Mechanistic Perspective Research Articles

Integration and Analysis of Omics Data Using Genome-Scale Metabolic Models

Constraint-based modelling and genome-scale metabolic models (GEMs) have been used extensively to analyze omics data, providing a mechanistic perspective on complex metabolic systems and networks [...]

Antimicrobial and antibiofilm potential of α-MSH derived cationic and hydrophobic peptides against Escherichia coli: Mechanistic insight through peptide-lipopolysaccharide interactions

The prevalence of infections caused by various Gram-negative pathogens specifically Escherichia coli continuously poses a significant challenge in health care as well as community settings owing to their ability to form biofilm and escalating tolerance towards available antibiotics. While most treatment regimes are targeted at eliminating the E. coli cells, the pathogenicity factors called endotoxin (lipopolysaccharides), associated with the sepsis initiation and the leading cause of death in intensive care units globally, are often ignored. In this study, the potency of alpha-Melanocyte Stimulating Hormone based-peptides, particularly Ana-9 and Ana-10 against E. coli was investigated through microbiological, biophysical, and microscopic assays. Both Ana-9 and Ana-10 demonstrated enhanced activity against planktonic E. coli cells, and retained their activity against biofilm, which was supported by confocal microscopy. From the mechanistic perspective, spectroscopic studies indicated that the binding of peptides with LPS led to structural alteration of peptides due to their insertion into the hydrophobic environment of LPS. The electrostatic interaction of the peptide with LPS leads to outer membrane disorganization, allowing the peptide to access the inner membrane, depolarize it and ultimately inhibit the bacterial cells within the biofilm. These observations were further confirmed by atomic force and scanning electron microscopy. Thus, this study deepens our understanding of the structural characteristics of peptides attached to LPS, which could lead to the gradual improvement in developing more potent, broad-spectrum endotoxin neutralizers.

The Chemistry of Levulinic Acid: Its Potential in the Production of Biomass‐based Chemicals

Biomass has been identified as the ultimate sustainable resource for all carbon‐based consumer products of the chemical industries in the future. Its catalytic conversion leads to the formation of various platform chemicals that could partially or even fully replace the fossil‐based building blocks that have been currently used in synthetic chemical processes. Among these compounds, levulinic acid (LA) has been recognized as a member of the "Top Value Added Chemicals from Biomass" and has attracted significant attention since the seminal paper reported by Werpy and Petersen in 2004. This review summarizes the properties, recent advances, and developments in the chemistry of levulinic acid. The production of LA from both plant and animal‐based carbohydrate feedstocks via 5‐hydroxymethylfurfural or furfuryl alcohol is discussed from a mechanistic perspective, highlighting intrinsic molecular‐level limitations to LA formation. The efficiencies of recently developed catalytic systems are also summarized and compared. Furthermore, the conversion of LA into high‐value‐added downstream chemicals, including its role in the synthesis of complex molecular structures, is overviewed. This section discussed the reactions of LA in the points of view of its various transformations on carbonyl‐, carboxy‐, methyl‐, and methylene functional groups. The reactions of these functionalities with C‐ ,N‐, O‐, and S‐nucleophiles, alcohols, amines, organometallic reagents, oxygen etc. were thematically summarized. Our review also outlooks to highlight the challenges and opportunities associated with the extensive research area of organic chemistry of levulinic acid.

Mechanistic Perspectives: Integration and Repairing Adaptation of Self‐Healing Electrolytes for Zinc Ion Batteries

AbstractSelf‐healing is a magical function that endows energy storage devices with extraordinary resilience and has become a promising strategy for advancing battery technology. This short review focus on the recent developments made in self‐healing chemistry for electrolytes in term of extrinsic and intrinsic dynamical concepts. Firstly, the fundamental mechanism of electrolyte self‐healing and repairing adaptation is introduced. The extrinsic self‐healing mechanism adopts capsule‐vascular networking while intrinsic self‐healing lean physical and chemical routes. The Former healing adaptation, generally follows strong physical networking and covalent linkages, which are more prevalent and practical, compared to the latter case of self‐healing. In addition to that, this review also evaluates the estimated healing capabilities and statistics using thermodynamic protocols. Finally, we propose some possible future research directions and development strategies to further apply the self‐healing phenomenon for zinc ion batteries.

Mechanistic Perspective on Oxygen Activation Chemistry by Flavoenzymes.

Flavin-dependent enzymes catalyze a panoply of chemical transformations essential for living organisms. Through oxygen activation, flavoenzymes could generate diverse flavin-oxygen species that mediate numerous redox and non-redox transformations. In this review, we highlight the extensive oxygen activation chemistry at two sites of the flavin cofactor: C4a and N5 sites. Oxygen activation at the C4a site generates flavin-C4aOO(H) species for various monooxygenation reactions, while activation at the N5 site produces negatively charged flavin-N5OOH species, which act as highly reactive nucleophiles or bases. The selective oxygen activation at either the C4a or N5 site depends on the nature of substrates and is controlled by the active site architecture. These insights have expanded our understanding of oxygen activation chemistry in flavoenzymes and will serve as a foundation for future efforts in enzyme engineering and redesign.

Harnessing luciferase chemistry in regulated cell death modalities and autophagy: overview and perspectives.

Regulated cell death is a fate of cells in (patho)physiological conditions during which extrinsic or intrinsic signals or redox equilibrium pathways following infection, cellular stress or injury are coupled to cell death modalities like apoptosis, necroptosis, pyroptosis or ferroptosis. An immediate survival response to cellular stress is often induction of autophagy, a process that deals with removal of aggregated proteins and damaged organelles by a lysosomal recycling process. These cellular processes and their regulation are crucial in several human diseases. Exploiting high-throughput assays which discriminate distinct cell death modalities and autophagy are critical to identify potential therapeutic agents that modulate these cellular responses. In the past few years, luciferase-based assays have been widely developed for assessing regulated cell death and autophagy pathways due to their simplicity, sensitivity, known chemistry, different spectral properties and high-throughput potential. Here, we review basic principles of bioluminescent reactions from a mechanistic perspective, along with their implication in vitro and in vivo for probing cell death and autophagy pathways. These include applying luciferase-, luciferin-, and ATP-based biosensors for investigating regulated cell death modalities. We discuss multiplex bioluminescence platforms which simultaneously distinguish between the various cell death phenomena and cellular stress recovery processes such as autophagy. We also highlight the recent technological achievements of bioluminescent tools for the prediction of drug effectiveness in pathways associated with regulated cell death.

Atypical Metastatic Patterns In Squamous Cell Carcinoma: Clinical Insights And Mechanistic Perspectives

Atypical Metastatic Patterns In Squamous Cell Carcinoma: Clinical Insights And Mechanistic Perspectives

Assessing the impact of artificial geotextile covers on glacier mass balance and energy fluxes

As global warming accelerates, leading to the retreat of glaciers, the effectiveness of artificial coverings, in particular geotextiles, in reducing glacier ablation has emerged as a topic of increasing concern. Nevertheless, a critical gap in knowledge persists regarding the specific physical processes involved in the mitigation provided by these coverings. This study explores the underlying mechanisms that govern the interaction through field observations and COSIPY model simulations at Bailanghe Glacier No. 21 in the Qilian Mountains from 26 June to 17 September 2023. It compares covered and uncovered areas to evaluate differences in mass and energy balance fluxes. It was discovered that geotextiles could decrease ice melt by up to 1000 mm w.e. in comparison to the surface of glaciers without cover, primarily because of a 23% increase in albedo compared to ice, leading to a decrease in net short-wave radiation and available melt energy. The effect of covering the entire glacier with a geotextile, which has varying albedo properties, was also simulated. It was found that, with every 5% increase in the albedo of the geotextile, ablation was reduced by 10%‒25%, resulting in a decrease in ice volume loss of approximately 2.5 × 105 m3. While artificially covering glaciers can reduce ablation rates, it faces challenges such as high costs, environmental risks, and issues with replicability. Ultimately, this study aims to analyze the feasibility of glacier coverage from a mechanistic perspective for glacier management amidst ongoing climate change.

Transition metal pincer catalysts for formic acid dehydrogenation: a mechanistic perspective.

The storage and transportation of hydrogen gas, a non-polluting alternative to carbon-based fuels, have always been challenging due to its extreme flammability. In this regard, formic acid (FA) is a promising liquid organic hydrogen carrier (LOHC), and over the past decades, significant progress has been made in dehydrogenating FA through transition metal catalysis. In this review, our goal is to provide a detailed insight into the existing processes to expose various mechanistic challenges associated with FA dehydrogenation (FAD). Specifically, methodologies catalyzed by pincer-ligated metal complexes were chosen. Pincer ligands are preferred as they provide structural rigidity to the complexes, making the isolation and analysis of reaction intermediates less challenging and consequently providing a better mechanistic understanding. In this perspective, the catalytic activity of the reported pincer complexes in FAD was overviewed, and more importantly, the catalytic cycles were examined in detail. Further attention was given to the structural modifications, role of additives, reaction medium, and their crucial effects on the outcome.

TMEM17 Promotes Tumor Progression in Glioblastoma by Activating the PI3K/AKT Pathway.

Glioblastoma (GBM) is a highly aggressive and fast-growing brain tumor, characterized by rapid progression, a very poor prognosis, and a high likelihood of recurrence. Thus, effective new therapeutic targets are urgently needed. Transmembrane proteins (TMEMs) have pro-cancer effects on multiple cancer types, but the mechanisms underlying the effects of TMEM17, particularly its role in GBM, remain unclear. We conducted bioinformatics analyses and immunohistochemistry to evaluate the role of TMEM17 in a variety of cancer types. Functional assays were conducted included the Cell Counting Kit-8 assay, annexin V-FITC/PI double staining, 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay, wound healing assay, transwell invasion assay, and dual luciferase assay. We found that TMEM17 is associated with a poor prognosis in GBM. Prognostic analyses confirmed that high TMEM17 expression predicted poorer survival, establishing its significance as an independent prognostic factor. Functional assays demonstrated that silencing TMEM17 in GBM cell lines inhibited proliferation and invasion, and induced apoptosis, underscoring its role in tumor aggressiveness. From a mechanistic perspective, we discovered that the Ying Yang 1 (YY1) transcription factor can bind to the promoter of TMEM17, regulating its upregulation. Regarding downstream mechanisms, knocking down TMEM17 inhibited the phosphoinositide 3-kinase/AKT pathway. These findings suggest that TMEM17 plays a significant role in GBM and may be a potential therapeutic target for this cancer. These data prove that TMEM17 plays a key role in the regulation of GBM and has great potential as a clinical therapeutic target for GBM.

Anti-inflammatory Principles of the Plant Family Amaryllidaceae.

There is considerable interest in the utilisation of plants against inflammation. Over 50 species of the plant family Amaryllidaceae are known for such usage in traditional medicine. This review was undertaken to identify the chemical principles responsible for these anti-inflammatory effects. It describes the findings from in vitro, in vivo and in silico studies, as well as the probes made on the mechanisms of action. The literature search returned over 600 hits, of which around 130 were chosen for their relevance to the text. Over 140 compounds have thus far been screened for anti-inflammatory effects. These were mostly isoquinoline alkaloids but also included other classes of secondary metabolites such as chromones, flavonoids and triterpenoids. In vitro studies were carried out in mononuclear cells such as lymphocytes, monocytes, neutrophils and macrophages, against which no serious side effects were observed. The constituents were also effective against inflammation induced by physical and chemical stimuli in a variety of murine test subjects. Chief among the compounds were the isoquinoline alkaloids lycorine and narciclasine, which displayed potent effects against pain, swelling, asthma and arthritis, amongst others. From a mechanistic perspective, several of the compounds were shown to mediate in inflammatory pathways, notably via the modulation of both pro-inflammatory (such as NF-κB, TNF-α and IL-1) and anti-inflammatory (such as IL-10 and TGF-β) factors. Useful insights also emerged from active-site docking studies of some of the compounds. The Amaryllidaceae affords a rich and diverse platform for the discovery of potential anti-inflammatory drugs.

How Natural Enzymes and Synthetic Ribozymes Generate Methylated Nucleotides in RNA.

Methylation of RNA nucleotides represents an important layer of gene expression regulation, and perturbation of the RNA methylome is associated with pathophysiology. In cells, RNA methylations are installed by RNA methyltransferases (RNMTs) that are specialized to catalyze particular types of methylation (ribose or different base positions). Furthermore, RNMTs must specifically recognize their appropriate target RNAs within the RNA-dense cellular environment. Some RNMTs are catalytically active alone and achieve target specificity via recognition of sequence motifs and/or RNA structures. Others function together with protein cofactors that can influence stability, S-adenosyl-L-methionine binding, and RNA affinity as well as aiding specific recruitment and catalytic activity. Association of RNMTs with guide RNAs represents an alternative mechanism to direct site-specific methylation by an RNMT that lacks intrinsic specificity. Recently, ribozyme-catalyzed methylation of RNA has been achieved in vitro, and here, we compare these different strategies for RNA methylation from structural and mechanistic perspectives.

Rhizosphere effects and microbial N limitations drive the root N limitations in the rhizosphere during secondary succession in a Pinus tabuliformis forest in North China.

Rhizosphere effects (REs) have recently been identified as important regulators of root and microbial nutrient acquisition and are positively involved in nutrient cycling of belowground carbon (C), nitrogen (N), and phosphorus (P). Nutrient conditions of the fine roots and soil N are likely to influence REs. Still, it is unclear how REs of soil nutrients themselves variably impact the supply of nutrients to plants in terms of the responses to soil N due to succession. In this study, we applied both fine roots and extracellular enzymes for vector analysis and stoichiometry of N:P to explore the metabolic limitations of roots and rhizospheric soil microbes and their relationships with REs across five levels of soil N (0, 5, 10, 15, and 20kg N m-2 year-1) along successional age classes of 42, 55, and 65 years in a Pinus tabuliformis forest. Overall, the metabolism of root and rhizospheric soil microbes was mediated by soil N. N limitation of roots initially decreased before increasing, whereas that of microbes demonstrated opposite trends to the N levels owing to competition for inorganic N between them by REs of NO3 --N. However, N limitations of both roots and microbes were alleviated in young stands and increased with succession after the application of N. In addition, root N limitations were manipulated by REs of three different soil N-related indicators, i.e., total N, NH4 +-N, and NO3 --N. Rhizospheric soil microbial N limitation was almost unaffected by REs due to their strong homeostasis but was an important driver in the regulation of root N limitation. Our results indicated that successional age was the most critical driver that directly and indirectly affected root N metabolism. However, the level of N application had a slight effect on root N limitation. Microbial N limitation and variations in the REs of N indicators regulated root N limitation in the rhizosphere. As a result, roots utilized REs to sequester N to alleviate N limitations. Thesefindings contribute to novel mechanistic perspectives on the sustainability of N nutrition by regulating N cycling in a system of plant-soil-microbes in the rhizosphere to adapt to global N deposition or the heterogeneous distribution of bioavailable soil N with succession.

SOH estimation of lithium-ion batteries based on multi-feature deep fusion and XGBoost

State of Health (SOH) is a crucial metric for battery management systems, and accurate estimation of battery SOH is essential for the underlying management and maintenance of batteries. Traditional data-driven approaches lack in-depth analysis of health features and fail to exploit the deep-level health information among these features. Therefore, this paper extracts six health features from both measurement and calculation perspectives based on actual measurable charging curve data, and conducts aging analysis of health features from a mechanistic perspective and Spearman correlation analysis from a quantitative perspective. Additionally, a strategy combining deep learning with ensemble learning is proposed. This strategy utilizes one-dimensional convolutional neural networks to deeply integrate multiple original features, extracting fusion features with deep-level health information. Subsequently, XGBoost is employed to learn the fusion features for estimating battery SOH. Finally, the effectiveness and superiority of the proposed method are verified on battery aging datasets from the University of Maryland and our laboratory. Experimental results demonstrate that the RMSE and MAE of the proposed method are both below 1 % and outperform other methods.

Characterization of antimalarial activity of artemisinin-based hybrid drugs.

In response to the spread of artemisinin (ART) resistance, ART-based hybrid drugs were developed, and their activity profile was characterized against drug-sensitive and drug-resistant Plasmodium falciparum parasites. Two hybrids were found to display parasite growth reduction, stage-specificity, speed of activity, additivity of activity in drug combinations, and stability in hepatic microsomes of similar levels to those displayed by dihydroartemisinin (DHA). Conversely, the rate of chemical homolysis of the peroxide bonds is slower in hybrids than in DHA. From a mechanistic perspective, heme plays a central role in the chemical homolysis of peroxide, inhibiting heme detoxification and disrupting parasite heme redox homeostasis. The hybrid exhibiting slow homolysis of peroxide bonds was more potent in reducing the viability of ART-resistant parasites in a ring-stage survival assay than the hybrid exhibiting fast homolysis. However, both hybrids showed limited activity against ART-induced quiescent parasites in the quiescent-stage survival assay. Our findings are consistent with previous results showing that slow homolysis of peroxide-containing drugs may retain activity against proliferating ART-resistant parasites. However, our data suggest that this property does not overcome the limited activity of peroxides in killing non-proliferating parasites in a quiescent state.

Immune-checkpoint inhibitor-mediated myocarditis: CTLA4, PD1 and LAG3 in the heart.

Immune-checkpoint inhibitors (ICIs) have revolutionized oncology, with nearly 50% of all patients with cancer eligible for treatment with ICIs. However, patients on ICI therapy are at risk for immune-related toxicities that can affect any organ. Inflammation of the heart muscle, known as myocarditis, resulting from ICI targeting cytotoxic Tlymphocyte-associated antigen 4 (CTLA4), programmed cell death protein 1 (PD1) and PD1 ligand 1 (PDL1) is an infrequent but potentially fatal complication. ICI-mediated myocarditis (ICI-myocarditis) is a growing clinical entity given the widespread use of ICIs, its increased clinical recognition and growing use of combination ICI treatment, a well-documented risk factor for ICI-myocarditis. In this Review, we approach ICI-myocarditis from a basic and mechanistic perspective, synthesizing the recent data from both preclinical models and patient samples. We posit that mechanistic understanding of the fundamental biology of immune-checkpoint molecules may yield new insights into disease processes, which will enable improvement in diagnostic and therapeutic approaches. The syndrome of ICI-myocarditis is novel, and our understanding of immune checkpoints in the heart is in its nascency. Yet, investigations into the pathophysiology will inform better patient risk stratification, improved diagnostics and precision-based therapies for patients.

Chemical Memory in Primitive Organisms: Evolutionary Insights and Mechanistic Perspectives

Memory, the cornerstone of adaptive behavior, has been extensively studied within the confines of neural systems. A comprehensive literature review was conducted using key academic databases such as PubMed, Web of Science, and Google Scholar. The methodology prioritized peer-reviewed papers, reviews, and primary research, with a particular emphasis on articles relevant to chemical memory in primitive organisms. This review sheds light on the less-explored territory of chemical memory in primitive organisms. From the complex neural pathways in humans to the basic chemical interactions in bacteria and protozoa, this study underscores the evolutionary significance and ubiquity of information storage in biology. A notable highlight is the exploration of the ability of plants to adaptively respond to their environment despite lacking a central nervous system, emphasizing the role of epigenetic markers in stress memory. In organisms devoid of advanced neural systems, chemical reactions, and interactions pave the way for memory mechanisms, offering insight into the foundational building blocks of memory. The findings presented challenges in traditional neuro-centric views, broadening our understanding of memory and highlighting its pivotal role in the evolutionary tapestry of life.

Effects of Metabolic Dysfunction-Associated Steatotic Liver Disease on Bone Density and Fragility Fractures: Associations and Mechanisms.

Metabolic dysfunction-associated steatotic liver disease (MASLD) has profound adverse effects on bone health and homeostasis. MASLD appears to be associated with changes in bone mineral density (BMD) and fracture rate. However, the data are ambiguous and conflicting. Although several studies have shown that children and adolescents with MASLD have decreased BMD, the data on the prevalence of fragility fractures among children are scarce. In adults, increasing evidence suggests that MASLD decreases BMD and increases the risk of fragility fractures, which appears to be due to deterioration of bone architecture in addition to a decrease in BMD. Effects of MASLD on bone health may also be age- and race-specific. MASLD does not seem to increase fracture risk in children and adolescents but increases the risk of fractures in elderly men, especially those of Asian origin. From a mechanistic perspective, bone remodeling is a continuous process between osteoblasts (bone-forming) and osteoclasts (bone-resorbing), with any imbalance resulting in metabolic bone disease. In individuals with MASLD, loss of anabolic insulin receptor signaling (insulin resistance) in osteoblasts and increased receptor activator of nuclear factor κB (RANK)/RANK ligand signaling in osteoclasts (proinflammatory cytokines) swings the pendulum toward accelerated bone loss. These processes are further complicated by the concomitant presence of obesity, type 2 diabetes mellitus, or sarcopenia in individuals with MASLD. This study reviews the current literature associated with the effects of MASLD on BMD and fragility fractures in children/adolescents and adults. This review also discusses the pathomechanisms that link MASLD with changes in BMD and fragility fractures.

A specific super-enhancer actuated by berberine regulates EGFR-mediated RAS–RAF1–MEK1/2–ERK1/2 pathway to induce nasopharyngeal carcinoma autophagy

Nasopharyngeal carcinoma (NPC), primarily found in the southern region of China, is a malignant tumor known for its highly metastatic characteristics. The high mortality rates caused by the distant metastasis and disease recurrence remain unsolved clinical problems. In clinic, the berberine (BBR) compound has widely been in NPC therapy to decrease metastasis and disease recurrence, and BBR was documented as a main component with multiple anti-NPC effects. However, the mechanism by which BBR inhibits the growth and metastasis of nasopharyngeal carcinoma remains elusive. Herein, we show that BBR effectively inhibits the growth, metastasis, and invasion of NPC via inducing a specific super enhancer (SE). From a mechanistic perspective, the RNA sequencing (RNA-seq) results suggest that the RAS–RAF1–MEK1/2–ERK1/2 signaling pathway, activated by the epidermal growth factor receptor (EGFR), plays a significant role in BBR-induced autophagy in NPC. Blockading of autophagy markedly attenuated the effect of BBR-mediated NPC cell growth and metastasis inhibition. Notably, BBR increased the expression of EGFR by transcription, and knockout of EGFR significantly inhibited BBR-induced microtubule associated protein 1 light chain 3 (LC3)-II increase and p62 inhibition, proposing that EGFR plays a pivotal role in BBR-induced autophagy in NPC. Chromatin immunoprecipitation sequencing (ChIP-seq) results found that a specific SE existed only in NPC cells treated with BBR. This SE knockdown markedly repressed the expression of EGFR and phosphorylated EGFR (EGFR-p) and reversed the inhibition of BBR on NPC proliferation, metastasis, and invasion. Furthermore, BBR-specific SE may trigger autophagy by enhancing EGFR gene transcription, thereby upregulating the RAS–RAF1–MEK1/2–ERK1/2 signaling pathway. In addition, in vivo BBR effectively inhibited NPC cells growth and metastasis, following an increase LC3 and EGFR and a decrease p62. Collectively, this study identifies a novel BBR-special SE and established a new epigenetic paradigm, by which BBR regulates autophagy, inhibits proliferation, metastasis, and invasion. It provides a rationale for BBR application as the treatment regime in NPC therapy in future.

Physiological Basis of Convergent Evolution in Animal Communication Systems

Synopsis To humans, the diverse array of display behaviors that animals use for communication can easily seem peculiar or bizarre. While ample research delves into the evolutionary principles that shape these signals’ effectiveness, little attention is paid to evolutionary patterning of signal design across taxa, particularly when it comes to the potential convergent evolution of many elaborate behavioral displays. By taking a mechanistic perspective, we explore the physiological and neurobiological mechanisms that likely influence the evolution of communication signals, emphasizing the utilization of pre-existing structures over novel adaptations. Central to this investigation are the concepts of perceptual bias and ritualization that we propose contribute to the convergence of elaborate display designs across species. Perceptual bias explains a phenomenon where pre-existing perceptual systems of receivers, used for innate behaviors such as food and predator recognition, select for certain traits of a communication signal from a signaler. Ritualization occurs when traits with no functional role in communication are co-opted through selection and transformed into a new communicative signal. Importantly, susceptibility for ritualization can be brought about through physiological modifications that occurred early in evolutionary time. In this way, perceptual bias can be a selective force that causes the co-option of non-communicative traits into a new communication signal through ritualization involving pre-existing modifications to physiological systems. If the perceptual bias, non-communicative signal, and physiological modifications that increase susceptibility to ritualization are highly conserved, then we may see the convergent evolution of the new communication signal with unrelated taxa facing similar sensory constraints. We explore this idea here using the foot-flagging frog system as a theoretical case study.