Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation.

The Phyllanthaceae family comprises a diverse range of plants with medicinal, edible, and ornamental value, extensively cultivated worldwide. Polyploid species commonly occur in Phyllanthaceae. Due to the rather complex genomes and evolutionary histories, their speciation process has been still lacking in research. In this study, we generated chromosome-scale haplotype-resolved genomes of two octoploid species (Phyllanthus emblica and Sauropus spatulifolius) in Phyllanthaceae family. Combined with our previously reported one tetraploid (Sauropus androgynus) and one diploid species (Phyllanthus cochinchinensis) from the same family, we explored their speciation history. The three polyploid species were all identified as allopolyploids with subgenome A/B. Each of their two distinct subgenome groups from various species was uncovered to independently share a common diploid ancestor (Ancestor-AA and Ancestor-BB). Via different evolutionary routes, comprising various scenarios of bifurcating divergence, allopolyploidization (hybrid polyploidization), and autopolyploidization, they finally evolved to the current tetraploid S. androgynus, and octoploid S. spatulifolius and P. emblica, respectively. We further discuss the variations in copy number of alleles and the potential impacts within the two octoploids. In addition, we also investigated the fluctuation of metabolites with medical values and identified the key factor in its biosynthesis process in octoploids species. Our study reconstructed the evolutionary history of these Phyllanthaceae species, highlighting the critical roles of polyploidization and hybridization in their speciation processes. The high-quality genomes of the two octoploid species provide valuable genomic resources for further research of evolution and functional genomics.

Multifunctional Gold Nanozyme-Engineered Amphotericin B for Enhanced Antifungal Infection Therapy.

Chronic wounds of significant severity and acute injuries are highly vulnerable to fungal infections, drastically impeding the expected wound healing trajectory. The clinical use of antifungal therapeutic drug is hampered by poor solubility, high toxicity and adverse reactions, thereby necessitating the urgent development of novel antifungal therapy strategy. Herein, this study proposes a new strategy to enhance the bioactivity of small-molecule antifungal drugs based on multifunctional metal nanozyme engineering, using amphotericin B (AmB) as an example. AmB-decorated gold nanoparticles (AmB@AuNPs) are synthesized by a facile one-pot reaction strategy, and the AmB@AuNPs exhibit superior peroxidase (POD)-like enzyme activity, with maximal reaction rates (Vmax ) 3.4 times higher than that of AuNPs for the catalytic reaction of H2 O2 . Importantly, the enzyme-like activity of AuNPs significantly enhanced the antifungal properties of AmB, and the minimum inhibitory concentrations of AmB@AuNPs against Candida albicans (C. albicans) and Saccharomyces cerevisiae (S. cerevisiae) W303 are reduced by 1.6-fold and 50-fold, respectively, as compared with AmB alone. Concurrent in vivo studies conducted on fungal-infected wounds in mice underscored the fundamentally superior antifungal ability and biosafety of AmB@AuNPs. The proposed strategy of engineering antifungal drugs with nanozymes has great potential for enhanced therapy of fungal infections and related diseases.

Trade-off in the partitioning of recent photosynthate carbon under global change.

There may be trade-offs in the allocation patterns of recent photosynthetic carbon (RPC) allocation in response to environmental changes, with a greater proportion of RPC being directed towards compartments experiencing limited resource availability. Alternatively, the allocation of RPC could shift from sources to sinks as plants processing excess photosynthates. It prompts the question: Does the pattern of RPC allocation vary under global changes? If so, is this variation driven by optimal or by residual C allocation strategies? We conducted a meta-analysis by complicating 273 pairwise observations from 55 articles with 13 C or 14 C pulse or continuous labeling to assess the partitioning of RPC in biomass (leaf, stem, shoot, and root), soil pools (soil organic C, rhizosphere, and microbial biomass C) and CO2 fluxes under elevated CO2 (eCO2 ), warming, drought and nitrogen (N) addition. We propose that the increased allocation of RPC to belowground under sufficient CO2 results from the excretion of excess photosynthates. Warming led to a significant reduction in the percentage of RPC allocated to shoots, alongside an increase in roots allocation, although this was not statistically significant. This pattern is due to the reduced water availability resulting from warming. In conditions of drought, there was a notable increase in the partitioning of RPC to stems (+7.25%) and roots (+36.38%), indicative of a greater investment of RPC in roots for accessing water from deeper soil. Additionally, N addition led to a heightened allocation of RPC in leaves (+10.18%) and shoots (+5.78%), while reducing its partitioning in soil organic C (-8.92%). Contrary to the residual C partitioning observed under eCO2 , the alterations in RPC partitioning in response to warming, drought, and N supplementation are more comprehensively explained through the lens of optimal partitioning theory, showing a trade-off in the partitioning of RPC under global change.

Structural characterization of a water-soluble acidic polysaccharide CSP-IV with potential anticoagulant activity from fruit pulp of Clausena lansium (Lour.) Skeels Guifei.

Four main water-soluble wampee fruit pulp polysaccharides, named CSP-I, CSP-II, CSP-III and CSP-IV, were isolated from Clausena lansium (Lour.) Skeels Guifei, therein CSP-IV content was higher than the others. All components possess certain anticoagulant activity demonstrated by prolonged activated partial thromboplastin time, especially CSP-IV, which suggests that CSP-IV plays anticoagulant effect through disturbing intrinsic coagulation pathway. The wampee polysaccharide CSP-IV with Mw of 510.1 kDa was mainly composed of Gal, Ara and GalA. Backbone of CSP-IV contains Gal, Ara and GalA, two kinds of side chains contain one monosaccharide Gal or Ara, both branch on Gal residue of backbone. CSP-IV has no the conformation of triple helix demonstrated by Congo red test. These results showed that CSP-IV is an acidic polysaccharide with potential anticoagulant activity via targeting intrinsic coagulation pathway.

Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding.

Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.

AI algorithms for accurate prediction of osteoporotic fractures in patients with diabetes: an up-to-date review.

Osteoporotic fractures impose a substantial burden on patients with diabetes due to their unique characteristics in bone metabolism, limiting the efficacy of conventional fracture prediction tools. Artificial intelligence (AI) algorithms have shown great promise in predicting osteoporotic fractures. This review aims to evaluate the application of traditional fracture prediction tools (FRAX, QFracture, and Garvan FRC) in patients with diabetes and osteoporosis, review AI-based fracture prediction achievements, and assess the potential efficiency of AI algorithms in this population. This comprehensive literature search was conducted in Pubmed and Web of Science. We found that conventional prediction tools exhibit limited accuracy in predicting fractures in patients with diabetes and osteoporosis due to their distinct bone metabolism characteristics. Conversely, AI algorithms show remarkable potential in enhancing predictive precision and improving patient outcomes. However, the utilization of AI algorithms for predicting osteoporotic fractures in diabetic patients is still in its nascent phase, further research is required to validate their efficacy and assess the potential advantages of their application in clinical practice.

Association of Body Fat Distribution and Risk of Breast Cancer in Pre- and Postmenopausal Women.

INTRODUCTION: Obesity is a risk factor for both the development of and mortality from breast cancer in postmenopausal but not in premenopausal women. However, which part of the fat mass is associated with risk remains unclear, and whether the difference in the risk for breast cancer is associated with discrepancy in the distribution of fat with menstrual status requires further study. METHODS: A dataset from the UK Biobank, which included 245,009 female participants and 5,402 females who developed breast cancer during a mean follow-up of 6.6 years, was analyzed. Body fat mass was measured according to bioelectrical impedance at baseline by trained technicians. Age- and multivariable-adjusted hazard ratios and corresponding 95% confidence intervals for associations between body fat distribution and the risk for breast cancer were estimated using Cox proportional-hazards regression. Height, age, education level, ethnicity, index of multiple deprivation, alcohol intake, smoking, physical activity, fruit consumption, age at menarche, age at first birth, number of births, hormone replacement therapy, family history of breast cancer, hysterectomy, and ovariotomy were adjusted for potential confounders. RESULTS: Fat distribution differed between pre- and postmenopausal women. After menopause, there was an increase in fat mass in different body segments (arms, legs, and trunk). After age- and multivariable adjustment, fat mass in different segments, BMI, and waist circumference were significantly associated with the risk for breast cancer among postmenopausal but not premenopausal women. CONCLUSION: Postmenopausal women exhibited more fat in different body segments, which are associated with increased risk for breast cancer, compared to premenopausal women. Fat mass control throughout the body may be beneficial in mitigating the risk for breast cancer and was not limited to abdominal fat alone among postmenopausal women.

Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa.

Rhodomyrtus tomentosa is an important fleshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world. However, studies on the evolution and genomic breeding of R. tomentosa were hindered by the lack of a reference genome. Here, we presented a chromosome-level gap-free T2T genome assembly of R. tomentosa using PacBio and ONT long read sequencing. We assembled the genome with size of 470.35 Mb and contig N50 of ~43.80 Mb with 11 pseudochromosomes. A total of 33 382 genes and 239.31 Mb of repetitive sequences were annotated in this genome. Phylogenetic analysis elucidated the independent evolution of R. tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species. We identified four major compounds of anthocyanins and their synthetic pathways in R. tomentosa. Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R. tomentosa tends to be determined by the activation of anthocyanin synthesis pathway. The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process. The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R. tomentosa. Expression analysis and pathway identification enriched the importance of starch degradation, response to stimuli, effect of hormones, and cell wall metabolism during the fleshy fruit development in Myrtaceae. Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R. tomentosa.

Elastin-Derived VGVAPG Fragment Decorated Cell-Penetrating Peptide with Improved Gene Delivery Efficacy.

Cell-penetrating peptides (CPPs) are attractive non-viral gene delivery vectors due to their high transfection capacity and safety. Previously, we have shown that cell-penetrating peptide RALA can be a promising gene delivery vector for chronic wound regeneration application. In this study, we engineered a novel peptide called RALA-E by introducing elastin-derived VGVAPG fragment into RALA, in order to target the elastin-binding protein on the cell surface and thus improve delivery efficacy of RALA. The transfection efficiency of RALA-E was evaluated by transfecting the HEK-293T and HeLa cell lines cells with RALA-E/pDNA complexes and the flow-cytometry results showed that RALA-E significantly increased the transfection efficiency by nearly 20% in both cell lines compared to RALA. Inhibition of pDNA transfection on HEK-293T cells via chlorpromazine, genistein and mßCD showed that the inhibition extent in transfection efficiency was much less for RALA-E group compared to RALA group. In addition, RALA-E/miR-146a complexes showed up to 90% uptake efficiency in macrophages, and can escape from the endosome and enter the nucleus to inhibit the expression of inflammation genes. Therefore, the developed RALA-E peptide has high potential as a safe and efficient vector for gene therapy application.

BMAL1 collaborates with CLOCK to directly promote DNA double-strand break repair and tumor chemoresistance.

Accumulating evidence indicates a correlation between circadian dysfunction and genomic instability. However, whether the circadian machinery directly regulates DNA damage repair, especially in double-strand breaks (DSBs), remains poorly understood. Here, we report that in response to DSBs, BMAL1 is activated by ATM-mediated phosphorylation at S183. Phosphorylated BMAL1 is then localized to DNA damage sites, where it facilitates acetylase CLOCK to load in the chromatin, regulating the acetylation of histone H4 (H4Ac) at DSB sites. In this way, the BMAL1-CLOCK-H4Ac axis promotes the DNA end-resection to generate single-stranded DNA (ssDNA) and the subsequent homologous recombination (HR). BMAL1 deficient cells display defective HR, accumulation of unrepaired DSBs and genome instability. Accordingly, depletion of BMAL1 significantly enhances the sensitivity of adrenocortical carcinoma (ACC) to DNA damage-based therapy in vitro and in vivo. These findings uncover non-canonical function of BMAL1 and CLOCK in HR-mediated DSB repair, which may have an implication in cancer therapeutics.

Effects of vitamin D supplementation on autoantibodies and thyroid function in patients with Hashimoto's thyroiditis: A systematic review and meta-analysis.

BACKGROUND: Hashimoto's thyroiditis (HT) is the prevailing form of autoimmune thyroiditis and the leading cause of hypothyroidism in iodine-sufficient regions worldwide. This study aims to evaluate the efficacy of vitamin D supplementation on HT through a meta-analysis of randomized controlled trials (RCTs). METHODS: The databases searched included PubMed, and others. We included RCTs that the treatment group received vitamin D, while the control group received either a placebo or no treatment. The studies measured the baseline and endpoint levels of 25-hydroxyvitamin D [25(OH)D], thyroid-stimulating hormone (TSH), free thyroxine (FT4), free triiodothyronine (FT3), anti-thyroid peroxidase antibody (TPO-Ab), and thyroglobulin antibody (TG-Ab). We performed a meta-analysis to calculate the standardized mean difference (SMD) and 95% confidence interval (CI). RESULTS: A total of 12 studies involving 862 individuals were included. Vitamin D supplementation has a significant impact on reducing the titers of TPO-Ab (SMD = -1.084, 95% CI = -1.624 to -0.545) and TG-Ab (SMD = -0.996, 95% CI = -1.579 to -0.413) in patients with HT, and it also improves thyroid function by decreasing TSH level (SMD = -0.167, 95% CI = -0.302 to 0.031) and increasing FT3 (SMD = 0.549, 95% CI = 0.077-1.020) and FT4 (SMD = 0.734, 95% CI = 0.184-1.285) levels. Active vitamin D (calcitriol) significantly reduces the titer of TPO-Ab compared to naive forms of vitamin D (vitamin D2 or D3); treatment durations > 12 weeks result in a more effective reduction of TPO-Ab levels and a more significant increase in FT4 and FT3 levels in patients with HT (meta-regression P < .05). CONCLUSION: Vitamin D supplementation may have beneficial effects on HT patients by modulating immune responses and improving thyroid function.

Polyploid Genome Assembly Provides Insights into Morphological Development and Ascorbic Acid Accumulation of Sauropus androgynus.

Sauropus androgynus (S. androgynus) (2n = 4x = 52) is one of the most popular functional leafy vegetables in South and Southeast Asia. With its rich nutritional and pharmaceutical values, it has traditionally had widespread use for dietary and herbal purposes. Here, the genome of S. androgynus was sequenced and assembled, revealing a genome size of 1.55 Gb with 26 pseudo-chromosomes. Phylogenetic analysis traced back the divergence of Sauropus from Phyllanthus to approximately 29.67 million years ago (Mya). Genome analysis revealed that S. androgynus polyploidized around 20.51 Mya and shared a γ event about 132.95 Mya. Gene function analysis suggested that the expansion of pathways related to phloem development, lignin biosynthesis, and photosynthesis tended to result in the morphological differences among species within the Phyllanthaceae family, characterized by varying ploidy levels. The high accumulation of ascorbic acid in S. androgynus was attributed to the high expression of genes associated with the L-galactose pathway and recycling pathway. Moreover, the expanded gene families of S. androgynus exhibited multiple biochemical pathways associated with its comprehensive pharmacological activity, geographic adaptation and distinctive pleasurable flavor. Altogether, our findings represent a crucial genomic asset for S. androgynus, casting light on the intricate ploidy within the Phyllanthaceae family.

Chromosome-level genome assembly and functional characterization of terpene synthases provide insights into the volatile terpenoid biosynthesis of Wurfbainia villosa.

Wurfbainia villosa is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of China. Its dried fruits (called Fructus Amomi) are broadly used in traditional Chinese medicine for curing gastrointestinal diseases and are rich in volatile terpenoids. Here, we report a high-quality chromosome-level genome assembly of W. villosa with a total size of approximately 2.80 Gb, 42 588 protein-coding genes, and a very high percentage of repetitive sequences (87.23%). Genome analysis showed that W. villosa likely experienced a recent whole-genome duplication event prior to the W. villosa-Zingiber officinale divergence (approximately 11 million years ago), and a recent burst of long terminal repeat insertions afterward. The W. villosa genome enabled the identification of 17 genes involved in the terpenoid skeleton biosynthesis pathway and 66 terpene synthase (TPS) genes. We found that tandem duplication events have an important contribution to the expansion of WvTPSs, which likely drove the production of volatile terpenoids. In addition, functional characterization of 18 WvTPSs, focusing on the TPS-a and TPS-b subfamilies, showed that most of these WvTPSs are multi-product TPS and are predominantly expressed in seeds. The present study provides insights into the genome evolution and the molecular basis of the volatile terpenoids diversity in W. villosa. The genome sequence also represents valuable resources for the functional gene research and molecular breeding of W. villosa.

Clinical and Genetic Analysis of a Patient With Coexisting 17a-Hydroxylase/17,20-Lyase Deficiency and Moyamoya Disease.

17a-Hydroxylase/17,20-lyase deficiency (17OHD) is caused by pathogenic mutations in CYP17A1. Female patients present with hypertension, hypokalemia, and sexual infantilism while males present with sex development disorder. Moyamoya disease (MMD) is a chronic cerebrovascular disease that frequently results in intracranial ischemia or hemorrhage. The present study describes a case of 17OHD and MMD in a 27-year-old phenotypically female (46, XY) patient and discusses the clinical features and characteristics of her genetic defect. Clinical, hormonal, radiological, and genetic analyses were performed and blood samples were collected for whole-exome sequencing (WES). The results of the WES revealed a homozygous intronic mutation (c.297+2T>C) in CYP17A1, which led to combined 17a-hydroxylase/17,20-lyase deficiency, as well as novel variants in PCNT and CNOT3 that might lead to MMD. To our knowledge, this study is the first to describe 17OHD accompanied by MMD. While several cases have previously described patients with 17OHD with histories of cerebral hemorrhage or cerebral ischemia, a correlation in genetic levels between 17OHD and MMD was not found. The risk of cerebrovascular accidents should be considered in patients with 17OHD and hypertension. Cerebrovascular examination in patients with 17OHD may be beneficial for the prevention of life-threatening intracranial vascular disease.

Simple method for microwave photonic temperature interrogation with high resolution and sensitivity.

We propose a microwave photonic temperature interrogation system with high resolution and sensitivity based on temperature-to-time mapping with a simple structure. In this work, a bidirectional chirped optical signal is constructed, and the temperature information is mapped to the time interval change of the output pulses by filtering the bidirectional chirped optical signal using the transmission spectrum of a Fabry-Perot filter. Only a low-speed oscilloscope is required to extract the time interval of the output pulses in the proposed scheme, and complex data processing as well as synchronizing processes are avoided. In a proof-of-concept experiment, a high temperature interrogation sensitivity of 18.24 µs/°C and a high resolution of 0.035°C are realized, demonstrating good potential for practical applications.

Complete genome sequence and phylogenetic analysis of medicinal plant Abrus cantoniensis for evolutionary research and germplasm utilization.

Abrus cantoniensis Hance, a native medicinal plant in southern China, is officially recorded in the Chinese Pharmacopoeia. Here, we presented the first high-quality genome in Abrus genus, A. cantoniensis genome, as well as the detailed genomic information. The assembled genome size was 381.27 Mb with a scaffold N50 of 18.95 Mb, and 98.97% of the assembled sequences were anchored on 11 pseudochromosomes. The A. cantoniensis genome comprised 25,058 protein-coding genes and 45.12% of the assemblies were repetitive sequences. Comparative genome analysis suggested that chromosome translocation and inversion played an important role in the differentiation of Abrus. In addition, 24 toxin-related genes were identified, which formed two tandem gene clusters on chromosomes 2 and 3. The chromosome-level genome of A. cantoniensis obtained in this work provides a valuable resource for understanding the evolution, active ingredient biosynthesis, and genetic improvement for A. cantoniensis and Abrus species.

Pitaya Genome and Multiomics Database (PGMD): A Comprehensive and Integrative Resource of Selenicereus undatus.

Pitaya (Selenicereus) is a kind of novel fruit with a delicious taste and superior horticulture ornamental value. The potential economic impact of the pitaya lies in its diverse uses not only as agricultural produce and processed foods but also in industrial and medicinal products. It is also an excellent plant material for basic and applied biological research. A comprehensive database of pitaya would facilitate studies of pitaya and the other Cactaceae plant species. Here, we constructed pitaya genome and multiomics database, which is a collection of the most updated and high-quality pitaya genomic assemblies. The database contains various information such as genomic variation, gene expression, miRNA profiles, metabolite and proteomic data from various tissues and fruit developmental stages of different pitaya cultivars. In PGMD, we also uploaded videos on the flowering process and planting tutorials for practical usage of pitaya. Overall, these valuable data provided in the PGMD will significantly facilitate future studies on population genetics, molecular breeding and function research of pitaya.

Methylesterification of cell-wall pectin controls the diurnal flower-opening times in rice.

Flowers are the core reproductive organ of plants, and flowering is essential for cross-pollination. Diurnal flower-opening time is thus a key trait influencing reproductive isolation, hybrid breeding, and thermostability in plants. However, the molecular mechanisms controlling this trait remain unknown. Here, we report that rice Diurnal Flower Opening Time 1 (DFOT1) modulates pectin methylesterase (PME) activity to regulate pectin methylesterification levels of the lodicule cell walls, which affect lodicule swelling to control diurnal flower-opening time. DFOT1 is specifically expressed in the lodicules, and its expression gradually increases with the approach to flowering but decreases with flowering. Importantly, a knockout of DFOT1 showed earlier diurnal flower opening. We demonstrate that DFOT1 interacts directly with multiple PMEs to promote their activity. Knockout of PME40 also resulted in early diurnal flower opening, whereas overexpression of PME42 delayed diurnal flower opening. Lower PME activity was observed to be associated with higher levels of pectin methylesterification and the softening of cell walls in lodicules, which contribute to the absorption of water by lodicules and cause them to swell, thus promoting early diurnal flower opening. Higher PME activity had the opposite effect. Collectively, our work uncovers a molecular mechanism underlying the regulation of diurnal flower-opening time in rice, which would help reduce the costs of hybrid breeding and improve the heat tolerance of flowering plants by avoiding higher temperatures at anthesis.

Natural variations in grain length 10 (GL10) regulate rice grain size.

Grain size is an important determinant of grain weight and yield in rice. Although several genes related to grain size have been identified, natural variations in these genes that affect grain size are poorly characterized. Here, we describe the grain length QTL GL10, encoding MADS56, which positively regulates grain length and grain weight. A natural allelic variation of NIL-gl10, containing an ∼1.0-kb deletion in the first exon that abolishes its transcription, results in shorter grain length, lower grain weight and delayed flowering in gl10 plants. The knockout of GL10 in the HJX74 background leads to grain phenotypes similar to that of NIL-gl10, while overexpression of GL10 results in increased grain length and weight and earlier heading date. GL10 regulates grain length by promoting greater longitudinal cell growth in the grain glume. Additionally, GL10 participates in the regulation of gibberellic acid (GA) signaling pathway genes in young panicle tissues. Analysis of GL10 haplotypes shows obvious divergence between the japonica and indica lineages. Our findings reveal an allelic variation of GL10 that may explain differences in grain length among modern cultivars and could be used to breed rice varieties with optimized grain shape.