Pan-Genome of Wild and Cultivated Soybeans.

Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.

Chemical interference with DSIF complex formation lowers synthesis of mutant huntingtin gene products and curtails mutant phenotypes.

Earlier work has shown that siRNA-mediated reduction of the SUPT4H or SUPT5H proteins, which interact to form the DSIF complex and facilitate transcript elongation by RNA polymerase II (RNAPII), can decrease expression of mutant gene alleles containing nucleotide repeat expansions differentially. Using luminescence and fluorescence assays, we identified chemical compounds that interfere with the SUPT4H-SUPT5H interaction and then investigated their effects on synthesis of mRNA and protein encoded by mutant alleles containing repeat expansions in the huntingtin gene (HTT), which causes the inherited neurodegenerative disorder, Huntington's Disease (HD). Here we report that such chemical interference can differentially affect expression of HTT mutant alleles, and that a prototypical chemical, 6-azauridine (6-AZA), that targets the SUPT4H-SUPT5H interaction can modify the biological response to mutant HTT gene expression. Selective and dose-dependent effects of 6-AZA on expression of HTT alleles containing nucleotide repeat expansions were seen in multiple types of cells cultured in vitro, and in a Drosophila melanogaster animal model for HD. Lowering of mutant HD protein and mitigation of the Drosophila "rough eye" phenotype associated with degeneration of photoreceptor neurons in vivo were observed. Our findings indicate that chemical interference with DSIF complex formation can decrease biochemical and phenotypic effects of nucleotide repeat expansions.

Interlamellar-Spacing Engineering of Stable and Toxicity-Reduced 2D Perovskite Single Crystal for High-Resolution X-ray Imaging.

Two-dimensional (2D) lead halide perovskites are excellent candidates for X-ray detection due to their high resistivity, high ion migration barrier, and large X-ray absorption coefficients. However, the high toxicity and long interlamellar distance of the 2D perovskites limit their wide application in high sensitivity X-ray detection. Herein, we demonstrate stable and toxicity-reduced 2D perovskite single crystals (SCs) realized by interlamellar-spacing engineering via a distortion self-balancing strategy. The engineered low-toxicity 2D SC detectors achieve high stability, large mobility-lifetime product, and therefore high-performance X-ray detection. Specifically, the detectors exhibit a record high sensitivity of 13488 µC Gy1- cm-2, a low detection limit of 8.23 nGy s-1, as well as a high spatial resolution of 8.56 lp mm-1 in X-ray imaging, all of which are far better than those of the high-toxicity 2D lead-based perovskite detectors. These advances provide a new technical solution for the low-cost fabrication of low-toxicity, scalable X-ray detectors.

Multi-Functional AIE Phototheranostic Agent Enhancing αPD-L1 Response for Oral Squamous Cell Carcinoma Immunotherapy.

Oral squamous cell carcinoma (OSCC) represents a prevalent head and neck malignancy with surgical intervention as the primary clinical option. Immunotherapy, particularly immune checkpoint blockade (ICB) targeting PD-1/PD-L1 shows great promise but is impeded by the immunosuppressive tumor microenvironment and low PD-L1 expression in OSCC. Herein, the "all-in-one" phototherapeutic nanoparticles (TSD NPs) are reported with balanced reactive oxygen species and photothermal conversion capacity for combined photoimmunotherapy and ICB immunotherapy against OSCC. A novel electron acceptor, 3-(dicyanomethylene)-2,3-dihydrobenzothiophene-1,1-dioxide (DTM), is introduced to develop the phototherapeutic agent with aggregation-induced emission (AIE) feature and NIR-II fluorescence centered at 1000 nm. Benefiting from the AIE feature and the DTM acceptor, the resultant TSD NPs also exhibit strong type I reactive oxygen species (ROS) generation and high photothermal conversion efficiency (45.3%), which can profoundly induce immunogenic cell death (ICD), activate cytotoxic T lymphocytes, and convert the immunosuppressive tumor microenvironment into an immune-supportive one. Additionally, TSD NPs upregulate the PD-L1 expression on OSCC cells, thus enhancing the efficacy of combined treatment with αPD-L1 ICB immunotherapy. This results show that the synergistic treatment of TSD NPs and αPD-L1 effectively eradicates solid OSCC tumors without adverse effects on normal tissues, proving a novel and promising strategy for OSCC management.

Rational Design of A-Site Cation for High Performance Lead-Free Perovskite X-Ray Detectors.

Design of hypotoxic lead-free perovskites, e.g. Bismuth(Bi)-based perovskites, is much beneficial for commercialization of perovskite X-ray detectors due to their strong radiation absorption. Nevertheless, the design principles governing the selection of A-site cations for achieving high-performance X-ray detectors remain elusive. Here, seven molecules (methylamine MA, amine NH3, dimethylbiguanide DGA, phenylethylamine PEA, 4-fluorophenethylamine p-FPEA, 1,3-propanediamine PDA, and 1,4-butanediamine BDA) and calculated their dipole moments and interaction strength with metal halide (BiI3) are selected. The first-principles calculations and related spectroscopy measurements confirm that organic molecules (DGA) with large dipole moments can have strong interactions with perovskite octahedron and improve the carrier transport between the organic and inorganic clusters. Consequently, zero-dimensional single crystal (SC) (DGA)BiI5∙H2O is synthesized. The (DGA)BiI5∙H2O SCs demonstrate an exceptional carrier mobility-lifetime product of 6.55 × 10-3 cm2 V-1, resulting in the high sensitivity of 5879.4 µCGyair -1cm-2, featuring a low detection limit (4.7 nGyair s-1) and remarkable X-ray irradiation stability even after 100 days of aging at a high electric field (100 V mm-1). Furthermore, the (DGA)BiI5∙H2O SCs for imaging, achieving a notable spatial resolution of 5.5 lp mm-1 are applied. This investigation establishes a pathway for systematically screening A-site cations to design low-dimensional SCs for high-performance X-ray detection.

Combined expert-in-the-loop-random forest multiclass segmentation U-net based artificial intelligence model: evaluation of non-small cell lung cancer in fibrotic and non-fibrotic microenvironments.

BACKGROUND: The tumor microenvironment (TME) plays a key role in lung cancer initiation, proliferation, invasion, and metastasis. Artificial intelligence (AI) methods could potentially accelerate TME analysis. The aims of this study were to (1) assess the feasibility of using hematoxylin and eosin (H&E)-stained whole slide images (WSI) to develop an AI model for evaluating the TME and (2) to characterize the TME of adenocarcinoma (ADCA) and squamous cell carcinoma (SCCA) in fibrotic and non-fibrotic lung. METHODS: The cohort was derived from chest CT scans of patients presenting with lung neoplasms, with and without background fibrosis. WSI images were generated from slides of all 76 available pathology cases with ADCA (n = 53) or SCCA (n = 23) in fibrotic (n = 47) or non-fibrotic (n = 29) lung. Detailed ground-truth annotations, including of stroma (i.e., fibrosis, vessels, inflammation), necrosis and background, were performed on WSI and optimized via an expert-in-the-loop (EITL) iterative procedure using a lightweight [random forest (RF)] classifier. A convolution neural network (CNN)-based model was used to achieve tissue-level multiclass segmentation. The model was trained on 25 annotated WSI from 13 cases of ADCA and SCCA within and without fibrosis and then applied to the 76-case cohort. The TME analysis included tumor stroma ratio (TSR), tumor fibrosis ratio (TFR), tumor inflammation ratio (TIR), tumor vessel ratio (TVR), tumor necrosis ratio (TNR), and tumor background ratio (TBR). RESULTS: The model's overall classification for precision, sensitivity, and F1-score were 94%, 90%, and 91%, respectively. Statistically significant differences were noted in TSR (p = 0.041) and TFR (p = 0.001) between fibrotic and non-fibrotic ADCA. Within fibrotic lung, statistically significant differences were present in TFR (p = 0.039), TIR (p = 0.003), TVR (p = 0.041), TNR (p = 0.0003), and TBR (p = 0.020) between ADCA and SCCA. CONCLUSION: The combined EITL-RF CNN model using only H&E WSI can facilitate multiclass evaluation and quantification of the TME. There are significant differences in the TME of ADCA and SCCA present within or without background fibrosis. Future studies are needed to determine the significance of TME on prognosis and treatment.

Lung nodule malignancy classification with associated pulmonary fibrosis using 3D attention-gated convolutional network with CT scans.

BACKGROUND: Chest Computed tomography (CT) scans detect lung nodules and assess pulmonary fibrosis. While pulmonary fibrosis indicates increased lung cancer risk, current clinical practice characterizes nodule risk of malignancy based on nodule size and smoking history; little consideration is given to the fibrotic microenvironment. PURPOSE: To evaluate the effect of incorporating fibrotic microenvironment into classifying malignancy of lung nodules in chest CT images using deep learning techniques. MATERIALS AND METHODS: We developed a visualizable 3D classification model trained with in-house CT dataset for the nodule malignancy classification task. Three slightly-modified datasets were created: (1) nodule alone (microenvironment removed); (2) nodule with surrounding lung microenvironment; and (3) nodule in microenvironment with semantic fibrosis metadata. For each of the models, tenfold cross-validation was performed. Results were evaluated using quantitative measures, such as accuracy, sensitivity, specificity, and area-under-curve (AUC), as well as qualitative assessments, such as attention maps and class activation maps (CAM). RESULTS: The classification model trained with nodule alone achieved 75.61% accuracy, 50.00% sensitivity, 88.46% specificity, and 0.78 AUC; the model trained with nodule and microenvironment achieved 79.03% accuracy, 65.46% sensitivity, 85.86% specificity, and 0.84 AUC. The model trained with additional semantic fibrosis metadata achieved 80.84% accuracy, 74.67% sensitivity, 84.95% specificity, and 0.89 AUC. Our visual evaluation of attention maps and CAM suggested that both the nodules and the microenvironment contributed to the task. CONCLUSION: The nodule malignancy classification performance was found to be improving with microenvironment data. Further improvement was found when incorporating semantic fibrosis information.

Comparison of lung cancer occurring in fibrotic versus non-fibrotic lung on chest CT.

PURPOSE: Evaluate the behavior of lung nodules occurring in areas of pulmonary fibrosis and compare them to pulmonary nodules occurring in the non-fibrotic lung parenchyma. METHODS: This retrospective review of chest CT scans and electronic medical records received expedited IRB approval and a waiver of informed consent. 4500 consecutive patients with a chest CT scan report containing the word fibrosis or a specific type of fibrosis were identified using the system M*Model Catalyst (Maplewood, Minnesota, U.S.). The largest nodule was measured in the longest dimension and re-evaluated, in the same way, on the follow-up exam if multiple time points were available. The nodule doubling time was calculated. If the patient developed cancer, the histologic diagnosis was documented. RESULTS: Six hundred and nine patients were found to have at least one pulmonary nodule on either the first or the second CT scan. 274 of the largest pulmonary nodules were in the fibrotic tissue and 335 were in the non-fibrotic lung parenchyma. Pathology proven cancer was more common in nodules occurring in areas of pulmonary fibrosis compared to nodules occurring in areas of non-fibrotic lung (34% vs 15%, p < 0.01). Adenocarcinoma was the most common cell type in both groups but more frequent in cancers occurring in non-fibrotic tissue. In the non-fibrotic lung, 1 of 126 (0.8%) of nodules measuring 1 to 6 mm were cancer. In contrast, 5 of 49 (10.2%) of nodules in fibrosis measuring 1 to 6 mm represented biopsy-proven cancer (p < 0.01). The doubling time for squamous cell cancer was shorter in the fibrotic lung compared to non-fibrotic lung, however, the difference was not statistically significant (p = 0.24). 15 incident lung nodules on second CT obtained ≤ 18 months after first CT scan was found in fibrotic lung and eight (53%) were diagnosed as cancer. CONCLUSIONS: Nodules occurring in fibrotic lung tissue are more likely to be cancer than nodules in the nonfibrotic lung. Incident pulmonary nodules in pulmonary fibrosis have a high likelihood of being cancer.

Expression profiles and characterization of microRNAs responding to chitin in Arthrobotrys oligospora.

Extracellular proteases, such as chitinases secreted by Arthrobotrys oligospora (A. oligospora), play a crucial role in the process of nematode infection. However, post-transcriptional regulation of gene expression involving microRNAs (miRNAs) in A. oligospora remains scarcely described. Hereto, transcriptome sequencing was carried out to analyze the expression profiles of chitin-responsive miRNAs in A. oligospora. Based on the RNA-seq data, the differential expression of miRNAs (DEmiRNAs) in response to chitin was screened, identified and characterized in A. oligospora. Meanwhile, the potential target genes were predicted by the online tools miRanda and Targetscan, respectively. Furthermore, the interaction of DEmiRNA with it's target gene was validated by a dual-luciferase reporter assay system. Among 85 novel miRNAs identified, 25 miRNAs displayed significant differences in expression in A. oligospora in response to chitin. Gene Ontology (GO) analysis showed that the potential genes targeted by DEmiRNAs were enriched in the biological processes such as bio-degradation, extracellular components and cell cycle. KEGG analysis revealed that the target genes were mainly involved in Hippo, carbon and riboflavin metabolic pathway. Outstandingly, chitinase AOL_s00004g379, which is involved in the hydrolysis metabolic pathway of chitin, was confirmed to be a target gene of differential miR_70. These findings suggest that chitin-responsive miRNAs are involved in the regulation of cell proliferation, predator hyphae growth and chitinase expression through the mechanisms of post-transcriptional regulation, which provides a new perspective to the molecular mechanisms underlying miRNAs-mediated control of gene expression in A. oligospora.

Molecular characterization and phylogenetic analysis of porcine epidemic diarrhea virus in Xinjiang, China, from 2020 to 2022.

In recent years, the pig industry in Xinjiang, China, has been severely impacted by outbreaks of porcine epidemic diarrhea (PED), despite vaccination efforts. In this study, we investigated the genetic characteristics of currently prevalent porcine epidemic diarrhea virus (PEDV) strains in the region. We collected 548 samples from animals with suspected PED on large-scale pig farms in Xinjiang. Of these, 258 tested positive for PEDV by RT-PCR, yielding an overall positivity rate of 47.08%. S1 gene sequencing and phylogenetic analysis were conducted on 23 randomly selected RT-PCR-positive samples. Three endemic strains of PEDV (PEDV/CH/XU/2020, PEDV/CH/XK/2020, and PEDV/CH/XA/2020) were isolated, and their complete genome sequences were analyzed for evidence of genetic recombination. Sequence comparison of the S gene indicated significant variations in the S1 gene of the Xinjiang strains compared to the vaccine strains CV777, AJ1102, and LWL, with 90.2%-98.5% nucleotide sequence identity. Notably, both the N-terminal and C-terminal domains of the S protein showed significant variation. Genetic evolutionary analysis identified the GIIa subtype as the dominant genotype among the epidemic strains in Xinjiang. Recombination analysis revealed inter-subtype recombination events in the PEDV/CH/XK/2020 and XJ1904-34 strains. These findings highlight the extensive genetic variation in the predominant GIIa genotype of PEDV in Xinjiang, which does not match the genotype of the currently used vaccine strains. These data may guide further efforts toward the development of effective vaccines for the control of PED.

Ultra-high flux mesh membranes coated with tannic acid-ZIF-8@MXene composites for efficient oil-water separation.

Oil/water separation has become a global concern due to the increasing discharge of multi-component harmful oily wastewater. Super wetting membranes have been shown to be an effective material for oil/water separation. Ultra-high flux stainless-steel meshes (SSM) with superhydrophilicity and underwater superoleophobicity were fabricated by tannic acid (TA) modified ZIF-8 nanoparticles (TZIF-8) and two-dimensional MXene materials for oil/water separation. The TZIF-8 increased the interlayer space of MXene, enhancing the flux permeation (69,093 L m-2h-1) and rejection of the composite membrane (TZIF-8@MXene/SSM). The TZIF-8@MXene/SSM membrane showed an underwater oil contact angle of 154.2°. The membrane maintained underwater superoleophobic after stability and durability tests, including various pH solutions, organic solvents, reusability, etc. In addition, the oil/water separation efficiency of TZIF-8@MXene/SSM membranes was higher than 99% after treatment in harsh conditions and recycling. The outstanding anti-fouling, stability, durability, and recyclability properties of TZIF-8@MXene/SSM membrane highlight the remarkable potential of membranes for complex oil/water separation process.

Correlation between the development of phage resistance and the original antibiotic resistance of host bacteria under the co-exposure of antibiotic and bacteriophage.

Bacteriophages (phages) are viruses capable of regulating the proliferation of antibiotic resistant bacteria (ARB). However, phages that directly cause host lethality may quickly select for phage resistant bacteria, and the co-evolutionary trade-offs under varying environmental conditions, including the presence of antibiotics, remains unclear as to their impact on phage and antibiotic resistance. Here, we report the emergence of phage resistance in three distinct E. coli strains with varying resistance to ß-lactam antibiotics, treated with different ampicillin (AMP) concentrations. Hosts exhibiting stronger antibiotic resistance demonstrated a higher propensity to develop and maintain stable phage resistance. When exposed to polyvalent phage KNT-1, the growth of AMP-sensitive E. coli K12 was nearly suppressed within 18 h, while the exponential growth of AMP-resistant E. coli TEM and super-resistant E. coli NDM-1 was delayed by 12 h and 8 h, respectively. The mutation frequency and mutated colony count of E. coli NDM-1 were almost unaffected by co-existing AMP, whereas for E. coli TEM and K12, these metrics significantly decreased with increasing AMP concentration from 8 to 50 µg/mL, becoming unquantifiable at 100 µg/mL. Furthermore, the fitness costs of phage resistance mutation and its impact on initial antibiotic resistance in bacteria were further examined, through analyzing AMP susceptibility, biofilm formation and EPS secretion of the isolated phage resistant mutants. The results indicated that acquiring phage resistance could decrease antibiotic resistance, particularly for hosts lacking strong antibiotic resistance. The ability of mutants to form biofilm contributes to antibiotic resistance, but the correlation is not entirely positive, while the secretion of extracellular polymeric substance (EPS), especially the protein content, plays a crucial role in protecting the bacteria from both antibiotic and phage exposure. This study explores phage resistance development in hosts with different antibiotic resistance and helps to understand the limitations and possible solutions of phage-based technologies.

MOTS-c is an effective target for treating cancer-induced bone pain through the induction of AMPK-mediated mitochondrial biogenesis.

Bone cancer pain (BCP), due to cancer bone metastasis and bone destruction, is a common symptom of tumors, including breast, prostate, and lung tumors. Patients often experience severe pain without effective treatment. Here, using a mouse model of bone cancer, we report that MOTS-c, a novel mitochondrial-derived peptide, confers remarkable protection against cancer pain and bone destruction. Briefly, we find that the plasma level of endogenous MOTS-c is significantly lower in the BCP group than in the sham group. Accordingly, intraperitoneal administration of MOTS-c robustly attenuates bone cancer-induced pain. These effects are blocked by compound C, an AMPK inhibitor. Furthermore, MOTS-c treatment significantly enhances AMPKα 1/2 phosphorylation. Interestingly, mechanical studies indicate that at the spinal cord level, MOTS-c relieves pain by restoring mitochondrial biogenesis, suppressing microglial activation, and decreasing the production of inflammatory factors, which directly contribute to neuronal modulation. However, in the periphery, MOTS-c protects against local bone destruction by modulating osteoclast and immune cell function in the tumor microenvironment, providing long-term relief from cancer pain. Additionally, we find that chronic administration of MOTS-c has little effect on liver, renal, lipid or cardiac function in mice. In conclusion, MOTS-c improves BCP through peripheral and central synergistic effects on nociceptors, immune cells, and osteoclasts, providing a pharmacological and biological rationale for the development of mitochondrial peptide-based therapeutic agents for cancer-induced pain.

Comparative Study of the Morphological Characteristics of Perforators of the Transverse and Descending Branches of the Lateral Circumflex Femoral Artery in Anterolateral Thigh Flap Surgery.

BACKGROUND: The anterolateral thigh flap (ALTF) is a kind of lateral thigh flap that uses branches of the lateral circumflex femoral artery (LCFA) as the vessel pedicle and is widely used in plastic surgery. During classic ALTF surgery, some perforators from the descending branch of the lateral circumflex femoral artery (LCFA-db) are hard to harvest due to their anatomical variants and individual differences; thus, it is necessary to design an appropriate alternative surgical plan. The transverse branch of the LCFA (LCFA-tb) has unique advantages and can be a potential complement to ALTF vascular pedicle selection. The aim of this study was to compare the difference in morphology between LCFA-db and LCFA-tb, and to verify the feasibility and clinical effect of ALTF with LCFA-tb as the source artery. METHODS: The morphological and clinical data of patients who underwent wound repair of the extremities with the ALTF pedicled with the LCFA-tb and LCFA-db were retrospectively analyzed. This study consisted of the clinical data of 62 patients who accepted an ALTF pedicled with LCFA-tb, and 45 patients accepted an ALTF pedicled with LCFA-db. RESULTS: A total of 68 cutaneous perforators originating from the LCFA-tb were found in the surgical field, of which 35 perforators were direct cutaneous perforators (51.5%), 28 perforators were septocutaneous perforators (41.2%), and 5 perforators were musculocutaneous perforators (7.3%). Seventy-four cutaneous perforators were found in the LCFA-db group. The proportions of septocutaneous perforators and musculocutaneous perforators were 23% and 77%, respectively, and the number of direct cutaneous perforators was 0. The harvest time of flaps pedicled with LCFA-tb was remarkably shortened. Regarding prognosis, there were no significant differences between the curative effects of the 2 types of flaps. CONCLUSIONS: This study verified that most LCFA-tb perforators are direct cutaneous perforators and that the piercing-in positions of LCFA-tb perforators on superficial fascia were higher than those of LCFA-db perforators. Furthermore, the ALTF pedicled with LCFA-tb can provide satisfactory soft tissue reconstruction and can be used as a useful supplement to the traditional flap design.

Study on the mechanism of action of methane production by co-fermentation of sludge and lignite.

To improve the methanogenic efficiency of lignite anaerobic fermentation and explore innovative approaches to sludge utilization, a co-fermentation technique involving lignite and sludge was employed for converting biomass into biomethane. Volatile suspended solids were introduced as a native enrichment of the sludge and mixed with lignite for fermentation. The synergistic fermentation mechanism between sludge and lignite for biomethane production was analyzed through biochemical methane potential experiments, measurement of various parameters pre- and post-fermentation, observation of bacterial population changes during the peak of reaction, carbon migration assessment, and evaluation of rheological characteristics. The results showed that the addition of sludge in the anaerobic fermentation process improved the microorganisms' ability to degrade lignite and bolstered biomethane production. Notably, the maximum methane production recorded was 215.52 mL/g-volatile suspended solids, achieved at a sludge to coal ratio of 3:1, with a synergistic growth rate of 25.37%. Furthermore, the removal rates of total suspended solids, and total chemical oxygen demand exhibited an upward trend with an increasing percentage of sludge in the mixture. The relative abundance and activity of the methanogens population were found to increase with an appropriate ratio of sludge to lignite. This observation confirmed the migration of carbon between the solid-liquid-gas phases, promoting enhanced system affinity. Additionally, the changes in solid-liquid phase parameters before and after the reaction indicated that the addition of sludge improved the system's degradation capacity. The results of the study hold significant implications in realizing the resource utilization of sludge and lignite while contributing to environmental protection endeavors.

Metagenomic insights into the mechanism of sophorolipid in facilitating co-anaerobic digestion of mushroom residues and cattle manure: Functional microorganisms and metabolic pathway analysis.

The present study aimed to enhance the co-anaerobic digestion system of mushroom residues and cattle manure by incorporating biosurfactant sophorolipid. Results demonstrated that the addition of 75 mg/L sophorolipid increased cumulative methane production by 33.68%, acetate content by 9-10 times, and the abundance of Methanosarcina by 69.22%. The electroactive microorganisms (Bacteroides, Petrimonas, etc.) were enriched, while the up-regulation of functional genes associated with carbohydrate metabolism and methane metabolism was observed. The metagenomic analysis revealed the significant involvement of inter-microbial communication and extracellular electron transfer in anaerobic digestion. Petrimonas was identified as the predominant host involved in cellular processes and environmental information processing. The supplementation of sophorolipid significantly enhanced its abundance during the late anaerobic digestion period (by 12.30%-64.84%). The results emphasize the crucial function of sophorolipid as biosurfactant in enhancing the efficiency of anaerobic digestion.

The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean.

Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean plants. The development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost begins. FUL belongs to the MADS-box transcription factor family and has several duplicated members in soybeans. In this study, we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity, while GmFULc knockout mutants exhibited late maturity. Chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) revealed that GmFULc could bind to the CArG, bHLH and homeobox motifs. Further investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 genes. Overexpression of GmZTL4 promoted soybean maturity, whereas the ztl4 mutants exhibited delayed maturity. Moreover, we found that the cis element box 4 motif of the GmZTL4 promoter, a motif of light response elements, played an important role in controlling the growth period. Deletion of this motif shortened the growth period by increasing the expression levels of GmZTL4. Functional investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb, ultimately resulting in the promotion of flowering and early maturation. Taken together, these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.

Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution.

Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.

Frontiers of soybean pan-genome studies.

Artificial domestication provided the original motivation to the blooming of agriculture, following with the dramatic change of the genetic background of crops and livestock. According to theory and technology upgradation that contributing to the omics, we appreciate using the pan-genome instead of single reference genome for crop study. By comparison and integration of multiple genomes under the guidance of pan-genome theory, we can estimate the genomic information range of a species, leading to a global understanding of its genetic diversity. Combining pan-genome with large size chromosomal structural variations, high throughput population resequencing, and multi-omics data, we can profoundly study the genetic basis behind species traits we focus on. Soybean is one of the most important commercial crops over the world. It is also essential to our food security. Dissecting the formation of genetic diversity and the causal loci of key agricultural traits of soybean will make the modern soybean breeding more efficiently. In this review, we summarize the core idea of pan-genome and clarified the characteristics of construction strategies of pan-genome such as de novo/mapping assembly, iterative assembly and graph-based genome. Then we used the soybean pan-genome work as a case study to introduce the general way to study pan-genome. We highlighted the contribution of structural variation (SV) to the evolution/domestication of soybean and its value in understanding the genetic bases of agronomy traits. By those, we approved the value of graph-based pan-genome for data integration and SV calculation. Future research directions are also discussed for crop genomics and data science.

Designed Additive to Regulated Crystallization for High Performance Perovskite Solar Cell.

It is a crucial role for enhancing the power conversion efficiency (PCE) of perovskite solar cells (PSCs) to prepare high-quality perovskite films, which can be achieved by delaying the crystallization of perovskite film. Hence, we designed difluoroacetic anhydride (DFA) as an additive to regulating crystallization process thus reducing defect formation during perovskite film formation. It was found DFA reacts with DMSO by forming two molecules, difluoroacetate thioether ester (DTE) and difluoroacetic acid (DA). The strong bonding DTE⋅PbI2 and DA⋅PbI2 retard perovskite crystallization process for high-quality film formation, which was monitored through in situ UV/Vis and PL tests. By using DFA additives, we prepared perovskite films with high-quality and low defects. Finally, a champion PCE of 25.28 % was achieved with excellent environmental stability, which retained 95.75 % of the initial PCE after 1152 h at 25 °C under 25 % RH.