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A dataset of tissue-specific gene expression dynamics during seed development in Brassica
No full textIn oilseed crops, e.g. oilseed rape (OSR; Brassica napus), a key developmental process is seed maturation, during which the embryo transitions from the early, globular state to the mature state. Seed development involves cell division, differentiation, and oil accumulation in specific tissue types (embryo, endosperm, and seed coat). These developmental processes impact seed quality and oil yield. High quality RNA from Brassica spp. seed tissues, from heart to mature developmental stages, was obtained using previously reported methods for five Brassica genotypes comprising winter, semi-winter and spring OSR varieties, a B. napus heritage kale and a rapid-cycling double-haploid Brassica oleracea line. RNA-seq was performed on 240 sets of samples. The resulting dataset contains detailed spatio-temporal expression profiles during seed development. In addition to the repository data, we provide easy access to this through the Seed Oilseed Rape Developmental Expression Resource (SeedORDER), which enables users to search for genes of interest and visualise expression patterns. Knowledge of where and when genes are expressed during seed development will inform future breeding effort
Long-term no-tillage farming mitigates waterlogging during extreme rainfall events in black soil (Mollisols) region of Northeast China
No full textThe increasing frequency of extreme rainfall events intensifies waterlogging-induced aeration stress on crops, highlighting the urgency for adaptive agricultural practices. This study evaluates the potential of long-term no-tillage (NT) farming to mitigate waterlogging risks on a silty clay loam in Northeast China by comparing with traditional moldboard plough (MP) farming using an 11-year field experiment. Rainfall simulation (40 mm h−1) and dye-tracing were employed to study the dynamics water infiltration, and X-ray computed tomography (CT) was applied to examine soil pore characteristics (0–60 cm depth) and their responses (0–5 cm layer) to raindrop splashing. Results demonstrated that NT significantly enhanced water infiltration capacity, with a 161 % higher maximum infiltration depth (MID), an 65 % increase in total stained area (TSA), and 95 % less surface ponding compared to MP. Although MP exhibited higher total porosity (εtotal), macroporosity (>0.04 mm pores, εX-ray), and increased pore connectivity in the 0–20 cm layer, it had fewer biopores and greater vertical stratification of macroporosity compared to NT across the 0–60 cm profile. During rainfall events, the MP plot experienced a 28 % reduction in porosity of pores sized 0.2–1.0 mm and a 19 % increase in porosity of pores <0.2 mm in the surface layer, likely due to raindrop splashing, while NT maintained pore integrity through straw mulching. We conclude that long-term NT is effective in enhance soil resilience to waterlogging by developing continuous vertical pore networks and maintaining surface mulch, thereby improving climate adaptability in the black soil region of Northeast Chin
Multiple soil and landscape properties are associated with the spatial variation of selenium concentration in maize grain in Malawi
No full textDietary selenium (Se) deficiency is widespread in Malawi, due to the limited supply of Se in the predominantly maize based-food system characterised by low Se concentration. In this study, the aim was to examine the spatial variation of Se in maize grains in Malawi, in relation to soil properties and landscape features. Co-located soil and maize grain samples were collected in a spatially representative survey. Selenium concentration in maize, soil properties, and environmental covariates were determined. Soil and environmental variables were tested as potential predictors of Se concentration in maize. A false discovery rate (FDR) control was used within a linear mixed model (LMM) framework. Selenium concentrations in maize ranged from below detection limits (7.69 µ g kg ^−1 ) to 1852 µ g kg ^−1 with mean and median values of 39.1 and 16.8 µ g kg ^−1 respectively. The ranges of concentrations of Se fractions in soil were (i) soluble Se 0.181–18.8 µ g kg ^−1 with mean and median values of 3.94 and 3.29 mg µ g kg ^−1 respectively; (ii) adsorbed Se 0.019–119 µ g kg ^−1 with mean and median values of 3.72 and 3.02 µ g kg ^−1 respectively; (iii) organically bound Se 9.43–1334 µ g kg ^−1 with mean and median values of 123 and 92.3 µ g kg ^−1 respectively. A LMM for maize Se concentration was used for which the independent log transformed variables of soil soluble Se, adsorbed Se, oxalate extracted oxides, soluble and exchangeable sulphur had predictive value ( p 0.01 in all cases, with FDR controlled at 0.05). Downscaled mean annual temperature also explained some of the spatial variation in grain Se concentration. Spatial variation of Se in maize showed relationships with soil and environmental variables, which can be used to identify areas most at risk of Se deficiency and thus inform policy responses. However, only a small proportion of the variation was explained indicating more analysis of Se geochemistry in soil may provide more explanatory insights
High-quality gemome assembly of Chironomus reparius and its population history in European populations
No full textThe aquatic midge Chironomus riparius is an established indicator taxon for the assessment of water quality as of the European Water Framework Directive. Here, we present a novel long-read genome assembly generated with PacBio HiFi and Hi-C sequencing, which achieves chromosome-scale resolution with an assembly size of 192 Mb, an N50 of 59 Mb, and a BUSCO completeness of 99.0%. Four chromosomes with their predicted centromeric regions and 10 unplaced scaffolds were assembled containing 15,439 protein-coding genes. Chromosome-level resolution in nonmodel species is often limited, posing challenges for population genomic studies that depend on high-quality reference genomes. Reanalyzing genomic data of natural C. riparius populations, we demonstrate the improved accuracy of population genomic estimators based on the high-quality reference genome. The high contiguity and completeness of the assembly enhanced demographic inference with Sequential Markovian Coalescent (MSMC2) modeling. Our results suggest that population divergence began in an ancestral lineage during the late Pleistocene to early Holocene, consistent with paleoclimate records from Central Europ
Communicating expected uncertainty in a geostatistical survey to support co-design with users of information
No full textMuch research has examined communication about the uncertainty in spatial information to users of that information, but an equally challenging task is enabling those users to understand a priori measures of uncertainty for surveys of different intensity (and cost) at the planning stage. While statisticians can relate sampling density to measures of uncertainty, such as prediction error variance, these do not necessarily help information users (e.g. agronomists, soil scientists, policymakers and health experts) to make rational decisions about how much of the budget should be assigned to field sampling to produce information of adequate quality. In this exploratory study, we considered four ways to communicate uncertainty associated with predictions made based on data from a geostatistical survey, to determine an appropriate sampling density to meet an information user's expectations. The first method, offset correlation, is a measure of the consistency of kriging predictions made from data on sample grids with the same spacing but different origins. The second and third methods are based on the conditional prediction distribution: the second is the width of the prediction interval, whereas the third is the overall probability that, at a site where the true value of the variable indicates the need for an intervention, the contrary is indicated by the prediction. Fourth, the implicit loss function is a method that allows the user to reflect on the valuation of losses from decisions based on uncertain information implicit in selecting some arbitrary sampling density. All of these methods depend on the model of spatial dependence for the target variable, but they interrogate it in different ways and do not provide the same information. The evaluation of the four communication methods was carried out using a questionnaire that gathered the opinions of experienced participants (with experience in survey planning) about the effectiveness of the method and the comprehensibility of the uncertainty measure and its trade-off with the sampling effort. Our results show significant differences in how participants responded to the methods: the conditional probability and implicit loss function approaches were not well understood, whereas the offset correlation was the most understood. During feedback sessions, the information users highlighted that they were more familiar with the concept of correlation, with a closed interval, in this instance of [0, 1], which is likely to account for the more consistent responses regarding this method. Offset correlation will likely be more useful to information users with little or no statistical background and to those who are unable to express their requirements with respect to information quality based on other measures of uncertainty. However, the results should not be generalized due to the small sample size, and there is the need for a more in-depth study with a larger sample size to explore this further
Assessing the role of servicing in enhancing sanitation-related quality of life among container-based sanitation users
No full textHere we evaluate the servicing of container-based sanitation (CBS)—which includes the collection, replacement and cleaning of cartridges—and its influence on sanitation-related quality of life (using the SanQoL-5 index) in informal settlements across Kenya, Peru and South Africa. We (1) compared the incidence and severity of problems associated with CBS toilets against other sanitation types, (2) assessed the quality of CBS servicing across different regions and implementations and (3) evaluated the relationship between servicing issues and sanitation-related quality of life, utilizing high-frequency longitudinal smartphone survey data collected at various intervals over 1 year. Results revealed significantly fewer and less severe issues were recorded for CBS toilets than other toilet types, such as pit latrines, sewers and open drains. CBS servicing was consistently well regarded in all countries. Participants in Kenya highlighted particular satisfaction with the frequency of container replacement, whereas, in Peru, the cleanliness of replacement containers was highly regarded. SanQoL-5 scores decreased when CBS servicing issues were recorded, particularly in Kenya. This study underscores the potential of CBS as a sustainable sanitation solution in urban informal settlements, provided that high-quality servicing is maintained
Spatiotemporal dynamics of non-floodplain ponded waterbodies in the upper Yangtze River Basin, China: A hydrological connectivity perspective
No full textNon-floodplain ponded waterbodies (NPWs) are key nodes in upland-stream hydrological continuums, playing essential roles in flood and drought mitigation and water quality improvement. The hydrological connectivity between NPWs and downstream water systems determines their ecological and hydrological function. Understanding NPW dynamics through the lens of hydrologic connectivity provides valuable insights for managing the resilience of water resources. However, this aspect has received limited attention in previous research. In the present study, NPWs in the upper Yangtze River Basin were identified using the Global Surface Water dataset. They were then classified into three hydrologic connectivity classes—shallow flow path NPWs (NPWSFP), mid-depth flow path NPWs (NPWMFP), and deep flow path NPWs (NPWDFP)—based on the depth of their flow paths to the nearest stream. Thereafter, the spatial distribution and changes of these waterbodies from 1990 to 2021 were analyzed. Further, the driving factors, including natural and human induced changes, were investigated across different hydrologic connectivity classes using Partial Least Squares Structural Equation Modelling. NPWSFP and NPWMFP were primarily distributed in the Sichuan Basin, while NPWDFP were mainly concentrated in the Jinsha, Mintuo, and Wu River basins. Between 1990 and 2021, the total area covered by NPWs increased significantly, with notable growth in NPWSFP and NPWDFP. The area of NPWSFP increased primarily due to reservoir construction to meet increasing water demand. In contrast, the area of NPWDFP increased as a result of greater water replenishment driven by climate change. Climate change affected NPW dynamics indirectly through its influence on vegetation. Human activities also shaped NPW changes, mainly by altering vegetation and modifying local climate conditions. These findings offer insights for the targeted conservation and restoration of surface waterbodies
Genome-wide mapping of cAMP receptor protein binding in enteroaggregative Escherichia coli reveals targeting of virulence-associated genes
No full textBacterial pathogens employ a diverse array of virulence factors to colonize and subsequently elicit disease in their host. These factors are often subject to extensive regulation at the transcriptional level to ensure that their expression is timely. Although many pathogens use bespoke transcription factors that primarily target virulence genes, global transcription factors also sometimes play a role in controlling these genes. Enteroaggregative Escherichia coli (EAEC) is a significant cause of watery and mucoid diarrhoea globally. The organism colonizes the small intestine before producing toxins that elicit disease, using a multitude of virulence factors that are encoded both chromosomally and on virulence plasmids. In this work, we have studied the cAMP receptor protein (CRP), a well-characterized bacterial global transcription factor, focusing on its role in the pathogenicity of the prototype EAEC strain 042. We show that, although most functional CRP binding sites on the chromosome are conserved between E. coli K-12 and 042, CRP has been co-opted to couple the expression of some virulence genes to the nutritional state of the cell. We report novel mechanisms for CRP-dependent regulation of genes whose products contribute to the maturation of a bacterial antibiotic, export of a polysaccharide capsule and production of a putative adhesin
North Atlantic Oscillation Modulates Long-Term ANPP Dynamics via 1 Precipitation or 2 Temperature, Depending on Soil Nutrient Levels
No full textPrecipitation and temperature are major controls of the inter-annual dynamics of Aboveground Net Primary Production (ANPP). However, the effect of humans, through fertilization, acts on ANPP in combination with environmental variations. This raises two questions that drive our research: (1) How do seasonal variations of global atmospheric patterns, such as the North Atlantic Oscillation (NAO), affect precipitation and temperature, and ultimately influence ANPP? (2) Does long-term fertilization modify the potential pathway from the NAO, through precipitation and temperature, to ANPP? We addressed these questions using data from plots with either ‘high’ or ‘low’ nutrient addition from the world longest ecological experiment (period used for this analysis: 1950 to 2018), ‘Park Grass’, at Rothamsted Research, England, UK. We evaluated the relationships between ANPP and interannual climate variations across both types of plots using a structural equation model, with the aim to understand how monthly variations in the NAO affected precipitation and temperature, and how these, in turn, affected ANPP. We observed a signal of NAO on ANPP. However, the signal differed between ‘low’ and ‘high’ nutrient addition plots. Under the ‘low’ nutrient addition level, the NAO signal from all months exerted some influence on ANPP (R2: 0.38, P-value: 0.001), and all pathways were associated with precipitation. Under ‘high’ nutrients addition, the NAO signal exerted a small influence on ANPP (R2: 0.17, P-value = 0.001) through April precipitation and May temperatures. These results shed light on the link between global atmospheric patterns and local ecosystem functioning. Our work also confirmed a shift from a precipitation-driven response to one mediated by temperature when shifting from ‘low’ to ‘high’ nutrient conditions. These contrasting patterns suggest there is no simple way to explain the mechanisms by which 34 global atmospheric patterns influence ecosystem functioning