Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea
Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-SerAGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-SerAGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
Sun et al. (2022) Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea. PeerJ 10:e13730 https://doi.org/10.7717/peerj.13730
Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region)
In June 2017, extreme fires along the southern Cape coast of South Africa burnt native fynbos and thicket vegetation and caused extensive damage to plantations and residential properties. Invasive alien plants (IAPs) occur commonly in the area and were thought to have changed the behaviour of these fires through their modification of fuel properties relative to that of native vegetation. This study experimentally compared various measures of flammability across groups of native and alien invasive shrub species in relation to their fuel traits. Live plant shoots of 30 species (10 species each of native fynbos, native thicket, and IAPs) were sampled to measure live fuel moisture, dry biomass, fuel bed porosity and the proportions of fine-, coarse- and dead fuels. These shoots were burnt experimentally, and flammability measured in terms of maximum temperature (combustibility), completeness of burn (consumability), and time-to-ignition (ignitability). Multiple regression models were used to assess the relationships between flammability responses and fuel traits, while the Kruskal-Wallis H test was used to establish if differences existed in flammability measures and fuel traits among the vegetation groups. Dry biomass significantly enhanced, while live fuel moisture significantly reduced, maximum temperature, whereas the proportion of fine fuels significantly increased completeness of burn. Unlike other similar studies, the proportion of dead fuels and fuel bed porosity were not retained by any of the models to account for variation in flammability. Species of fynbos and IAPs generally exhibited greater flammability in the form of higher completeness of burn and more rapid ignition than species of thicket. Little distinction in flammability and fuel traits could be made between species of fynbos and IAPs, except that fynbos species had a greater proportion of fine fuels. Thicket species had higher proportions of coarse fuels and greater dry biomass (~fuel loading) than species of fynbos and IAPs. Live fuel moisture did not differ among the vegetation groups, contrary to the literature often ascribing variation in flammability to fuel moisture differences. The fuel traits investigated only explained 21–53% of the variation in flammability and large variation was evident among species within vegetation groups suggesting that species-specific and in situ community-level investigations are warranted, particularly in regard fuel moisture and chemical contents.
Kraaij et al. (2022) Fuel trait effects on flammability of native and invasive alien shrubs in coastal fynbos and thicket (Cape Floristic Region). PeerJ 10:e13765 https://doi.org/10.7717/peerj.13765
Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings
Elymus sibiricus is a highly valuable perennial forage that is widely planted in the Qinghai-Tibet Plateau (QTP) region. However, E. sibiricus artificial grasslands have a short utilization lifespan, and reach the highest yield in the 2nd and 3rd year of plantation, then rapidly drop its productivity. We hypothesized that autotoxicity is one of the mechanisms for the reduction of the productivity. To test this hypothesis, we prepared the water extract from rhizosphere soils of E. sibiricus planted for 3, 4, 5, and 8 years and examined the effects of the extract concentrations at 0.05, 0.1, 0.2, and 0.5 g/mL on seed germination, seedling growth, physiological characteristics and phytohormones in the aboveground and roots of E. sibiricus. The results showed that the soil extract concentration, planting years, and their interaction had significant influences on the most of these indices. The soil extract inhibited the seed germination and growth of seedlings, and the inhibitory effects appeared to be stronger at the 0.5 g/mL rhizosphere soil extract for 5 and 8 years. The superoxide dismultase and peroxide activities, the free proline concentration, soluble sugar concentration were altered. The malondialdehyde concentration was, in general, increased, especially in 8 years soil extract. The indole acetic acid and gibberellic acids concentrations were lowered, while the abscisic acid concentration varied. These changes were depending on the extract concentration and the years of planting, without clear patterns in some of them in response to the extract concentration and planting years. In summary, autotoxicity can be a contributor to the retardation of the growth and development of artificial E. sibiricus grasslands. The inhibitory effects could be attribute to impaired antioxidant capacity and disturbance of osmortic-regulatory substances and plant hormones, and are more profound on the root than on the aboveground part of the seedlings.
Yang et al. (2022) Autotoxicity effect of water extracts from rhizosphere soil of Elymus sibiricus in different planting years on seed germination, physiological characteristics and phytohormones of seedlings. PeerJ 10:e13768 https://doi.org/10.7717/peerj.13768
Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity
Rotational strip intercropping (RSI) of cereals and legumes has been developed and widely carried out to alleviate continuous cropping obstacles, to control erosion and to improve field use efficiency. In this study, a four-year fixed-field experiment was carried out in northeast China with three treatments: continuous cropping of maize, continuous cropping of peanuts and rotational strip intercropping of maize and peanut. The results show that crop rotation improved the main-stem height, branch number, lateral branch length, and yield and quality of peanuts; the yield was the highest in 2018, when it was increased by 39.5%. RSI improved the contents of total N, available N, total P, available P, total K and available K; the content of available N was the highest in 2018, with an increase of 70%. Rhizosphere soil urease and catalase activities were significantly increased and were the highest in 2017, reaching 183.13% and 91.21%, respectively. According to a high-throughput sequencing analysis, the rhizosphere soil bacterial richness and specific OTUs decreased in peanut rhizosphere soil, while the fungal increased. There were differences in the bacterial and fungal community structures; specifically, the abundance of Acidobacteria and Planctomycetes increased among bacteria and the abundance of beneficial microorganisms such as Ascomycota increased among fungi. In conclusion, rotational strip intercropping of maize and peanut increased the yield and quality of peanuts and conducive to alleviating the obstacles facing the continuous cropping of peanuts. Among then, soil physicochemical properties, enzyme activity and microbial diversity were significantly affected the yield of peanut.
Han et al. (2022) Maize-peanut rotational strip intercropping improves peanut growth and soil properties by optimizing microbial community diversity. PeerJ 10:e13777 https://doi.org/10.7717/peerj.13777
Quality of care and prescription patterns among patients with diabetic kidney disease—a large-scale cohort study from Taiwanese clinics
Aims To investigate the quality of care and prescription patterns of patients with diabetic kidney disease (DKD) receiving primary care at local clinics in Taiwan. Methods A retrospective chart review was conducted in 43 primary care clinics in Taiwan. The patients’ baseline characteristics, laboratory tests, presence of complications and antidiabetic agents prescribed were analyzed. Results 7,200 patients with type 2 diabetes mellitus were enrolled. Percentage of HbA1c, blood pressure (BP), and low density lipoprotein cholesterol (LDL-C) goals reached were 52.5% in HbA1c < 7%, 40.9% in BP < 130/80 mmHg and 79.7% in LDL-C < 2.59 mmol/L. 18.3% achieved all three ABC goals. However, patients with DKD had a lower rate of ABC goal attainment and higher rate of complications. Among DKD patients with eGFR ≥ 30 ml/min/1.73 m2 and on monotherapy, metformin was most frequently prescribed. As for dual therapy, the most common combinations were metformin with sulfonylurea and metformin with DPP-4 inhibitors. Conclusions Diabetes patients in Taiwan receiving primary diabetes care at local clinics had generally satisfactory management performance. However, more aggressive HbA1c, BP, and LDL-C management among DKD patients should be emphasized. Contrary to current recommendations, SGLT-2 inhibitors and GLP-1 receptor agonists as frontline therapy were under-prescribed.
Tsai et al. (2022) Quality of care and prescription patterns among patients with diabetic kidney disease—a large-scale cohort study from Taiwanese clinics. PeerJ 10:e13636 https://doi.org/10.7717/peerj.13636
Spatial variation in diatom abundance and composition in Biwase Bay and Hamanaka Bay (Eastern Hokkaido, Japan), with reference to environmental features
This study aims to examine the spatial variation of diatom abundance and composition along the nearshore areas of Biwase Bay and Hamanaka Bay, eastern Hokkaido. Terrestrial input via Kiritappu Wetland is expected to affect variation and composition differently depending on the position of the two bays. We conducted an oceanographic survey in June 2014 to measure seawater temperature, salinity, colored dissolved organic matter (CDOM) absorption, nutrient concentrations, and total and size-fractionated chlorophyll (Chl) a concentration at 11 stations of the shallowest (<5 m) parts of the bays. These were grouped into four areas (Areas 1 and 2 in Biwase Bay, and Areas 3 and 4 in Hamanaka Bay) based on the distance of the location from the wetland outlet (nearest in Area 1 to the farthest in Area 4). Diatoms are the major primary producers in the water column. Therefore, we also determined genus level cell abundance and diversity of diatoms to compare similarity among areas. Sea surface temperature was the lowest at Area 4, whereas sea surface salinity was the lowest at Area 1. The contribution of CDOM absorption, an indicator of wetland-influenced river discharge, and silica concentration was highest at Area 1. Total amount of nitrite and nitrate concentrations was the highest at Area 4. Total amount of Chl a concentration was also lowest in Area 1. Our size-fractionated Chl a results revealed that while the size composition of phytoplankton varied among areas, micro-sized (>10 µm) phytoplankton were predominant in Area 4. Finally, diatom composition at the genus level differed greatly among areas. Pennate diatoms were predominant in Areas 1 and 2, but centric diatoms dominated in Areas 3 and 4. Our results suggested great spatial variability in oceanographic conditions among areas, with less influence of wetland and more influence of Coastal Oyashio Water based on distance from the wetland outlet. Diatom composition showed geographical division between Biwase and Hamanaka Bays.
Ahn et al. (2022) Spatial variation in diatom abundance and composition in Biwase Bay and Hamanaka Bay (Eastern Hokkaido, Japan), with reference to environmental features. PeerJ 10:e13705 https://doi.org/10.7717/peerj.13705
Postoperative pain intensity and incidence following single visit root canal treatment with different obturation techniques: a randomized clinical trial
Background There are few studies in the literature about the effect of obturation techniques on postoperative pain. Besides, GuttaFlow2 was used for the first time in this study regarding postoperative pain. This study aimed to compare the postoperative pain levels and incidence following single-visit root canal treatment with different canal filling techniques; cold lateral compaction (CLC), thermoplasticised solid-core carrier (GuttaCore) based filling and cold free-flow compaction (GuttaFlow2) technique. Methods The patients (n = 93) having single-rooted teeth with a single canal diagnosed with asymptomatic irreversible pulpitis or single-rooted vital teeth with a single canal requiring endodontic treatment because of prosthetic reasons were enrolled in this study. Patients were randomized into three groups (n = 31) according to the obturation technique. A single operator performed all the treatments in a single visit. Data on obturation levels, postoperative pain and analgesic intake frequency were recorded at postoperative 6, 12 and 24 h and daily afterward until the 7th day. Postoperative pain was measured by visual analogue scale (VAS). The date were statistically analyzed with chi-squared tests (for the analyses of the categorical data), the nonparametric Kruskal-Wallis test (for the comparisons of VAS score) and with the Friedman test (for the assessments of the changes in VAS scores over time). Results The GuttaCore group recorded the higher pain levels, except first 12 h, on the other hand, the GuttaFlow2 group recorded the lower pain levels at all time periods. Significant differences occurred among the groups during the first 4 days (p < 0.05), except at 12 h (p = 0.054). The patients in the CLC and GuttaFlow2 groups did not need to use the prescribed analgesic; however, one patient in the GuttaCore group used it once. Conclusions Postoperative pain levels following root canal therapy were affected by the obturation technique especially first 4 days following obturation.
Koçer et al. (2022) Postoperative pain intensity and incidence following single visit root canal treatment with different obturation techniques: a randomized clinical trial. PeerJ 10:e13756 https://doi.org/10.7717/peerj.13756
Effects of bone morphogenetic protein 4 on TGF-β1-induced cell proliferation, apoptosis, activation and differentiation in mouse lung fibroblasts via ERK/p38 MAPK signaling pathway
Fibroblasts, in particular myofibroblasts, are the critical effector cells in idiopathic pulmonary fibrosis (IPF), a deadly lung disease characterized by abnormal lung remodeling and the formation of “fibroblastic foci”. Aberrant activation of TGF-β1 is frequently encountered and promotes fibroblast proliferation, activation, and differentiation in pulmonary fibrosis. Hence, the inhibition of TGF-β1-induced lung fibroblast activation holds promise as a therapeutic strategy for IPF. The present study aimed to investigate the potential effect and underlying mechanisms of bone morphogenetic protein 4 (BMP4) on TGF-β1-induced proliferation, apoptosis, activation and myofibroblast differentiation of adult lung fibroblasts. Here, we demonstrated that BMP4 expression was significantly decreased in TGF-β1-stimulated mouse primary lung fibroblasts (PLFs). BMP4 inhibited proliferation and apoptosis resistance of TGF-β1-stimulated mouse PLFs. BMP4 suppressed TGF-β1-induced fibroblast activation and differentiation in mouse PLFs. We also found that BMP4 inhibited TGF-β1-induced ERK and p38 MAPK phosphorylation. Our findings indicate that BMP4 exerts its anti-fibrotic effects by regulating fibroblast proliferation, apoptosis, activation and differentiation via the inhibition of the ERK/p38 MAPK signaling pathway, and thus has a potential for the treatment of pulmonary fibrosis.
Cai et al. (2022) Effects of bone morphogenetic protein 4 on TGF-β1-induced cell proliferation, apoptosis, activation and differentiation in mouse lung fibroblasts via ERK/p38 MAPK signaling pathway. PeerJ 10:e13775 https://doi.org/10.7717/peerj.13775
Effects of six weeks outdoor versus treadmill running on physical fitness and body composition in recreationally active young males: a pilot study
Background Running as exercise may be performed either on an outdoor surface or treadmill surface. However, previous research has indicated that the nature of both the surfaces differ significantly and therefore the training outcomes from running in these surfaces may also vary. Aim Therefore, the aim of this pilot study was to compare the effects of 6-weeks of supervised outdoor running (OT) vs treadmill running (TT) on physical fitness and body composition in recreationally active young males. Methods Participants (age: 19.82 ± 1.28 years, height: 172.6 ± 4.9 cm, body mass: 64.3 ± 8.7 kg) were randomly assigned to OT (n = 14) or TT (n = 14), and assessed for physical fitness, i.e., 50 m sprint, cardiorespiratory endurance (i.e., 1,600 m run time-trial), standing long jump (SLJ), flexibility (i.e., sit-and-reach test), and upper-body muscle endurance (i.e., push-ups repetitions), alongside body composition, i.e., body mass, body mass index (BMI), fat percentage, fat free mass, and leg skeletal muscle mass (SMM). A two (pre-post intervention) by two (OT, TT) mixed ANOVA analysed exercise-specific effects. For significant group-by-time interactions, Bonferroni adjusted paired (within-group) and independent (between-group comparisons at post) t-tests were used for post-hoc analyses. Results Significant time-effect was found in all physical fitness variables (all p < 0.001, ηp2 = 0.67–0.91), body mass (p = 0.23, ηp2 = 0.18), BMI (p = 0.009, ηp2 = 0.24), body fat percentage (p = 0.001, ηp2 = 0.38), and leg SMM (p = 0.002–0.007, ηp2 = 0.25–0.33). Significant group-by-time interaction was found for 50 m sprint (p = < 0.001, ηp2 = 0.74), 1,600 m run (p = 0.001, ηp2 = 0.35), and SLJ (p < 0.001, ηp2 = 0.43), favouring OT. Group-specific post-hoc tests showed improvements in all physical fitness variables after OT (p = < 0.001–0.001, g = 0.69–2.32, %Δ = 3.0–12.4) and TT (p = < 0.001–0.017, g = 0.15–0.65, %Δ = 0.9–11.7), and fat percentage after OT and TT (p = 0.002–0.041, g = 0.14–0.26, %Δ = 4.3–6.0). However, leg SMM decreased in TT (p = 0.001–0.004, g = 0.14–0.15, %Δ = 6.2–6.7). Conclusions Both OT and TT improved physical fitness and decreased fat percentage. However, compared to TT, the OT intervention preserved leg SMM and induced greater physical fitness improvements.
Singh et al. (2022) Effects of six weeks outdoor versus treadmill running on physical fitness and body composition in recreationally active young males: a pilot study. PeerJ 10:e13791 https://doi.org/10.7717/peerj.13791
Weight change-related factors during the COVID-19 pandemic: a population-based cross-sectional study using social cognitive theory
Background Published studies during the Coronavirus-19 (COVID-19) pandemic have focused on eating and exercise behaviors and failed to portray a comprehensive understanding of the factors associated with weight change in a setting of a behavioral change framework. This study explores factors associated with weight change during the COVID-19 pandemic among Lebanese residents using the Social Cognitive Theory (SCT) framework, integrating behavioral, environmental, and cognitive factors. Materials & Methods This study uses a cross-sectional design using an anonymous online survey. Participants were recruited from a tertiary hospital patient portal and social media posts. The survey included four domains: demographics, cognitive, behavioral, psychological, and environmental factors. Multiple validated self-reported instruments were included Generalized Anxiety Disorder-2 items (GAD-2), Patient Health Questionnaire-2 (PHQ-2), General Self Efficacy Scale (GSES), Alcohol Use Disorders Identification Test-Concise (AUDIT-C), and the dietary pattern evaluation tool. Results A sample of 335 complete responses was obtained. Mean age was 39.0 ± 13.4 years old. Participants were mostly females (n = 224, 66.9%), employed (n = 191, 57.4%), nonsmokers (n = 227, 70.5%), reporting depression (n = 224, 80.3%) and anxiety (n = 242, 84.3%). Mean weight change was −7.0 ± 6.0 kg in the decrease weight group and 6.4 ± 5.0 kg in the increase group. When compared to stable weight, the multinomial logistic model factors that were found to correlate significantly to weight gain were: overeating/binge eating (p-value = 0.001) and unbalanced food pattern (p-value = 0.012). Baseline BMI (p-value = 0.003), anxiety (p-value = 0.020) and smoking (p-value = 0.004) were significant factors of weight loss as compared to stable weight. Conclusions COVID-19-related weight change is multifactorial and is associated with specific behavior and individual characteristics. Hence, addressing people’s behaviors and relationship to food is vital to control weight change during this continuing and future pandemic or natural occurrence.
Assaf et al. (2022) Weight change-related factors during the COVID-19 pandemic: a population-based cross-sectional study using social cognitive theory. PeerJ 10:e13829 https://doi.org/10.7717/peerj.13829