Biochemical Information Research Articles

Enhancing mitochondrial one-carbon metabolism is neuroprotective in Alzheimer’s disease models

Alzheimer’s disease (AD) is the most common form of age-related dementia. In AD, the death of neurons in the central nervous system is associated with the accumulation of toxic amyloid β peptide (Aβ) and mitochondrial dysfunction. Mitochondria are signal transducers of metabolic and biochemical information, and their impairment can compromise cellular function. Mitochondria compartmentalise several pathways, including folate-dependent one-carbon (1C) metabolism and electron transport by respiratory complexes. Mitochondrial 1C metabolism is linked to electron transport through complex I of the respiratory chain. Here, we analysed the proteomic changes in a fly model of AD by overexpressing a toxic form of Aβ (Aβ-Arc). We found that expressing Aβ-Arc caused alterations in components of both complex I and mitochondrial 1C metabolism. Genetically enhancing mitochondrial 1C metabolism through Nmdmc improved mitochondrial function and was neuroprotective in fly models of AD. We also found that exogenous supplementation with the 1C donor folinic acid improved mitochondrial health in both mammalian cells and fly models of AD. We found that genetic variations in MTHFD2L, the human orthologue of Nmdmc, were linked to AD risk. Additionally, Mendelian randomisation showed that increased folate intake decreased the risk of developing AD. Overall, our data suggest enhancement of folate-dependent 1C metabolism as a viable strategy to delay the progression and attenuate the severity of AD.

Vertical Graphene-Based Multiparametric Sensing Array for Integration of Smart Catheter to Electrochemically Monitor Peritoneal Dialysis.

Renal failure is typical chronic kidney disease that required peritoneal dialysis as the primary treatment, but current catheter devices lack functionality to monitor changes in chemical analytes during peritoneal dialysis. Fabrication of miniatured sensing modules with good electrochemical performance in tiny catheter devices is the key to realize the smart monitoring of peritoneal dialysis. In this work, a vertical graphene-based multiparametric sensing array (VG-MSA) is developed to continuously measure fluctuations of various analyte concentrations for peritoneal dialysis monitoring. Vertical graphene (VG) electrode with good electrochemical properties serves as the core module in VG-MSA, allowing the development of miniatured sensing modules with sufficient electrochemical performance. The VG-MSA enables sensitive and multiplexed measurement of dialysate components like metabolites (reactive oxygen species, uric acid, and glucose) and ions (K+, Ca2+, and H+). The VG-MSA is demonstrated to effectively detect biochemical signals in peritoneal dialysate in vivo on rat models. The VG-MSA catheter can be inserted into abdominal cavity, allowing full contact with dialysate for in situ, real-time, and continuous collection of biochemical information during peritoneal dialysis. The VG-MSA catheter device offers a valuable tool for monitoring dialysis quality and facilitating treatment adjustments, potentially as a promising platform for high-quality therapy of renal failure.

A consumer-oriented approach to define breeding targets for molecular breeding.

Flavor is a crucial aspect of the eating experience, reflecting evolving consumer preferences for fruits with enhanced quality. Modern fruit breeding programs prioritize improving quality traits aligned with consumer tastes. However, defining fruit-quality attributes that significantly impact consumer preference is a current challenge faced by the industry and breeders. This study proposes a data-driven approach to statistically model the relationship between fruit-quality parameters and consumers' overall liking. Our primary hypothesis suggests that the interplay between fruit-quality attributes and consumer preferences may reach a critical value, serving as new empirical benchmarks for fruit quality. Using extensive historical datasets accounting for sensory, biochemical, and genomic information described in blueberry, we first demonstrated that multivariate adaptive regression splines (MARS) could be used to identify specific values of fruit-quality traits that significantly affect consumer perception by using nonlinear spline regressions on estimating threshold points. We harnessed genomic information and carried out genomic selection (GS) for five fruit-quality traits evaluated on the original scale and after classified via the MARS approach. This study provides a pioneering consumer-centric and data-driven approach to defining fruit-quality standards and supporting molecular breeding that has broad applications to breeding programs from any species.

Rapid diagnosis and severity scale of post-COVID condition using advanced spectroscopy

The COVID-19 pandemic has resulted in a persistent health challenge known as Post-COVID Condition (PCC), characterized by symptoms lasting at least three months after the initial SARS-CoV-2 infection and potentially persisting for several years. While studies on PCC using lipidomics and proteomics have been conducted, these methods are costly and time-consuming. The comprehensive analysis of UV–VIS–NIR–MIR spectroscopy is explored here as an alternative for the rapid and cheap diagnosis and quantification of the severity of PCC. Blood samples from 65 PCC patients, previously analyzed in lipidomic and proteomic studies, along with samples from 65 new patients, were examined to develop a model that quantifies the severity of PCC based solely on spectrophotometric data. Significant spectral variability was observed in the UV–VIS region, particularly between 297 and 600 nm, correlating strongly with patient symptoms. Unsupervised clustering algorithms in this spectral region effectively differentiated between asymptomatic and symptomatic patients, achieving a Jaccard similarity score of 0.667 when compared with clinical symptom classifications. Comparative analysis with proteomic and lipidomic studies indicated that UV–VIS spectroscopy captures clinically relevant biochemical information. The results of the model developed in this work to quantify the severity of PCC demonstrated robustness with new patient data, underscoring the method’s potential as a rapid, non-invasive, and cost-effective diagnostic tool. This study highlights the strengths of spectroscopic techniques, suggesting their suitability for widespread clinical application in diagnosing and monitoring PCC, and emphasizes the need for further refinement and integration of these methods into healthcare practice, particularly for their potential implementation in portable devices.

Vagus nerve stimulation for epilepsy: A narrative review of factors predictive of response.

Vagus nerve stimulation (VNS) is an established therapy for drug-resistant epilepsy. However, there is a lack of reliable predictors of VNS response in clinical use. The identification of factors predictive of VNS response is important for patient selection and stratification as well as tailored stimulation programming. We conducted a narrative review of the existing literature on prognostic markers for VNS response using clinical, demographic, biochemical, and modality-specific information such as from electroencephalography (EEG), magnetoencephalography, and magnetic resonance imaging (MRI). No individual marker demonstrated sufficient predictive power for individual patients, although several have been suggested, with some promising initial findings. Combining markers from underresearched modalities such as T1-weighted MRI morphometrics and EEG may provide better strategies for treatment optimization.

Plasma proteome and incident myocardial infarction: sex-specific differences.

Few population-based cohort studies, including both men and women, have explored circulating proteins associated with incident myocardial infarction (MI). This study investigated the relationships between circulating cardiometabolic-related proteins and MI risk using cohort-based and Mendelian randomization (MR) analyses and explored potential sex-specific differences. The discovery cohort included 11 751 Swedish adults (55-93 years). Data on 259 proteins assessed with Olink proximity extension assays, biochemical, and questionnaire-based information were used. Participants were followed up for incident MI and death over 8 years through linkage to Swedish registers. Replication analyses were conducted on the UK Biobank sample (n = 51 613). In MR analyses, index cis-genetic variants strongly related to the proteins were used as instrumental variables. Genetic association summary statistic data for MI were obtained from the CARDIoGRAMplusC4D consortium and FinnGen. Forty-five proteins were associated with incident MI in discovery and replication samples following adjustment for potential confounders and multiple testing. In the secondary analysis, 13 of the protein associations were sex-specific, with most associations identified among women. In MR analysis, genetically predicted higher levels of renin, follistatin, and retinoic acid receptor responder protein 2 were linked to an increased risk of MI. Tissue factor pathway inhibitor, tumor necrosis factor receptors 1 and 2, placenta growth factor had an inverse association with MI. This study identified both new and confirmed previously established associations between circulating proteins and incident MI and, for the first time, suggested sex-specific patterns in multiple protein-MI associations.

Use of [<sup>18</sup>F]FDG/PET to access the rosmarinic acid anti-inflammatory effect in a mouse sponge implant model

Positron emission tomography (PET) is one of the most sensitive and effective imaging techniques for detecting very low concentrations of specific radiotracers. It is suitable for analyzing biochemical, metabolic, physiological and functional information at the molecular level in vivo and non-invasively. PET using 2-deoxy-2[18F]-fluoro-D-glucose ([18F]FDG) can be used to identify sites of inflammation and other pathologies and to monitor the efficacy of treatment. This technique can be used to study the effect of rosmarinic acid (RA) in various preclinical models. RA is a natural compound with promising antioxidant and anti-inflammatory effects. Therefore, the aim of this study is to investigate the anti-inflammatory potential of RA and the efficacy of PET/[18F]FDG in localizing inflammation and assessing response to treatment. A sponge implant model in mice was used for this purpose. All experiments were performed with male BALB/c mice aged 6 to 9 weeks and weighing 18 to 22 g, with 5 animals per group (10 animals in total throughout the study). Methods: The mice were implanted with sponge-like polyurethane discs to induce local inflammation. The animals were divided into two experimental groups: those treated with a vehicle and those treated with RA. PET scans with [18F]FDG were performed to evaluate the inflammatory process. Results: The results obtained with [18F]FDG showed a decrease in inflammatory cell infiltrates in the sponge after treatment with RA. Conclusion: The use of [18F]FDG demonstrated its efficacy in quantitatively evaluating the inflammatory process in the mouse subcutaneous sponge model as well as the anti-inflammatory effect of RA.

Elucidation of the noncovalent interactions driving enzyme activity guides branching enzyme engineering for α-glucan modification

Branching enzymes (BEs) confer to α-glucans, the primary energy-storage reservoir in nature, a variety of features, like slow digestion. The full catalytic cycle of BEs can be divided in six steps, namely two covalent catalytic steps involving glycosylation and transglycosylation, and four noncatalytic steps involving substrate binding and transfers (SBTs). Despite the ever-growing wealth of biochemical and structural information on BEs, clear mechanistic insights into SBTs from an industrial-performance perspective are still missing. Here, we report a Rhodothermus profundi BE (RpBE) endowed with twice as much enzymatic activity as the Rhodothermus obamensis BE currently used in industry. Furthermore, we focus on the SBTs for RpBE by means of large-scale computations supported by experiment. Engineering of the crucial positions responsible for the initial substrate-binding step improves enzymatic activity significantly, while offering a possibility to customize product types. In addition, we show that the high-efficiency substrate-transfer steps preceding glycosylation and transglycosylation are the main reason for the remarkable enzymatic activity of RpBE, suggestive of engineering directions for the BE family.

Methodology for Studying Interactions of Vitamin A Membrane Receptors and Opsin Protein with their Ligands in Generating the Retinylidene Protein.

Distribution of dietary vitamin A/all-trans retinol (ROL) throughout the body is critical for maintaining retinoid function in peripheral tissues and generating the retinylidene protein for visual function. RBP4-ROL is the complex of ROL with retinol-binding protein 4 (RBP4), which is present in the blood. Two membrane receptors, Retinol Binding Protein 4 Receptor 2 (RBPR2) in the liver and STimulated by Retinoic Acid 6 Retinol (STRA6) in the eye, bind circulatory RBP4 and this mechanism is critical for internalizing ROL into cells. Establishing methods to investigate receptor-ligand kinetics is essential in understanding the physiological function of vitamin A receptors for retinoid homeostasis. Using Surface Plasmon Resonance (SPR) assays, we can analyze the binding affinities and kinetic parameters of vitamin A membrane receptors with its physiological ligand RBP4. These methodologies can reveal new structural and biochemical information of RBP4-binding motifs in RBPR2 and STRA6, which are critical for understanding pathological states of vitamin A deficiency. In the eye, internalized ROL is metabolized to 11-cis retinal, the visual chromophore that binds to opsin in photoreceptors to form the retinylidene protein, rhodopsin. The absorbance of light causes the cis-to-trans isomerization of 11-cis retinal, inducing conformational changes in rhodopsin and the subsequent activation of the phototransduction cascade. Decreased concentrations of serum and ocular ROL can impact retinylidene protein formation, which in turn can cause rhodopsin mislocalization, apoprotein opsin accumulation, night blindness, and photoreceptor outer segment degeneration, leading to Retinitis Pigmentosa or Leber Congenital Amaurosis. Therefore, spectrophotometric methodologies to quantify the G protein-coupled receptor opsin-11-cis retinal complex in the retina are critical for understanding mechanisms of retinal cell degeneration in the above-mentioned pathological states. With these comprehensive methodologies, investigators will be able to better assess dietary vitamin A supply in maintaining systemic and ocular retinoid homeostasis, which is critical for generating and maintaining retinylidene protein concentrations in photoreceptors, which is critical for sustaining visual function in humans.

Role of Gluten-Free Diet on HbA1c Level in Children with Type 1 Diabetes Mellitus and Celiac Disease

Background: Due to autoimmune mechanisms, celiac disease (CD) may affect patients with type 1 diabetes mellitus (T1DM) more than the general population. Objectives: We evaluated the effect of a gluten-free diet (GFD) on HbA1c levels in patients with both type 1 diabetes and CD. Methods: In this cross-sectional study, biochemical and clinical information was gathered from 174 children with T1DM from January 2013 to January 2019. Results: We assessed 174 children with T1DM (93 girls and 81 boys). Celiac disease was diagnosed in 18 out of 174 cases (10.34%). Height and weight percentiles showed significant differences between children with CD and those without CD (P = 0.015 and P = 0.026, respectively). The average HbA1c in the celiac group was 8.61 ± 2.20 (95% CI: 5.1 - 12.1) prior to GFD therapy. HbA1c was assessed six and twelve months following the initiation of the GFD and was found to be 8.32 ± 1.46 (95% CI: 6 - 9.8) and 8.37 ± 1.67 (95% CI: 6.1 - 10.2), respectively. No significant change in HbA1c was observed before and after therapy (P = 0.501). Conclusions: Diabetic children with CD exhibit lower weight and height compared to those without CD. Gluten-free diet therapy in patients with CD did not affect HbA1c levels.

A Proteins of ANL Family FACLs and FAALs, Next Anti TB Drug Targets.

The adenylating enzymes (AEs) of the ANL family contribute to the lipid synthesis process in Mycobacterium tuberculosis (MTB). FAALs (Fatty Acyl-AMP Ligase) and FACLs (Fatty Acyl-CoA Ligase) are members of the ANL enzyme family and are closely associated with the metabolism of mycobacterial lipids responsible for successful infections. Therefore, given their role in both biosynthesis and breakdown processes within fatty acid metabolism, these two groups of proteins might be potential drug targets. The growing abundance of structural, biochemical, and genetic information on mycobacterial FAAL and FACL enzymes could provide a solid foundation for the creation of next-generation anti-tuberculosis drugs, via rational drug designing.

Piercing the Shadows: Exploring the Influence of Signal Preprocessing on Interpreting Ultrasensitive Bioelectronic Sensor Data.

The development of ultrasensitive electronic sensors for in vitro diagnostics is essential for the reliable monitoring of asymptomatic individuals before illness proliferation or progression. These platforms are increasingly valued for their potential to enable timely diagnosis and swift prognosis of infectious or progressive diseases. Typically, the responses from these analytical tools are recorded as digital signals, with electronic data offering simpler processing compared to spectral and optical data. However, preprocessing electronic data from potentiometric biosensor arrays is still in its infancy compared to more established optical technologies. This study utilized the Single-Molecule with a Large Transistor (SiMoT) array, which has achieved a Technology Readiness Level of 5, to explore the impact of data preprocessing on electronic biosensor outcomes. A dataset consisting of plasma and cyst fluid samples from 37 patients with pancreatic precursor cyst lesions was analyzed. The findings revealed that standard signal preprocessing can produce misleading conclusions due to artifacts introduced by mathematical transformations. The study offers strategies to mitigate these effects, ensuring that data interpretation remains accurate and reflective of the underlying biochemical information in the samples.

Intrinsically Disordered Proteins on Au Surfaces

Intrinsically disordered protein Tau, is a neuronal protein and one of the biomarkers of neurodegenerative diseases. Tau protein undergoes conformational changes, post-translational modifications, and aggregation, and is a viable drug target. We reported on using electrochemical impedance spectroscopy and cyclic voltammetry to study various aspects of tau protein biochemistry on Au surfaces (1-2). By immobilizing the tau protein onto the Au surface, the interactions with other proteins, ligands, and enzymes were investigated. Data show that the electrochemical methods are viable biophysical tools that provide new biochemical information which is not always possible with traditional biochemical methods. References A) Carlin, N., Martic-Milne, S. (2018). Anti-tau antibodies based electrochemical sensor for detection of tau protein. J. Electrochem. Soc.165: G3018-G3025. B) Jahshan, A., Esteves, J.O.V., Martic-Milne, S. (2016). Evaluation of ferritin and transferrin binding to tau protein. J. Inorg. Biochem. 162: 127-134. Trzeciakiewicz, H., Esteves, J.O.V., Carlin, N., Martic, S. (2015). Electrochemistry of heparin binding to tau protein on Au surfaces. Electrochim. Acta. 162: 24-30.

(Keynote) Soft Microfluidic Analysis Systems for the Skin

Recent advances in materials science, chemical engineering and mechanics design establish the foundations for high performance classes of microfluidic lab-on-a-chip technologies that have physical properties matched those of the human skin. The resulting devices can integrate with the surface of the skin in a water-tight yet physically imperceptible fashion, to provide real-time measurements of sweat rate and total sweat loss, along with continuous, clinical-quality biochemical information on physiological status using a combination of colorimetric and electrochemical techniques. This talk summarizes the key ideas and presents application examples in sports performance, worker safety, medical diagnostics and nutritional monitoring.

Ultrasound-guided photoacoustic (US-PA) tomography of the breast: Biochemical differentiation using intrinsic tissue markers—lipids, collagen and hemoglobin with histopathologic correlation

In this pilot study, we investigated the utility of handheld ultrasound-guided photoacoustic (US-PA) imaging probe for analyzing ex-vivo breast specimens obtained from female patients who underwent breast-conserving surgery (BCS). We aimed to assess the potential of US-PA in detecting biochemical markers such as collagen, lipids, and hemoglobin, and compare these findings with routine imaging modalities (mammography, ultrasound) and histopathology results, particularly across various breast densities. Twelve ex-vivo breast specimens were obtained from female patients with a mean age of 59.7 ± 9.5 years who underwent BCS. The tissues were illuminated using handheld US-PA probe between 700 and 1100 nm across all margins and analyzed for collagen, lipids, and hemoglobin distribution. The obtained results were compared with routine imaging and histopathological assessments. Our findings revealed that lipid intensity and distribution decreased with increasing breast density, while collagen exhibited an opposite trend. These observations were consistent with routine imaging and histopathological analyses. Moreover, collagen intensity significantly differed (P < 0.001) between cancerous and normal breast tissue, indicating its potential as an additional biomarker for risk stratification across various breast conditions. The study results suggest that a combined assessment of PA biochemical information, such as collagen and lipid content, superimposed on grey-scale ultrasound findings could aid in distinguishing between normal and malignant breast conditions, as well as assist in BCS margin assessment. This underscores the potential of US-PA imaging as a valuable tool for enhancing breast cancer diagnosis and management, offering complementary information to existing imaging modalities and histopathology.

Inverse metabolic engineering based on metabonomics for efficient production of hydroxytyrosol by Saccharomyces cerevisiae

Metabolic engineering provides a powerful approach to efficiently produce valuable compounds, with the aid of emerging gene editing tools and diverse metabolic regulation strategies. However, apart from the current known biochemical pathway information, a variety of unclear constraints commonly limited the optimization space of cell phenotype. Hydroxytyrosol is an important phenolic compound that serves various industries with prominent health-beneficial properties. In this study, the inverse metabolic engineering based on metabolome analysis was customized and implemented to disclose the hidden rate-limiting steps and thus to improve hydroxytyrosol production in Saccharomyces cerevisiae (S. cerevisiae). The potential rate-limiting steps involved three modules that were eliminated individually via reinforcing and balancing metabolic flow, optimizing cofactor supply, and weakening the competitive pathways. Ultimately, a 118.53 % improvement in hydroxytyrosol production (639.84 mg/L) was achieved by inverse metabolic engineering.

SERS microscopy as a tool for comprehensive biochemical characterization in complex samples.

Surface enhanced Raman scattering (SERS) spectra of biomaterials such as cells or tissues can be used to obtain biochemical information from nanoscopic volumes in these heterogeneous samples. This tutorial review discusses the factors that determine the outcome of a SERS experiment in complex bioorganic samples. They are related to the SERS process itself, the possibility to selectively probe certain regions or constituents of a sample, and the retrieval of the vibrational information in order to identify molecules and their interaction. After introducing basic aspects of SERS experiments in the context of biocompatible environments, spectroscopy in typical microscopic settings is exemplified, including the possibilities to combine SERS with other linear and non-linear microscopic tools, and to exploit approaches that improve lateral and temporal resolution. In particular the great variation of data in a SERS experiment calls for robust data analysis tools. Approaches will be introduced that have been originally developed in the field of bioinformatics for the application to omics data and that show specific potential in the analysis of SERS data. They include the use of simulated data and machine learning tools that can yield chemical information beyond achieving spectral classification.

Flexible and multi-functional three-dimensional scaffold based on enokitake-like Au nanowires for real-time monitoring of endothelial mechanotransduction

Endothelial cells are sensitive to mechanical force and can convert it into biochemical signals to trigger mechano-chemo-transduction. Although conventional techniques have been used to investigate the subsequent modifications of cellular expression after mechanical stimulation, the in situ and real-time acquiring the transient biochemical information during mechanotransduction process remains an enormous challenge. In this work, we develop a flexible and multi-functional three-dimensional conductive scaffold that integrates cell growth, mechanical stimulation, and electrochemical sensing by in situ growth of enokitake-like Au nanowires on a three-dimensional porous polydimethylsiloxane substrate. The conductive scaffold possesses stable and desirable electrochemical sensing performance toward nitric oxide under mechanical deformation. The prepared e-AuNWs/CC/PDMS scaffold exhibits a good electrocatalytic ability to NO with a linear range from 2.5 nM to 13.95 μM and a detection limit of 8 nM. Owing to the excellent cellular compatibility, endothelial cells can be cultured directly on the scaffold and the real-time inducing and recording of nitric oxide secretion under physiological and pathological conditions were achieved. This work renders a reliable sensing platform for real-time monitoring cytomechanical signaling during endothelial mechanotransduction and is expected to promote other related biological investigations based on three-dimensional cell culture.

Synchrotron nano-FTIR spectroscopy for probing anticancer drugs at subcellular scale

The cellular response to cisplatin was assessed in human osteosarcoma cells, using synchrotron-based (SR) Fourier Transform InfraRed nanospectroscopy (nano-FTIR) at the MIRIAM beamline B22 of Diamond Light Source (UK). This label-free mapping method delivered simultaneous morphological and biochemical information on a subcellular level (i.e. 100 s nanometer or better). Based on specific spectral biomarkers, the main biochemical constituents affected by the drug were identified at distinct locations within the cell´s inner body. Cisplatin was shown to have a noteworthy effect on proteins, mostly within the cytoplasm. A clear drug impact on cellular lipids was also observed. Within current literature on s-SNOM, this nanospectroscopy work represents a first successful application in life sciences providing full fingerprint nano-FTIR spectra across intact human cancer cells.

Discovery of a new class of bacterial heme-containing C[dbnd]C cleaving oxygenases

Previously, some bacteria were shown to harbour enzymes capable of catalysing the oxidative cleavage of the double bond of t-anethole and related compounds. The cofactor dependence of these enzymes remained enigmatic due to a lack of biochemical information. We report on catalytic and structural details of a representative of this group of oxidative enzymes: t-anethole oxygenase from Stenotrophomonas maltophilia (TAOSm). The bacterial enzyme could be recombinantly expressed and purified, enabling a detailed biochemical study that has settled the dispute on its cofactor dependence. We have established that TAOSm contains a tightly bound b-type heme and merely depends on dioxygen for catalysis. It was found to accept t-anethole, isoeugenol and O-methyl isoeugenol as substrates, all being converted into the corresponding aromatic aldehydes without the need of any cofactor regeneration. The elucidated crystal structure of TAOSm has revealed that it contains a unique active site architecture that is conserved for this distinct class of heme-containing bacterial oxygenases. Similar to other hemoproteins, TAOSm has a histidine (His121) as proximal ligand. Yet, unique for TAOs, an arginine (Arg89) is located at the distal axial position. Site directed mutagenesis confirmed crucial roles for these heme-liganding residues and other residues that form the substrate binding pocket. In conclusion, the results reported here reveal a new class of bacterial heme-containing oxygenases that can be used for the cleavage of alkene double bonds, analogous to ozonolysis in organic chemistry.