Genome-wide association study of carotenoids in maize kernel.

In this study, the contents of four carotenoids in 244 maize inbred lines were detected and about three million single nucleotide polymorphisms (SNPs) for genome-wide association study to preliminarily analyze the genetic mechanism of maize kernel carotenoids. We identified 826 quantitative trait loci (QTLs) were significantly associated with carotenoids contents, and two key candidate genes Zm00001d029526 (CYP18) and Zm00001d023336 (wrky91) were obtained. In addition, we found a germplasm IL78 with higher carotenoids. The results of this study can provide a theoretical basis for screening genes that guide kernel carotenoids selection breeding.

Enhanced immune reconstitution with albuvirtide in HIV-infected immunological non-responders.

Background: Incomplete immune recovery in people living with HIV/AIDS (PLWHA) remains an important clinical challenge with the lack of an effective strategy currently available to restore their T-cell immune response. This study aimed to evaluate the effect of Albuvirtide (ABT) on immune recovery in immunological non-responders (INRs) and attempted to explore potential mechanisms of ABT on the functionality of immune cells. Methods: In this prospective, open-label, controlled clinical study, participants with incomplete immune reconstitution (continuous ART over 5 years and CD4+T lymphocyte absolute count of <500 cells/µl or ART for 2-5 years and CD4+T cell count of <200 cells/µl with undetectable viral load) were received intensive treatment with ABT or maintained on the original ART regimen at a ratio of 1:1. Immune response and safety were examined within 24 weeks. In the cytological study, T subsets, cell apoptosis and cell autophagy were analyzed using immunofluorescence staining and flow cytometry from 25 blood specimens. Results: Both groups (n=25 each) were comparable in age, gender, and ART duration. At week 12, CD4+T cell count increased significantly in the intensive ABT group compared with control group (the change from baseline in CD4+T cell count: 45 vs. -5 cells/µL, p<0.001). After ABT discontinuation, CD4+T cell counts remained significantly higher in the intensive ABT group at week 24 (55 vs. -5 cells/µL, p=0.012). In laboratory analysis, naïve CD4+ T cell amounts were lowest among participants with unsatisfactory immune response (uIR) to ABT (p=0.001). The proportion of caspase 3+CD45RA+CD31+CD4+ T cells was significantly lower in participants with satisfactory immune response (sIR) to ABT (p<0.05). Conclusion: Significant CD4+T cell count increase suggests ABT enhances immune function in INRs which may be attributed to its antiviral properties as well as its ability to increase thymic cell output and decrease cell apoptosis.

Whole-genome sequencing of a worldwide collection of sugarcane cultivars (Saccharum spp.) reveals the genetic basis of cultivar improvement.

Sugarcane is the main source of sugar worldwide, and 80% of the sucrose production comes from sugarcane. However, the genetic differentiation and basis of agronomic traits remain obscure. Here, we sequenced the whole-genome of 219 elite worldwide sugarcane cultivar accessions. A total of approximately 6 million high-quality genome-wide single nucleotide polymorphisms (SNPs) were detected. A genome-wide association study identified a total of 2198 SNPs that were significantly associated with sucrose content, stalk number, plant height, stalk diameter, cane yield, and sugar yield. We observed homozygous tendency of favor alleles of these loci, and over 80% of cultivar accessions carried the favor alleles of the SNPs or haplotypes associated with sucrose content. Gene introgression analysis showed that the number of chromosome segments from Saccharum spontaneum decreased with the breeding time of cultivars, while those from S. officinarum increased in recent cultivars. A series of selection signatures were identified in sugarcane improvement procession, of which 104 were simultaneously associated with agronomic traits and 45 of them were mainly associated with sucrose content. We further proposed that as per sugarcane transgenic experiments, ShN/AINV3.1 plays a positive role in increasing stalk number, plant height, and stalk diameter. These findings provide comprehensive resources for understanding the genetic basis of agronomic traits and will be beneficial to germplasm innovation, screening molecular markers, and future sugarcane cultivar improvement.

[Effect of Exogenous Chitosan on Physiological Properties, Antioxidant Activity, and Cadmium Uptake of Wheat (Triticum aestivum L.) Seedlings Under Cadmium Stress].

This research aimed to clarify the effects of exogenously applied chitosan on the physiological characteristics, antioxidant activities, and Cd accumulation of wheat (Triticum aestivum L.) seedlings under cadmium (Cd) stress and to identify the key indicators based on the partial least squares model. The wheat variety studied was Bainong207 (BN207), and Cd-stress was achieved by growing seedlings in a hydroponic culture experiment with 10 and 25 µmol·L-1 Cd2+ added to the culture solution. It was found that both Cd-stress at 10 and 25 µmol·L-1 significantly inhibited the chlorophyll content, photosynthesis, and biomass accumulation of wheat seedlings. Seedling roots became shorter and thicker, and the lateral roots decreased under Cd-stress. The Cd-stress also increased H2O2 and MDA accumulation and the degree of cell membrane lipid peroxidation and affected the activities of antioxidant enzymes such as superoxide dismutase (SOD) and peroxidase (POD). Under Cd stress, exogenous chitosan decreased the Cd content in the aboveground and underground parts of wheat by 13.22 %-21.63 % and 7.92 %-28.32 % and reduced Cd accumulation in the aboveground and underground parts by 5.37 %-6.71 % and 1.91 %-4.09 %, respectively. Whereas exogenous chitosan application significantly reduced the content of H2O2 in roots and aboveground parts of wheat by 38.21 %-47.46 % and 45.81 %-55.73 % and MDA content by 37.65 %-48.12 % and 29.87 %-32.51 %, it increased the activities of SOD and POD in roots by 2.78 %-5.61 % and 13.81 %-18.33 %, respectively. In summary, exogenous chitosan can improve the photosynthetic characteristics and antioxidant enzyme activities of wheat seedlings under Cd stress, reduce the content and accumulation of Cd in the root and aboveground parts of wheat, and alleviate the damage of lipid peroxidation to the cell membrane. All of these results provide the basal data for the application of exogenous chitosan to alleviate Cd toxicity to wheat seedlings.

[Mitigative Effect of Rare Earth Element Cerium on the Growth of Zinc-stressed Wheat （Triticum aestivum L.）Seedlings].

This research aimed to clarify the mitigative effect of exogenously applied rare earth element cerium （Ce） on the growth， zinc （Zn） accumulation， and physiological characteristics of wheat （Triticum aestivum L.） seedlings under Zn stress. The wheat variety studied was Bainong307 （BN307）， and Zn stress was achieved by growing seedlings in a hydroponic culture experiment with 500 µmol·L-1 Zn2 + added to the culture solution. It was found that Zn stress at 500 µmol·L-1 significantly inhibited the chlorophyll content， photosynthesis， and biomass accumulation of wheat seedlings. Seedling roots became shorter and thicker， and the lateral roots decreased under Zn stress. The Zn stress also increased MDA accumulation and the degree of cell membrane lipid peroxidation and reduced soluble protein contents and the activities of antioxidant enzymes such as superoxide dismutase （SOD）， catalase （CAT）， and ascorbate peroxidase （APX）. On the contrary， exogenous Ce decreased the adsorption and transport of Zn by the root system and alleviated the damage of Zn stress to wheat seedlings. Specifically， the increase in chlorophyll content （chlorophyll a， chlorophyll b， and total chlorophyll） and photosynthetic parameters， the enhancement of antioxidant enzymes activities and soluble protein levels， and the reduction in MDA content and the damage of lipid peroxidation to the cell membrane were all driven by exogenous Ce， which ultimately led to the increase in dry matter biomass of the root system and shoot. In summary， these results provide basic data for the application of exogenous Ce to alleviate Zn toxicity to plants.

Spatial and Temporal Disparity Analyses of Glycosylated Benzaldehyde and Identification and Expression Pattern Analyses of Uridine Diphosphate Glycosyltransferase Genes in Prunus mume.

The species Prunus mume consists of uniquely aromatic woody perennials with large amounts of free aromatic substances in the flower cells. Uridine diphosphate glycosyltransferase (UGT) modifies these free aromatic substances into water-soluble glycoside-bound volatiles (GBVs) which play an important role in regulating the use of volatiles by plants for information exchange, defense, and stress tolerance. To investigate the changes in the glycosidic state of aromatic substances during the flowering period of P. mume and discern the location and expression of glycoside synthesis genes, we extracted and enzymatically hydrolyzed GBVs of P. mume and then utilized gas chromatography-mass spectrometry (GC-MS) to characterize and analyze the types and contents of GBV glycosides. Further, we identified and classified the members of the UGT gene family of P. mume using the bioinformatic method and analyzed the correlation between the expression of the UGT family genes in P. mume and the changes in glycosidic content. The results showed that the benzenoids were the main aromatic substance that was glycosylated during flowering in P. mume and that glycosidic benzaldehyde was the most prevalent compound in different flower parts and at different flowering stages. The titer of glycoside benzaldehyde gradually increased during the bud stage and reached the highest level at the big bud stage (999.6 µg·g-1). Significantly, titers of glycoside benzaldehyde significantly decreased and stabilized after flowering while the level of free benzaldehyde, in contrast, significantly increased and then reached a plateau after the flowering process was completed. A total of 155 UGT family genes were identified in the P. mume genome, which were divided into 13 subfamilies (A-E, G-N); according to the classification of Arabidopsis thaliana UGT gene subfamilies, the L subfamily contains 17 genes. The transcriptome analysis showed that PmUGTL9 and PmUGTL13 were highly expressed in the bud stage and were strongly correlated with the content of the glycosidic form of benzaldehyde at all stages of flowering. This study provides a theoretical basis to elucidate the function of UGT family genes in P. mume during flower development, to explore the mechanism of the storage and transportation of aromatic compounds in flower tissues, and to exploit industrial applications of aromatic products from P. mume.

Microbial metabolite enhances immunotherapy efficacy by modulating T cell stemness in pan-cancer.

The immune checkpoint blockade (ICB) response in human cancers is closely linked to the gut microbiota. Here, we report that the abundance of commensal Lactobacillus johnsonii is positively correlated with the responsiveness of ICB. Supplementation with Lactobacillus johnsonii or tryptophan-derived metabolite indole-3-propionic acid (IPA) enhances the efficacy of CD8+ T cell-mediated αPD-1 immunotherapy. Mechanistically, Lactobacillus johnsonii collaborates with Clostridium sporogenes to produce IPA. IPA modulates the stemness program of CD8+ T cells and facilitates the generation of progenitor exhausted CD8+ T cells (Tpex) by increasing H3K27 acetylation at the super-enhancer region of Tcf7. IPA improves ICB responsiveness at the pan-cancer level, including melanoma, breast cancer, and colorectal cancer. Collectively, our findings identify a microbial metabolite-immune regulatory pathway and suggest a potential microbial-based adjuvant approach to improve the responsiveness of immunotherapy.

Causal association of gut microbiota on spondyloarthritis and its subtypes: a Mendelian randomization analysis.

Background: Despite establishing an association between gut microbiota and spondyloarthritis (SpA) subtypes, the causal relationship between them remains unclear. Methods: Gut microbiota data were obtained from the MiBioGen collaboration, and SpA genome-wide association study (GWAS) summary data were obtained from the FinnGen collaboration. We conducted a two-sample Mendelian randomization (MR) analysis using the inverse-variance-weighted method supplemented with four additional MR methods (MR-Egger, weighted median, simple mode, and weighted mode). Pleiotropy and heterogeneity were also assessed. Reverse MR analysis was used to detect reverse causal relationships. Results: We identified 23 causal links between specific gut microbiota taxa and SpA levels. Of these, 22 displayed nominal causal associations, and only one demonstrated a robust causal connection. Actinobacteria id.419 increased the risk of ankylosing spondylitis (AS) (odds ratio (OR) = 1.86 (95% confidence interval (CI): 1.29-2.69); p = 8.63E-04). The family Rikenellaceae id.967 was associated with a reduced risk of both AS (OR = 0.66 (95% CI: 0.47-0.93); p = 1.81E-02) and psoriatic arthritis (OR = 0.70 (95% CI: 0.50-0.97); p = 3.00E-02). Bacillales id.1674 increased the risk of AS (OR = 1.23 (95% CI: 1.00-1.51); p = 4.94E-02) and decreased the risk of enteropathic arthritis (OR = 0.56 (95% CI: 0.35-0.88); p = 1.14E-02). Directional pleiotropy, or heterogeneity, was not observed. No reverse causal associations were observed between the diseases and the gut microbiota. Conclusion: Our MR analysis suggested a genetic-level causal relationship between specific gut microbiota and SpA, providing insights into the underlying mechanisms behind SpA development mediated by gut microbiota.

Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize.

BACKGROUND: Maize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour traits, an association panel including 244 superior maize inbred lines was used to measure and analyse the six traits related to kernel colour in two environments and was then combined with the about 3 million SNPs covering the whole maize genome in this study. Two models (Q + K, PCA + K) were used for genome-wide association analysis (GWAS) of kernel colour traits. RESULTS: We identified 1029QTLs, and two SNPs contained in those QTLs were located in coding regions of Y1 and R1 respectively, two known genes that regulate kernel colour. Fourteen QTLs which contain 19 SNPs were within 200 kb interval of the genes involved in the regulation of kernel colour. 13 high-confidence SNPs repeatedly detected for specific traits, and AA genotypes of rs1_40605594 and rs5_2392770 were the most popular alleles appeared in inbred lines with higher levels. By searching the confident interval of the 13 high-confidence SNPs, a total of 95 candidate genes were identified. CONCLUSIONS: The genetic loci and candidate genes of maize kernel colour provided in this study will be useful for uncovering the genetic mechanism of maize kernel colour, gene cloning in the future. Furthermore, the identified elite alleles can be used to molecular marker-assisted selection of kernel colour traits.

Comparison of results and age-related changes in establishing reference intervals for CEA, AFP, CA125, and CA199 using four indirect methods.

•The reference intervals calculated using RefineR, Kosmic, TMC, and non-parametric methods are similar.•TMC algorithm is more robust, demonstrates a high pass rate among the four methods and has the ability to automatically isolate outliers.•The reference intervals of CA125 and CA199 showed significant differences between age and sex.