Increased α-ketoglutarate links the C3-C4 intermediate state to C4 photosynthesis in the genus Flaveria.

As a complex trait, C4 photosynthesis has multiple independent origins in evolution. Phylogenetic evidence and theoretical analysis suggest that C2 photosynthesis, which is driven by glycine decarboxylation in the bundle sheath cell, may function as a bridge from C3 towards C4 photosynthesis. However, the exact molecular mechanism underlying the transition between C2 photosynthesis towards C4 photosynthesis remains elusive. Here, we provide evidence suggesting a role of higher α-ketoglutarate (AKG) concentration during this transition. Metabolomic data of 12 Flaveria species, including multiple photosynthetic types, show that AKG concentration initially increased in the C3-C4 intermediate with a further increase in C4 species. Petiole feeding of AKG increases the concentrations of C4 related metabolites in C3-C4 and C4 species but not the activity of C4 related enzymes. Sequence analysis shows that glutamate synthase (Fd-GOGAT), which catalyzes the generation of glutamate using AKG, was under strong positive selection during the evolution of C4 photosynthesis. Simulations with a constraint-based model for C3-C4 intermediate further show that decreasing the activity of Fd-GOGAT facilitated the transition from a C2-dominant to a C4-dominant CO2 concentrating mechanism. All these results provide insight into the mechanistic switch from C3-C4 intermediate to C4 photosynthesis.

Regulatory NADH dehydrogenase-like complex optimizes C4 photosynthetic carbon flow and cellular redox in maize.

C4 plants typically operate a CO2 concentration mechanism from mesophyll (M) cells into bundle sheath (BS) cells. NADH dehydrogenase-like (NDH) complex is enriched in the BS cells of many NADP-malic enzyme (ME) type C4 plants and is more abundant in C4 than in C3 plants, but to what extent it is involved in the CO2 concentration mechanism remains to be experimentally investigated. We created maize and rice mutants deficient in NDH function and then used a combination of transcriptomic, proteomic, and metabolomic approaches for comparative analysis. Considerable decreases in growth, photosynthetic activities, and levels of key photosynthetic proteins were observed in maize but not rice mutants. However, transcript abundance for many cyclic electron transport (CET) and Calvin-Benson cycle components, as well as BS-specific C4 enzymes, was increased in maize mutants. Metabolite analysis of the maize ndh mutants revealed an increased NADPH : NADP ratio, as well as malate, ribulose 1,5-bisphosphate (RuBP), fructose 1,6-bisphosphate (FBP), and photorespiration intermediates. We suggest that by optimizing NADPH and malate levels and adjusting NADP-ME activity, NDH functions to balance metabolic and redox states in the BS cells of maize (in addition to ATP supply), coordinating photosynthetic transcript abundance and protein content, thus directly regulating the carbon flow in the two-celled C4 system of maize.

Exploring the feasibility of using long-term stored newborn dried blood spots to identify metabolic features for congenital heart disease screening.

Congenital heart disease (CHD) represents a significant contributor to both morbidity and mortality in neonates and children. There's currently no analogous dried blood spot (DBS) screening for CHD immediately after birth. This study was set to assess the feasibility of using DBS to identify reliable metabolite biomarkers with clinical relevance, with the aim to screen and classify CHD utilizing the DBS. We assembled a cohort of DBS datasets from the California Department of Public Health (CDPH) Biobank, encompassing both normal controls and three pre-defined CHD categories. A DBS-based quantitative metabolomics method was developed using liquid chromatography with tandem mass spectrometry (LC-MS/MS). We conducted a correlation analysis comparing the absolute quantitated metabolite concentration in DBS against the CDPH NBS records to verify the reliability of metabolic profiling. For hydrophilic and hydrophobic metabolites, we executed significant pathway and metabolite analyses respectively. Logistic and LightGBM models were established to aid in CHD discrimination and classification. Consistent and reliable quantification of metabolites were demonstrated in DBS samples stored for up to 15 years. We discerned dysregulated metabolic pathways in CHD patients, including deviations in lipid and energy metabolism, as well as oxidative stress pathways. Furthermore, we identified three metabolites and twelve metabolites as potential biomarkers for CHD assessment and subtypes classifying. This study is the first to confirm the feasibility of validating metabolite profiling results using long-term stored DBS samples. Our findings highlight the potential clinical applications of our DBS-based methods for CHD screening and subtype classification.

High-throughput quantitation of amino acids and acylcarnitine in cerebrospinal fluid: identification of PCNSL biomarkers and potential metabolic messengers.

Background: Due to the poor prognosis and rising occurrence, there is a crucial need to improve the diagnosis of Primary Central Nervous System Lymphoma (PCNSL), which is a rare type of non-Hodgkin's lymphoma. This study utilized targeted metabolomics of cerebrospinal fluid (CSF) to identify biomarker panels for the improved diagnosis or differential diagnosis of primary central nervous system lymphoma (PCNSL). Methods: In this study, a cohort of 68 individuals, including patients with primary central nervous system lymphoma (PCNSL), non-malignant disease controls, and patients with other brain tumors, was recruited. Their cerebrospinal fluid samples were analyzed using the Ultra-high performance liquid chromatography - tandem mass spectrometer (UHPLC-MS/MS) technique for targeted metabolomics analysis. Multivariate statistical analysis and logistic regression modeling were employed to identify biomarkers for both diagnosis (Dx) and differential diagnosis (Diff) purposes. The Dx and Diff models were further validated using a separate cohort of 34 subjects through logistic regression modeling. Results: A targeted analysis of 45 metabolites was conducted using UHPLC-MS/MS on cerebrospinal fluid (CSF) samples from a cohort of 68 individuals, including PCNSL patients, non-malignant disease controls, and patients with other brain tumors. Five metabolic features were identified as biomarkers for PCNSL diagnosis, while nine metabolic features were found to be biomarkers for differential diagnosis. Logistic regression modeling was employed to validate the Dx and Diff models using an independent cohort of 34 subjects. The logistic model demonstrated excellent performance, with an AUC of 0.83 for PCNSL vs. non-malignant disease controls and 0.86 for PCNSL vs. other brain tumor patients. Conclusion: Our study has successfully developed two logistic regression models utilizing metabolic markers in cerebrospinal fluid (CSF) for the diagnosis and differential diagnosis of PCNSL. These models provide valuable insights and hold promise for the future development of a non-invasive and reliable diagnostic tool for PCNSL.

Altered expression of the L-arginine/nitric oxide pathway in ovarian cancer: metabolic biomarkers and biological implications.

MOTIVATION: Ovarian cancer (OC) is a highly lethal gynecological malignancy. Extensive research has shown that OC cells undergo significant metabolic alterations during tumorigenesis. In this study, we aim to leverage these metabolic changes as potential biomarkers for assessing ovarian cancer. METHODS: A functional module-based approach was utilized to identify key gene expression pathways that distinguish different stages of ovarian cancer (OC) within a tissue biopsy cohort. This cohort consisted of control samples (n = 79), stage I/II samples (n = 280), and stage III/IV samples (n = 1016). To further explore these altered molecular pathways, minimal spanning tree (MST) analysis was applied, leading to the formulation of metabolic biomarker hypotheses for OC liquid biopsy. To validate, a multiple reaction monitoring (MRM) based quantitative LCMS/MS method was developed. This method allowed for the precise quantification of targeted metabolite biomarkers using an OC blood cohort comprising control samples (n = 464), benign samples (n = 3), and OC samples (n = 13). RESULTS: Eleven functional modules were identified as significant differentiators (false discovery rate, FDR < 0.05) between normal and early-stage, or early-stage and late-stage ovarian cancer (OC) tumor tissues. MST analysis revealed that the metabolic L-arginine/nitric oxide (L-ARG/NO) pathway was reprogrammed, and the modules related to "DNA replication" and "DNA repair and recombination" served as anchor modules connecting the other nine modules. Based on this analysis, symmetric dimethylarginine (SDMA) and arginine were proposed as potential liquid biopsy biomarkers for OC assessment. Our quantitative LCMS/MS analysis on our OC blood cohort provided direct evidence supporting the use of the SDMA-to-arginine ratio as a liquid biopsy panel to distinguish between normal and OC samples, with an area under the ROC curve (AUC) of 98.3%. CONCLUSION: Our comprehensive analysis of tissue genomics and blood quantitative LC/MSMS metabolic data shed light on the metabolic reprogramming underlying OC pathophysiology. These findings offer new insights into the potential diagnostic utility of the SDMA-to-arginine ratio for OC assessment. Further validation studies using adequately powered OC cohorts are warranted to fully establish the clinical effectiveness of this diagnostic test.

Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase.

Methylations on nucleosomal histones play fundamental roles in regulating eukaryotic transcription. Jumonji C domain-containing histone demethylases (JMJs) dynamically control the level of histone methylations. However, how JMJ activity is generally regulated is unknown. We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. Chromatin-bound KGDH catalyzes α-KG decarboxylation and thus may limit its local availability to KGDH-coupled JMJs, inhibiting histone demethylation. Thus, our results uncover a regulatory mechanism for histone demethylations by JMJs.

Cheilolejeunea zhui (Lejeuneaceae, Marchantiophyta), a new species with moniliate ocelli from Guangxi, China.

A new ocellate liverwort species, Cheilolejeunea zhui (Lejeuneaceae), is described from Guangxi, China. The new species is similar to the neotropical C. urubuensis in having moniliate ocelli in the leaf lobes and in general appearances but differs in having obliquely spreading leaves, obtuse to subacute leaf apex, thin-walled leaf cells with distinct trigones, shallowly bifid female bracteole apex, and numerous ocelli in its perianths. Molecular phylogeny of data from three regions (nrITS, trnL-F, and trnG) confirmed the systematic position of this new species to be sister to C. urubuensis, well apart from the remaining members of the genus. Based on morphological and molecular evidence, Cheilolejeunea sect. Moniliocella sect. nov. is proposed to accommodate C. urubuensis and C. zhui. The discovery of C. zhui represents the fourth known species in Cheilolejeunea with linearly arranged ocelli.

One-Step Fabrication of Coconut-Like Capsules via Competitive Reactions at an All-Aqueous Interface for Enzyme Immobilization.

A concept of interfacial competitive reaction between biomineralization and alginate gelation at an all-aqueous single-emulsion droplet interface to prepare robust coconut-like capsules (inner hard wall and outer soft wall) is developed. The concept is further applied for enzyme immobilization with high encapsulation efficiency, enzyme loading, mass transfer coefficient, and recyclability. The thickness and swelling properties of the shell are simply tunable by a competitive reaction. Our platform may open a green, facile, and efficient way to prepare organic-inorganic hybrid sustainable materials with tailored compositions and structures.

Microstructure and morphology of the soldering interface of Sn-2.0Ag-1.5Zn low Ag content lead-free solder ball and different substrates.

Eutectic Sn-Ag-Cu lead-free solder has limited applications due to cost and reliability issues. Sn-Ag-Zn solder has the advantages of low melting point, good mechanical properties and reliable welding interface. However, the research system of low silver content Sn-Ag-Zn solder is incomplete. In this paper, Sn-2.0Ag-1.5Zn low silver content alloy solder is soldered to different substrates. The interfacial reaction after soldering and the microstructure and reliability under different aging treatment conditions are studied. Sn-2.0Ag-1.5Zn solder is made into solder balls by direct melting method. The solder balls are placed in a solder strength tester to be heated and welded to the substrate, and then the solder joints are placed in a heating furnace for aging treatment. The results show that the solder is soldered to the bare Cu substrate, and a dense double-layer Intermetallic Compound (IMC) structure of Cu5Zn8 and Ag3Sn is formed at the interface after aging treatment. The double-layer structure blocks each other, limiting the development of copper-tin IMCs. The solder is soldered with the Cu substrate electroplated with Ni barrier layer, and the soldering interface forms a thin layer of Ni3Sn4 metal compound. After aging for 1000 h, the thickness of Ni3Sn4 is about 1 µm, the thickness of Ni barrier layer is kept at 2-3 µm, and the barrier effect of Ni barrier layer is stable. Sn-2.0Ag-1.5Zn solder has excellent loss performance in long aging treatment. It has good heat-resistance aging treatment, good quality of solder connection, high interface reliability and less environmental pollution. The low silver content in Sn-2.0Ag-1.5Zn solder results in a significant cost reduction. Coarse IMC Ag3Sn is not easily formed. The optimized ratio of Ag and Zn in Sn-2.0Ag-1.5Zn solder improves the strength and toughness of the solder joint. The performance has been improved, and it is a very promising alloy solder.

Evolution of gene regulatory network of C4 photosynthesis in the genus Flaveria reveals the evolutionary status of C3-C4 intermediate species.

C4 photosynthesis evolved from ancestral C3 photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4 metabolic pathway have been intensively studied and well documented; however, the transcription factors (TFs) that regulate these C4 metabolic genes are not yet well understood. In particular, how the TF regulatory network of C4 metabolic genes was rewired during the evolutionary process is unclear. Here, we constructed gene regulatory networks (GRNs) for four closely evolutionarily related species from the genus Flaveria, which represent four different evolutionary stages of C4 photosynthesis: C3 (F. robusta), type I C3-C4 (F. sonorensis), type II C3-C4 (F. ramosissima), and C4 (F. trinervia). Our results show that more than half of the co-regulatory relationships between TFs and core C4 metabolic genes are species specific. The counterparts of the C4 genes in C3 species were already co-regulated with photosynthesis-related genes, whereas the required TFs for C4 photosynthesis were recruited later. The TFs involved in C4 photosynthesis were widely recruited in the type I C3-C4 species; nevertheless, type II C3-C4 species showed a divergent GRN from C4 species. In line with these findings, a 13CO2 pulse-labeling experiment showed that the CO2 initially fixed into C4 acid was not directly released to the Calvin-Benson-Bassham cycle in the type II C3-C4 species. Therefore, our study uncovered dynamic changes in C4 genes and TF co-regulation during the evolutionary process; furthermore, we showed that the metabolic pathway of the type II C3-C4 species F. ramosissima represents an alternative evolutionary solution to the ammonia imbalance in C3-C4 intermediate species.

Proton-Mediated and Ir-Catalyzed Iron/Iron-Oxide Redox Kinetics for Enhanced Rechargeability and Durability of Solid Oxide Iron-Air Battery.

Long duration energy storage (LDES) is an economically attractive approach to accelerating clean renewable energy deployment. The newly emerged solid oxide iron-air battery (SOIAB) is intrinsically suited for LDES applications due to its excellent low-rate performance (high-capacity with high efficiency) and use of low-cost and sustainable materials. However, rechargeability and durability of SOIAB are critically limited by the slow kinetics in iron/iron-oxide redox couples. Here the use of combined proton-conducting BaZr0.4 Ce0.4 Y0.1 Yb0.1 O3 (BZC4YYb) and reduction-promoting catalyst Ir to address the kinetic issues, is reported. It is shown that, benefiting from the facilitated H+ diffusion and boosted FeOx -reduction kinetics, the battery operated under 550 °C, 50% Fe-utilization and 0.2 C, exhibits a discharge specific energy density of 601.9 Wh kg-1 -Fe with a round-trip efficiency (RTE) of 82.9% for 250 h of a cycle duration of 2.5 h. Under 500 °C, 50% Fe-utilization and 0.2 C, the same battery exhibits 520 Wh kg-1 -Fe discharge energy density with an RTE of 61.8% for 500 h. This level of energy storage performance promises that SOIAB is a strong candidate for LDES applications.

An integrated isotopic labeling and freeze sampling apparatus (ILSA) to support sampling leaf metabolomics at a centi-second scale.

BACKGROUND: Photosynthesis close interacts with respiration and nitrogen assimilation, which determine the photosynthetic efficiency of a leaf. Accurately quantifying the metabolic fluxes in photosynthesis, respiration and nitrogen assimilation benefit the design of photosynthetic efficiency improvement. To accurately estimate metabolic fluxes, time-series data including leaf metabolism and isotopic abundance changes should be collected under precisely controlled environments. But for isotopic labelled leaves under defined environments the, time cost of manually sampling usually longer than the turnover time of several intermediates in photosynthetic metabolism. In this case, the metabolic or physiological status of leaf sample would change during the sampling, and the accuracy of metabolomics data could be compromised. RESULTS: Here we developed an integrated isotopic labeling and freeze sampling apparatus (ILSA), which could finish freeze sampling automatically in 0.05 s. ILSA can not only be used for sampling of photosynthetic metabolism measurement, but also suit for leaf isotopic labeling experiments under controlled environments ([CO2] and light). Combined with HPLC-MS/MS as the metabolic measurement method, we demonstrated: (1) how pool-size of photosynthetic metabolites change in dark-accumulated rice leaf, and (2) variation in photosynthetic metabolic flux between rice and Arabidopsis thaliana. CONCLUSIONS: The development of ILSA supports the photosynthetic research on metabolism and metabolic flux analysis and provides a new tool for the study of leaf physiology.

Binary Iron Sulfide as a Low-Cost and High-Performance Anode for Lithium-/Sodium-Ion Batteries.

Iron-based sulfides have been deemed as an appealing anode material for lithium-ion batteries (LIBs) and sodium-ion batteries (SIBs) for their high theoretical capacity and low cost. However, their practical application is limited by drastic volume expansion during cycling and low-intrinsic electronic conductivity. In this work, we report a FeS2/Fe7S8-rGO composite synthesized via a facile solvothermal method as an LIB/SIB anode. The FeS2/Fe7S8-rGO anode exhibits an excellent Li-storage capacity of 514 mAh g-1 at 2.0 A g-1 after 3000 cycles and a Na-storage capacity of 650 mAh g-1 at 0.2 A g-1 after 250 cycles, respectively. The rGO matrix is deemed responsible for providing good electron conduction and alleviating volume expansion during cycling. The electrokinetic analysis confirms a large portion of intercalational pseudocapacitance as a major contribution to the superior rate performance. In situ X-ray diffraction further reveals details of a combined intercalational and conversional Li-ion storage mechanisms in this Fe-sulfide-based anode. Finally, density functional theory calculations suggest that there exists a synergistic effect at the heterointerface between FeS2 and Fe7S8 to promote electrokinetics.

Aqueous Two-Phase Droplet-Templated Colloidosomes Composed of Self-Formed Particles via Spatial Confined Biomineralization.

A facile and green approach is developed for fabricating colloidosomes with well-controlled size and structure from the microfluidic-generated aqueous two-phase system (ATPS) emulsion droplet. Unlike other methods that rely on self-assembly of externally added colloidal particles at the emulsion interface, urease-mediated biomineralization induced by "drainage" is introduced to form CaCO3 particles at the alginate emulsion interface for preparing Ca-alg@CaCO3 colloidosomes. Two types of bioactive molecules (bovine serum albumin and catalase) can be encapsulated with high efficiency (>85%) because of the partitioning effect of the ATPS and high viscosity of alginate solution. The encapsulated bioactive molecules can be controllably released by regulating the compactness of colloidosomes. Moreover, after being freeze-dried or dried at 37 °C, the activity of catalase in colloidosomes is obviously higher than that in alginate hydrogels, which confirms that the Ca-alg@CaCO3 structure has strong protection for inclusions. We believe that the biocompatible and controllable Ca-alg@CaCO3 colloidosomes possess great potential applications in bioencapsulation for foods, daily chemicals, and synthetic protocell formation.

Monodisperse Alginate Microcapsules with Spatially Confined Bioactive Molecules via Microfluid-Generated W/W/O Emulsions.

A simple process is developed for the one-step preparation of dual-compartment alginate microcapsules with controlled size and structure from microfluid-generated water-in-water-in-oil (W/W/O) emulsion droplet. Unlike other methods that rely on transient W/W/O emulsion droplet, we introduce an aqueous two-phase system (ATPS) to form a stable W/W/O emulsion droplet as a template for preparing dual-compartment alginate microcapsules. Two different bioactive molecules are able to be spatially confined encapsulated in the shell and core of alginate microcapsules due to the partitioning effect of ATPS and the high viscosity of alginate solution. Moreover, an enzyme cascade reaction with a spatial confined glucose oxidase and horseradish peroxidase in the shell and core of alginate microcapsules confirms its excellent biocompatibility and high activity. This method provides a green platform for enzyme-catalyzed tandem reactions and controlled sequential release of multiple drugs based on alginate microcapsules.

The genome of broomcorn millet.

Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.

Complete Genome Sequence of Bacillus megaterium Strain TG1-E1, a Plant Drought Tolerance-Enhancing Bacterium.

Based on a combination of next-generation sequencing and single-molecule sequencing, we obtained the whole-genome sequence of Bacillus megaterium strain TG1-E1, which is a highly salt-tolerant rhizobacterium that enhances plant tolerance to drought stress. The complete genome is estimated to be approximately 5.48 Mb containing a total of 5,858 predicted protein-coding DNA sequences.

Species composition and diversity of ground bryophytes across a forest edge-to-interior gradient.

Understanding diversity patterns and community structure of bryophytes will help integrate nature conservation at multiple biotic-group levels. We conducted a survey of ground bryophytes in a subtropical forest along an edge-to-interior gradient in South China. We recorded 11 liverwort species from 10 genera of seven families, and 26 moss species from 23 genera of 16 families in three transects. A two-way cluster analysis detected the environmental gradient between the forest edge and forest interior for bryophytes with habitat specificity. Functional diversity of bryophytes differed significantly across an edge-to-interior gradient. The range and median in both structural and functional diversity decreased remarkably from the forest edge to the interior. Multi-response permutation procedures showed significant differences in species composition between the forest-edge and forest-interior, and between the intermediate and forest-interior transects. Seven species were detected with a significant indicator value for indicating environmental conditions in the forest edge, while only one such species was found indicative of the intermediate transect. Our results demonstrate that remarkable edge effects exist for species composition and functional diversity patterns, and the forest edge is a marginal habitat with high biotic heterogeneity. Furthermore, functional diversity metrics are more sensitive to the edge effect than species diversity.

Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a High-Salinity Environment.

Here, we report the complete genome sequence for Bacillus megaterium strain YC4-R4, a highly salt-tolerant rhizobacterium that promotes growth in plants. The sequencing process was performed by combining pyrosequencing and single-molecule sequencing techniques. The complete genome is estimated to be approximately 5.44 Mb, containing a total of 5,673 predicted protein-coding DNA sequences (CDSs).