Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot.

Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibirica, P. mandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for P. zhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of P. zhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.

Sustainable electro-Fenton simultaneous reduction of Cr (VI) and degradation of organic pollutants via dual-site porous carbon cathode driving uncoordinated molybdenum sites conversion.

Simultaneous removal of heavy metals and organic contaminants remains a substantial challenge in the electro-Fenton (EF) system. Herein, we propose a facile and sustainable "iron-free" EF system capable of simultaneously removing hexavalent chromium (Cr (VI)) and para-chlorophenol (4-CP). The system comprises a nitrogen-doped and carbon-deficient porous carbon (dual-site NPC-D) cathode coupled with a MoS2 nanoarray promoter (MoS2 NA). The NPC-D/MoS2 NA system exhibits exceptional synergistic electrocatalytic activity, with removal rates for Cr (VI) and 4-CP that are 20.3 and 4.4 times faster, respectively, compared to the NPC-D system. Mechanistic studies show that the dual-site structure of NPC-D cathode favors the two-electron oxygen reduction pathway with a selectivity of 81 %. Furthermore, an electric field-driven uncoordinated Mo valence state conversion of MoS2 NA enchances the generation of dynamic singlet oxygen and hydroxyl radicals. Notably, this system shows outstanding recyclability, resilience in real wastewater, and sustainability during a 3 L scale-up operation, while effectively mitigating toxicity. Overall, this study presents an effective approach for treating multiple-component wastewater and highlights the importance of structure-activity correlation in synergistic electrocatalysis.

Enhanced ammonia oxidation by a photoelectrocatalysis­chlorine system: The role of ClO• and free chlorine.

The decomposition of ammonia-N to environmental-friendly N2 remains a fundamental problem for water treatment. We proposed a way to selectively and efficiently oxidize ammonia to N2 through an integrated photoeletrocatalysis­chlorine reactions (PECCl) system based on a bifunctional TiO2 nanotube photoanode. The ·OH and HClO can be simultaneously generated on the TiO2 nanotube photoanode in this system, which can in situ form ClO· for efficient ammonia removal. Compared with electrochemical­chlorine (EC-Cl), photocatalysis­chlorine (PC-Cl) and photoelectrocatalysis (PEC) systems, the PEC-Cl system exhibited much higher electrocatalytic activity due to the synergetic effect of photoelectrocatalyst and electrocatalyst in bifunctional TiO2 nanotube electrode. The removal efficiency of ammonia-N and total-N reached 100.0 % and 93.3 % at 0.3 V (vs Ag/AgCl) in the PEC-Cl system. Moreover, the system was efficient under various pH conditions. The reactions between ClO-/ClO· and the N-containing intermediates contributed to the high performance of the system, which expanded the reactions from the electrode surface to the electrolyte. Furthermore, radical scavenging and free chlorine determination experiments confirmed that ClO· and free chlorine were the main active species that enabled the ammonia oxidation. This study presents new understanding on the role of active species for ammonia removal in wastewater.

Evaluation of the lncRNA-miRNA-mRNA ceRNA network in lungs of miR-147 -/- mice.

Background: Previous studies have documented important roles for microRNA-147 (miR-147) in inflammation, radiation-induced injury, cancer, and a range of other diseases. Murine lungs exhibit high levels of miRNA, mRNA, and lncRNA expression. However, very little research to date has focused on the lncRNA-miRNA-mRNA competing endogenous RNA (ceRNA) networks associated with miR-147, and the regulation of lncRNAs and miRNAs in this setting remains poorly understood. Methods: After establishing a miR-147-/- model mouse, samples of lung tissue were harvested for RNA-sequencing, and differentially expressed lncRNAs, miRNAs, and mRNAs were identified. The miRNA targets of these lncRNAs and the identified miRNAs were first overlapped to facilitate the prediction of target mRNAs, with analyses then examining the overlap between these targets and mRNAs that were differentially expressed. Then, these target mRNAs were subjected to pathway enrichment analyses. These results were ultimately used to establish a miR-147-related ceRNA network. Results: Relative to wild-type mice, the lungs of miR-147-/- mice exhibited 91, 43, and 71 significantly upregulated lncRNAs, miRNAs, and mRNAs, respectively, together with 114, 31, and 156 that were significantly downregulated. The lncRNA-miRNA-mRNA network established based on these results led to the identification of Kcnh6 as a differentially expressed hub gene candidate and enabled the identification of a range of regulatory relationships. KEGG pathway enrichment showed that the mRNA targets of differentially expressed lncRNAs and miRNAs in the mice were associated with tumor-related signaling, endometrial cancer, bladder cancer, and ErbB signaling. Conclusion: These results suggest that the identified ceRNA network in miR-147-/- mice shapes tumor-associated signaling activity, with miR-147 potentially regulating various lncRNAs and miRNAs through Kcnh6, ultimately influencing tumorigenesis. Future studies of the lncRNA, miRNA, and mRNA regulatory targets shown to be associated with miR-147 in the present study may ultimately lead to the identification of novel clinically relevant targets through which miR-147 shapes the pathogenesis of cancer and other diseases.

High-throughput identification of meat ingredients in adulterated foods based on centrifugal integrated purification-CRISPR array.

Rapid, accurate, and sensitive analytical methods for the detection of food fraud are now an urgent requirement in the global food industry to ensure food quality. In response to this demand, a centrifugal integrated purification-CRISPR array for meat adulteration (CIPAM) was established. In detail, CIPAM system combines microneedles for DNA extraction and RAA-CRISPR/Cas12a integrated into a centrifugal microfluidic chip for the detection of meat adulteration. The RAA-CRISPR/Cas12a reaction reagents were pre-embedded into the different reaction chambers on the microfluidic chip to achieve the streamline of operations, markedly simplifying the detection process. The whole reaction was completed within 30 min with a detection limit of 0.1 % (w/w) in pig, chicken, duck, and lamb products. Referring to the results of the standard method, CIPAM system achieved 100 % accuracy. The automatic multiplex detection process implemented in the developed CIPAM system met the needs of food regulatory authorities.

Evaluating the efficacy of auricular acupuncture for chemotherapy-induced taste alterations: A pilot randomized controlled trial.

PURPOSE: Irrespective of the development of acupuncture-based interventions, clinical evidence regarding their efficacy remains controversial owing to issues with the study design and an unclear risk of bias. This study aimed to evaluate the efficacy of auricular acupuncture in managing taste alterations in patients with cancer undergoing platinum-based chemotherapy. METHODS: We conducted a pilot randomized controlled trial involving 73 patients randomly assigned to an auricular acupuncture or a control group. The primary outcome was the severity of chemotherapy-induced taste alterations, and the secondary outcomes included quality of life and negative emotions of the patients. RESULTS: A total of 49 participants completed the study. Compared to the control group, patients in the auricular acupuncture group showed significant reductions in discomfort, general taste alterations, and total scores on the Chemotherapy-induced Taste Alteration Scale (all p < 0.05). Furthermore, we observed significant improvements in quality of life, including physical function (p = 0.007), role function (p = 0.006), emotional function (p = 0.016), nausea and vomiting (p = 0.021), appetite loss (p = 0.046), and significant improvements in anxiety and depression (p < 0.01). CONCLUSIONS: Our findings suggest that auricular acupuncture may be a beneficial intervention for managing chemotherapy-induced taste alterations in patients with cancer receiving platinum-based chemotherapy. It may also contribute to improvements in quality of life and negative emotions. However, these results are preliminary, and further evaluation with larger randomized controlled trials is necessary.

Discovery of novel dual Bruton's tyrosine kinase (BTK) and Janus kinase 3 (JAK3) inhibitors as a promising strategy for rheumatoid arthritis.

Rheumatoid arthritis (RA) is a chronically systemic autoimmune disorder, which is related with various cellular signal pathways. Both BTK (Bruton's Tyrosine Kinase) and JAK3 (Janus Kinase 3) play important roles in the pathogenesis of rheumatoid arthritis. Herein, we reported the discovery of dual BTK/JAK3 inhibitors through bioisosterism and computer-aided drug design based on the structure of BTK inhibitor ibrutinib. We reported the discovery of dual BTK/JAK3 inhibitors which are based on the structure of BTK inhibitor ibrutinib via the method of bioisosterism and computer-aided drug design) Most of the target compounds exhibited moderate to strong inhibitory activities against BTK and JAK3. Among them, compound XL-12 stood out as the most promising candidate targeting BTK and JAK3 with potent inhibitory activities (IC50 = 2.0 nM and IC50 = 14.0 nM respectively). In the in vivo studies, compound XL-12 (40 mg/kg) exhibited more potent antiarthritic activity than ibrutinib (10 mg/kg) in adjuvant arthritis (AA) rat model. Furthermore, compound XL-12 (LD50 > 1600 mg/kg) exerted improved safety compared with ibrutinib (LD50 = 750 mg/kg). These results indicated that compound XL-12, the dual BTK/JAK3 inhibitor, might be a potent drug candidate for the treatment of RA.

The structural and molecular mechanisms of type II PETases: a mini review.

The advent of plastics has led to significant advances for humans, although the accompanying pollution has also been a source of concern for countries globally. Consequently, a biological method to effectively degrade polyethylene terephthalate (PET) has been an area of significant scientific interest. Following the report of the highly efficient PET hydrolase from the bacterium Ideonella sakaiensis strain 201-F6 (i.e., IsPETase) in 2016, its structure has been extensively studied, showing that it belongs to the type II PETase group. Unlike type I PETases that include most known cutinases, structural investigations of type II PETases have only been conducted since 2017. Type II PETases are further divided into type IIa and IIb enzymes. Moreover, even less research has been conducted on type IIa plastic-degrading enzymes. Here, we present a review of recent studies of the structure and mechanism of type II PETases, using the known structure of the type IIa PETase PE-H from the marine bacterium Pseudomonas aestusnigri in addition to the type IIb enzyme IsPETase as representatives. These studies have provided new insights into the structural features of type II PETases that exhibit PET catalytic activity. In addition, recent studies investigating the rational design of IsPETases are reviewed and summarized alongside a discussion of controversies surrounding PETase investigations.

Analysis of lncRNA-miRNA-mRNA Expression in the Troxerutin-Mediated Prevention of Radiation-Induced Lung Injury in Mice.

Background: Radiation-induced lung injury (RILI) is a critical factor that leads to pulmonary fibrosis and other diseases. LncRNAs and miRNAs contribute to normal tissue damage caused by ionizing radiation. Troxerutin offers protection against radiation; however, its underlying mechanism remains largely undetermined. Methods: We established a model of RILI in mice pretreated with troxerutin. The lung tissue was extracted for RNA sequencing, and an RNA library was constructed. Next, we estimated the target miRNAs of differentially expressed (DE) lncRNAs, and the target mRNAs of DE miRNAs. Then, functional annotations of these target mRNAs were performed using GO and KEGG. Results: Compared to the control group, 150 lncRNA, 43 miRNA, and 184 mRNA were significantly up-regulated, whereas, 189 lncRNA, 15 miRNA, and 146 mRNA were markedly down-regulated following troxerutin pretreatment. Our results revealed that the Wnt, cAMP, and tumor-related signaling pathways played an essential role in RILI prevention via troxerutin using lncRNA-miRNA-mRNA network. Conclusion: These evidences revealed that the abnormal regulation of RNA potentially leads to pulmonary fibrosis. Therefore, targeting lncRNA and miRNA, along with a closer examination of competitive endogenous RNA (ceRNA) networks are of great significance to the identification of troxerutin targets that can protect against RILI.

Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX.

Aptamers are ligand-binding RNA or DNA molecules and have been widely examined as biosensors, diagnostic tools, and therapeutic agents. The application of aptamers as biosensors commonly requires an expression platform to produce a signal to report the aptamer-ligand binding event. Traditionally, aptamer selection and expression platform integration are two independent steps and the aptamer selection requires the immobilization of either the aptamer or the ligand. These drawbacks can be easily overcome through the selection of allosteric DNAzymes (aptazymes). Herein, we used the technique of Expression-SELEX developed in our laboratory to select for aptazymes that can be specifically activated by low concentrations of l-phenylalanine. We chose a previous DNA-cleaving DNAzyme known as II-R1 as the expression platform for its low cleavage rate and used stringent selection conditions to drive the selection of high-performance aptazyme candidates. Three aptazymes were chosen for detailed characterization and these DNAzymes were found to exhibit a dissociation constant for l-phenylalanine as low as 4.8 µM, a catalytic rate constant improvement as high as 20 000-fold in the presence of l-phenylalanine, and the ability to discriminate against closely related l-phenylalanine analogs including d-phenylalanine. This work has established the Expression-SELEX as an effective SELEX method to enrich high-quality ligand-responsive aptazymes.

Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding.

Hybrid potato breeding will transform the crop from a clonally propagated tetraploid to a seed-reproducing diploid. Historical accumulation of deleterious mutations in potato genomes has hindered the development of elite inbred lines and hybrids. Utilizing a whole-genome phylogeny of 92 Solanaceae and its sister clade species, we employ an evolutionary strategy to identify deleterious mutations. The deep phylogeny reveals the genome-wide landscape of highly constrained sites, comprising ∼2.4% of the genome. Based on a diploid potato diversity panel, we infer 367,499 deleterious variants, of which 50% occur at non-coding and 15% at synonymous sites. Counterintuitively, diploid lines with relatively high homozygous deleterious burden can be better starting material for inbred-line development, despite showing less vigorous growth. Inclusion of inferred deleterious mutations increases genomic-prediction accuracy for yield by 24.7%. Our study generates insights into the genome-wide incidence and properties of deleterious mutations and their far-reaching consequences for breeding.

Metagenomic next-generation sequencing for pulmonary infections diagnosis in patients with diabetes.

BACKGROUND: Diabetes mellitus is a major cause of high mortality and poor prognosis in patients with pulmonary infections. However, limited data on the application of metagenomic next-generation sequencing (mNGS) are available for diabetic patients. This study aimed to evaluate the diagnostic performance of mNGS in diabetic patients with pulmonary infections. METHODS: We retrospectively reviewed 184 hospitalized patients with pulmonary infections at Guizhou Provincial People's Hospital between January 2020 to October 2021. All patients were subjected to both mNGS analysis of bronchoalveolar lavage fluid (BALF) and conventional testing. Positive rate by mNGS and the consistency between mNGS and conventional testing results were evaluated for diabetic and non-diabetic patients. RESULTS: A total of 184 patients with pulmonary infections were enrolled, including 43 diabetic patients and 141 non-diabetic patients. For diabetic patients, the microbial positive rate by mNGS was significantly higher than that detected by conventional testing methods, primarily driven by bacterial detection (microbes: 95.3% vs. 67.4%, P = 0.001; bacteria: 72.1% vs. 37.2%, P = 0.001). mNGS and traditional tests had similar positive rates with regard to fungal and viral detection in diabetic patients. Klebsiella pneumoniae was the most common pathogen identified by mNGS in patients with diabetes. Moreover, mNGS identified pathogens in 92.9% (13/14) of diabetic patients who were reported negative by conventional testing. No significant difference was found in the consistency of the two tests between diabetic and non-diabetic groups. CONCLUSIONS: mNGS is superior to conventional microbiological tests for bacterial detection in diabetic patients with pulmonary infections. mNGS is a valuable tool for etiological diagnosis of pulmonary infections in diabetic patients.

Autophagy-related gene LAPTM4B promotes the progression of renal clear cell carcinoma and is associated with immunity.

Renal cell carcinoma (RCC) is a common urologic disease. Currently, surgery is the primary treatment for renal cancer; immunotherapy is not as effective a treatment strategy as expected. Hence, understanding the mechanism in the tumor immune microenvironment (TME) and exploring novel immunotherapeutic targets are considered important. Recent studies have demonstrated that autophagy could affect the immune environment of renal cell carcinoma and induce proliferation and apoptosis of cancer cells. By comparing lysosomal genes and regulating autophagy genes, we identified the LAPTM4B gene to be related to RCC autophagy. By analyzing the TCGA-KIRC cohort using bioinformatics, we found M2 macrophages associated with tumor metastasis to be significantly increased in the immune microenvironment of patients with high expression of LAPTM4B. GO/KEGG/GSEA/GSVA results showed significant differences in tumor autophagy- and metastasis-related pathways. Single-cell sequencing was used to compare the expression of LAPTM4B in different cell types and obtain the differences in lysosomal and autophagy pathway activities in different ccRCC cells. Subsequently, we confirmed the differential expression of LAPTM4B in renal cell carcinoma of different Fuhrman grades using western blotting. Downregulation of LAPTM4B expression significantly reduced the proliferation of renal cell carcinoma cells and promoted cell apoptosis through cell experiments. Overall, our study demonstrated that the autophagy-related gene LAPTM4B plays a critical role in the TME of RCC, and suggested that LAPTM4B is a potential therapeutic target for RCC immunotherapy.

Construction and validation of a competing endogenous RNA network in the thymus of miR-147-/- mice.

BACKGROUND: Prior evidence has demonstrated that miR-147 can regulate cellular proliferation, migration, apoptotic death, inflammatory responses, and the replication of viruses through its interactions with specific mRNA targets. LncRNA-miRNA-mRNA interactions are often found in various biological processes. No studies have documented lncRNA-miRNA-mRNA regulatory interactions in miR-147-/- mice. METHODS: Thymus tissue samples from miR-147-/- mice were systematically analyzed to detect patterns of lncRNA, miRNA, and mRNA dysregulation in the absence of this biologically important miRNA. Briefly, RNA-sequencing was used to analyze samples of thymus tissue from wild-type (WT) and miR-147-/- mice. Radiation damage models of miR-147-/- mice were prepared and prophylactic intervention with the drug trt was performed. The validation of miR-47, PDPK1,AKT and JNK were carried out by qRT-PCR, western blot and fluorescence in situ hybridization. Apoptosis was detected by Hoechst staining, and histopathological changes were detected by HE staining. RESULTS: We showed the identification of 235 mRNAs, 63 lncRNAs, and 14 miRNAs that were significantly upregulated in miR-147-/- mice as compared to WT controls, as well as 267 mRNAs, 66 lncRNAs and 12 miRNAs exhibiting significant downregulation. Predictive analyses of the miRNAs targeted by dysregulated lncRNAs and their associated mRNAs were further performed, highlighting the dysregulation of pathways including the Wnt signaling pathway, Thyroid cancer, Endometrial cancer (include PI3K/AKT) and Acute myeloid leukemia pathway(include PI3K/AKT) pathways. Troxerutin (TRT) upregulated PDPK1 via targeting miR-147 to promote AKT activation and inhibit JNK activation in the lungs of mice in radioprotection. CONCLUSION: Together, these results highlight the potentially important role of miR-147 as a key regulator of complex lncRNA-miRNA-mRNA interacting networks. Further research focusing on PI3K/AKT pathways in miR-147-/- mice in radioprotection will thus benefit current knowledge of miR-147 while also informing efforts to improve radioprotection.

Integrating anodic sulfate activation with cathodic H2O2 production/activation to generate the sulfate and hydroxyl radicals for the degradation of emerging organic contaminants.

Conventional electrocatalytic degradation of pollutants involves either cathodic reduction or anodic oxidation process, which caused the low energy utilization efficiency. In this study, we successfully couple the anodic activation of sulfates with the cathodic H2O2 production/activation to boost the generation of sulfate radical (SO4·-) and hydroxyl radical (·OH) for the efficient degradation of emerging contaminants. The electrocatalysis reactor is composed of a modified-graphite-felt (GF) cathode, in-situ prepared by the carbonization of polyaniline (PANI) electrodeposited on a GF substrate, and a boron-doped diamond (BDD) anode. In the presence of sulfates, the electrocatalysis system shows superior activities towards the degradation of pharmaceutical and personal care products (PPCPs), with the optimal performance of completely degrading the representative pollutant carbamazepine (CBZ, 0.2 mg L-1) within 150 s. Radicals quenching experiments indicated that ·OH and SO4·- act as the main reactive oxygen species for CBZ decomposition. Results from the electron paramagnetic resonance (EPR) and chronoamperometry studies verified that the sulfate ions were oxidized to SO4·-radicals at the anode, while the dissolve oxygen molecules were reduced to H2O2 molecules which were further activated to produce ·OH radicals at the cathode. It was also found that during the catalytic reactions SO4·-radicals could spontaneously convert into peroxydisulfate (PDS) which were subsequently reduced back to SO4·-at the cathodes. The quasi-steady-state concentrations of ·OH and SO4·-were estimated to be 0.51×10-12 M and 0.56×10-12 M, respectively. This study provides insight into the synergistic generation of ·OH/SO4·- from the integrated electrochemical anode oxidation of sulfate and cathode reduction of dissolved oxygen, which indicates a potential practical approach to efficiently degrade the emerging organic water contaminants.

Novel B and N Sites of One-Dimensional Boron Nitride Fiber: Efficient Performance and Mechanism in the Formaldehyde Capture Process.

Identification of adsorption centers with atomic levels of adsorbents is crucial to study the adsorption of formaldehyde (HCHO), especially for an in-depth understanding of the mechanism of HCHO capture. Herein, we investigate the HCHO adsorption performance of one-dimensional (1D) nanoporous boron nitride (BN) fiber, and explore the adsorption mechanism by density functional theory (DFT) calculations, including adsorption energy change and Bader charge change, and experimental study as well. Research shows that the 1D nanoporous BN fiber possesses a high concentration of Lewis pairs, which act as Lewis acid and Lewis base sites associated with the fiber's electron-deficient and electron-rich features. It is worth noting that the HCHO removal efficiency of a typical sample is as high as 91%. This work may open the door to the field of adsorption of other pollutants by constructing Lewis pairs in the future.

IC50: an unsuitable measure for large-sized prostate cancer spheroids in drug sensitivity evaluation.

Preclinical models of tumors have the potential to become valuable tools for commercial drug research and development, and 3D culture systems are gaining traction in this area, particularly in prostate cancer (PCa) research. However, nearly all 3D drug design and screening assessments are based on 2D experiments, suggesting limitations of 3D drug testing. To simulate the natural response of human cells to the drug, we detected the half-maximal inhibitory concentration (IC50) changes of 2D/3D LNCaP cells in the drug docetaxel, as well as the sensitivity of different morphologies of 2D/3D LNCaP to docetaxel treatment. In contrast to 2D LNCaP cells, the evaluation of LNCaP spheroids' susceptibility to treatment was more complicated; the fitness of IC50 curves of 2D and 3D tumor cell preclinical models differs significantly. IC50 curves were unsuitable for large-sized LNCaP spheroids. More evaluation indexes (such as max inhibition) and experiments (such as spheroids formation) should be explored and performed to evaluate the susceptibility systematically.

Graph pangenome captures missing heritability and empowers tomato breeding.

Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits1,2. The solution to this problem is to identify all causal genetic variants and to measure their individual contributions3,4. Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largely due to resolving incomplete linkage disequilibrium through the inclusion of additional causal structural variants identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, structural variants improve the power to identify genetic factors underlying agronomically important traits leading to, for example, the identification of two new genes potentially contributing to soluble solid content. The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

Changes of distribution and chemical speciation of metals in hexavalent chromium loaded algal-bacterial aerobic granular sludge before and after hydrothermal treatment.

Algal-bacterial aerobic granular sludge (AGS) was applied for hexavalent chromium (Cr(VI)) biosorption from wastewater and the dynamic distribution and mobility of different metals in granules were systematically examined before and after hydrothermal treatment. The loaded Cr on algal-bacterial AGS was found to mainly localize in microbial cells and mineral particles; little Cr was detected in extracellular polymeric substances (EPS) after 6 h contact, which increased to 5.1% after 24 h biosorption. Along with Cr localization, 9.3-22.8% of Mg and 11.5-26.4% of Ca in algal-bacterial AGS were released from loosely bound EPS, then replenished to maintain their stable proportion in EPS, probably contributing to granular stability. In addition, chemical fractionation showed that the Cr mobility in algal-bacterial AGS, indicated by a low mobility factor of 4.7%, decreased to 1.4% with the co-existence of mineral salts and acetate during biosorption, which was further declined to 0 after hydrothermal treatment.

Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites.

BACKGROUND: Long-term domestication and intensive breeding of crop plants aim to establish traits desirable for human needs, and characteristics related to yield, disease resistance, and postharvest storage have traditionally received considerable attention. These processes have led also to negative consequences, as is the case of loss of variants controlling fruit quality, for instance in tomato. Tomato fruit quality is directly associated to metabolite content profiles; however, a full understanding of the genetics affecting metabolite content during tomato domestication and improvement has not been reached due to limitations of the single detection methods previously employed. Here, we aim to reach a broad understanding of changes in metabolite content using a genome-wide association study (GWAS) with eigenvector decomposition (EigenGWAS) on tomato accessions. RESULTS: An EigenGWAS was performed on 331 tomato accessions using the first eigenvector generated from the genomic data as a "phenotype" to understand the changes in fruit metabolite content during breeding. Two independent gene sets were identified that affected fruit metabolites during domestication and improvement in consumer-preferred tomatoes. Furthermore, 57 candidate genes related to polyphenol and polyamine biosynthesis were discovered, and a major candidate gene chlorogenate: glucarate caffeoyltransferase (SlCGT) was identified, which affected the quality and diseases resistance of tomato fruit, revealing the domestication mechanism of polyphenols. CONCLUSIONS: We identified gene sets that contributed to consumer liking during domestication and improvement of tomato. Our study reports novel evidence of selective sweeps and key metabolites controlled by multiple genes, increasing our understanding of the mechanisms of metabolites variation during those processes. It also supports a polygenic selection model for the application of tomato breeding.