Search Results (1,185)

Nuclear Factor Y A (NF-YA) transcription factors are widely involved in multiple plant biological processes, such as embryogenesis, abscisic acid signaling, and abiotic stress response. This study presents a comprehensive genome-wide identification and expression profiling of NF-YA transcription factors in blueberry (Vaccinium corymbosum), an important economic crop with good adaptability, under abiotic stress conditions. Given the economic significance and health benefits of blueberries, understanding their responses to environmental stresses, such as salt, drought, and temperature extremes, is crucial. A total of 24 NF-YA transcription factors were identified through bioinformatics analyses, including sequence alignment, phylogenetic tree construction, and conserved motif analysis. The expression patterns of these NF-YA genes were evaluated in various tissues (roots, stems, and leaves) and under different stress treatments (abscisic acid, salt, and cold) using quantitative real-time PCR (qRT-PCR). The results indicated that most VcNF-YA genes exhibited higher expression levels in stems and leaves compared to roots. Most VcNF-YAs were responsive to the stress treatment. Furthermore, cis-acting element analysis revealed that the promoters of VcNF-YAs were enriched with elements responsive to abiotic stress, suggesting their pivotal role in stress adaptation. This research unveils the expressional responses of NF-YA transcription factors in blueberry upon abiotic stresses and lays the groundwork for future studies on improving crop adaptation. Full article

Broadening the genetic base of an elite breeding gene pool is one important goal in a successful long-term plant breeding program. This goal is largely achieved through the search for and introgression of exotic germplasm with adaptive traits. However, little is known about the genetic backgrounds of acquired exotic germplasm, as germplasm selection is mainly based on trait information. Here, we expanded an average pairwise dissimilarity (APD) analysis to samples with SNP genotypes associated with genes for specific characters of breeding interest. Specifically, we explored a gene-associated APD analysis in a genomic characterization of 2643 rice lines based on their published FASTQ data. Published contigs for cloned genes conditioning heat tolerance, cold tolerance, fertility, and seed size were downloaded as gene reference sequences for SNP calling, along with those SNP calls based on the rice reference genome and published indels. Totally, eight SNP or indel data sets were formed for each of three sample groups (All2643, Indica1789, and Japonica854). APD estimation was made for each of the 24 data sets. For each sample group, four novel sets of the 25 most genetically distinct rice lines, each for an assayed character, were identified. Further analyses of APD estimates also revealed some interesting APD properties. Four contig-based SNP data sets for four specific characters displayed similar APD frequency distributions and positive high correlations of APD estimates. Contig-based APD estimates were negatively correlated with genome-based APD estimates and nearly uncorrelated with indel-based APD estimates. These findings are significant for plant germplasm characterization and germplasm utilization in plant breeding. Full article

The objective of this study was to identify the Hsp70s in Paracoccus marginatus and explore their roles in P. marginatus’s resistance to temperature and insecticide stress. The full-length cDNA sequences of PmHsp70s were obtained by PCR cloning and sequencing. The physicochemical and structural characteristics of PmHsp70s were analyzed, and a phylogenetic tree was constructed. The gene expressions of PmHsp70s were detected using qRT-PCR to explore the impacts of temperature and insecticide stress on P. marginatus. A total of 12 PmHsp70s were identified and cloned. The amino acids encoded by PmHsp70s were found to contain highly conserved regions characteristic of the Hsp70 family. The subcellular localization results showed that the majority of PmHsp70s were located in the cytoplasm. A total of 13 unique conserved motifs were identified for the PmHsp70s, of which 9 were shared motifs. The phylogenetic tree showed that the 12 PmHsp70s could be clustered into five branches, with the closest evolutionary relationship observed with the Phenacoccus solenopsis. The expression of the majority of PmHsp70s was up-regulated in P. marginatus when subjected to heat stress, with the higher expression fold change observed for PmHsp70-9, PmHsp70-11, and PmHsp70-12. The expression of specific PmHsp70s was notably suppressed under cold stress, whereas the expression of others was markedly enhanced. Upon exposure to chlorfenapyr and lambda-cyhalothrin, the expressions of PmHsp70-11 and PmHsp70-12 were significantly up-regulated with the highest expression fold change, respectively. The results revealed the significance of specific PmHsp70s in the resistance of P. marginatus to temperature and insecticide stress. This study improved our understanding of the mechanisms underlying P. marginatus’s adaptive responses to unfavorable environmental conditions. Full article

RNA plays important roles in the regulation of gene expression in response to environmental stimuli. SVALKA, a long noncoding cis-natural antisense RNA, is a key component of regulating the response to cold temperature in Arabidopsis thaliana. There are three mechanisms through which SVALKA fine tunes the transcriptional response to cold temperatures. SVALKA regulates the expression of the CBF1 (C-Repeat Dehydration Binding Factor 1) transcription factor through a collisional transcription mechanism and a dsRNA and DICER mediated mechanism. SVALKA also interacts with Polycomb Repressor Complex 2 to regulate the histone methylation of CBF3. Both CBF1 and CBF3 are key components of the COLD REGULATED (COR) regulon that direct the plant’s response to cold temperature over time, as well as plant drought adaptation, pathogen responses, and growth regulation. The different isoforms of SVALKA and its potential to form dynamic RNA conformations are important features in regulating a complex gene network in concert with several other noncoding RNA. This review will summarize the three mechanisms through which SVALKA participates in gene regulation, describe the ways that dynamic RNA structures support the function of regulatory noncoding RNA, and explore the potential for improving agricultural genetic engineering with a better understanding of the roles of noncoding RNA. Full article

This study introduces a quantitative risk assessment (QRA) model aimed at evaluating the risk of invasive listeriosis linked to the consumption of ready-to-eat (RTE) smoked and gravad fish. The QRA model, based on published data, simulates the production process from fish harvest through to consumer intake, specifically focusing on smoked brine-injected, smoked dry-salted, and gravad fish. In a reference scenario, model predictions reveal substantial probabilities of lot and pack contamination at the end of processing (38.7% and 8.14% for smoked brined fish, 34.4% and 6.49% for smoked dry-salted fish, and 52.2% and 11.1% for gravad fish), although the concentrations of L. monocytogenes are very low, with virtually no packs exceeding 10 CFU/g at the point of sale. The risk of listeriosis for an elderly consumer per serving is also quantified. The lot-level mean risk of listeriosis per serving in the elderly population was 9.751 × 10⁻⁸ for smoked brined fish, 9.634 × 10⁻⁸ for smoked dry-salted fish, and 2.086 × 10⁻⁷ for gravad fish. Risk reduction strategies were then analyzed, indicating that the application of protective cultures and maintaining lower cold storage temperatures significantly mitigate listeriosis risk compared to reducing incoming fish lot contamination. The model also addresses the effectiveness of control measures during processing, such as minimizing cross-contamination. The comprehensive QRA model has been made available as a fully documented qraLm R package. This facilitates its adaptation for risk assessment of other RTE seafood, making it a valuable tool for public health officials to evaluate and manage food safety risks more effectively. Full article

Bees play important roles in socio-economic development, biodiversity conservation, and ecosystem stability. However, during the cold season, resources become limited, leading to significant losses in bee colonies. Although many studies have described the characteristics of winter bees and demonstrated that notable changes occur in their gut microflora, the underlying mechanisms remain yet to be fully elucidated. Therefore, this study was conducted to compare the gut microbiota dynamics of overwintering bees. Sample acquisition involved randomly selecting ten colonies each from three bee farms containing Apis cerana (AC) and Apis mellifera (AM), followed by dissection for further analysis. DNA was extracted, and 16S rDNA sequencing, along with various bioinformatics tools, was used to assess microbial diversity, functional differences, and species comparisons between AC and AM gut microbiota. AC exhibited lower β diversity in the gut microbiota than AM during winter. Moreover, Gilliamella and Apibacter were relatively more abundant in AC. Regarding microbial functions, key pathways included the phosphotransferase system, galactose metabolism, the pentose phosphate pathway, and carbohydrate transport and metabolism. These results suggest the presence of microbial diversity differences between AC and AM, with the differential microbial functions mainly enriched in metabolic pathways that facilitate adaptation to cold environmental stress. Full article

Amid global climate change, recurrent drought events pose significant challenges to regional water resource management and the sustainability of socio-economic growth. Thus, understanding drought characteristics and regional development patterns is essential for effective drought monitoring, prediction, and the creation of robust adaptation strategies. Most prior research has analyzed drought events independently in spatial and temporal dimensions, often overlooking their dynamic nature. In this study, we employ a three-dimensional methodology that accounts for spatiotemporal continuity to identify and extract meteorological drought events based on a 3-month standardized precipitation evapotranspiration index (SPEI3). Measured by the SPEI3 index, the incidence of drought increased in the middle part of the basin, especially in some parts of Sichuan and Yunnan province, and the frequency of drought events decreased in the upper reaches. We evaluate drought events within the Yangtze River basin from 1980 to 2016 by examining five variables: chronology, extent, severity, duration, and epicenter locations. The results show that a total of 97 persisting drought events lasting at least 3 months have been identified in Yangtze River basin. Most events have a duration between 4 and 7 months. The findings indicate that while the number of drought events in the Yangtze River basin has remained unchanged, the intensity, duration, and severity of these events have shown a slight increase from 1980 to 2016. The drought events gradually moved from the western and southeastern parts of the basin to the central region. The most severe drought event occurred between January 2011 and October 2011, with a duration of 10 months and an affected area of 0.94 million km², impacting over fifty percent of the basin. Changes in wetness and dryness in the Yangtze River basin are closely related to El Niño/Southern Oscillation (ENSO) events, with a positive correlation between the intensity of cold events and the probability of extreme drought. This study enhances our understanding of the dynamics and evolution of drought events in the Yangtze River basin, providing crucial insights for better managing water resources and developing effective adaptation strategies. Full article

The GARP transcription factor family is integral to the regulation of plant growth, development, hormone signaling pathways, circadian rhythms, and responses to both biotic and abiotic stressors. Despite its recognized importance, a comprehensive characterization of the GARP gene family in Glycine max remains unexplored. In this study, we identified 126 GmGARP genes across the 16 chromosomes of G. max and elucidated their diverse physicochemical properties. Phylogenetic classification grouped the GmGARP genes into eight distinct subfamilies, based on conserved motifs and gene structures, suggesting functional and evolutionary conservation within these clusters. The discovery of 56 segmentally duplicated gene pairs highlights gene duplication as a key driver of family expansion. Promoter analysis revealed various cis-regulatory elements, while expression profiling demonstrated that GmGARP genes possess significant tissue specificity. Furthermore, qRT-PCR analysis indicated that GmGARP genes are highly responsive to exogenous hormones, such as ABA, MeJA, and GA, as well as to abiotic stresses, including cold, salt, and drought conditions. Notably, GmGARP120 and GmGARP98 contain specific cis-elements linked to hormone responses, with their interaction verified through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Additionally, 11,195 potential target genes were predicted, underscoring the regulatory potential of the GmGARP transcription factors. These findings provide significant insights into the GmGARP gene family, laying a strong foundation for future studies on its role in G. max development and adaptive responses to environmental stressors. Full article

There is currently no established information for assessing the general welfare conditions and behavior of dairy cows housed in compost-bedded pack barns (CBPs) that allow access to pasture. Therefore, the objective of this study was to evaluate and classify the welfare and behavior of dairy cows in three different housing conditions within CBPs in southern Brazil. During both the cold and hot seasons, nine farms were divided into three groups: CONV (conventional, large, full-time barns), ADAP (conventionally adapted, full-time barns), and PART (part-time barns). The European Welfare Quality^® (WQ^®) protocol takes into account the characteristics of the animals, animal housing, and farm management to set an overall score to assess animal welfare, which is why WQ^® was used in this study. Daytime behavior was monitored over a period of four consecutive hours on two days. The 29 WQ^® measures were grouped into 11 criteria, then into four principles, and finally into the general welfare category. The experimental design employed was a randomized block design in a 2 × 3 factorial scheme (two climatic seasons and three groups), with the means of the measures, principles, and criteria for each group, season, and interaction (group × season) compared using the Tukey test. The diurnal behavior of the cows was described by the average absolute frequency of each observed behavioral measure. There were no differences among the groups in any of the measures assessed by the WQ^® protocol. However, there was a significant increase in both the incidence of diarrhea and the duration of lying down during the cold season. Only the principle of appropriate behavior varied among the groups, with the PART group demonstrating superior scores. Regardless of the season, the welfare of dairy cows maintained in CBPs was classified as “improved”. No abnormalities in behavior were observed among cows housed in the different groups or seasons. Cows in the PART group laid down less frequently during the hot season. Overall, the CBP system provided favorable welfare and behavioral conditions for cows in Brazil, and access to grazing further enhanced the welfare of animals housed in the PART group. Full article

Separation of duplex strands of nucleic acids is a vital process in the nucleic acid metabolism and survival of all living organisms. Helicases are defined as enzymes that are intended to unwind the double-stranded nucleic acids. Helicases play a prominent role in the cold adaptation of plants and bacteria. Cold stress can increase double-strand DNA breaks, generate reactive oxygen species, cause DNA methylation, and stabilize the secondary structure of RNA molecules. In this review, we discuss how helicases play important roles in adaptive responses to cellular stress caused by low temperature conditions, particularly in bacteria and plants. We also provide a glimpse of the eminence of helicase function over nuclease when an enzyme has both helicase and nuclease functions. Full article

Aimed at the high cost of cold chain distribution of fresh agricultural products within a specified time window, a joint optimization method based on a bi-level programming model for cold chain logistics is proposed for the location of front warehouses and distribution path planning. At the upper level of the bi-level programming model, k-means clustering analysis is used to obtain all accurate information about alternative locations for the front warehouse for site selection, thereby providing the corresponding foundation for the lower level algorithm. At the lower level of the model, a fusion algorithm of particle swarm optimization (PSO) and a genetic algorithm (GA) is used for solving. To accelerate the convergence speed of the population and lower the running time of the algorithm, the parameter values in the algorithm are determined adaptively. An adaptive hybrid algorithm combining the particle swarm optimization algorithm and the genetic algorithm (APSOGA) is used to reallocate the location information on backup points for the front-end warehouse, ultimately determining the facility location of the front-end warehouse and planning the end path from the front-end warehouse to the customer point, achieving joint optimization of the front-end warehouse’s location and path. A comparative analysis of algorithm optimization shows that using the APSOGA hybrid algorithm can reduce the total cost of the logistics network by 14.57% compared to a traditional single-algorithm PSO solution and reduce it by 5.21% compared to using a single GA. This proves the effectiveness of the APSOGA hybrid algorithm in solving location and path planning problems for cold chain logistics distribution companies. Full article

Hibernation serves as an energy-conserving strategy that enables animals to withstand harsh environments by reducing their metabolic rate significantly. However, the mechanisms underlying energy adaptation in hibernating ectotherms, such as Pelodiscus sinensis, remain contentious. This paper first reports the decrease in lipid levels and the expression of metabolism-related genes in P. sinensis during hibernation. The results of physiological and biochemical analysis showed that adipocyte cell size was reduced and liver lipid droplet (LD) contents were decreased during hibernation in P. sinensis. Concurrently, serum levels of triglycerides (TGs), total cholesterol (TC), non-esterified fatty acids (NEFAs), high-density lipoprotein cholesterol (HDLC), and low-density lipoprotein cholesterol (LDLC) were diminished (n = 8, p < 0.01), while an increase in serum glucose (Glu) (n = 8, p < 0.01) was noted among hibernating P. sinensis. These observations suggest a shift in energy metabolism during hibernation. To gain insights into the molecular mechanisms, we performed integrated transcriptomic and lipidomic analyses of adipose tissue and livers from summer-active versus overwintering P. sinensis, which revealed downregulation of free fatty acids (FFAs), triglycerides (TGs), diglycerides (DGs), and ceramides (Cers) during hibernation. The results of GSEA analysis showed that metabolic pathways associated with lipid metabolism, including glycerolipid metabolism and regulation of lipolysis in adipocytes, were suppressed significantly. Notably, acute cold exposure induced significant downregulation of genes related to lipolysis such as PNPLA2, ABHD5, LPL, CPT1A, and PPARα. The results indicate that lipolysis is suppressed during hibernation in P. sinensis. Collectively, these findings deepen our understanding of survival mechanisms and elucidate the unique energy adaptation strategies employed by hibernating ectotherms. Future research should explore the implications of these findings for the conservation of ectotherms and the applications for artificially inducing hibernation. Full article

To clarify the adaptation strategies of cold-tolerant wheat against global warming, this study examined the effects of daily temperature, precipitation, and sunshine duration on wheat yield in Hokkaido, Japan, over 13 years (2011–2023). Yield components were also analyzed over 20 years (2004–2023). The number of snow-cover days decreased by about 24 days over the 20-year period. As a result, the growth of overwintered wheat accelerated, with the heading and maturity of plants advancing by about 8 and 5 days, respectively, and the grain-filling period extending from about 44 to about 48 days. Multiple regression analysis was conducted using wheat yield as the objective variable and weather conditions as explanatory variables. Three weather conditions were selected: precipitation for 8 days from 27 March, sunshine hours for 8 days from 21 March, and sunshine hours for 12 days from 13 June, which yielded a coefficient of determination of 0.953. Despite the highest mean summer temperatures on record being registered in 2023, high yields were ensured by the number of sunshine hours, which were approximately 1.5 times the normally recorded hours. This highlights the importance of this parameter in mitigating the impact of high summer temperatures. Full article

In the winter of 2023/2024, the mass death of swans was observed on Lake Karakol on the eastern coast of the Caspian Sea. From 21 December 2023 to 25 January 2024, 1132 swan corpses (Cygnus olor, Cygnus cygnus) were collected and disposed of on the coast by veterinary services and ecologists. Biological samples were collected from 18 birds for analysis at different dates of the epizootic. It was found that the influenza outbreak was associated with a high concentration of migrating birds at Lake Karakol as a result of a sharp cold snap in the northern regions. At different dates of the epizootic, three avian influenza A/H5N1 viruses of clade 2.3.4.4.b were isolated from dead birds and identified as highly pathogenic viruses (HPAIs) based on the amino acid sequence of the hemagglutinin multi-base proteolytic cleavage site (PLREKRRRKR/G). A phylogenetic analysis showed that the viruses isolated from the swans had reassortations in the PB2, PB1, and NP genes between highly pathogenic (HP) and low-pathogenic (LP) avian influenza viruses. Avian influenza viruses A/Cygnus cygnus/Karakol lake/01/2024(H5N1) and A/Mute swan/Karakol lake/02/2024(H5N1) isolated on 10 January 2024 received PB2, PB1, and NP from LPAIV, while A/Mute swan/Mangystau/9809/2023(H5N1) isolated on 26 December 2023 received PB1 and NP from LPAIV, indicating that the H5N1 viruses in this study are new reassortants. All viruses showed amino acid substitutions in the PB2, PB1, NP, and NS1 segments, which are critical for enhanced virulence or adaptation in mammals. An analysis of the genomes of the isolated viruses showed that bird deaths during different periods of the epizootic were caused by different reassortant viruses. Kazakhstan is located at the crossroads of several migratory routes of migratory birds, and the possible participation of wild birds in the introduction of various pathogens into the regions of Kazakhstan requires further study. Full article

Comparative analysis based on the mitogenomes of hares in Xinjiang, China, is limited. In this study, the complete mitochondrial genomes of seven hare samples including four hare species and their hybrids from different environments were sequenced, assembled, and annotated. Subsequently, we performed base content and bias analysis, tRNA analysis, phylogenetic analysis, and amino acid sequence analysis of the annotated genes to understand their characteristics and phylogenetic relationship. Their mitogenomes are circular molecules (from 16,691 to 17,598 bp) containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region, which are similar with other Lepus spp. worldwide. The relative synonymous codon usage analysis revealed that the adaptation of Lepus yarkandensis to its unique arid and hot environment might be associated with synthesizing amino acids like alanine, leucine, serine, arginine, and isoleucine and the terminator caused by the different usage of codons. Further, we utilized the MEME model and identified two positive selection genes (ND4, ND5) in Lepus tibetanus pamirensis and one (ND5) in L. yarkandensis that might be important to their adaptation to the plateau and dry and hot basin environments, respectively. Meanwhile, Lepus tolai lehmanni and Lepus timidus may have evolved different adaptive mechanisms for the same cold environment. This study explored the evolutionary dynamics of Xinjiang hares’ mitochondrial genomes, providing significant support for future research into their adaptation mechanisms in extreme environments. Full article