Identification and functional analysis of a chromosome 2D fragment harboring TaFPF1 gene with the potential for yield improvement using a late heading wheat mutant.

KEY MESSAGE: A chromosome fragment influencing wheat heading and grain size was identified using mapping of m406 mutant. The study of TaFPF1 in this fragment provides more insights into wheat yield improvement. In recent years, wheat production has faced formidable challenges driven by rapid population growth and climate change, emphasizing the importance of improving specific agronomic traits such as heading date, spike length, and grain size. To identify potential genes for improving these traits, we screened a wheat EMS mutant library and identified a mutant, designated m406, which exhibited a significantly delayed heading date compared to the wild-type. Intriguingly, the mutant also displayed significantly longer spike and larger grain size. Genetic analysis revealed that a single recessive gene was responsible for the delayed heading. Surprisingly, a large 46.58 Mb deletion at the terminal region of chromosome arm 2DS in the mutant was identified through fine mapping and fluorescence in situ hybridization. Thus, the phenotypes of the mutant m406 are controlled by a group of linked genes. This deletion encompassed 917 annotated high-confidence genes, including the previously studied wheat genes Ppd1 and TaDA1, which could affect heading date and grain size. Multiple genes in this region probably contribute to the phenotypes of m406. We further investigated the function of TaFPF1 using gene editing. TaFPF1 knockout mutants showed delayed heading and increased grain size. Moreover, we identified the direct upstream gene of TaFPF1 and investigated its relationship with other important flowering genes. Our study not only identified more genes affecting heading and grain development within this deleted region but also highlighted the potential of combining these genes for improvement of wheat traits.

Association between systemic immune-inflammation index and post-stroke depression: a cross-sectional study of the national health and nutrition examination survey 2005-2020.

Background: Less research has linked the Systemic Immune Inflammatory Index (SII) with post-stroke depression (PSD). This study aims to look at any potential connections between SII and PSD. Methods: The National Health and Nutrition Examination Survey (NHANES), conducted in a population that embodied complete SII and stroke data from 2005 to 2020, was used to perform the current cross-sectional survey. A fitted smoothed curve was used to depict the nonlinear link between SII and PSD, and multiple linear regression analysis demonstrated a positive correlation between SII and PSD. Results: Multiple linear regression analysis showed that SII and PSD were markedly related [1.11(1.05, 1.17)]. Interaction tests showed that the association between SII and PSD was not statistically different between strata, and age, sex, BMI, income poverty ratio, education level, smoking status, diabetes mellitus, coronary heart disease, and heart failure did not have a significant effect on this positive association (p > 0.05 for interaction). In addition, a nonlinear association between SII and PSD was found using a two-stage linear regression model. Conclusion: The results of our research support the existence of a significant positive correlation between SII levels and PSD. Further prospective trials are required to comprehend SII, which is for the PSD thoroughly.

Ultrasound Microbubble-Stimulated miR-145-5p Inhibits Malignant Behaviors of Breast Cancer Cells by Targeting ACTG1.

ABSTRACT: Ultrasound-targeted microbubble destruction (UTMD) technology combines ultrasound with a variety of functional microbubble vectors to enhance the transfection and expression of target genes, and has become a promising noninvasive method for localized gene transfer, which is widely used in gene therapy for cancer. This research aimed to explore the role of UTMD-mediated miR-145-5p on breast cancer (BC) tumorigenesis and the underlying mechanisms. To achieve UTMD-mediated miR-145-5p overexpression, BC cells were cotransfected with microbubbles (MBs) and miR-145-5p mimics. The BC cell malignant phenotypes were assessed through CCK-8, wound healing, and transwell assays. MiR-145-5p and actin gamma 1 (ACTG1) binding relationship was verified through luciferase reporter and RNA pull-down assays. MiR-145-5p and ACTG1 levels in BC cells and tissues were detected through RT-qPCR and Western blotting. ACTG1 was upregulated, whereas miR-145-5p was downregulated in BC cells and tissues. MiR-145-5p targeted ACTG1 and negatively regulated its level in BC cells. Overexpressing miR-145-5p restrained BC cell growth, migration, and invasion. Ultrasound-targeted microbubble destruction improved the overexpression efficiency of miR-145-5p and enhanced the suppressive influence on BC cell malignant phenotypes. In addition, ACTG1 overexpression compromises the repression of UTMD-mediated miR-145-5p on cellular behaviors in BC. Ultrasound-targeted microbubble destruction-delivered miR-145-5p hindered malignant behaviors of BC cells through downregulating ACTG1.

Predicting the effects of mutations on protein solubility using graph convolution network and protein language model representation.

Solubility is one of the most important properties of protein. Protein solubility can be greatly changed by single amino acid mutations and the reduced protein solubility could lead to diseases. Since experimental methods to determine solubility are time-consuming and expensive, in-silico methods have been developed to predict the protein solubility changes caused by mutations mostly through protein evolution information. However, these methods are slow since it takes long time to obtain evolution information through multiple sequence alignment. In addition, these methods are of low performance because they do not fully utilize protein 3D structures due to a lack of experimental structures for most proteins. Here, we proposed a sequence-based method DeepMutSol to predict solubility change from residual mutations based on the Graph Convolutional Neural Network (GCN), where the protein graph was initiated according to predicted protein structure from Alphafold2, and the nodes (residues) were represented by protein language embeddings. To circumvent the small data of solubility changes, we further pretrained the model over absolute protein solubility. DeepMutSol was shown to outperform state-of-the-art methods in benchmark tests. In addition, we applied the method to clinically relevant genes from the ClinVar database and the predicted solubility changes were shown able to separate pathogenic mutations. All of the data sets and the source code are available at https://github.com/biomed-AI/DeepMutSol.

Identification of the early leaf senescence gene ELS3 in bread wheat (Triticum aestivum L.).

MAIN CONCLUSION: Characterization of the early leaf senescence mutant els3 and identification of its causal gene ELS3, which encodes an LRR-RLK protein in wheat. Leaf senescence is an important agronomic trait that affects both crop yield and quality. However, few senescence-related genes in wheat have been cloned and functionally analyzed. Here, we report the characterization of the early leaf senescence mutant els3 and fine mapping of its causal gene ELS3 in wheat. Compared with wild-type Yanzhan4110 (YZ4110), the els3 mutant had a decreased chlorophyll content and a degraded chloroplast structure after the flowering stage. Further biochemical assays in flag leaves showed that the superoxide anion and hydrogen peroxide contents increased, while the activities of antioxidant enzymes, including catalase, superoxide dismutase and glutathione reductase, decreased gradually after the flowering stage in the els3 mutant. To clone the causal gene underlying the phenotype of leaf senescence, a genetic map was constructed using 10,133 individuals of F2:3 populations, and ELS3 was located in a 2.52 Mb region on chromosome 2DL containing 16 putative genes. Subsequent sequence analysis and gene annotation identified only one SNP (C to T) in the first exon of TraesCS2D02G332700, resulting in an amino acid substitution (Pro329Ser), and TraesCS2D02G332700 was preliminarily considered as the candidate gene of ELS3. ELS3 encodes a leucine-rich repeat receptor-like kinase (LRR-RLK) protein that is localized on the cell membrane. We also found that the transient expression of mutant TraesCS2D02G332700 can induce leaf senescence in N. benthamiana. Taken together, TraesCS2D02G332700 is likely to be the candidate gene of ELS3 and may have a function in regulating leaf senescence.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement.

Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.

Retrospective analysis of the endometrial preparation protocols for frozen-thawed embryo transfer cycles in women with endometriosis.

BACKGROUND: There was inconsistency in optimal endometrial preparation protocol for frozen-thawed embryo transfer (FET) in patients with endometriosis. We conducted this study to investigate the effect of different endometrial preparation protocols on the pregnancy outcomes in patients with endometriosis undergoing FET cycles, and determine the optimal number of GnRHa injections in GnRHa-HRT protocols. METHOD(S): This was a retrospective cohort analysis of women with endometriosis who underwent FET cycles at a single university-based center. This study retrospectively analyzed 2048 FET cycles in our center from 2011 to 2020. According to the endometrial preparation protocols, patients were divided into 4 groups: gonadotropin releasing hormone agonist-hormone replacement therapy(GnRHa-HRT), hormone replacement therapy(HRT), ovulation induction(OI), and natural cycle(NC). In the GnRHa-HRT group, patients were further divided into 3 groups: one injection of GnRHa, two injections of GnRHa, and three or more injections of GnRHa. The primary outcome was the clinical pregnancy rate. Propensity score matching was used to adjust for potential non-similarities among the groups. Multivariate logistic regression analysis was performed to figure out the risk factors for pregnancy outcomes. RESULT(S): There were no statistical differences in pregnancy outcomes among the four endometrial preparation protocols in FET cycles with endometriosis patients, the results retained after propensity score matching(PSM). And in endometriosis patients complicated with adenomyosis, the results remained similar. In patients with GnRHa-HRT protocol, there were no differences in clinical pregnancy rate and live birth rate with different numbers of GnRHa injections, the early miscarriage rate were 18% in the two injections of GnRHa group and 6.5% in the one injection of GnRHa group(P = 0.017). Multifactorial logistic regression analysis showed that two injections of GnRHa before FET was associated with increased early miscarriage rate compared with one injection of GnRHa[adjusted OR (95% CI): 3.116(1.079-8.998),p = 0.036]. CONCLUSION(S): The four kinds of endometrial preparation protocols for FET, GnRHa-HRT, HRT, OI and NC had similar pregnancy outcomes in patients with endometriosis. In endometriosis patients complicated with adenomyosis, the results remained similar. In patients with endometriosis undergoing GnRHa-HRT protocol for FET, more injections of GnRHa had no more advantages in pregnancy outcomes, on the contrary, it might increase the early miscarriage rate.

A Glu209Lys substitution in DRG1/TaACT7, which disturbs F-actin organization, reduces plant height and grain length in bread wheat.

Plant height and grain size are two important agronomic traits that are closely related to crop yield. Numerous dwarf and grain-shape mutants have been studied to identify genes that can be used to increase crop yield and improve breeding programs. In this study, we characterized a dominant mutant, dwarf and round grain 1 (drg1-D), in bread wheat (Triticum aestivum L.). drg1-D plants exhibit multiple phenotypic changes, including dwarfism, round grains, and insensitivity to brassinosteroids (BR). Cell structure observation in drg1-D mutant plants showed that the reduced organ size is due to irregular cell shape. Using map-based cloning and verification in transgenic plants, we found that a Glu209Lys substitution in the DRG1 protein is responsible for the irregular cell size and arrangement in the drg1-D mutant. DRG1/TaACT7 encodes an actin family protein that is essential for polymerization stability and microfilament (MF) formation. In addition, the BR response and vesicular transport were altered by the abnormal actin cytoskeleton in drg1-D mutant plants. Our study demonstrates that DRG1/TaACT7 plays an important role in wheat cell shape determination by modulating actin organization and intracellular material transport, which could in the longer term provide tools to better understand the polymerization of actin and its assembly into filaments and arrays.

Potential active compounds and common mechanisms of Evodia rutaecarpa for Alzheimer's disease comorbid pain by network pharmacology analysis.

Evodia rutaecarpa (Evodia) is a Chinese herbal medicine with analgesic and anti-neurodegenerative properties. However, whether Evodia compounds can be applied for the comorbid pain of Alzheimer's disease (AD) and the underlying mechanisms remain unclear. Herein, 137 common targets of Evodia between AD and pain were predicted from drug and disease target databases. Subsequently, protein-protein interaction (PPI) network, protein function module construction, and bioinformatics analyses were used to analyze the potential relationship among targets, pathways, and diseases. Evodia could simultaneously treat AD comorbid pain through multi-target, multi-component, and multi-pathway mechanisms, and inflammation was an important common phenotype of AD and pain. The relationship between important transcription factors such as RELA, NF-κB1, SP1, STAT3, and JUN on IL-17, TNF, and MAPK signaling pathways might be potential mechanisms of Evodia. Additionally, 10 candidate compounds were predicted, and evodiamine might be the effective active ingredient of Evodia in treating AD or pain. In summary, this study provided a reference for subsequent research and a novel understanding and direction for the clinical use of evodiamine to treat AD patients with comorbid pain.

Removal characteristics of microplastics in sewage flowing through a long-term operation surface flow wetland.

Microplastics (MPs) in sewage pose significant threats to aquatic system. Surface flow wetland (SFW) is a common natural wetland type, and is also used as a cheap and easy-to-build sewage treatment system for small and scattered settlements. However, seasonal variation patterns of MPs in sewage removed by SFW are still limited. Therefore, a field investigation was conducted in an SFW that has been operated for 17 years. The concentration of microplastics in the influent of the SFW (CMPs, in) ranged from 56 ± 6 to 250 ± 14 items L-1. The dominant plastic types were fibers and polyethylene terephthalate (PET). CMPs, in were high in summer and winter, significantly related to the seasonal dressing habits. The removal efficiencies of MPs in SFW were 48.03-92.32 % in different seasons, and the mechanisms of MP removal were different with traditional pollutants. Before flowing out occasionally or by heavy precipitation, MPs were primarily trapped in the SFW and underwent certain oxidation. Simulation experiments demonstrated that 47.5-92.9 % of MPs would be trapped in the SFW, and plants would significantly enhance the trapping capacities. This study sheds light on the seasonal variation characteristics and patterns of MPs in actual sewage, and clarifies the fate of MPs in a long-term operation SFW.

GSK3 regulates VRN1 to control flowering time in wheat.

GLYCOGEN SYNTHASE KINASE 3 physically interacts with VRN1 and regulates its accumulation to mediate flowering in wheat.

Extracellular matrix-regulator MMPA is required for the orderly proliferation of neoblasts and differentiation of ectodermal progenitor cells in the planarian Dugesia japonica.

Matrix metalloproteinases (MMPs) are members of a family of zinc-dependent metallopeptidase proteins that are widely found in plants, animals, and microorganisms. As the regulators of the extracellular matrix and basement membrane, MMPs play an important role in embryogenesis, development, innate immunity, and regeneration. However, the function of MMP family in planarian, a model for regeneration research, is still ambiguous. Here, we cloned 5 MMPs genes from Dugesia japonica and found that DjMMPA was associated with the process of regeneration, neoblasts cell maintenance confusion and destruction. Loss of DjMMPA led to homeostasis confusion and eventually death, owing to neoblasts proliferation disorder. Additionally, DjMMPA RNAi-treated animals had impaired regeneration after amputation. Furthermore, knockdown of DjMMPA had noticeable defects in cell differentiation of ectoderm, especially in eyes and neural progenitor cells, possibly by inhibiting Wnt signaling. Our results suggest that extracellular matrix-regulator MMPA is required for the orderly proliferation of neoblasts and differentiation of ectodermal progenitor cells in the planarian, which provide valuable information for further explorations into the molecular mechanism of MMPS, stem cells, and regeneration.

HIGD1A inactivated by DNA hypermethylation promotes invasion of kidney renal clear cell carcinoma.

Hypoxia contributes to the tumorigenesis and metastasis of the tumor. However, the detailed mechanisms underlying hypoxia and kidney renal clear cell carcinoma (KIRC) development and progression remain unclear. Here, we investigated the role of the system HIG1 hypoxia inducible domain family member 1 A (HIGD1A) in the proliferation and metastasis of KIRC and elucidated the underlying molecular mechanisms. The expression of HIGD1A is significantly downregulated in KIRC due to promoter hypermethylation. HIGD1A could serve as a valuable diagnostic biomarker in KIRC. In addition, ectopic overexpression of HIGD1A significantly suppressed the growth and invasive capacity of KIRC cells in vitro under normal glucose conditions. Interestingly, the suppressive efficacy in invasion is much more significant when depleted glucose, but not in proliferation. Furthermore, mRNA expression of HIGD1A positively correlates with CDH1 and EPCAM, while negatively correlated with VIM and SPARC, indicating that HIGD1A impedes invasion of KIRC by regulating epithelial-mesenchymal transition (EMT). Our data suggest that HIGD1A is a potential diagnostic biomarker and tumor suppressor in KIRC.

Deficits in psychological resilience and problem-solving ability in adolescents with suicidal ideation.

OBJECTIVES: This study aimed to explore differences between psychological resilience and problem-solving ability in grade one junior middle school adolescents with and without suicidal ideation, focusing on the relationship between these factors and suicidal ideation. METHODS: Ninety-nine adolescents (aged 10 to 14) were divided into Suicidal Ideation (SI, n = 49) and Non-Suicidal Ideation (NSI, n = 50) grouped by the Self-rating Idea of Suicide Scale (SIOSS). The Psychological Resilience Scale (PRS) and Tower of Hanoi task (TOH) were applied to assess psychological resilience and problem-solving ability, respectively. RESULTS: The SI group scored significantly lower than the NSI group on PRS (p < 0.001) and performed more poorly on TOH than the NSI group, with more mistakes in the number of errors index (p < 0.001) and requiring a longer time in the task completion time index (p < 0.05). Among all the participants in this study, a significant negative correlation was observed between PRS and SIOSS (r = - 0.413, p < 0.01). The sub-dimensions of PRS including emotional control, family support, and interpersonal assistance were significantly negatively correlated with the SIOSS total score (r = - 0.361, - 0.360, - 0.382; p < 0.01). CONCLUSIONS: This study profiled the characteristics and differences in psychological resilience and problem-solving ability between adolescents with and without suicidal ideation. The data suggested adolescents with SI might have deficits in psychological resilience and problem-solving ability, which may serve as potential targets for suicide intervention.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat.

Wheat (Triticum aestivum, BBAADD) is an allohexaploid species that originated from two polyploidization events. The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii, respectively. Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome. However, whether Ae. speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae. speltoides and the B subgenome remain unclear. Here, we assembled a high-quality reference genome for Ae. speltoides, resequenced 53 accessions from seven species (Aegilops bicornis, Aegilops longissima, Aegilops searsii, Aegilops sharonensis, Ae. speltoides, Aegilops mutica [syn. Amblyopyrum muticum], and Triticum dicoccoides) and revealed their genomic contributions to the wheat B subgenome. Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae. speltoides and the B subgenome. We classified five groups of conserved and non-conserved genes between Aegilops and Triticum, revealing their biological characteristics, differentiation in gene expression patterns, and collinear relationships between Ae. speltoides and the wheat B subgenome. We also identified gene families that expanded in Ae. speltoides during its evolution and 789 genes specific to Ae. speltoides. These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress. The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.

Subfertile Chinese patients with diminished ovarian reserve: An analysis of pregnancy outcomes of ART cycles.

Objective: To analyze the pregnancy outcomes of patients presenting with infertility solely due to diminished ovarian reserve (DOR) and treated by assisted reproductive technology (ART), including artificial insemination by husband (AIH) and in vitro fertilization (IVF). Methods: This was a retrospective study of subfertile patients due to DOR attending the Center for Reproductive Medicine in Guangzhou, China, between January 2010 and October 2015. Patients were assigned into either the AIH or IVF group. Within each group, these patients were further subgrouped based on their serum basal follicle-stimulating hormone (bFSH) level (10 ≤ bFSH ≤ 12IU/L and bFSH > 12IU/L) and age (20-30, 31-35, 36-40, and 41-45 years). The live birth rates were compared among these groups and subgroups. Result: A total of 1,003 patients with a median age of 38.91 (21-45) years were enrolled in the study. The live birth rate following AIH was 5.61% (25/446), which was significantly lower than that following IVF (25.13%; 140/557). In the subgroup analysis, the cumulative live birth rates in AIH group were significantly lower than those in the IVF groups (in the 10-12 IU/L bFSH subgroup, 13.74% vs. 41.13% (P<0.05) for patients aged ≤35 years, and 4.82% vs. 19.77% (P<0.05) for patients aged >35 years; in the >12 IU/L bFSH subgroup, 9.52% vs. 29.91% (P<0.05) for patients aged ≤35 years, and 5.71% vs. 20.55% (P<0.05) for patients aged >35 years). Longitudinal analysis showed that majority of live births, in AIH or IVF groups, were achieved in the first two cycles. Conclusions: In subfertile women with DOR, live birth rates following AIH were significantly lower than IVF, especially for the aged women. Considering the low efficacy of AIH and that majority of live births were achieved in the first two cycles, we suggest no more than two AIH treatment attempts for the aged women with DOR.

Corrosion Inhibition Mechanism of Ultra-High-Temperature Acidizing Corrosion Inhibitor for 2205 Duplex Stainless Steel.

The acidizing corrosion inhibitors reported so far have a poor effect on duplex stainless steel in high-temperature and high-concentration acid systems and cannot effectively inhibit the occurrence of selective corrosion. In this paper, a new acidizing corrosion inhibitor was designed, which was mainly composed of Mannich base and antimony salt. The inorganic substance in the corrosion inhibitor had good stability at high temperatures and could quickly form a complex with the metal matrix to enhance the binding ability. The organic substance can make up for the non-dense part of the inorganic film. The properties of developed corrosion inhibitors were analyzed by quantum chemical calculation, molecular dynamics simulation, and scanning electron microscopy. The results showed that a double-layer membrane structure could be constructed after adding the corrosion inhibitor, which could play a good role in blocking the diffusion of acid solution at high-temperature. The uniform corrosion rate of 2205 duplex stainless steel after adding acidizing corrosion inhibitor immersion in a simulated service condition (9 wt.% HCl + 1.5 wt.% HF + 3 wt.% CH3COOH + 4~6 wt.%) at 140 °C, 160 °C and 180 °C for a 4 h test is 6.9350 g·m-2·h-1, 6.3899 g·m-2·h-1 and 12.1881 g·m-2·h-1, respectively, which shows excellent corrosion inhibition effect and is far lower than that of the commonly accepted 81 g·m-2·h-1 and no selective corrosion could be detected.

GSK3 phosphorylates and regulates the Green Revolution protein Rht-B1b to reduce plant height in wheat.

The utilization of stabilized DELLA proteins Rht-B1b and Rht-D1b was crucial for increasing wheat (Triticum aestivum) productivity during the Green Revolution. However, the underlying mechanisms remain to be clarified. Here, we cloned a gain-of-function allele of the GSK3/SHAGGY-like kinase-encoding gene GSK3 by characterizing a dwarf wheat mutant. Furthermore, we determined that GSK3 interacts with and phosphorylates the Green Revolution protein Rht-B1b to promote it to reduce plant height in wheat. Specifically, phosphorylation by GSK3 may enhance the activity and stability of Rht-B1b, allowing it to inhibit the activities of its target transcription factors. Taken together, we reveal a positive regulatory mechanism for the Green Revolution protein Rht-B1b by GSK3, which might have contributed to the Green Revolution in wheat.