Soybean is an important legume crop and has significant agricultural and economic value. Previous research has shown that the AT-Hook Motif Nuclear Localized (AHL) gene family is highly conserved in ...land plants, playing crucial roles in plant growth and development. To date, however, the AHL gene family has not been studied in soybean.
To investigate the roles played by the AHL gene family in soybean, genome-wide identification, expression patterns and gene structures were performed to analyze. We identified a total of 63 AT-hook motif genes, which were characterized by the presence of the AT-hook motif and PPC domain in soybean. The AT-hook motif genes were distributed on 18 chromosomes and formed two distinct clades (A and B), as shown by phylogenetic analysis. All the AHL proteins were further classified into three types (I, II and III) based on the AT-hook motif. Type-I was belonged to Clade-A, while Type-II and Type-III were belonged to Clade-B. Our results also showed that the main type of duplication in the soybean AHL gene family was segmented duplication event. To discern whether the AHL gene family was involved in stress response in soybean, we performed cis-acting elements analysis and found that AHL genes were associated with light responsiveness, anaerobic induction, MYB and gibberellin-responsiveness elements. This suggest that AHL genes may participate in plant development and mediate stress response. Moreover, a co-expression network analysis showed that the AHL genes were also involved in energy transduction, and the associated with the gibberellin pathway and nuclear entry signal pathways in soybean. Transcription analysis revealed that AHL genes in Jack and Williams82 have a common expression pattern and are mostly expressed in roots, showing greater sensitivity under drought and submergence stress. Hence, the AHL gene family mainly reacts on mediating stress responses in the roots and provide comprehensive information for further understanding of the AT-hook motif gene family-mediated stress response in soybean.
Sixty-three AT-hook motif genes were identified in the soybean genome. These genes formed into two distinct phylogenetic clades and belonged to three different types. Cis-acting elements and co-expression network analyses suggested that AHL genes participated in significant biological processes. This work provides important theoretical basis for the understanding of AHLs biological functions in soybean.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Coastal aquaculture has made an important contribution to global food security and the economic development of coastal zones in recent decades. However, it has also damaged these coastal zones’ ...ecosystems. Moreover, coastal aquaculture is poised to play a key role in the achievement of Sustainable Development Goals (SDGs). Consequently, extracting aquaculture has become crucial and valuable. However, due to the limitations of remote sensing image spatial resolution and traditional extraction methods, most research studies focus on aquaculture areas containing dikes rather than individually separable aquaculture ponds (ISAPs). This is not an accurate estimation of these aquaculture areas’ true size. In our study, we propose a rapid and effective object-based method of extracting ISAPs. We chose multi-scale segmentation to generate semantically meaningful image objects for various types of land cover, and then built a decision tree classifier according to the unique features of ISAPs. The results show that our method can remove small rivers and other easily confused features, which has thus far been difficult to accomplish with conventional methods. We obtained an overall precision value of 85.61% with a recall of 84.04%; compared to the support vector machine’s (SVM) overall precision value of 78.85% and recall rate of 61.21%, our method demonstrates greater accuracy and efficiency. We used this method to test the transferability of the algorithm to nearby areas, and the obtained accuracy exceeded 80%. The method proposed in this study could provide a readily available solution for the simple and efficient extracting of ISAPs and shows high spatiotemporal transferability.
Mangrove forests, as important ecological and economic resources, have suffered a loss in the area due to natural and human activities. Monitoring the distribution of and obtaining accurate ...information on mangrove species is necessary for ameliorating the damage and protecting and restoring mangrove forests. In this study, we compared the performance of UAV Rikola hyperspectral images, WorldView-2 (WV-2) satellite-based multispectral images, and a fusion of data from both in the classification of mangrove species. We first used recursive feature elimination‒random forest (RFE-RF) to select the vegetation’s spectral and texture feature variables, and then implemented random forest (RF) and support vector machine (SVM) algorithms as classifiers. The results showed that the accuracy of the combined data was higher than that of UAV and WV-2 data; the vegetation index features of UAV hyperspectral data and texture index of WV-2 data played dominant roles; the overall accuracy of the RF algorithm was 95.89% with a Kappa coefficient of 0.95, which is more accurate and efficient than SVM. The use of combined data and RF methods for the classification of mangrove species could be useful in biomass estimation and breeding cultivation.
•The imbalance in ES supply and demand was found coupling with a high level of landscape ecological risk in Beijing.•Ecosystem service supply–demand and landscape ecological risk exhibited a ...significant negative correlation.•Land use, distance to settlement, and vegetation cover influenced the distributions of ES supply–demand ratio and landscape ecological risk.•We built a “status identification - relationship analysis - factor detection” framework for efficiency land use planning.
The balance between ecosystem service supply–demand and landscape ecological risk are two crucial aspects influencing the sustainable development of regional ecosystems. Current evaluations ignore these aspects and lead to partial landscape planning in urban areas. As a result, a framework was built for regional planning in urban areas based on multidimensional evaluations of ecosystems for high-efficiency land use planning. First, to determine the ecosystem service balance in regional scale, the supply and demand of five ecosystem services were quantified—biodiversity conservation, carbon sequestration, water conservation, food production, and landscape recreation. Second, landscape ecological risks were identified using the “natural–social–landscape” research framework combined with spatial principal component analysis. Third, spatial clustering analysis of ecosystem service supply–demand ratios and landscape ecological risks was then performed through spatial autocorrelation, which aimed to identify areas for protection and restoration priority. Finally, GeoDetector was used to determine the main factors influencing ecosystem service balance and landscape ecological risks and develop targeted planning measures. The results revealed an imbalance in total ecosystem service supply–demand in Beijing's plain area, coupled with a high level of landscape ecological risk. The combined ecosystem service supply–demand ratios exhibited a significant negative correlation and aggregation with landscape ecological risk, and the significant area accounted for approximately 31.9% of the total area. Priority areas for protection and restoration accounted for 10.39% and 19.94%, respectively, of the total regional area. Land use, distance to settlements, and vegetation cover were the primary environmental variables influencing the distributions of the combined ecosystem service supply–demand ratios and landscape ecological risk. So, this study emphasizes the need to strengthen intensive land use and prevent the uncontrolled expansion of urban land and settlements. It is crucial to enhance urban green infrastructure construction, promote the development of biodiversity-friendly agriculture, and implement measures such as afforestation restoration to increase regional vegetation cover. Overall, by integrating a framework of ecosystem services and landscape ecological risk, a comprehensive scientific reference can be provided for the efficient land use and sustainable development planning in urban areas.
Reaction kinetics in biodegradation process is the basis and key of bioremediation technology, which can be used to predict the interaction between microorganisms and environmental states in the ...system. In this study, the kinetic model (Monod, Moser, Tessier and Cotonis) and kinetic parameters of aerobic biodegradation of functional bacteria in simulated wastewater polluted by aromatic volatile organic compounds (VOCs) were determined by shaking flask experiment. Monod, Moser, Tessier and Contois models were used to fit the experimental data and determine the kinetic parameters based on nonlinear regression analysis. Experimental results demonstrated that the removal rate of aromatic VOCs at 72 h was between 34.78 and 99.75% depending on the initial concentration of aromatic VOCs. The specific growth rate μ and degradation rate q increased with the increase of substrate concentration. The model of Monod, Moser and Tessier could be used to simulate microbial growth and substrate degradation in simulated aromatic VOCs polluted wastewater. Then the model and corresponding kinetic parameters were used to predict the limit concentration of biodegradation and provide theoretical support for the subsequent dynamic simulation and field engineering.
•An improved local outlier factor algorithm with a rotating search area (LOFR) was developed for ICESat-2 ATLAS data.•The LOFR algorithm can adaptively adjust the search area and direction.•The LOFR ...algorithm was evaluated in four sites across China.•The LOFR performs well for terrain and forest height estimation.
ICESat-2 (Ice, Cloud, and Land Elevation Satellite-2) was launched in 2018 with a photon-counting LiDAR (Light Detection and Ranging) system, ATLAS (Advanced Topographic Laser Altimeter System). It is collecting massive earth elevation data all over the world, which has shown the potential of large-scale forest monitoring. However, the energy emitted by the LiDAR system is low, and the received signals are easily affected by noise. Accurate classification of photons is an important step for forest parameter retrieval. Given the limitations of existing photon classification algorithms in areas with complex terrain, we proposed an improved local outlier factor algorithm with a rotating search area (LOFR). First, photons are transformed to the along-track direction, and noise photons are preliminarily filtered out by using the elevation histogram and elevation statistical methods. Next, ground photons are extracted by using the LOF (Local Outlier Factor) with the horizontal ellipse search area algorithm (LOFE) during an initial classification stage to filter photons that are far away from the ground. During the refined classification stage, which is the core of the algorithm, the terrain slope is calculated according to the ground photons extracted during initial classification. The elliptic search area is then rotated to align its long axis with the terrain slope. Finally, the LOFR scores of the photons are calculated to remove noise photons and signal photons are classified into top-of-canopy photons, canopy photons, and ground photons. The results show that the algorithm can effectively classify photons. Both estimated terrain height and canopy height derived using the classified photons are in good agreement with airborne LiDAR data. The mean absolute error (MAE) of the estimated terrain height relative to airborne data was 1.45 m and the root mean square error (RMSE) was 2.82 m. For canopy height validation, the correlation coefficient (R2), MAE, and RMSE at the best study scale (80 m) were 0.86, 1.82 m, and 2.72 m, respectively. These results demonstrated that the proposed LOFR algorithm can improve photon classification over complex terrain without prior knowledge of the terrain. Therefore, it could provide a robust approach for large-scale ATLAS data processing.
With the intensification of global climate change, there is an increasing emphasis on protecting natural resources. Mangrove forests, critical to tropical and subtropical intertidal ecosystems, have ...garnered considerable attention in recent years for their strong carbon sink capacity, rich species diversity, and abundant natural resources. This study utilizes the 2020 global mangrove vector data as a baseline to construct a reasonable buffer zone by calculating the increase in mangrove crown width. The Google Earth Engine (GEE) platform and its Sentinel-2 data from 2022 are employed to acquire synthetic images across all regions using the mosaic algorithm. Then, mangrove forests are extracted using the Otsu algorithm, and a map depicting the global spatial distribution of mangrove forests in 2022 is obtained. The average overall accuracy of the extracted mangrove forests in this study reaches 92.4%, and it is determined that the global mangrove forest area expanded by 4920.6 km2 between 2020 and 2022, This study provides crucial data support for the global monitoring of mangrove changes and holds significant importance for protecting and restoring mangrove ecosystems.
Geographically isolated islands are under great stress due to global climate change, as well as the social and environmental issues relating to human activities. It is necessary to monitor and ...analyze the spatial–temporal changes of the land surface environment in species-rich tropical islands in order to realize the sustainable development and protection of island areas. In this study, we extracted the land cover and coastline information of three tropical islands from 1990 to 2020 based on the Google Earth Engine platform and the Random Forest algorithm. The results showed that: (1) different tropical islands have similar characteristics in terms of land surface environment changes, with the amount of artificial surface and cultivated land increasing, the forest and mangrove areas decreasing, and the amount of artificial coastline increasing; (2) human disturbance plays an important role in changes in the land surface environment. Population growth, immigration policies, food security, and human activities related to achieving economic profits are likely responsible for these land cover changes; and (3) the main factors driving coastline changes include natural processes (topography, ecological ecosystems, sea-level rise, sea waves, and storms) and human activities (sand mining, tourism, port construction, aquaculture expansion, and mangrove deforestation). Understanding these changes will help tropical islands and coastal zones to make suitable policies for land management and respond to climate change and sustainable development challenges.
Histone methylation occurs primarily on lysine residues and requires a set of enzymes capable of reading, writing, and erasing to control its establishment and deletion, which is essential for ...maintaining chromatin structure and gene expression. Histone methylation and demethylation are contributed to plant growth and development, and are involved in adapting to environmental stresses. The JmjC domain-containing proteins are extensively studied for their function in histone lysine demethylation in plants, and play a critical role in sustaining histone methylation homeostasis. In this study, a total of 21 JmjC domain-containing histone demethylase proteins (JHDMs) in birch were identified and classified into five subfamilies based on structural characteristics and phylogenetic relationships among Arabidopsis, rice, maize, and birch. Although the BpJMJ genes displayed significant schematic variation, their distribution on the chromosomes is relatively uniform. Additionally, the BpJMJ genes in birch have never experienced a tandem-duplication event proved by WGD analysis and were remaining underwent purifying selection (Ka/Ks < < 1). A typical JmjC domain was found in all BpJMJ genes, some of which have other essential domains for their functions. In the promoter regions of BpJMJ genes, cis-acting elements associated with hormone and abiotic stress responses were overrepresented. Under abiotic stresses, the transcriptome profile reveals two contrasting expression patterns within 21 BpJMJ genes. Furthermore, it was established that most BpJMJ genes had higher expression in young tissues under normal conditions, with BpJMJ06/16 having the highest expression in germinating seeds and participating in the regulation of BpGA3ox1/2 gene expression. Eventually, BpJMJ genes were found to directly interact with genes involved in the "intracellular membrane" in respond to cold stress. The present study will provide a foundation for future experiments on histone demethylases in birch and a theoretical basis for epigenetic research on growth and development in response to abiotic stresses.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Buyang Huanwu Decoction (BHD) is a traditional Chinese herbal medicine that is effective for treating cerebral ischemia (CI). However, the molecular mechanisms of BHD in CI have not been fully ...elucidated. In this study, we integrated the circular RNA (circRNA)-microRNA (miRNA)-messenger RNA (mRNA) network of middle cerebral artery occlusion (MACO) rats treated with BHD.
SD rats were randomly divided into a control group, model group, model+BHD group (2.5, 5, 10 g/kg) and model+butylphthalide (NBP) group (54 mg/kg). The neurological functions of the rats were evaluated by a modified neurological severity scoring (mNSS) system. Pathological lesions were assessed by Nissl staining, and the effects of BHD on neurovascular unit (NVU) associated protein microtubule-associated protein 2 (MAP2), glial fibrillary acidic protein (GFAP) and von Willebrand factor (VWF) were assessed by immunohistochemistry. CeRNA and miRNA microarrays were used to establish the circRNA, miRNA, and mRNA profiles. Finally, a circRNA-miRNA-mRNA ternary transcription network was constructed.
BHD improved the neurobehavioral test scores (P < 0.01) and the histopathological changes in ischemic brain tissue in MCAO rats. The expression of MAP2 and VWF decreased and the expression of GFAP increased in the ischemic side brain tissue of MCAO rats (P < 0.01), and treatment with BHD reversed the above changes (P < 0.01 or 0.05). We identified seven, three, and 86 significantly dysregulated circRNAs, miRNAs, and mRNAs, respectively, that were associated with the neuroprotective effects of BHD. Furthermore, bioinformatics analysis showed that these targets may exert therapeutic effects through multiple pathways, such as the VEGF and Hippo signaling pathways. Finally, we constructed a circRNA-miRNA-mRNA network.
In brief, our study provides novel insights into ceRNA-mediated gene regulation in the progression of NVU after CI and the mechanism of action for BHD.
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•Buyang Huanwu Decoction (BHD) improved the neurobehavioral scores in middle cerebral artery occlusion (MACO) rats.•BHD reversed the injury of neurovascular units in MCAO rats.•BHD decoction may protect the neurovascular units of MCAO rats by affecting the circRNA-miRNA-mRNA transcription network.
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