Monitoring cyanobacterial toxins in a large reservoir: relationships with water quality parameters
Cyanobacteria are widely distributed in fresh, brackish, and ocean water environments, as well as in soil and on moist surfaces. Changes in the population of cyanobacteria can be an important indicator of alterations in water quality. Metabolites produced by blooms of cyanobacteria can be harmful, so cell counts are frequently monitored to assess the potential risk from cyanobacterial toxins. A frequent uncertainty in these types of assessments is the lack of strong relationships between cell count numbers and algal toxin concentrations. In an effort to use ion concentrations and other water quality parameters to determine the existence of any relationships with cyanobacterial toxin concentrations, we monitored four cyanobacterial toxins and inorganic ions in monthly water samples from a large reservoir over a 2-year period. Toxin concentrations during the study period never exceeded safety limits. In addition, toxin concentrations at levels above the limit of quantitation were infrequent during the 2-year sampling period; non-detects were common. Microcystin-LA was the least frequently detected analyte (86 of 89 samples were ND), followed by the other microcystins (microcystin-RR, microcystin-LR). Cylindrospermopsin and saxitoxin were the most frequently detected analytes. Microcystin and anatoxin concentrations were inversely correlated with Cl−, SO ${}_{4}^{-2}$ 4 − 2 , Na+, and NH ${}_{4}^{+}$ 4 + , and directly correlated with turbidity and total P. Cylindrospermopsin and saxitoxin concentrations in water samples were inversely correlated with Mg+2 and directly correlated with water temperature. Results of our study are expected to increase the understanding of potential relationships between human activities and water quality.
Subbiah et al. (2019) Monitoring cyanobacterial toxins in a large reservoir: relationships with water quality parameters. PeerJ 7:e7305 https://doi.org/10.7717/peerj.7305
Selection of reliable reference genes for quantitative RT-PCR in garlic under salt stress
Quantitative real-time reverse-transcriptase PCR (qRT-PCR) has been frequently used for detecting gene expression. To obtain reliable results, selection of suitable reference genes is a fundamental and necessary step. Garlic (Allium sativum), a member from Alliaceae family, has been used both as a food flavoring and as a traditional medicine. In the present study, garlic plants were exposed to salt stress (200 mM NaCl) for 0, 1, 4 and 12 h, and garlic roots, bulbs, and leaves were harvested for subsequent analysis. The expression stability of eight candidate reference genes, eukaryotic translation initiation factor 4α (eIF-4α), actin (ACTIN), tubulin β-7 (TUB7), TAP42-interacting protein of 41 kDa (TIP41), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), SAND family protein (SAND), elongation factor 1 alpha (EF-1α), and protein phosphatase 2A (PP2A) were evaluated by geNorm, NormFinder, and BestKeeper. All genes tested displayed variable expression profiles under salt stress. In the leaf and root group, ACTIN was the best reference gene for normalizing gene expression. In garlic clove, ACTIN and SAND were the least variable, and were suitable for gene expression studies under salt stress; these two genes also performed well in all samples tested. Based on our results, we recommend that it is essential to use specific reference genes in different situations to obtain accurate results. Using a combination of multiple stable reference genes, such as ACTIN and SAND, to normalize gene expression is encouraged. The results from the study will be beneficial for accurate determination of gene expression in garlic and other plants.
Wang et al. (2019) Selection of reliable reference genes for quantitative RT-PCR in garlic under salt stress. PeerJ 7:e7319 https://doi.org/10.7717/peerj.7319
Herbivore corridors sustain genetic footprint in plant populations: a case for Spanish drove roads
Habitat fragmentation is one of the greatest threats to biodiversity conservation and ecosystem productivity mediated by direct human impact. Its consequences include genetic depauperation, comprising phenomena such as inbreeding depression or reduction in genetic diversity. While the capacity of wild and domestic herbivores to sustain long-distance seed dispersal has been proven, the impact of herbivore corridors in plant population genetics remains to be observed. We conducted this study in the Conquense Drove Road in Spain, where sustained use by livestock over centuries has involved transhumant herds passing twice a year en route to winter and summer pastures. We compared genetic diversity and inbreeding coefficients of Plantago lagopus populations along the drove road with populations in the surrounding agricultural matrix, at varying distances from human settlements. We observed significant differences in coefficients of inbreeding between the drove road and the agricultural matrix, as well as significant trends indicative of higher genetic diversity and population nestedness around human settlements. Trends for higher genetic diversity along drove roads may be present, although they were only marginally significant due to the available sample size. Our results illustrate a functional landscape with human settlements as dispersal hotspots, while the findings along the drove road confirm its role as a pollinator reservoir observed in other studies. Drove roads may possibly also function as linear structures that facilitate long-distance dispersal across the agricultural matrix, while local P. lagopus populations depend rather on short-distance seed dispersal. These results highlight the role of herbivore corridors for conserving the migration capacity of plants, and contribute towards understanding the role of seed dispersal and the spread of invasive species related to human activities.
García-Fernández et al. (2019) Herbivore corridors sustain genetic footprint in plant populations: a case for Spanish drove roads. PeerJ 7:e7311 https://doi.org/10.7717/peerj.7311
Scenarios of availability of water due to overexploitation of the aquifer in the basin of Laguna de Santiaguillo, Durango, Mexico
Background The importance of water to life is unquestionable. Most of the fresh water we use for daily activities comes from the aquifers, which in many cases due to misuse are overexploited and at risk. This article studies the aquifer that appeared in Laguna de Santiaguillo basin; it should be noted that the most important economic activity in the basin is agriculture. Methods By analyzing vector and demographic information, using GIS and with some field trips, the impact and risk on the level of disposition in every micro-basin that forms the basin were determined. Results The different modeling scenarios demonstrate that the basin and sub-basins that conform Santiaguillo are overexploited. Discussion The volumes concessioned are of such magnitude that they generate a condition of vulnerability to the activities of the basin and sustain the overexploitation conditions of the aquifer.
Corral-Bermudez et al. (2019) Scenarios of availability of water due to overexploitation of the aquifer in the basin of Laguna de Santiaguillo, Durango, Mexico. PeerJ 7:e6814 https://doi.org/10.7717/peerj.6814
Comparison of integrated PET/MRI with PET/CT in evaluation of endometrial cancer: a retrospective analysis of 81 cases
Background The objective of this study was to compare the diagnostic value of integrated PET/MRI with PET/CT for assessment of regional lymph node metastasis and deep myometrial invasion detection of endometrial cancer. Methods Eighty-one patients with biopsy-proven endometrial cancer underwent preoperative PET/CT (n = 37) and integrated PET/MRI (n = 44) for initial staging. The diagnostic performance of PET/CT and integrated PET/MRI for assessing the extent of the primary tumor and metastasis to the regional lymph nodes was evaluated by two experienced readers. Histopathological and follow-up imaging results were used as the gold standard. McNemar’s test was employed for statistical analysis. Results Integrated PET/MRI and PET/CT both detected 100% of the primary tumors. Integrated PET/MRI proved significantly more sensitivity and specificity than PET/CT in regional lymph node metastasis detection (P = 0.015 and P < 0.001, respectively). The overall accuracy of myometrial invasion detection for PET/CT and Integrated PET/MRI was 45.9% and 81.8%, respectively. Integrated PET/MRI proved significantly more accurate than PET/CT (P < 0.001). Conclusion Integrated PET/MRI, which complements the individual advantages of MRI and PET, is a valuable technique for the assessment of the lymph node metastasis and myometrial invasion in patients with endometrial cancer.
Bian et al. (2019) Comparison of integrated PET/MRI with PET/CT in evaluation of endometrial cancer: a retrospective analysis of 81 cases. PeerJ 7:e7081 https://doi.org/10.7717/peerj.7081
Trajectories of change after a health-education program in Japan: decay of impact in anxiety, depression, and patient-physician communication
Background Health education can benefit people with chronic diseases. However, in previous research those benefits were small, and reinforcement to maintain them was not effective. A possible explanation is that the benefits appeared to be small and reinforcement appeared to be ineffective because those analyses mixed data from two latent groups: one group of people who needed reinforcement and one group of people who did not. The hypothesis is that mixing the data from those two different groups caused the true effects to be “diluted.” Methods To test that hypothesis we used data from the Chronic Disease Self-Management Program in Japan, focusing on anxiety, depression, and patient-physician communication. To identify latent trajectories of change after the program, we used growth-mixture modeling. Then, to find out which baseline factors were associated with trajectory-group membership, we used logistic regression. Results Growth-mixture modeling revealed two trajectories—two groups that were defined by distinct patterns of change after the program. One of those patterns was improvement followed by backsliding: decay of impact. On anxiety and depression the decay of impact was large enough to be clinically important, and its prevalence was as high as 50%. Next, logistic regression analysis revealed that being in the decay-of-impact group could be predicted from multimorbidity, low self-efficacy, and high scores on anxiety or depression at baseline. In addition, one unexpected finding was an association between multimorbidity and better patient-physician communication. Conclusions These results support the hypothesis that previous findings (i.e., apparently small effect sizes and apparently ineffective reinforcement) actually reflect “dilution” of large effects, which was caused by mixing of data from distinct groups. Specifically, there was one group with decay of impact and one without. Thus, evaluations of health education should include analyses of trajectory-defined groups. These results show how the group of people who are most likely to need reinforcement can be identified even before the educational program begins. Extra attention and reinforcement can then be tailored. They can be focused specifically to benefit the people with the greatest need.
Park et al. (2019) Trajectories of change after a health-education program in Japan: decay of impact in anxiety, depression, and patient-physician communication. PeerJ 7:e7229 https://doi.org/10.7717/peerj.7229
Diversity, ecology and distribution of benthic diatoms in thermo-mineral springs in Auvergne (France) and Sardinia (Italy)
This study investigated and compared the diatom flora from thermo-mineral springs in Auvergne (France) and Sardinia (Italy). Samples were collected from rock/cobbles and fine sediments in 16 springs between January 2015 and March 2017. A total of 207 taxa (59 genera) were found. Multivariate analyses revealed significant differences in species composition and abundance among diatom assemblages both within each geographic region and between Auvergne and Sardinia (global R = 0.516; p = 0.002), suggesting the importance of local and climatic factors in species distribution. Based on abundance and common occurrence in multiple sites, some taxa can be considered more representative of springs in each region: Crenotia thermalis for Auvergne and Lemnicola exigua, Nitzschia amphibia, N. inconspicua and Rhopalodia operculata for Sardinia. pH, conductivity and HCO3− were the most significant environmental variables for diatom assemblages. Our results highlight the high heterogeneity of these spring systems. Future taxonomic insights can be useful to define the identity of some abundant and dominant taxa not identified at the species level in this study. Their identification is a crucial step for a more precise ecological characterization and comparison of these peculiar spring systems.
Lai et al. (2019) Diversity, ecology and distribution of benthic diatoms in thermo-mineral springs in Auvergne (France) and Sardinia (Italy). PeerJ 7:e7238 https://doi.org/10.7717/peerj.7238
Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions
Although coral skeletons generally comprise aragonite crystals, changes in the molar Mg/Ca ratio (mMg/Ca) in seawater result in the incorporation of calcite crystals. The formation mechanism of aragonite and calcite crystals in the scleractinian coral Acropora tenuis was therefore investigated by RNA-seq analysis, using early growth stage calcite (mMg/Ca = 0.5) and aragonite (mMg/Ca = 5.2)-based corals. As a result, 1,287 genes were up-regulated and 748 down-regulated in calcite-based corals. In particular, sixty-eight skeletogenesis-related genes, such as ectin, galaxin, and skeletal aspartic acid-rich protein, were detected as up-regulated, and six genes, such as uncharacterized skeletal organic matrix protein 5, down-regulated, in low-Mg/Ca conditions. Since the number of down-regulated genes associated with the skeletal organic matrix of aragonite skeletons was much lower than that of up-regulated genes, it is thought that corals actively initiate construction of an aragonite skeleton by the skeletal organic matrix in low-Mg/Ca conditions. In addition, different types of skeletal organic matrix proteins, extracellular matrix proteins and calcium ion binding proteins appeared to change their expression in both calcite-formed and normal corals, suggesting that the composition of these proteins could be a key factor in the selective formation of aragonite or calcite CaCO3.
Yuyama et al. (2019) Differential gene expression in skeletal organic matrix proteins of scleractinian corals associated with mixed aragonite/calcite skeletons under low mMg/Ca conditions. PeerJ 7:e7241 https://doi.org/10.7717/peerj.7241
A green garlic (Allium sativum L.) based intercropping system reduces the strain of continuous monocropping in cucumber (Cucumis sativus L.) by adjusting the micro-ecological environment of soil
The continuous cropping obstacle of cucumber (Cucumis sativus L.) under facility cultivation is more prevalent in China. This is associated with an imbalance in soil microbial and ecological environment in long-term monocultures. It was postulated that intercropping with green garlic would relieve the continuous cropping obstacle of cucumber by altering the soil micro-ecology status. A pot-based experiment was conducted to investigate the green garlic-cucumber intercropping and cucumber monocropping systems. The results showed that the cucumber shoot biomass was improved by intercropping with green garlic. However, the population of soil bacteria and actinomycetes increased, while the fungal population decreased. The fatty acid methyl ester (FAME) profiles indicated that soil contained more fungal FAME biomarkers (18:1ω9c, 18:2ω6, 9) and higher fungal:bacterial ratio in the monoculture system, whereas clustering of more bacterial FAME biomarkers (cy17:0, cy19:0, 16:1ω7c10, Me16:0, 10Me17:0, 10Me18:0) was observed under intercropping conditions. Moreover, significantly (P < 0.05) higher soil invertase and alkaline phosphatase activities, organic matter, and available N, P and K contents were observed under intercropping systems. These were high in both bulk and rhizosphere soils in the intercropping system when compared to monocropping system. These findings suggest that intercropping with green garlic can alleviate continuous cropping obstacle of cucumber by improving the diverse composition of soil microbial community, enzyme activities, and nutrient availability.
Xiao et al. (2019) A green garlic (Allium sativum L.) based intercropping system reduces the strain of continuous monocropping in cucumber (Cucumis sativus L.) by adjusting the micro-ecological environment of soil. PeerJ 7:e7267 https://doi.org/10.7717/peerj.7267
The aridity index governs the variation of vegetation characteristics in alpine grassland, Northern Tibet Plateau
The vegetation dynamic (e.g., community productivity) is an important index used to evaluate the ecosystem function of grassland ecosystem. However, the critical factors that affect vegetation biomass are disputed continuously, and most of the debates focus on mean annual precipitation (MAP) or temperature (MAT). This article integrated these two factors, used the aridity index (AI) to describe the dynamics of MAP and MAT, and tested the hypothesis that vegetation traits are influenced primarily by the AI. We sampled 275 plots at 55 sites (five plots at each site, including alpine steppe and meadow) across an alpine grassland of the northern Tibet Plateau, used correlation analysis and redundancy analysis (RDA) to explore which key factors determine the biomass dynamic, and explained the mechanism by which they affect the vegetation biomass in different vegetation types via structural equation modelling (SEM). The results supported our hypothesis, in all of the environmental factors collected, the AI made the greatest contribution to biomass variations in RDA , and the correlation between the AI and biomass was the largest (R = 0.85, p < 0.05). The final SEM also validated our hypothesis that the AI explained 79.3% and 84.4% of the biomass variations in the alpine steppe and the meadow, respectively. Furthermore, we found that the soils with higher carbon to nitrogen ratio and soil total nitrogen had larger biomass, whereas soil organic carbon had a negative effect on biomass in alpine steppe; however, opposite effects of soil factors on biomass were observed in an alpine meadow. The findings demonstrated that the AI was the most critical factor affecting biomass in the alpine grasslands, and different reaction mechanisms of biomass response to the AI existed in the alpine steppe and alpine meadow.
Liu et al. (2019) The aridity index governs the variation of vegetation characteristics in alpine grassland, Northern Tibet Plateau. PeerJ 7:e7272 https://doi.org/10.7717/peerj.7272