Integrated transcriptome and microRNA analysis reveals molecular responses to high-temperature stress in the liver of American shad (Alosa sapidissima).

BACKGROUND: Fish reproduction, development and growth are directly affected by temperature, investigating the regulatory mechanisms behind high temperature stress is helpful to construct a finer molecular network. In this study, we systematically analyzed the transcriptome and miRNA information of American shad (Alosa sapidissima) liver tissues at different cultivation temperatures of 24 â„ƒ (Low), 27 â„ƒ (Mid) and 30 â„ƒ (High) based on a high-throughput sequencing platform. RESULTS: The results showed that there were 1594 differentially expressed genes (DEGs) and 660 differentially expressed miRNAs (DEMs) in the LowLi vs. MidLi comparison group, 473 DEGs and 84 DEMs in the MidLi vs. HighLi group, 914 DEGs and 442 DEMs in the LowLi vs. HighLi group. These included some important genes and miRNAs such as calr, hsp90b1, hsp70, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p. The DEGs were mainly enriched in the protein folding, processing and export pathways of the endoplasmic reticulum; the target genes of the DEMs were mainly enriched in the focal adhesion pathway. Furthermore, the association analysis revealed that the key genes were mainly enriched in the metabolic pathway. Interestingly, we found a significant increase in the number of genes and miRNAs involved in the regulation of heat stress during the temperature change from 24 °C to 27 °C. In addition, we examined the tissue expression characteristics of some key genes and miRNAs by qPCR, and found that calr, hsp90b1 and dre-miR-125b-2-3p were significantly highly expressed in the liver at 27 â„ƒ, while novel-m0481-5p, ssa-miR-125a-3p, ssa-miR-92b-5p, dre-miR-15a-3p and novel-m1018-5p had the highest expression in the heart at 30℃. Finally, the quantitative expression trends of 10 randomly selected DEGs and 10 DEMs were consistent with the sequencing data, indicating the reliability of the results. CONCLUSIONS: In summary, this study provides some fundamental data for subsequent in-depth research into the molecular regulatory mechanisms of A. sapidissima response to heat stress, and for the selective breeding of high temperature tolerant varieties.

Proteomics and metabolomics analysis of American shad (Alosa sapidissima) liver responses to heat stress.

The dramatic changes in the global climate pose a major threat to the survival of many organisms, including fish. To date, the regulatory mechanisms behind the physiological responses of fish to temperature changes have been studied, and a comprehensive analysis of the regulatory mechanisms of temperature tolerance will help to propose effective strategies for fish to cope with global warming. In this study, we investigated the expression profiles of proteins and metabolites in liver tissues of American shad (Alosa sapidissima) corresponding to different water temperatures (24 °C, 27 °C and 30 °C) at various times (1-month intervals) under natural culture conditions. Proteomic analysis showed that the expression levels of the heat shock protein family (e.g. HSPE1, HSP70, HSPA5 and HSPA.1) increase significantly with temperature and that many differentially expressed proteins were highly enriched especially in pathways related to the endoplasmic reticulum, oxidative phosphorylation and glycolysis/gluconeogenesis processes. In addition, the results of conjoint metabolomics and proteomics analysis suggested that the contents of several important amino acids and chemical compounds, including L-serine, L-isoleucine, L-cystine, choline and betaine, changed significantly under high-temperature environmental stress, affecting the metabolic levels of starch, amino acid and glucose, which is thought to represent a possible energy conservation method for A. sapidissima to cope with rapid changes in external temperature. In summary, our findings demonstrate that living under high temperatures for a long period of time leads to different physiological defense responses in A. sapidissima, which provides some new ideas for analyzing the molecular regulatory patterns of adaptation to high temperature and also provides a theoretical basis for the subsequent improvement of fish culture in response to global warming.

Molecular characterization and function of hif1a and fih1 in response to acute thermal stress in American shad (Alosa sapidissima).

In order to evaluate the function of hypoxia-inducible factor-1 alpha (hif1α) and factor inhibiting hif1α (fih1) in response to thermal stress, we first conducted a functional analysis of A. sapidissima hif1α and fih1, and determined hif1α and fih1 expressions in different tissues in response to thermal stress based on identified housekeeping genes (HKGs). The results showed that hif1α and fih1 were mainly located in the nucleus and cytoplasm. The full length cDNA sequence of hif1α and fih1 was 4073 bp and 2759 bp, respectively. The cDNA sequence of hif1α includes 15 exons encoding 750 amino acid residues, and the full length cDNA sequence of fih1 contains 9 exons encoding 354 amino acid residues. During the acute thermal stress transferring from 16 ± 0.5 °C (control) to 20 ± 0.5 °C, 25 ± 0.5 °C, and 30 ± 0.5 °C for 15 min, it was found that the expression trends of hif1α and fih1 showed an inhibitory regulation in the heart, while they consistently expressed in brain, intestine, muscle, gill, kidney and liver. In conclusion, this is the first study to identify the tissue-specific HKGs in A. sapidissima and found that ef1α and ß-actin are the most suitable HKGs. Hif1α and Fih1 are mainly the nuclear and cytoplasmic proteins, respectively, having high levels in the heart and brain. Alosa sapidissima countered a temperature increase from 16 to 25 ℃ by regulating the expressions of hif1α and fih1, but their physiological regulatory functions were unable to cope with acute thermal stress when the temperature difference was 14 ℃ (from 16 to 30 ℃).

Survey data on livelihoods and inputs and outputs of crop production in Quzhou county on the North China Plain.

Farmers' decisions on crop choice, management practices, and livelihood strategies are essential to agricultural sustainability. This data article describes three datasets on crop production in Quzhou, a county in the central part of North China Plain. The three datasets cover different scales. The village dataset assembles basic data on all 342 villages of Quzhou county, including information on population, land area, crop grown, labour, irrigation and markets. Data was sourced from the yearbook data of 2017 and a village cadres survey in 2018. The village dataset was used to create a village typology from which 35 villages belonging to seven village types (five for each type) were selected for stratified random sampling to collect information on farm characteristics and cropping practices. We surveyed these 35 villages, interviewing fifteen farmer households per village (525 in total) in 2020. The interviewees represented two farm management models: smallholder farms and business farms. The resulting household dataset provides farm-level data, including demographic data of farming decision-makers and the number of household members, land use and machinery resources, crop production management practices, and government subsidies. The crop-level dataset was derived from the household survey and included input-output inventories for each crop grown during one year on each field greater than 1/30th ha (1/2 mu) on the 525 surveyed farms within a year. This dataset comprises information on cropping practices in 1352 fields. The three datasets provide a basis for analyses on cropping practices and sustainability attributes of farms and crops in a typical agricultural county on the North China Plain.

Spatio-temporal effects of built environment on running activity based on a random forest approach in nanjing, China.

Running activity is closely related to the urban built environment in terms of mental and physical health, and this relationship can change as a result of spatio-temporal changes. Most studies, however, do not account for this and assume a linear relationship exists between the built environment and running activity. This study, therefore, collected running data spanning 2019-2022, studied spatial distribution of four-year running activity, established built environment indicators, used a random forest approach to investigate the non-linear relationship between them, and evaluated spatio-temporal changes in the relationships over time. The findings suggested that running activities are spatially clustered and the degree of clustering varies over time, and nonlinear relationships and threshold effects between the built environment and running activity can be found through the random forest algorithm and partial dependence plots. Urban park green space, greenway, and the normalized difference vegetation index had the most significant effects on running activity. The effects of population, buildings, streets, road intersections, and points of interest on running activity changed during the Coronavirus disease 2019 pandemic. In 2022, however, these effects were consistent with those during the pre-pandemic period. Our findings fill research gaps by using spatio-temporal analysis and a non-linear approach; they can also provide a reference for urban planners in building running-suitable and healthy cities.

High-temperature stress response: Insights into the molecular regulation of American shad (Alosa sapidissima) using a multi-omics approach.

High temperature is an important abiotic stressor that limits the survival and growth of aquatic organisms. American shad (Alosa sapidissima), a migratory fish suitable for culturing at low temperatures, is known for its delicious taste and thus has high economic value. Studies concerning changes in A. sapidissima under high temperature are limited, especially at the gene expression and protein levels. High-temperature stress significantly reduced the survival rates and increased vacuolar degeneration and inflammatory infiltration in the gills and liver. High temperature increased the activities of SOD, CAT, and cortisol, with a trend of initial increase followed by decreases in MDA, ALP, and LDH, and irregular changes in T-AOC and Na-K-ATPase. Comprehensive analysis of the transcriptome, proteome, and metabolome of gills from fish treated with different culture temperatures (24, 27, and 30 °C) revealed that differentially expressed genes, proteins, and metabolites were highly enriched in pathways involved in protein digestion and absorption, protein processing in endoplasmic reticulum, metabolic pathways, and purine metabolism. Gene expression and protein profiles indicated that genes coding for antioxidants (i.e., cat and alpl) and members of the heat shock protein (i.e., HSP70, HSP90AA1, and HSP5) were significantly upregulated. Additionally, a conjoint analysis revealed that several key enzymes, including nucleoside diphosphate kinase 2, adenosine deaminase, and ectonucleoside triphosphate diphosphohydrolase 5/6 were altered, thereby affecting the metabolism of guanosine, guanine, and inosine. An interaction network further confirmed that levels of the essential amino acids DL-arginine and L-histidine were significantly reduced, and corticosterone levels were significantly increased, suggesting that A. sapidissima may be more dependent on amino acids for energy in vivo. Overall, this work suggests that living in a high-temperature environment leads to differential defense responses in fishes. The results provide novel perspectives for studying the molecular basis of adaptation to climate change in A. sapidissima and for genetic selection.

Farmers perceive diminishing ecosystem services, but overlook dis-services in intensively used agricultural landscapes in the North China Plain.

The UN sustainable development goals ask countries to advance sustainable production methods in agriculture. While the need for a transition to sustainable agricultural production is widely felt, there is little insight into local stakeholders' perceptions regarding agroecosystem (dis)services in areas with intensive production methods. The North China Plain is an agricultural production area with intensive production systems and simplified agricultural landscapes. We conducted a survey with 267 farmers in Quzhou county in the North China Plain in 2020 to measure the perceived level of agroecosystem (dis)services supply and the changes therein between 2015 and 2020. We analyzed which explanatory factors were associated with farmers' perceptions. Provisioning services were at a high level, while the regulating and supporting ecosystem services were considered to be in low supply, as evidenced by low scores for the presence of natural enemies and earthworms, and for natural habitats such as hedgerows and windbreaks. Most of the participants did not perceive dis-services from agriculture. Differences in perception between villages with contrasting biophysical and socio-economic conditions highlight the relevance of contextualized policy development for agricultural landscape composition and configuration to manage ecosystem (dis)services.

The effects of controlled release urea on maize productivity and reactive nitrogen losses: A meta-analysis.

Application of controlled release urea (CRU) is recommended to reduce the undesirable environmental effects resulting from urea application. However, the overall effects of CRU on maize productivity and reactive nitrogen (N) losses remain unclear. Our global meta-analysis based on 866 observations of 120 studies indicated that application of CRU instead of urea (same N rate) increased maize yield by 5.3% and nitrogen use efficiency (NUE) by 24.1%, and significantly decreased nitrous oxide (N2O) emission, N leaching and ammonia (NH3) volatilization by 23.8%, 27.1% and 39.4%, respectively. The increase of NUE and reduction of N2O emission by CRU application were greater with medium and high N rates (150 ≤ N < 200 and N ≥ 200 kg N ha-1) than with low N rates. The reduction in N2O emission and N leaching with CRU application were enhanced when soil organic carbon (SOC) content was <15.0 g kg-1, and soil texture was medium or coarse. The reduction in N2O emission and NH3 volatilization with CRU were greater in soils with pH ≥ 6.0. We concluded that use of CRU should be encouraged for maize production, especially on light-textured soils with low organic matter content.