Mapping of reads to reference sequences is an essential step in a wide range of biological studies. The large size of datasets generated with next-generation sequencing technologies motivates the development of fast mapping software. Here, I describe URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves high accuracy (precision 0.998, sensitivity 0.982 and F-measure 0.990) with the strelka2 caller. However, GIAB reference variants are shown to be biased against repetitive regions which are difficult to map and may therefore pose an unrealistically easy challenge to read mappers and variant callers.
Edgar (2020) URMAP, an ultra-fast read mapper. PeerJ 8:e9338 https://doi.org/10.7717/peerj.9338
Ocean warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea (Ehrenberg, 1834) in the Eastern Mediterranean Sea
Climate, which sets broad limits for migrating species, is considered a key filter to species migration between contrasting marine environments. The Southeast Mediterranean Sea (SEMS) is one of the regions where ocean temperatures are rising the fastest under recent climate change. Also, it is the most vulnerable marine region to species introductions. Here, we explore the factors which enabled the colonization of the endemic Red Sea octocoral Melithaea erythraea (Ehrenberg, 1834) along the SEMS coast, using sclerite oxygen and carbon stable isotope composition (δ18OSC and δ13CSC), morphology, and crystallography. The unique conditions presented by the SEMS include a greater temperature range (∼15 °C) and ultra-oligotrophy, and these are reflected by the lower δ13CSCvalues. This is indicative of a larger metabolic carbon intake during calcification, as well as an increase in crystal size, a decrease of octocoral wart density and thickness of the migrating octocoral sclerites compared to the Red Sea samples. This suggests increased stress conditions, affecting sclerite deposition of the SEMS migrating octocoral. The δ18Osc range of the migrating M. erythraea indicates a preference for warm water sclerite deposition, similar to the native depositional temperature range of 21–28 °C. These findings are associated with the observed increase of minimum temperatures in winter for this region, at a rate of 0.35 ± 0.27 °C decade−1 over the last 30 years, and thus the region is becoming more hospitable to the Indo-Pacific M. erythraea. This study shows a clear case study of “tropicalization” of the Mediterranean Sea due to recent warming.
Grossowicz et al. (2020) Ocean warming is the key filter for successful colonization of the migrant octocoral Melithaea erythraea (Ehrenberg, 1834) in the Eastern Mediterranean Sea. PeerJ 8:e9355 https://doi.org/10.7717/peerj.9355
Biofilm modelling on the contact lenses and comparison of the in vitro activities of multipurpose lens solutions and antibiotics
During the contact lens (CL) usage, microbial adhesion and biofilm formation are crucial threats for eye health due to the development of mature biofilms on CL surfaces associated with serious eye infections such as keratitis. For CL related eye infections, multi drug resistant Pseudomonas aeruginosa or Staphylococcus aureus (especially MRSA) and Candida albicans are the most common infectious bacteria and yeast, respectively. In this study, CL biofilm models were created by comparing them to reveal the differences on specific conditions. Then the anti-biofilm activities of some commercially available multipurpose CL solutions (MPSs) and antibiotic eye drops against mature biofilms of S. aureus, P. aeruginosa, and C. albicans standard and clinical strains were determined by the time killing curve (TKC) method at 6, 24 and 48 h. According to the biofilm formation models, the optimal biofilms occurred in a mixture of bovine serum albumin (20% v/v) and lysozyme (2 g/L) diluted in PBS at 37 °C for 24 h, without shaking. When we compared the CL types under the same conditions, the strongest biofilms according to their cell density, were formed on Pure Vision ≥ Softens 38 > Acuve 2 ∼ Softens Toric CLs. When we compared the used CLs with the new ones, a significant increase at the density of biofilms on the used CLs was observed. The most active MPS against P. aeruginosa and S. aureus biofilms at 24 h was Opti-Free followed by Bio-True and Renu according to the TKC analyses. In addition, the most active MPS against C. albicans was Renu followed by Opti-Free and Bio-True at 48 h. None of the MPSs showed 3 Log bactericidal/fungicidal activity, except for Opti-Free against S. aureus and P. aeruginosa biofilms during 6 h contact time. Moreover, all studied antibiotic eye drops were active against S. aureus and P. aeruginosa biofilms on CLs at 6 h and 24 h either directly or as 1/10 concentration, respectively. According to the results of the study, anti-biofilm activities of MPSs have changed depending on the chemical ingredients and contact times of MPSs, the type of infectious agent, and especially the CL type and usage time.
Dosler et al. (2020) Biofilm modelling on the contact lenses and comparison of the in vitro activities of multipurpose lens solutions and antibiotics. PeerJ 8:e9419 https://doi.org/10.7717/peerj.9419
A new species of frog (Terrarana, Strabomantidae, Phrynopus) from the Peruvian Andean grasslands
We describe a new, medium-sized species of terrestrial frog of the genus Phrynopus from a single locality in the central Andes of Peru (Departamento de Huánuco) at 3,730 meters of elevation. Phylogenetic analyses supported Phrynopus remotum sp. nov. as an independent lineage, sister to most of its congeners. The new species is morphologically distinguishable by the presence of small tubercles on upper eyelids and heels, an areolate venter, and the absence of dorsolateral folds or ridges. This species inhabits the highlands adjacent to the Marañón Dry valley. The only sympatric amphibian species recorded is the marsupial frog Gastrotheca peruana.
Chávez et al. (2020) A new species of frog (Terrarana, Strabomantidae, Phrynopus) from the Peruvian Andean grasslands. PeerJ 8:e9433 https://doi.org/10.7717/peerj.9433
A new large canopy-dwelling species of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of the state of Bahia, Northeastern Brazil
The known diversity of treefrogs of the genus Phyllodytes has rapidly increased in recent years, currently comprising 14 species. Recent field work in the Atlantic Rainforest of the state of Bahia lead to the discovery of a new large species of Phyllodytes which is herein described based on multiple evidence including morphological, acoustical and genetic data. Phyllodytes sp. nov. is one of the largest species within the genus and presents immaculate yellowish dorsum and limbs. The advertisement call of the species is composed of 7–31 notes (half pulsed/pulsatile-half harmonic) with frequency-modulated harmonics. Phyllodytes sp. nov. has a karyotype of 2n = 22 chromosomes, as also found in other species of the genus. Genetic distance values of the 16S mitochondrial rRNA among Phyllodytes sp. nov. and its congeners range between 6.4 to 10.2%. The description of another new species for this state reinforces the need for further taxonomic work with Phyllodytes in this region that has been revealed as a priority area for research and conservation of this genus.
Dias et al. (2020) A new large canopy-dwelling species of Phyllodytes Wagler, 1930 (Anura, Hylidae) from the Atlantic Forest of the state of Bahia, Northeastern Brazil. PeerJ 8:e8642 https://doi.org/10.7717/peerj.8642
Effects of Stellera chamaejasme removal on the nutrient stoichiometry of S. chamaejasme-dominated grasslands in the Qinghai–Tibetan plateau
Background Stoichiometric relations drive powerful constraints in several fundamental ecosystem processes. However, limited studies have been conducted on the ecological stoichiometry of plants after the change of community composition induced by Stellera chamaejasme removal in alpine grassland in the Qinghai–Tibetan Plateau. Methods We investigated the effects of S. chamaejasme removal on ecological stoichiometry by estimating the C:N:P stoichiometry in species, functional group and community levels of the ecosystem. The interactions between different species, functional groups and correlation with soil nutrient, responding to S. chamaejasme removal were also analyzed. Results For the plants that became dominant after S. chamaejasme removal (SR), N content decreased and their C:N increased. S. chamaejasme removal significantly affected the nutrient stoichiometry of different functional groups. Specifically, Gramineae in the SR sites had decreased N content and N:P, and increased C:N; however, forbs had increased N content, C:P and N:P and decreased P content and C:N. At the community level, N content was lower and C:N higher in SR communities compared to CK. The N content of the plant community was positively correlated with soil total N content. S. chamaejasme removal could change the nutrient balance from species level, to functional group level, and to community level. Thus, supplementary measures might be cooperated with S. chamaejasme removal for the recovery of S. chamaejasme-dominated degraded grassland. These results provide insight into the role of S. chamaejasme in ecological protection and conservation, and the conclusions from this study could be used to develop effective and sustainable measures for S. chamaejasme control in the Qinghai–Tibetan Plateau.
Song et al. (2020) Effects of Stellera chamaejasme removal on the nutrient stoichiometry of S. chamaejasme-dominated grasslands in the Qinghai–Tibetan plateau. PeerJ 8:e9239 https://doi.org/10.7717/peerj.9239
Modelling of climate change impact on flow conditions in the lowland anastomosing river
The progressive degradation of freshwater ecosystems worldwide requires action to be taken for their conservation. Nowadays, protection strategies need to step beyond the traditional approach of managing protected areas as they have to deal with the protection or recovery of natural flow regimes disrupted by the effects of future climate conditions. Climate change affects the hydrosphere at catchment scale altering hydrological processes which in turn impact hydrodynamics at the river reach scale. Therefore, conservation strategies should consider mathematical models, which allow for an improved understanding of ecosystem functions and their interactions across different spatial and temporal scales. This study focuses on an anastomosing river system in north-eastern Poland, where in recent decades a significant loss of the anabranches has been observed. The objective was to assess the impact of projected climate change on average flow conditions in the anastomosing section of the Narew River. The Soil and Water Assessment Tool (SWAT software) for the Narew catchment was coupled with the HEC-RAS one-dimensional unsteady flow model. The study looked into projected changes for two future time horizons 2021–2050 and 2071–2100 under the Representative Concentration Pathway 4.5 using an ensemble of nine EURO-CORDEX model scenarios. Results show that low flow conditions in the anastomosing section of the Narew National Park will remain relatively stable in 2021–2050 compared to current conditions and will slightly increase in 2071–2100. Duration of low flows, although projected to decrease on an annual basis, will increase for August–October, when the loss on anastomoses was found to be the most intense. Hydraulic modeling indicated extremely low flow velocities in the anastomosing arm (<0.1 m/s) nowadays and under future projections which is preferable for in-stream vegetation development and their gradual sedimentation and closure.
Spatial and Geographic Information Science
© 2020 Marcinkowski and Mirosław-Świątek
Marcinkowski et al. (2020) Modelling of climate change impact on flow conditions in the lowland anastomosing river. PeerJ 8:e9275 https://doi.org/10.7717/peerj.9275
Feasibility of a smartphone app to enhance physical activity in progressive MS: a pilot randomized controlled pilot trial over three months
Background People with chronic progressive multiple sclerosis (CPMS) have limited options in medical treatment. Enhancing physical activity (PA) might promote neuroregeneration in multiple sclerosis (MS) and positively influence disability, thus providing an alternative to medical treatment. Previous studies indicate that evidence-based patient information (EBPI) is essential for inducing behavioral change, e.g. enhancing PA. Objective To investigate feasibility of a smartphone app providing EBPI about the benefit of PA and a simple activity feedback to enhance PA in people with CPMS in a pilot randomized controlled trial over 3 months. Methods Thirty-eight people with CPMS (mean age 51 years, median Expanded Disability Status Scale 4.0) were 1:1 randomized into either a control group (n = 20) or an intervention group (n = 18). The intervention group received access to a multimedia EBPI app including activity feedback, texts, figures and videos. In the control group, participants received a leaflet with unspecific information about exercising in general. The EPBI itself was designed based on a systematic review. At baseline and after 3 months, all participants underwent clinical performance tests, filled in questionnaires and received an activity monitor (Actigraph®) for 7 days. The primary endpoint was the rate of responders defined as participants with a 20% increase of physical acitivity (time of moderate or vigiorous PA—MVPA) or 20% increase of the number of steps, both assessed with the activity monitor. As secondary endpoints, we compared accelerometry, performance and questionnaires adjusted for baseline measurments between the groups (ANCOVA). Moreover, we used questionnaires to compare knowledge about exercise (activity requiring physical effort, carried out to improve or improve health and fitness) in MS, usability of the app in general and motivation towards a more active lifestyle after 3 months in both groups. Results The groups showed significant differences in disease duration and PA according to the Godin–Leisure Time Exercise Questionnaire at baseline. After 3 months, we detected no difference in the rate of responders, which was an overall 22%. However, MVPA significantly increased in both groups (p < 0.001) and the intervention group tended to have a higher motivation towards a more active lifestyle (Cohens D = 0.7, p = 0.09) as measured by the questionnaire. Reponses also showed, that participants appreciated the app but claimed a lack of interactivity as a short-coming. Conclusion Just providing information in a multimedia smartphone app did not enhance physical activitiy more than a simple leaflet in this small pilot trial in CPMS. However, the group of app users tended to have a higher motivation towards a more active lifestyle. Overall, the concept of a smartphone app to support an active lifestyle in MS is highly appreciated by participants.
Nasseri et al. (2020) Feasibility of a smartphone app to enhance physical activity in progressive MS: a pilot randomized controlled pilot trial over three months. PeerJ 8:e9303 https://doi.org/10.7717/peerj.9303
Longitudinal relationships between changes in body composition and changes in selected metabolic risk factors (abdominal obesity and blood pressure) among South African adolescents
Background Incidence of childhood high blood pressure (BP) is increasing worldwide. This study examined the longitudinal relationship between changes in body composition (i.e. body mass index (BMI), waist circumference (WC) and percentage body fat) and selected metabolic risk factors (abdominal obesity and BP) among adolescents from the Tlokwe municipality in the North West Province of South Africa. Method One hundred and eight-six adolescents (81 boys and 105 girls) aged 14 to 16 years participated in the study. Body composition was measured following the International Society of the Advancement of Kinanthropometry standard procedures. BMI, abdominal obesity using WC measurement, and resting BP were determined. Analysis of variance (ANOVA) for repeated measures was calculated to determine changes in anthropometric measures and body composition as well as changes in BP. Additionally, Univariate analysis of variance with repeated measures and participants as a random sample was applied. Diastolic BP (DBP) and systolic BP (SBP) were used as dependent variables and sex, age, BMI, WC, and waist-to-height ratio as independent variables. Results Significant changes were found for stature, BMI, body mass, WC, SBP, and DBP. BMI for the total group was significant and positively related to abdominal obesity in 2012 (r = 0.55; p < 0.01) and in 2013 (r = 0.77; p < 0.01) and to SBP (r = 0.26; p < 0.05) in 2012 and (r = 0.17; p = 0.43) in 2013. BMI among the boys was significantly and positively related to abdominal obesity in 2012 (r = 0.83; p < 0.01) and 2013 (r = 0.91; p < 0.01). For the girls, BMI was significantly and positively related to abdominal obesity (r = 0.49; p < 0.01) and to SBP (r = 0.32; p = 0.05) in 2012. Boys with a higher WC in 2012 had significantly increased DBP (p < 0.05). Boys measured in 2012 with greater WC and BMI show a significant increase in SBP. Conclusions BMI was positively related to BP and abdominal obesity over time. Relatively high BMI and abdominal obesity significantly increased the likelihood of elevated BP over time, especially in boys. BMI was a predictor of abdominal obesity in boys, while in girls, BMI was a predictor of both abdominal obesity and SBP. In view of the future health implications of both abdominal obesity and elevated BP, urgent strategic interventions programs aimed at increasing physical activity and advocating for well-balanced dietary practices as well as importance of keeping normal blood pressure among South African adolescents are needed.
Masocha et al. (2020) Longitudinal relationships between changes in body composition and changes in selected metabolic risk factors (abdominal obesity and blood pressure) among South African adolescents. PeerJ 8:e9331 https://doi.org/10.7717/peerj.9331
Marsupial and monotreme milk—a review of its nutrient and immune properties
All mammals are characterized by the ability of females to produce milk. Marsupial (metatherian) and monotreme (prototherian) young are born in a highly altricial state and rely on their mother’s milk for the first part of their life. Here we review the role and importance of milk in marsupial and monotreme development. Milk is the primary source of sustenance for young marsupials and monotremes and its composition varies at different stages of development. We applied nutritional geometry techniques to a limited number of species with values available to analyze changes in macronutrient composition of milk at different stages. Macronutrient energy composition of marsupial milk varies between species and changes concentration during the course of lactation. As well as nourishment, marsupial and monotreme milk supplies growth and immune factors. Neonates are unable to mount a specific immune response shortly after birth and therefore rely on immunoglobulins, immunological cells and other immunologically important molecules transferred through milk. Milk is also essential to the development of the maternal-young bond and is achieved through feedback systems and odor preferences in eutherian mammals. However, we have much to learn about the role of milk in marsupial and monotreme mother-young bonding. Further research is warranted in gaining a better understanding of the role of milk as a source of nutrition, developmental factors and immunity, in a broader range of marsupial species, and monotremes.
Stannard et al. (2020) Marsupial and monotreme milk—a review of its nutrient and immune properties. PeerJ 8:e9335 https://doi.org/10.7717/peerj.9335