The rise of baobab trees in Madagascar.

The baobab trees (genus Adansonia) have attracted tremendous attention because of their striking shape and distinctive relationships with fauna1. These spectacular trees have also influenced human culture, inspiring innumerable arts, folklore and traditions. Here we sequenced genomes of all eight extant baobab species and argue that Madagascar should be considered the centre of origin for the extant lineages, a key issue in their evolutionary history2,3. Integrated genomic and ecological analyses revealed the reticulate evolution of baobabs, which eventually led to the species diversity seen today. Past population dynamics of Malagasy baobabs may have been influenced by both interspecific competition and the geological history of the island, especially changes in local sea levels. We propose that further attention should be paid to the conservation status of Malagasy baobabs, especially of Adansonia suarezensis and Adansonia grandidieri, and that intensive monitoring of populations of Adansonia za is required, given its propensity for negatively impacting the critically endangered Adansonia perrieri.

VvbHLH036, a basic helix-loop-helix transcription factor regulates the cold tolerance of grapevine.

Cold stress is an adverse environmental factor that limits the growth and productivity of horticulture crops such as grapes (Vitis vinifera). In this study, we identified a grapevine cold-induced basic helix-loop-helix (bHLH) transcription factor (VvbHLH036). Overexpression and CRISPR/Cas9-mediated knockout (KO) of VvbHLH036 enhanced and decreased cold tolerance in grapevine roots, respectively. Transcriptome analysis of VvbHLH036-overexpressed roots identified threonine synthase (VvThrC1) as a potential downstream target of VvbHLH036. We confirmed that VvbHLH036 could bind the VvThrC1 promoter and activate its expression. Both the transcripts of VvThrC1 and the content of threonine were significantly induced in the leaves and roots of grapevine under cold treatment compared to controls. Conversely, these dynamics were significantly suppressed in the roots of CRISPR/Cas9-induced knockout of VvbHLH036. These observations support the regulation of threonine accumulation by VvbHLH036 through VvThrC1 during cold stress in grapevine. Furthermore, overexpression and CRISPR/Cas9-mediated knockout of VvThrC1 also confirmed its role in regulating threonine content and cold tolerance in transgenic roots at low temperature. Exogenous threonine treatment increased cold tolerance and reduced the accumulation of superoxide anions and hydrogen peroxide in grapevine leaves. Together, these findings point to the pivotal role of VvbHLH036 and VvThrC1 in the cold stress response in grapes by regulating threonine biosynthesis.

Identifying the protective effects of miR-874-3p/ATF3 axis in intervertebral disc degeneration by single-cell RNA sequencing and validation.

Intervertebral disc degeneration (IVDD) severely affects the work and the quality of life of people. We previously demonstrated that silencing activation transcription factor 3 (ATF3) blocked the IVDD pathological process by regulating nucleus pulposus cell (NPC) ferroptosis, apoptosis, inflammation, and extracellular matrix (ECM) metabolism. Nevertheless, whether miR-874-3p mediated the IVDD pathological process by targeting ATF3 remains unclear. We performed single-cell RNA sequencing (scRNA-seq) and bioinformatics analysis to identify ATF3 as a key ferroptosis gene in IVDD. Then, Western blotting, flow cytometry, ELISA, and animal experiments were performed to validate the roles and regulatory mechanisms of miR-874-3p/ATF3 signalling axis in IVDD. ATF3 was highly expressed in IVDD patients and multiple cell types of IVDD rat, as revealed by scRNA-seq and bioinformatics analysis. GO analysis unveiled the involvement of ATF3 in regulating cell apoptosis and ECM metabolism. Furthermore, we verified that miR-874-3p might protect against IVDD by inhibiting NPC ferroptosis, apoptosis, ECM degradation, and inflammatory response by targeting ATF3. In vivo experiments displayed the protective effect of miR-874-3p/ATF3 axis on IVDD. These findings propose the potential of miR-874-3p and ATF3 as biomarkers of IVDD and suggest that targeting the miR-874-3p/ATF3 axis may be a therapeutic target for IVDD.

Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia.

BACKGROUND: Interest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea's niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models. RESULTS: There was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures). CONCLUSION: Our study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.

Alginate Oligosaccharides Enhance Gut Microbiota and Intestinal Barrier Function, Alleviating Host Damage Induced by Deoxynivalenol in Mice.

BACKGROUND: Alginate oligosaccharides (AOS) exhibits notable effects in terms of anti-inflammatory, antibacterial, and antioxidant properties. Deoxynivalenol (DON) has the potential to trigger intestinal inflammation by upregulating pro-inflammatory cytokines and apoptosis, thereby compromising the integrity of the intestinal barrier function and perturbing the balance of the gut microbiota. OBJECTIVES: We assessed the impact of AOS on mitigating DON-induced intestinal damage and systemic inflammation in mice. METHODS: After a 1-wk acclimatization period, the mice were divided into 4 groups. For 3 wk, the AOS and AOS + DON groups were gavaged daily with 200 µL of AOS [200 mg/kg body weight (BW)], whereas the CON and DON groups received an equivalent volume of sterile Phosphate-Buffered Saline (PBS). Subsequently, for 1 wk, the DON and AOS + DON groups received 100 µL of DON (4.8 mg/kg BW) daily, whereas the control (CON) and AOS groups continued receiving PBS. RESULTS: After administering DON via gavage to mice, there was a significant decrease (P < 0.05) in body weights compared with the CON group. Interestingly, AOS exhibited a tendency to mitigate this weight loss in the AOS + DON group. In the feces of mice treated with both AOS and DON, the concentration of DON significantly increased (P < 0.05) compared with the DON group alone. Histological analysis revealed that DON exposure caused increased intestinal damage, including shortened villi and eroded epithelial cells, which was ameliorated by presupplementation with AOS, alleviating harm to the intestinal barrier function. In both jejunum and colon tissues, DON exposure significantly reduced (P < 0.05) the expression of tight junction proteins (claudin and occludin in the colon) and the mucin protein mucin 2, compared with the CON group. Prophylactic administration of AOS alleviated these reductions, thereby improving the expression levels of these key proteins. Additionally, AOS supplementation protected DON-exposed mice by increasing the abundance of probiotics such as Bifidobacterium, Faecalibaculum, and Romboutsia. These gut microbes are known to enhance (P < 0.05) anti-inflammatory responses and the production of short-chain fatty acids (SCFAs), including total SCFAs, acetate, and valerate, compared with the DON group. CONCLUSIONS: This study unveils that AOS not only enhances gut microbiota and intestinal barrier function but also significantly mitigates DON-induced intestinal damage.

Plasma-derived exosomal protein SHP2 deficiency induces neutrophil hyperactivation in Behcet's uveitis.

To investigate the effect of plasma-derived exosomal proteins on neutrophil hyperactivation in Behcet's uveitis (BU), we treated neutrophils from healthy controls with plasma-derived exosomes from active BU patients, and determined the level of neutrophil activation by real-time quantitative PCR (RT-qPCR) and cytokine detection assay. The results revealed that exosomes from active BU patients could activate neutrophils as shown by increasing the expression levels of pro-inflammatory cytokines (IL-17 and IL-6), chemokines (IL-8 and MCP-1), and NETs (MPO and ELANE). Label-free quantitative proteomic analysis of plasma-derived exosomes from patients and healthy controls found a remarkably distinct protein profile and identified differentially expressed proteins (DEPs) between the two groups. The results of GO, KEGG, and GSEA enrichment analysis showed that DEPs were enriched in innate immune-mediated and neutrophil hyperactivation-related signaling pathways. The protein-protein interaction (PPI) analysis determined that SHP2 was a downregulated key hub protein in the exosomes of active BU patients. Knockdown of SHP2 in human neutrophil cell lines (NB4 cells) was shown to promote the secretion of pro-inflammatory cytokines, chemokines, and NETs. The converse effects were observed following SHP2 overexpression. In conclusion, we highlighted a pathogenic role of plasma-derived exosomal SHP2 deficiency in facilitating neutrophil activation and suggested that SHP2 might be an immunoprotective factor in BU pathologic process.

Systemic inflammation markers and the prevalence of hypertension in 8- to 17-year-old children and adolescents: A NHANES cross-sectional study.

BACKGROUND AND AIMS: The recent emphasis on systemic inflammation markers has focused primarily on their association with cardiac disorders, particularly the prevalence of hypertension, in adults but not children and adolescents. This research aimed to explore the associations between systemic inflammation markers and the occurrence of hypertension in 8- to 17-year-old children and adolescents in the United States. METHODS AND RESULTS: Data from 6095 participants under 18 years of age were obtained from the National Health and Nutritional Examination Survey (NHANES: 1999-2020). This study examined the associations between the incidence of hypertension and four indicators of systemic inflammation: the systemic immune-inflammation index (SII), neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and lymphocyte-to-monocyte ratio (LMR). Multivariate logistic regression analysis results are represented as odds ratios (ORs) and 95 % confidence intervals (CIs), and subgroup analyses were conducted to further explore associations. After fully adjusting for potential confounding covariates, the SII, NLR, and PLR were positively associated with hypertension. Compared with individuals in the bottom quartiles, those in the top SII, NLR, and PLR quartiles were 2.12, 2.11, and 1.57 times more likely to have hypertension, respectively. Conversely, the LMR was negatively associated with hypertension incidence, particularly among those in the highest LMR quartiles (OR = 0.59, 95 % CI = 0.39-0.88; P = 0.009). Subgroup analyses revealed that the four indicators exhibited strong correlations with hypertension in male subjects. CONCLUSION: This study revealed significant relationships between systemic inflammatory markers and hypertension incidence, highlighting the potential of these markers as hypertension risk indicators, particularly among male patients.

Association between Body Mass Index and Serum Uric Acid: mediation analysis involving liver enzymes indicators.

BACKGROUND: Numerous studies have indicated a growing prevalence of hyperuricemia. Elevated levels of serum uric acid (SUA) have been established as influential factors in conditions such as obesity, metabolic syndrome, diabetes mellitus, gout, and cardiovascular disease. Overweight and obesity are closely related to an increase in SUA. Our objective is to demonstrate the mediating role of liver enzyme in the correlation between body mass index (BMI) and SUA. METHODS: A total of 5925 adults aged 18 to 65 were included in this cross-sectional study. Logistic regression and mediation analysis were used to investigate the relationship between BMI and hyperuricemia as well as liver enzyme levels. Standard methods were used to determine the biochemical indexes, including SUA, liver enzymes, and blood lipids in the collected samples. RESULTS: The study revealed that the prevalence of hyperuricemia was 28.0%. Furthermore, the prevalence of overweight and obesity was as high as 48.5%, with 70.7% of this subgroup presenting with hyperuricemia. There was a positive correlation between BMI and hyperuricemia, and elevated levels of liver enzymes (ALT, AST, GGT) were associated with a higher risk of hyperuricemia. The study also observed a positive correlation between BMI and liver enzymes (ALT, AST, GGT). The study findings suggested that ALT, AST, and GGT played significant mediating roles in the relationship between BMI and SUA. Specifically, the unadjusted model revealed that ALT and GGT accounted for 22.12% and 18.13% of the mediation effects, respectively. CONCLUSIONS: The study found that BMI is associated with hyperuricemia, where liver enzyme abnormalities may have a mediating role. It is suggested that being overweight or obese may affect liver enzyme levels, leading to increased SUA levels. Controlling weight and liver enzyme levels may help prevent and treat hyperuricemia.

Anesthetic Management of One-Lung Ventilation in Patients With Tracheal Bronchus: A Narrative Review.

Tracheal bronchus is a rare congenital tracheal abnormality that generally refers to the right upper lobe bronchus of the lung that originates from the trachea. Tracheal bronchus is usually asymptomatic and is often accidentally detected by fiberoptic bronchoscopy or computed tomography for other conditions. Depending on the location of the tracheal bronchial opening and possible anatomical variations, the management of 1-lung ventilation in patients with tracheal bronchus is a significant challenge for anesthesiologists. To provide a reference for anesthesiologists to better manage anesthesia in such patients, we review the pathophysiology, definition, and Conacher classification of tracheal bronchus and then discuss the diagnosis of tracheal bronchus and management of 1-lung ventilation during anesthesia according to the Conacher classification.

Ecological restoration reduces mercury in corn kernel and the distinction of mercury in corn plants in rural China - A case in Wuchuan mercury mining area.

Corn is a crucial crop in China and is widely cultivated in the mercury (Hg) mining region of Guizhou. This study analyzed the Hg content in soil and corn plant samples from the Wuchuan Hg mining area (WCMA) and the surrounding non-Hg mining regions (SNMR). The findings suggest that ongoing ecological rehabilitation and environmental conservation measures in the WCMA have significantly decreased the Hg content in corn kernels. The Hg concentration in different parts of the corn plant varied, being higher in the roots, tassels, and leaves and lower in kernels and stalks. Hg stored in corn plant growing in the WCMA primarily originates from the soil (55.4%), while in the SNMR, it mainly comes from the atmosphere (74.9%). Despite counted only about 7% of the total plant mass, corn roots play a crucial role in soil Hg pollution remediation when corn is used for remediation. Household corn residues burning release about 58.5% and 66.9% of the stored Hg in corn plants growing in the WCMA and the SNMR, respectively, into the atmosphere. Our findings indicate that corn cultivation acts as a reservoir for both soil and atmospheric Hg in the SNMR, while in the WCMA, it serves as a source of atmospheric Hg.

Exploring the Timing of Disengagement From Nondriving Related Tasks in Scheduled Takeovers With Pre-Alerts: An Analysis of Takeover-Related Measures.

OBJECTIVES: This study aimed to investigate drivers' disengagement from nondriving related tasks (NDRT) during scheduled takeovers and to evaluate its impact on takeover performance. BACKGROUND: During scheduled takeovers, drivers typically have sufficient time to prepare. However, inadequate disengagement from NDRTs can introduce safety risks. METHOD: Participants experienced scheduled takeovers using a driving simulator, undergoing two conditions, with and without an NDRT. We assessed their takeover performance and monitored their NDRT disengagement from visual, cognitive, and physical perspectives. RESULTS: The study examined three NDRT disengagement timings (DTs): DT1 (disengaged before the takeover request), DT2 (disengaged after the request but before taking over), and DT3 (not disengaged). The impact of NDRT on takeover performance varied depending on DTs. Specifically, DT1 demonstrated no adverse effects; DT2 impaired takeover time, while DT3 impaired both takeover time and quality. Additionally, participants who displayed DT1 exhibited longer eye-off-NDRT duration and a higher eye-off-NDRT count during the prewarning stage compared to those with DT2 and DT3. CONCLUSION: Drivers can benefit from earlier disengagement from NDRTs, demonstrating resilience to the adverse effects of NDRTs on takeover performance. The disengagement of cognition is often delayed compared to that of eyes and hands, potentially leading to DT3. Moreover, visual disengagement from NDRTs during the prewarning stage could distinguish DT1 from the other two. APPLICATION: Our study emphasizes considering NDRT disengagement in designing systems for scheduled takeovers. Measures should be taken to promote early disengagement, facilitate cognitive disengagement, and employ visual disengagement during the prewarning period as predictive indicators of DTs.

11B NMR of the Morphological Evolution of Traditional Chinese Medicine Borax.

This article applies nuclear magnetic resonance technology to the study of boron-containing traditional Chinese medicine, in order to explore the morphological evolution of boron elements in traditional Chinese medicine. Borax is a traditional Chinese medicine with anti-corrosion, anti-inflammatory, antibacterial, and anticonvulsant effects. It is made by boiling, removing stones, and drying borax minerals like borate salts. This article introduces an 11B nuclear magnetic resonance method for identifying and characterizing boron-containing compounds in TCM. We applied this technology to borax aqueous solutions in different chemical environments and found that with boron mixed in the form of SP2 hybridization in equilateral triangles and SP3 hybridization in equilateral tetrahedra, the pH changes in alkaline environments significantly affected the ratio of the two. At the same time, it was found that in addition to the raw material peak, boron signals of other boron-containing compounds were also detected in 20 commercially available boron-containing TCM preparations. These new boron-containing compounds may be true pharmaceutical active ingredients, and adding them directly to the formula can improve quality and safety. This article describes the detection of 11B NMR in boron-containing traditional Chinese medicine preparations. It is simple, non-destructive, and can provide chemical fingerprint studies for boron-containing traditional Chinese medicine.

Spatiotemporal response of the optical characteristics of dissolved organic matter to seasonality and land use in tropical island rivers.

Dissolved organic matter (DOM), a pivotal component in the global carbon cycle, plays a crucial role in maintaining the productivity and functionality of aquatic ecosystems. However, the driving factors of variations in the properties of riverine DOM in tropical islands still remain unclear. In this study, the spatiotemporal response of the optical characteristics of riverine DOM to seasonality and land use on Hainan Island in southern China was investigated. Our results revealed that DOM in the rivers of Hainan Island exhibited a relatively high proportion of fulvic acid and demonstrated strong terrestrial sources. The optical properties of DOM exhibited significant variations both seasonally and spatially. Land use exerted a dominant influence on riverine DOM. Specifically, during the wet season, riverine DOM exhibited larger molecular weight, increased chromophoric DOM (CDOM) abundance, and higher Fmax compared to the dry season. Furthermore, riverine DOM influenced by grassland and farmland showed higher CDOM abundance, Fmax, and humification degree in contrast to those impacted by forest and urban. Random forest and correlation analysis results indicated that grassland and farmland enhanced the Fmax of DOM by increasing levels of TP, NO3--N, Chl a, and NH4+-N in the dry season. However, during the wet season, the increased Fmax of DOM induced by grassland and farmland relied on the increments of Chl a and TP concentrations. This study improves our understanding of the spatiotemporal fluctuations of DOM in the rivers of Hainan Island, highlighting the effects of season and land use on DOM. It offers valuable support for improving water quality and contributes to enhancing human comprehension of the global carbon cycle.

Phylogenomic Analyses of Alismatales Shed Light into Adaptations to Aquatic Environments.

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptations to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptations, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the three main clades that was best explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light- or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and WGDs using phylogenomics.

Two-Dimensional Ultrathin Graphic Carbon Nitrides with Extended π-Conjugation as Extraordinary Efficient Hydrogen Evolution Photocatalyst.

Construction of 2D graphic carbon nitrides (g-CNx ) with wide visible light adsorption range and high charge separation efficiency concurrently is of great urgent demand and still very challenging for developing highly efficient photocatalysts for hydrogen evolution. To achieve this goal, a two-step pyrolytic strategy has been applied here to create ultrathin 2D g-CNx with extended the π-conjugation. It is experimentally proven that the extension of π-conjugation in g-CNx is not only beneficial to narrowing the bandgap, but also improving the charge separation efficiency of the g-CNx . As an integral result, extraordinary apparent quantum efficiencies (AQEs) of 57.3% and 7.0% at short (380 nm) and long (520 nm) wavelength, respectively, are achieved. The formation process of the extended π-conjugated structures in the ultrathin 2D g-CNx has been investigated using XRD, FT-IR, Raman, XPS, and EPR. Additionally, it has been illustrated that the two-step pyrolytic strategy is critical for creating ultrathin g-CNx nanosheets with extended π-conjugation by control experiments. This work shows a feasible and effective strategy to simultaneously expand the light adsorption range, enhance charge carrier mobility and depress electron-hole recombination of g-CNx for high-efficient photocatalytic hydrogen evolution.

Simultaneous diagnosis of tuberculous pleurisy and malignant pleural effusion using metagenomic next-generation sequencing (mNGS).

BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a powerful tool for pathogen detection, but the value of human sequencing reads generated from it is underestimated. METHODS: A total of 138 patients with pleural effusion (PE) were diagnosed with tuberculous pleurisy (TBP, N = 82), malignant pleural effusion (MPE, N = 35), or non-TB infection (N = 21), whose PE samples all underwent mNGS analysis. Clinical TB tests including culture, Acid-Fast Bacillus (AFB) test, Xpert, and T-SPOT, were performed. To utilize mNGS for MPE identification, 25 non-MPE samples (20 TBP and 5 non-TB infection) were randomly selected to set human chromosome copy number baseline and generalized linear modeling was performed using copy number variant (CNV) features of the rest 113 samples (35 MPE and 78 non-MPE). RESULTS: The performance of TB detection was compared among five methods. T-SPOT demonstrated the highest sensitivity (61% vs. culture 32%, AFB 12%, Xpert 35%, and mNGS 49%) but with the highest false-positive rate (10%) as well. In contrast, mNGS was able to detect TB-genome in nearly half (40/82) of the PE samples from TBP subgroup, with 100% specificity. To evaluate the performance of using CNV features of the human genome for MPE prediction, we performed the leave-one-out cross-validation (LOOCV) in the subcohort excluding the 25 non-MPE samples for setting copy number standards, which demonstrated 54.1% sensitivity, 80.8% specificity, 71.7% accuracy, and an AUC of 0.851. CONCLUSION: In summary, we exploited the value of human and non-human sequencing reads generated from mNGS, which showed promising ability in simultaneously detecting TBP and MPE.

Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.

BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities. METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP)161-180 was investigated using a similarity search in the NCBI protein BLAST program (BLASTP). Enzyme-linked Immunosorbent Assay (ELISA) was performed to evaluate the cross-reactive responses of experimental autoimmune uveitis (EAU)-derived lymphocytes and BU patients-derived peripheral blood mononuclear cells (PBMCs) against homologous peptides. The area under the curve (AUC) analysis was used to test the sensitivity and specificity of gut microbial biomarkers. RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP161-180. In vitro experiments showed that lymphocytes from EAU or PBMCs from BU patients reacted to this peptide antigen as shown by the production of IFN-γ and IL-17. Addition of the SteTDR peptide to the classical IRBP immunization protocol exacerbated EAU severity. Gut microbial marker profiles consisted of 24 species and 32 species respectively differentiated BU and VKH from each other as well as from the other four immune-mediated diseases and healthy controls. Protein annotation identified 148 and 119 specific microbial proteins associated with BU and VKH, respectively. For metabolic function analysis, 108 and 178 metabolic pathways were shown to be associated with BU and VKH, respectively. CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.

Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica.

Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.

Evolution of 101 Apocynaceae plastomes and phylogenetic implications.

Apocynaceae are one of the ten species-richest angiosperm families. However, the backbone phylogeny of the family is yet less well supported, and the evolution of plastome structure has not been thoroughly studied for the whole family. Herein, a total of 101 complete plastomes including 35 newly sequenced, 24 reassembled from public raw data and the rest from the NCBI GenBank database, representing 26 of 27 tribes of Apocynaceae, were used for comparative plastome analysis. Phylogenetic analyses were conducted using a combined plastid data matrix of 77 protein-coding genes from 162 taxa, encompassing all tribes and 41 of 49 subtribes of Apocynaceae. Plastome lengths ranged from 150,897 bp in Apocynum venetum to 178,616 bp in Hoya exilis. Six types of boundaries between the inverted repeat (IR) regions and single copy (SC) regions were identified. Different sizes of IR expansion were found in three lineages, including Alyxieae, Ceropegieae and Marsdenieae, suggesting multiple expansion events of the IRs over the SC regions in Apocynaceae. The IR regions of Marsdenieae evolved in two ways: expansion towards the large single copy (LSC) region in Lygisma + Stephanotis + Ruehssia + Gymnema (Cosmopolitan clade), and expansion towards both LSC and small single copy (SSC) region in Dischidia-Hoya alliance and Marsdenia (Asia-Pacific clade). Six coding genes and five non-coding regions were identified as highly variable, including accD, ccsA-ndhD, clpP, matK, ndhF, ndhG-ndhI, trnG(GCC)-trnfM(CAU), trnH(GUG)-psbA, trnY(GUA)-trnE(UUC), ycf1, and ycf2. Maximum likelihood and Bayesian phylogenetic analyses resulted in nearly identical tree topologies and produced a well-resolved backbone comprising 15 consecutive dichotomies that subdivided Apocynaceae into 15 clades. The subfamily Periplocoideae were embedded in the Apocynoid grade and were sister to the Echiteae-Odontadenieae-Mesechiteae clade with high support values. Three tribes (Melodineae, Vinceae, and Willughbeieae), the subtribe Amphineuriinae, and four genera (Beaumontia, Ceropegia, Hoya, and Stephanotis) were not resolved as monophyletic. Our work sheds light on the backbone phylogenetic relationships in the family Apocynaceae and offers insights into the evolution of Apocynaceae plastomes using the most densely sampled plastome dataset to date.

An updated phylogeny, biogeography, and PhyloCode-based classification of Cornaceae based on three sets of genomic data.

PREMISE: A major goal of systematic biology is to uncover the evolutionary history of organisms and translate that knowledge into stable classification systems. Here, we integrate three sets of genome-wide data to resolve phylogenetic relationships in Cornaceae (containing only Cornus s.l.), reconstruct the biogeographic history of the clade, and provide a revised classification using the PhyloCode to stabilize names for this taxonomically controversial group. METHODS: We conducted phylogenetic analyses using 312 single-copy nuclear genes and 70 plastid genes from Angiosperms353 Hyb-Seq, plus numerous loci from RAD-Seq. We integrated fossils using morphological data and produced a dated phylogeny for biogeographical analysis. RESULTS: A well-resolved, strongly supported, comprehensive phylogeny was obtained. Biogeographic analyses support an origin and rapid diversification of Cornus into four morphologically distinct major clades in the Northern Hemisphere (with an eastern Asian ancestor) during the late Cretaceous. Dispersal into Africa from eastern Asia likely occurred along the Tethys Seaway during the Paleogene, whereas dispersal into South America likely occurred during the Neogene. Diversification within the northern hemisphere likely involved repeated independent colonization of new areas during the Paleogene and Neogene along the Bering Land Bridge, the North Atlantic Land Bridge, and the Tethys Seaway. Thirteen strongly supported clades were named following rules of the PhyloCode. CONCLUSIONS: Our study provides an example of integrating genomic and morphological data to produce a robust, explicit species phylogeny that includes fossil taxa, which we translate into an updated classification scheme using the PhyloCode to stabilize names.