Large-scale gene flow in the barnacle Jehlius cirratus and contrasts with other broadly-distributed taxa along the Chilean coast
We evaluate the population genetic structure of the intertidal barnacle Jehlius cirratus across a broad portion of its geographic distribution using data from the mitochondrial cytochrome oxidase I (COI) gene region. Despite sampling diversity from over 3,000 km of the linear range of this species, there is only slight regional structure indicated, with overall Φ CT of 0.036 (p < 0.001) yet no support for isolation by distance. While these results suggest greater structure than previous studies of J. cirratus had indicated, the pattern of diversity is still far more subtle than in other similarly-distributed species with similar larval and life history traits. We compare these data and results with recent findings in four other intertidal species that have planktotrophic larvae. There are no clear patterns among these taxa that can be associated with intertidal depth or other known life history traits.
Guo et al. (2017) Large-scale gene flow in the barnacle Jehlius cirratus and contrasts with other broadly-distributed taxa along the Chilean coast. PeerJ 5:e2971 https://doi.org/10.7717/peerj.2971
Evolutionary and functional implications of hypervariable loci within the skin virome
Localized genomic variability is crucial for the ongoing conflicts between infectious microbes and their hosts. An understanding of evolutionary and adaptive patterns associated with genomic variability will help guide development of vaccines and antimicrobial agents. While most analyses of the human microbiome have focused on taxonomic classification and gene annotation, we investigated genomic variation of skin-associated viral communities. We evaluated patterns of viral genomic variation across 16 healthy human volunteers. Human papillomavirus (HPV) and Staphylococcus phages contained 106 and 465 regions of diversification, or hypervariable loci, respectively. Propionibacterium phage genomes were minimally divergent and contained no hypervariable loci. Genes containing hypervariable loci were involved in functions including host tropism and immune evasion. HPV and Staphylococcus phage hypervariable loci were associated with purifying selection. Amino acid substitution patterns were virus dependent, as were predictions of their phenotypic effects. We identified diversity generating retroelements as one likely mechanism driving hypervariability. We validated these findings in an independently collected skin metagenomic sequence dataset, suggesting that these features of skin virome genomic variability are widespread. Our results highlight the genomic variation landscape of the skin virome and provide a foundation for better understanding community viral evolution and the functional implications of genomic diversification of skin viruses.
Hannigan et al. (2017) Evolutionary and functional implications of hypervariable loci within the skin virome. PeerJ 5:e2959 https://doi.org/10.7717/peerj.2959
The concept of Watson’s carative factors in nursing and their (dis)harmony with patient satisfaction
Background Constant reviews of the caring behavior of nurses and patient satisfaction help to improve the quality of nursing. The aim of our research was to explore relationships between the level of nursing education, the perception of nurses and nursing assistants of Watson’s carative factors, and patient satisfaction. Methods A questionnaire survey using a convenience sample of 1,098 members of nursing teams and a purposive sample of 1,123 patients in four health care institutions in Slovenia was conducted in August 2012. A demographic questionnaire and the Caring Nurse-Patient Interactions Scale (nurse version) were delivered to the nurses. A Hospital Consumer Assessment of Health Plans Survey was delivered to discharged patients. Data were analyzed using descriptive and inferential statistics. Results Carative factor sensibility was related to the level of nursing education. Patients were satisfied with the care received from nurses, nursing assistants and hospitals, although we found differences between the perceptions of nurses and nursing assistants of carative factors and patient satisfaction. By comparing only the perceptions of nurses and nursing assistants of carative factors in health care institutions, differences were found for seven out of ten carative factors. Discussion We did not find major significant differences between carative factors and level of nurse education, except in one carative factor. Differences in perceptions of carative factors between health care institutions are probably the result of different institutional factors. The results can be of great benefit to nurse administrators and educators, indicating the factors that must be taken into account for enhancing patient satisfaction. Emphasis on caring theories should be placed in nursing education and their application in nursing practice.
Pajnkihar et al. (2017) The concept of Watson’s carative factors in nursing and their (dis)harmony with patient satisfaction. PeerJ 5:e2940 https://doi.org/10.7717/peerj.2940
Differences in pollination success between local and foreign flower color phenotypes: a translocation experiment with Gentiana lutea (Gentianaceae)
Background The adaptive maintenance of flower color variation is frequently attributed to pollinators partly because they preferentially visit certain flower phenotypes. We tested whether Gentiana lutea—which shows a flower color variation (from orange to yellow) in the Cantabrian Mountains range (north of Spain)—is locally adapted to the pollinator community. Methods We transplanted orange-flowering individuals to a population with yellow-flowering individuals and vice versa, in order to assess whether there is a pollination advantage in the local morph by comparing its visitation rate with the foreign morph. Results Our reciprocal transplant experiment did not show clear local morph advantage in overall visitation rate: local orange flowers received more visits than foreign yellow flowers in the orange population, while both local and foreign flowers received the same visits in the yellow population; thus, there is no evidence of local adaptation in Gentiana lutea to the pollinator assemblage. However, some floral visitor groups (such as Bombus pratorum, B. soroensis ancaricus and B. lapidarius decipiens) consistently preferred the local morph to the foreign morph whereas others (such as Bombus terrestris) consistently preferred the foreign morph. Discussion We concluded that there is no evidence of local adaptation to the pollinator community in each of the two G. lutea populations studied. The consequences for local adaptation to pollinator on G. lutea flower color would depend on the variation along the Cantabrian Mountains range in morph frequency and pollinator community composition.
Guitián et al. (2017) Differences in pollination success between local and foreign flower color phenotypes: a translocation experiment with Gentiana lutea (Gentianaceae). PeerJ 5:e2882 https://doi.org/10.7717/peerj.2882
Vascular plant biodiversity of the lower Coppermine River valley and vicinity (Nunavut, Canada): an annotated checklist of an Arctic flora
The Coppermine River in western Nunavut is one of Canada’s great Arctic rivers, yet its vascular plant flora is poorly known. Here, we report the results of a floristic inventory of the lower Coppermine River valley and vicinity, including Kugluk (Bloody Falls) Territorial Park and the hamlet of Kugluktuk. The study area is approximately 1,200 km2, extending from the forest-tundra south of the treeline to the Arctic coast. Vascular plant floristic data are based on a review of all previous collections from the area and more than 1,200 new collections made in 2014. Results are presented in an annotated checklist, including citation of all specimens examined, comments on taxonomy and distribution, and photographs for a subset of taxa. The vascular plant flora comprises 300 species (311 taxa), a 36.6% increase from the 190 species documented by previous collections made in the area over the last century, and is considerably more diverse than other local floras on mainland Nunavut. We document 207 taxa for Kugluk (Bloody Falls) Territorial Park, an important protected area for plants on mainland Nunavut. A total of 190 taxa are newly recorded for the study area. Of these, 14 taxa (13 species and one additional variety) are newly recorded for Nunavut (Allium schoenoprasum, Carex capitata, Draba lonchocarpa, Eremogone capillaris subsp. capillaris, Sabulina elegans, Eleocharis quinqueflora, Epilobium cf. anagallidifolium, Botrychium neolunaria, Botrychium tunux, Festuca altaica, Polygonum aviculare, Salix ovalifolia var. arctolitoralis, Salix ovalifolia var. ovalifolia and Stuckenia pectinata), seven species are newly recorded for mainland Nunavut (Carex gynocrates, Carex livida, Cryptogramma stelleri, Draba simmonsii, Festuca viviparoidea subsp. viviparoidea, Juncus alpinoarticulatus subsp. americanus and Salix pseudomyrsinites) and 56 range extensions are reported. The psbA-trnH and rbcL DNA sequence data were used to help identify the three Botrychium taxa recorded in the study area. Three new combinations are proposed: Petasites frigidus subsp. sagittatus (Banks ex Pursh) Saarela, Carex petricosa subsp. misandroides (Fernald) Saarela and Carex simpliciuscula subsp. subholarctica (T. V. Egorova) Saarela.
Saarela et al. (2017) Vascular plant biodiversity of the lower Coppermine River valley and vicinity (Nunavut, Canada): an annotated checklist of an Arctic flora. PeerJ 5:e2835 https://doi.org/10.7717/peerj.2835
Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands
Background The páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants. Methods Field expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny. Results Phylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other. Conclusions Our data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them.
Diazgranados et al. (2017) Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands. PeerJ 5:e2968 https://doi.org/10.7717/peerj.2968
A new glimpse on Mesozoic zooplankton—150 million-year-old lobster larvae
Larvae of malacostracan crustaceans represent a large fraction of modern day zooplankton. Plankton is not only a major part of the modern marine ecosystem, but must have played an important role in the ecosystems of the past as well. Unfortunately, our knowledge about plankton composition of the past is still quite limited. As an important part of today’s zooplankton, malacostracan larvae are still a rarity in the fossil record; many types of malacostracan larvae dominating the modern plankton have so far not been found as fossils. Here we report a new type of fossil malacostracan larva, found in the 150 million years old lithographic limestones of southern Germany (Solnhofen Lithographic Limestones). The three rather incomplete specimens mainly preserve the telson. A pronounced middle spine on the posterior edge of these specimens indicates that they are either larval forms of a clawed lobster or of an axiidean lobster, or of a closer relative to one of the two groups. The tergo-pleura are drawn out into distinct spines in one specimen, further supporting the interpretation as a larva of a clawed lobster or an early relative. The telson morphology also shows adaptations to a prolonged planktic life style, the latero-posterior edges are drawn out into distinct spines. Similar adaptations are known in larvae of the modern homarid lobster Nephrops norvegicus, not necessarily indicating a closer relationship, but convergent life styles. The new finds provide an important new insight into the composition of Mesozoic zooplankton and demonstrate the preservation potential of lithographic limestones.
Haug et al. (2017) A new glimpse on Mesozoic zooplankton—150 million-year-old lobster larvae. PeerJ 5:e2966 https://doi.org/10.7717/peerj.2966
Effects of rhodomyrtone on Gram-positive bacterial tubulin homologue FtsZ
Rhodomyrtone, a natural antimicrobial compound, displays potent activity against many Gram-positive pathogenic bacteria, comparable to last-defence antibiotics including vancomycin and daptomycin. Our previous studies pointed towards effects of rhodomyrtone on the bacterial membrane and cell wall. In addition, a recent molecular docking study suggested that the compound could competitively bind to the main bacterial cell division protein FtsZ. In this study, we applied a computational approach (in silico), in vitro, and in vivo experiments to investigate molecular interactions of rhodomyrtone with FtsZ. Using molecular simulation, FtsZ conformational changes were observed in both (S)- and (R)-rhodomyrtone binding states, compared with the three natural states of FtsZ (ligand-free, GDP-, and GTP-binding states). Calculations of free binding energy showed a higher affinity of FtsZ to (S)-rhodomyrtone (−35.92 ± 0.36 kcal mol−1) than the GDP substrate (−23.47 ± 0.25 kcal mol−1) while less affinity was observed in the case of (R)-rhodomyrtone (−18.11 ± 0.11 kcal mol−1). In vitro experiments further revealed that rhodomyrtone reduced FtsZ polymerization by 36% and inhibited GTPase activity by up to 45%. However, the compound had no effect on FtsZ localization in Bacillus subtilis at inhibitory concentrations and cells also did not elongate after treatment. Higher concentrations of rhodomyrtone did affect localization of FtsZ and also affected localization of its membrane anchor proteins FtsA and SepF, showing that the compound did not specifically inhibit FtsZ but rather impaired multiple divisome proteins. Furthermore, a number of cells adopted a bean-like shape suggesting that rhodomyrtone possibly possesses further targets involved in cell envelope synthesis and/or maintenance.
Saeloh et al. (2017) Effects of rhodomyrtone on Gram-positive bacterial tubulin homologue FtsZ. PeerJ 5:e2962 https://doi.org/10.7717/peerj.2962
Medial knee joint contact force in the intact limb during walking in recently ambulatory service members with unilateral limb loss: a cross-sectional study
Background Individuals with unilateral lower limb amputation have a high risk of developing knee osteoarthritis (OA) in their intact limb as they age. This risk may be related to joint loading experienced earlier in life. We hypothesized that loading during walking would be greater in the intact limb of young US military service members with limb loss than in controls with no limb loss. Methods Cross-sectional instrumented gait analysis at self-selected walking speeds with a limb loss group (N = 10, age 27 ± 5 years, 170 ± 36 days since last surgery) including five service members with transtibial limb loss and five with transfemoral limb loss, all walking independently with their first prosthesis for approximately two months. Controls (N = 10, age 30 ± 4 years) were service members with no overt demographical risk factors for knee OA. 3D inverse dynamics modeling was performed to calculate joint moments and medial knee joint contact forces (JCF) were calculated using a reduction-based musculoskeletal modeling method and expressed relative to body weight (BW). Results Peak JCF and maximum JCF loading rate were significantly greater in limb loss (184% BW, 2,469% BW/s) vs. controls (157% BW, 1,985% BW/s), with large effect sizes. Results were robust to probabilistic perturbations to the knee model parameters. Discussion Assuming these data are reflective of joint loading experienced in daily life, they support a “mechanical overloading” hypothesis for the risk of developing knee OA in the intact limb of limb loss subjects. Examination of the evolution of gait mechanics, joint loading, and joint health over time, as well as interventions to reduce load or strengthen the ability of the joint to withstand loads, is warranted.
Miller et al. (2017) Medial knee joint contact force in the intact limb during walking in recently ambulatory service members with unilateral limb loss: a cross-sectional study. PeerJ 5:e2960 https://doi.org/10.7717/peerj.2960
Demographic, ecological, and physiological responses of ringed seals to an abrupt decline in sea ice availability
To assess whether demographic declines of Arctic species at the southern limit of their range will be gradual or punctuated, we compared large-scale environmental patterns including sea ice dynamics to ringed seal (Pusa hispida) reproduction, body condition, recruitment, and stress in Hudson Bay from 2003 to 2013. Aerial surveys suggested a gradual decline in seal density from 1995 to 2013, with the lowest density occurring in 2013. Body condition decreased and stress (cortisol) increased over time in relation to longer open water periods. The 2010 open water period in Hudson Bay coincided with extremes in large-scale atmospheric patterns (North Atlantic Oscillation, Arctic Oscillation, El Nino-Southern Oscillation) resulting in the earliest spring breakup and the latest ice formation on record. The warming event was coincident with high stress level, low ovulation rate, low pregnancy rate, few pups in the Inuit harvest, and observations of sick seals. Results provide evidence of changes in the condition of Arctic marine mammals in relation to climate mediated sea ice dynamics. We conclude that although negative demographic responses of Hudson Bay seals are occurring gradually with diminishing sea ice, a recent episodic environmental event played a significant role in a punctuated population decline.
Ferguson et al. (2017) Demographic, ecological, and physiological responses of ringed seals to an abrupt decline in sea ice availability. PeerJ 5:e2957 https://doi.org/10.7717/peerj.2957