Quantitative trait locus analysis of gray leaf spot resistance in the maize IBM Syn10 DH population.

KEY MESSAGE: The exploration and dissection of a set of QTLs and candidate genes for gray leaf spot disease resistance using two fully assembled parental genomes may help expedite maize resistance breeding. The fungal disease of maize known as gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is a significant concern in China, Southern Africa, and the USA. Resistance to GLS is governed by multiple genes with an additive effect and is influenced by both genotype and environment. The most effective way to reduce the cost of production is to develop resistant hybrids. In this study, we utilized the IBM Syn 10 Doubled Haploid (IBM Syn10 DH) population to identify quantitative trait loci (QTLs) associated with resistance to gray leaf spot (GLS) in multiple locations. Analysis of seven distinct environments revealed a total of 58 QTLs, 49 of which formed 12 discrete clusters distributed across chromosomes 1, 2, 3, 4, 8 and 10. By comparing these findings with published research, we identified colocalized QTLs or GWAS loci within eleven clustering intervals. By integrating transcriptome data with genomic structural variations between parental individuals, we identified a total of 110 genes that exhibit both robust disparities in gene expression and structural alterations. Further analysis revealed 19 potential candidate genes encoding conserved resistance gene domains, including putative leucine-rich repeat receptors, NLP transcription factors, fucosyltransferases, and putative xyloglucan galactosyltransferases. Our results provide a valuable resource and linked loci for GLS marker resistance selection breeding in maize.

An activatable fluorescent-photoacoustic dual-modal probe for highly sensitive imaging of nitroxyl in vivo.

Nitroxyl (HNO) plays a vital role in various biological functions and pharmacological activities, so the development of an excellent near-infrared fluorescent (NIRF) and photoacoustic (PA) dual-modality probe is crucial for understanding HNO-related physiological and pathological progression. Herein, we proposed and synthesized a novel NIRF/PA dual probe (QL-HNO) by substituting an indole with quinolinium in hemicyanine for the sensitive detection of exogenous and endogenous HNO in vivo. The designed probe showed the highest sensitivity in NIRF mode and a desirable PA signal-to-noise ratio for HNO detection in vitro and was further applied for NIRF/PA dual-modal imaging of HNO with high contrast in living cells and tumor-bearing animals. Based on the excellent performance of QL-HNO, we believe that this study provides a promising molecular tool for further understanding of HNO-related physiological and pathological progression.

Genomic analysis and biological properties of the novel Serratia liquefaciens phage vB_SlqM_MQ-4.

A novel lytic Serratia liquefaciens phage, named vB_SlqM_MQ-4, was isolated from sewage. BLASTn analysis showed that the genome sequence of phage vB_SlqM_MQ-4 shared only 15% query coverage with that of Escherichia phage vB_EcoM-ep3, with 80.52% identity. Genomic analysis demonstrated that phage vB_SlqM_MQ-4 has a 43,534-bp dsDNA genome with 56% GC content and might be a member of a new genus in the order Caudoviricetes. Moreover, vB_SlqM_MQ-4 exhibited strong lytic performance with a short latent period (10 min) and a high burst size (267 PFU per cell) as well as a wide range of thermal (below 70 ℃) and pH tolerance (pH 4-12).

Enzyme-targeted near-infrared fluorescent probe for organophosphorus pesticide residue detection.

Pesticide residues significantly affect food safety and harm human health. In this work, a series of near-infrared fluorescent probes were designed and developed by acylating the hydroxyl group of the hemicyanine skeleton with a quenching moiety for monitoring the presence of organophosphorus pesticides in food and live cells. The carboxylic ester bond on the probe was hydrolyzed catalytically in the presence of carboxylesterase and thereby the fluorophore was released with near-infrared emission. Notably, the proposed probe 1 exhibited excellent sensitivity against organophosphorus based on the carboxylesterase inhibition mechanism and the detection limit for isocarbophos achieved 0.1734 µg/L in the fresh vegetable sample. More importantly, probe 1 allowed for situ visualization of organophosphorus in live cells and bacteria, meaning great potential for tracking the organophosphorus in biological systems. Consequently, this study presents a promising strategy for tracking pesticide residues in food and biological systems.

Combined QTL mapping and RNA-Seq pro-filing reveal candidate genes related to low-temperature tolerance in maize.

Maize (Zea mays L.) is the most important food crop in the world, with significant acreage and production across the globe. However, it is affected by low temperatures throughout its growth process, especially during germination. Therefore, it is important to identify more QTLs or genes associated with germination under low-temperature conditions. For the QTL analysis of traits related to low-temperature germination, we used a high-res genetic map of 213 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, which had 6618 bin markers. We detected 28 QTLs of eight phenotypic characteristics associated with low-temperature germination, while they explained the phenotypic contribution rate of 5.4 ~ 13.34%. Additionally, 14 overlapping QTLs produced six QTL clusters on every chromosome, except for 8 and 10. RNA-Seq found six genes related to low-temperature tolerance in these QTLs, while qRT-PCR analysis demonstrated that the expression trends of the Zm00001d045568 gene in the LT_BvsLT_M group and the CK_BvsCK_M group were highly significantly different at all four-time points (P < 0.01), and encoded the RING zinc finger protein. It was located on qRTL9-2 and qRSVI9-1 and is related to the total length and simple vitality index. These results provided potential candidate genes for further gene cloning and improving the low-temperature tolerance of maize. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01297-6.

Analysis of QTLs and Candidate Genes for Tassel Symptoms in Maize Infected with Sporisorium reilianum.

Heat smut is a fungal soil-borne disease caused by Sporisorium reilianum, and affects the development of male and female tassels. Our previous research found that the tassel symptoms in maize infected with Sporisorium reilianum significantly differed in inbred lines with Sipingtou blood, and exhibited stable heredity over time at multiple locations. In this study, cytological analysis demonstrated that the cellular organization structures of three typical inbred lines (Huangzao4, Jing7, and Chang7-2) showed significant discrepancies at the VT stage. QTLs that control the different symptoms of maize tassels infected with Sporisorium reilianum were located in two F2 populations, which were constructed using three typical inbred lines. The BSA (bulked segregation analysis) method was used to construct mixed gene pools based on typical tassel symptoms. The QTLs of different symptoms of maize tassels infected with Sporisorium reilianum were detected with 869 SSR markers covering the whole maize genome. The mixed gene pools were screened with polymorphic markers between the parents. Additional SSR markers were added near the above marker to detect genotypes in partially single plants in F2 populations. The QTL controlling tassel symptoms in the Huangzao4 and Jing7 lines was located on the bin 1.06 region, between the markers of umc1590 and bnlg1598, and explained 21.12% of the phenotypic variation with an additive effect of 0.6524. The QTL controlling the tassel symptoms of the Jing7 and Chang7-2 lines was located on the bin 2.07 region, between the markers of umc1042 and bnlg1335, and explained 11.26% phenotypic variation with an additive effect of 0.4355. Two candidate genes (ZmABP2 and Zm00001D006403) were identified by a conjoint analysis of label-free quantification proteome sequencings.

CRISPR/cas9 mediated knockout of an intergenic variant rs6927172 identified IL-20RA as a new risk gene for multiple autoimmune diseases.

Genetic variants near the tumor necrosis factor-α-induced protein 3 gene (TNFAIP3) at the chromosomal region 6q23 demonstrated significant associations with multiple autoimmune diseases. The signals of associations have been explained to the TNFAIP3 gene, the most likely causal gene. In this study, we employed CRISPR/cas9 genome-editing tool to generate cell lines with deletions including a candidate causal variant, rs6927172, at 140 kb upstream of the TNFAIP3 gene. Interestingly, we observed alterations of multiple genes including IL-20RA encoding a subunit of the receptor for interleukin 20. Using Electrophoretic mobility shift assay (EMSA), Western blotting, and chromatin conformation capture we characterized the molecular mechanism that the DNA element carrying the variant rs6927172 influences expression of IL-20RA and TNFAIP3 genes. Additionally, we developed a new use of the transcription activator-like effector (TALE) to study the role of the variant in regulating expressions of its target genes. In summary, we generated deletion knockouts that included the candidate causal variant rs6927172 in HEK293T cells provided new evidence and mechanism for IL-20RA gene as a risk factor for multiple autoimmune diseases.

Mitochondrion-Targeting Fluorescence Probe via Reduction Induced Charge Transfer for Fast Methionine Sulfoxide Reductases Imaging.

Methionine sulfoxide reductases (Msrs) play essential roles in maintaining mitochondrial function and are recognized as potential therapeutic targets. However, current probes for Msrs fail to target mitochondria and exhibit a relatively slow response and limited sensitivity. Here we develop a novel turn-on fluorescence probe that facilitates imaging of mitochondrial Msrs in living cells. The probe is constructed by conjugating a methyl phenyl sulfoxide, a mimic Msrs substrate, to an electron-withdrawing hydrophobic cation, methylpyridinium. The probe of acceptor-acceptor structure is initially nonemissive. Msrs catalyzed reduction of sulfoxide to sulfide generated a fluorophore of distinct donor-acceptor structure. The probe is demonstrated to exhibit high sensitivity, fast response, and high selectivity toward MsrA in vitro. Furthermore, the probe is successfully introduced to detect and image Msrs in living cells with excellent mitochondrial-targeting capability. Moreover, the probe also reveals decreased Msrs activity in a cellular Parkinson's disease model. Our probe affords a powerful tool for detecting and visualizing mitochondrial Msrs in living cells.

Modulation of hypoxia-inducible factor-1α/cyclo-oxygenase-2 pathway associated with attenuation of intestinal mucosa inflammatory damage by Acanthopanax senticosus polysaccharides in lipopolysaccharide-challenged piglets.

Intestinal barrier inflammatory damage is commonly accompanied by hypoxia. The hypothesis that dietary Acanthopanax senticosus polysaccharides (ASPS) might modulate the hypoxia-inducible factor-1α (HIF-1α) signalling pathway and contribute to attenuate intestinal injury was tested in lipopolysaccharide (LPS)-challenged piglets. Thirty-six weaned pigs were randomly allocated to one of the following three groups: (1) basal diet + saline challenge; (2) basal diet + LPS challenge; (3) basal diet with 800 mg/kg ASPS + LPS challenge. LPS was injected at 15, 18 and 21 d, and intestinal sections were sampled following blood collection at 21 d . The results showed ASPS reversed (P < 0·05) LPS-induced decrease in average daily feed intake and rise (P < 0·05) of diarrhoea incidence and index. Biochemical index reflecting gut barrier damage and function involving ileal pro-inflammatory cytokines (TNF-α and IL-1ß) and enzyme activity (diamine oxidase and lactase), as well as circulatory d-xylose, was normalised (P < 0·05) in LPS-challenged piglets receiving ASPS. ASPS also ameliorated intestinal morphological deterioration of LPS-challenged piglets, proved by elevated ileal villus height (P < 0·05) and improved appearance of epithelial villus and tight junction ultrastructure. Moreover, ASPS prevented LPS-induced amplification of inflammatory mediators, achieved by depressed ileal mRNA abundance of TNF-α, inducible NO synthase and IL-1ß concentration. Importantly, ileal protein expressions of HIF-1α, cyclo-oxygenase-2 (COX-2) and NFκB p65 were also suppressed with ASPS administration (P < 0·05). Collectively, these results suggest the improvement of mucosal inflammatory damage and diarrhoea in immune stress piglets is possibly associated with a novel finding where HIF-1α/COX-2 pathway down-regulation is involved in NFκB p65-inducible releasing of inflammatory cytokines by dietary ASPS.

A near infrared fluorescent probe for the detection and imaging of prolyl aminopeptidase activity in living cells.

Prolyl aminopeptidase (PAP) is an important exopeptidase which might be a biomarker for pathogen infection and a potential therapeutic target. However, very few fluorescent probes have been developed for detecting PAP activity. Here we report the development of the first near infrared (NIR) turn-on fluorescent probe (NIR-PAP) for detecting and imaging PAP in living cells. The probe is prepared by reacting a cysteine-proline dipeptide with an acryloylated NIR fluorophore via a facile thiol-Michael addition reaction. NIR-PAP exhibits a dynamic response toward PAP in the range of 0.02-2.5 U mL-1 with an estimated limit of detection of 0.013 U mL-1. In vitro studies also reveal that the probe displays high specificity and robust responses toward PAP under physiological pH and temperature conditions. Moreover, NIR-PAP is successfully introduced to detect and differentiate PAP activity in four different cell lines via both confocal fluorescence imaging and flow cytometry. Therefore, our probe may hold great promise in diagnosing infectious diseases caused by pathogens and screening therapeutic drugs in vivo.

Analysis of Cytology and Expression of Resistance Genes in Maize Infected with Sporisorium reilianum.

Head smut, caused by the fungus Sporisorium reilianum, is a devastating global disease of maize (Zea mays). In the present study, maize seedlings were artificially inoculated with compatible mating-type strains of S. reilianum by needle inoculation of mesocotyls (NIM) or by soaking inoculation of radicles (SIR). After NIM or SIR, Huangzao4 mesocotyls exhibited severe damage with brownish discoloration and necrosis, whereas Mo17 mesocotyls exhibited few lesions. Fluorescence and electron microscopy showed that S. reilianum infected maize within 0.5 day after SIR and mainly colonized the phloem. With longer incubation, the density of S. reilianum hyphae increased in the vascular bundles, concentrated mainly in the phloem. In Mo17, infected cells exhibited apoptosis-like features, and hyphae became sequestered within dead cells. In contrast, in Huangzao4, pathogen invasion resulted in autophagy that failed to prevent hyphal spreading. The growth of S. reilianum hyphae diminished at 6 days after inoculation when expression of the R genes ZmWAK and ZmNL peaked. Thus, 6 days after SIR inoculation might be an important time for inhibiting the progress of S. reilianum infection in maize. The results of this study will provide a basis for further analysis of the mechanisms of maize resistance to S. reilianum.

Engineering Organelle-Specific Molecular Viscosimeters Using Aggregation-Induced Emission Luminogens for Live Cell Imaging.

Subcellular viscosity is essential for cell functions and may indicate its physiological status. We screen two fluorescent probes by engineering tetraphenylethene (TPE) for measuring viscosity in mitochondria and lysosomes, respectively. These two probes are only weakly emissive in nonviscous medium and the emission signals are greatly enhanced in viscous medium due to the restriction of intramolecular motion. The presence of pyridium has endowed one probe with mitochondrial specificity, while the presence of indole ring has granted the other probe with lysosome-targeting ability. Their optical properties are characterized in vitro and their applications in imaging viscosity variations in mitochondria and lysosomes are also demonstrated in living cells under different stimulated processes. In addition, an increase in both mitochondrial and lysosomal viscosity during mitophagy was revealed for the first time with our probes. To our knowledge, this is the first time that TPE is engineered to be fluorescent molecular viscosimeters that possess desirable aqueous solubility, red-shifted emission, and organelle specificity.

Activatable Fluorescence Probe via Self-Immolative Intramolecular Cyclization for Histone Deacetylase Imaging in Live Cells and Tissues.

Histone deacetylases (HDACs) play essential roles in transcription regulation and are valuable theranostic targets. However, there are no activatable fluorescent probes for imaging of HDAC activity in live cells. Here, we develop for the first time a novel activatable two-photon fluorescence probe that enables in situ imaging of HDAC activity in living cells and tissues. The probe is designed by conjugating an acetyl-lysine mimic substrate to a masked aldehyde-containing fluorophore via a cyanoester linker. Upon deacetylation by HDAC, the probe undergoes a rapid self-immolative intramolecular cyclization reaction, producing a cyanohydrin intermediate that is spontaneously rapidly decomposed into the highly fluorescent aldehyde-containing two-photon fluorophore. The probe is shown to exhibit high sensitivity, high specificity, and fast response for HDAC detection in vitro. Imaging studies reveal that the probe is able to directly visualize and monitor HDAC activity in living cells. Moreover, the probe is demonstrated to have the capability of two-photon imaging of HDAC activity in deep tissue slices up to 130 µm. This activatable fluorescent probe affords a useful tool for evaluating HDAC activity and screening HDAC-targeting drugs in both live cell and tissue assays.

An Autoimmune Disease-Associated Risk Variant in the TNFAIP3 Gene Plays a Protective Role in Brucellosis That Is Mediated by the NF-κB Signaling Pathway.

Naturally occurring functional variants (rs148314165 and rs200820567, collectively referred to as TT>A) reduce the expression of the tumor necrosis factor alpha-induced protein 3 (TNFAIP3) gene, a negative regulator of NF-κB signaling, and predispose individuals to autoimmune disease. In this analysis, we conducted a genetic association study of the TT>A variants in 1,209 controls and 150 patients with brucellosis, an infectious disease, and further assessed the role of the variants in brucellosis. Our data demonstrated that the TT>A variants were correlated with cases of brucellosis (P = 0.002; odds ratio [OR] = 0.34) and with individuals who had a positive serum agglutination test (SAT) result (titer of >1/160) (P = 4.2 × 10-6; OR = 0.23). A functional study demonstrated that brucellosis patients carrying the protective allele (A) showed significantly lower expression levels of the TNFAIP3 gene in their peripheral blood mononuclear cells and showed increased NF-κB signaling. Monocytes from individuals carrying the A allele that were stimulated with Brucella abortus had lower mRNA levels of TNFAIP3 and produced more interleukin-10 (IL-10), IL-6, and IL-1ß than those from TT allele carriers. These data showed that autoimmune disease-associated risk variants, TT>A, of the TNFAIP3 locus play a protective role in the pathogenesis of brucellosis. Our findings suggest that a disruption of the normal function of the TNFAIP3 gene might serve as a therapeutic target for the treatment of brucellosis.

Effects of 2-amino-9H-pyrido[2,3-b]indole (AαC) metabolic bio-activation on oxidative DNA damage in human hepatoma G2 (HepG2) cells.

2-Amino-9H-pyrido[2,3-b]indole (AαC), which is a hazardous compound present in cigarette smoke, has been listed as probable human carcinogens (Group 2B). The carcinogenicity and genotoxicity of AαC were activated by the process of metabolic bio-activation. Whereas, few studies about genotoxicity induced by AαC have been reported. In this study, we took HepG2 cells as the model to investigate the relationship between oxidative DNA damage induced by AαC and metabolic bio-activation of AαC, which is of importance to unveil the mechanism of AαC genotoxicity. Firstly, the HepG2 cells were treated with 10 and 20 µg/mL AαC, respectively. Then different concentrations of protein ranging from 0 to 1 mg/mL in S9 mixture solution were utilized to make cells have different capacities for metabolic activation. Intracellular AαC hydroxylated metabolites and 8-OHdG were estimated by using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). The results showed that, at the same concentration of AαC, with the increment of concentration of protein in S9 mixture solution, the levels of hydroxylated metabolites and 8-OHdG/106dG increased. And at the same concentration of protein in S9 mixture solution, with the increment of concentration of AαC, the levels of hydroxylated metabolites and 8-OHdG/106dG increased. The hydroxylated metabolites and 8-OHdG were positively related by correlation analysis. In addition, the correlation coefficients of N-OH-AαC and 8-OHdG were maximum (R2 = 0.73 and 0.66). Taken together, these results indicated that the metabolic bio-activation of AαC might result in oxidative DNA damage.

Mitochondrion-Targeting, Environment-Sensitive Red Fluorescent Probe for Highly Sensitive Detection and Imaging of Vicinal Dithiol-Containing Proteins.

Mitochondrial vicinal dithiol-containing proteins (VDPs) are key regulators in cellular redox homeostasis and useful markers for diagnostics of redox-dependent diseases. Current probes fail to target mitochondrial VDPs and show limited sensitivity and response rate. We develop a novel fluorescent probe using an engineered benzoxadiazole fluorophore that allows selective targeting of mitochondria and exhibits highly sensitive environment responsiveness. This probe is almost nonfluorescent in aqueous media, while delivering intense fluorescence upon binding to VDPs via a cyclic dithiaarsane ligand. The fluorescence probe is shown to have rapid response within 30 s and high sensitivity for detecting reduced bovine serum albumin (rBSA) in the concentration range from 0 to 0.1 µM with a detection limit of 2 nM. To our knowledge, this is the first fluorescence probe for VDPs which exhibits deep red emission, instantaneous response, high turn-on fluorescence ratio, and specific mitochondrial localization. It may provide a new tool for in situ monitoring mitochondrial VDPs.

A ratiometric fluorescent pH probe based on keto-enol tautomerization for imaging of living cells in extreme acidity.

6-(Diethylamino)-2,3-dihydro-1H-xanthene-4-carbaldehyde (DDXC), a reported synthetic intermediate for near-infrared fluorescent dyes, was developed into a fluorescent pH probe for extreme acidity. The unique sensing mechanism of DDXC for pH is based on the reversible protonation of the carbonyl oxygen followed by keto-enol tautomerization. The probe displays a linear ratiometric fluorescence response (I512/I580) to H+ over the extremely acidic range of pH 2.0-4.0 with a pKa of 3.11, and features high fluorescence quantum yield (Φ = 0.60) and excellent selectivity. More importantly, the probe can be applied to ratiometric fluorescence imaging of pH changes in living cells, making it a potential molecular tool for pH-related cell biology study.

A novel two-photon fluorescent probe with a long Stokes shift and a high signal-to-background ratio for human NAD(P)H:quinone oxidoreductase 1 (hNQO1) detection and imaging in living cells and tissues.

In recent years, many activatable fluorescent probes have been developed for hNQO1 detection. However, most of the reported fluorescent probes are susceptible to the interferences of endogenous fluorescence and have the drawback of inadequate penetration depth. Very recently, researchers have reported a two-photon excitation (TPE) fluorescent probe for hNQO1 detection. Nevertheless, this probe only exhibits a compromised signal-to-background ratio, and has not been applied to image hNQO1 in living tissues. Herein, a novel TPE fluorescent probe, trimethyl locked quinone caged Acedan (Q3CA-P), has been developed for hNQO1 detection and imaging in living cells and tissues. Q3CA-P displays over 25-fold enhancement in fluorescence intensity toward hNQO1 with a Stokes shift over 100 nm in one-photon excitation and exhibits a very low detection limit of 5.6 ng mL-1. The imaging experiments performed in tumour cells and tissue slices using Q3CA-P demonstrate that Q3CA-P could image the endogenous hNQO1 with high selectivity and sensitivity with a TPE probing depth of 120 µm. Thus, our probe may have great potential for use in cancer diagnosis and image-guided surgery.

A novel off-on fluorescent probe for sensitive imaging of mitochondria-specific nitroreductase activity in living tumor cells.

Sensitive and selective detection and imaging of nitroreductase (NTR) in cancer cells is of great importance for better understanding their biological functions. Since there are a few fluorescent probes concerning NTR activity specifically located in mitochondria, we developed a novel fluorescent benzoindocyanine probe (BICP) for mitochondrial NTR activity monitoring and imaging via extending a benzoindole moiety into a benzoindocyanine based fluorophore (BICF) with a strong intramolecular charge transfer (ICT) effect and incorporating 4-nitrobenzyl as a fluorescence-quenching and enzyme-responsive moiety. Live cell imaging of HeLa and A549 demonstrates that the developed BICP is able to realize sensitive and selective mitochondrial NTR activity probing with high-contrast "off-on" fluorescence. These findings implied the great potential of the developed probe for monitoring mitochondrial-specific NTR activities in living cells and related applications in cell biology.