutes a biodiversity hotspot where over the last years, Potter Cove annual air temperatures averages increased by 0.66 °C, coastal glaciers declined, and suspended particulate matter increased due to ice melting. Macroalgae are the main energy source for all consumers and detritivores of Potter Cove. Some effects of climate change favor pioneer macroalgae species that exploit new ice-free areas and can also decline rates of photosynthesis and intensify competition between species due to the increase of suspended particulate matter. In this study, we evaluated possible consequences of climate change at Potter Cove food web by simulating the extinction of macroalgae and detritus using a topological approach with thresholds of extinction. Thresholds represent the minimum number of incoming links necessary for species’ survival. When we simulated the extinctions of macroalgae species at random, a threshold of extinction beyond 50% was necessary to obtain a significant number of secondary extinctions, while with a 75% threshold a real collapse of the food web occurred. Our results indicate that Potter Cove food web is relative robust to macroalgae extinction. This is dramatically different from what has been found in other food webs, where the reduction of 10% in prey intake caused a disproportionate increase of secondary extinctions. Robustness of the Potter Cove food web was mediated by omnivory and redundancy, which had an important relevance in this food web. When we eliminated larger-biomass species more secondary extinctions occurred, a similar response was observed when more connected species were deleted, yet there was no correlation between species of larger-biomass and high-degree. This similarity could be explained because both criteria involved key species that produced an emerging effect on the food web. In this way, large-biomass and high-degree species could be acting as source for species with few trophic interactions or low redundancy. Based on this work, we expect the Potter Cove food web to be robust to changes in macroalgae species caused by climate change until a high threshold of stress is reached, and then negative effects are expected to spread through the entire food web leading to its collapse.
Cordone et al. (2018) Effects of macroalgae loss in an Antarctic marine food web: applying extinction thresholds to food web studies. PeerJ 6:e5531 https://doi.org/10.7717/peerj.5531
An overview report on the application of heteropoly acids on supporting materials in the photocatalytic degradation of organic pollutants from aqueous solutions
Organic pollutants contaminate water resources and the environment when discharged into water streams. Also, the presence of these materials in incompletely treated or untreated wastewater leads to serious environmental hazards. The hydroxyl radicals and holes are regarded as the most oxidant species in the degradation of organic pollutants using the studied composites. The results of this review show that heteropoly acids on supporting materials could be considered as appropriate photocatalysts in the removal of organic pollutant from aqueous solutions.
Environmental Contamination and Remediation
Nikoonahad et al. (2018) An overview report on the application of heteropoly acids on supporting materials in the photocatalytic degradation of organic pollutants from aqueous solutions. PeerJ 6:e5501 https://doi.org/10.7717/peerj.5501
Deep divergence of Red-crowned Ant Tanager (Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica
Many neotropical species have a complex history of diversification as a result of the influence of geographical, ecological, climatic, and geological factors that determine the distribution of populations within a lineage. Phylogeography identifies such populations, determines their geographic distributions, and quantifies the degree of genetic divergence. In this work we explored the genetic structure of Habia rubica populations, a polytypic taxon with 17 subspecies described, in order to obtain hypotheses about their evolutionary history and processes of diversification. We undertook multilocus analyses using sequences of five molecular markers (ND2, ACOI-I9, MUSK, FGB-I5 and ODC), and sampling from across the species’ distribution range, an area encompassing from Central Mexico throughout much of South America. With these data, we obtained a robust phylogenetic hypothesis, a species delimitation analysis, and estimates of divergence times for these lineages. The phylogenetic hypothesis of concatenated molecular markers shows that H. rubica can be divided in three main clades: the first includes Mexican Pacific coast populations, the second is formed by population from east of Mexico to Panama and the third comprises the South American populations. Within these clades we recognize seven principal phylogroups whose limits have a clear correspondence with important geographical discontinuities including the Isthmus of Tehuantepec in southern Mexico, the Talamanca Cordillera, and the Isthmus of Panama in North America. In South America, we observed a marked separation of two phylogroups that include the populations that inhabit mesic forests in western and central South America (Amazon Forest) and those inhabiting the seasonal forest from the eastern and northern regions of the South America (Atlantic Forest). These areas are separated by an intervening dry vegetation “diagonal” (Chaco, Cerrado and Caatinga). The geographic and genetic structure of these phylogroups describes a history of diversification more active and complex in the northern distribution of this species, producing at least seven well-supported lineages that could be considered species.
Ramírez-Barrera et al. (2018) Deep divergence of Red-crowned Ant Tanager (Habia rubica: Cardinalidae), a multilocus phylogenetic analysis with emphasis in Mesoamerica. PeerJ 6:e5496 https://doi.org/10.7717/peerj.5496
The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome
Chemerin is an adipocyte derived signalling molecule (adipokine) that serves as a ligand activator of Chemokine-like receptor 1(CMKLR1). Chemerin/CMKLR1 signalling is well established to regulate fundamental processes in metabolism and inflammation. The composition and function of gut microbiota has also been shown to impact the development of metabolic and inflammatory diseases such as obesity, diabetes and inflammatory bowel disease. In this study, we assessed the microbiome composition of fecal samples isolated from wildtype, chemerin, or CMKLR1 knockout mice using Illumina-based sequencing. Moreover, the knockout mice and respective wildtype mice used in this study were housed at different universities allowing us to compare facility-dependent effects on microbiome composition. While there was no difference in alpha diversity within samples when compared by either facility or genotype, we observed a dramatic difference in the presence and abundance of numerous taxa between facilities. There were minor differences in bacterial abundance between wildtype and chemerin knockout mice, but significantly more differences in taxa abundance between wildtype and CMKLR1 knockout mice. Specifically, CMKLR1 knockout mice exhibited decreased abundance of Akkermansia and Prevotella, which correlated with body weight in CMKLR1 knockout, but not wildtype mice. This is the first study to investigate a linkage between chemerin/CMKLR1 signaling and microbiome composition. The results of our study suggest that chemerin/CMKLR1 signaling influences metabolic processes through effects on the gut microbiome. Furthermore, the dramatic difference in microbiome composition between facilities might contribute to discrepancies in the metabolic phenotype of CMKLR1 knockout mice reported by independent groups. Considered altogether, these findings establish a foundation for future studies to investigate the relationship between chemerin signaling and the gut microbiome on the development and progression of metabolic and inflammatory disease.
Dranse et al. (2018) The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome. PeerJ 6:e5494 https://doi.org/10.7717/peerj.5494
Antiviral therapy effectively improves liver hemodynamics as evidenced by serum biomarker and contrast-enhanced ultrasound examinations in patients with hepatitis B cirrhosis
Background and Aims To prospectively evaluate the effects of antiviral therapy on liver hemodynamics in patients with hepatitis B cirrhosis. Methods Seventy consecutive eligible HBV-related cirrhotic inpatients were enrolled in the prospective study. Fifty-two received different nucleoside analogs monotherapy and 18 denied antiviral therapy. Their liver biochemistry profiles and HBV-DNA were measured at the baseline and every 3 months. Peripheral blood vWF and sCD163, as well as liver ultrasound Doppler parameters including portal vein diameter (PVD), portal vein velocity (PVV), portal vein congestion index (PV-CI), hepatic vein damping index (HV-DI), hepatic arterial arrival time (HAAT), hepatic vein arrival time (HVAT) and intrahepatic cycle time (HV-HA), were measured at the baseline and the follow-up periods. Results In the antiviral group, all patients achieved complete virologic and liver biochemical responses after 3-month antiviral treatment. Furthermore, the response states were maintained till the follow-up endpoint. However, in the non-antiviral group, HBV DNA replication resulted in higher levels of ALT and AST compared to the baseline values (P < 0.05). In the antiviral group, PVD, PV-CI, HV-DI, vWF-Ag and sCD163 were all significantly reduced than the baseline values (P < 0.05), and PVV was significantly increased than the baseline value (P < 0.05). Conclusions Antiviral therapy could effectively suppress hepatocyte inflammation and alleviate the dysfunction of intrahepatic vascular endothelial and hepatic macrophages, which might improve hepatic hemodynamic function in HBV-related cirrhosis.
Xu et al. (2018) Antiviral therapy effectively improves liver hemodynamics as evidenced by serum biomarker and contrast-enhanced ultrasound examinations in patients with hepatitis B cirrhosis. PeerJ 6:e5484 https://doi.org/10.7717/peerj.5484