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Abstract Background DNA methylation contributes to the epigenetic regulation of nuclear gene expression, and is associated with plant growth, development, and stress responses. Compelling evidence has emerged that long non-coding RNA (lncRNA) regulates DNA methylation. Previous genetic and physiological evidence indicates that lncRNA-CRIR1 plays a positive role in the responses of cassava plants to cold stress. However, it is unclear whether global DNA methylation changes with CRIR1-promoted cold tolerance. Results In this study, a comprehensive comparative analysis of DNA methylation and transcriptome profiles was performed to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression. Compared with the wild-type plants, CRIR1-overexpressing plants present gained DNA methylation in over 37,000 genomic regions and lost DNA methylation in about 16,000 genomic regions, indicating a global decrease in DNA methylation after CRIR1 overexpression. Declining DNA methylation is not correlated with decreased/increased expression of the DNA methylase/demethylase genes, but is associated with increased transcripts of a few transcription factors, chlorophyll metabolism and photosynthesis-related genes, which could contribute to the CRIR1-promoted cold tolerance. Conclusions In summary, a first set of transcriptome and epigenome data was integrated in this study to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression, with the identification of several TFs, chlorophyll metabolism and photosynthesis-related genes that may be involved in CRIR1-promoted cold tolerance. Therefore, our study has provided valuable data for the systematic study of molecular insights for plant cold stress response.

Abstract Background Auxin/induced-3-acetic acid (Aux/IAA) is an important plant hormone that affects plant growth and resistance to abiotic stresses. Drought stress is a vital factor in reducing plant biomass yield and production quality. Alfalfa (Medicago sativa L.) is the most widely planted leguminous forage and one of the most economically valuable crops in the world. Aux/IAA is one of the early responsive gene families of auxin, playing a crucial role in response to drought stress. However, the characteristics of the Aux/IAA gene family in alfalfa and its potential function in response to drought stress are still unknown. Result A total of 41 Aux/IAA gene members were identified in alfalfa genome. The physicochemical, peptide structure, secondary and tertiary structure analysis of proteins encoded by these genes revealed functional diversity of the MsIAA gene. A phylogenetic analysis classified the MsIAA genes into I-X classes in two subgroups. And according to the gene domain structure, these genes were classified into typical MsIAA and atypical MsIAA. Gene structure analysis showed that the MsIAA genes contained 1–4 related motifs, and except for the third chromosome without MsIAAs, they were all located on 7 chromosomes. The gene duplication analysis revealed that segmental duplication and tandem duplication greatly affected the amplification of the MsIAA genes. Analysis of the Ka/Ks ratio of duplicated MsAux/IAA genes suggested purification selection pressure was high and functional differences were limited. In addition, identification and classification of promoter cis-elements elucidated that MsIAA genes contained numerous elements associated to phytohormone response and abiotic stress response. The prediction protein–protein interaction network showed that there was a complex interaction between the MsAux/IAA genes. Gene expression profiles were tissue-specific, and MsAux/IAA had a broad response to both common abiotic stress (ABA, salt, drought and cold) and heavy metal stress (Al and Pb). Furthermore, the expression patterns analysis of 41 Aux/IAA genes by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that Aux/IAA genes can act as positive or negative factors to regulate the drought resistance in alfalfa. Conclusion This study provides useful information for the alfalfa auxin signaling gene families and candidate evidence for further investigation on the role of Aux/IAA under drought stress. Future studies could further elucidate the functional mechanism of the MsIAA genes response to drought stress.

With the increasing demand for seamless urban transportation, there is a growing need to establish a high-quality transportation service system that improves the efficiency of comprehensive passenger transportation hubs and provides superior passenger transport services. The taxi travel system at Terminal T2 of Shanghai Hongqiao Airport, as a crucial component of transportation in a world-class hub city, has a significant impact on travelers’ satisfaction with transportation services. This study utilizes fieldwork and interviews to investigate the composition and current operational modes of the taxi travel system at Terminal T2. Using the simulation software FlexSim, we model and simulate the existing system, revealing the critical need for enhanced system performance, particularly in terms of stay time in queue and passenger output. Subsequently, we propose a performance optimization strategy, based on process analysis, involving the introduction of push-pull control to enhance supply and demand equilibrium, and the refinement of the boarding process to improve bottleneck capability. Our simulation experiments show that process enhancements, including a 5-second reduction in boarding activity and the implementation of push-pull control, can elevate the number of passengers served by 6.4% and reduce the average waiting time for passengers and taxis by 60 seconds and 110 seconds, respectively, thereby significantly heightening travel satisfactions.

Abstract Background B-box (BBX) family is a class of zinc finger transcription factors (TFs) that play essential roles in regulating plant growth, development, as well as abiotic stress. However, no systematic analysis of BBX genes has yet been conducted in alfalfa (Medica go sativa L.), and their functions have not been elucidated up to now. Results In this study, 28 MsBBX genes were identified from the alfalfa genome, which were clustered into 4 subfamilies according to an evolutionary tree of BBX proteins. Exon-intron structure and conserved motif analysis reflected the evolutionary conservation of MsBBXs in alfalfa. Collinearity analysis showed that segmental duplication promoted the expansion of the MsBBX family. Analysis of cis-regulatory elements suggested that the MsBBX genes possessed many growth/development-, light-, phytohormone-, and abiotic stress-related elements. MsBBX genes were differentially expressed in leaves, flowers, pre-elongated stems, elongated stems, roots and nodules, and most MsBBXs were remarkably induced by drought, salt and various plant growth regulators (ABA, JA, and SA). Further functional verification demonstrated that overexpressing of the MsBBX11 gene clearly promoted salt tolerance in transgenic Arabidopsis by regulating growth and physiological processes of seedlings. Conclusions This research provides insights into further functional research and regulatory mechanisms of MsBBX family genes under abiotic stress of alfalfa.

A snowstorm event followed by the elevated thunderstorm occurred in Henan Province from February 24 to 25 in 2021. The operational forecast of all meteorological stations failed to capture the thunderstorm of this event, with the snowfall being underestimated. Using the conventional meteorological observations, the dual polarization weather radar products, and the NCEP/NCAR reanalysis with special resolution of 1° and temporal resolution of 6 h, we conducted the analysis of the synoptic conditions and the characteristics of the dual polarization radar parameters for the elevated thunderstorm during this event. Results are as follows. (1) Due to the interaction of synoptic scale systems such as the mid-latitude upper trough moving eastward and deepening, the southwest jet developing northward at 700 hPa, and the cold air diffusing southward from the surface, the convection is triggered, which resulted in the elevated thunderstorms during the snowstorm event. (2) The strongest water vapor transport is located at 700 hPa, the great value belt of water vapor flux is located in the region along the Yellow River in Henan, and there is the abundant water vapor over Henan in this event, which provide favorable thermodynamic condition for the establishment of unstable stratification in the middle level and the triggering of convection. (3) The superposition of upward branches of two secondary circulations in front of the trough provides strong upward motion for the occurrence of thunderstorms and the maintenance of snowfall. The strong vertical wind shear at 0-6 km is beneficial to the development of symmetric instability. The instability energy in the mid-and upper-level is released due to the convergence of southwest wind jet at 700 hPa and the large-scale forcing by the upper trough, thus triggering convection. (4) When the elevated thunderstorm occurs, the intensity of radar echo is greater than or equal to 45 dBz and its top height is over -20 ℃. The "bull's eye" structure and maintain of the convergence rising area are favorable for generating the thunderstorm. The main characteristics of dual polarization radar parameters during the elevated thunderstorm are that the correlation coefficient (CC) is low of 0.7-0.9, the specific differential phase (KDP) is high of 0.5°- 0.7°·km-1, and the differential reflectivity factor (ZDR) is more than 2 dB. Echo intensity over 55 dBz with large KDP of 0.5°-0.7°·km-1 corresponds to the period of frequent lightning and heavy snowfall.

Drought stress impairs plant growth and other physiological functions. MeHDZ14, a homeodomain-leucine zipper I transcription factor, is strongly induced by drought stress in various cassava cultivars. However, the role of MeHDZ14 in cassava growth regulation has remained unclear. Here we report that MeHDZ14 affected plant height, such that a dwarf phenotype and altered internode elongation were observed in transgenic cassava lines. MeHDZ14 was found to negatively regulate the biosynthesis of lignin. Its overexpression resulted in abaxially rolled leaves. The morphogenesis of leaf epidermal cells was inhibited by overexpression of MeHDZ14, with decreased auxin and gibberellin and increased cytokinin contents. MeHDZ14 was found to regulate many drought-responsive genes, including genes involved in cell wall synthesis and expansion. MeHDZ14 bound to the promoter of caffeic acid 3-O-methyltransferase 1 (MeCOMT1), acting as a transcriptional repressor of genes involved in cell wall development. MeHDZ14 appears to act as a negative regulator of internode elongation and epidermal cell morphogenesis during cassava leaf development.

Chilling-induced accumulation of reactive oxygen species (ROS) is harmful to plants, which usually produce anthocyanins to scavenge ROS as protection from chilling stress. As a tropical crop, cassava is hypersensitive to chilling, but the biochemical basis of this hypersensitivity remains unclear. We previously generated MeMYB2-RNAi transgenic cassava with increased chilling tolerance. Here we report that MeMYB2-RNAi transgenic cassava accumulated less ROS but more cyanidin-3-O-glucoside than the wild type under early chilling stress. Under this stress, the anthocyanin biosynthesis pathway was more active in MeMYB2-RNAi lines than in the wild type, and several genes involved in the pathway, including MeTT8, were up-regulated by MeMYB2-RNAi in the transgenic cassava. MeMYB2 bound to the MeTT8 promoter and blocked its expression under both normal and chilling conditions, thereby inhibiting anthocyanin accumulation. MeTT8 was shown to bind to the promoter of Dihydroflavonol 4-reductase (MeDFR-2) and increased MeDFR-2 expression. MeMYB2 appears to act as an inhibitor of chilling-induced anthocyanin accumulation during the rapid response of cassava to chilling stress.

Abstract Background Elevated fasting plasma glucose (FPG) levels can increase morbidity and mortality even when it is below the diagnostic threshold of type 2 diabetes mellitus (T2DM). We conducted a genome-wide DNA methylation analysis to detect DNA methylation (DNAm) variants potentially related to FPG in Chinese monozygotic twins. Methods Genome-wide DNA methylation profiling in whole blood of twins was performed using Reduced Representation Bisulfite Sequencing (RRBS), yielding 551,447 raw CpGs. Association between DNAm of single CpG and FPG was tested using a generalized estimation equation. Differentially methylated regions (DMRs) were identified using comb-P approach. ICE FALCON method was utilized to perform the causal inference. Candidate CpGs were quantified and validated using Sequenom MassARRAY platform in a community population. Weighted gene co-expression network analysis (WGCNA) was conducted using gene expression data from twins. Results The mean age of 52 twin pairs was 52 years (SD: 7). The relationship between DNAm of 142 CpGs and FPG reached the genome-wide significance level. Thirty-two DMRs within 24 genes were identified, including TLCD1, MRPS31P5, CASZ1, and CXADRP3. The causal relationship of top CpGs mapped to TLCD1, MZF1, PTPRN2, SLC6A18, ASTN2, IQCA1, GRIN1, and PDE2A genes with FPG were further identified using ICE FALCON method. Pathways potentially related to FPG were also identified, such as phospholipid-hydroperoxide glutathione peroxidase activity and mitogen-activated protein kinase p38 binding. Three CpGs mapped to SLC6A18 gene were validated in a community population, with a hypermethylated direction in diabetic patients. The expression levels of 18 genes (including SLC6A18 and TLCD1) were positively correlated with FPG levels. Conclusions We detect many DNAm variants that may be associated with FPG in whole blood, particularly the loci within SLC6A18 gene. Our findings provide important reference for the epigenetic regulation of elevated FPG levels and diabetes.

Soil salinity is a major factor threatening the production of crops around the world. Smooth bromegrass (Bromus inermis L.) is a high-quality grass in northern and northwestern China. Currently, selecting and utilizing salt-tolerant genotypes is an important way to mitigate the detrimental effects of salinity on crop productivity. In our research, salt-tolerant and salt-sensitive varieties were selected from 57 accessions based on a comprehensive evaluation of 22 relevant indexes, and their salt-tolerance physiological and molecular mechanisms were further analyzed. Results showed significant differences in salt tolerance between 57 genotypes, with Q25 and Q46 considered to be the most salt-tolerant and salt-sensitive accessions, respectively, compared to other varieties. Under saline conditions, the salt-tolerant genotype Q25 not only maintained significantly higher photosynthetic performance, leaf relative water content (RWC), and proline content but also exhibited obviously lower relative conductivity and malondialdehyde (MDA) content than the salt-sensitive Q46 (p < 0.05). The transcriptome sequencing indicated 15,128 differentially expressed genes (DEGs) in Q46, of which 7,885 were upregulated and 7,243 downregulated, and 12,658 DEGs in Q25, of which 6,059 were upregulated and 6,599 downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the salt response differences between Q25 and Q46 were attributed to the variable expression of genes associated with plant hormone signal transduction and MAPK signaling pathways. Furthermore, a large number of candidate genes, related to salt tolerance, were detected, which involved transcription factors (zinc finger proteins) and accumulation of compatible osmolytes (glutathione S-transferases and pyrroline-5-carboxylate reductases), etc. This study offers an important view of the physiological and molecular regulatory mechanisms of salt tolerance in two smooth bromegrass genotypes and lays the foundation for further identification of key genes linked to salt tolerance.

Abstract In order to solve the requirements of real-time detection on metallic gaskets of wheelset assembly under the condition of limited hardware resources, here we propose an improved lightweight YOLOX-like network that can be deployed on mobile devices with low computing resource consumption. Firstly, the basic components of ShuffleNetV2 network structure are trimmed to reduce the computation intensity and the number of training parameters. Thus the lightweight ShuffleNetV2 is used as the backbone structure of YOLOX. The prediction layer for $$20\times 20$$ 20 × 20 size large targets is also removed from the head of this structure to further reduce the calculation time and improve the inference speed. Besides, the channel-attention enhancement module efficient channel attention is added into the network to improve the capability of feature extraction and the accuracy of target detection. Finally, the verification of inference for the proposed model is carried out on mobile terminal devices.The results show that the improved lightweight algorithm proposed in this paper not only ensures the detection accuracy, but also greatly reduces training parameters and computing resources, and it particularly can be run rapidly on mobile terminal devices with low-cost of computation.

Abstract Background Hypertension is a crucial risk factor for developing cardiovascular disease and reducing life expectancy. We aimed to detect DNA methylation (DNAm) variants potentially related to systolic blood pressure (SBP) and diastolic blood pressure (DBP) by conducting epigenome-wide association studies in 60 and 59 Chinese monozygotic twin pairs, respectively. Methods Genome-wide DNA methylation profiling in whole blood of twins was performed using Reduced Representation Bisulfite Sequencing, yielding 551,447 raw CpGs. Association between DNAm of single CpG and blood pressure was tested by applying generalized estimation equation. Differentially methylated regions (DMRs) were identified by comb-P approach. Inference about Causation through Examination of Familial Confounding was utilized to perform the causal inference. Ontology enrichment analysis was performed using Genomic Regions Enrichment of Annotations Tool. Candidate CpGs were quantified using Sequenom MassARRAY platform in a community population. Weighted gene co-expression network analysis (WGCNA) was conducted using gene expression data. Results The median age of twins was 52 years (95% range 40, 66). For SBP, 31 top CpGs (p

Alfalfa is an excellent leguminous forage crop that is widely cultivated worldwide, but its yield and quality are often affected by drought and soil salinization. Hyperosmolality-gated calcium-permeable channel (OSCA) proteins are hyperosmotic calcium ion (Ca2+) receptors that play an essential role in regulating plant growth, development, and abiotic stress responses. However, no systematic analysis of the OSCA gene family has been conducted in alfalfa. In this study, a total of 14 OSCA genes were identified from the alfalfa genome and classified into three groups based on their sequence composition and phylogenetic relationships. Gene structure, conserved motifs and functional domain prediction showed that all MsOSCA genes had the same functional domain DUF221. Cis-acting element analysis showed that MsOSCA genes had many cis-regulatory elements in response to abiotic or biotic stresses and hormones. Tissue expression pattern analysis demonstrated that the MsOSCA genes had tissue-specific expression; for example, MsOSCA12 was only expressed in roots and leaves but not in stem and petiole tissues. Furthermore, RT–qPCR results indicated that the expression of MsOSCA genes was induced by abiotic stress (drought and salt) and hormones (JA, SA, and ABA). In particular, the expression levels of MsOSCA3, MsOSCA5, MsOSCA12 and MsOSCA13 were significantly increased under drought and salt stress, and MsOSCA7, MsOSCA10, MsOSCA12 and MsOSCA13 genes exhibited significant upregulation under plant hormone treatments, indicating that these genes play a positive role in drought, salt and hormone responses. Subcellular localization results showed that the MsOSCA3 protein was localized on the plasma membrane. This study provides a basis for understanding the biological information and further functional analysis of the MsOSCA gene family and provides candidate genes for stress resistance breeding in alfalfa.

Abstract Hydrate reservoirs in the South China Sea belong to muddy silt‐type hydrate reservoirs with low permeability. Horizontal well fracturing is one of the main stimulation methods for low‐permeability oil and gas reservoirs. For muddy silt‐type hydrate reservoirs, the stability and effectiveness of hydraulic fractures may be a severe problem due to poor reservoir cementation, reservoir deformation, and sand production. In this paper, the time variability of fracture conductivity is considered for the first time. According to the geological data at offshore gas hydrate production test site in the South China Sea, a multilayer hydrate reservoir model was established, and the influence of the time variable fracture conductivity on the production behavior in the process of horizontal well fracturing was analyzed. The simulation results show that, compared with the case of constant fracture conductivity, the gas production rate with the case of time variable fracture conductivity is greatly reduced, and the 5‐year cumulative gas production is reduced by 49.9%. Sensitivity analysis shows that the larger the initial fracture conductivity, the higher the peak gas production rate; the larger the attenuation magnitude of the fracture conductivity, the lower the gas production rate in the late production period; the larger the decline rate coefficient of the fracture conductivity, the higher the gas production rate in the early production period. The analysis of the orthogonal experimental design shows that the influence of the attenuation magnitude of fracture conductivity, the initial conductivity of fracture, and the decline rate coefficient of fracture conductivity on the cumulative gas production decreases in order. The actual production process should try to avoid excessive attenuation magnitude of fracture conductivity, while improving the initial fracture conductivity as much as possible to ensure high cumulative gas production.

Sonic vibration sampling technology is widely used due to its high sample fidelity, low disturbance to the stratum and environmental protection. The influence of the diameter variation of sonic drill string caused by the sampling tube on the axial vibration of the system is still unclear, which restricts the improvement of coring efficiency. In this study, an axial vibration model of a sonic drilling string with a sampling tool is established, which takes into account the section variation. Adopting numerical simulations, the influence of the drill string on the vibration characteristics of the system, the relationship between the excitation and the amplitude of the sampling bit, and the effect of the cross-sectional area on the bearing capacity of the drill string with the sampling tube are obtained. With the longer the sampling tube and the thicker the wall thickness, the lower the inherent frequency and the higher the bearing capacity. The results show that the discontinuity of the drill string section caused by the sampling tube inevitably affects the natural frequency and response of the drill string system. The model can provide a theoretical basis for the research of sonic vibration sampling engineering. Properly balancing parameters can improve drilling and sampling performance.

Traditional hub location problems are usually based on deterministic circumstances. However, many uncertain factors can cause demand to vary in the long run, which increases the difficulty of strategic hub location planning. The hub location problem for fresh agricultural products is studied considering the perishability of the products and the uncertainty of customer demands. An uncertain demand variable is described by an affine function of the nominal mean and several independent uncertainty sources and is further adjusted by the deterioration rate. An uncapacitated robust hub location model for fresh agricultural products with uncertain demand is first established and solved using the Lagrangian relaxation approach. Then, a robust optimization model for the corresponding capacitated hub location problem is given. A numerical study based on the Australian Post data set (AP20) shows that the deterioration rate of fresh agricultural products, the uncertainty of demand and the degree of conservatism of decision makers all have significant impacts on the total transportation profit. Furthermore, the capacitated model yields more profit than the uncapacitated model because it allows the effects of the deterioration rate and uncertainty to be moderated through flow reallocation. The proposed models are useful for helping decision makers determine the locations and capacities of hubs for fresh agricultural products in accordance with different risk preferences.

Drought is one of the most common abiotic stressors in plants. Melatonin (MT) is a high-efficiency and low-toxicity growth regulator that plays an important role in plant responses to drought stress. As a wild relative of wheat, Agropyron mongolicum has become an important species for the improvement of degraded grasslands and the replanting of sandy grasslands. However, the physiological and molecular mechanisms by which exogenous MT regulates drought stress in A. mongolicum remain unclear. To assess the effectiveness of MT intervention (100 mg·L−1), polyethylene glycol 6000 was used to simulate drought stress, and its ameliorating effects on drought stress in A. mongolicum seedlings were investigated through physiology, transcriptomics, and metabolomics. Physiological analysis indicated that MT treatment increased the relative water content and chlorophyll content and decreased the relative conductivity of A. mongolicum seedlings. Additionally, MT decreased malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation by enhancing antioxidant enzyme activities. The transcriptome and metabolite profiling analysis of A. mongolicum seedlings treated with and without MT under drought stress identified the presence of 13,466 differentially expressed genes (DEGs) and 271 differentially expressed metabolites (DEMs). The integrated analysis of transcriptomics and metabolomics showed that DEGs and DEMs participated in diverse biological processes, such as flavonoid biosynthesis and carbohydrate metabolism. Moreover, MT may be involved in regulating the correlation of DEGs and DEMs in flavonoid biosynthesis and carbohydrate metabolism during drought stress. In summary, this study revealed the physiological and molecular regulatory mechanisms of exogenous MT in alleviating drought stress in A. mongolicum seedlings, and it provides a reference for the development and utilization of MT and the genetic improvement of drought tolerance in plants from arid habitats.

Abstract Depression is currently the leading cause of disability around the world. We conducted an epigenome-wide association study (EWAS) in a sample of 58 depression score-discordant monozygotic twin pairs, aiming to detect specific epigenetic variants potentially related to depression and further integrate with gene expression profile data. Association between the methylation level of each CpG site and depression score was tested by applying a linear mixed effect model. Weighted gene co-expression network analysis (WGCNA) was performed for gene expression data. The association of DNA methylation levels of 66 CpG sites with depression score reached the level of P < 1 × 10−4. These top CpG sites were located at 34 genes, especially PTPRN2, HES5, GATA2, PRDM7, and KCNIP1. Many ontology enrichments were highlighted, including Notch signaling pathway, Huntington disease, p53 pathway by glucose deprivation, hedgehog signaling pathway, DNA binding, and nucleic acid metabolic process. We detected 19 differentially methylated regions (DMRs), some of which were located at GRIK2, DGKA, and NIPA2. While integrating with gene expression data, HELZ2, PTPRN2, GATA2, and ZNF624 were differentially expressed. In WGCNA, one specific module was positively correlated with depression score (r = 0.62, P = 0.002). Some common genes (including BMP2, PRDM7, KCNIP1, and GRIK2) and enrichment terms (including complement and coagulation cascades pathway, DNA binding, neuron fate specification, glial cell differentiation, and thyroid gland development) were both identified in methylation analysis and WGCNA. Our study identifies specific epigenetic variations which are significantly involved in regions, functional genes, biological function, and pathways that mediate depression disorder.

In the long-term growth process, alfalfa rhizosphere forms specific microbiome to provide nutrition for its growth and development. However, the effects of different perennial alfalfa cultivars on changes in the rhizosphere soil characteristics and microbiome are not well understood. In this study, 12 perennial alfalfa cultivars were grown continuously for eight years. Rhizosphere samples were tested using Illumina sequencing of the 16S rRNA gene coupled with co-occurrence network analysis to explore the relationship between alfalfa (biomass and crude protein content), soil properties, and the microbial composition and diversity. Redundancy analysis showed SOC and pH had the greatest impact on the composition of the rhizosphere microbial community. Moreover, microbial diversity also contributes to microbial composition. Soil properties (AP, EC, SOC and pH) exhibited a significant positive correlation with soil bacterial communities, which was attributed to the differences between plant cultivars. Partial least squares path modeling (PLS-PM) revealed that microbial biomass and community composition rather than diversity, are the dominant determinants in the rhizosphere soil nitrogen content of perennial alfalfa. Our findings demonstrate that the soil microbial biomass and composition of rhizosphere bacterial communities are strongly affected by cultivar, driving the changes in soil nitrogen content, and variances in the selective capacities of plants.

As a high-quality legume forage, alfalfa is restricted by various abiotic stresses during its growth and development. Melatonin is a multifunctional signaling molecule that involves in plant defense against multiple stresses. However, little is known about its downstream signaling pathway and regulatory mechanisms in salt stress of alfalfa. In this study, we investigated the protective effects and key regulatory pathways of melatonin on alfalfa under salt tolerance. The results showed that melatonin promoted the growth of alfalfa seedlings under salt stress, as demonstrated by higher plant height, leaf area, and fresh weight. Melatonin treatment resulted in an increase in the photosynthetic capacity and starch content of alfalfa. Moreover, melatonin decreased cell membrane damage and reactive oxygen species (ROS) accumulation by enhancing antioxidant defense activity under salt stress conditions. Transcriptome sequencing (RNA-seq) analysis revealed that melatonin mainly induced the transcription of genes involved in Ca2+ signaling (cyclic nucleotide gated channel, CNGCs; cam modulin/calmodulin-like protein, CAM/CMLs and calcium-dependent protein kinase, CDPKs), starch and sucrose metabolism (α-amylase, AMYs; β-amylase, BAMs; starch synthase, SSs and sucrose synthase, SUSs), plant hormone signal transduction (auxin/indole acetic acid protein, AUX/IAAs; ABA receptor, PYL4; protein phosphatase 2C, PP2Cs; scarecrow-like protein, SCLs and ethylene-responsive transcription factor 1B, ERF1B), and key transcription factors (C3Hs, MYBs, ERFs, and WRKYs). Specifically, we focused on starch and sucrose metabolism and plant hormone signal transduction pathways. The interactions between melatonin and other phytohormones occurred via regulation of the expression of genes involved in hormone signaling pathways. In addition, melatonin increased the contents of endogenous melatonin, auxin, gibberellic acid (GA3), salicylic acid, brassinosteroids, and ethylene, while decreasing the abscisic acid content under salt stress. In summary, this study established a regulatory network for melatonin-induced key signaling pathways and functional genes under salt stress and provided a theoretical basis for salt tolerance breeding in alfalfa.

In the two test productions that have been conducted in the hydrate reservoir test development zone in the South China Sea, the gas production capacity of single wells is low and the exploitation difficulty with the cost is too high for commercial demand economically. The low permeability of the hydrate-bearing layer (HBL) acts as the major barrier for pressure propagation during depressurization. Hydraulic fracturing by the combined depressurization is considered a promising hydrate production enhancement technology that can effectively improve the seepage state in the reservoir. In this study, to evaluate the effectiveness of the development methods association with fracturing, we established an idealized Class II hydrate reservoir and studied it using a multi-stage fractured horizontal well to assist in depressurization extraction. In order to evaluate the production enhancement effect of this method, we compared the gas production results of four methods, including single vertical well, vertical fractured well, horizontal well, and multistage fractured horizontal well through numerical simulation. In order to investigate the influence of key fracture parameters on the production enhancement effect, a sensitivity analysis of the production effect of Class II hydrate reservoirs with different fracture spacing, number of fractures, fracture conductivity, and fracture length was conducted, and the results were analyzed in terms of gas production and water production behavior curves as well as physical field evolution over time. The simulation results show that the multi-stage fractured horizontal wells have the best production increase in the comparison of well types. In the analysis of fracture parameters, it can be found that the selection of proper fracture spacing and dimensionless fracture conductivity can lead to a significant increase in gas production.

Electroacupuncture (EA) has been extensively considered as a tool for treating diseases and relieving various pains. However, understanding the molecular mechanisms underlying its effect is of high importance. In this study, we performed a weighted gene co-expression network analysis (WGCNA) on data collected from a microarray experiment to investigate the relationship underlying EA within three factors, time, frequency and tissue regions (periaqueductal grey (PAG) and spinal dorsal horn (DH)) as well as the biological implication of gene expression changes. Gene expression on rats in PAG-DH regions induced by EA with 2 Hz and 100 Hz at l h and 24 h were measured using microarray technology. The WGCNA was performed to identify distinct network modules related to EA effects. To find the biological function of genes and pathways, the gene ontology (GO) Consortium was applied and the gene-gene interaction network of top genes in important modules was visualized. We identified one network module (466 genes) which is significantly associated with time, another module (402 genes) significantly related to frequency, and three modules each consisting of 1144, 402 and 3148 genes that are significantly associated with tissue regions. Furthermore, meaningful biological pathways were enriched in association with each of the experimental factors during EA stimulation.Our analysis showed the robustness of WGCNA and revealed important genes within specific modules and pathways which might be activated in response to EA analgesia. The findings may help to clarify the underlying mechanisms of EA and provide references for future verification of this study.

Background Classical acupuncture is being used in the treatment of rheumatoid arthritis (RA). To explore the biological response to acupuncture, a network-based analysis was performed on gene expression data collected from an animal model of RA treated with acupuncture. Methods Gene expression data were obtained from published microarray studies on blood samples from rats with collagen induced arthritis (CIA) and non-CIA rats, both treated with manual acupuncture. The weighted gene co-expression network analysis was performed to identify gene clusters expressed in association with acupuncture treatment time and RA status. Gene ontology and pathway analyses were applied for functional annotation and network visualization. Results A cluster of 347 genes were identified that differentially downregulated expression in association with acupuncture treatment over time; specifically in rats with CIA with module-RA correlation at 1 hour after acupuncture (−0.27; p < 0.001) and at 34 days after acupuncture (−0.33; p < 0.001). Functional annotation showed highly significant enrichment of porphyrin-containing compound biosynthetic processes (p < 0.001). The network-based analysis also identified a module of 140 genes differentially expressed between CIA and non-CIA in rats (p < 0.001). This cluster of genes was enriched for antigen processing and presentation of exogenous peptide antigen (p < 0.001). Other functional gene clusters previously reported in earlier studies were also observed. Conclusion The identified gene expression networks and their hub-genes could help with the understanding of mechanisms involved in the pathogenesis of RA, as well understanding the effects of acupuncture treatment of RA.

Abstract Background Large numbers of autosomal sites are found differentially methylated in the aging genome. Due to analytical difficulties in dealing with sex differences in X-chromosome content and X-inactivation (XCI) in females, this has not been explored for the X chromosome. Methods Using data from middle age to elderly individuals (age 55+ years) from two Danish cohorts of monozygotic twins and the Scottish Lothian Birth Cohort 1921, we conducted an X-chromosome-wide analysis of age-associated DNA methylation patterns with consideration of stably inferred XCI status. Results Through analysing and comparing sex-specific X-linked DNA methylation changes over age late in life, we identified 123, 293 and 55 CpG sites significant (FDR

Hub location problems are network design problems on the level of strategic decision-making processes. During strategic planning, input data, such as flows and set-up costs, are not always known in advance. Hence, decisions have to be made in an uncertain environment. In this paper, two sources of uncertainty are considered: the flows from origins to destinations and the set-up costs of hubs. A robust optimization formulation is proposed for both single and multiple allocation cases, in which the flow between each pair of nodes is assumed to be uncertain and correlated. In addition, the set-up cost of a hub is related to the total flow through the hub. Nonlinear integer program models are presented for both single and multiple allocation cases, and they are solved using CPLEX. Computational tests using the Civil Aeronautics Board and Australian Post datasets are provided. The numerical results suggest that the robust optimization strategy locates more hubs than in the deterministic case with a relatively small cost increase, and the total cost of the robust solution calculated for the multiple allocation case is marginally lower than that for the single allocation case. The robust optimization strategy is proven to be effective for protecting the solution against the worst case for different uncertain parameters.

Based on traditional titanium-based composites and the design concept of biomimetic laminated structures, the continuous SiC ceramic fiber, ductile metal Ti foil, and intermetallic Ti2AlNb foil were selected as structural components, which were alternately stacked in the sequence of Ti2AlNb-Ti-SiCf-Ti-Ti2AlNb to prepare the continuous SiC ceramic fiber-reinforced titanium-based laminated composite. The methods adopted were vacuum hot-pressing and ceramic fiber braiding. In the prepared state, the composite’s structural components were metallurgically bonded ideally, and the continuous SiC ceramic fiber was equidistantly distributed in the ductile metal Ti matrix. This composite’s phase is mainly composed of α-Ti, β-Ti, SiC, TiC, O, and B2 phases. In addition, along the ceramic SiC fiber lengthwise, the tensile test was performed on this composite at room temperature and a high temperature of 600°C, with the ultimate tensile strength being 948.76 MPa and 526.62 MPa, respectively, and, in this process, the fiber was debonded and pulled out. Meanwhile, the composite’s bending strength was measured to be 1506.21 MPa in a three-point bending test, and, under this bending load, the mode of crack propagation and failure mechanism were analyzed.

The prediction of gas productivity and reservoir stability of natural gas hydrate (NGH) reservoirs plays a vital role in the exploitation of NGH. In this study, we developed a THMC (thermal-hydrodynamic-mechanical-chemical) numerical model for the simulation of gas production behavior and the reservoir response. The model can describe the phase change, multiphase flow in porous media, heat transfer, and deformation behavior during the exploitation of NGH reservoirs. Two different production scenarios were employed for the simulation: depressurization and depressurization coupled with CO2 exchange. The simulation results suggested that the injection of CO2 promotes the dissociation of NGH between the injection well and the production well compared with depressurization only. The cumulative production of gas and water increased by 27.88% and 2.90%, respectively, based on 2000 days of production simulation. In addition, the subsidence of the NGH reservoir was lower in the CO2 exchange case compared with the single depressurization case for the same amount of cumulative gas production. The simulation results suggested that CO2 exchange in NGH reservoirs alleviates the issue of reservoir subsidence during production and maintains good reservoir stability. The results of this study can be used to provide guidance on field production from marine NGH reservoirs.

Alfalfa (Medicago sativa L.) is an important forage crop, and its productivity is severely affected by salt stress. Although proline is a compatible osmolyte that plays an important role in regulating plant abiotic stress resistance, the basic mechanism of proline requires further clarification regarding the effect of proline in mitigating the harmful effects of salinity. Here, we investigate the protective effects and regulatory mechanisms of proline on salt tolerance of alfalfa. The results show that exogenous proline obviously promotes seed germination and seedling growth of salt-stressed alfalfa. Salt stress results in stunted plant growth, while proline application alleviates this phenomenon by increasing photosynthetic capacity and antioxidant enzyme activities and decreasing cell membrane damage and reactive oxygen species (ROS) accumulation. Plants with proline treatment maintain a better K+/Na+ ratio by reducing Na+ accumulation and increasing K+ content under salt stress. Additionally, proline induces the expression of genes related to antioxidant biosynthesis (Cu/Zn-SOD and APX) and ion homeostasis (SOS1, HKT1, and NHX1) under salt stress conditions. Proline metabolism is mainly regulated by ornithine-δ-aminotransferase (OAT) and proline dehydrogenase (ProDH) activities and their transcription levels, with the proline-treated plants displaying an increase in proline content under salt stress. In addition, OAT activity in the ornithine (Orn) pathway rather than Δ1-pyrroline-5-carboxylate synthetase (P5CS) activity in the glutamate (Glu) pathway is strongly increased under salt stress, made evident by the sharp increase in the expression level of the OAT gene compared to P5CS1 and P5CS2. Our study provides new insight into how exogenous proline improves salt tolerance in plants and that it might be used as a significant practical strategy for cultivating salt-tolerant alfalfa.

Cognitive aging is one of the major problems worldwide, especially as people get older. This study aimed to perform global gene expression profiling of cognitive function to identify associated genes and pathways and a novel transcriptional regulatory network analysis to identify important regulons. We performed single transcript analysis on 400 monozygotic twins using an assumption-free generalized correlation coefficient (GCC), linear mixed-effect model (LME) and kinship model and identified six probes (one significant at the standard FDR < 0.05 while the other results were suggestive with 0.18 ≤ FDR ≤ 0.28). We combined the GCC and linear model results to cover diverse patterns of relationships, and meaningful and novel genes like APOBEC3G, H6PD, SLC45A1, GRIN3B, and PDE4D were detected. Our exploratory study showed the downregulation of all these genes with increasing cognitive function or vice versa except the SLC45A1 gene, which was upregulated with increasing cognitive function. Linear models found only H6PD and SLC45A1, the other genes were captured by GCC. Significant functional pathways (FDR < 3.95e-10) such as focal adhesion, ribosome, cysteine and methionine metabolism, Huntington's disease, eukaryotic translation elongation, nervous system development, influenza infection, metabolism of RNA, and cell cycle were identified. A total of five regulons (FDR< 1.3e-4) were enriched in a transcriptional regulatory analysis in which CTCF and REST were activated and SP3, SRF, and XBP1 were repressed regulons. The genome-wide transcription analysis using both assumption-free GCC and linear models identified important genes and biological pathways implicated in cognitive performance, cognitive aging, and neurological diseases. Also, the regulatory network analysis revealed significant activated and repressed regulons on cognitive function.

We propose a new chaotic krill herd (CKH) in terms of the recently developed krill herd (KH) algorithm, to solve global numerical optimization problems. In CKH, chaos characteristics are introduced into the KH so as to further enhance its global search ability. The elitism scheme is also applied to store the best krill during the process when updating the krill. This new approach can speed up the global convergence, while preserving the advantage of the standard KH, thus making the approach more feasible for a wider range of practical applications. Here, thirteen different chaotic maps are used to tune the time interval of the krill in the KH algorithm. Twenty-four standard benchmark functions are utilized to verify the effects of the CKH and it has been demonstrated that, in most cases, the performance of CKH with a proper chaotic map is superior to, or at least highly competitive with, the standard KH and other population-based optimization methods. Highlights A new meta-heuristic algorithm, namely CKH is proposed for global optimization. 13 different chaotic maps are applied to tune the main parameter of the KH algorithm. The elitism scheme is applied to keep the best fitness krill. The CKH algorithm is compared with ten well-known methods.

Abstract Background Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneously assess the transcriptomes of pathogen and host. This method greatly helps to understand the responses of pathogen and host to each other and discover the potential pathogenic mechanism. Results Plantlets of two economically important banana cultivars, Foc TR4 less susceptible cultivar NK and susceptible cultivar BX, were used to research the Foc-banana interaction mechanism. Notably, the infected NK had more significantly up-regulated genes on the respiration machinery including TCA cycle, glyoxylate, glycerol, and glycolysis compared to BX at 27 h post inoculation (hpi). In addition, genes involved in plant-pathogen interaction, starch, sucrose, linolenic acid and sphingolipid metabolisms were uniquely more greatly induced in BX than those in NK during the whole infection. Genes related to the biosynthesis and metabolism of SA and JA were greatly induced in the infected NK; while auxin and abscisic acid metabolisms related genes were strongly stimulated in the infected BX at 27 hpi. Furthermore, most of fungal genes were more highly expressed in the roots of BX than in those of NK. The fungal genes related to pathogenicity, pectin and chitin metabolism, reactive oxygen scavenging played the important roles during the infection of Foc. CCP1 (cytochrome c peroxidase 1) was verified to involve in cellulose utilization, oxidative stress response and pathogenicity of fungus. Conclusion The transcriptome indicated that NK had much faster defense response against Foc TR4 than BX and the expression levels of fungal genes were higher in BX than those in NK. The metabolisms of carbon, nitrogen, and signal transduction molecular were differentially involved in pathogen infection in BX and NK. Additionally, the putative virulence associated fungal genes involved in colonization, nutrition acquirement and transport provided more insights into the infection process of Foc TR4 in banana roots.

Abstract Background Multiple epigenome-wide association studies have been performed to identify DNA methylation patterns regulated by aging or correlated with risk of death. However, the inter-relatedness of the epigenetic basis of aging and mortality has not been well investigated. Methods Using genome-wide DNA methylation data from the Lothian Birth Cohorts, we conducted a genome-wide association analysis of all-cause mortality and compared this with age-associated methylation patterns reported on the same samples. Results Survival analysis using the Cox regression model identified 2552 CpG sites with genome-wide significance (false discovery rate

Seed germination requirements may determine the kinds of habitat in which plants can survive. We tested the hypothesis that nitrogen (N) addition can change seed germination trait-environmental filter interactions and ultimately redistribute seed germination traits in alpine meadows. We determined the role of N addition on germination trait selection in an alpine meadow after N addition by combining a 3-year N addition experiment in an alpine meadow and laboratory germination experiments. At the species level, germination percentage, germination rate (speed) and breadth of temperature niche for germination (BTN) were positively related to survival of a species in the fertilized community. In addition, community-weighted means of germination percentage, germination rate, germination response to alternating temperature and BTN increased. However, germination response to wet-cold storage (cold stratification) and functional richness of germination traits was lower in alpine meadows with high-nitrogen addition than in those with no, low and medium N addition. Thus, N addition had a significant influence on environmental filter-germination trait interactions and generated a different set of germination traits in the alpine meadow. Further, the effect of N addition on germination trait selection by environmental filters was amount-dependent. Low and medium levels of N addition had less effect on redistribution of germination traits than the high level.

Phosphorus is one of the essential macronutrients required by plant growth and development, but phosphate resources are finite and diminishing rapidly because of the huge need in global agriculture. In this study, 11 genes were found in the Phosphate Transporter 1 (PHT1) family of Medicago truncatula. Seven genes of the PHT1 family were available by qRT-PCR. Most of them were expressed in roots, and almost all genes were induced by low-phosphate stress in the nodule. The expression of MtPT6 was relatively high in nodules and induced by low-phosphate stress. The fusion expression of MtPT6 promoter-GUS gene in M. truncatula suggested that the expression of MtPT6 was induced in roots and nodules by phosphate starvation. In roots, MtPT6 was mainly expressed in vascular tissue and tips, and it was also expressed in cortex under low-phosphate stress; in nodules, it was mainly expressed in vascular bundles, cortical cells, and fixation zone cells. MtPT6 had a close relationship with other PHT1 family members according to amino acid alignment and phylogenetic analysis. Subcellular localization analysis in tobacco revealed that MtPT6 protein was localized to the plasma membrane. The heterologous expression of MtPT6 in Arabidopsis knockout mutants of pht1.1 and pht1.4 made seedlings more susceptible to arsenate treatment, and the phosphate concentrations in pht1.1 were higher in high phosphate condition by expressing MtPT6. We conclude that MtPT6 is a typical phosphate transporter gene and can promote phosphate acquisition efficiency of plants.

This paper develops a two-echelon green supply chain that consists of one green manufacturer and one retailer. The green manufacturer has both online direct and offline retail channels. Considering manufacturer’s risk attitude and product’s green level, the paper constructs centralized and decentralized game models when the online channel’s demand is uncertain. Furthermore, this paper analyzes the impacts of a set of factors, including consumer environmental awareness (CEA), product green level, and risk attitude on decision-making in the supply chain. Finally, we present numerical examples. The main findings are as follows: the manufacturer and the retailer will benefit from the improvement of CEA; hence, they could invest more to obtain more profits by improving CEA; manufacturer’s risk attitude has a negative impact on the pricing and profits of the supply chain; as such, the members of the supply chain should improve the accuracy of their demand forecast, so as to minimize risks and losses resulting from uncertainty in demand.

The Xihu Sag in the East China Sea Shelf Basin contains abundant oil and gas reserves and is a focus for hydrocarbon exploration and development. Source rocks are mainly coals and coal-measures mudstones in the Paleogene Pinghu and Huagang formations. Samples from the Pinghu Formation in the Xihu Sag were collected for petrology, total organic carbon, and Rock-Eval analysis for the purpose of investigating macerals component and their contributions to hydrocarbon generation potential. The coaly source rocks from the Pinghu Formation are dominated by vitrinite (average 86.18%) but have an obviously elevated content of liptinite (average 12.59%) and a much lower amount of inertinite (average 1.23%). Liptinite of the samples is mainly composed of resinite, with a small amount of cutinite, sporinite and alginate in descending order. TOC values are 37.55%–65.58% (average 49.16%). Effective HI values are 167–281 mg HC/g TOC (average 223.5 mg HC/g TOC), suggesting the organic matter is type II kerogen. Relatively high HI values and macerals components suggest that the coaly source rocks can generate both oil and gas. Although the liptinite in the coaly source rocks has a content lower than vitrinite values, it makes a significant contribution to both total hydrocarbon and liquid hydrocarbon generation. The contributions of vitrinite, liptinite and inertinite to the total hydrocarbon generation approximately are 63.21%, 36.46% and 0.33%, respectively. The contributions of vitrinite and liptinite to the liquid hydrocarbon generation are approximately 40.95% and 59.05%, respectively. These results demonstrate that the coaly source rocks are dominated by vitrinite macerals with a relatively higher content of liptinite macerals, especially resinite, and these source rocks are more prone to both total hydrocarbon and liquid hydrocarbon generation. Paleogene coaly source rocks from other parts of the world should be considered for their oil-prone nature.

Background: Although increased age is associated with higher systolic blood pressure (SBP) in general, there may be variation across individuals in how SBP changes over time. The goal of this paper is to identify heterogeneity in SBP trajectories among young adults with similar initial values and identify personal characteristics associated with different trajectory patterns. This may have important implications for prevention and prognosis. Methods: A cohort of 12,468 individuals aged 18–35 years in the Qingdao Port Cardiovascular Health Study in China was followed yearly during 2000–2011. Individuals were categorized into three strata according to their baseline SBP: ≤110 mmHg, 111–130 mmHg, and >130 mmHg. Within each stratum, group-based trajectory analyses were conducted to identify distinct SBP trajectory patterns, and their association with sociodemographic and baseline health characteristics was assessed by ordinal logistic regression. Results: Five distinct groups of individuals exhibiting divergent patterns of increasing, stable or decreasing SBP trends were identified within each stratum. This is a first report to identify a subgroup with decreasing trend in SBP. Individuals with more advanced age, having less than high school education, family history of cardiovascular diseases, greater body mass index, greater waist circumference, and hyperlipidemia at baseline were more likely to experience trajectories of higher SBP within each stratum. Conclusions: The diverging trajectories among young adults with similar initial SBP highlight the need for prevention and feasibility of effective blood pressure control, while the identified risk factors may inform targeted interventions.

Abstract Background Glutathione S-transferases (GSTs) have been reported to regulate the plant tolerance to environmental stresses. Many plant GSTs exhibited the roles on promoting tolerance to drought stress, oxidative stress and plant hormones. The biological function of GSTs has been well characterized in Arabidopsis thaliana in response to exogenous environmental stresses. However, their regulation function under exogenous environmental stresses regulating leaf abscission in cassava (Manihot esculenta Crantz) remained unknown. Results Here, 83 GSTs were identified from tropical plant cassava. The amino acid motifs and phylogenetic analyses indicated that MeGSTs were divided into 9 classes. The global expression analyses were carried out to analyze the gene expression patterns of MeGST in cassava abscission zones by comparing the MeGST genes expression patterns in both ethylene and drought induced cassava leaf abscission. Totally, 34 GSTs were detected to express in both ethylene and drought induced leaf abscission in cassava abscission zones. Comparison of GST expression profiling between ethylene and drought induced leaf abscission suggested that Tau GST genes showed with the similar expression in both treatments induced leaf abscission in cassava abscission zone. GO annotation indicated that all 17 Tau GST genes participated in the pathway of toxin catabolism (GO: 0009407). The expression levels of 17 Tau MeGST genes were analyzed in two cassava cultivars, ‘SC124’ and ‘Arg7’, the two cultivars exhibit different levels of leaf abscission when suffered from the same environmental stress. Higher expression levels of Tau MeGSTs were detected in the precocious abscission Arg7 cultivar, while lower expression levels in delayed abscission SC124 cultivar. All the results indicated that Tau MeGSTs have the function in regulation the cassava leaf abscission under environmental stresses. Conclusion Analysis of the expression patterns of GSTs in various abscission-promoting treatments in cassava abscission zones helps us to understand the possible roles of GSTs in cassava leaf abscission.

Abstract Background Preterm birth is a leading cause of perinatal mortality and long-term health consequences. Epigenetic mechanisms may have been at play in preterm birth survivors, and these could be persistent and detrimental to health later in life. Methods We performed a genome-wide DNA methylation profiling in adult twins of premature birth to identify genomic regions under differential epigenetic regulation in 144 twins with a median age of 33 years (age range 30–36). Results Association analysis detected three genomic regions annotated to the SDHAP3, TAGLN3 and GSTT1 genes on chromosomes 5, 3 and 22 (FWER: 0.01, 0.02 and 0.04) respectively. These genes display strong involvement in neurodevelopmental disorders, cancer susceptibility and premature delivery. The three identified significant regions were successfully replicated in an independent sample of twins of even older age (median age 66, range 56–80) with similar regulatory patterns and nominal p values

Abstract Background Bananas (Musa spp.) are the most important fruit crops worldwide due to their high nutrition value. Fusarium wilt of banana, caused by fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc 4), is considered as the most destructive disease in the world and results in extensive damage leading to productivity loss. The widespread use of plant resistance inducers (PRIs), such as benzothiadiazole (BTH), is a novel strategy to stimulate defense responses in banana plants to protect against pathogens infection. The recent focus on the crop defense against fungal infections has led to a renewed interest on understanding the molecular mechanisms of specific PRIs-mediated resistance. This transcriptome study aimed to identify genes that are associated with BTH-induced resistance. Patterns of gene expression in the leaves and roots of BTH-sprayed banana plants were studied using RNA-Seq. Results In this study, 18 RNA-Seq libraries from BTH-sprayed and untreated leaves and roots of the Cavendish plants, the most widely grown banana cultivar, were used for studying the transcriptional basis of BTH-related resistance. Comparative analyses have revealed that 6689 and 3624 differentially expressed genes were identified in leaves and roots, respectively, as compared to the control. Approximately 80% of these genes were differentially expressed in a tissue-specific manner. Further analysis showed that signaling perception and transduction, transcription factors, disease resistant proteins, plant hormones and cell wall organization-related genes were stimulated by BTH treatment, especially in roots. Interestingly, the ethylene and auxin biosynthesis and response genes were found to be up-regulated in leaves and roots, respectively, suggesting a choice among BTH-responsive phytohormone regulation. Conclusions Our data suggests a role for BTH in enhancing banana plant defense responses to Foc 4 infection, and demonstrates that BTH selectively affect biological processes associated with plant defenses. The genes identified in the study could be further studied and exploited to develop Foc 4-resistant banana varieties.

Abstract Background Numerous regulatory genes participate in plant thermotolerance. In Arabidopsis, HEAT-INDUCED TAS1 TARGET2 (HTT2) is an important thermotolerance gene that is silenced by ta-siR255, a trans-acting siRNA. ta-siR255 is absent from heading Chinese cabbage (Brassica rapa ssp. pekinensis). Our previous attempt to overexpress the endogenous BrpHTT2 gene of heading Chinese cabbage (B. rapa ssp. pekinensis) failed because of cosuppression. In theory, heading Chinese cabbage can overexpress Arabidopsis HTT2 to improve thermotolerance in the absence of ta-siR255-mediated gene silencing and the weak potential of coexpression. Results To test the potential application of HTT2 in improving crop thermotolerance, we transferred p35S::HTT2 to heading Chinese cabbage. We tested the leaf electrical conductivity, hypocotyl elongation, and survival percentage of p35S::HTT2 plants subjected to high-temperature (38 °C) and heat-shock (46 °C) treatment. The leaf electrical conductivity of p35S::HTT2 seedlings under high temperature decreased but did negligibly change under heat shock. The hypocotyl length of p35S::HTT2 seedlings increased under high temperature and heat shock. The survival rate of p35S::HTT2 seedlings increased under heat shock. BrpHsfs, a subset of heat-shock factor genes, were upregulated in p35S::HTT2 plants under high-temperature and heat shock conditions. In the field, transgenic plants with HTT2 appeared greener and formed leafy heads earlier than wild-type plants. Conclusions Exogenous HTT2 increased the survival rates of heat-shocked heading Chinese cabbage by promoting thermotolerance through decreasing electrical conductivity and extending hypocotyl length. Our work provides a new approach to the genetic manipulation of thermotolerance in crops through the introduction of exogenous thermotolerance genes.

Abstract Background The therapeutic management of obesity is challenging, hence further elucidating the underlying mechanisms of obesity development and identifying new diagnostic biomarkers and therapeutic targets are urgent and necessary. Here, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) to identify significant genes and specific modules related to BMI based on gene expression profile data of 7 discordant monozygotic twins. Results In the differential gene expression analysis, it appeared that 32 differentially expressed genes (DEGs) were with a trend of up-regulation in twins with higher BMI when compared to their siblings. Categories of positive regulation of nitric-oxide synthase biosynthetic process, positive regulation of NF-kappa B import into nucleus, and peroxidase activity were significantly enriched within GO database and NF-kappa B signaling pathway within KEGG database. DEGs of NAMPT, TLR9, PTGS2, HBD, and PCSK1N might be associated with obesity. In the WGCNA, among the total 20 distinct co-expression modules identified, coral1 module (68 genes) had the strongest positive correlation with BMI (r = 0.56, P = 0.04) and disease status (r = 0.56, P = 0.04). Categories of positive regulation of phospholipase activity, high-density lipoprotein particle clearance, chylomicron remnant clearance, reverse cholesterol transport, intermediate-density lipoprotein particle, chylomicron, low-density lipoprotein particle, very-low-density lipoprotein particle, voltage-gated potassium channel complex, cholesterol transporter activity, and neuropeptide hormone activity were significantly enriched within GO database for this module. And alcoholism and cell adhesion molecules pathways were significantly enriched within KEGG database. Several hub genes, such as GAL, ASB9, NPPB, TBX2, IL17C, APOE, ABCG4, and APOC2 were also identified. The module eigengene of saddlebrown module (212 genes) was also significantly correlated with BMI (r = 0.56, P = 0.04), and hub genes of KCNN1 and AQP10 were differentially expressed. Conclusion We identified significant genes and specific modules potentially related to BMI based on the gene expression profile data of monozygotic twins. The findings may help further elucidate the underlying mechanisms of obesity development and provide novel insights to research potential gene biomarkers and signaling pathways for obesity treatment. Further analysis and validation of the findings reported here are important and necessary when more sample size is acquired.

Abstract Aging is a complex biological process regulated by multiple cellular pathways and molecular mechanisms including epigenetics. Using genome-wide DNA methylation data measured in a large collection of Scottish old individuals, we performed discovery association analysis to identify age-methylated CpGs and replicated them in two independent Danish cohorts. The double-replicated CpGs were characterized by distribution over gene regions and location in relation to CpG islands. The replicated CpGs were further characterized by involvement in biological pathways to study their functional implications in aging. We identified 67,604 age-associated CpG sites reaching genome-wide significance of FWER

Control of the grouting pressure within the critical grouting pressure for crack propagation in Ordovician limestone can not only ensure grout penetration length, but also prevent the risk of creating an artificial water channel. Based on the fracture mechanics theory, a formula was proposed to calculate the critical grouting pressure of mixed mode I-II cracks in Ordovician limestone. The necessary conditions for tilted crack opening, the rationality of the existing empirical value of the maximum allowable grouting pressure was investigated based on the mechanical model. The RFPA2D-Flow numerical simulation software was used to evaluate the deduced theory. The research results show that the deduced theoretical calculation formula of the critical grouting pressure agrees with the numerical simulation results; when the mixed mode I-II fracture initiation occurs, the grouting pressure exceeds the perpendicular stress of the overlying rock; the greater the density of the overlying rock mass, the greater the value of grouting pressure for fracture initiation; when the side pressure coefficient was ≥1, crack dip angle increased and the grouting pressure for fracture initiation tended to decrease; and the empirical grouting pressure at the maximum allowable grouting pressure is 2.0–2.5 pw, which will not cause propagation and failure of the existing crack.

Serum uric acid (SUA), as the end product of purine metabolism, has proven emerging roles in human disorders. Here based on a sample of 379 middle and old-aged Chinese twin pairs, we aimed to explore the magnitude of genetic impact on SUA variation by performing sex-limitation twin modeling analyses and further detect specific genetic variants related to SUA by conducting a genome-wide association study. Monozygotic (MZ) twin correlation for SUA level (rMZ = 0.56) was larger than for dizygotic (DZ) twin correlation (rDZ = 0.39). The common effects sex-limitation model provided the best fit with additive genetic parameter (A) accounting for 46.3%, common or shared environmental parameter (C) accounting for 26.3% and unique/nonshared environmental parameter (E) accounting for 27.5% for females and 29.9, 33.1, and 37.0% for males, respectively. Although no SUA-related genetic variants reached genome-wide significance level, 25 SNPs were suggestive of association (P

Abiotic stress negatively impacts cassava (Manihot esculenta) growth and yield. Several molecular mechanisms of plant response to cold and drought have been identified and described in the literature, however, little is known about the crosstalk of the responses of cassava to these two stresses. To elucidate this question, transcriptome analysis of cassava seedlings under cold or PEG-simulated drought stress treatment was performed. Our results showed that 6103 and 7462 transcripts were significantly regulated by cold and drought stress, respectively. Gene Ontology annotation revealed that the abscisic and jasmonic acid signaling pathways shared between the two stresses responses. We further identified 2434 common differentially expressed genes (DEGs), including 1130 up-regulated and 841 down-regulated DEGs by the two stresses. These co-induced or co-suppressed genes are grouped as stress signal perception and transduction, transcription factors (TFs), metabolism as well as transport facilitation according to the function annotation. Furthermore, a large proportion of well characterized protein kinases, TF families and ubiquitin proteasome system related genes, such as RLKs, MAPKs, AP2/ERFBPs, WRKYs, MYBs, E2 enzymes and E3 ligases, including three complexes of interacting proteins were shown as key points of crosstalk between cold and drought stress signaling transduction pathways in a hierarchical manner. Our research provides valuable information and new insights for genetically improving the tolerance of crops to multiple abiotic stresses.