Machine learning phenotyping and GWAS reveal genetic basis of Cd tolerance and absorption in jute.

Cadmium (Cd) is a dangerous environmental contaminant. Jute (Corchorus sp.) is an important natural fiber crop with strong absorption and excellent adaptability to metal-stressed environments, used in the phytoextraction of heavy metals. Understanding the genetic and molecular mechanisms underlying Cd tolerance and accumulation in plants is essential for efficient phytoremediation strategies and breeding novel Cd-tolerant cultivars. Here, machine learning (ML) and hyperspectral imaging (HSI) combining genome-wide association studies (GWAS) and RNA-seq reveal the genetic basis of Cd resistance and absorption in jute. ML needs a small number of plant phenotypes for training and can complete the plant phenotyping of large-scale populations with efficiency and accuracy greater than 90%. In particular, a candidate gene for Cd resistance (COS02g_02406) and a candidate gene (COS06g_03984) associated with Cd absorption are identified in isoflavonoid biosynthesis and ethylene response signaling pathways. COS02g_02406 may enable plants to cope with metal stress by regulating isoflavonoid biosynthesis involved in antioxidant defense and metal chelation. COS06g_03984 promotes the binding of Cd2+ to ETR/ERS, resulting in Cd absorption and tolerance. The results confirm the feasibility of high-throughput phenotyping for studying plant Cd tolerance by combining HSI and ML approaches, facilitating future molecular breeding.

CsMIKC1 regulates inflorescence development and grain production in Cannabis sativa plants.

Female inflorescence is the primary output of medical Cannabis. It contains hundreds of cannabinoids that accumulate in the glandular trichomes. However, little is known about the genetic mechanisms governing Cannabis inflorescence development. In this study, we reported the map-based cloning of a gene determining the number of inflorescences per branch. We named this gene CsMIKC1 since it encodes a transcription factor that belongs to the MIKC-type MADS subfamily. Constitutive overexpression of CsMIKC1 increases inflorescence number per branch, thereby promoting flower production as well as grain yield in transgenic Cannabis plants. We further identified a plant-specific transcription factor, CsBPC2, promoting the expression of CsMIKC1. CsBPC2 mutants and CsMIKC1 mutants were successfully created using the CRISPR-Cas9 system; they exhibited similar inflorescence degeneration and grain reduction. We also validated the interaction of CsMIKC1 with CsVIP3, which suppressed expression of four inflorescence development-related genes in Cannabis. Our findings establish important roles for CsMIKC1 in Cannabis, which could represent a previously unrecognized mechanism of inflorescence development regulated by ethylene.

Vision transformer empowered physics-driven deep learning for omnidirectional three-dimensional holography.

The inter-plane crosstalk and limited axial resolution are two key points that hinder the performance of three-dimensional (3D) holograms. The state-of-the-art methods rely on increasing the orthogonality of the cross-sections of a 3D object at different depths to lower the impact of inter-plane crosstalk. Such strategy either produces unidirectional 3D hologram or induces speckle noise. Recently, learning-based methods provide a new way to solve this problem. However, most related works rely on convolution neural networks and the reconstructed 3D holograms have limited axial resolution and display quality. In this work, we propose a vision transformer (ViT) empowered physics-driven deep neural network which can realize the generation of omnidirectional 3D holograms. Owing to the global attention mechanism of ViT, our 3D CGH has small inter-plane crosstalk and high axial resolution. We believe our work not only promotes high-quality 3D holographic display, but also opens a new avenue for complex inverse design in photonics.

Identification of Single Nucleotide Polymorphic Loci and Candidate Genes for Seed Germination Percentage in Okra under Salt and No-Salt Stresses by Genome-Wide Association Study.

Excessive soil salinity is a major stressor inhibiting crops' growth, development, and yield. Seed germination is a critical stage of crop growth and development, as well as one of the most salt-sensitive stages. Salt stress has a significant inhibitory effect on seed germination. Okra is a nutritious vegetable, but its seed germination percentage (GP) is low, whether under salt stress conditions or suitable conditions. In this study, we used 180 okra accessions and conducted a genome-wide association study (GWAS) on the germination percentage using 20,133,859 single nucleotide polymorphic (SNP) markers under 0 (CK, diluted water), 70 (treatment 1, T1), and 140 mmol/L (treatment 2, T2) NaCl conditions. Using the mixed linear model (MLM) in Efficient Mixed-model Association eXpedated (EMMAX) and Genome-wide Efficient Mixed Model Association (GEMMA) software, 511 SNP loci were significantly associated during germination, of which 167 SNP loci were detected simultaneously by both programs. Among the 167 SNPs, SNP2619493 on chromosome 59 and SNP2692266 on chromosome 44 were detected simultaneously under the CK, T1, and T2 conditions, and were key SNP loci regulating the GP of okra seeds. Linkage disequilibrium block analysis revealed that nsSNP2626294 (C/T) in Ae59G004900 was near SNP2619493, and the amino acid changes caused by nsSNP2626294 led to an increase in the phenotypic values in some okra accessions. There was an nsSNP2688406 (A/G) in Ae44G005470 near SNP2692266, and the amino acid change caused by nsSNP2688406 led to a decrease in phenotypic values in some okra accessions. These results indicate that Ae59G004900 and Ae44G005470 regulate the GP of okra seeds under salt and no-salt stresses. The gene expression analysis further demonstrated these results. The SNP markers and genes that were identified in this study will provide reference for further research on the GP of okra, as well as new genetic markers and candidate genes for cultivating new okra varieties with high GPs under salt and no-salt stress conditions.

Methyl Ferulic Acid Alleviates Neuropathic Pain by Inhibiting Nox4-induced Ferroptosis in Dorsal Root Ganglia Neurons in Rats.

Neuropathic pain is a disease that has become one of the major public health problems and a global burden. Nox4-induced oxidative stress can lead to ferroptosis and neuropathic pain. Methyl ferulic acid (MFA) can inhibit the Nox4-induced oxidative stress. This study aimed to estimate whether methyl ferulic acid alleviates neuropathic pain by inhibiting the expression of Nox4 and its induction of ferroptosis. Adult male Sprague-Dawley rats were subjected to spared nerve injury (SNI) model to induce neuropathic pain. After the establishment of the model, methyl ferulic acid was given 14 days by gavage. Nox4 overexpression was induced by microinjection of the AAV-Nox4 vector. All groups measured paw mechanical withdrawal threshold (PMWT), paw thermal withdrawal latency (PTWL), and paw withdrawal cold duration (PWCD). The expression of Nox4, ACSL4, GPX4, and ROS was investigated by Western blot and immunofluorescence staining. The changes in iron content were detected by a tissue iron kit. The morphological changes in mitochondria were observed by transmission electron microscopy. In the SNI group, the paw mechanical withdrawal threshold, the paw withdrawal cold duration decreased, the paw thermal withdrawal latency did not change, the Nox4, ACSL4, ROS, and iron content increased, the GPX4 decreased, and the number of abnormal mitochondria increased. Methyl ferulic acid can increase PMWT and PWCD but does not affect PTWL. Methyl ferulic acid can inhibit Nox4 protein expression. Meanwhile, ferroptosis-related protein ACSL4 expression was decreased, GPX4 expression was increased, ROS, iron content and abnormal mitochondrial number were decreased. By overexpressing Nox4, the PMWT, PWCD, and ferroptosis of rats were more severe than those of the SNI group, but they could be reversed after treatment with methyl ferulic acid. In conclusion, methyl ferulic acid can alleviate neuropathic pain, which is related to Nox4-induced ferroptosis.

Unsupervised Pre-Training for Detection Transformers.

DEtection TRansformer (DETR) for object detection reaches competitive performance compared with Faster R-CNN via a transformer encoder-decoder architecture. However, trained with scratch transformers, DETR needs large-scale training data and an extreme long training schedule even on COCO dataset. Inspired by the great success of pre-training transformers in natural language processing, we propose a novel pretext task named random query patch detection in Unsupervised Pre-training DETR (UP-DETR). Specifically, we randomly crop patches from the given image and then feed them as queries to the decoder. The model is pre-trained to detect these query patches from the input image. During the pre-training, we address two critical issues: multi-task learning and multi-query localization. (1) To trade off classification and localization preferences in the pretext task, we find that freezing the CNN backbone is the prerequisite for the success of pre-training transformers. (2) To perform multi-query localization, we develop UP-DETR with multi-query patch detection with attention mask. Besides, UP-DETR also provides a unified perspective for fine-tuning object detection and one-shot detection tasks. In our experiments, UP-DETR significantly boosts the performance of DETR with faster convergence and higher average precision on object detection, one-shot detection and panoptic segmentation. Code and pre-training models: https://github.com/dddzg/up-detr.

Phytoremediation with kenaf (Hibiscus cannabinus L.) for cadmium-contaminated paddy soil in southern China: translocation, uptake, and assessment of cultivars.

Kenaf (Hibiscus cannabinus L.) is suitable for growing in heavy metal-polluted soil for non-food purposes and can be used as a potential crop to remediate heavy metal-contaminated soil. The main objective of this study was to investigate kenaf phytoextraction of cadmium (Cd), including uptake, translocation, and accumulation differences in tissues among kenaf cultivars. A field experiment was conducted in a Cd contaminated paddy field in southern China area with 13 kenaf cultivars in 2015 and 2016. Agronomic performance, Cd concentrations in plant tissues (root, xylem, and phloem), and biomass of different tissues of each cultivar were measured and evaluated. Significant differences in Cd concentrations and accumulation among tissues and cultivars were observed. The phloem had the highest Cd accumulation and transfer capability compared with the roots and xylem. Approximately 35 ~ 65 g of Cd could be taken up by the aerial parts of different kenaf cultivars within every hectare of soil. The percentage of Cd uptake by the phloem ranged from 47 to 61% and by the xylem ranged from 38 to 53%. By evaluating the agronomic traits and Cd bioaccumulation capacity, Fuhong 952, Fuhong 992, and Fuhong R1 were regarded as Cd accumulators for the phytoremediation of Cd-contaminated soil. Our study clearly demonstrated that a significant level of Cd in the soil was taken up through the phytoremediation with kenaf. In addition, harmless utilization of kenaf planting in Cd-contaminated paddy soil was discussed.

Multi-omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius).

Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.

Prediction of Left Double-Lumen Tube Size by Measurement of Cricoid Cartilage Transverse Diameter by Ultrasound and CT Multi-Planar Reconstruction.

Background: Currently, there is no uniform standard for selecting the left double lumen tubes (LDLT). Advantages, such as safety and convenience of the ultrasonic technology, and measurement accuracy, make it more widely applied in the clinical anesthesia, and computed tomography (CT) multi-planar reconstruction (MPR) technology will certainly provide a more accurate measurement. For better application for thoracic surgery choice LDLT, relieving the injury to patients, and reducing the complications, this study will compare the two approaches. Methods: The first part, 120 cases of patients were selected according to the height and gender; recording the patient's optimum LDLT and measurement the transverse diameter of the cricoid cartilage (TD-C) by ultrasound and CT MPR, and then obtained the TD-C range measurement by ultrasound and CT MPR corresponding to different types of LDLT. The second part, total of 102 patients were divided into the ultrasound group and the CT MPR group. In the ultrasound group, TD-C was measured by ultrasound, the corresponding size for intubation was selected based on the conclusions derived from the first part. In the CT MPR group, TD-C was measured by CT MPR, the corresponding size of LDLT based on the conclusions derived from the first part. Results: In the first part, 120 patients were no significant difference in the basic characteristics (P > 0.05). The accuracy of selecting the LDLT by conventional experience, namely height and gender was 58.3%. Ultrasonic measurement TD-C range was as follows: 32 Fr <15.88, 35 Fr: 15.88-16.80, 37 Fr: 16.75-17.81, and 39 Fr > 17.80. CT MPR measurement TD-C range was as follows: 32 Fr <15.74, 35 Fr: 15.74-16.65, 37 Fr: 16.56-17.68, and 39 Fr > 17.65. In the second part, there was no significant difference in the basic characteristics between the two groups (P > 0.05). The accuracy of intubation in the ultrasound group was 90.2% and the corresponding in the CT MPR group was 94.1% (P > 0.05). Conclusions: The accuracy of selecting the LDLT based on TD-C is significantly higher than conventional experience; it can significantly reduce the post-operative complications and there was no statistical significance in the accuracy of LDLT selected for TD-C measurement by ultrasound vs. CT, and both of them could be safely used for the evaluation before intubation under anesthesia in thoracic surgery.

Establishment of an Agrobacterium-mediated genetic transformation and CRISPR/Cas9-mediated targeted mutagenesis in Hemp (Cannabis Sativa L.).

Hemp (Cannabis sativa L.) is an annual and typically dioecious crop. Due to the therapeutic potential for human diseases, phytocannabinoids as a medical therapy is getting more attention recently. Several candidate genes involved in cannabinoid biosynthesis have been elucidated using omics analysis. However, the gene function was not fully validated due to few reports of stable transformation for Cannabis tissues. In this study, we firstly report the successful generation of gene-edited plants using an Agrobacterium-mediated transformation method in C. sativa. DMG278 achieved the highest shoot induction rate, which was selected as the model strain for transformation. By overexpressing the cannabis developmental regulator chimera in the embryo hypocotyls of immature grains, the shoot regeneration efficiency was substantially increased. We used CRISPR/Cas9 technology to edit the phytoene desaturase gene and finally generated four edited cannabis seedlings with albino phenotype. Moreover, we propagated the transgenic plants and validated the stable integration of T-DNA in cannabis genome.

Insights into the mechanism of multi-walled carbon nanotubes phytotoxicity in Arabidopsis through transcriptome and m6A methylome analysis.

With the increasing production and wide application of carbon nanotubes (CNTs), they are inevitably released into the natural environment and ecosystems, where plants are the main primary producers. Hence, it is imperative to understand the toxic effects of CNTs on plants. The molecular mechanisms underlying the toxic effects of CNTs on plants are still unclear. Therefore, in the present study, we investigated the effects of high concentrations of multi-walled CNTs (MWCNTs) on Arabidopsis. Root elongation and leaf development were severely inhibited after MWCNT exposure. Excess production of H2O2, O2-, and malondialdehyde was observed, indicating that MWCNTs induced oxidative stress. The antioxidant system was activated to counter MWCNTs-induced oxidative stress. Combinatorial transcriptome and m6A methylome analysis revealed that MWCNTs suppressed auxin signaling and photosynthesis. Reactive oxygen species metabolism, toxin metabolism, and plant responses to pathogens were enhanced to cope with the phytotoxicity of MWCNTs. Our results provide new insights into the molecular mechanisms of CNT phytotoxicity and plant defense responses to CNTs.

Differential Proteomic Analysis to Identify Proteins Associated with Apomeiosis in Boehmeria tricuspis (Hance) Makino Using an iTRAQ-Based Strategy.

Numerous candidate genes related to apomixis have been identified through transcriptomics; however, the molecular mechanism underlying apomixis remains unclear. Elucidation of the underlying mechanisms is essential to expand its application in crop breeding. Therefore, here, we employed the isobaric tags for a relative and absolute quantification labeling technology to investigate the protein expression in Boehmeria tricuspis generated through different reproductive modes at the functional megaspore stage. We identified 40 differential abundance proteins associated with apomeiosis, most of which were involved in "response to stress". Functional analysis suggested that lower levels of reactive oxygen species (ROS) play a role in inducing the development of apomeiosis. Proteins related to ROS regulation, cell wall modifications, and stability under heat stress play a crucial role in the development of diplosporic apomeiosis. Our results give evidence to the insight that stress can induce a switch from apomixis to sexuality by ROS content, and an increased composition of stress tolerance as well as secondary metabolites can buffer ROS effects. Precise coordination of these proteins involved in inter-related regulatory control mechanisms may act together in the transition from the sexual to apomixis development.

Isoflurane post-conditioning attenuates cerebral ischemia/reperfusion injury by reducing apoptotic through activating the BMP7/SMAD signaling pathway in rats.

The expressions of different temporal patterns of bone morphogenetic proteins (BMPs) have changed after ischemic strokes, and ischemic preconditioning-induced neuroprotection was attenuated when BMP7 was inhibited. In the previous study, the neuroprotection of isoflurane postconditioning (ISPOC) against cerebral ischemia-reperfusion (I/R) injury has been addressed, with particular relevance to the role of BMP7. Consequently, in the present study, we continued to explore the mechanisms involved in the BMP7 signal mediated the neuroprotection of ISPOC. A rat model of the middle cerebral artery occlusion was used in this study. Rats were administered 1.5 % isoflurane, 60 min after 90 min of ischemia, followed by a 24 h reperfusion period. The 1.5 % ISPOC significantly ameliorated the cerebral infarct volumes, neurologic deficit scores, damaged neurons, and apoptotic neurons. Moreover, ISPOC unregulated the expressions of BMP7, p-Smad1/5/9, and p-p38. Whereas, the neuroprotective effect was weakened by LDN-193189 and SB203580, respectively, a BMP7/Smad1/5/9 and p38MAPK signaling pathway inhibitor. Furthermore, LDN-193189 downregulated the expression of p-p38. The present results of this study indicated that the neuroprotection of 1.5 % isoflurane postconditioning to cerebral ischemia-reperfusion injury is related to the activating of BMP7/Smad1/5/9 and p38MAPK signal pathway.

Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.).

BACKGROUND: Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species. RESULTS: There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue. CONCLUSION: We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops.

Isoflurane Postconditioning Upregulates Phosphorylated Connexin 43 in the Middle Cerebral Artery Occlusion Model and Is Probably Associated with the TGF-ß1/Smad2/3 Signaling Pathway.

AIM: Connexin 43 (Cx43) has been identified to be important for cerebral ischemia/reperfusion (I/R) injury as well as protection from it. This study was aimed at investigating the relationship between phosphorylated Cx43 (p-Cx43), transforming growth factor-ß1 (TGF-ß1 (TGF. METHODS: The middle cerebral artery occlusion (MCAO) model was induced in 96 male Sprague-Dawley rats, weighing 250-300 g. The rats were randomized into 12 groups, namely, sham, middle cerebral artery occlusion (MCAO)/I/R, I/R+1.5% ISPOC, I/R+LY2157299 (blocker of TGF-ß1 (TGF-ß1 (TGF-ß1 (TGF-ß1 (TGF. RESULTS: Neurological deficit scores, brain infarct volume, and damaged neurons in the I/R group significantly increased compared to those in the sham group (P < 0.05). However, in the ISPOC group, damage of the brain was significantly ameliorated (P < 0.05). However, in the ISPOC group, damage of the brain was significantly ameliorated (P < 0.05). However, in the ISPOC group, damage of the brain was significantly ameliorated (ß1 (TGF-P < 0.05). However, in the ISPOC group, damage of the brain was significantly ameliorated (ß1 (TGF-P < 0.05). However, in the ISPOC group, damage of the brain was significantly ameliorated (ß1 (TGF-ß1 (TGF-P < 0.05). However, in the ISPOC group, damage of the brain was significantly ameliorated (. CONCLUSION: Isoflurane postconditioning (ISPOC) may alleviate cerebral I/R injury through upregulating the expression of p-Cx43, and the TGF-ß1/Smad2/3 signaling pathway may be involved in the process.ß1 (TGF.

Construction of a high-resolution genetic map and identification of quantitative trait loci for salt tolerance in jute (Corchous spp.).

BACKGROUND: Jute (Corchorus spp.) is the most important natural fiber crop after cotton in terms of cultivation area and production. Salt stress greatly restricts plant development and growth. A high-density genetic linkage map is the basis of quantitative trait locus (QTLs) mapping. Several high-density genetic maps and QTLs mapping related to salt tolerance have been developed through next-generation sequencing in many crop species. However, such studies are rare for jute. Only several low-density genetic maps have been constructed and no salt tolerance-related QTL has been mapped in jute to date. RESULTS: We developed a high-density genetic map with 4839 single nucleotide polymorphism markers spanning 1375.41 cM and an average distance of 0.28 cM between adjacent markers on seven linkage groups (LGs) using an F2 jute population, LGs ranged from LG2 with 299 markers spanning 113.66 cM to LG7 with 1542 markers spanning 350.18 cM. In addition, 99.57% of gaps between adjacent markers were less than 5 cM. Three obvious and 13 minor QTLs involved in salt tolerance were identified on four LGs explaining 0.58-19.61% of the phenotypic variance. The interval length of QTL mapping varied from 1.3 to 20.2 cM. The major QTL, qJST-1, was detected under two salt stress conditions that explained 11.81 and 19.61% of the phenotypic variation, respectively, and peaked at 19.3 cM on LG4. CONCLUSIONS: We developed the first high-density and the most complete genetic map of jute to date using a genotyping-by-sequencing approach. The first QTL mapping related to salt tolerance was also carried out in jute. These results should provide useful resources for marker-assisted selection and transgenic breeding for salt tolerance at the germination stage in jute.

TGF-ß2 Induces Gli1 in a Smad3-Dependent Manner Against Cerebral Ischemia/Reperfusion Injury After Isoflurane Post-conditioning in Rats.

Isoflurane (ISO) post-conditioning attenuates cerebral ischemia/reperfusion (I/R) injury, but the underlying mechanism is incompletely elucidated. Transforming growth factor beta (TGF-ß) and hedgehog (Hh) signaling pathways govern a wide range of mechanisms in the central nervous system. We aimed to investigate the effect of the TGF-ß2/Smad3 and sonic hedgehog (Shh)/Glioblastoma (Gli) signaling pathway and their crosstalk in the hippocampus of rats with ISO post-conditioning after cerebral I/R injury. Adult male Sprague-Dawley rats were subjected to middle cerebral artery occlusion (MCAO), 1.5 h occlusion and 24 h reperfusion (MCAO/R). To assess the effect of ISO after I/R injury, various approaches were used, including neurobehavioral tests, TTC staining, HE staining, Nissl staining, TUNEL staining, immunofluorescence (IF), qRT-PCR (quantitative real-time polymerase chain reaction) and Western blot. The ISO post-conditioning group (ISO group) received 1 h ISO post-conditioning when reperfusion was initiated, leading to lower infarct volumes and neurologic deficit scores, more surviving neurons, and less damaged and apoptotic neurons. IF staining, qRT-PCR and Western blot showed high expression levels of TGF-ß2, Shh and Gli1 in the hippocampal CA1 of the ISO group. Phosphorylated Smad3 (p-Smad3), Patched (Ptch), and Smoothed (Smo) were also increased at protein level in the ISO group, whereas total Smad3 expression did not change in all groups. When TGF-ß2 inhibitor, pirfenidone, or Smad3 inhibitor, SIS3 HCl, were administered, the expression levels of p-Smad3 and Gli1 were reduced, and surviving pyramidal neurons decreased. By contrast, the expression levels of TGF-ß2 and p-Smad3 did not change significantly after pre-injection of Smo inhibitor cyclopamine, but reduced the expression levels of Shh, Ptch, and Gli1. Moreover, Gli showed the lowest expression levels with pirfenidone combined with cyclopamine. These findings indicate that the TGF-ß and hedgehog signaling pathways mediate the neuroprotection of ISO post-conditioning after cerebral I/R injury, and crosstalk between two pathways at the Gli1 level.

Combined genome-wide association analysis and transcriptome sequencing to identify candidate genes for flax seed fatty acid metabolism.

Flax seeds have a high oil content and are rich in unsaturated fatty acids, which have advantageous effects in preventing chronic diseases, such as cardiovascular diseases. At present, flax seeds are mainly developed for oil. Therefore, it is of practical significance to identify the candidate genes of fatty acid metabolism in flax seeds for breeding flax seeds with high oil content. In the present study, a natural population of flax containing 224 samples planted in 3 different environments was studied. The genome-wide association analysis (GWAS) of seed fatty acid content was conducted based on specific length amplified fragment sequencing (SLAF-seq) data. Transcriptome sequencing (RNA-seq) of samples from 3 different periods (14 d, 21 d and 28 d after anthesis) during seed development of the low oil variety Shuangya 4 and the high oil variety NEW was performed. The candidate genes for seed fatty acid metabolism were identified by combined analysis of these 2 methods. GWAS detected 16 SNP loci significantly associated with seed fatty acid content, and RNA-seq analysis identified 11,802 differentially expressed genes between high and low oil samples. Pathway enrichment analysis revealed that some differentially expressed genes were classified into fatty acid-related pathways. After comparison of these differentially expressed genes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 20 genes homologous to other species were obtained. After analysis, 10 candidate genes were screened by GWAS and RNA-seq screening. Of these 10 genes, qRT-PCR assays using flax seeds in 5 different developmental stages showed that the expression levels of 6 candidate genes were significantly correlated with 5 fatty acid contents in seeds of the high oil variety NEW. Through metabolic pathway analysis found that 6 genes were involved in important fatty acid metabolic pathways, and some of them also have upstream and downstream regulation relations. The present study combined GWAS and RNA-seq methods to identify candidate genes for fatty acid metabolism in flax seeds, which provided reference for screening of candidate genes with complex traits.

A Full-Length Reference Floral Transcriptome of Boehmeria tricuspis Provides Insights into Apomeiosis and Polyploidy.

Boehmeria tricuspis (Hance) Makino constitutes a hardy herbaceous or shrubby perennial native to East Asia that includes different ploidy levels and reproductive modes (diplosporous to sexual). Although several apomeiosis-associated genes have been described, the genetic control and molecular mechanisms underlying apomeiosis remain poorly understood. Moreover, the basis of the correlation between polyploidy and apomixis has not yet been clarified. We utilized long-read sequencing to produce a full-length reference floral transcriptome of B. tricuspis. Based on the generated database, gene expression of the female flowers of different ploidy levels and reproductive mode cytotypes was compared. Overall, 1,387 genes related to apomeiosis, 217 genes related to ploidy, and 9 genes associated with both apomixis and ploidy were identified. Gene Ontology analyses of this set of transcripts indicated reproductive genes, especially those related to "cell differentiation" and "cell cycle process," as significant factors regulating apomeiosis. Furthermore, our results suggested that different expressions of stress response genes might be important in the preparation for apomeiosis transition. In addition, our observations indicated that the expression of apomeiosis may not depend on polyploidy but rather on deregulation of the sexual pathway in B. tricuspis.

Wnt/ß-catenin signaling pathway contributes to isoflurane postconditioning against cerebral ischemia-reperfusion injury and is possibly related to the transforming growth factorß1/Smad3 signaling pathway.

AIM: The Wnt/ß-catenin signaling pathway plays an important role in ischemia-reperfusion(I/R) injury, and the transforming growth factor(TGF)-ß/Smad signaling pathway participates in the neuroprotection effect induced by isoflurane(ISO) postconditioning. In this study, we aimed to explore the role of the Wnt/|[beta]|-catenin ß-catenin signaling pathway in the neuroprotection effect induced by ISO postconditioning, and investigate the interaction of Wnt/ß-catenin and TGF-ß/Smad signaling pathway in this neuroprotection effect. METHODS: Cerebral I/R injury was established in Sprague-Dawley rats by using the middle cerebral artery occlusion (MCAO) model for 90 min followed by 24 h reperfusion. Postconditioning by inhalation of ISO was performed for 60 min after ischemia at the onset of reperfusion. Neurological deficit scoring, 2,3,5-triphenyl tetrazolium chloride staining and Nissl staining were adopted to evaluate brain injury. Apoptosis of the hippocampus and cortex neurons was detected by TUNEL staining. The expression levels of Wnt3a, GSK-3ß, ß-catenin, Cyclin D1, VEGF, Caspase 3, TGF-ß1, Smad3 and p-Smad3 were determined by immunofluorescence (IF) staining, quantitative real-time polymerase chain reaction (qRT-PCR), and Western blot. Various targeted inhibitors were administered via intraperitoneal injection or lateral ventricle injection. RESULTS: In the cortex region, the neurological deficit score, infarct volumes and neuron apoptosis increased, and the expression level of the Wnt3a, GSK-3ß, ß-catenin, VEGF and Cyclin D1 decreased in the MCAO group compared with the Sham group. In the MCAO + ISO group, the neurological deficit score, infarct volumes and neuron apoptosis reduced significantly, the expression levels of Wnt3a, ß-catenin, VEGF and Cyclin D1 increased, while the expression level of GSK-3ß and Caspase 3 decreased relative to MCAO group. When Wnt inhibitor(DKK-1) was given in advance followed by ISO postconditioning, the neurological deficit score, infarct volumes, neuron apoptosis and the expression level of GSK-3ß and Caspase 3 increased. qRT-PCR and IF showed similar changes in the protein levels of all groups. However, the expression level of ß-catenin in nuclear and cytoplasm both decreased significantly after pre-injection with the TGF-ß1 inhibitor(LY2157299) and Smad3 inhibitor(SIS3), whereas the expression levels of TGF-ß1, Smad3 and p-Smad3 were almost unchanged. The expression levels of all the related proteins and morphological changes in the hippocampus region were consistent with that of the cortex. CONCLUSION: ISO postconditioning can reduce cerebral I/R injury by activating the Wnt/ß-catenin signaling pathway and may be related to the TGF-ß/Smad3 signaling pathway.