Carbon dioxide transport and carbonic anhydrase in blood and muscle

Advancing extracorporeal carbon dioxide removal technology: bridging basic science and clinical practice

Recently, advancements in extracorporeal carbon dioxide removal (ECCO 2 R) technology have markedly enhanced its clinical applicability and efficacy for managing severe respiratory conditions. This review highlights critical innovations in ECCO 2 R, such as advanced catheter technologies, active mixing methods, and biochemical enhancements, which have substantially improved gas exchange efficiency and broadened the scope of ECCO 2 R applications. Integrating ECCO 2 R into acute and chronic respiratory care has led to a shift toward more mobile and less invasive modalities, promising for extending ECCO 2 R usage from intensive care units to home settings. By examining these technological advancements and their clinical impacts, this paper outlines the potential future directions of ECCO 2 R technology, emphasizing its role in transforming respiratory care practices and enhancing patient outcomes.

Role of channels in the O₂ permeability of murine red blood cells. III. Mathematical modeling and simulations

In this third of three papers, we develop a reaction-diffusion model for O 2 offloading from a red blood cell (RBC), treated as a sphere with diameter approximating RBC thickness. Stopped-flow (SF) analysis (paper #1) of hemoglobin/oxyhemoglobin (Hb/HbO 2 ) absorbance spectra during O 2 efflux from intact murine RBCs show that membrane-impermeant inhibitor p-chloromercuribenzenesulfonate (pCMBS) reduces the HbO 2 -deoxygenation rate constant (k HbO2 ) by ~61%. SF experiments show that k HbO2 falls by (1) 9% for aquaporin-1 knockouts (AQP1-KOs), (2) 17% for Rhesus A-glycoprotein knockouts (RhAG-KOs), (3) 30% for double knockouts (dKOs), and (4) ~78% in dKOs/pCMBS. Here, we simulate HbO 2 dissociation (rate constant, k HbO2 → Hb); HbO 2 , Hb, and O 2 diffusion through RBC cytosol; transmembrane O 2 diffusion; and O 2 diffusion through extracellular unconvected fluid (EUF) to bulk extracellular fluid. Informed by automated-hematology data (paper #1) and imaging-flow-cytometry data (paper #2), simulations predict that observed k HbO2 decreases cannot reflect changes in RBC size/shape or [Hb/HbO 2 ]. Instead, membrane O 2 permeability ( P M,O2 ) must fall by (1) 22% to account for AQP1-KO data, (2) 36% for RhAG-KOs, (3) 55% for dKOs, and (4) 91% for dKOs/pCMBS. Exploring predicted k HbO2 sensitivities to eight key parameters (e.g., [Hb/HbO 2 ], diffusion constants, k HbO2 → Hb, thickness EUF , diameter Sphere ) shows that no reasonable changes explain the k HbO2 data. We introduce a linear-combination approach to accommodate for the presence of poikilocytes. Finally, contrary to common beliefs, the model predicts that, in the absence of inhibitors, the RBC membrane represents >30% of total diffusive "resistance" to O 2 offloading, even for a WT mouse.

The Role of Ion-Transporting Proteins on Crosstalk Between the Skeletal Muscle and Central Nervous Systems Elicited by Physical Exercise

A paradigm shift in the understanding of bidirectional interactions between peripheral and central nervous systems is essential for development of rehabilitation and preventive interventions based on physical exercise. Although a causal relationship has not been completely established, modulation of voltage-dependent ion channels (Ca2+, Cl-, K+, Na+, lactate-, H+) in skeletal and neuronal cells provides opportunities to maintain force production during exercise and reduce the risk of disease. However, there are caveats to consider when interpreting the effects of physical exercise on this bidirectional axis, since exercise protocol details (e.g., duration and intensity) have variable effects on this crosstalk. Therefore, an integrative perspective of the skeletal muscle and brain's communication pathway is discussed, and the role of physical exercise on such communication highway is explained in this review.

Soft Biological Actuators for Meter-Scale Homeostatic Biohybrid Robots

Skeletal muscle's elegant protein-based architecture powers motion throughout the animal kingdom, with its constituent actomyosin complexes driving intra- and extra-cellular motion. Classical motors and recently developed soft actuators cannot match the packing density and contractility of individual muscle fibers that scale to power the motion of ants and elephants alike. Accordingly, the interdisciplinary fields of robotics and tissue engineering have combined efforts to build living muscle actuators that can power a new class of robots to be more energy-efficient, dexterous, and safe than existing motor-powered and hydraulic paradigms. Doing so ethically and at scale─creating meter-scale tissue constructs from sustainable muscle progenitor cell lines─has inspired innovations in biomaterials and tissue culture methodology. We weave discussions of muscle cell biology, materials chemistry, tissue engineering, and biohybrid design to review the state of the art in soft actuator biofabrication. Looking forward, we outline a vision for meter-scale biohybrid robotic systems and tie discussions of recent progress to long-term research goals.

Modeling Krebs cycle from liver, heart and hepatoma mitochondria, supported Complex I as target for specific inhibition of cancer cell proliferation

Introduction

The Krebs cycle (KC) is an important pathway for cancer cells because it produces reduced coenzymes for ATP synthesis and precursors for cellular proliferation. Described changes in cancer KC enzyme activities suggested modifications in the reactions that control the KC flux compared to normal cells.

Methods

In this work, kinetic metabolic models of KC of mitochondria from cancer (HepM), liver (RLM) and heart (RHM) to identify targets to decrease the KC flux were constructed from kinetic parameters (Vmax and Km) of enzymes here determined.

Results

The enzymes Vmax values were higher in the following order: RHM > HepM > RLM; meanwhile, Km values were similar. Kinetic modeling indicated that the NADH consumption reaction (complex I) exerted higher control on the Krebs cycle flux in HepM versus RLM and to a lesser extent in RHM. These results suggested that cancer cells may be more sensitive to complex I inhibition than heart and other non-cancer cells. Indeed, cancer cell proliferation was more sensitive to rotenone (a complex I inhibitor) than heart and non-cancer cells. In contrast, cell proliferation had similar sensitivities to malonate, an inhibitor of succinate dehydrogenase, an enzyme that does not exert control.

Discussion

Our results showed that kinetic modeling and metabolic control analysis allow the identification of high flux-controlling targets in cancer cells that help to design strategies to specifically inhibit their proliferation. This can minimize the toxic effects in normal cells, such as the cardiac ones that are highly sensitive to conventional chemotherapy.

Exhaled Breath Analysis: From Laboratory Test to Wearable Sensing

Breath analysis and monitoring have emerged as pivotal components in both clinical research and daily health management, particularly in addressing the global health challenges posed by respiratory and metabolic disorders. The advancement of breath analysis strategies necessitates a multidisciplinary approach, seamlessly integrating expertise from medicine, biology, engineering, and materials science. Recent innovations in laboratory methodologies and wearable sensing technologies have ushered in an era of precise, real-time, and in situ breath analysis and monitoring. This comprehensive review elucidates the physical and chemical aspects of breath analysis, encompassing respiratory parameters and both volatile and non-volatile constituents. It emphasizes their physiological and clinical significance, while also exploring cutting-edge laboratory testing techniques and state-of-the-art wearable devices. Furthermore, the review delves into the application of sophisticated data processing technologies in the burgeoning field of breathomics and examines the potential of breath control in human-machine interaction paradigms. Additionally, it provides insights into the challenges of translating innovative laboratory and wearable concepts into mainstream clinical and daily practice. Continued innovation and interdisciplinary collaboration will drive progress in breath analysis, potentially revolutionizing personalized medicine through entirely non-invasive breath methodology.

Unveiling tomorrow: Carbonic anhydrase activators and inhibitors pioneering new frontiers in Alzheimer's disease

Alzheimer's disease (AD) is a neurodegenerative disorder and a principal basis of dementia in the elderly population globally. Recently, human carbonic anhydrases (hCAs, EC 4.2.1.1) were demonstrated as possible new targets for treating AD. hCAs are vital for maintaining pH balance and performing other physiological processes as they catalyze the reversible hydration of carbon dioxide to bicarbonate and a proton. Current research indicates that hCA plays a role in brain functions critical for transmitting neural signals. Activation of carbonic anhydrase (CA) has emerged as a promising avenue in addressing memory loss and cognitive issues. Conversely, the exploration of CA inhibition represents a novel frontier in this field. By enhancing glial fitness and cerebrovascular health and blocking amyloid-β (Aβ)-induced mitochondrial dysfunction pathways, cytochrome C (CytC) release, caspase 9 activation, and H2O2 generation in neurons, CA inhibitors improve cognition and lessen the pathology caused by Aβ. Recent research has pushed hCAs into the spotlight as critical players in AD pathogenesis and precise therapeutic targets. The captivating dilemma of choosing between hCA inhibitors and activators looms large, as inhibitors reduce Aβ aggregation and improve cerebral blood flow, while activators enhance cerebrovascular functions and restore pH balance. The current review sheds light on the clinical evidence for hCAs and the roles of inhibitors and activators in AD. Additionally, this review offers a fascinating outlook on the data that may aid medicinal chemists in designing and developing new leads that are more effective and selective for upcoming in vitro and in vivo studies, allowing for the discovery and introduction of novel drug candidates for the treatment of AD to the market and into the clinical pipeline.

mRNA biomarkers sensitive and specific to micro-dose erythropoietin treatment at sea level and altitude

Recombinant human erythropoietin (rhEPO) is prohibited by the World Anti-Doping Agency. rhEPO abuse can be indirectly detected via the athlete biological passport (ABP). However, altitude exposure challenges interpretation of the ABP. This study investigated whether 5'-aminolevulinate synthase 2 (ALAS2) and carbonic anhydrase 1 (CA1) in capillary dried blood spots (DBSs) are sensitive and specific markers of rhEPO treatment at altitude. ALAS2 and CA1 expression was monitored in DBS collected weekly before, during, and after a 3-week period at sea level or altitude. Participants were randomly assigned to receive 20 IU kg bw-1 epoetin alpha (rhEPO) or placebo injections every second day for 3 weeks while staying at sea level (rhEPO, n = 25; placebo, n = 9) or altitude (rhEPO, n = 12; placebo, n = 27). ALAS2 and CA1 expression increased up to 300% and 200%, respectively, upon rhEPO treatment at sea-level and altitude (P-values <0.05). When a blinded investigator interpreted the results, ALAS2 and CA1 expression had a sensitivity of 92%. Altitude did not confound the interpretation. Altitude affected ALAS2 and CA1 expression less than actual ABP markers when compared between sea level and altitude results. An individual athlete passport-like approach simulation confirmed the biomarker potential of ALAS2 and CA1. ALAS2 and CA1 were sensitive and specific biomarkers of micro-dose rhEPO treatment at sea level and altitude. Altitude seemed less a confounding factor for these biomarkers, especially when they are combined. Thus, micro-dose rhEPO injections can be detected in a longitudinal blinded setting using mRNA biomarkers in DBS.

Comparative study of lysine acetylation in Vesicomyidae clam Archivesica marissinica and the manila clam Ruditapes philippinarum: adaptation mechanisms in cold seep environments

BACKGROUND

The deep-sea cold seep zone is characterized by high pressure, low temperature, darkness, and oligotrophy. Vesicomyidae clams are the dominant species within this environment, often forming symbiotic relationships with chemosynthetic microbes. Understanding the mechanisms by which Vesicomyidae clams adapt to the cold seep environment is significant. Acetylation modification of lysine is known to play a crucial role in various metabolic processes. Consequently, investigating the role of lysine acetylation in the adaptation of Vesicomyidae clams to deep-sea environments is worthwhile. So, a comparative study of lysine acetylation in cold seep clam Archivesica marissinica and shallow water shellfish Ruditapes philippinarum was conducted.

RESULTS

A total of 539 acetylated proteins were identified with 1634 acetylation sites. Conservative motif enrichment analysis revealed that the motifs -KacR-, -KacT-, and -KacF- were the most conserved. Subsequent gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted on significantly differentially expressed acetylated proteins. The GO enrichment analysis indicated that acetylated proteins are crucial in various biological processes, including cellular response to stimulation, and other cellular processes ( p < 0.05 and false discovery rate (FDR) < 0.25). The results of KEGG enrichment analysis indicated that acetylated proteins are involved in various cellular processes, including tight junction, motor proteins, gap junction, phagosome, cGMP-PKG signaling pathways, endocytosis, glycolysis/gluconeogenesis, among others (p < 0.05 and FDR < 0.25). Notably, a high abundance of lysine acetylation was observed in the glycolysis/glycogenesis pathways, and the acetylation of glyceraldehyde 3-phosphate dehydrogenase might facilitate ATP production. Subsequent investigation into acetylation modifications associated with deep-sea adaptation revealed the specific identification of key acetylated proteins. Among these, the adaptation of cold seep clam hemoglobin and heat shock protein to high hydrostatic pressure and low temperature might involve an increase in acetylation levels. Acetylation of arginine kinase might be related to ATP production and interaction with symbiotic bacteria. Myosin heavy chain (Ama01085) has the most acetylation sites and might improve the actomyosin system stability through acetylation. Further validation is required for the acetylation modification from Vesicomyidae clams.

CONCLUSION

A novel comparative analysis was undertaken to investigate the acetylation of lysine in Vesicomyidae clams, yielding novel insights into the regulatory role of lysine acetylation in deep-sea organisms. The findings present many potential proteins for further exploration of acetylation functions in cold seep clams and other deep-sea mollusks.

The physiological significance of plasma-accessible carbonic anhydrase in the respiratory systems of fishes

Carbonic anhydrase (CA) activity is ubiquitously found in all vertebrate species, tissues and cellular compartments. Most species have plasma-accessible CA (paCA) isoforms at the respiratory surfaces, where the enzyme catalyzes the conversion of plasma bicarbonate to carbon dioxide (CO2) that can be excreted by diffusion. A notable exception are the teleost fishes that appear to lack paCA at their gills. The present review: (i) recapitulates the significance of CA activity and distribution in vertebrates; (ii) summarizes the current evidence for the presence or absence of paCA at the gills of fishes, from the basal cyclostomes to the derived teleosts and extremophiles such as the Antarctic icefishes; (iii) explores the contribution of paCA to organismal CO2 excretion in fishes; and (iv) the functional significance of its absence at the gills, for the specialized system of O2 transport in most teleosts; (v) outlines the multiplicity and isoform distribution of membrane-associated CAs in fishes and methodologies to determine their plasma-accessible orientation; and (vi) sketches a tentative time line for the evolutionary dynamics of branchial paCA distribution in the major groups of fishes. Finally, this review highlights current gaps in the knowledge on branchial paCA function and provides recommendations for future work.

Effects of sodium bicarbonate ingestion on ventilatory and cerebrovascular responses in resting heated humans

Hyperthermia stimulates ventilation in humans. This hyperthermia-induced hyperventilation may be mediated by the activation of peripheral chemoreceptors implicated in the regulation of respiration in reaction to various chemical stimuli, including reductions in arterial pH. Here, we investigated the hypothesis that during passive heating at rest, the increases in arterial pH achieved with sodium bicarbonate ingestion, which could attenuate peripheral chemoreceptor activity, mitigate hyperthermia-induced hyperventilation. We also assessed the effect of sodium bicarbonate ingestion on cerebral blood flow responses, which are associated with hyperthermia-induced hyperventilation. Twelve healthy men ingested sodium bicarbonate (0.3 g/kg body weight) or sodium chloride (0.208 g/kg). One hundred minutes after the ingestion, the participants were passively heated using hot-water immersion (42°C) combined with a water-perfused suit. Increases in esophageal temperature (an index of core temperature) and minute ventilation (V̇E) during the heating were similar in the two trials. Moreover, when V̇E is expressed as a function of esophageal temperature, there were no between-trial differences in the core temperature threshold for hyperventilation (38.0 ± 0.3 vs. 38.0 ± 0.4°C, P = 0.469) and sensitivity of hyperthermia-induced hyperventilation as assessed by the slope of the core temperature-V̇E relation (13.5 ± 14.2 vs. 15.8 ± 15.5 L/min/°C, P = 0.831). Furthermore, middle cerebral artery mean blood velocity (an index of cerebral blood flow) decreased similarly with heating duration in both trials. These results suggest that sodium bicarbonate ingestion does not mitigate hyperthermia-induced hyperventilation and the reductions in cerebral blood flow index in resting heated humans.NEW & NOTEWORTHY Hyperthermia leads to hyperventilation and associated cerebral hypoperfusion, both of which may impair heat tolerance. This hyperthermia-induced hyperventilation may be mediated by peripheral chemoreceptors, which can be activated by reductions in arterial pH. However, our results suggest that sodium bicarbonate ingestion, which can increase arterial pH, is not an effective intervention in alleviating hyperthermia-induced hyperventilation and cerebral hypoperfusion in resting heated humans.

The potential of carbonic anhydrase enzymes as a novel target for anti-cancer treatment

Carbonic anhydrase (CA) is a zinc-dependent metal enzyme that maintains the pH and carbon dioxide (CO2) homeostasis in cells by catalyzing the reversible hydration and dehydration of CO2 and bicarbonate (HCO3-). In mammals, there are 16 isozymes of CA existed, namely CAI to CAXIV, but only 15 isozymes are found in humans except CAXV. Human CAs have highly conserved catalytic domains, all of which are distributed in different tissues and play important physiological roles. Changes in their functions may disrupt the typical distribution of CAs throughout human body and therefore CAs can be used as diagnostic biomarkers for many diseases. Furthermore, the expression of CAs is correlated to the progression of numerous tumors, therapeutic sensitivity and patient prognosis. In this review, we discuss thoroughly the structure of CAs, their functional activities in human physiology, dysregulations and diseases related to CAs, and different types of CA inhibitors that can reverse their dysregulation.

The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM

The principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. Uniquely among jawed vertebrates, crocodilians possess Hb that shows a profound drop in oxygen affinity in the presence of bicarbonate ions. This allows them to stay underwater for extended periods by consuming almost all the oxygen present in the blood-stream, as metabolism releases carbon dioxide, whose conversion to bicarbonate and hydrogen ions is catalysed by carbonic anhydrase. Despite the apparent universal utility of bicarbonate as an allosteric regulator of Hb, this property evolved only in crocodilians. We report here the molecular structures of both human and a crocodilian Hb in the deoxy and liganded states, solved by cryo-electron microscopy. We reveal the precise interactions between two bicarbonate ions and the crocodilian protein at symmetry-related sites found only in the T state. No other known effector of vertebrate Hbs binds anywhere near these sites.

Engineering Synthetic Erythrocytes as Next-Generation Blood Substitutes

Blood scarcity is one of the main causes of healthcare disruptions worldwide, with blood shortages occurring at an alarming rate. Over the last decades, blood substitutes has aimed at reinforcing the supply of blood, with several products (e.g., hemoglobin-based oxygen carriers, perfluorocarbons) achieving a limited degree of success. Regardless, there is still no widespread solution to this problem due to persistent challenges in product safety and scalability. In this Review, we describe different advances in the field of blood substitution, particularly in the development of artificial red blood cells, otherwise known as engineered erythrocytes. We categorize the different strategies into natural, synthetic, or hybrid approaches, and discuss their potential in terms of safety and scalability. We identify synthetic engineered erythrocytes as the most powerful approach, and describe erythrocytes from a materials engineering perspective. We review their biological structure and function, as well as explore different methods of assembling a material-based cell. Specifically, we discuss how to recreate size, shape, and deformability through particle fabrication, and how to recreate the functional machinery through synthetic biology and nanotechnology. We conclude by describing the versatile nature of synthetic erythrocytes in medicine and pharmaceuticals and propose specific directions for the field of erythrocyte engineering.

Monitoring CO2 kinetics as a marker of cardiopulmonary efficiency

PURPOSE OF REVIEW

To describe current and near future developments and applications of CO2 kinetics in clinical respiratory and cardiovascular monitoring.

RECENT FINDINGS

In the last years, we have witnessed a renewed interest in CO2 kinetics in relation with a better understanding of volumetric capnography and its derived parameters. This together with technological advances and improved measurement systems have expanded the monitoring potential of CO2 kinetics including breath by breath continuous end-expiratory lung volume and continuous noninvasive cardiac output. Dead space has slowly been gaining relevance in clinical monitoring and prognostic evaluation. Easy to measure dead space surrogates such as the ventilatory ratio have demonstrated a strong prognostic value in patients with acute respiratory failure.

SUMMARY

The kinetics of carbon dioxide describe many relevant physiological processes. The clinical introduction of new ways of assessing respiratory and circulatory efficiency based on advanced analysis of CO2 kinetics are paving the road to a long-desired goal in clinical monitoring of critically ill patients: the integration of respiratory and circulatory monitoring during mechanical ventilation.

Biomedical applications of prokaryotic carbonic anhydrases: an update

INTRODUCTION

This review offers an updated perspective on the biomedical applications of prokaryotic carbonic anhydrases (CAs), emphasizing their potential as targets for drug development against antibiotic-resistant bacterial infections. A systematic review of literature from PubMed, Web of Science, and Google Scholar has been conducted to provide a comprehensive analysis.

AREA COVERED

It delves into the pivotal roles of prokaryotic CAs in bacterial metabolism and their distinctions from mammalian CAs. The review explores the diversity of CA classes in bacteria, discusses selective inhibitors targeting bacterial CAs, and explores their potential applications in biomedical research. Furthermore, it analyzes clinical trials investigating the efficacy of carbonic anhydrase inhibitors (CAIs) and patented approaches for developing antibacterial CAIs, highlighting their translational potential in creating innovative antibacterial agents.

EXPERT OPINION

Recent years have witnessed increased recognition of CA inhibition as a promising strategy against bacterial infections. Challenges persist in achieving selectivity over human isoforms and optimizing therapeutic efficacy. Structural biology techniques provide insights into unique active site architectures, guiding selective inhibitor design. The review underscores the importance of interdisciplinary collaborations, innovative drug delivery systems, and advanced drug discovery approaches in unlocking the full therapeutic potential of prokaryotic CA inhibitors. It emphasizes the significance of these efforts in addressing antibiotic resistance and improving patient outcomes.

PCO 2 Gradient Between Inlet and Outlet Blood of Extracorporeal Respiratory Support Is a Reliable Marker of CO 2 Elimination

Our objective was to assess the relationship between the pre-/post-oxygenator gradient of the partial pressure of carbon dioxide (∆ EC PCO 2 ; dissolved form) and CO 2 elimination under extracorporeal respiratory support. All patients who were treated with veno-venous extracorporeal membrane oxygenation and high-flow extracorporeal CO 2 removal in our intensive care unit over 18 months were included. Pre-/post-oxygenator blood gases were collected every 12 h and CO 2 elimination was calculated for each pair of samples (pre-/post-oxygenator total carbon dioxide content in blood [ ct CO 2 ] × pump flow [extracorporeal pump flow {Q EC }]). The relationship between ∆ EC PCO 2 and CO 2 elimination, as well as the origin of CO 2 removed. Eighteen patients were analyzed (24 oxygenators and 293 datasets). Each additional unit of ∆ EC PCO 2 × Q EC was associated with an increase in CO 2 elimination of 5.2 ml (95% confidence interval [CI], 4.7-5.6 ml; p < 0.001). Each reduction of 1 ml STPD/dl of CO 2 across the oxygenator was associated with a reduction of 0.63 ml STPD/dl (95% CI, 0.60-0.66) of CO 2 combined with water, 0.08 ml STPD/dl (95% CI, 0.07-0.09) of dissolved CO 2 , and 0.29 ml STPD/dl (95% CI, 0.27-0.31) of CO 2 in erythrocytes. The pre-/post-oxygenator PCO 2 gradient under extracorporeal respiratory support is thus linearly associated with CO 2 elimination; however, most of the CO 2 removed comes from combined CO 2 in plasma, generating bicarbonate.

Neurovascular coupling is optimized to compensate for the increase in proton production from nonoxidative glycolysis and glycogenolysis during brain activation and maintain homeostasis of pH, pCO2, and pO2

During transient brain activation cerebral blood flow (CBF) increases substantially more than cerebral metabolic rate of oxygen consumption (CMRO2) resulting in blood hyperoxygenation, the basis of BOLD-fMRI contrast. Explanations for the high CBF versus CMRO2 slope, termed neurovascular coupling (NVC) constant, focused on maintenance of tissue oxygenation to support mitochondrial ATP production. However, paradoxically the brain has a 3-fold lower oxygen extraction fraction (OEF) than other organs with high energy requirements, like heart and muscle during exercise. Here, we hypothesize that the NVC constant and the capillary oxygen mass transfer coefficient (which in combination determine OEF) are co-regulated during activation to maintain simultaneous homeostasis of pH and partial pressure of CO2 and O2 (pCO2 and pO2). To test our hypothesis, we developed an arteriovenous flux balance model for calculating blood and brain pH, pCO2, and pO2 as a function of baseline OEF (OEF0), CBF, CMRO2, and proton production by nonoxidative metabolism coupled to ATP hydrolysis. Our model was validated against published brain arteriovenous difference studies and then used to calculate pH, pCO2, and pO2 in activated human cortex from published calibrated fMRI and PET measurements. In agreement with our hypothesis, calculated pH, pCO2, and pO2 remained close to constant independently of CMRO2 in correspondence to experimental measurements of NVC and OEF0. We also found that the optimum values of the NVC constant and OEF0 that ensure simultaneous homeostasis of pH, pCO2, and pO2 were remarkably similar to their experimental values. Thus, the high NVC constant is overall determined by proton removal by CBF due to increases in nonoxidative glycolysis and glycogenolysis. These findings resolve the paradox of the brain's high CBF yet low OEF during activation, and may contribute to explaining the vulnerability of brain function to reductions in blood flow and capillary density with aging and neurovascular disease.

Synthesis, molecular docking analysis, drug-likeness evaluation, and inhibition potency of new pyrazole-3,4-dicarboxamides incorporating sulfonamide moiety as carbonic anhydrase inhibitors

A series of novel pyrazole-dicarboxamides were synthesized from pyrazole-3,4-dicarboxylic acid chloride and various primary and secondary sulfonamides. The structures of the new compounds were confirmed by FT-IR, 1H-NMR, 13C-NMR, and HRMS. Then the inhibition effects of newly synthesized molecules on human erythrocyte hCA I and hCA II isoenzymes were investigated. Ki values of the compounds were in the range of 0.024-0.496 µM for hCA I and 0.006-5.441 µM for hCA II. Compounds 7a and 7i showed nanomolar level of inhibition of hCA II, and these compounds exhibited high selectivity for this isoenzyme. Molecular docking studies were performed between the most active compounds 7a, 7b, 7i, and the reference inhibitor AAZ and the hCAI and hCAII to investigate the binding mechanisms between the compounds and the isozymes. These compounds showed better interactions than the AAZ. ADMET and drug-likeness analyses for the compounds have shown that the compounds can be used pharmacologically in living organisms.

Erythrocyte metabolism

Our aim is to present an updated overview of the erythrocyte metabolism highlighting its richness and complexity. We have manually collected and connected the available biochemical pathways and integrated them into a functional metabolic map. The focus of this map is on the main biochemical pathways consisting of glycolysis, the pentose phosphate pathway, redox metabolism, oxygen metabolism, purine/nucleoside metabolism, and membrane transport. Other recently emerging pathways are also curated, like the methionine salvage pathway, the glyoxalase system, carnitine metabolism, and the lands cycle, as well as remnants of the carboxylic acid metabolism. An additional goal of this review is to present the dynamics of erythrocyte metabolism, providing key numbers used to perform basic quantitative analyses. By synthesizing experimental and computational data, we conclude that glycolysis, pentose phosphate pathway, and redox metabolism are the foundations of erythrocyte metabolism. Additionally, the erythrocyte can sense oxygen levels and oxidative stress adjusting its mechanics, metabolism, and function. In conclusion, fine-tuning of erythrocyte metabolism controls one of the most important biological processes, that is, oxygen loading, transport, and delivery.

Impaired O2 unloading from stored blood results in diffusion-limited O2 release at tissues: evidence from human kidneys

ABSTRACT

The volume of oxygen drawn from systemic capillaries down a partial pressure gradient is determined by the oxygen content of red blood cells (RBCs) and their oxygen-unloading kinetics, although the latter is assumed to be rapid and, therefore, not a meaningful factor. Under this paradigm, oxygen transfer to tissues is perfusion-limited. Consequently, clinical treatments to optimize oxygen delivery aim at improving blood flow and arterial oxygen content, rather than RBC oxygen handling. Although the oxygen-carrying capacity of blood is increased with transfusion, studies have shown that stored blood undergoes kinetic attrition of oxygen release, which may compromise overall oxygen delivery to tissues by causing transport to become diffusion-limited. We sought evidence for diffusion-limited oxygen release in viable human kidneys, normothermically perfused with stored blood. In a cohort of kidneys that went on to be transplanted, renal respiration correlated inversely with the time-constant of oxygen unloading from RBCs used for perfusion. Furthermore, the renal respiratory rate did not correlate with arterial O2 delivery unless this factored the rate of oxygen-release from RBCs, as expected from diffusion-limited transport. To test for a rescue effect, perfusion of kidneys deemed unsuitable for transplantation was alternated between stored and rejuvenated RBCs of the same donation. This experiment controlled oxygen-unloading, without intervening ischemia, holding all non-RBC parameters constant. Rejuvenated oxygen-unloading kinetics improved the kidney's oxygen diffusion capacity and increased cortical oxygen partial pressure by 60%. Thus, oxygen delivery to tissues can become diffusion-limited during perfusion with stored blood, which has implications in scenarios, such as ex vivo organ perfusion, major hemorrhage, and pediatric transfusion. This trial was registered at www.clinicaltrials.gov as #ISRCTN13292277.

Design, synthesis, and biological investigation of selective human carbonic anhydrase II, IX, and XII inhibitors using 7-aryl/heteroaryl triazolopyrimidines bearing a sulfanilamide scaffold

A novel library of human carbonic anhydrase (hCA) inhibitors based on the 2-sulfanilamido[1,2,4]triazolo[1,5-a]pyrimidine skeleton modified at its 7-position was prepared by an efficient convergent procedure. These derivatives were evaluated in vitro for their inhibition properties against a representative panel of hCA isoforms (hCA I, II, IV, IX, and XII). The target tumour-associated isoforms hCA IX and XII were potently inhibited with KIs in the low nanomolar range of 5-96 nM and 4-72 nM, respectively. Compounds 1d, 1j, 1v, and 1x were the most potent hCA IX inhibitors with KIs of 5.1, 8.6, 4.7, and 5.1 nM, respectively. Along with derivatives 1d and 1j, compounds 1r and 1ab potently inhibited hCA XII isoform with KIs in a single-digit nanomolar range of 8.8, 5.4, 4.3, and 9.0 nM, respectively. Compounds 1e, 1m, and 1p exhibited the best selectivity against hCA IX and hCA XII isoforms over off-target hCA II, with selectivity indexes ranging from 5 to 14.

Harnessing large language models (LLMs) for candidate gene prioritization and selection

BACKGROUND

Feature selection is a critical step for translating advances afforded by systems-scale molecular profiling into actionable clinical insights. While data-driven methods are commonly utilized for selecting candidate genes, knowledge-driven methods must contend with the challenge of efficiently sifting through extensive volumes of biomedical information. This work aimed to assess the utility of large language models (LLMs) for knowledge-driven gene prioritization and selection.

METHODS

In this proof of concept, we focused on 11 blood transcriptional modules associated with an Erythroid cells signature. We evaluated four leading LLMs across multiple tasks. Next, we established a workflow leveraging LLMs. The steps consisted of: (1) Selecting one of the 11 modules; (2) Identifying functional convergences among constituent genes using the LLMs; (3) Scoring candidate genes across six criteria capturing the gene's biological and clinical relevance; (4) Prioritizing candidate genes and summarizing justifications; (5) Fact-checking justifications and identifying supporting references; (6) Selecting a top candidate gene based on validated scoring justifications; and (7) Factoring in transcriptome profiling data to finalize the selection of the top candidate gene.

RESULTS

Of the four LLMs evaluated, OpenAI's GPT-4 and Anthropic's Claude demonstrated the best performance and were chosen for the implementation of the candidate gene prioritization and selection workflow. This workflow was run in parallel for each of the 11 erythroid cell modules by participants in a data mining workshop. Module M9.2 served as an illustrative use case. The 30 candidate genes forming this module were assessed, and the top five scoring genes were identified as BCL2L1, ALAS2, SLC4A1, CA1, and FECH. Researchers carefully fact-checked the summarized scoring justifications, after which the LLMs were prompted to select a top candidate based on this information. GPT-4 initially chose BCL2L1, while Claude selected ALAS2. When transcriptional profiling data from three reference datasets were provided for additional context, GPT-4 revised its initial choice to ALAS2, whereas Claude reaffirmed its original selection for this module.

CONCLUSIONS

Taken together, our findings highlight the ability of LLMs to prioritize candidate genes with minimal human intervention. This suggests the potential of this technology to boost productivity, especially for tasks that require leveraging extensive biomedical knowledge.

Keto-bridged dual triazole-linked benzenesulfonamides as potent carbonic anhydrase and cathepsin B inhibitors

Background: Inhibition of human carbonic anhydrase (hCA) isoforms IX and XII with concurrent inhibition of cathepsin B is a promising approach for targeting cancers. Methods/results: 28 keto-bridged dual triazole-containing benzenesulfonamides were synthesized and tested, following the multitarget approach, for their efficacy as inhibitors of cathepsin B and hCA isoforms (I, II, IX, XII). The synthesized compounds showed excellent inhibition of CA isoforms (IX and XII) and cathepsin B. Compound 8i exhibited better and more selective inhibition of the cancer-associated isoform hCA IX as compared with acetazolamide (reference drug) and SLC-0111 (potent lead as carbonic anhydrase inhibitor). Molecular docking studies were also carried out. Conclusion: The present work gives important generalizations for the development of isoform-selective hCA inhibitors endowed with anti-cathepsin properties.

Single Functional Group Platform for Multistimuli Responsivities: Tertiary Amine for CO2/pH/ROS-Triggered Cargo Release in Nanocarriers

The design of multistimuli-responsive soft nanoparticles (NPs) often presents synthetic complexities and limited breadth in exploiting changes surrounding physiological environments. Nanocarriers that could collectively take advantage of several endogenous stimuli can offer a powerful tool in nanomedicine. Herein, we have capitalized on the chemical versatility of a single tertiary amine to construct miktoarm polymer-based nanocarriers that respond to dissolved CO2, varied pH, reactive oxygen species (ROS), and ROS + CO2. Curcumin (Cur), an anti-inflammatory phytopharmaceutic, was loaded into micelles, and we validated the sensitivity of the tertiary amine in tuning Cur release. An in vitro evaluation indicated that Cur encapsulation strongly suppressed its toxicity at high concentrations, significantly inhibited nigericin-induced secretion of interleukin-1β by THP-1 macrophages, and the proportion of M2/M1 (anti-inflammatory/pro-inflammatory macrophages) was higher for Cur-loaded NPs than for free Cur. Our approach highlights the potential of a simple-by-design strategy in expanding the scope of polymeric NPs in drug delivery.

Venous Minus Arterial Carbon Dioxide Gradients in the Monitoring of Tissue Perfusion and Oxygenation: A Narrative Review

According to Fick's principle, the total uptake of (or release of) a substance by tissues is the product of blood flow and the difference between the arterial and the venous concentration of the substance. Therefore, the mixed or central venous minus arterial CO₂ content difference depends on cardiac output (CO). Assuming a linear relationship between CO₂ content and partial pressure, central or mixed venous minus arterial PCO₂ differences (P_cv-aCO₂ and P_mv-aCO₂) are directly related to CO. Nevertheless, this relationship is affected by alterations in the CO₂Hb dissociation curve induced by metabolic acidosis, hemodilution, the Haldane effect, and changes in CO₂ production (VCO₂). In addition, P_cv-aCO₂ and P_mv-aCO₂ are not interchangeable. Despite these confounders, CO is a main determinant of P_cv-aCO₂. Since in a study performed in septic shock patients, P_mv-aCO₂ was correlated with changes in sublingual microcirculation but not with those in CO, it has been proposed as a monitor for microcirculation. The respiratory quotient (RQ)-RQ = VCO₂/O₂ consumption-sharply increases in anaerobic situations induced by exercise or critical reductions in O₂ transport. This results from anaerobic VCO₂ secondary to bicarbonate buffering of anaerobically generated protons. The measurement of RQ requires expired gas analysis by a metabolic cart, which is not usually available. Thus, some studies have suggested that the ratio of P_cv-aCO₂ to arterial minus central venous O₂ content (P_cv-aCO₂/C_a-cvO₂) might be a surrogate for RQ and tissue oxygenation. In this review, we analyze the physiologic determinants of P_cv-aCO₂ and P_cv-aCO₂/C_a-cvO₂ and their potential usefulness and limitations for the monitoring of critically ill patients. We discuss compelling evidence showing that they are misleading surrogates for tissue perfusion and oxygenation, mainly because they are systemic variables that fail to track regional changes. In addition, they are strongly dependent on changes in the CO₂Hb dissociation curve, regardless of changes in systemic and microvascular perfusion and oxygenation.

Conformationally Restricted Glycoconjugates Derived from Arylsulfonamides and Coumarins: New Families of Tumour-Associated Carbonic Anhydrase Inhibitors

The involvement of carbonic anhydrases (CAs) in a myriad of biological events makes the development of new inhibitors of these metalloenzymes a hot topic in current Medicinal Chemistry. In particular, CA IX and XII are membrane-bound enzymes, responsible for tumour survival and chemoresistance. Herein, a bicyclic carbohydrate-based hydrophilic tail (imidazolidine-2-thione) has been appended to a CA-targeting pharmacophore (arylsulfonamide, coumarin) with the aim of studying the influence of the conformational restriction of the tail on the CA inhibition. For this purpose, the coupling of sulfonamido- or coumarin-based isothiocyanates with reducing 2-aminosugars, followed by the sequential acid-promoted intramolecular cyclization of the corresponding thiourea and dehydration reactions, afforded the corresponding bicyclic imidazoline-2-thiones in good overall yield. The effects of the carbohydrate configuration, the position of the sulfonamido motif on the aryl fragment, and the tether length and substitution pattern on the coumarin were analysed in the in vitro inhibition of human CAs. Regarding sulfonamido-based inhibitors, the best template turned out to be a d-galacto-configured carbohydrate residue, meta-substitution on the aryl moiety (9b), with K_i against CA XII within the low nM range (5.1 nM), and remarkable selectivity indexes (1531 for CA I and 181.9 for CA II); this provided an enhanced profile in terms of potency and selectivity compared to more flexible linear thioureas 1-4 and the drug acetazolamide (AAZ), used herein as a reference compound. For coumarins, the strongest activities were found for substituents devoid of steric hindrance (Me, Cl), and short linkages; derivatives 24h and 24a were found to be the most potent inhibitors against CA IX and XII, respectively (K_i = 6.8, 10.1 nM), and also endowed with outstanding selectivity (K_i > 100 µM against CA I, II, as off-target enzymes). Docking simulations were conducted on 9b and 24h to gain more insight into the key inhibitor-enzyme interactions.

Carbonic anhydrase in elasmobranchs and implications of the current climate change scenario

The enzyme carbonic anhydrase (CA) has well-known functions in acid-base balance, respiratory gas exchange, and osmoregulation in teleost fishes. However, studies concerning the role of CA in elasmobranchs are still scarce. Therefore, the aim of this study is to present the current status of CA studies in sharks and rays, as well as to identify gaps and emerging needs, in order to guide future studies. This review is organized according to the main roles of CA, with further considerations on climate change and CA effects indicated as paramount, as strategies in the face of climate change can be crucial for species response. The literature review revealed a reduction in publications on CA over the years. In addition, a historical research differentiation is noted, where the first assessments on the subject addressed investigations on basic CA functions, while the most recent studies present a comparative approach among species as well as interdisciplinary discussions, such as ecology and phylogeny. Considering that most elasmobranchs are threatened, future studies should prioritize non-lethal methodologies, in addition to expanding studies to climate change effects on CA.

Functional divergence of teleost carbonic anhydrase 4

The functional role of membrane-bound carbonic anhydrases (CAs) has been of keen interest in the past decade, and in particular, studies have linked CA in red muscle, heart, and eye to enhanced tissue oxygen extraction in bony fishes (teleosts). However, the number of purported membrane-bound CA isoforms in teleosts, combined with the imperfect system of CA isoform nomenclature, present roadblocks for ascribing physiological functions to particular CA isoforms across different teleost lineages. Here we developed an organizational framework for membrane-bound CAs in teleosts, providing the latest phylogenetic analysis of extant CA4 and CA4-like isoforms. Our data confirm that there are three distinct isoforms of CA4 (a, b, and c) that are conserved across major teleost lineages, with the exception of CA4c gene being lost in salmonids. Tissue distribution analyses suggest CA4a functions in oxygen delivery across teleost lineages, while CA4b may be specialized for renal acid-base balance and ion regulation. This work provides an important foundation for researchers to elucidate the functional significance of CA4 isoforms in fishes.

Mathematical modelling of bicarbonate supplementation and acid-base chemistry in kidney failure patients on hemodialysis

Acid-base regulation by the kidneys is largely missing in end-stage renal disease patients undergoing hemodialysis (HD). Bicarbonate is added to the dialysis fluid during HD to replenish the buffers in the body and neutralize interdialytic acid accumulation. Predicting HD outcomes with mathematical models can help select the optimal patient-specific dialysate composition, but the kinetics of bicarbonate are difficult to quantify, because of the many factors involved in the regulation of the bicarbonate buffer in bodily fluids. We implemented a mathematical model of dissolved CO2 and bicarbonate transport that describes the changes in acid-base equilibrium induced by HD to assess the kinetics of bicarbonate, dissolved CO2, and other buffers not only in plasma but also in erythrocytes, interstitial fluid, and tissue cells; the model also includes respiratory control over the partial pressures of CO2 and oxygen. Clinical data were used to fit the model and identify missing parameters used in theoretical simulations. Our results demonstrate the feasibility of the model in describing the changes to acid-base homeostasis typical of HD, and highlight the importance of respiratory regulation during HD.

Nanobiotechnological basis of an oxygen carrier with enhanced carbonic anhydrase for CO2 transport and enhanced catalase and superoxide dismutase for antioxidant function

This is a mini review on the biotechnological aspects of the most extensively developed hemoglobin-based oxygen carriers The emphasis is on the most recent Polyhemoglobin-catalase-superoxide dismutase-carbonic anhydrase (PolyHb-CAT-SOD-CA), which is a nanobiotechnological complex that is being investigated and scaled up with the potential for clinical use as nanobiotherapeutics. Hemoglobin, a tetramer, is an excellent oxygen carrier. However, in the body it is converted into toxic dimers. Diacid or glutaraldehyde can crosslink hemoglobin into polyhemoglobin (PolyHb) and prevent its breakdown into toxic dimers. This has been developed and tested in clinical trials. A bovine polyhemoglobin has been approved for routine clinical use for surgical procedures in South Africa and Russia. Clinical trials with human PolyHb in hemorrhagic shock were effective but with a very slight increase in non-fatal myocardial ischemia. This could be due to a number of reasons. For those conditions with ischemia-reperfusion, one would need an oxygen carrier with antioxidant properties. One approach to remedy this is with prepared polyhemoglobin-catalase-superoxide dismutase (PolyHb-CAT-SOD). Another reason is an increase in intracellular pCO₂. We therefore added an enhanced level of carbonic anhydrase to prepare a PolyHb-CAT-SOD-CA. The result is an oxygen carrier with enhanced Carbonic Anhydrase for CO₂ transport and enhanced Catalase and Superoxide Dismutase for antioxidant functions. Detailed efficacy and safety studies have led to the industrial scale up towards clinical trial. In the meantime, oxygen carriers are being investigated around the world for use in ex vivo biotechnological fluid for organ preservation for transplantation, with one already approved in France.

Base (HCO3-/CO32-) Transport Properties of SLC4 Proteins: New Insights in Acid-Base Kidney Physiology

H+ or base transporters and channels in the mammalian genome play important roles in the maintenance of numerous cellular biochemical and physiologic processes throughout the body. Among the known base transporters, those within the SLC4 and SLC26 gene families are involved in cell, transepithelial, and whole organ function. Whether the functional properties of these transporters involve HCO3-, CO32-, or HCO3-/CO32- stimulated H+ (or OH-) transport has not received widespread attention in the literature. Accordingly, "bicarbonate" is the term typically used in most textbooks without greater specificity. Moreover, clinicians and physiologists have historically focused on the blood HCO3- concentration as the base term in the Henderson-Hasselbalch equation in the analysis of clinical acid-base abnormalities, thus, bicarbonate has been assumed to be the species reabsorbed along the nephron as required to maintain the blood [HCO3-] at approximately 25 mM. However, accumulating data in the literature suggest that carbonate, rather than bicarbonate, is the species absorbed across the proximal tubule basolateral membrane, whereas in the collecting duct, bicarbonate is indeed transported. Various experimental approaches leading to this new concept are herein reviewed.

Carbonic anhydrase IX: A tumor acidification switch in heterogeneity and chemokine regulation

The primary physiological process of respiration produces carbon dioxide (CO₂) that reacts with water molecules which subsequently liberates bicarbonate (HCO-₃) and protons. Carbonic anhydrases (CAs) are the primary catalyst involved in this conversion. More than 16 isoforms of human CAs show organ or subcellular specific activity. Dysregulation of each CA is associated with multiple pathologies. Out of these members, the overexpression of membrane-bound carbonic anhydrase IX (CAIX) is associated explicitly with hypoxic tumors or various solid cancers. CAIX helps tumors deal with higher CO₂ by sequestering it with bicarbonate ions and helping cancer cells to grow in a comparatively hypoxic or acidic environment, thus acting as a pH adaptation switch. CAIX-mediated adaptations in cancer cells include angiogenesis, metabolic alterations, tumor heterogeneity, drug resistance, and regulation of cancer-specific chemokines. This review comprehensively collects and describe the cancer-specific expression mechanism and role of CAIX in cancer growth, progression, heterogeneity, and its structural insight to develop future combinatorial targeted cancer therapies.

Interplay of carbon dioxide and peroxide metabolism in mammalian cells

The carbon dioxide/bicarbonate (CO₂/HCO₃^-) molecular pair is ubiquitous in mammalian cells and tissues, mainly as a result of oxidative decarboxylation reactions that occur during intermediary metabolism. CO₂ is in rapid equilibrium with HCO₃^-via the hydration reaction catalyzed by carbonic anhydrases. Far from being an inert compound in redox biology, CO₂ enhances or redirects the reactivity of peroxides, modulating the velocity, extent, and type of one- and two-electron oxidation reactions mediated by hydrogen peroxide (H₂O₂) and peroxynitrite (ONOO^-/ONOOH). Herein, we review the biochemical mechanisms by which CO₂ engages in peroxide-dependent reactions, free radical production, redox signaling, and oxidative damage. First, we cover the metabolic formation of CO₂ and its connection to peroxide formation and decomposition. Next, the reaction mechanisms, kinetics, and processes by which the CO₂/peroxide interplay modulates mammalian cell redox biology are scrutinized in-depth. Importantly, CO₂ also regulates gene expression related to redox and nitric oxide metabolism and as such influences oxidative and inflammatory processes. Accumulated biochemical evidence in vitro, in cellula, and in vivo unambiguously show that the CO₂ and peroxide metabolic pathways are intertwined and together participate in key redox events in mammalian cells.

Development of 4-((3-oxo-3-phenylpropyl)amino)benzenesulfonamide derivatives utilizing tail/dual-tail approaches as novel carbonic anhydrase inhibitors

In the current work, we adopted the tail/dual tail approaches to design and synthesize the benzenesulfonamide derivatives 6a-b, 8, 10a-b, 12a-b, 14, and 16 as new SLC-0111 analogs endowed with carbonic anhydrase (CA) inhibitory activity. All the prepared benzenesulfonamide derivatives were tested for their inhibitory action towards hCA isoforms; hCA I, II, IX, and XII. The results revealed their ability to affect the examined isoforms in variable degrees with KI ranges: 49.3-6459 nM for CA I, 5.1-4171 nM for CA II, 9.4-945.1 nM for CA IX, and 5.2-1159 nM for CA XII. As expected, appending a second hydrophilic tail (ethanolamine) in compound 16 significantly enhanced the inhibitory activities towards hCA IX and hCA XII isoforms by about 5-fold in comparison to its single tail analogue 6c (KI = 51.5 and 28.2 nM for 6cvs. 10.2 and 5.2 nM for 16, respectively). Moreover, SAR analysis pointed out the significance of grafting the sulfamoyl functionality at para-position, as well as the incorporation of a bulky hydrophobic tail for CA inhibitory activity. The most potent hCA IX inhibitors (6f and 16) displayed efficient cell growth inhibitory activity against breast cancer cell lines; T-47D (IC50 = 19 and 10.9 μM, respectively) and MCF-7 (IC50 = 7.5 and 5.7 μM, respectively).

The whole-cell kinetic metabolic model of the pH regulation mechanisms in human erythrocytes

Mathematical modeling in recent years helped to obtain answers to questions that were difficult or even impossible to answer experimentally, to predict several unexpected connections in cell metabolism and to understand and importance of certain biochemical reactions. Due to the complexity and variety of processes underlying the mechanisms of intracellular pH (pHi) regulation, mathematical modeling and metabolome analysis are powerful tools for their analysis. In this regard, a mathematical metabolic model for human erythrocytes was created, which combines cellular metabolism with acid-base processes and gas exchange. The model consists of the main metabolic pathways, such as glycolysis, the pentose phosphate pathway, some membrane transport systems, and interactions between hemoglobin and metabolites. The Jacobs-Stewart cycle, which is fundamental in gas exchange and pH regulation, was included to these pathways. The model was created in the COPASI environment, consisted of 85 reactions, the rate of which is based on accurate kinetic equations. The time dependences of reaction flows and metabolite concentrations, as an outcome of calculations, allowed us to reproduce the behaviour of the metabolic system after its disturbance in vitro and to establish the recovery mechanisms or approximation to stationary states. The COPASI simulation environment provides model flexibility by reproducing any experimental design by optimizing direct quantitative comparisons between measured and predicted results. Thus, the procedure of parameters optimization (Parameter Estimation) followed by the solution of the model’s differential equations (Time Course procedure) was used to predict the behaviour of all measured and unmeasured variables over time. The initial intracellular concentrations of CO2, HCO3– in human erythrocytes used for incubation in a phosphate buffer medium were calculated. Changes in CO2, HCO3– content over time were shown. It was established that the regulation of pH in erythrocytes placed in a buffer medium takes place with the participation of two types of processes – fast (takes place in 1.3 s) and slow. It is shown that fast processes are aimed at restoring the intracellular balance between CO2 and HCO3–, slow processes are aimed at establishing the balance of H+ between the cell and the extracellular environment. The role of carbonic anhydrase (CA) and hemoglobin in the processes of pH stabilization is shown and analyzed. The physiological role of the metabolon between band 3 protein (AE1), CA, aquaporin and hemoglobin in maintaining pH homeostasis in the conditions of in vitro experiments are discussed.

Modeling surface pH measurements of oocytes

The transport of gases across cell membranes plays a key role in many different cell functions, from cell respiration to pH control. Mathematical models play a central role in understanding the factors affecting gas transport through membranes, and are the tool needed for testing the novel hypothesis of the preferential crossing through specific gas channels. Since the surface pH of cell membrane is regulated by the transport of gases such as CO₂and NH₃, inferring the membrane properties can be done indirectly from pH measurements. Numerical simulations based on recent models of the surface pH support the hypothesis that the presence of a measurement device, a liquid-membrane pH sensitive electrode on the cell surface may disturb locally the pH, leading to a systematic bias in the measured values. To take this phenomenon into account, it is necessary to equip the model with a description of the micro-environment created by the pH electrode. In this work we propose a novel, computationally lightweight numerical algorithm to simulate the surface pH data. The effect of different parameters of the model on the output are investigated through a series of numerical experiments with a physical interpretation.

Genome-Wide Association Studies and Haplotype-Sharing Analysis Targeting the Egg Production Traits in Shaoxing Duck

Age at first egg (AFE) and egg number (EN) are economically important traits related to egg production, as they directly influence the benefits of the poultry industry, but the molecular genetic research that affects those traits in laying ducks is still sparse. Our objective was to identify the genomic regions and candidate genes associated with AFE, egg production at 43 weeks (EP43w), and egg production at 66 weeks (EP66w) in a Shaoxing duck population using genome-wide association studies (GWASs) and haplotype-sharing analysis. Single-nucleotide polymorphism (SNP)-based genetic parameter estimates showed that the heritability was 0.15, 0.20, and 0.22 for AFE, EP43w, and EP66w, respectively. Subsequently, three univariate GWASs for AFE, EP43w, and EP66w were carried out independently. Twenty-four SNPs located on chromosome 25 within a 0.01-Mb region that spans from 4.511 to 4.521 Mb were associated with AFE. There are two CIs that affect EP43w, i.e., twenty-five SNPs were in strong linkage disequilibrium region spanning from 3.186 to 3.247 Mb on chromosome 25, a region spanning from 4.442 to 4.446 Mb on chromosome 25, and two interesting genes, ACAD8 and THYN1, that may affect EP43w in laying ducks. There are also two CIs that affect EP66w, i.e., a 2.412-Mb region that spans from 127.497 to 129.910 Mb on chromosome 2 and a 0.355-Mb region that spans from 4.481 to 4.837 Mb on chromosome 29, and CA2 and GAMT may be the putative candidate genes. Our study also found some haplotypes significantly associated with these three traits based on haplotype-sharing analysis. Overall, this study was the first publication of GWAS on egg production in laying ducks, and our findings will be helpful to provide some candidate genes and haplotypes to improve egg production performance based on breeding in laying duck. Additionally, we learned from a method called bootstrap test to verify the reliability of a GWAS with small experimental samples that users can access at https://github.com/xuwenwu24/Bootstrap-test.

Influence of physical training on intracellular and extracellular zinc concentrations

Background

Physical exercise affects zinc (Zn) homeostasis. This study aimed to analyze the influence of physical training on extracellular (serum, plasma, and urine) and intracellular (erythrocytes and platelets) concentrations of Zn.

Methods

Forty young men, divided into a training group (TG; n = 20; 18.15 ± 0.27 years; 68.59 ± 4.18 kg; 1.76 ± 0.04 m) and a control group (CG; n = 20; 19.25 ± 0.39 years; 73.45 ± 9.04 kg; 1.79 ± 0.06 m), participated in this study. The TG was formed by semiprofessional soccer players from a youth category with a regular training plan of 10 h/week. The CG was formed by healthy men who did not practice physical exercise and had not followed any specific training plan. Plasma, serum, urine, erythrocyte, and platelet samples of Zn were obtained and analyzed by inductively coupled plasma mass spectrometry.

Results

The TG showed elevated plasma Zn concentrations (p < 0.01) despite similar intakes. However, TG showed reduced absolute (p < 0.01) and relative (p < 0.05) Zn concentrations in erythrocytes.

Conclusions

Athletes who underwent regular physical training showed elevated plasma and reduced erythrocyte Zn concentrations despite similar intakes to the CG.

Trans-cerebral HCO3- and PCO2 exchange during acute respiratory acidosis and exercise-induced metabolic acidosis in humans

This study investigated trans-cerebral internal jugular venous-arterial bicarbonate ([HCO3-]) and carbon dioxide tension (PCO2) exchange utilizing two separate interventions to induce acidosis: 1) acute respiratory acidosis via elevations in arterial PCO2 (PaCO2) (n = 39); and 2) metabolic acidosis via incremental cycling exercise to exhaustion (n = 24). During respiratory acidosis, arterial [HCO3-] increased by 0.15 ± 0.05 mmol ⋅ l-1 per mmHg elevation in PaCO2 across a wide physiological range (35 to 60 mmHg PaCO2; P < 0.001). The narrowing of the venous-arterial [HCO3-] and PCO2 differences with respiratory acidosis were both related to the hypercapnia-induced elevations in cerebral blood flow (CBF) (both P < 0.001; subset n = 27); thus, trans-cerebral [HCO3-] exchange (CBF × venous-arterial [HCO3-] difference) was reduced indicating a shift from net release toward net uptake of [HCO3-] (P = 0.004). Arterial [HCO3-] was reduced by -0.48 ± 0.15 mmol ⋅ l-1 per nmol ⋅ l-1 increase in arterial [H+] with exercise-induced acidosis (P < 0.001). There was no relationship between the venous-arterial [HCO3-] difference and arterial [H+] with exercise-induced acidosis or CBF; therefore, trans-cerebral [HCO3-] exchange was unaltered throughout exercise when indexed against arterial [H+] or pH (P = 0.933 and P = 0.896, respectively). These results indicate that increases and decreases in systemic [HCO3-] - during acute respiratory/exercise-induced metabolic acidosis, respectively - differentially affect cerebrovascular acid-base balance (via trans-cerebral [HCO3-] exchange).

Long-term exposure of mice to 890 ppm atmospheric CO2 alters growth trajectories and elicits hyperactive behaviours in young adulthood

Atmospheric carbon dioxide (CO₂ ) levels are currently at 418 parts per million (ppm), and by 2100 may exceed 900 ppm. The biological effects of lifetime exposure to CO₂ at these levels is unknown. Previously we have shown that mouse lung function is altered by long-term exposure to 890 ppm CO₂ . Here, we assess the broader systemic physiological responses to this exposure. Mice were exposed to either 460 or 890 ppm from preconception to 3 months of age, and assessed for effects on developmental, renal and osteological parameters. Locomotor, memory, learning and anxiety-like behaviours of the mice were also assessed. Exposure to 890 ppm CO₂ increased birthweight, decreased female body weight after weaning, and, as young adults, resulted in reduced engagement in memory/learning tasks, and hyperactivity in both sexes in comparison to controls. There were no clear anxiety, learning or memory changes. Renal and osteological parameters were minimally affected. Overall, this study shows that exposure of mice to 890 ppm CO₂ from preconception to young adulthood alters growth and some behaviours, with limited evidence of compensatory changes in acid-base balance. These findings highlight the potential for a direct effect of increased atmospheric CO₂ on mammalian health outcomes. KEY POINTS: Long-term exposure to elevated levels of atmospheric CO₂ is an uncontrolled experiment already underway. This is the first known study to assess non-respiratory physiological impacts of long-term (conception to young adulthood) exposure of mice to CO₂ at levels that may arise in the atmosphere due to global emissions. Exposure to elevated CO₂ , in comparison to control mice, altered growth patterns in early life and resulted in hyperactive behaviours in young adulthood. Renal and bone parameters, which are important to balance acid-base levels to compensate for increased CO₂ exposure, remained relatively unaffected. This work adds to the body of evidence regarding the effects of carbon emissions on mammalian health and highlights a potential future burden of disease.

Carbon Dioxide Sensing-Biomedical Applications to Human Subjects

Carbon dioxide (CO2) monitoring in human subjects is of crucial importance in medical practice. Transcutaneous monitors based on the Stow-Severinghaus electrode make a good alternative to the painful and risky arterial "blood gases" sampling. Yet, such monitors are not only expensive, but also bulky and continuously drifting, requiring frequent recalibrations by trained medical staff. Aiming at finding alternatives, the full panel of CO2 measurement techniques is thoroughly reviewed. The physicochemical working principle of each sensing technique is given, as well as some typical merit criteria, advantages, and drawbacks. An overview of the main CO2 monitoring methods and sites routinely used in clinical practice is also provided, revealing their constraints and specificities. The reviewed CO2 sensing techniques are then evaluated in view of the latter clinical constraints and transcutaneous sensing coupled to a dye-based fluorescence CO2 sensing seems to offer the best potential for the development of a future non-invasive clinical CO2 monitor.

Proteomic profiling of carbonic anhydrase CA3 in skeletal muscle

INTRODUCTION

Carbonic anhydrase (CA) is a key enzyme that mediates the reversible hydration of carbon dioxide. Skeletal muscles contain high levels of the cytosolic isoform CA3. This enzyme has antioxidative function and plays a crucial role in the maintenance of intracellular pH homeostasis.

AREAS COVERED

Since elevated levels of serum CA3, often in combination with other muscle-specific proteins, are routinely used as a marker of general muscle damage, it was of interest to examine recent analyses of this enzyme carried out by modern proteomics. This review summarizes the mass spectrometry-based identification and evaluation of CA3 in normal, adapting, dystrophic, and aging skeletal muscle tissues.

EXPERT OPINION

The mass spectrometric characterization of CA3 confirmed this enzyme as a highly useful marker of both physiological and pathophysiological alterations in skeletal muscles. Cytosolic CA3 is clearly enriched in slow-twitching type I fibers, which makes it an ideal marker for studying fiber type shifting and muscle adaptations. Importantly, neuromuscular diseases feature distinct alterations in CA3 in skeletal muscle tissues versus biofluids, such as serum. Characteristic changes of CA3 in age-related muscle wasting and dystrophinopathy established this enzyme as a suitable biomarker candidate for differential diagnosis and monitoring of disease progression and therapeutic impact.

2-Aminobenzoxazole-appended coumarins as potent and selective inhibitors of tumour-associated carbonic anhydrases

We have carried out the design, synthesis, and evaluation of a small library of 2-aminobenzoxazole-appended coumarins as novel inhibitors of tumour-related CAs IX and XII. Substituents on C-3 and/or C-4 positions of the coumarin scaffold, and on the benzoxazole moiety, together with the length of the linker connecting both units were modified to obtain useful structure-activity relationships. CA inhibition studies revealed a good selectivity towards tumour-associated CAs IX and XII (K_i within the mid-nanomolar range in most of the cases) in comparison with CAs I, II, IV, and VII (K_i > 10 µM); CA IX was found to be slightly more sensitive towards structural changes. Docking calculations suggested that the coumarin scaffold might act as a prodrug, binding to the CAs in its hydrolysed form, which is in turn obtained due to the esterase activity of CAs. An increase of the tether length and of the substituents steric hindrance was found to be detrimental to in vitro antiproliferative activities. Incorporation of a chlorine atom on C-3 of the coumarin moiety achieved the strongest antiproliferative agent, with activities within the low micromolar range for the panel of tumour cell lines tested.

ZnO-based micromotors fueled by CO2: the first example of self-reorientation-induced biomimetic chemotaxis

Synthetic chemotactic micro/nanomotors are envisioned to actively ‘seek out’ targets by following specific chemicals, but they are mainly powered by bioincompatible fuels and only show pseudochemotaxis (or advanced chemokinesis) due to their weak self-reorientation capabilities. Here we demonstrate that synthetic ZnO-based Janus micromotors can be powered by the alternative biocompatible fuel of CO₂, and further provide the first example of self-reorientation-induced biomimetic chemotaxis using them. The ZnO-based micromotors are highly sensitive to dissolved CO₂ in water, which enables the corrosion of ZnO to continuously occur by providing H⁺ through hydration. Thus, they can autonomously move even in water exposed to air based on self-diffusiophoresis. Furthermore, they can sense the local CO₂ gradient and perform positive chemotaxis by self-reorientations under the phoretic torque. Our discovery opens a gate to developing intelligent micro/nanomotors powered by, and sensitive to, biocompatible atmospheric or endogenous gaseous chemicals for biomedical and environmental applications.

Non-invasive carbon dioxide monitoring in neonates: methods, benefits, and pitfalls

Wide fluctuations in partial pressure of carbon dioxide (PaCO2) can potentially be associated with neurological and lung injury in neonates. Blood gas measurement is the gold standard for assessing gas exchange but is intermittent, invasive, and contributes to iatrogenic blood loss. Non-invasive carbon dioxide (CO2) monitoring has become ubiquitous in anesthesia and critical care and is being increasingly used in neonates. Two common methods of non-invasive CO2 monitoring are end-tidal and transcutaneous. A colorimetric CO2 detector (a modified end-tidal CO2 detector) is recommended by the International Liaison Committee on Resuscitation (ILCOR) and the American Academy of Pediatrics to confirm endotracheal tube placement. Continuous CO2 monitoring is helpful in trending PaCO2 in critically ill neonates on respiratory support and can potentially lead to early detection and minimization of fluctuations in PaCO2. This review includes a description of the various types of CO2 monitoring and their applications, benefits, and limitations in neonates.

Cell Physiology and Molecular Mechanism of Anion Transport by Erythrocyte Band 3/AE1

The major transmembrane protein of the red blood cell, known as band 3, AE1, and SLC4A1, has two main functions: 1) catalysis of Cl^-/HCO₃^- exchange, one of the steps in CO₂ excretion; 2) anchoring the membrane skeleton. This review summarizes the 150 year history of research on red cell anion transport and band 3 as an experimental system for studying membrane protein structure and ion transport mechanisms. Important early findings were that red cell Cl^- transport is a tightly coupled 1:1 exchange and band 3 is labeled by stilbenesulfonate derivatives that inhibit anion transport. Biochemical studies showed that the protein is dimeric or tetrameric (paired dimers) and that there is one stilbenedisulfonate binding site per subunit of the dimer. Transport kinetics and inhibitor characteristics supported the idea that the transporter acts by an alternating access mechanism with intrinsic asymmetry. The sequence of band 3 cDNA provided a framework for detailed study of protein topology and amino acid residues important for transport. The identification of genetic variants produced insights into the roles of band 3 in red cell abnormalities and distal renal tubular acidosis. The publication of the membrane domain crystal structure made it possible to propose concrete molecular models of transport. Future research directions include improving our understanding of the transport mechanism at the molecular level and of the integrative relationships among band 3, hemoglobin, carbonic anhydrase, and gradients (both transmembrane and subcellular) of HCO₃^-, Cl^-, O₂, CO₂, pH, and NO metabolites during pulmonary and systemic capillary gas exchange.

Pathophysiology and clinical implications of the veno-arterial PCO2 gap

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2021. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2021 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .