Energy Pathways Research Articles

Metagenomic and metabolomic analysis showing the adverse risk–benefit trade-off of the ketogenic diet

BackgroundKetogenic diets are increasingly popular for addressing obesity, but their impacts on the gut microbiota and metabolome remain unclear. This paper aimed to investigate how a ketogenic diet affects intestinal microorganisms and metabolites in obesity.MethodsMale mice were provided with one of the following dietary regimens: normal chow, high-fat diet, ketogenic diet, or high-fat diet converted to ketogenic diet. Body weight and fat mass were measured weekly using high-precision electronic balances and minispec body composition analyzers. Metagenomics and non-targeted metabolomics data were used to analyze differences in intestinal contents.ResultsObese mice on the ketogenic diet exhibited notable improvements in weight and body fat. However, these were accompanied by a significant decrease in intestinal microbial diversity, as well as an increase in Firmicutes abundance and a 247% increase in the Firmicutes/Bacteroidetes ratio. The ketogenic diet also altered multiple metabolic pathways in the gut, including glucose, lipid, energy, carbohydrate, amino acid, ketone body, butanoate, and methane pathways, as well as bacterial secretion and colonization pathways. These changes were associated with increased intestinal inflammation and dysbiosis in obese mice. Furthermore, the ketogenic diet enhanced the secretion of bile and the synthesis of aminoglycoside antibiotics in obese mice, which may impair the gut microbiota and be associated with intestinal inflammation and immunity.ConclusionsThe study suggest that the ketogenic diet had an unfavorable risk–benefit trade-off and may compromise metabolic homeostasis in obese mice.

The Flavoring Agent Ethyl Vanillin Induces Cellular Stress Responses in HK-2 Cells.

Flavored e-cigarettes are a popular alternative to cigarette smoking; unfortunately, the extrapulmonary effects are not well-characterized. Human proximal tubule cells were cultured for 24 or 48 h with 0-1000 µM ethyl vanillin (ETH VAN) and cytotoxicity evaluated. Mitochondrial health was significantly diminished following 48 h of exposure, accompanied by significantly decreased spare capacity, coupling efficiency, and ATP synthase expression. ETH VAN at 24 h inhibited glycolysis. The endoplasmic reticulum (ER) stress marker C/EBP homologous protein (CHOP) was increased at 100 μM relative to 500-1000 μM. The downstream proapoptotic marker cleaved caspase-3 subsequently showed a decreasing trend in expression after 48 h of exposure. The autophagy biomarkers microtubule-associated proteins 1A/1B light chain 3 (LC3B-I and LC3B-II) were measured by Western blot. LC3B-II levels and the LC3B-II/LC3B-I ratio increased at 24 h, which suggested activation of autophagy. In contrast, by 48 h, the autophagy biomarker LC3B-II decreased, resulting in no change in the LC3B-II/LC3B-I ratio. Mitophagy biomarker PTEN-induced putative kinase 1 (PINK1) expression decreased after 48 h of exposure. The downstream marker Parkin was not significantly changed after 24 or 48 h. These findings indicate that the flavoring ETH VAN can induce energy pathway dysfunction and cellular stress responses in a renal model.

Transcriptomic and metabolomic analysis of prebiotics utilization by Bifidobacterium animalis.

In this study, the utilization mechanism of oligosaccharides by Bifidobacterium was investigated through the transcriptome sequencing and non-targeted metabolomics technology of Bifidobacterium animalis cultured with fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS). The results showed that FOS affected the synthesis of adenosine triphosphate binding transporters (ABC transporters) by increasing the expression levels of msmE, msmG, and gluA. Similarly, GOS improved aminoacyl-tRNA synthases by upregulating the expression of tRNA-Ala, tRNA-Pro, and tRNA-Met. Bifidobacterium animalis cultured with FOS and GOS produced different metabolites, such as histamine, tartaric acid, and norepinephrine, with the functions of inhibiting inflammation, alleviating depression and diseases related to brain and nervous system and maintaining body health. Furthermore, the transcriptome and metabolome analysis results revealed that FOS and GOS promoted the growth and metabolism of Bifidobacterium animalis by regulating the related pathways of carbohydrate, energy, and amino acid metabolism. Overall, the experimental results provided significant insights into the prebiotic effects of FOS and GOS.

Analyzing the impact of T7L variants overexpression on the metabolic profile of Escherichia coli.

Exploring metabolic changes within host E. coli through an untargeted metabolomic study of T7L variants overexpression to optimize engineered endolysins for clinical/therapeutic use. This study aims to assess the impact of overexpressing T7L variants on the metabolic profiles of E. coli. The two variants considered include T7L-H37A, which has enhanced lytic activity compared to its wild-type protein, and T7L-H48K, a dead mutant with no significant activity. 1H NMR-based metabolomics was employed to compare the metabolic profiles of E. coli cells overexpressing T7L wild-type protein and its variants. Overexpression of the T7L wild-type (T7L-WT) protein and its variants (T7L-H48K and T7L-H37A) was compared to RNAP overexpression in E. coli cells using 1H NMR-based metabolomics, analyzing a total of 75 annotated metabolites, including organic acids, amino acids, sugars, and nucleic acids. The results showed distinct clustering patterns for the two T7L variant groups compared with the WT, in which the dead mutant (H48K) group showed clustering close to that of RNAP. Pathway impact analysis revealed different effects of T7L variants on E. coli metabolic profiles, with T7L-H48K showing minimal alterations in energy and amino acid pathways linked to osmotic stress compared to noticeable alterations in these pathways for both T7L-H37A and T7L-WT. This study uncovered distinct metabolic fingerprints when comparing the overexpression of active and inactive mutants of T7L lytic enzymes in E. coli cells. These findings could contribute to the optimization and enhancement of suitable endolysins as potential alternatives to antibiotics.

Genomic Deletion of PFKFB3 Decreases In Vivo Tumorigenesis.

Rapidly proliferative processes in mammalian tissues including tumorigenesis and embryogenesis rely on the glycolytic pathway for energy and biosynthetic precursors. The enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 (PFKFB3) plays an important regulatory role in glycolysis by activating the key rate-limiting glycolytic enzyme, 6-phosphofructo-1-kinase (PFK-1). We have previously determined that decreased PFKFB3 expression reduced glycolysis and growth in transformed cells in vitro and suppressed xenograft growth in vivo. In earlier studies, we created a constitutive knockout mouse to interrogate the function of PFKFB3 in vivo but failed to generate homozygous offspring due to the requirement for PFKFB3 for embryogenesis. We have now developed a novel transgenic mouse model that exhibits inducible homozygous pan-tissue Pfkfb3 gene deletion (Pfkfb3fl/fl). We have induced Pfkfb3 genomic deletion in these mice and found that it effectively decreased PFKFB3 expression and activity. To evaluate the functional consequences of Pfkfb3 deletion in vivo, we crossed Cre-bearing Pfkfb3fl/fl mice with oncogene-driven tumor models and found that Pfkfb3 deletion markedly decreased their glucose uptake and growth. In summary, our studies reveal a critical regulatory function for PFKFB3 in glycolysis and tumorigenesis in vivo and characterize an effective and powerful model for further investigation of its role in multiple biological processes.

How much hydrogen could we need in New Zealand? Understanding the diverse hydrogen applications and their regional mapping

ABSTRACT Green hydrogen could become a key solution for the decarbonisation of diverse sectors in the energy transition. Beyond supplying the current demand for ammonia, methanol, and steel, new applications like aviation fuels, high-temperature heat and seasonal storage are promising. While initial efforts have been made to understand the future of hydrogen in New Zealand, there has been no comprehensive quantification of hydrogen demands. In this study, using systems analysis, we quantify the potential demand for 20 hydrogen applications in the country, including their spatial allocation to each of the 16 regions. We sort these applications using the so-called Clean Hydrogen Ladder concept. The associated database is open source. The results show that New Zealand's total demand for green hydrogen would be around 2.8 Mt if all technically feasible applications switched to hydrogen. Prioritising the demand for applications in rungs A and B of the Clean Hydrogen Ladder concept, we estimate approximately 0.24 and 0.77 metric tons, respectively. The findings of this research contribute to the development of a hydrogen strategy and serve as inputs for optimal planning of integrated energy pathways for New Zealand.

Tumor-targeted nano-assemblies for energy-blocking cocktail therapy in cancer

Starvation therapy aims to “starve” tumor cells by cutting off their nutritional supply. However, due to the complex and varied energy metabolism of tumors, targeting a single nutrient supply often fails to yield significant therapeutic benefits. This study proposes a tumor energy cocktail therapy that combines metformin, an oxidative phosphorylation inhibitor, with 2-deoxy-d-glucose (2-DG), a glycolysis inhibitor, to target tumor cells. To minimize the dosage of both drugs, we have developed a drug delivery strategy that prepared metformin as a nanoderivative, denoted as MA-dots. These MA-dots not only preserve the antitumor properties of metformin but also serve as a targeted delivery platform for 2-DG, ensuring its direct reach to the tumor site. Upon reaching the acidic tumor environment, the composite disintegrates, releasing 2-DG to inhibit glycolysis by targeting hexokinase 2 (HK2), the key enzyme in glycolysis, while MA-dots inhibit mitochondrial OXPHOS. This dual action significantly reduces ATP production in tumor cells, leading to apoptosis. In human lung tumor cells, the half-maximal inhibitory concentration (IC50) of 2-DG@MA-dots was significantly lower than that of either metformin or 2-DG alone, showing a nearly 100-fold and 30-fold reduction in IC50 values to 11.78 µg mL−1, from 1159 µg mL−1 and 351.20 µg mL−1, respectively. In studies with A549 tumor-bearing mice, the combination of low-dose 2-DG and metformin did not impede tumor growth, whereas 2-DG@MA-dots markedly decreased tumor volume, with the mean final tumor volume in the combination treatment group being approximately 89 times greater than that in the 2-DG@MA-dot group. Statement of significanceMetformin is a promising antitumor agent capable of modulating mitochondrial oxidative phosphorylation to inhibit cancer growth. However, its antitumor efficacy is limited when used alone due to compensatory energy mechanisms. Hence, we introduced glycolysis inhibitor 2-deoxy-d-glucose (2-DG) to inhibit an alternative tumor energy pathway. In our study, we developed a drug delivery strategy using metformin-derived nanomedicine (MA-dots) to load 2-DG. This approach enables the co-delivery of both drugs and their synergistic effect at the tumor site, disrupting both energy pathways and introducing an innovative “energy cocktail therapy”.

In vitro digestive and fermentation characterization of Polygonatum cyrtonema polysaccharide and its effects on human gut microbiota

Polygonatum cyrtonema polysaccharide (PCP) was subjected to simulated gastrointestinal digestion, followed by in vitro fermentation using human gut microbiota organisms. The results indicated that PCP did not degrade under simulated salivary conditions; however, a certain increase in reducing sugars and monosaccharides, and a slight reduction in the molecular weight of PCP in the gastrointestinal tract were observed, suggesting the partial degradation of PCP. During in vitro fermentation, a large proportion of PCP was degraded by the gut microbiota in fecal samples from both healthy and obese people. The utilization of PCP by the gut microbiota resulted in the generation of abundant short-chain fatty acids (SCFAs), leading to a reduction in environmental pH and stimulation of the proliferation of beneficial bacteria, such as Collinsella and Dialister, while impeding the growth of detrimental bacteria like Flavonifractor. The gut microbiota of healthy individuals exhibited greater efficiency in utilizing PCP compared to that of obese individuals. PICRUSt prediction analysis indicated that the regulation of the gut microbiota by PCP was mainly linked to carbohydrate, amino acid, energy, and lipid metabolic pathways. These results suggested that PCP may promote host health by modulating the gut microbiota and exhibiting potential prebiotic properties.

Serum metabolomics analysis of patients with chronic obstructive pulmonary disease and 'frequent exacerbator' phenotype.

Chronic obstructive pulmonary disease (COPD) exacerbations accelerate loss of lung function and increased mortality. The complex nature of COPD presents challenges in accurately predicting and understanding frequent exacerbations. The present study aimed to assess the metabolic characteristics of the frequent exacerbation of COPD (COPD‑FE) phenotype, identify potential metabolic biomarkers associated with COPD‑FE risk and evaluate the underlying pathogenic mechanisms. An internal cohort of 30 stable patients with COPD was recruited. A widely targeted metabolomics approach was used to detect and compare serum metabolite expression profiles between patients with COPD‑FE and patients with non‑frequent exacerbation of COPD (COPD‑NE). Bioinformatics analysis was used for pathway enrichment analysis of the identified metabolites. Spearman's correlation analysis assessed the associations between metabolites and clinical indicators, while receiver operating characteristic (ROC) analysis evaluated the ability of metabolites to distinguish between two groups. An external cohort of 20 patients with COPD validated findings from the internal cohort. Out of the 484 detected metabolites, 25 exhibited significant differences between COPD‑FE and COPD‑NE. Metabolomic analysis revealed differences in lipid, energy, amino acid and immunity pathways. Spearman's correlation analysis demonstrated associations between metabolites and clinical indicators of acute exacerbation risk. ROC analysis demonstrated that the area under the curve (AUC) values for D‑fructose 1,6‑bisphosphate (AUC=0.871), arginine (AUC=0.836), L‑2‑hydroxyglutarate (L‑2HG; AUC=0.849), diacylglycerol (DG) (16:0/20:5) (AUC=0.827), DG (16:0/20:4) (AUC=0.818) and carnitine‑C18:2 (AUC=0.804) were >0.8, highlighting their discriminative capacity between the two groups. External validation results demonstrated that DG (16:0/20:5), DG (16:0/20:4), carnitine‑C18:2 and L‑2HG were significantly different between patients with COPD‑FE and those with COPD‑NE. In conclusion, the present study offers insights into early identification, mechanistic understanding and personalized management of the COPD‑FE phenotype.

Comparison of floating and traditional artificial reef areas using an ecosystem-based approach in the Dashentang area of Bohai Bay, China

Instead of the conventional fishery survey-based approach, this study used an ecosystem-based approach to evaluate the ecological impacts of artificial reefs (ARs). Trophic models were initially employed for floating artificial reef area (FARA), traditional artificial reef area (TARA), and reef-free control area (CONA) in the Dashentang area of Bohai Bay, China. Ecosystem-based analyses of FARA and TARA highlighted similar trophic functioning characteristics. A substantial proportion of energy occurred at trophic levels I and II, and most of the primary production was utilized through grazing pathways. As a structuring group, zoobenthos played a pivotal role in enabling pelagic-benthic coupling in both ecosystems. Additionally, the top-down control in the FARA and TARA ecosystems was enhanced. Conventional surveys and comparative ecosystem-based analyses revealed distinct differences between the two ecosystems. In FARA, a significant increase was observed in pelagic fish and zoobenthos, with increases of 3.60- and 4.44-fold, respectively, compared with CONA. Conversely, TARA showed a considerable increase in demersal fish, approximately 2.6 times greater than that of CONA. Based on the biomass disparity between the two ARs, the ecosystem-based approach revealed that the FARA ecosystem led to enhanced energy pathways from detritus, greater total system throughput, higher energy cycle proportion, and more efficient nutrient transfer. Furthermore, the FARA ecosystem showed relatively high stability and maturity (total primary production/total respiration, 1.616<1.946) compared to the TARA ecosystem, suggesting a greater potential to withstand disturbances. Consequently, marine ecosystems respond differently to AR management initiatives. This study emphasizes the reliability of ecosystem-based evaluations during the initial phases of AR construction. Despite being a preliminary pilot study, this study offers insights into the impact on AR ecosystems, especially the role of floating ARs in coastal management.

Amber free energy tools: Interoperable software for free energy simulations using generalized quantum mechanical/molecular mechanical and machine learning potentials

We report the development and testing of new integrated cyberinfrastructure for performing free energy simulations with generalized hybrid quantum mechanical/molecular mechanical (QM/MM) and machine learning potentials (MLPs) in Amber. The Sander molecular dynamics program has been extended to leverage fast, density-functional tight-binding models implemented in the DFTB+ and xTB packages, and an interface to the DeePMD-kit software enables the use of MLPs. The software is integrated through application program interfaces that circumvent the need to perform “system calls” and enable the incorporation of long-range Ewald electrostatics into the external software’s self-consistent field procedure. The infrastructure provides access to QM/MM models that may serve as the foundation for QM/MM–ΔMLP potentials, which supplement the semiempirical QM/MM model with a MLP correction trained to reproduce ab initio QM/MM energies and forces. Efficient optimization of minimum free energy pathways is enabled through a new surface-accelerated finite-temperature string method implemented in the FE-ToolKit package. Furthermore, we interfaced Sander with the i-PI software by implementing the socket communication protocol used in the i-PI client–server model. The new interface with i-PI allows for the treatment of nuclear quantum effects with semiempirical QM/MM–ΔMLP models. The modular interoperable software is demonstrated on proton transfer reactions in guanine-thymine mispairs in a B-form deoxyribonucleic acid helix. The current work represents a considerable advance in the development of modular software for performing free energy simulations of chemical reactions that are important in a wide range of applications.

A comparative well-to-wheel analysis of renewable energy pathways for hydrogen and battery electric vehicles

Renewable hydrogen and batteries are pivotal not only for promoting renewable energy adoption but also for serving as key components in electric vehicles. While multiple hydrogen-based and battery-based pathways exist for linking renewable energy to automotive powertrains, comprehensive evaluations of them are lacking, especially in the context of long-distance energy transmission in China. This study aims to fill this gap by offering an in-depth well-to-wheel (WTW) analysis of costs and CO2 emissions across various pathways. The pathways involve two energy storage mediums - hydrogen and battery, five transport options, and three automotive powertrains - Internal Combustion Engine Vehicle (ICEV), Fuel Cell Electric Vehicle (FCEV), and Battery Electric Vehicle (BEV). How the electricity price, storage duration, and transport distance influence these pathways is also examined. The results show that the battery-based pathway offers the lowest WTW cost and CO2 emissions in BEV applications. Hydrogen-based pathways are not economically feasible for ICEVs. Importantly, the indirect use of hydrogen in BEVs - H2 for power generation - outperforms its direct use in FCEVs and ICEVs in both cost and emissions. The battery-based pathway is significantly affected by storage duration and becomes less feasible for durations exceeding one day. The most cost-efficient hydrogen transport methods are identified for different transport distances and electricity prices. This research may provide valuable insights for the planning of the hydrogen industry, automotive decarbonization and renewable energy development in China.

Metabolomics Reveals Tyrosine Kinase Inhibitor Resistance-Associated Metabolic Events in Human Metastatic Renal Cancer Cells.

The development of resistance to tyrosine kinase inhibitors (TKIs) is a major cause of treatment failure in metastatic renal cell carcinoma (mRCC). A deeper understanding of the metabolic mechanisms associated with TKI resistance is critical for refining therapeutic strategies. In this study, we established resistance to sunitinib and pazopanib by exposing a parental Caki-1 cell line to increasing concentrations of sunitinib and pazopanib. The intracellular and extracellular metabolome of sunitinib- and pazopanib-resistant mRCC cells were investigated using a nuclear magnetic resonance (NMR)-based metabolomics approach. Data analysis included multivariate and univariate methods, as well as pathway and network analyses. Distinct metabolic signatures in sunitinib- and pazopanib-resistant RCC cells were found for the first time in this study. A common metabolic reprogramming pattern was observed in amino acid, glycerophospholipid, and nicotinate and nicotinamide metabolism. Sunitinib-resistant cells exhibited marked alterations in metabolites involved in antioxidant defence mechanisms, while pazopanib-resistant cells showed alterations in metabolites associated with energy pathways. Sunitinib-resistant RCC cells demonstrated an increased ability to proliferate, whereas pazopanib-resistant cells appeared to restructure their energy metabolism and undergo alterations in pathways associated with cell death. These findings provide potential targets for novel therapeutic strategies to overcome TKI resistance in mRCC through metabolic regulation.

Life cycle cost assessment of geothermal energy assisted hydrogen liquefaction for sustainable and renewable energy applications: Case study and adaptation for Afyon geothermal power plant

This study presents a comprehensive Life Cycle Cost Assessment (LCCA) of geothermal-assisted hydrogen liquefaction, explicitly focusing on the Afyon Geothermal Power Plant (AGPP) as a case study. The study evaluates the economic viability and sustainability of integrating geothermal energy into hydrogen liquefaction. The results of the LCCA contribute to the ongoing discourse on sustainable energy solutions, offering a nuanced understanding of the economic considerations associated with geothermal-assisted hydrogen liquefaction. The study serves as a model for assessing the economic feasibility of similar systems, fostering informed decision-making in the pursuit of cleaner and more economically sustainable energy pathways. This study has conducted a technical and economic investigation of liquid hydrogen production using geothermal heat and electricity effects. Geothermal water pre-cools the hydrogen by providing heat to the absorption system. Then, the electricity generated in the geothermal plant is used to work in the liquefaction cycle. The generated electricity is used to liquefy hydrogen in the liquefaction cycle. The capacity of the electricity generated from the AGPP produced here is 2621 kW. The proposed system can be achieved by pre-cooling unit H2 up to −30 °C at 120 °C and 150 kg/s geothermal source. In the liquefaction cycle, 0.84 kg/s H2 can be liquefied. As a result, the total energy efficiency of the proposed system can be calculated as 32.4% and exergy efficiency as 15.4%. The system's net present value (NPV) was calculated as 65,320,000 $. When life cycle cost analysis was performed using the levelized annual cost (LAC) method, the project's levelized cost was calculated as 7,673,000 $/yr. The unit cost of the liquid hydrogen produced is 1.252 $/kg. This system's discounted payback period (Ndpp) is calculated as 3.48.

Optimized system for combined production of electricity/green hydrogen for multiple energy pathways: a case study of Egypt

Abstract By optimal sizing of a wind/photovoltaic hybrid renewable-energy (RE) system, trimming the surplus capacity to reduce the fluctuations in the electricity supplied to the grid, and using it to produce green hydrogen through electrolysis, a stable output with maximum possible capacity factor (CF) is generated to maintain the electricity grid stability. Simultaneously, the trimmed energy is used in a secondary conversion path that minimizes the weighted average cost of the energy generated from the entire plant. This surplus power-to-gas conversion allows the use of green hydrogen to produce electricity, methanol, or ammonia subject to the resource availability, site characteristics, and financial feasibility. Based on robust site selection criteria, the best performance is obtained at two sites: Ras Ghareb and Minya, achieving the lowest energy cost with some variance in their performance. For the Ras Ghareb site, the optimally sized RE plant provided the grid with a quasi-steady capacity of 423 MW with a CF of 80.04% and was capable of injecting 2965.8648 GWh throughout the year with the lowest cost of 2.4355 ¢/kWh. A surplus of 3.9% of the total energy produced from the plant was directed to produce 1922-ton H2/year, achieving the lowest cost of hydrogen production of $1.9745/kg H2. For the other selected site, Minya, the clipped energy is used to produce 3330.47-ton H2/year with an optimized lowest cost of $3.5268/kg H2. The difference in hydrogen costs was attributed to the number of full operating hours of the electrolyser in both sites. The cost is mainly affected by the electricity price and the electrolyser cost. With both tending to decrease, future forecasts show hydrogen cost reductions.

Apoptosis, a Metabolic "Head-to-Head" between Tumor and T Cells: Implications for Immunotherapy.

Induction of apoptosis represents a promising therapeutic approach to drive tumor cells to death. However, this poses challenges due to the intricate nature of cancer biology and the mechanisms employed by cancer cells to survive and escape immune surveillance. Furthermore, molecules released from apoptotic cells and phagocytes in the tumor microenvironment (TME) can facilitate cancer progression and immune evasion. Apoptosis is also a pivotal mechanism in modulating the strength and duration of anti-tumor T-cell responses. Combined strategies including molecular targeting of apoptosis, promoting immunogenic cell death, modulating immunosuppressive cells, and affecting energy pathways can potentially overcome resistance and enhance therapeutic outcomes. Thus, an effective approach for targeting apoptosis within the TME should delicately balance the selective induction of apoptosis in tumor cells, while safeguarding survival, metabolic changes, and functionality of T cells targeting crucial molecular pathways involved in T-cell apoptosis regulation. Enhancing the persistence and effectiveness of T cells may bolster a more resilient and enduring anti-tumor immune response, ultimately advancing therapeutic outcomes in cancer treatment. This review delves into the pivotal topics of this multifaceted issue and suggests drugs and druggable targets for possible combined therapies.

Global proteomic analyses of lysine acetylation, malonylation, succinylation, and crotonylation in human sperm reveal their involvement in male fertility

Protein lysine modifications (PLMs) are hotspots of post-translational modifications and are involved in many diseases; however, their role in human sperm remains obscure. This study examined the presence and functional roles of a classical PLM (lysine acetylation, Kac) and three novel PLMs (lysine malonylation, Kmal; lysine succinylation, Ksucc; lysine crotonylation, Kcr) in human sperm. Immunoblotting and immunofluorescence assays revealed modified proteins (15–150 kDa) in the tails of human sperm. An immunoaffinity approach coupled with liquid chromatography/tandem mass spectrometry revealed 1423 Kac sites in 680 proteins, 196 Kmal sites in 118 proteins, 788 Ksucc sites in 251 proteins, and 1836 Kcr sites in 645 proteins. These modified proteins participate in a variety of biological processes and metabolic pathways. Crosstalk analysis demonstrated that proteins involved in the sperm energy pathways of glycolysis, oxidative phosphorylation, the citrate cycle, fatty acid oxidation, and ketone body metabolism were modified by at least one of these modifications. In addition, these modifications were found in 62 male fertility-related proteins that weave a protein-protein interaction network associated with asthenoteratozoospermia, asthenozoospermia, globozoospermia, spermatogenic failure, hypogonadotropic hypogonadism, and polycystic kidney disease. Our findings shed light on the functional role of PLMs in male reproduction. SignificanceProtein lysine modifications (PLMs) are hotspots of posttranslational modifications and are involved in many diseases. This study revealed the presence of a classical PLM (lysine acetylation) and three novel PLMs (lysine malonylation, lysine succinylation, and lysine crotonylation) in human sperm tails. The modified proteins participate in a variety of biological processes and metabolic pathways. In addition, these modifications were found in 62 male infertility-associated proteins and could serve as potential diagnostic markers and therapeutic targets for male infertility.

Significance of extracellular vesicles in orchestration of immune responses in Mycobacterium tuberculosis infection.

Mycobacterium tuberculosis (M.tb), the causative agent of Tuberculosis, is an intracellular bacterium well known for its ability to subvert host energy and metabolic pathways to maintain its intracellular survival. For this purpose, the bacteria utilize various mechanisms of which extracellular vehicles (EVs) related mechanisms attracted more attention. EVs are nanosized particles that are released by almost all cell types containing active biomolecules from the cell of origin and can target bioactive pathways in the recipient cells upon uptake. It is hypothesized that M.tb dictates the processes of host EV biogenesis pathways, selectively incorporating its molecules into the host EV to direct immune responses in its favor. During infection with Mtb, both mycobacteria and host cells release EVs. The composition of these EVs varies over time, influenced by the physiological and nutritional state of the host environment. Additionally, different EV populations contribute differently to the pathogenesis of disease at various stages of illness participating in a complex interplay between host cells and pathogens. These interactions ultimately influence immune responses and disease outcomes. However, the precise mechanisms and roles of EVs in pathogenicity and disease outcomes remain to be fully elucidated. In this review, we explored the properties and function of EVs in the context of M.tb infection within the host microenvironment and discussed their capacity as a novel therapeutic strategy to combat tuberculosis.

Replacing a Cysteine Ligand by Selenocysteine in a [NiFe]-Hydrogenase Unlocks Hydrogen Production Activity and Addresses the Role of Concerted Proton-Coupled Electron Transfer in Electrocatalytic Reversibility.

Hydrogenases catalyze hydrogen/proton interconversion that is normally electrochemically reversible (having minimal overpotential requirement), a special property otherwise almost exclusive to platinum metals. The mechanism of [NiFe]-hydrogenases includes a long-range proton-coupled electron-transfer process involving a specific Ni-coordinated cysteine and the carboxylate of a nearby glutamate. A variant in which this cysteine has been exchanged for selenocysteine displays two distinct changes in electrocatalytic properties, as determined by protein film voltammetry. First, proton reduction, even in the presence of H2 (a strong product inhibitor), is greatly enhanced relative to H2 oxidation: this result parallels a characteristic of natural [NiFeSe]-hydrogenases which are superior H2 production catalysts. Second, an inflection (an S-shaped "twist" in the trace) appears around the formal potential, the small overpotentials introduced in each direction (oxidation and reduction) signaling a departure from electrocatalytic reversibility. Concerted proton-electron transfer offers a lower energy pathway compared to stepwise transfers. Given the much lower proton affinity of Se compared to that of S, the inflection provides compelling evidence that concerted proton-electron transfer is important in determining why [NiFe]-hydrogenases are reversible electrocatalysts.

Inferring the Molecular Basis for Dissolved Organic Matter Photochemical and Optical Properties.

Despite the widespread use of photochemical and optical properties to characterize dissolved organic matter (DOM), a significant gap persists in our understanding of the relationship among these properties. This study infers the molecular basis for the optical and photochemical properties of DOM using a comprehensive framework and known structural moieties within DOM. Utilizing Suwannee River Fulvic Acid (SRFA) as a model DOM, carboxylated aromatics, phenols, and quinones were identified as dominant contributors to the absorbance spectra, and phenols, quinones, aldehydes, and ketones were identified as major contributors to radiative energy pathways. It was estimated that chromophores constitute ∼63% w/w of dissolved organic carbon in SRFA and ∼47% w/w of overall SRFA. Notably, estimations indicate the pool of fluorescent compounds and photosensitizing compounds in SRFA are likely distinct from each other at wavelengths below 400 nm. This perspective offers a practical tool to aid in the identification of probable chemical groups when interpreting optical and photochemical data and challenges the current "black box" thinking. Instead, DOM photochemical and optical properties can be closely estimated by assuming the DOM is composed of a mixture of individual compounds.