Assessment of the impact of land use in an agricultural catchment area on water quality of lowland rivers
In several countries around the world, agricultural land area exceeds 70% (Uruguay 82.6%, Kazakhstan 80.4%, Turkmenistan 72.0%, Great Britain 71.7%, Ukraine 71.6% and others). This poses a serious risk of dissipating nitrates into the aquatic environment in agricultural catchments. The aim of this study was to assess the impact of land use on water quality parameters in an agricultural catchment area. It was decided to select for analysis the catchment of the Orla River (river length of 88 km, catchment area of 1,546 km2). The catchment area is predominantly agricultural in character and its entire area has been declared as an agricultural nitrate vulnerable zone (NVZ). A total of 27 survey sites were selected on the main watercourse and its tributaries. Analyses were conducted in the years 2010–2012 to determine physical and chemical parameters of water (pH reaction, conductivity, dissolved oxygen, total nitrogen, organic nitrogen, ammonia nitrogen, nitrates, total and reactive phosphorus) as well as six macrophyte metrics of ecological status assessment (MIR, IBMR, RMNI, MTR, TIM, RI). The average values of most physico-chemical parameters of water quality repeatedly exceeded limits of good ecological status, both in the Orla River and its tributaries. As many as 18 survey sites were classified as moderate ecological status, five sites as poor and only four as good ecological status. The results indicate the impact of land use in the catchment on water conductivity. Differences were observed in the concentrations of biotic components in the main watercourse and its tributaries, and in water quality in the southern part of the catchment in relation to the rest of the study area. This is probably connected with a greater share of forests and surface waters in that area.
Kupiec et al. (2021) Assessment of the impact of land use in an agricultural catchment area on water quality of lowland rivers. PeerJ 9:e10564 https://doi.org/10.7717/peerj.10564
Scoping review of distribution models for selected Amblyomma ticks and rickettsial group pathogens
The rising prevalence of tick-borne diseases in humans in recent decades has called attention to the need for more information on geographic risk for public health planning. Species distribution models (SDMs) are an increasingly utilized method of constructing potential geographic ranges. There are many knowledge gaps in our understanding of risk of exposure to tick-borne pathogens, particularly for those in the rickettsial group. Here, we conducted a systematic scoping review of the SDM literature for rickettsial pathogens and tick vectors in the genus Amblyomma. Of the 174 reviewed articles, only 24 studies used SDMs to estimate the potential extent of vector and/or pathogen ranges. The majority of studies (79%) estimated only tick distributions using vector presence as a proxy for pathogen exposure. Studies were conducted at different scales and across multiple continents. Few studies undertook original data collection, and SDMs were mostly built with presence-only datasets from public database or surveillance sources. The reliance on existing data sources, using ticks as a proxy for disease risk, may simply reflect a lag in new data acquisition and a thorough understanding of the tick-pathogen ecology involved.
Spatial and Geographic Information Science
Lippi et al. (2021) Scoping review of distribution models for selected Amblyomma ticks and rickettsial group pathogens. PeerJ 9:e10596 https://doi.org/10.7717/peerj.10596
Density estimation of tiger and leopard using spatially explicit capture–recapture framework
The conservation of large carnivores often requires precise and accurate estimates of their populations. Being cryptic and occurring at low population densities, obtaining an unbiased population estimate is difficult in large carnivores. To overcome the uncertainties in the conventional capture–recapture (CR) methods used to estimate large carnivore densities, more robust methods such as spatially explicit capture-recapture (SECR) framework are now widely used. We modeled the CR data of tiger (Panthera tigris tigris) and leopard (Panthera pardus fusca) in the SECR framework with biotic and abiotic covariates likely believed to influence their densities. An effort of 2,211 trap nights resulted in the capture of 33 and 38 individual tigers and leopards. A total of 95 and 74 detections of tigers and leopards were achieved using 35 pairs of camera traps. Tiger and leopard density were estimated at 4.71 ± 1.20 (3.05–5.11) and 3.03 ± 0.78 (1.85–4.99) per 100 km2. Our results show that leopard density increased with high road density, high terrain ruggedness and habitats with high percentage of cropland and natural vegetation. The tiger density was positively influenced by the mosaic of cropland and natural vegetation. This study provides the first robust density estimates of tiger and leopard within the study area. Our results support the notion that large carnivores can attain moderate densities within human-dominated regions around protected areas relying on domestic livestock. Broader management strategies aimed at maintaining wild prey in the human-dominated areas around protected areas are necessary for large and endangered carnivores’ sustenance in the buffer zones around protected areas.
Rather et al. (2021) Density estimation of tiger and leopard using spatially explicit capture–recapture framework. PeerJ 9:e10634 https://doi.org/10.7717/peerj.10634
Sleep disturbance and its association with quality of life among psychiatric nurses in China
Background Sleep disturbance is associated with a number of negative adverse outcomes. This study examined the prevalence of sleep disturbance and its association with demographic and clinical characteristics and quality of life (QOL) in psychiatric nurses in China. Methods This is a multi-center, cross-sectional study involving 11 psychiatric hospitals in China. Three types of sleep disturbance (difficulty initiating sleep (DIS), difficulty maintaining sleep (DMS) and early-morning awakening (EMA)) and QOL were measured by standardized questions or instruments. Results A total of 1,847 psychiatric nurses participated. The overall prevalence of at least one type of sleep disturbance was 71.5% (95% CI [69.3–73.5]); the prevalence of DIS, DMS and EMA was 58.5% (95% CI [56.2–60.8]), 53.7% (95% CI [51.4–56.0]) and 54.6% (95% CI [52.3–56.9]), respectively. Nurses with sleep disturbance had significantly lower QOL in physical (F(1, 1,846) = 219.12, P < 0.001), psychological (F(1, 1,846) = 72.18, P < 0.001), social (F(1, 1,846) = 37.57, P < 0.001) and environmental domains (F(1, 1,846) = 95.45, P < 0.001). Multivariable logistic regression analyses revealed that shift work (DIS, OR = 1.6, 95% CI [1.28–1.98]; DMS, OR = 1.2, 95% CI [1.001–1.54]; EMA, OR = 1.3, 95% CI [1.02–1.58]) and alcohol use (DIS, OR = 1.8, 95% CI [1.46–2.32]; DMS, OR = 1.8, 95% CI [1.43–2.23]; EMA, OR = 1.7, 95% CI [1.33–2.07]) were positively associated with sleep disturbance, while higher monthly income (DIS, OR = 0.5, 95% CI [0.38–0.75]; DMS, OR = 0.7, 95% CI [0.51–0.98]) was negatively associated with sleep disturbance. Conclusion Sleep disturbance was common among nurses in psychiatric hospitals in China, particularly those on shifts and having alcohol use. Health authorities should develop effective measures to reduce risk of sleep disturbance in this population.
Lu et al. (2021) Sleep disturbance and its association with quality of life among psychiatric nurses in China. PeerJ 9:e10659 https://doi.org/10.7717/peerj.10659
Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer
To date, most data regarding the crosstalk between the Wnt signaling pathway and the YAP/TAZ transcriptional coactivators focuses on the Wnt/β-catenin branch of the pathway. In contrast, the relationship between the non-canonical Wnt pathway and YAP/TAZ remains significantly less explored. Wnt5a is usually regarded as a prototypical non-canonical Wnt ligand, and its expression has been related to cancer progression. On the other hand, YAP/TAZ transcriptional coactivators act in concert with TEAD transcription factors to control gene expression. Although one article has shown previously that WNT5A is a YAP/TEAD target gene, there is a need for further evidence supporting this regulatory relationship, because a possible YAP/Wnt5a regulatory circuit might have profound implications for cancer biology. This article analyzes publicly available ChIP-Seq, gene expression, and protein expression data to explore this relationship, and shows that WNT5A might be a YAP/TEAD target gene in several contexts. Moreover, Wnt5a and YAP expression are significantly correlated in specific cancer types, suggesting that the crosstalk between YAP/TAZ and the Wnt pathway is more intricate than previously thought.
Astudillo (2021) Analysis in silico of the functional interaction between WNT5A and YAP/TEAD signaling in cancer. PeerJ 9:e10869 https://doi.org/10.7717/peerj.10869
Expression, purification, crystallization and preliminary X-ray crystallographic studies of a mitochondrial membrane-associated protein Cbs2 from Saccharomyces cerevisiae
Background Mitochondria are unique organelles that are found in most eukaryotic cells. The main role of the mitochondria is to produce ATP. The nuclear genome encoded proteins Cbs1 and Cbs2 are located at the mitochondrial inner membrane and are reported to be essential for the translation of mitochondrial cytochrome b mRNA. Genetic studies show that Cbs2 protein recognizes the 5′ untranslated leader sequence of mitochondrial cytochrome b mRNA. However, due to a lack of biochemical and structural information, this biological process remains unclear. To investigate the structural characteristics of how Saccharomyces cerevisiae (S. cerevisiae) Cbs2 tethers cytochrome b mRNA to the mitochondrial inner membrane, a preliminary X-ray crystallographic study was carried out and is reported here. Methods The target gene from S. cerevisiae was amplified by polymerase chain reaction. The PCR fragment was digested by the NdeI and XhoI restriction endonucleases and then inserted into expression vector p28. After sequencing, the plasmid was transformed into Escherichia coli C43 competent cells. The selenomethionine derivative Cbs2 protein was overexpressed using M9 medium based on a methionine-biosynthesis inhibition method. The protein was first purified to Ni2+-nitrilotriacetate affinity chromatography and then further purified by Ion exchange chromatography and Gel-filtration chromatography. The purified Se-Cbs2 protein was concentrated to 10 mg/mL. The crystallization trials were performed using the sitting-drop vapor diffusion method at 16 °C. The complete diffraction data was processed and scaled with the HKL2000 package and programs in the CCP4 package, respectively. Results Cbs2 from S. cerevisiae was cloned, prokaryotic expressed and purified. The analysis of the size exclusion chromatography showed that the Cbs2 protein peaked at a molecular weight of approximately 90 KDa. The crystal belonged to the space group C2, with unit-cell parameters of a = 255.11, b = 58.10, c = 76.37, and β = 95.35°. X-ray diffraction data was collected at a resolution of 2.7 Å. The Matthews coefficient and the solvent content were estimated to be 3.22 Å 3 Da-1 and 61.82%, respectively. Conclusions In the present study Cbs2 from S. cerevisiae was cloned, expressed, purified, and crystallized for structural studies. The molecular weight determination results indicated that the biological assembly of Cbs2 may be a dimer.The preliminary X-ray crystallographic studies indicated the presence of two Cbs2 molecules in the asymmetric unit. This study will provide an experimental basis for exploring how Cbs2 protein mediates cytochrome b synthesis.
Wu et al. (2021) Expression, purification, crystallization and preliminary X-ray crystallographic studies of a mitochondrial membrane-associated protein Cbs2 from Saccharomyces cerevisiae. PeerJ 9:e10901 https://doi.org/10.7717/peerj.10901
Mental health status and quality of life in elderly patients with coronary heart disease
Background Coronary heart disease (CHD) is the leading cause of morbidity and mortality among elderly individuals. Patients with CHD are at high risk for mental health disorders, and psychological issues may affect the quality of life (QoL) of these patients. Nevertheless, there is little evidence regarding the psychological issues and QoL of patients with CHD among the elderly population. This study aimed to investigate the relationship between comorbidities and mental status as well as QoL among elderly patients with CHD. Methods Overall, 216 patients were included in this cross-sectional, observational, single-center study. The demographics and clinical manifestations of the patients were collected from electronic medical records. All patients were interviewed using the Chinese version of Symptom Checklist 90 (SCL-90) to assess the mental health status and the World Health Organization Quality of Life-BREF questionnaire (WHOQOL-BREF) to assess the QoL. Results In total, 96 men and 120 women, with a mean age of 71.69 ± 8.30 years, were included. When controlling for the patients’ sex, marital status and stroke, multiple stepwise linear regression analyses suggested that for CHD patients, comorbid type 2 diabetes mellitus had the significant influence on average positive factors (Coef., 5.809; 95% CI [2.467–9.152] p = 0.001); when controlling for the patients’ sex, marital status and type 2 diabetes mellitus, multiple stepwise linear regression analyses suggested that for CHD patients, comorbid stroke had the significant influence on average positive factors (Coef., 8.680; 95% CI [4.826–12.534]; p < 0.001); when controlling for the patients’ sex, marital status, type 2 diabetes mellitus and stroke, multiple stepwise linear regression analyses suggested that for CHD patients, comorbid primary hypertension had the significant influence on phobic anxiety (Coef., 0.178; 95% CI [0.010–0.347]; p = 0.038). Conclusions For elderly CHD patients, comorbid type 2 diabetes mellitus and stroke were at risk for psychological problems and lower QoL. Our findings may guide patients and clinicians to make better decisions and achieve better outcomes.
Tang et al. (2021) Mental health status and quality of life in elderly patients with coronary heart disease. PeerJ 9:e10903 https://doi.org/10.7717/peerj.10903
Biomarker identification of isolated compartments of the cell wall, cytoplasm and vacuole from the internodal cell of characean Nitellopsis obtusa
Cells of characean algae are attractive for plant cell physiologists because of their large size and their close relation to higher plant cells. The objective of our study was to evaluate the purity of the compartments (cell wall, cytoplasm with plastids, mitochondria, nuclei and endomembrane system, and vacuole) separated mechanically from the internodal cells of Nitellopsis obtusa using enzymatic markers. These included α-mannosidase and malate dehydrogenase, vacuolar and cytoplasmic enzymes, respectively. The biomarkers applied revealed the degree of compartment contamination with the material from unwanted cell parts. The cell wall was contaminated slightly by vacuole and cytoplasm residuals, respectively by 12.3 and 1.96% of corresponding biomarker activities. Relatively high activity of vacuolar marker in the cell wall could be associated with the cell vacuoles in the multicellular structure of the nodes. The biomarkers confirmed highly purified vacuolar (99.5%) and cytoplasmic (86.7%) compartments. Purity estimation of the cell fractions enabled reevaluating nCuO related Cu concentrations in the compartments of charophyte cell. The internalisation of CuO nanoparticles in N. obtusa cell occurred already after 0.5h. In general, the approach seems to be useful for assessing the accumulation and distribution of various xenobiotics and/or metabolites within plant cell. All this justifies N.obtusa internodal cells as a model organism for modern studies in cell biology and nanotoxicology.
Gylytė et al. (2021) Biomarker identification of isolated compartments of the cell wall, cytoplasm and vacuole from the internodal cell of characean Nitellopsis obtusa. PeerJ 9:e10930 https://doi.org/10.7717/peerj.10930
Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa
The AT-hook motif nuclear-localized (AHL) family is a plant transcription factor family, which plays an important role in growth and development and stress responses. We identified and analyzed 37 AHL genes in poplar (Populus trichocarpa). Phylogenetic analysis classified the PtrAHL members into three subfamilies based on their conserved domain. All PtrAHL paralogous pairs evolved under purifying selection. The promoter analysis revealed the presence of stress-related and phytohormone-related cis-elements of the PtrAHL genes. Our analysis of the tissue-specific expression pattern of PtrAHL genes indicated their significance in tissue and organ development. Network-based prediction suggested that PtrAHL genes may interact with histone deacetylases (HDAC) and participate in the development of organs, such as roots. Drought negatively impacts plant growth and development. ABA is produced under osmotic stress condition, and it takes an important part in the stress response and tolerance of plants. Real-time quantitative PCR (qRT-PCR) showed that PtrAHL genes were induced by drought stress and ABA treatment. These insights into the expression of PtrAHL genes under stress provide a basis for PtrAHL gene functional analysis. Our study will help develop new breeding strategies to improve drought tolerance in poplar.
Wang et al. (2021) Comprehensive analysis of AHL gene family and their expression under drought stress and ABA treatment in Populus trichocarpa. PeerJ 9:e10932 https://doi.org/10.7717/peerj.10932
Phylogenetically-controlled correlates of primate blinking behaviour
Eye blinking is an essential maintenance behaviour for many terrestrial animals, but is also a risky behaviour as the animal is unable to scan the environment and detect hazards while its eyes are temporarily closed. It is therefore likely that the length of time that the eyes are closed and the length of the gap between blinks for a species may reflect aspects of the ecology of that species, such as its social or physical environment. An earlier published study conducted a comparative study linking blinking behaviour and ecology, and detailed a dataset describing the blinking behaviour of a large number of primate species that was collected from captive animals, but the analysis presented did not control for the nonindependence of the data due to common evolutionary history. In the present study, the dataset is reanalysed using phylogenetic comparative methods, after reconsideration of the parameters describing the physical and social environments of the species. I find that blink rate is best described by the locomotion mode of a species, where species moving through arboreal environments blink least, ground-living species blink most, and species that use both environments show intermediate rates. The duration of a blink was also related to locomotion mode, and positively correlated with both mean species group size and mean species body mass, although the increase in relation to group size is small. How a species moves through the environment therefore appears to be important for determining blinking behaviour, and suggests that complex arboreal environments may require less interruption to visual attention. Given that the data were collected with captive individuals, caution is recommended for interpreting the correlations found.
Rands (2021) Phylogenetically-controlled correlates of primate blinking behaviour. PeerJ 9:e10950 https://doi.org/10.7717/peerj.10950