Search

Wide exposure to endocrine-disrupting chemicals (EDCs) poses a great risk on human health. However, few large-scale cohort studies have comprehensively estimated the association between EDCs exposure and mortality risk. This study aimed to investigate the association of urinary EDCs exposure with mortality risk and quantify attributable mortality and economic loss. Multivariable Cox proportional hazards regression models were performed to investigate the association of 38 representative EDCs exposure with mortality risk in the National Health and Nutrition Examination Survey (NHANES). During a median follow-up of 7.7 years, 47,279 individuals were enrolled. All-cause mortality was positively associated with 1-hydroxynaph-thalene, 2-hydroxynaphthalene, cadmium, antimony, cobalt, and monobenzyl phthalate. Cancer mortality was positively associated with cadmium. Cardiovascular disease (CVD) mortality was positively associated with 1-hydroxynaphthalene, 2-hydroxynaph-thalene, and 2-hydroxyfluorene. Nonlinear U-shaped relationships were found between all-cause mortality and cadmium and cobalt, which was also identified between 2-hydroxyfluorene and CVD mortality. J-shaped association of cadmium exposure with cancer mortality was also determined. EDCs exposure may cause 56.52% of total deaths (1,528,500 deaths) and around 1,897 billion USD in economic costs. Exposure to certain phthalates, polycyclic aromatic hydrocarbons, phytoestrogens, or toxic metals, even at substantially low levels, is significantly associated with mortality and induces high economic costs.

In this paper, we studied the structure, expression and function of black carp insulin gene. The complete Mylopharyngodon piceus insulin (Mp-Ins) gene is 1,965 bp long and includes a 1,499 bp 5ʹ-untranslated region (UTR), a 139 bp 3′-UTR with a poly(A) tail, and an open reading frame (ORF) of 327 bp. The predicted molecular weight of the recombinant Mp-Ins(rMp-Ins) protein is 11.87 kDa. The mRNA expression of Mp-Ins is upregulated in the brain and liver. After the injection of rMp-Ins, Mp-Ins mRNA transcript abundance was significantly upregulated in the liver. The rMp-Ins protein could inhibit the concentration of glycogen phosphorylase (GP), growth hormone (GH), fatty acid synthase (FAS), and insulin-like growth factors-1 (IGF-1), and it also significantly increased the concentration of PI3K. Additionally, the injection of rMp-Ins did not have a significant impact on the glucose-6-phosphatase (G6Pase) content in blood. In situ hybridization results showed that the positive signal of the Mp-Ins gene was mainly concentrated in the cell nucleus of brain tissue and the cell membrane of liver tissue and muscle tissue. Together, these results demonstrated that Mp-Ins plays an important role in growth and metabolism in M. piceus.

Increasing plant density can increase cereal crop yields. However, the physiological and anatomical mechanisms of grain yield increase at high plant densities in maize-based intercropping systems are not well understood. A two-year field experiment was conducted in 2018 and 2019 to investigate grain yield, photosynthetic characteristics, stomatal traits, and leaf anatomy of maize plants in an intercropping system with high plant densities. Two cropping patterns (monocropping and intercropping) and three plant densities (D1, 78,000 plants ha−1; D2, 103,500 plants ha−1; D3, 129,000 plants ha−1) were arranged in a randomized block design. Increasing maize plant density significantly increased maize yield, and intercropping gave a significant yield advantage over monocropping under the same plant density. Intercropping combined with high plant density increased the leaf area and SPAD value of maize, increasing the photosynthesis rates after the harvest of pea. At the twelfth leaf stage, the stomatal density and stomatal area of intercrops combined with medium plant density increased by respectively 10.5% and 18.4% relative to their values for the corresponding density of monocrops. Although leaf thickness of maize was reduced by increasing plant density, the chloroplast number and grana lamella number were higher in intercropping than in monocropping under different plant densities. These positive changes in leaf anatomy resulted in increased photosynthesis, suggesting a physiological basis for the increase in grain yield.

Introduction Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. Objectives Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. Methods We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. Results We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of “QTL-hotspot” identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, ‘Legumepedia’. Conclusion This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.

Paraquat is one of the most widely used nonselective herbicides in agriculture. Due to its wide use, paraquat resistant weeds have emerged and is becoming a potential threat to agriculture. The molecular mechanisms of paraquat resistance in weeds remain largely unknown. Physiological studies indicated that the impaired translocation of paraquat and enhanced antioxidation could improve paraquat resistance in plants. However, the detoxification of paraquat via active metabolism by plants has not been reported to date. Here we report that an activated expression of At1g01600 encoding the P450 protein CYP86A4 confers paraquat resistance as revealed by the gain-of-function mutant paraquat tolerance 11D (pqt11D), in which a T-DNA with four 35S enhancers was inserted at 1646 bp upstream the ATG of At1g01600. The paraquat resistance can be recapitulated in Arabidopsis wild type by overexpressing AtPQT11 (At1g01600), while its knockout mutant is hypersensitive to paraquat. Moreover, AtPQT11 also confers paraquat resistance in E. coli when overexpressed. We further demonstrate that AtPQT11 has P450 enzyme activity that converts paraquat to N-demethyl paraquat nontoxic to Arabidopsis, therefore detoxifying paraquat in plants. Taken together, our results unequivocally demonstrate that AtPQT11/ CYP86A4 detoxifies paraquat via active metabolism, thus revealing a novel molecular mechanism of paraquat resistance in plants and providing a means potentially enabling crops to resist paraquat.

Telomeres are protective, nucleoprotein structures at the end of chromosomes that have been associated with lifespan across taxa. However, the extent to which these associations can be attributed to absolute length vs. the rate of telomere shortening prior to sampling remains unresolved. In a longitudinal study, we examined the relationship between lifespan, telomere length and the rate of telomere shortening in wild, purple-crowned fairy-wrens (Malurus coronatus coronatus). To this end, we measured telomere length using quantitative polymerase chain reaction in the blood of 59 individuals sampled as nestlings and 4-14 months thereafter, and in 141 known-age individuals sampled on average three times across adulthood. We applied within-subject centring analyses to simultaneously test for associations between lifespan and average telomere length and telomere shortening. We reveal that the rate of telomere shortening and to a lesser extent telomere length in the first year of life independently predicted lifespan, with individuals with faster shortening rates and/or shorter telomeres living less long. In contrast, in adulthood neither telomere shortening nor telomere length predicted lifespan, despite a considerably larger data set. Our results suggest that telomere length measured very early in life (during development) and longitudinal assessments of telomere shortening during the first year of life constitute more useful biomarkers of total life expectancy than either telomere length measured after development, or telomere shortening later in adulthood.

A self-regulated anti-diabetic drug release device mimicking pancreatic cells is highly desirable for the therapy of diabetes. Herein, a glucose-mediated dual-responsive drug delivery system, which combines pH- and H2O2-responsive block copolymer grafted hollow mesoporous silica nanoparticles (HMSNs) with microneedle (MN) array patch, has been developed to achieve self-regulated administration. The poly[4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzyl acrylate]-b-poly[2-(dimethylamino)ethyl methacrylate] (PPBEM-b-PDM) polymer serves as gate keeper to prevent drug release from the cavity of HMSNs at normoglycemic level. In contrast, the drug release rate is significantly enhanced upon H2O2 and pH stimuli due to the chemical change of H2O2 sensitive PPBEM block and acid responsive PDM block. Therefore, incorporation of anti-diabetic drug and glucose oxidase (GOx, which can oxidize glucose to gluconic acid and in-situ produce H2O2) into stimulus polymer coated HMSNs results in a glucose-mediated MN device after depositing the drug-loaded nanoparticles into MN array patch. Both in vitro and in vivo results show this MN device presents a glucose mediated self-regulated drug release characteristic, which possesses a rapid drug release at hyperglycemic level but retarded drug release at normoglycemic level. The result indicates that the fabricated smart drug delivery system is a good candidate for the therapy of diabetes.

Nitrogen removal is a critical process in water treatment plants (WTPs) and wastewater treatment plants (WWTPs). The recent discovery of a novel bacterial process, complete ammonia oxidation (comammox, CMX), has refuted a century-long perception of the two-step conversion of NH3 to NO3–. Compared with canonical nitrifiers, CMX bacteria offer undeniable advantages, such as a high growth yield propensity and adaptability to nutrient- and growth-limiting conditions, which collectively draw attention to validate the aptness of CMX bacteria to wastewater treatment. As there has been no comprehensive review on the relevance of CMX bacteria for sustainable water and wastewater treatment, this review is intended to discuss the roles and applications of CMX in the removal of nitrogen and pollutants from water and wastewater. We took into account insights into the metabolic versatilities of CMX bacteria at the clade and subclade levels. We focused on the distribution of CMX bacteria in engineered systems, niche differentiation, co-occurrence and interactions with canonical nitrifiers for a better understanding of CMX bacteria in terms of their ecophysiology. Conceptualized details on the reactor adaptability and stress response of CMX bacteria are provided. The potential of CMX bacteria to degrade micropollutants either directly or co-metabolically was evaluated, and these insights would be an indispensable advantage in opening the doors for wider applications of CMX bacteria in WWTPs. Finally, we summarized future directions of research that are imperative in improving the understanding of CMX biology.

Hypertension is a leading risk factor for stroke, heart disease, chronic kidney disease, vascular cognitive impairment, and Alzheimer’s disease. Previous genetic studies have nominated hundreds of genes linked to hypertension, and renal and cognitive diseases. Some have been advanced as candidate genes by showing that they can alter blood pressure or renal and cerebral vascular function in knockout animals; however, final validation of the causal variants and underlying mechanisms has remained elusive. This review chronicles 40 years of work, from the initial identification of adducin (ADD) as an ACTIN-binding protein suggested to increase blood pressure in Milan hypertensive rats, to the discovery of a mutation in ADD1 as a candidate gene for hypertension in rats that were subsequently linked to hypertension in man. More recently, a recessive K572Q mutation in ADD3 was identified in Fawn-Hooded Hypertensive (FHH) and Milan Normotensive (MNS) rats that develop renal disease, which is absent in resistant strains. ADD3 dimerizes with ADD1 to form functional ADD protein. The mutation in ADD3 disrupts a critical ACTIN-binding site necessary for its interactions with actin and spectrin to regulate the cytoskeleton. Studies using Add3 KO and transgenic strains, as well as a genetic complementation study in FHH and MNS rats, confirmed that the K572Q mutation in ADD3 plays a causal role in altering the myogenic response and autoregulation of renal and cerebral blood flow, resulting in increased susceptibility to hypertension-induced renal disease and cerebral vascular and cognitive dysfunction.

Photodynamic therapy (PDT) is an efficacious noninvasive therapeutic modality that utilizes nontoxic photosensitizers (PSs) to transform oxygen into highly cytotoxic reactive oxygen species (ROS) u...

Root branching and mycorrhizal symbioses are two major mechanisms for soil resources acquisition by trees. Understanding the relationship between these two mechanisms and their responses to varied environmental conditions are crucial for predicting the responses of foraging strategies of roots to environmental changes. This study was conducted in 11 Chinese fir (Cunninghamia lanceolata) plantations distributed in different environmental conditions in Subtropical China to assess the relationship between root tip traits related to nutrient foraging (branching ratio of 1st order roots to 2nd order roots and arbuscular mycorrhizal (AM) colonization) and their environmental variables including annual mean precipitation (MAP), annual mean temperature (MAT), soil C, soil N, soil P and soil pH. Results Root branching was more sensitive to environmental conditions than mycorrhizal symbioses. The branching ratio and AM colonization of Chinese fir were significantly related to several environmental variables. The branching ratios were positively correlated with MAT but negatively correlated with soil C, soil N and soil pH (P P P

Slugging represents one of the major regimes in fluidization, which occurs in small diameter beds with large bed height-to-diameter ratio or in large diameter beds with internals that resemble multiple small diameter fluidized beds. Slug types include round-nosed slug, wall slug and square-nosed slug. Studies of the slugs have been mainly focused on round-nosed or wall slugs known as half slug, typically occurring in Geldart group A particle fluidization. The square-nosed slug typically occurring for Geldart group D particles appears to be regarded as simple in its structure. The Electrical Capacitance Volume Tomography (ECVT) imaging of the square-nosed slugging phenomena conducted in this study reveals otherwise. That is the structure of the square-nosed slug is, in fact, complex, particularly with respect to its dynamic variation in fluidization. More broadly, this study examines experimentally the hydrodynamic characteristics of the square-nosed fluidization regime. Specifically, simultaneous measurements from multiple ECVT sensors provide non-invasive, continuous, 3-dimensional imaging of the entire flow region of the slugging bed and hence enabling the dynamic characterization of the evolution of the slugs. The analysis of the 3D images reconstructed for real-time gas–solid volume fraction profile of the slugging fluidized bed indicates that there are three different zones, namely, the bottom fluidization zone, the gas slug zone, and the solid slug zone, co-existing in the bed. The three zones present different hydrodynamic characteristics during the slug evolution. It is found that varying the gas velocity of the slugging bed mainly varies the maximum length of the gas slug zone, while it only has a minor effect on the lengths of the bottom fluidization zone and solid slug zone. It also has an insignificant effect on the solid volume fraction of the three zones.

Epigenetic regulation of mitochondrial DNA (mtDNA) is an emerging and fast-developing field of research. Compared to regulation of nucler DNA, mechanisms of mtDNA epigenetic regulation (mitoepigenetics) remain less investigated. However, mitochondrial signaling directs various vital intracellular processes including aerobic respiration, apoptosis, cell proliferation and survival, nucleic acid synthesis, and oxidative stress. The later process and associated mismanagement of reactive oxygen species (ROS) cascade were associated with cancer progression. It has been demonstrated that cancer cells contain ROS/oxidative stress-mediated defects in mtDNA repair system and mitochondrial nucleoid protection. Furthermore, mtDNA is vulnerable to damage caused by somatic mutations, resulting in the dysfunction of the mitochondrial respiratory chain and energy production, which fosters further generation of ROS and promotes oncogenicity. Mitochondrial proteins are encoded by the collective mitochondrial genome that comprises both nuclear and mitochondrial genomes coupled by crosstalk. Recent reports determined the defects in the collective mitochondrial genome that are conducive to breast cancer initiation and progression. Mutational damage to mtDNA, as well as its overproliferation and deletions, were reported to alter the nuclear epigenetic landscape. Unbalanced mitoepigenetics and adverse regulation of oxidative phosphorylation (OXPHOS) can efficiently facilitate cancer cell survival. Accordingly, several mitochondria-targeting therapeutic agents (biguanides, OXPHOS inhibitors, vitamin-E analogues, and antibiotic bedaquiline) were suggested for future clinical trials in breast cancer patients. However, crosstalk mechanisms between altered mitoepigenetics and cancer-associated mtDNA mutations remain largely unclear. Hence, mtDNA mutations and epigenetic modifications could be considered as potential molecular markers for early diagnosis and targeted therapy of breast cancer. This review discusses the role of mitoepigenetic regulation in cancer cells and potential employment of mtDNA modifications as novel anti-cancer targets.

Purpose Anti-CD19 chimeric antigen receptor T-cell immunotherapy (19CAR-T) has achieved impressive clinical results in adult and pediatric relapsed/refractory (r/r) B-lineage acute lymphoblastic leukemia (B-ALL). However, the application and effect of CAR-T therapy in B-ALL patients with extramedullary relapse are rarely issued even disqualified in some clinical trials. Here, we examined the efficacy of 19CAR-T in patients with both bone marrow and extramedullary involvement. Materials and methods CAR-T cells were generated by transfection of primary human T lymphocytes with a lentiviral vector expressing anti-CD19 single chain antibody fragments (scFvs) with the cytoplasmic domains of 4-1BB and CD3ζ, and used to infuse patients diagnosed as having r/r B-ALL with extramedullary origination. Clinical responses were evaluated by the use of bone marrow aspiration, imaging, and flow cytometry. Results Eight patients received 19CAR-T infusion and all attained complete remission (CR). Only one patient was bridged to hematopoietic stem cell transplantation (HSCT). Although three patients relapsed after infusion, they received 19/22CAR-T infusion sequentially and attained a second remission. To date, five patients are in continuous CR and all eight patients are still alive. The mean follow-up time was 21.9 months, while the 24-month estimated event-free survival is 51.4%. Conclusion Anti-CD19 CAR-T therapy can lead to clinical remission for extramedullary relapsed pediatric B-ALL patients. However, the problem of CD19+ relapses after CAR-T remained to be solved. For patients relapsing after CAR-T, a second CAR-T therapy creates another opportunity for remission for subsequent HSCT.

The high mortality in larval-to-juvenile transition is a big problem in aquaculture which is related to the shifting from endogenous to exogenous feeding. However, the underlying causes remain poorly understood. Autophagy, an evolutionary regulated cellular mechanism, is highly conserved in eukaryotic organisms to maintain energy homeostasis against stress including starvation. To investigate whether autophagy plays a role during larval-to-juvenile transition, we generated atg7 and beclin1 zebrafish mutant lines using CRISPR/Cas9 gene editing technology. In this study, both atg7 and beclin1 null zebrafish died during larval-to-juvenile transition because atg7 and beclin1 mutants were unable to cope with the metabolic stress after yolk absorption and fail to activate autophagy in response to nutrient restriction. Meanwhile, dramatic defects in the intestine architecture and metabolic functions in the liver of these mutants were observed even though refeeding them. Treatment with rapamycin, an activator of autophagy, could effectively extend the survival time of both atg7 and beclin1 null zebrafish through decreasing the metabolic rate while it couldn't activate autophagy in mutants via the canonical pathway. Thus, our results revealed that autophagy played a crucial role in zebrafish ontogeny during larval-to-juvenile transition, and it could be considered as one of the most important endogenous factors judging the survival rate of the developing embryos during this period.

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI), such as Erlotinib, have demonstrated remarkable efficacy in the treatment of non-small cell lung cancer (NSCLC) patients with mutated EGFR. However, the efficacy of EGFR-TKIs in wild-type (wt) EGFR tumours has been shown to be marginal. Methods that can sensitize Erlotinib to EGFR wild-type NSCLC remain rare. Herein, we developed a multifunctional superparamagnetic nanotheranostic agent as a novel strategy to potentiate Erlotinib to EGFR-wt NSCLCs. Our results demonstrate that the nanoparticles can co-escort Erlotinib and a vascular epithermal growth factor (VEGF) inhibitor, Bevacizumab (Bev), to EGFR-wt tumours. The nanotheranostic agent exhibits remarkable effects as an inhibitor of EGFR-wt tumour growth. Moreover, Bev normalizes the tumour embedded vessels, further promoting the therapeutic efficacy of Erlotinib. In addition, the tumour engagement of the nanoparticles and the vascular normalization could be tracked by magnetic resonance imaging (MRI). Collectively, our study, for the first time, demonstrated that elaborated nanoparticles could be employed as a robust tool to potentiate Erlotinib to EGFR-wt NSCLC, paving the way for imaging-guided nanotheranostics for refractory NSCLCs expressing EGFR wild-type genes.

The microRNAs (miRNAs) play an important role in regulating myogenesis by targeting mRNA. However, the understanding of miRNAs in skeletal muscle development and diseases is unclear. In this study, we firstly performed the transcriptome profiling in differentiating C2C12 myoblast cells. Totally, we identified 187 miRNAs and 4260 mRNAs significantly differentially expressed that were involved in myoblast differentiation. We carried out validation of microarray data based on 5 mRNAs and 5 miRNAs differentially expressed and got a consistent result. Then we constructed and validated the significantly up- and down-regulated mRNA-miRNA interaction networks. Four interaction pairs (miR-145a-5p-Fscn1, miR-200c-5p-Tmigd1, miR-27a-5p-Sln and miR-743a-5p-Mob1b) with targeted relationships in differentiated myoblast cells were demonstrated. They are all closely related to myoblast development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated cell cycle signals important for exploring skeletal muscle development and disease. Functionally, we discovered that miR-743a targeting gene Mps One Binder Kinase Activator-Like 1B (Mob1b) gene in differentiated C2C12. The up-regulated miR-743a can promote the differentiation of C2C12 myoblast. While the down-regulated Mob1b plays a negative role in differentiation. In addition, the expression profile of miR-743a and Mob1b are consistent with skeletal muscle recovery after Cardiotoxin (CTX) injury. Our study revealed that miR-743a-5p regulates myoblast differentiation by targeting Mob1b involved in skeletal muscle development and regeneration. Our findings made a further exploration for mechanisms in myogenesis and might provide potential possible miRNA-based target therapies for skeletal muscle regeneration and disease in the near future.

Background The transcription factor NFIL3 exerts comprehensive effects on the immune system. Previous studies revealed that NFIL3 is related to the function and development of different immune cell subsets. Experimental autoimmune encephalomyelitis (EAE) is mediated by immune cells which results in inflammatory demyelination in the central nervous system (CNS). However, how NFIL3 affects EAE has not been thoroughly studied. Objectives The current study aimed to investigate how NFIL3 affects EAE, especially the changes of T cells and dendritic cells as well as the crosstalk between them. Methods We used NFIL3-/- mice and C57BL/6J mice (wildtype) to establish MOG35-55-induced EAE. The clinical scores were recorded daily. The immune cells within and outside the CNS of EAE mice were analyzed by flow cytometry. Histology was used to evaluated the neuroinflammation and demyelination in the CNS. Besides, CD11c+ dendritic cells (DCs) were cocultured with T cells and the interplay was measured. Results At the peak of EAE, Th17 cells decreased within the CNS accompanying with lower clinical scores and milder neuroinflammation and demyelination in NFIL3 knockout EAE mice. Outside the CNS, PD-1 and ICOS on CD4+T cells increased, whereas Th2, Th9, CD8+CD103+T cells and GM-CSF+CD4+T cells decreased. Besides, the pro-inflammatory capacity of NFIL3-/- CD11c+ dendritic cells was impaired while the anti-inflammatory capacity was promoted. Conclusions This study suggests that NFIL3 deficiency could alleviate MOG35-55-induced EAE through regulating different immune cell subsets, which is not only related with adaptive immunity and innate immunity, but also related with the cross-talk between them, especially CD4+ T cells and CD11c+ dendritic cells.

Tissue inhibitor of metalloproteinases (TIMPs/Timps) are an endogenous family of widely expressed matrisome-associated proteins that were initially identified as inhibitors of matrix metalloproteinase activity (Metzincin family proteases). Consequently, TIMPs are often considered simply as protease inhibitors by many investigators. However, an evolving list of new metalloproteinase-independent functions for TIMP family members suggests that this concept is outdated. These novel TIMP functions include direct agonism/antagonism of multiple transmembrane receptors, as well as functional interactions with matrisome targets. While the family was fully identified over two decades ago, there has yet to be an in-depth study describing the expression of TIMPs in normal tissues of adult mammals. An understanding of the tissues and cell-types that express TIMPs 1 through 4, in both normal and disease states are important to contextualize the growing functional capabilities of TIMP proteins, which are often dismissed as non-canonical. Using publicly available single cell RNA sequencing data from the Tabula Muris Consortium, we analyzed approximately 100,000 murine cells across eighteen tissues from non-diseased organs, representing seventy-three annotated cell types, to define the diversity in Timp gene expression across healthy tissues. We describe the unique expression profiles across tissues and organ-specific cell types that all four Timp genes display. Within annotated cell-types, we identify clear and discrete cluster-specific patterns of Timp expression, particularly in cells of stromal and endothelial origins. RNA in-situ hybridization across four organs expands on the scRNA sequencing analysis, revealing novel compartments associated with individual Timp expression. These analyses provide evidence of the biological significance of Timp expression in the identified cell sub-types, which are consistent with novel roles in normal tissue homeostasis and changing roles in disease progression. This understanding of the tissues, specific cell types and microenvironment conditions in which Timp genes are expressed adds important physiological context to the growing array of novel functions for TIMP proteins.

Bactrocera dorsalis and its larvae have evolved to cope with the hypoxic environment during their lifetime. In this study, we sequenced the transcriptomes of B. dorsalis under and post anoxia stress. Our data revealed the different biological mechanisms of B. dorsalis in response to anoxia and during recovery from anoxia. The induction of heat shock proteins (HSPs) might be one of the important mechanisms for B. dorsalis to tolerate anoxia. Furthermore, our data showed B. dorsalis acquires energy through gluconeogenesis rather than glycolysis under anoxia and upregulated its lipid metabolism post anoxia. The up-regulation of the genes involved in the Hippo signaling pathway might also play a role in eliminating damaged cells as a result of anoxia. Furthermore, the HIF system of B. dorsalis did not change in response to anoxia stress in this study. We hypothesized that the HIF system in B. dorsalis might be activated by a specific duration of anoxia.

The secondary salinization of soil in facility agriculture is becoming increasingly serious. Cucumber is a moderately salt-sensitive crop, but because of the weak root system and poor resistance to salt stress in cucumber seedlings, it is sensitive to the accumulation of salt in facility soils. Hydrogen, a selective antioxidant and signal molecule, is nontoxic and harmless, and can repair damage in plants under stress. Therefore, the aim of the present paper was to understand the specific mechanism by which hydrogen-rich water (HRW) alleviated salt stress in cucumber seedlings (Cucumis sativus L.). Our results showed that the addition of 50% saturation HRW significantly promoted seedling growth, development and photosynthetic efficiency. Pretreatment with HRW significantly alleviated salt stress symptoms, including the inhibition of fresh and dry weight, root length, lateral roots, and the root/shoot ratio of cucumber seedlings. Pretreatment with HRW increased the chlorophyll content, chlorophyll a/b ratio, and photochemical reaction efficiency, and reduced energy dissipation. These responses to HRW pretreatment were consistent with significant decreases in the superoxide anion, hydrogen peroxide, and malondialdehyde contents and the degree of lipid peroxidation, and increases in the activities of SOD, POD, CAT, APX and GR, and the contents of ASA and GSH in cucumber seedlings under salt stress. In addition, HRW pretreatment under salt stress inhibited the expression of the protein kinase ROP1, which promoted the production of reactive oxygen, but upregulated the protein kinase LecRLK. The transcription factor TGA5, which was involved in osmotic stress, ion stress and ROS clearance, and the expression of NHX1 and SOS2, which were parts of the SOS signaling pathway. HRW enhanced the expression of genes that encoded antioxidant enzymes, including SOD, CAT and POD, and the expressions of GR and APX2, which were key genes in the ASA-GSH cycle under salt stress. Taken together, these results suggested that HRW enhanced the active oxygen scavenging ability in cucumber seedlings, promoted the redox balance in cells, and reduced the degree of oxidative damage in plants under salt stress by reducing the content of active oxygen. Therefore, the application of HRW might be a promising strategy for improving salt stress tolerance in cucumber seedlings.

Extracellular cold‐inducible RNA‐binding protein (CIRP) is a proinflammatory mediator that aggravates ischaemia‐reperfusion injury (IRI). Normothermic machine perfusion (NMP) could effectively alleviate the IRI of the liver, but the underlying mechanism remains to be explored. We show that human DCD livers secreted a large amount of CIRP during static cold storage (CS), which is released into the circulation after reperfusion. The expression of CIRP was related to postoperative IL‐6 levels and liver function. In a rat model, the CIRP expression was upregulated during warm ischaemia and cold storage. Then, rat DCD livers were preserved using CS, hypothermic oxygenated machine perfusion (HOPE) and NMP. C23, a CIRP inhibitor, was administrated in the HOPE group. Compared with CS, NMP significantly inhibited CIRP expression and decreased oxidative stress by downregulating NADPH oxidase and upregulating UCP2. NMP markedly inhibited the mitochondrial fission‐related proteins Drp‐1 and Fis‐1. Further, NMP increased the mitochondrial biogenesis‐related protein, TFAM. NMP significantly reduced inflammatory reactions and apoptosis after reperfusion, and NMP‐preserved liver tissue had higher bile secretion and ICG metabolism compared to the CS group. Moreover, C23 administration attenuated IRI in the HOPE group. Additionally, HL‐7702 cells were stimulated with rhCIRP and C23. High rhCIRP levels increased oxidative stress and apoptosis. In summary, NMP attenuates the IRI of DCD liver by inhibiting CIRP‐mediated oxidative stress and mitochondrial fission.

Backgroud Streptococcus agalactiae is a common colonizer of the rectovaginal tract and lead to infectious diseases of neonatal and non-pregnant adults, which also causes infectious disease in fish and a zoonotic risk as well. Lysine crotonylation (Kcr) is a kind of histone post-translational modifications discovered in 2011. In yeast and mammals, Kcr function as potential enhancers and promote gene expression. However, lysine crotonylation in S. agalactiae has not been studied yet. Methods In this study, the crotonylation profiling of fish pathogen, S. agalactiae was investigated by combining affinity enrichment with LC MS/MS. The Kcr modification of several selected proteins were further validated by Western blotting. Results In the present study, we conducted the proteome-wide profiling of Kcr in S. agalactiae and identified 241 Kcr sites from 675 screened proteins for the first time. Bioinformatics analysis showed that 164 sequences were matched to a total of six definitively conserved motifs, and many of them were significantly enriched in metabolic processes, cellular process, and single-organism processes. Moreover, four crotonylation modified proteins were predicted as virulence factors or to being part of the quorum sensing system PTMs on bacteria. The data are available via ProteomeXchange with identifier PXD026445. Conclusions These data provide a promising starting point for further functional research of crotonylation in bacterial virulence in S. agalactiae.

Osteoporosis, fracture, large-scale craniofacial defects and osteonecrosis are hot topics and are still underdiagnosed and undertreated in the clinic. It is urgent to understand the molecular mechanisms corresponding to the regulation of bone formation. CMTM3 (CKLF-like MARVEL transmembrane domain containing 3) connects the classic chemokine to the transmembrane 4 superfamily and plays an important role in intracellular vesicles transport, EGF receptor function maintenance and cancer development. However, its expression and function in bone remain unclear. In this paper, we found that the bone volume/total volume, trabecular number, trabecular thickness and bone surface area/bone volume of Cmtm3 KO mice increased significantly, and trabecular separation and trabecular pattern factor decreased in Cmtm3 KO mice compared with WT mice by microcomputed tomography. Moreover, the bone mineral content, bone mineral density, ultimate force and stiffness were also increased in Cmtm3 KO mice. Using in vitro analysis, we showed that CMTM3 expression decreases during the differentiation of hBMSCs to osteoblasts. Knockdown of CMTM3 promoted ALP and mineralization of hBMSCs and facilitated osteoblastic differentiation with increasing RUNX2 expression. However, overexpression of CMTM3 got the opposite results. These results proved that CMTM3 was essential for osteogenic differentiation. In addition, knockdown of CMTM3 enhanced p-Erk1/2, but had no significant effect on p-Akt or p-STAT3 in hBMSCs and MC3T3-E1 cells. Taken together, our results indicated that Erk1/2 and RUNX2 pathways mediated by CMTM3 were involved in the process of osteogenic differentiation, and CMTM3 might be a new potential target in the treatment of bone formation-related disease.

As the overuse of nitrogen fertilizer has caused series of environmental problems, improving the nitrogen use efficiency of rice crop has been drawing much attention. Since developing nitrogen-efficient rice genotypes is a feasible solution, illustrating the microbiological characteristics of the nitrogen-efficient rice genotypes is of great importance. We performed a field experiment, and planted 16 genotypes of rice. The nitrogen utilization efficiencies and yields of rice were examined. Real-time PCR and Illumina sequencing were employed to investigate the abundance of the nitrogen-cycle related genes and the bacterial community structure of the rhizosphere. The results revealed that rice genotypes enriched specific bacterial communities to inhabit in the rhizosphere at both the taxonomic and functional levels. The enriched bacteria were mainly involved in the functions of nitrogen transformation, ferric iron reduction, organic compound biodegradation, and sulfur transformation. We observed a strong correlation between the yield and the abundance of rhizospheric functional bacteria, especially the groups of Proteobacteria and Chloroflexi. The analysis of nitrite reductase and denitrifying genes showed that the denitrification activity in the rhizosphere inversely correlate with the efficiency of nitrogen utilization. We reason that a smaller denitrifying bacteria population leads to less the nitrogen loss in the rhizosphere, thus an increase of available nitrogen and a higher rice yield. This research revealed how functional bacteria assembled in the rhizosphere of rice genotypes with varied nitrogen use efficiencies, which may provide valuable information with regard to the improvement of nitrogen use efficiency and reduction of fertilizer application.

Hepatitis E, a significant global public health issue in China, is caused by sporadic infections with regional hepatitis E virus (HEV) genotypes 1, 3, and 4. To date, most immunoassays currently used to test human sera for the presence of anti-HEV antibodies cannot identify HEV at the genotype level. However, such information would be useful for identifying the source of infecting virus. Therefore, here we describe the development of a competitive enzyme-linked immunosorbent assay (ELISA) for detecting anti-genotype 1 HEV antibodies in human sera. Using recombinant genotype 1 HEV ORF3 protein as immunogen, traditional hybridoma technology was employed to generate seven monoclonal antibodies (mAbs), of which two mAbs specifically reacted with the immunogen. One of these two mAbs, 1D2, was labeled with horseradish peroxidase (HRP) for use in competitive ELISA (cELISA). After cELISA optimization using a checkerboard assay design, the amount of ORF3SAR−55 as coating antigen (100 ng/well), HRP-1D2 mAb concentration (1 μg/mL), and test serum dilution (1:10) were selected and a result ≥ 19.5 was used as the cutoff for a positive result. Importantly, cross-genotype cELISA results indicated that the cELISA could not detect anti-genotype 3 rabbit and 4 swine HEV antibodies. Moreover, human sera confirmed as negative for anti-HEV antibodies using the commercial ELISA kit were all negative via cELISA. However, because the commercial ELISA kit detects anti-all genotypes HEV antibodies and the cELISA only detects anti-genotype 1 HEV antibodies, the consistence rate of two assays detecting positive sera is low. In summary, here a cELISA for detecting anti-genotype 1 HEV antibodies was developed for use in epidemiological investigations of genotype 1 HEV infections in humans. • Seven mAbs were produced using genotype 1 HEV ORF3 protein as immunogen. • One mAb that specifically bound to genotype 1 HEV ORF3 protein was selected and labeled for use in a cELISA to detect anti-genotype 1 HEV antibodies. • The competitive ELISA developed here will aid clinical diagnosis of HEV infections and will be useful for large-scale serological testing of genotype 1 HEV infections in humans.

Objective: PD-L1 and PD-L2 expression levels determine immune evasion and the therapeutic efficacy of immune checkpoint blockade. The factors that drive inducible PD-L1 expression have been extensively studied, but mechanisms that result in constitutive PD-L1 expression in cancer cells are largely unknown. Methods: DNA elements were deleted in cells by CRISPR/Cas9-mediated knockout. Protein function was inhibited by chemical inhibitors. Protein levels were examined by Western blot, mRNA levels were examined by real-time RT-PCR, and surface protein expression was determined by cellular immunofluorescence and flow cytometry. Immune evasion was examined by in vitro T cell-mediated killing. Results: We determined the core regions (chr9: 5, 496, 378–5, 499, 663) of a previously identified PD-L1L2-super-enhancer (SE). Through systematic analysis, we found that the E26 transformation-specific (ETS) variant transcription factor (ETV4) bound to this core DNA region but not to DNA surrounding PD-L1L2SE. Genetic knockout of ETV4 dramatically reduced the expressions of both PD-L1 and PD-L2. ETV4 transcription was dependent on ERK activation, and BRAF/TAK1-induced ERK activation was dependent on extracellular signaling from αvβ3 integrin, which profoundly affected ETV4 transcription and PD-L1/L2 expression. Genetic silencing or pharmacological inhibition of components of the PD-L1L2-SE-associated pathway rendered cancer cells susceptible to T cell-mediated killing. Conclusions: We identified a pathway originating from the extracellular matrix that signaled via integrin/BRAF/TAK1/ERK/ETV4 to PD-L1L2-SE to induce PD-L1-mediated immune evasion. These results provided new insights into PD-L1L2-SE activation and pathways associated with immune checkpoint regulation in cancer.

Paulownias are among the fastest growing trees in the world, but they often suffer tremendous loss of wood production due to infection by Paulownia witches' broom (PaWB) phytoplasmas. In this study, we have sequenced and assembled a high-quality nuclear genome of Paulownia fortunei, a commonly cultivated paulownia species. The assembled genome of P. fortunei is 511.6 Mb in size, with 93.2% of its sequences anchored to 20 pseudo-chromosomes, and it contains 31 985 protein-coding genes. Phylogenomic analyses show that the family Paulowniaceae is sister to a clade composed of Phrymaceae and Orobanchaceae. Higher photosynthetic efficiency is achieved by integrating C3 photosynthesis and the crassulacean acid metabolism pathway, which may contribute to the extremely fast growth habit of paulownia trees. Comparative transcriptome analyses reveal modules related to cambial growth and development, photosynthesis, and defense responses. Additional genome sequencing of PaWB phytoplasma, combined with functional analyses, indicates that the effector PaWB-SAP54 interacts directly with Paulownia PfSPLa, which in turn causes the degradation of PfSPLa by the ubiquitin-mediated pathway and leads to the formation of witches' broom. Taken together, these results provide significant insights into the biology of paulownias and the regulatory mechanism for the formation of PaWB.

Native plant communities are commonly invaded by invasive plants to different degrees. However, the relative contribution of the invasive plant abundance vs. phylogenetic evenness to the responses of wetland communities to different degrees of invasion is still unclear. In addition, whether such contribution varies with environmental conditions such as flooding is also unclear. To address these questions, we chose Alternanthera philoxeroides as the invasive plant, and set up four invasive degrees by changing the community species composition under both flooding and non-flooding conditions. The relative abundance of A. philoxeroides and phylogenetic evenness changed simultaneously with the change in the community invasion degree. The invasion degree significantly affected the individual biomass of A. philoxeroides and some native species. Variation partitioning showed that the relative abundance of A. philoxeroides contributed more to variation in community indicators than phylogenetic evenness, regardless of flooding. Spearman rank correlation test showed that the relative abundance of A. philoxeroides was negatively correlated with the individual biomass of A. philoxeroides and some native species, while the phylogenetic evenness was positively correlated with only a few native species. And their correlation strength and significance were all affected by specific species and flooded environment. In conclusion, our results suggest that the relative abundance of A. philoxeroides can more effectively explain the wetland community response to different invasion degrees than phylogenetic evenness, regardless of flooding.

Genetic recombination produces new allelic combinations, thereby introducing variation for domestication. Allopolyploidization has increased the evolutionary potential of hexaploid common wheat by conferring the advantages of heterosis and gene redundancy, but whether a relationship exists between allopolyploidization and genetic recombination is currently unknown. To study the impact of allopolyploidization on genetic recombination in the ancestral D genome of wheat, we generated new synthetic hexaploid wheats by crossing tetraploid Triticum turgidum with multiple diploid Aegilops tauschii accessions, with subsequent chromosome doubling, to simulate the evolutionary hexaploidization process. Using the DArT-Seq approach, we determined the genotypes of two new synthetic hexaploid wheats with their parents, F2 plants in a diploid population (2x, D1D1 × D2D2) and its new synthetic hexaploid wheat-derived population (6x, AABBD1D1 × AABBD2D2). About 11% of detected SNP loci spanning the D genome of Ae. tauschii were eliminated after allohexaploidization, and the degree of segregation distortion was increased in their hexaploid offspring from the F2 generation. Based on codominant genotypes, the mean genetic interval length and recombination frequency between pairs of adjacent and linked SNPs on D genome of the hexaploid F2 population were 2.3 fold greater than those in the diploid F2 population, and the recombination frequency of Ae. tauschii was increased by their hexaploidization with T. turgidum. In conclusion, allopolyploidization increases genetic recombination of the ancestral diploid D genome of wheat, and DNA elimination and increased segregation distortion also occur after allopolyploidization. Increased genetic recombination could have produced more new allelic combinations subject to natural or artificial selection, helping wheat to spread rapidly to become a major global crop and thereby accelerating the evolution of wheat via hexaploidization.

The diverse members of the genus Daphne are prized for their fragrant flowers. Despite being promising ornamental plants in many countries, genetic information of Daphne is scarce. In this study, the plastomes of four species and one variety of Daphne were sequenced and analyzed. The plastomes were typical and contained a pair of inverted repeat (IR) regions that separated the large single-copy (LSC) region from the small single-copy (SSC) region. With a length ranging from 132,869 bp (D. genkwa) to 174,773 bp (Daphne championii), 106 to 141 genes were predicted. Comparative plastome analysis of the newly sequenced plastomes with four publicly available Daphne plastomes identified an expansion of the IRs, sequence variations, and mutational hotspots. Phylogenetic analyses indicated that the genus Daphne in its current circumscription is polyphyletic. Daphne genkwa was nested within the genus Wikstroemia, while D. championii was well resolved as sister to Edgeworthia. These findings concurred with results from our study that used nuclear ribosomal internal transcribed spacer sequence data. The conflicts on the molecular placement of D. championii and D. genkwa and the present taxonomic classification in Daphne suggest that a new intergeneric classification system of Daphneae warrants consideration.

Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes (plastomes) of flowering plants in diverse habitats, yet our knowledge of the evolution of plastid posttranscriptional modifications is limited. In this study, we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium, a genus with diverse trophic lifestyles. Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives. This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex, but independent pseudogenization of ndh genes has also occurred in the epiphyte C. mannii, which was reported to use strong crassulacean acid metabolism photosynthesis. RNA editing sites are abundant but variable in number among Cymbidium plastomes. The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial, mycoheterotrophic, and C. mannii plastomes. The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed, leading to nonrandom loss of ancestral edited sites via reduced editing efficiency. This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus. We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.

Dansylamide (DNSA) is a typical ICT probe that has a favorable serum albumin sensitivity. Inspired by this, we designed a microenvironment sensitive fluorescent probe 4C-G through introducing DNSA into pillar[5]arene. Unlike DNSA, 4C-G displayed differentiated sensitivity to multiple proteins, which was benefit from pillar[5]arene assisted the probe to form complexes with proteins. 4C-G could not only be applied in imaging of HepG2, but also act as a favorable drug carrier for regorafenib (REG) encapsulation. The 4C-G-REG complex would aggregate into high drug-loading fluorescent nanoparticles in a physiological environment (pH 7.4). Such nanoparticles exhibited pH-triggered enrichment ability, which rapidly enriched REG in the acidic environment (pH 6.0). Furthermore, the complexation between 4C-G and REG maintained the imaging property of the probe and the excellent anticancer activity of the drug on HepG2.

Intra-articular injection of mesenchymal stem cells (MSCs) is a promising strategy for osteoarthritis (OA) treatment. However, more and more studies reveal that the injected MSCs have poor adhesion, migration, and survival in the joint cavity. A recent study shows that tropoelastin (TE) regulates adhesion, proliferation and phenotypic maintenance of MSCs as a soluble additive, indicating that TE could promote MSCs-homing in regenerative medicine. In this study, we used TE as injection medium, and compared it with classic media in MSCs intra-articular injection such as normal saline (NS), hyaluronic acid (HA), and platelet-rich plasma (PRP). We found that TE could effectively improve adhesion, migration, chondrogenic differentiation of infrapatellar fat pad MSCs (IPFP-MSCs) and enhance matrix synthesis of osteoarthritic chondrocytes (OACs) in indirect-coculture system. Moreover, TE could significantly enhance IPFP-MSCs adhesion via activation of integrin β1, ERK1/2 and vinculin (VCL) in vitro. In addition, intra-articular injection of TE-IPFP MSCs suspension resulted in a short-term increase in survival rate of IPFP-MSCs and better histology scores of rat joint tissues. Inhibition of integrin β1 or ERK1/2 attenuated the protective effect of TE-IPFP MSCs suspension in vivo. In conclusion, TE promotes performance of IPFP-MSCs and protects knee cartilage from damage in OA through enhancement of cell adhesion and activation of integrin β1/ERK/VCL pathway. Our findings may provide new insights in MSCs intra-articular injection for OA treatment., Graphical abstract Image 1, Highlights • Tropoelastin promotes adhesion and migration of IPFP MSCs. • Tropoelastin promotes IPFP MSCs survival and adhesion in joint cavity. • Injection of IPFP MSCs in tropoelastin reduces OA progression.

A more complete profiling of vaginal microbial communities and their variability enables a more accurate description of women microbiome. However, there is a distinct lack of information regarding the Chinese women. Composition of the vaginal microbiota during pregnancy and 6 weeks postpartum of 454 Chinese women thus was characterized in this study by sequencing V3-V4 regions of the 16S ribosomal RNA (rRNA). It showed that the vaginal microbiome varied during pregnancy and postpartum in response to abortion history, hypertensive disorders (HBP), delivery mode and maternal age. Co-variation of 21 bacterial taxa, including Lactobacillus and two of its species, may account for the common characteristics of vaginal microbiome under different medical histories and pregnancy outcomes. On the contrary, discriminant bacteria were significantly different between premature rupture of membranes related preterm birth (PROM-PTB) and non-PROM related PTB, and community state type (CST) I without any predominant Lactobacillus species in microbiota was more prevalent during pregnancy in PROM-PTB, suggesting that specific bacteria could be considered to distinguish different types of PTB. Through adding the data from Chinese women, the study will enrich the knowledge of human microbiome and likewise contribute to a better understanding of the association between the vaginal microbiome and reproductive health.

Information on the tiller development of hybrid bromegrass (Bromus inermis × Bromus riparius) is limited. The objective of this study was to evaluate the effect of clipping frequency at the vegetative and reproductive stages on the tiller development and concentrations of sugars of c.v ‘AC Knowles’ hybrid bromegrass compared with c.v ‘Kirk’ crested wheatgrass (Agropyron cristatum L.). This experiment was conducted in a greenhouse using the tillers of the vernalized plants dug from the field. The experimental design was a randomized complete block design (RCBD). Grasses were clipped once or four times at either vegetative or reproductive stage. Regardless of the growth stage, four clippings reduced the tiller number of hybrid bromegrass by 25.9% compared with the undefoliated control, while single clipping had no impact. The four clippings had no impact on the tiller number of crested wheatgrass, while single clipping increased its tiller number on average by 50.4% at both growth stages. Crested wheatgrass produced 16.6% more tillers than hybrid bromegrass under the single clipping. The two grass species had a similar number of axillary buds under different clipping treatments. The axillary bud size of crested wheatgrass was larger than hybrid bromegrass. All axillary buds were viable under the two clipping treatments for both grasses. Four clippings significantly decreased the stem base glucose concentration of the two grasses and the root sucrose concentration of crested wheatgrass. Hybrid bromegrass was less tolerant to frequent clippings than crested wheatgrass. Therefore, intensive grazing of hybrid bromegrass pasture may result in a thin stand.

Plant photosynthetic capacity directly determines crop yield. Light quality regulates photosynthetic capacity. This review discusses plant responses to far-red light from the phenotypic to the molecular level, focusing specifically on the improvement of photosynthetic capacity by adjustment of photosynthetic electron transport and the path of light energy. Far-red light can also regulate leaf angle and increase plant height and leaf area, via expression of associated genes, to capture more light energy. Thus, far-red light regulates plant morphology and photosynthetic capacity. Identifying the mechanism of this regulation may lead to increased crop yields.

Publication of the complete genome sequence of Arabidopsis thaliana, the first plant reference genome, in December 2000 heralded the beginning of the plant genome era. Over the past 20 years reference genomes have been generated for hundreds of plant species, spanning non-vascular to flowering plants. Releasing these plant genomes has dramatically advanced studies in all disciplines of plant biology. Importantly, multiple reference-level genomes have been generated for the major crops and their progenitors, enabling the creation of pan-genomes and exploration of domestication history and natural variations that can be adopted by modern crop breeding. We summarize the progress of plant genome sequencing and the challenges of sequencing more complex plant genomes and generating pan-genomes.

Bacterial blight (BB), which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is an important rice disease responsible for significant yield losses. In the rice-growing regions of South China where BB outbreaks are common, the resistance of cultivars with BB resistance genes Xa4 and Xa21 has been lost because of rapid changes in the Xoo population structure and virulence. In this study, 421 diverse rice accessions were evaluated regarding their resistance to two Xoo strains, namely GD1358 (C5) and IV, which are prevalent pathotypes in South China and overcame the resistance of Xa4 and Xa21, respectively. Using the 4.8mio filtered SNP dataset, we conducted a genome-wide association study, which identified 13 loci associated with BB resistance, including eight new quantitative trait loci (QTL) and five QTL harboring known BB resistance genes: Xa3/Xa26, xa5, Xa35(t), Xa36(t), Xa40, Xa43(t), and xa44(t). Intriguingly, a steep peak was detected on chromosomes 5 and 11. Six QTL including three new ones, were distributed on chromosome 11, whereas a new QTL qBB5.1 and a known QTL were detected on chromosome 5. Haplotype analyses indicated that the LOC_Os05g01610 (OsPRAF2) gene within the qBB5.1 region, which encodes a PRAF protein, is associated with BB resistance. Furthermore, OsPRAF2 knockout lines generated using the CRISPR-Cpf1 system were significantly more resistant to Xoo strains than the wild-type plants. Our results provide researchers and breeders with useful information regarding QTL and gene resources, which may be relevant for developing new BB-resistant rice cultivars.