Multiomics Analyses Reveal MsC3H29 Positively Regulates Flavonoid Biosynthesis to Improve Drought Resistance of Autotetraploid Cultivated Alfalfa (Medicago sativa L.).

Alfalfa (Medicago sativa subsp. sativa), the "queen of forage," is the most important perennial legume, with high productivity and an excellent nutritional profile. Medicago sativa subsp. falcata is a subspecies of the alfalfa complex and exhibits better drought tolerance. However, drought stress significantly hampers their development and yield. The molecular mechanisms underlying the aboveground and underground tissues of sativa and falcata responding to drought stress remain obscure. Here, we performed a comprehensive comparative analysis of the physiological and transcriptomic responses of sativa and falcata under drought stress. The results showed that photosynthesis was inhibited, and antioxidant enzymes were activated under drought stress. MsC3H29, a CCCH-type zinc finger protein, was identified as a hub gene through weighted gene coexpression network analysis (WGCNA) and was significantly induced by drought in underground tissue. The MsC3H29 protein was localized in the nucleus. Overexpression (OE) of MsC3H29 can increase the primary root length and fresh weight of transgenic alfalfa hairy roots, while RNA interference (RNAi) decreases them under drought stress. The 2',7'-dichlorodihydrofluorescein diacetate (H2DCFDA) staining revealed that MsC3H29 promoted drought tolerance of alfalfa hairy roots through decreasing ROS accumulation. The targeted metabolome analysis showed that the overexpression of MsC3H29 resulted in higher levels of accumulation for flavonoid monomers, including vicenin, daidzein, apigenin, isorhamnetin, quercetin, and tricin, in transgenic alfalfa hairy roots before and after drought stress, while RNAi led to a reduction. Our study provided a key candidate gene for molecular breeding to improve drought resistance in alfalfa.

MODMS: a multi-omics database for facilitating biological studies on alfalfa (Medicago sativa L.).

Alfalfa (Medicago sativa L.) is a globally important forage crop. It also serves as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Multi-omics data on alfalfa continue to accumulate owing to recent advances in high-throughput techniques, and integrating this information holds great potential for expediting genetic research and facilitating advances in alfalfa agronomic traits. Therefore, we developed a comprehensive database named MODMS (multi-omics database of M. sativa) that incorporates multiple reference genomes, annotations, comparative genomics, transcriptomes, high-quality genomic variants, proteomics, and metabolomics. This report describes our continuously evolving database, which provides researchers with several convenient tools and extensive omics data resources, facilitating the expansion of alfalfa research. Further details regarding the MODMS database are available at https://modms.lzu.edu.cn/.

Preoperative US Integrated Random Forest Model for Predicting Delphian Lymph Node Metastasis in Patients with Papillary Thyroid Cancer.

BACKGROUND: Delphian lymph node (DLN) has been considered to be a gate that predicts widespread lymph node involvement, higher recurrence and mortality rates of head and neck cancer. OBJECTIVE: This study aimed to establish a preoperative ultrasonography integrated machine learning prediction model to predict Delphian lymph node metastasis (DLNM) in patients with diagnosed papillary thyroid carcinoma (PTC). METHODS: Ultrasonographic and clinicopathologic variables of PTC patients from 2014 to 2021 were retrospectively analyzed. The risk factors associated with DLNM were identified and validated through a developed random forest (RF) algorithm model based on machine learning and a logistic regression (LR) model. RESULTS: A total of 316 patients with 402 thyroid lesions were enrolled for the training dataset and 280 patients with 341 lesions for the validation dataset, with 170 (28.52%) patients developed DLNM. The elastography score of ultrasonography, central lymph node metastasis, lateral lymph node metastasis, and serum calcitonin were predictive factors for DLNM in both models. The RF model has better predictive performance in the training dataset and validation dataset (AUC: 0.957 vs. 0.890) than that in the LR model (AUC: 0.908 vs. 0.833). CONCLUSION: The preoperative ultrasonography integrated RF model constructed in this study could accurately predict DLNM in PTC patients, which may provide clinicians with more personalized clinical decision-making recommendations preoperatively. Machine learning technology has the potential to improve the development of DLNM prediction models in PTC patients.

Differentiation of Seven Isomeric n-Pentylquinoline Radical Cations Based on Energy-Resolved Medium-Energy Collision-Activated Dissociation.

Asphaltenes, a major and undesirable component of heavy crude oil, contain many different types of large aromatic compounds. These compounds include nitrogen-containing heteroaromatic compounds that are thought to be the main culprit in the deactivation of catalysts in crude oil refinery processes. Unfortunately, prevention of this is challenging as the structures and properties of the nitrogen-containing heteroaromatic compounds are poorly understood. To facilitate their structural characterization, an approach based on ion-trap collision-activated dissociation (ITCAD) tandem mass spectrometry followed by energy-resolved medium-energy collision-activated dissociation (ER-MCAD) was developed for the differentiation of seven isomeric molecular radical cations of n-pentylquinoline. The fragmentation of each isomer was found to be distinctly different and depended largely on the site of the alkyl side chain in the quinoline ring. In order to better understand the observed fragmentation pathways, mechanisms for the formation of several fragment ions were delineated based on quantum chemical calculations. The fast benzylic α-bond cleavage that dominates the fragmentation of analogous nonheteroaromatic alkylbenzenes was only observed for the 3-isomer as the major pathway due to the lack of favorable low-energy rearrangement reactions. All the other isomeric ions underwent substantially lower-energy rearrangement reactions as their alkyl chains were found to interact mostly via 6-membered transition states either with the quinoline nitrogen (2- and 8-isomers) or the adjacent carbon atom in the quinoline core (4-, 5-, 6-, and 7-isomers), which lowered the activation energies of the fragmentation reactions. The presented analytical approach will facilitate the structural characterization of nitrogen-containing heteroaromatic compounds in asphaltenes.

Energy-Resolved Mass Spectrometry as a Tool for Identification of Lignin Depolymerization Products.

Lignin is the largest source of bio-based aromatic compounds in nature, and its valorization is essential to the sustainability of lignocellulosic biorefining. Characterizing lignin-derived compounds remains challenging due to the heterogeneity of this biopolymer. Tandem mass spectrometry is a promising tool for lignin structural analytics, as fragmentation patterns of model compounds can be extrapolated to identify characteristic moieties in complex samples. This work extended previous resonance excitation-type collision-induced dissociation (CID) methods that identified lignin oligomers containing ß-O-4, ß-5, and ß-ß bonds, to also identify characteristics of 5-5, ß-1, and 4-O-5 dimers, enabled by quadrupole time-of-flight (QTOF) CID with energy-resolved mass spectrometry (ERMS). Overall, QTOF-ERMS offers in-depth structural information and could ultimately contribute to tools for high-throughput lignin dimer identification.

Mixed plastics waste valorization through tandem chemical oxidation and biological funneling.

Mixed plastics waste represents an abundant and largely untapped feedstock for the production of valuable products. The chemical diversity and complexity of these materials, however, present major barriers to realizing this opportunity. In this work, we show that metal-catalyzed autoxidation depolymerizes comingled polymers into a mixture of oxygenated small molecules that are advantaged substrates for biological conversion. We engineer a robust soil bacterium, Pseudomonas putida, to funnel these oxygenated compounds into a single exemplary chemical product, either ß-ketoadipate or polyhydroxyalkanoates. This hybrid process establishes a strategy for the selective conversion of mixed plastics waste into useful chemical products.

Genome-wide identification of the MADS-box transcription factor family in autotetraploid cultivated alfalfa (Medicago sativa L.) and expression analysis under abiotic stress.

BACKGROUND: Alfalfa, the "queen of forage", is the most extensively cultivated forage legume in the world. The development and yield of alfalfa are seriously limited by abiotic stress. MADS-box transcription factors are one of the largest gene families and play a pivotal role in plant development and abiotic stress. However, little is known regarding the MADS-box transcription factors in autotetraploid cultivated alfalfa. RESULTS: In the present study, we identified 120 MsMADS-box genes in the alfalfa genome. Phylogenetic analysis indicated that 75 type-I MsMADS-box genes were classified into the Mα, Mß, and Mγ subgroups, and 45 type-II MsMADS-box genes were classified into 11 subgroups. The promoter region of MsMADS-box genes containing several hormone and stress related elements. Chromosomal location analysis revealed that 117 MsMADS-box genes were unevenly distributed on 32 chromosomes, and the remaining three genes were located on unmapped scaffolds. A total of nine pairs of segmental duplications and four groups of tandem duplications were found. Expression analysis showed that MsMADS-box genes were differentially expressed in various tissues and under abiotic stresses. qRT-PCR analysis revealed that the expression profiles of eight selected MsMADS-box genes were distinct under various stresses. CONCLUSIONS: In this study, MsMADS-box genes were identified in the cultivated alfalfa genome based on autotetraploid level, and further confirmed by Gene Ontology (GO) analysis, phylogenetic analysis, sequence features and expression analysis. Taken together, these findings will provide clues for further study of MsMADS-box functions and alfalfa molecular breeding. Our study is the first to systematically identify and characterize the MADS-box transcription factors in autotetraploid cultivated alfalfa (Medicago sativa L.), and eight MsMADS-box genes were significantly involved in response to various stresses.

Free-Radical-Mediated Glycan Isomer Differentiation.

The inherent structural complexity and diversity of glycans pose a major analytical challenge to their structural analysis. Radical chemistry has gained considerable momentum in the field of mass spectrometric biomolecule analysis, including proteomics, glycomics, and lipidomics. Herein, seven isomeric disaccharides and two isomeric tetrasaccharides with subtle structural differences are distinguished rapidly and accurately via one-step radical-induced dissociation. The free-radical-activated glycan-sequencing reagent (FRAGS) selectively conjugates to the unique reducing terminus of glycans in which a localized nascent free radical is generated upon collisional activation and simultaneously induces glycan fragmentation. Higher-energy collisional dissociation (HCD) and collision-induced dissociation (CID) are employed to provide complementary structural information for the identification and discrimination of glycan isomers by providing different fragmentation pathways to generate informative, structurally significant product ions. Furthermore, multiple-stage tandem mass spectrometry (MS3 CID) provides supplementary and valuable structural information through the generation of characteristic parent-structure-dependent fragment ions.

Insight into molecular characteristics of a Chinese coal via separation, characterization, and data processing.

Dayan lignite was subjected to thermal dissolution sequentially with cyclohexane, acetone, and methanol. Each thermal dissolution extract was subjected to further separation/enrichment using column chromatography, which was sequentially eluted with petroleum ether, a mixture of ethyl acetate and petroleum ether (vol:vol = 1:1), and ethyl acetate. The three thermal dissolution extracts and nine enrichment subfractions were characterized by an Orbitrap mass spectrometry equipped with an atmospheric pressure chemical ionization ion source. The mass spectrometry data were also statistically analyzed by principal component analysis, which can reduce the dimensionality of data and classify multiple samples according to principal components. Identified compounds in the extracts and subfractions are classified into eight classes according to the heteroatom distribution. Hydrocarbon class is mainly presented in the petroleum ether fraction, and oxygen class, nitrogen class, and oxygen-nitrogen class are distributed in both petroleum ether/ethyl acetate and ethyl acetate subfractions. The combination of different analytical methods enhances the understanding of coal at the molecular level and provides important data for downstream refining processes.

Evaluation of coal-related model compounds using tandem mass spectrometry.

RATIONALE: Gas chromatography/mass spectrometry (GC/MS) is a routine and basic instrumental method for the analysis of complex coal conversion products in the chemical industry. To further enhance the practical potential of GC/MS in chemical industry, a tandem MS method for the selection of ion pairs applied in monitoring coal conversions was established using GC/quadrupole time-of-flight MS (GC/Q-TOF MS). The corresponding fragmentation pathways were explored and suitable ion pairs were screened. METHODS: Fourteen coal-related model compounds (CRMCs) were analyzed using GC/Q-TOF MS with different collision-induced dissociation (CID) energies (5-20 eV). The fragmentation pathways can offer a better understanding of chemical bond breaking, hydrogen transfer, rearrangement reactions and elimination of neutral fragments for CRMCs during the CID process. RESULTS: The precursor ions of aromatic hydrocarbons without alkyl chains were difficult to fragment with a CID energy of 20 eV. But aromatic hydrocarbons with branched chains were prone to fragment via the loss of alkyl chains and further fragmented through ring-opening reactions. Compared with the Calk Car bond, the Car Car bond was difficult to fragment due to its high bond dissociation energy. The existence of heteroatoms facilitated fragmentation that was conducive to the screening of ion pairs. CONCLUSIONS: The CID technique of GC/Q-TOF MS will contribute to studies on the organic composition of coals and to building monitoring methods for coal conversions via fragmentation and ion pair selection.

Application of paper spray-MS in PK studies using sunitinib and benzethonium as model compounds.

AIM: Current bioanalytical methods applied in nonclinical PK studies for screening drug candidates demand significant amount of time and resources, hence, the need to develop alternative methods. RESULTS: A proof-of-concept paper spray-MS method for the detection and quantitation of small molecules in plasma has been developed and validated using sunitinib and benzethonium as model compounds. The method includes single oral or intravenous administration of sunitinib to mice and serial micro-volume (20 µl) blood collection at different time intervals. The method is rapid with overall analysis time of 1 min and a full PK profile of sunitinib was obtained from a single mouse. CONCLUSION: The paper spray-MS approach is simple, sensitive and can potentially enable significant reduction of animal use and cost.

A covalent reporter of ß-lactamase activity for fluorescent imaging and rapid screening of antibiotic-resistant bacteria.

Bacterial resistance to antibiotics poses a great clinical challenge in fighting serious infectious diseases due to complicated resistant mechanisms and time-consuming testing methods. Chemical reaction-directed covalent labeling of resistance-associated bacterial proteins in the context of a complicated environment offers great opportunity for the in-depth understanding of the biological basis conferring drug resistance, and for the development of effective diagnostic approaches. In the present study, three fluorogenic reagents LRBL1-3 for resistant bacteria labeling have been designed and prepared on the basis of fluorescence resonance energy transfer (FRET). The hydrolyzed probes could act as reactive electrophiles to attach the enzyme, ß-lactamase, and thus facilitated the covalent labeling of drug resistant bacterial strains. SDS electrophoresis and MALDI-TOF mass spectrometry characterization confirmed that these probes were sensitive and specific to ß-lactamase and could therefore serve for covalent and localized fluorescence labeling of the enzyme structure. Moreover, this ß-lactamase-induced covalent labeling provides quantitative analysis of the resistant bacterial population (down to 5%) by high resolution flow cytometry, and allows single-cell detection and direct observation of bacterial enzyme activity in resistant pathogenic species. This approach offers great promise for clinical investigations and microbiological research.

Functional divergence of FimX in PilZ binding and type IV pilus regulation.

Type IV pili (T4P) are polar surface structures that play important roles in bacterial motility, biofilm formation, and pathogenicity. The protein FimX and its orthologs are known to mediate T4P formation in the human pathogen Pseudomonas aeruginosa and some other bacterial species. It was reported recently that FimX(XAC2398) from Xanthomonas axonopodis pv. citri interacts with PilZ(XAC1133) directly through the nonenzymatic EAL domain of FimX(XAC2398). Here we present experimental data to reveal that the strong interaction between FimX(XAC2398) and PilZ(XAC1133) is not conserved in P. aeruginosa and likely other Pseudomonas species. In vitro and in vivo binding experiments showed that the interaction between FimX and PilZ in P. aeruginosa is below the measurable limit. Surface plasmon resonance assays further confirmed that the interaction between the P. aeruginosa proteins is at least more than 3 orders of magnitude weaker than that between the X. axonopodis pv. citri pair. The N-terminal lobe region of FimX(XAC2398) was identified as the binding surface for PilZ(XAC1133) by amide hydrogen-deuterium exchange and site-directed mutagenesis studies. Lack of several key residues in the N-terminal lobe region of the EAL domain of FimX is likely to account for the greatly reduced binding affinity between FimX and PilZ in P. aeruginosa. All together, the results suggest that the interaction between PilZ and FimX in Xanthomonas species is not conserved in P. aeruginosa due to the evolutionary divergence among the FimX orthologs. The precise roles of FimX and PilZ in bacterial motility and T4P biogenesis are likely to vary among bacterial species.

Binding of cyclic diguanylate in the non-catalytic EAL domain of FimX induces a long-range conformational change.

FimX is a multidomain signaling protein required for type IV pilus biogenesis and twitching motility in the opportunistic pathogen Pseudomonas aeruginosa. FimX is localized to the single pole of the bacterial cell, and the unipolar localization is crucial for the correct assembly of type IV pili. FimX contains a non-catalytic EAL domain that lacks cyclic diguanylate (c-di-GMP) phosphodiesterase activity. It was shown that deletion of the EAL domain or mutation of the signature EVL motif affects the unipolar localization of FimX. However, it was not understood how the C-terminal EAL domain could influence protein localization considering that the localization sequence resides in the remote N-terminal region of the protein. Using hydrogen/deuterium exchange-coupled mass spectrometry, we found that the binding of c-di-GMP to the EAL domain triggers a long-range (∼ca. 70 Å) conformational change in the N-terminal REC domain and the adjacent linker. In conjunction with the observation that mutation of the EVL motif of the EAL domain abolishes the binding of c-di-GMP, the hydrogen/deuterium exchange results provide a molecular explanation for the mediation of protein localization and type IV pilus biogenesis by c-di-GMP through a remarkable allosteric regulation mechanism.