In vivo urea cycle flux distinguishes and correlates with phenotypic severity in disorders of the urea cycle

Impact of the delay in cryopreservation timing during biobanking procedures on human liver tissue metabolomics

The liver is a highly specialized organ involved in regulating systemic metabolism. Understanding metabolic reprogramming of liver disease is key in discovering clinical biomarkers, which relies on robust tissue biobanks. However, sample collection and storage procedures pose a threat to obtaining reliable results, as metabolic alterations may occur during sample handling. This study aimed to elucidate the impact of pre-analytical delay during liver resection surgery on liver tissue metabolomics. Patients were enrolled for liver resection during which normal tissue was collected and snap-frozen at three timepoints: before transection, after transection, and after analysis in Pathology. Metabolomics analyses were performed using 1H Nuclear Magnetic Resonance (NMR) and Liquid Chromatography-Mass Spectrometry (LC-MS). Time at cryopreservation was the principal variable contributing to differences between liver specimen metabolomes, which superseded even interindividual variability. NMR revealed global changes in the abundance of an array of metabolites, namely a decrease in most metabolites and an increase in β-glucose and lactate. LC-MS revealed that succinate, alanine, glutamine, arginine, leucine, glycerol-3-phosphate, lactate, AMP, glutathione, and NADP were enhanced during cryopreservation delay (all p<0.05), whereas aspartate, iso(citrate), ADP, and ATP, decreased (all p<0.05). Cryopreservation delays occurring during liver tissue biobanking significantly alter an array of metabolites. Indeed, such alterations compromise the integrity of metabolomic data from liver specimens, underlining the importance of standardized protocols for tissue biobanking in hepatology.

Self-adhesive, surface adaptive, regenerable SERS substrates for in-situ detection of urea on bio-surfaces

Wearable SERS substrates have gained substantial attention for health monitoring and other applications. Current designs often rely on conventional polymer substrates, leading to discomfort and complexity due to the need of additional adhesive layers. To address the issues, we fabricate a flexible, uniform, ultrathin, transparent and porous SERS substrate via depositing Ag nanoparticles (AgNPs) onto the CdS nanowires (CdSNWs) grown on the surface of a prepared nanofilm (AgNPs-CdSNWs/nanofilm). Unlike the wearable SERS substrates reported in literature, the one presented in this work is self-adhesive to a variety of surfaces, which simplifies structure, enhances comfort and improves performance. Importantly, the new SERS substrate as developed is highly stable and reusable. Artificial sample tests revealed that the substrate showed a great enhancement factor (EF) of 4.2 × 107 and achieved a remarkable detection limit (DL) of 1.0 × 10-14 M for rhodamine 6G (R6G), which are among the highest records observed in wearable SERS substrates reported in literature. Moreover, the substrate enables at real-time and in-situ reliable monitoring of urea dynamics in human sweat and plant leaves, indicating its applicability for health analysis and in precision agriculture.

Flux analysis of inborn errors of metabolism

Patients with an inborn error of metabolism (IEM) are deficient of an enzyme involved in metabolism, and as a consequence metabolism reprograms itself to reach a new steady state. This new steady state underlies the clinical phenotype associated with the deficiency. Hence, we need to know the flux of metabolites through the different metabolic pathways in this new steady state of the reprogrammed metabolism. Stable isotope technology is best suited to study this. In this review the progress made in characterizing the altered metabolism will be presented. Studies done in patients to estimate the residual flux through the metabolic pathway affected by enzyme deficiencies will be discussed. After this, studies done in model systems will be reviewed. The focus will be on glycogen storage disease type I, medium-chain acyl-CoA dehydrogenase deficiency, propionic and methylmalonic aciduria, urea cycle defects, phenylketonuria, and combined D,L-2-hydroxyglutaric aciduria. Finally, new developments are discussed, which allow the tracing of metabolic reprogramming in IEM on a genome-wide scale. In conclusion, the outlook for flux analysis of metabolic derangement in IEMs looks promising.

Stable isotope compounds - production, detection, and application

Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.

Targeting CPS1 in the treatment of Carbamoyl phosphate synthetase 1 (CPS1) deficiency, a urea cycle disorder

INTRODUCTION

Carbamoyl phosphate synthetase 1 (CPS1) deficiency (CPS1D) is a rare autosomal recessive urea cycle disorder (UCD), which can lead to life-threatening hyperammonemia. Unless promptly treated, it can result in encephalopathy, coma and death, or intellectual disability in surviving patients. Over recent decades, therapies for CPS1D have barely improved leaving the management of these patients largely unchanged. Additionally, in many cases, current management (protein-restriction and supplementation with citrulline and/or arginine and ammonia scavengers) is insufficient for achieving metabolic stability, highlighting the importance of developing alternative therapeutic approaches. Areas covered: After describing UCDs and CPS1D, we give an overview of the structure- function of CPS1. We then describe current management and potential novel treatments including N-carbamoyl-L-glutamate (NCG), pharmacological chaperones, and gene therapy to treat hyperammonemia. Expert opinion: Probably, the first novel CPS1D therapies to reach the clinics will be the already commercial substance NCG, which is the standard treatment for N-acetylglutamate synthase deficiency and has been proven to rescue specific CPS1D mutations. Pharmacological chaperones and gene therapy are under development too, but these two technologies still have key challenges to be overcome. In addition, current experimental therapies will hopefully add further treatment options.

In vivo monitoring of urea cycle activity with (13)C-acetate as a tracer of ureagenesis

BACKGROUND

The hepatic urea cycle is the main metabolic pathway for detoxification of ammonia. Inborn errors of urea cycle function present with severe hyperammonemia and a high case fatality rate. Long-term prognosis depends on the residual activity of the defective enzyme. A reliable method to estimate urea cycle activity in-vivo does not exist yet. The aim of this study was to evaluate a practical method to quantify (13)C-urea production as a marker for urea cycle function in healthy subjects, patients with confirmed urea cycle defect (UCD) and asymptomatic carriers of UCD mutations.

METHODS

(13)C-labeled sodium acetate was applied orally in a single dose to 47 subjects (10 healthy subjects, 28 symptomatic patients, 9 asymptomatic carriers).

RESULTS

The oral (13)C-ureagenesis assay is a safe method. While healthy subjects and asymptomatic carriers did not differ with regards to kinetic variables for urea cycle flux, symptomatic patients had lower (13)C-plasma urea levels. Although the (13)C-ureagenesis assay revealed no significant differences between individual urea cycle enzyme defects, it reflected the heterogeneity between different clinical subgroups, including male neonatal onset ornithine carbamoyltransferase deficiency. Applying the (13)C-urea area under the curve can differentiate between severe from more mildly affected neonates. Late onset patients differ significantly from neonates, carriers and healthy subjects.

CONCLUSION

This study evaluated the oral (13)C-ureagenesis assay as a sensitive in-vivo measure for ureagenesis capacity. The assay has the potential to become a reliable tool to differentiate UCD patient subgroups, follow changes in ureagenesis capacity and could be helpful in monitoring novel therapies of UCD.

Understanding strategy of nitrate and urea assimilation in a Chinese strain of Aureococcus anophagefferens through RNA-seq analysis

Aureococcus anophagefferens is a harmful alga that dominates plankton communities during brown tides in North America, Africa, and Asia. Here, RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. The number of differentially expressed genes between urea-grown and mixture N-grown cells were much less than those between urea-grown and nitrate-grown cells. Compared with nitrate-grown cells, mixture N-grown cells contained much lower levels of transcripts encoding proteins that are involved in nitrate transport and assimilation. Together with profiles of nutrient changes in media, these results suggest that A. anophagefferens primarily feeds on urea instead of nitrate when urea and nitrate co-exist. Furthermore, we noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid and nucleotide transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source.

Natural isotopic signatures of variations in body nitrogen fluxes: a compartmental model analysis

Body tissues are generally ¹⁵N-enriched over the diet, with a discrimination factor (Δ¹⁵N) that varies among tissues and individuals as a function of their nutritional and physiopathological condition. However, both ¹⁵N bioaccumulation and intra- and inter-individual Δ¹⁵N variations are still poorly understood, so that theoretical models are required to understand their underlying mechanisms. Using experimental Δ¹⁵N measurements in rats, we developed a multi-compartmental model that provides the first detailed representation of the complex functioning of the body's Δ¹⁵N system, by explicitly linking the sizes and Δ¹⁵N values of 21 nitrogen pools to the rates and isotope effects of 49 nitrogen metabolic fluxes. We have shown that (i) besides urea production, several metabolic pathways (e.g., protein synthesis, amino acid intracellular metabolism, urea recycling and intestinal absorption or secretion) are most probably associated with isotope fractionation and together contribute to ¹⁵N accumulation in tissues, (ii) the Δ¹⁵N of a tissue at steady-state is not affected by variations of its P turnover rate, but can vary according to the relative orientation of tissue free amino acids towards oxidation vs. protein synthesis, (iii) at the whole-body level, Δ¹⁵N variations result from variations in the body partitioning of nitrogen fluxes (e.g., urea production, urea recycling and amino acid exchanges), with or without changes in nitrogen balance, (iv) any deviation from the optimal amino acid intake, in terms of both quality and quantity, causes a global rise in tissue Δ¹⁵N, and (v) Δ¹⁵N variations differ between tissues depending on the metabolic changes involved, which can therefore be identified using simultaneous multi-tissue Δ¹⁵N measurements. This work provides proof of concept that Δ¹⁵N measurements constitute a new promising tool to investigate how metabolic fluxes are nutritionally or physiopathologically reorganized or altered. The existence of such natural and interpretable isotopic biomarkers promises interesting applications in nutrition and health.

Body proteins ensure vital functions, and their constancy is maintained through the tight coordination of many nitrogen metabolic fluxes, but our understanding of how this flux system is regulated, and sometimes dysregulated, remains fragmentary and incomplete. Besides, body tissues are generally naturally enriched in the heavier stable nitrogen isotope (¹⁵N) over the diet: this ¹⁵N bioaccumulation (Δ¹⁵N) varies depending on tissues and metabolic orientations, likely as the result of isotope effects associated to some metabolic pathways. We used a novel approach, combining multi-tissue Δ¹⁵N measurements and their analysis using modeling, to understand how body Δ¹⁵N values relate to nitrogen fluxes. The multi-tissue model we have developed provides a clearer understanding of the metabolic processes that generate isotopic fractionation, and of how tissue Δ¹⁵N values are modulated in response to changes in the body distribution of specific nitrogen fluxes. We show that Δ¹⁵N values tend to rise when the amino acids intake does not optimally fit the metabolic demand, and that Δ¹⁵N values constitute natural and interpretable signatures of nutritionally-induced variations in nitrogen fluxes. This approach constitutes a new promising tool to investigate how nitrogen metabolism is nutritionally or physiopathologically reorganized or altered, and promises interesting applications in many areas (nutrition, pathology, ecology, paleontology, etc).

Fast reconstruction of compact context-specific metabolic network models

Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for fast algorithms. We present fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that are known to be active in the context of interest (e.g., cell or tissue), and it searches for a flux consistent subnetwork of the global network that contains all reactions from the core set and a minimal set of additional reactions. Our key observation is that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network, and fastcore iteratively computes such a set via a series of linear programs. Experiments on liver data demonstrate speedups of several orders of magnitude, and significantly more compact reconstructions, over a rival method. Given its simplicity and its excellent performance, fastcore can form the backbone of many future metabolic network reconstruction algorithms.

Chloroplast-mitochondria cross-talk in diatoms

Diatoms are unicellular, mainly photosynthetic, eukaryotes living within elaborate silicified cell walls and believed to be responsible for around 40% of global primary productivity in the oceans. Their abundance in aquatic ecosystems is such that they have on different occasions been described as the insects, the weeds, or the cancer cells of the ocean. In contrast to higher plants and green algae which derive from a primary endosymbiosis, diatoms are now believed to originate from a serial secondary endosymbiosis involving both green and red algae and a heterotrophic exosymbiont host. As a consequence of their dynamic evolutionary history, they appear to have red algal-derived chloroplasts empowered largely by green algal proteins, working alongside mitochondria derived from the non-photosynthetic exosymbiont. This review will discuss the evidence for such an unusual assemblage of organelles in diatoms, and will present the evidence implying that it has enabled them with unorthodox metabolisms that may have contributed to their profound ecological success.

Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism

The first computational approach for the rapid generation of genome-scale tissue-specific models from a generic species model.

A genome scale model of human liver metabolism, which is comprehensively tested and validated using cross-validation and the ability to carry out complex hepatic metabolic functions.

The model's flux predictions are shown to correlate with flux measurements across a variety of hormonal and dietary conditions, and are successfully used to predict biomarker changes in genetic metabolic disorders, both with higher accuracy than the generic human model.

The study of normal human metabolism and its alterations is central to the understanding and treatment of a variety of human diseases, including diabetes, metabolic syndrome, neurodegenerative disorders, and cancer. A promising systems biology approach for studying human metabolism is through the development and analysis of large-scale stoichiometric network models of human metabolism. The reconstruction of these network models has followed two main paths: the former being the reconstruction of generic (non-tissue specific) models, characterizing the complete metabolic potential of human cells, based mostly on genomic data to trace enzyme-coding genes (Duarte et al, 2007; Ma et al, 2007), and the latter is the reconstruction of cell type- and tissue-specific models (Wiback and Palsson, 2002; Chatziioannou et al, 2003; Vo et al, 2004), based on a similar methodology to that described above, with the extra complexity of manual curation of literature evidence for the cell/system specificity of metabolic enzymes and pathways.

On this background, we present in this study, to the best of our knowledge, the first computational approach for a rapid generation of genome-scale tissue-specific models. The method relies on integrating the previously reconstructed generic human models with a variety of high-throughput molecular ‘omics' data, including transcriptomic, proteomic, metabolomic, and phenotypic data, as well as literature-based knowledge, characterizing the tissue in hand (Figure 1). Hence, it can be readily used to quite rapidly build and use a large array of human tissue-specific models. The resulting model satisfies stoichiometric, mass-balance, and thermodynamic constraints. It serves as a functional metabolic network that can then be used to explore the metabolic state of a tissue under various genetic and physiological conditions, simulating enzymatic inhibition or drug applications through standard constraint-based modeling methods, without requiring additional context-specific molecular data.

We applied this approach to build a genome scale model of liver metabolism, which is then comprehensively tested and validated. The model is shown to be able to simulate complex hepatic metabolic functions, as well as depicting the pathological alterations caused by urea cycle deficiencies. The liver model was applied to predict measured intra-cellular metabolic fluxes given measured metabolite uptake and secretion rates at different hepatic metabolic conditions. The predictions were tested using a comprehensive set of flux measurements performed by (Chan et al, 2003), showing that the liver model obtained more accurate predictions compared to those obtained by the original, generic human model (an overall prediction accuracy of 0.67 versus 0.46). Furthermore, it was applied to identify metabolic biomarkers for liver in-born errors of metabolism—once again, displaying superiority vs. the predictions generated by the generic human model (accuracy of 0.67 versus 0.59).

From a biotechnological standpoint, the liver model generated here can serve as a basis for future studies aiming to optimize the functioning of bio artificial liver devices. The application of the method to rapidly construct metabolic models of other human tissues can obviously lead to many other important clinical insights, e.g., concerning means for metabolic salvage of ischemic heart and brain tissues. Last but not least, the application of the new method is not limited to the realm of human modeling; it can be used to generate tissue models for any multi-tissue organism for which a generic model exists, such as the Mus musculus (Quek and Nielsen, 2008; Sheikh et al, 2005) and the model plant Arabidopsis thaliana (Poolman et al, 2009).

The computational study of human metabolism has been advanced with the advent of the first generic (non-tissue specific) stoichiometric model of human metabolism. In this study, we present a new algorithm for rapid reconstruction of tissue-specific genome-scale models of human metabolism. The algorithm generates a tissue-specific model from the generic human model by integrating a variety of tissue-specific molecular data sources, including literature-based knowledge, transcriptomic, proteomic, metabolomic and phenotypic data. Applying the algorithm, we constructed the first genome-scale stoichiometric model of hepatic metabolism. The model is verified using standard cross-validation procedures, and through its ability to carry out hepatic metabolic functions. The model's flux predictions correlate with flux measurements across a variety of hormonal and dietary conditions, and improve upon the predictive performance obtained using the original, generic human model (prediction accuracy of 0.67 versus 0.46). Finally, the model better predicts biomarker changes in genetic metabolic disorders than the generic human model (accuracy of 0.67 versus 0.59). The approach presented can be used to construct other human tissue-specific models, and be applied to other organisms.

Measuring in vivo ureagenesis with stable isotopes

Stable isotopes have been an invaluable adjunct to biomedical research for more than 70years. Indeed, the isotopic approach has revolutionized our understanding of metabolism, revealing it to be an intensely dynamic process characterized by an unending cycle of synthesis and degradation. Isotopic studies have taught us that the urea cycle is intrinsic to such dynamism, since it affords a capacious mechanism by which to eliminate waste nitrogen when rates of protein degradation (or dietary protein intake) are especially high. Isotopes have enabled an appreciation of the degree to which ureagenesis is compromised in patients with urea cycle defects. Indeed, isotopic studies of urea cycle flux correlate well with the severity of cognitive impairment in these patients. Finally, the use of isotopes affords an ideal tool with which to gauge the efficacy of therapeutic interventions to augment residual flux through the cycle.

New insights in nutritional management and amino acid supplementation in urea cycle disorders

Sodium phenylbutyrate is used in the pharmacological treatment of urea cycle disorders to create alternative pathways for nitrogen excretion. The primary metabolite, phenylacetate, conjugates glutamine in the liver and kidney to form phenylacetylglutamine that is readily excreted in the urine. Patients with urea cycle disorders taking sodium phenylbutyrate have a selective reduction in the plasma concentrations of branched chain amino acids despite adequate dietary protein intake. Moreover, this depletion is usually the harbinger of a metabolic crisis. Plasma branched chain amino acids and other essential amino acids were measured in control subjects, untreated ornithine transcarbamylase deficiency females, and treated patients with urea cycle disorders (ornithine transcarbamylase deficiency and argininosuccinate synthetase deficiency) in the absorptive state during the course of stable isotope studies. Branched chain amino acid levels were significantly lower in treated patients with urea cycle disorders when compared to untreated ornithine transcarbamylase deficiency females or control subjects. These results were replicated in control subjects who had low steady-state branched chain amino acid levels when treated with sodium phenylbutyrate. These studies suggested that alternative pathway therapy with sodium phenylbutyrate causes a substantial impact on the metabolism of branched chain amino acids in patients with urea cycle disorders, implying that better titration of protein restriction can be achieved with branched chain amino acid supplementation in these patients who are on alternative pathway therapy.

Contiguous gene deletion syndrome in a female with ornithine transcarbamylase deficiency

OTC deficiency, a partially dominant X-linked trait, is the most frequent inborn error of the urea cycle. We describe a female patient with a contiguous gene deletion syndrome encompassing the OTC, DMD, RPGR, CYBB and XK genes, amongst others, only manifesting features of OTC deficiency. Molecular characterization was ascertained by MLPA and confirmed by CGH microarray, which revealed an 8.7 Mb deletion of the X-chromosome. Complete de novo deletion of the OTC gene led to a severe clinical phenotype in the proband. The application of high resolution molecular genetic techniques such as MLPA and array CGH, in mutation negative OTC cases allows the identification of chromosomal rearrangements, such as large deletions and provides information for accurate genetic counseling and prenatal diagnosis.

Effects of a single dose of N-carbamylglutamate on the rate of ureagenesis

We studied the effect on ureagenesis of a single dose of N-carbamylglutamate (NCG) in healthy young adults who received a constant infusion (300 min) of NaH(13)CO(3). Isotope ratio-mass spectrometry was used to measure the appearance of label in [(13)C]urea. At 90 min after initiating the H(13)CO3-infusion each subject took a single dose of NCG (50 mg/kg). In 5/6 studies the administration of NCG increased the formation of [(13)C]urea. Treatment with NCG significantly diminished the concentration of blood alanine, but not that of glutamine or arginine. The blood glucose concentration was unaffected by NCG administration. No untoward side effects were observed. The data indicate that treatment with NCG stimulates ureagenesis and could be useful in clinical settings of acute hyperammonemia of various etiologies.

Liver cell transplantation: basic investigations for safe application in infants and small children

Liver cell transplantation (LCT) is a very promising method for the use in pediatric patients. It is significantly less invasive than whole organ transplantation, but has the potential to cure or at least to substantially improve severe disorders like inborn errors of metabolism or acute liver failure. Prior to a widespread use of the technique in children, some important issues regarding safety and efficacy must be addressed. We developed a mathematical model to estimate total hepatocyte counts in relation to bodyweight to make possible more appropriate dose calculations. Different liver cell suspensions were studied at different flow rates and different catheter sizes to determine mechanical damage of cells by shear forces. At moderate flow rates, no significant loss of viability was observed even at a catheter diameter of 4.2F. Addition of heparin to the cell suspension is favored, which is in contrast to previous animal experiments. Mitochondrial function of the hepatocytes was determined with the WST-1 assay and was not substantially altered by cryopreservation. We conclude that especially with the use of small catheters, human LCT should be safe and efficient even in small infants and neonates.

Systemic hypertension in two patients with ASL deficiency: a result of nitric oxide deficiency?

Argininosuccinic aciduria (ASA) is an inborn error of ureagenesis which if untreated leads to hyperammonemia, accumulation of argininosuccinic acid and arginine depletion. The presence of high blood pressure in patients with ASA has been reported so far as transient in one newborn. We describe the first two patients, one child and one young adult, with ASA and persistent systemic hypertension. Extensive evaluation of both patients excluded secondary causes of systemic hypertension. The intriguing link between nitric oxide (NO) production and hypertension lead us to hypothesize that the deficiency of endogenously synthesized arginine caused by ASL deficiency is responsible for the increased blood pressure.

Ammonia toxicity and its prevention in inherited defects of the urea cycle

The urea cycle is the final pathway for removal of surplus nitrogen from the body, and the major route in humans for detoxification of ammonia. The full complement of enzymes is expressed only in liver. Inherited deficiencies of urea cycle enzymes lead to hyperammonaemia, which causes brain damage. Severe defects present with hyperammonaemic crises in neonates. Equally devastating episodes may occur in previously asymptomatic adults with mild defects, most often X-linked ornithine transcarbamylase (OTC) deficiency. Several mechanisms probably contribute to pathogenesis. Treatment aims to reduce plasma ammonia quickly, reduce production of waste nitrogen, dispose of waste nitrogen using alternative pathways to the urea cycle and replace arginine. These therapies have increased survival and probably improve the neurological outcome. Arginine, sodium benzoate, sodium phenylbutyrate and, less often, sodium phenylacetate are used. Long-term correction is achieved by liver transplantation. Gene therapy for OTC deficiency is effective in animals, and work is ongoing to improve persistence and safety.

Study of serum argininosuccinate lyase determination for diagnosis of liver diseases

The objectives of this research were to establish an automatic analysis method for the determination of serum argininosuccinate lyase (ASL) and to investigate the value of serum ASL test in the diagnosis of various liver disorders. According to the chemical reaction catalyzed by ASL, an enzyme-coupled reaction system was designed, and a methodology evaluation of this method was performed. A total of 291 patients with various liver diseases, 247 patients with nonliver disease and 32 healthy controls, were recruited, their serum levels of ASL and traditional hepatopathy markers, including alanine aminotransferase (ALT), aspartate aminotransferase (AST), gamma-glutamyltransferase (GGT), lactate dehydrogenase (LDH), alkaline phosphatase (ALP), and total bilirubin (TBil), were all determined, and their diagnostic values in liver diseases were analyzed and compared. Liver biopsy and the score of histopathological inflammation grading were performed in 31 patients with hepatopathy to explore the correlation between serum ASL level and hepatic histopathological change. A continuous monitoring assay method of serum ASL activity was established, which could be performed with automatic biochemistry analyzer. Methodological evaluation exhibited that the precision of this method was good indicated by the 4.0% intraassay coefficient of variation (CV), and 5.9% interassay CV. The mean recovery was 100.5%, linear range was from 0 to 167.7 U/L, and the lowest detection limit was approximately 0 U/L. All of the tested hepatopathy markers listed above were significantly increased in the liver disease group. However, levels of traditional markers of hepatopathy were all significantly increased at different degrees (all P<0.001) in patients with nonliver diseases; in contrast, there were no significantly increased ASL levels in all non-hepatopathy groups (P=0.335). The receiver operating characteristic (ROC) curve showed that the sensitivity and specificity of ASL were 100% and 91.1% (cutoff value=8 U/L), respectively, in the assessment of liver diseases. In contrast, ALT levels were 97.6% and 24.7%, and AST levels were 83.8% and 28.3% (both cutoff values=40.0 U/L), respectively. A positive correlation (r=0.417, P=0.019) was observed between serum ASL levels (86.9+/-26.5) and scores of histopathological inflammation grading (SHIG) (9.83+/-3.36). The sensitivity and specificity of ALS is much higher than that of ALT and AST for the diagnosis of liver diseases. ASL may be a more valuable marker for estimating hepatopathy.

New indications and controversies in arginine therapy

Arginine is an important, versatile and a conditionally essential amino acid. Besides serving as a building block for tissue proteins, arginine plays a critical role in ammonia detoxification, and nitric oxide and creatine production. Arginine supplementation is an essential component for the treatment of urea cycle defects but recently some reservations have been raised with regards to the doses used in the treatment regimens of these disorders. In recent years, arginine supplementation or restriction has been proposed and trialled in several disorders, including vascular diseases and asthma, mitochondrial encephalopathy lactic acidosis and stroke-like episodes (MELAS), glutaric aciduria type I and disorders of creatine metabolism, both production and transportation into the central nervous system. Herein we present new therapeutic indications and controversies surrounding arginine supplementation or deprivation.

Liver cell transplantation for the treatment of inborn errors of metabolism

Over the last 15 years, liver cell transplantation (LCT) has developed from an experimental laboratory technique to a potentially life-saving therapeutic option. Because of its minimally invasive nature, the method is especially attractive for (small) children. In children with liver-based inborn errors of metabolism, this transfer of enzyme activity can be regarded as a gene therapy, which can be installed independently and additionally to conservative treatment concepts. To date 14 children with inherited metabolic diseases have undergone LCT in various centres. Although individual results are encouraging, different treatment protocols, difficulties in the objective assessment of function of the transplant, and finally the lack of a controlled study make it difficult to judge the overall significance of LCT in the treatment of metabolic diseases and call for collaborative clinical research.

Interaction between murine spf-ash mutation and genetic background yields different metabolic phenotypes

The spf-ash mutation in mice results in reduced hepatic and intestinal ornithine transcarbamylase. However, a reduction in enzyme activity only translates in reduced ureagenesis and hyperammonemia when an unbalanced nitrogen load is imposed. Six-week-old wild-type control and spf-ash mutant male mice from different genetic backgrounds (B6 and ICR) were infused intravenously with [(13)C(18)O]urea, l-[(15)N(2)]arginine, l-[5,5 D(2)]ornithine, l-[6-(13)C, 4,4,5,5, D(4)]citrulline, and l-[ring-D(5)]phenylalanine to investigate the interaction between genetic background and spf-ash mutation on ureagenesis, arginine metabolism, and nitric oxide production. ICR(spf-ash) mice maintained ureagenesis (5.5 +/- 0.3 mmol.kg(-1).h(-1)) and developed mild hyperammonemia (145 +/- 19 micromol/l) when an unbalanced nitrogen load was imposed; however, B6(spf-ash) mice became hyperammonemic (671 +/- 15 micromol/l) due to compromised ureagenesis (3.4 +/- 0.1 mmol.kg(-1).h(-1)). Ornithine supplementation restored ureagenesis and mitigated hyperammonemia. A reduction in citrulline entry rate was observed due to the mutation in both genetic backgrounds (wild-type: 128, spf-ash: 60; SE 4.0 micromol.kg(-1).h(-1)). Arginine entry rate was only reduced in B6(spf-ash) mice (B6(spf-ash): 332, ICR(spf-ash): 453; SE 20.6 micromol.kg(-1).h(-1)). Genetic background and mutation had an effect on nitric oxide production (B6: 3.4, B6(spf-ash): 2.8, ICR: 9.0, ICR(spf-ash): 4.6, SE 0.7 micromol.kg(-1).h(-1)). Protein breakdown was the main source of arginine during the postabsorptive state and was higher in ICR(spf-ash) than in B6(spf-ash) mice (phenylalanine entry rate 479 and 327, respectively; SE 18 micromol.kg(-1).h(-1)). Our results highlight the importance of the interaction between mutation and genetic background on ureagenesis, arginine metabolism, and nitric oxide production. These observations help explain the wide phenotypic variation of ornithine transcarbamylase deficiency in the human population.

Heritability of plasma amino acid levels in different nutritional states

Significant heritability has been shown for several plasma amino acid levels, but the results may have been confounded by sampling in a variety of nutritional states. We studied a group of families on a low protein steady-state diet in fasting and non-fasting states. Heritability of individual amino acids varied according to the nutritional state, suggesting the amount of genetic and environmental influences differ among the operative systems that control individual amino acid homeostasis throughout the feed/fast cycle.

Inborn errors of metabolism: the flux from Mendelian to complex diseases

Inborn errors of metabolism are characterized by dysregulation of the metabolic networks that underlie development and homeostasis, and constitute an important and expanding group of genetic disorders in humans. Diagnostic methods that are based on molecular genetic tools have a limited ability to correlate phenotypes with subtle changes in metabolic fluxes. We argue that the direct and dynamic measurement of metabolite flux will facilitate the integration of environmental, genetic and biochemical factors with phenotypic information. Ultimately, this integration will lead to new diagnostic and therapeutic approaches that are focused on the manipulation of these pathways.

Hyperammonemia increases sensitivity to LPS

Metabolic and cognitive alterations occur during hyperammonemia. Here, we report that chronic hyperammonemia also leads to increased sensitivity to LPS. Sparse-fur mice were challenged i.p. with LPS or saline control and then tested for motivation to investigate a novel juvenile over 24 h. Cytokine, ammonia, and urea concentration were quantified at the peak of sickness (2 h post injection). Chronic hyperammonemic Otc(spf-ash) mice displayed more pronounced and prolonged sickness behavior in response to LPS (P=0.02). LPS significantly (P<0.0001) increased plasma concentrations of TNFalpha, IL-1 beta, IL-6, IL-15, IL-9, IL-2, IL-1 alpha, IL-1 beta, Rantes, MIP1 alpha, MIP1 beta, MCP-1, KC, GM-CSF, G-CSF, Eotaxin, IL-13, and IL-12 in both wild type and Otc(spf-ash) mice. No significant genotype/treatment interactions (P>0.1) were detected for any cytokine. Adult Otc(spf-ash) mice (168+/-41 microM) had four times higher plasma ammonia compared to wild type mice (40 +/- 6 microM) (P=0.002). Two hours after LPS injection, plasma ammonia concentrations tended (P=0.08) to decrease in both wild type and Otc(spf-ash) mice. Learning and memory behaviors were assessed in mice under basal conditions to determine the impact of chronic hyperammonemia on cognition. Otc(spf-ash) mice performed significantly poorer in the two trial Y-maze (P=0.02) and the Morris water maze (P=0.001) than their littermate wild type controls. Taken together, these data indicate that chronic hyperammonemia results in impaired cognition and creates a state of LPS hypersensitivity.

Genetic counseling issues in urea cycle disorders

The goal of counseling families that have a urea cycle disorder (UCD) is to facilitate the process of scientific understanding, emotional acceptance, and decision-making in a nondirective way. A proper understanding of the genes involved, inheritance patterns, available testing, and complicating factors is critical to serving the families' needs. This article summarizes the needed information, in particular describing the complexities of prenatal testing and counseling issues for each UCD. Included case histories illustrate the genetic counseling process and the decision-making scenarios for two families.

In vivo urea kinetic studies in conscious mice

Stable isotope studies in conscious mice have been limited by the invasive catheterization procedures and relatively large sample size required. We developed minimally invasive catheterization protocols that together with the ability to analyze small samples have allowed for the study of urea kinetics in conscious mice. A single dose of 15N15N-urea followed by multiple sampling in mice (n = 6) showed that a primary pool of urea exchanged rapidly [70.65 +/- 14.96 mmol/(kg x h)] with a secondary pool. The urea entry rate determined with this protocol was 3.36 +/- 0.30 mmol/(kg x h). Continuous infusion of 15N15N-urea (n = 6) achieved plateau enrichment values at 3.3 +/- 0.2.h from which the urea entry rate was determined by isotope dilution [3.24 +/- 0.23 mmol/(kg x h)]. The urea entry rate measured by the single dose or continuous infusion protocol did not differ (P = 0.76). The minimally invasive methods described allow us to study not only ureagenesis and urea cycle disorders in vivo, but also urea transport and transporter function and nitrogen metabolism in general in mouse models. This is especially relevant because mouse targeting technologies will likely facilitate the generation of organ and tissue specific nulls of the various urea cycle enzymes.

Considerations in the Difficult-to-Manage Urea Cycle Disorder Patient

Today, patients with urea cycle disorder (UCD) may survive well beyond infancy. The goal of keeping them in consistent nitrogen balance can be undermined by changing metabolic needs throughout various stages of life, resulting in hyperammonemia in the short term, and poor growth and development in the long term. The specific UCD genotype can affect the risk of metabolic destabilization and management difficulties, as can variable protein tolerance secondary to changing growth demands, biochemical complications, and environmental influences. Preventing catabolic stress is as important as controlling dietary protein intake for avoiding metabolic decompensation. Optimal treatment, specifically pharmacologic therapy, possible branched chain amino acid (BCAA) supplementation, accurate laboratory monitoring, and psychosocial support, requires thorough understanding and careful application of each component.

Hyperargininemia due to liver arginase deficiency

The urea cycle is a series of six reactions necessary to rid the body of the nitrogen generated by the metabolism, primarily of amino acids, from the diet or released as the result of endogenous protein catabolism. Arginase is the sixth and final enzyme of this cycle. Arginase catalyzes the conversion of arginine to urea and ornithine, the latter recycled to continue the cycle. Hyperargininemia due to arginase deficiency is inherited in an autosomal recessive manner and gene for arginase, designated AI, has been cloned. Unlike the other urea cycle enzymes, a second gene encoding arginase, with similar structural properties and enzyme characteristics, exists and has been named Arginase II (AII). Comprehensive histories and physical examinations confirm a strikingly uniform clinical picture and one notably different from patients with other urea cycle disorders. This condition rarely presents in the neonatal period and first symptoms typically present in children between 2 and 4 years of age. First symptoms are often neurologically based. If untreated, symptoms are progressive with a gradual loss of developmental milestones. With adherence to a dietary and drug regimen, a favorable outcome can be expected, with cessation of further neurological deterioration and in some instances, of improvement. This article summarizes the clinical course of selected patients who represent the full spectrum of presentations of arginase deficiency. In addition to the clinical characterization of this disorder; the biochemical, enzymatic, and molecular evidence of disease is summarized. Treatment and prenatal diagnosis are also discussed.

Clinical consequences of urea cycle enzyme deficiencies and potential links to arginine and nitric oxide metabolism

Urea cycle disorders (UCD) are human conditions caused by the dysregulation of nitrogen transfer from ammonia nitrogen into urea. The biochemistry and the genetics of these disorders were well elucidated. Earlier diagnosis and improved treatments led to an emerging, longer-lived cohort of patients. The natural history of some of these disorders began to point to pathophysiological processes that may be unrelated to the primary cause of acute morbidity and mortality, i.e., hyperammonemia. Carbamyl phosphate synthetase I single nucleotide polymorphisms may be associated with altered vascular resistance that becomes clinically relevant when specific environmental stressors are present. Patients with argininosuccinic aciduria due to a deficiency of argininosuccinic acid lyase are uniquely prone to chronic hepatitis, potentially leading to cirrhosis. Moreover, our recent observations suggest that there may be an increased prevalence of essential hypertension. In contrast, hyperargininemia found in patients with arginase 1 deficiency is associated with pyramidal tract findings and spasticity, without significant hyperammonemia. An intriguing potential pathophysiological link is the dysregulation of intracellular arginine availability and its potential effect on nitric oxide (NO) metabolism. By combining detailed natural history studies with the development of tissue-specific null mouse models for urea cycle enzymes and measurement of nitrogen flux through the cycle to urea and NO in UCD patients, we may begin to dissect the contribution of different sources of arginine to NO production and the consequences on both rare genetic and common multifactorial diseases.

Effect of alternative pathway therapy on branched chain amino acid metabolism in urea cycle disorder patients

Urea cycle disorders (UCDs) are a group of inborn errors of hepatic metabolism caused by the loss of enzymatic activities that mediate the transfer of nitrogen from ammonia to urea. These disorders often result in life-threatening hyperammonemia and hyperglutaminemia. A combination of sodium phenylbutyrate and sodium phenylacetate/benzoate is used in the clinical management of children with urea cycle defects as a glutamine trap, diverting nitrogen from urea synthesis to alternatives routes of excretion. We have observed that patients treated with these compounds have selective branched chain amino acid (BCAA) deficiency despite adequate dietary protein intake. However, the direct effect of alternative therapy on the steady state levels of plasma branched chain amino acids has not been well characterized. We have measured steady state plasma branched chain and other essential non-branched chain amino acids in control subjects, untreated ornithine transcarbamylase deficiency females and treated null activity urea cycle disorder patients in the fed steady state during the course of stable isotope studies. Steady-state leucine levels were noted to be significantly lower in treated urea cycle disorder patients when compared to either untreated ornithine transcarbamylase deficiency females or control subjects (P<0.0001). This effect was reproduced in control subjects who had depressed leucine levels when treated with sodium phenylacetate/benzoate (P<0.0001). Our studies suggest that this therapeutic modality has a substantial impact on the metabolism of branched chain amino acids in urea cycle disorder patients. These findings suggest that better titration of protein restriction could be achieved with branched chain amino acid supplementation in patients with UCDs who are on alternative route therapy.

Problems in the management of urea cycle disorders

Several recent reviews describe the management of urea cycle disorders. There is much agreement on diet, alternative pathway therapy, maintenance of arginine and ornithine levels in acute and chronic management, sick-day regimens, and some aspects of monitoring. However, differences remain in several areas, and physicians at most treatment centers have relatively little experience, because these disorders are rare. Early suspicion of the diagnosis of a urea cycle disorder, and prompt referral to a tertiary center is vital. Drug treatment using chronic administration of sodium benzoate has been abandoned by some centers, but the acceptability of phenylbutyrate is an issue for many patients. Using citrulline chronically is not always successful in recommended doses, and may result in an arginine level too low for maximum control. Appetite and nutrition problems are common. One major concern is the early identification and management of chronic catabolism, theoretically easy, but hard in practice. Biochemical measurement problems complicate monitoring, and there are disagreements about the optimum way of identifying OTC carriers. It is not always clear whom to treat. Within a kindred with an early-onset phenotype, an asymptomatic newborn girl may need treatment for some undetermined time, but target values for monitoring are not clear. In late-onset phenotypes, management of asymptomatic males identified by family screening is also difficult. Most centers do not have sufficient cases to solve these conundrums, some of which require further multicenter study. This paper examines the recommendations of a consensus conference on management, outlines some remaining problems, and incorporates in the text the points raised in open discussion during a session of a symposium held in Sydney in 2003 entitled "New Developments in Urea Cycle Disorders."

Differential utilization of systemic and enteral ammonia for urea synthesis in control subjects and ornithine transcarbamylase deficiency carriers

BACKGROUND

Female carriers of ornithine transcarbamylase deficiency (OTCD) have nearly normal rates of total urea synthesis, but they derive less urea from systemic glutamine amide nitrogen than do healthy persons.

OBJECTIVE

The objective of the study was to investigate whether females with symptomatic OTCD rely on alternative pathways to compensate for the reduced urea synthesis activity observed in this disorder.

DESIGN

The 5-d study involved 6 control subjects (3 males, 3 females) and 6 female OTCD carriers who had a fixed energy intake of 133 kJ. kg(-)(1). d(-)(1) and a protein intake of 0.8 g. kg(-)(1). d(-)(1). They underwent two 12-h periods of isotopic tracer administration, separated by 2 d. On both occasions, [(18)O] or [(13)C]urea was infused intravenously, and the subjects consumed hourly meals. During the first period, [(15)N]NH(4)Cl was given intravenously; during the second period, the tracer was given as hourly oral doses.

RESULTS

OTCD carriers produced less urea (P < 0.05) but had a higher (P < 0.05) mean ammonia appearance rate and plasma ammonia concentration than did control subjects. OTCD carriers incorporated a lower (P < 0.001) mean (+/- SE) proportion of the intravenous [(15)N]NH(4)Cl dose into circulating urea than did control subjects (16 +/- 1% compared with 36 +/- 2%), but there was no genotypic difference in the incorporation of orally administered tracer (81 +/- 4% compared with 72 +/- 4%, respectively).

CONCLUSION

A good degree of dietary protein tolerance seemed to be retained in OTCD carriers by the maintenance of higher ammonia appearance rates, expansion of the plasma ammonia pool, and reliance on the ability of the perivenous hepatocytes to clear excess ammonia via glutamine synthesis.

Urea Cycle Disorders

Urea cycle disorders comprise a group of inborn errors of metabolism that represent unique gene-nutrient interactions whose significant morbidity arises from acute and chronic neurotoxicity associated with often massive hyperammonemia. Current paradigms of treatment are focused on controlling the flux of nitrogen transfer through the hepatic urea cycle by a combination of dietary and pharmacologic approaches. Evolving paradigms include the development of cell and gene therapies. Current research is focused on understanding the pathophysiology of ammonia-mediated toxicity and prevention of neural injury.

Urea-cycle disorders as a paradigm for inborn errors of hepatocyte metabolism

Urea-cycle disorders (UCDs) are a group of inborn errors of hepatocyte metabolism that are caused by the loss of enzymes involved in the process of transferring nitrogen from ammonia to urea, via the urea cycle (UC). Recent genetic analyses of inherited disorders that present with hyperammonemia demonstrate the function of cellular transporters that regulate the availability of UC intermediates. The regulation of UC intermediates, such as arginine, could have far reaching implications on nitric-oxide synthesis and vascular tone. Hence, each UCD and UC-related disorder constitutes a unique gene-nutrient interaction that is crucial for postnatal homeostasis. Recent advances in the diagnosis and management of UCDs include the application of in vivo metabolic-flux measurements. Cumulative morbidity is still high despite dietary and pharmacological therapies and, hence, both cell and gene therapies are being pursued as possible long-term corrective treatments. Although gene-replacement therapy has suffered recent clinical setbacks, new vector developments offer hope for the treatment of cell-autonomous defects of hepatocyte metabolism.

Metabolic bases of amino acid requirements in acute diseases

Acute diseases are characterized by a catabolic state, resulting in a negative nitrogen balance and muscle wasting. Increasing protein intake often proves to have little effect in limiting muscle protein loss. This suggests a qualitative inadequacy of the usual nutritional supports to meet the amino acid requirements of the critically ill patient. Therefore, it can be assumed that the additional intake of limiting amino acids would allow the sparing of muscle proteins. The aim of this review is to examine whether metabolic and kinetics studies using labelled amino acids can help identify the pathways activated in injury and their specific amino acid requirements. The kinetics of cysteine, arginine and glutamine, which are mainly cited as conditionally indispensable in stress situations, are presented. Moreover, amino acids can act as mediators or signal molecules and modulate numerous functions. The optimal conditions allowing the best expression of these activities are discussed.

An integrated approach to the diagnosis and prospective management of partial ornithine transcarbamylase deficiency

Ornithine transcarbamylase deficiency (OTCD) is the most common inherited urea cycle disorder, and is transmitted as an X-linked trait. Female OTCD heterozygotes exhibit wide clinical severities, ranging from being apparently asymptomatic to having the profound neurologic impairment observed in affected males. However, clinical and laboratory diagnosis of partial OTCD during asymptomatic periods is difficult, and correlation of phenotypic severity with either DNA mutation and/or in vitro enzyme activity is imprecise. Provocative testing, including protein load and allopurinol challenge used in the diagnosis of OTCD females, is not without risk and subject to both false positives and negatives. Although definitive when successful, DNA-based diagnosis is unable to detect mutations in all cases. We have previously used the ratio of isotopic enrichments of [(15)N]urea/[(15)N]glutamine ((15)N-U/G) derived from physiologic measurements of ureagenesis by stable isotope infusion as a sensitive index of in vivo urea cycle activity. We have now applied this method in combination with traditional biochemical testing to aid in the diagnosis of a symptomatic OTCD female in whom mutation in the ornithine transcarbamylase (OTC) gene was not found. The (15)N-U/G ratio in this patient showed that she had severe reduction of in vivo urea cycle activity on par with affected male subjects. This was correlated with partially deficient OTC activity in her liver, degree of orotic aciduria, and history of suspected recurrent hyperammonemic episodes before age 3. The measurement of in vivo urea cycle activity in combination with traditional biochemical indices optimizes a diagnostic approach to the at-risk partial OTCD patient, especially in those in whom molecular testing is unproductive. Together they contribute to the risk versus benefit considerations regarding the pursuit of medical therapy versus surgical, ie, orthotopic liver transplantation (OLT) therapy. The decision to resort to OLT in females with partial OTC activity is controversial, requiring consideration of phenotypic severity, failure of medical therapy, access to tertiary care centers experienced in the management of acute hyperammonemia, and social factors. In this patient, the use of in vivo and in vitro measures of urea cycle activity in conjunction with a consideration of her clinical history and medical-social situation led to a decision for OLT.

Metabolism 2000: the emperor needs new clothes

Metabolism is one of the corner stones of nutritional science. As biology enters the post-genomic era and with functional genomics beginning to takeoff, we anticipate that the study of metabolism will play an increasingly important role in helping to link advances made via the reductionist paradigm, that has been so successful in molecular and cellular biology, with those emerging from observational studies in animals and human subjects. A reconstructive metabolically-focused approach offers a timely paradigm for enhancing the elegance of nutritional science. Here we give particular attention to the use of tracers as phenotyping tools and discuss the application of our metaprobe concepts with respect to some novel features of metabolism, including 'underground metabolism', 'metabolic hijacking', 'catalytic promiscuity' and 'moonlighting proteins'. The opportunities for enhancing the study of metabolism by new and emerging technologies, and the importance of the interdisciplinary research enterprise are also touched upon. We conclude that: (1) the metaprobe concepts and approach, discussed herein, potentially yield a quantitative physiological (metabolic) phenotype against which to elaborate partial or focused genotypes; (2) physiological (metabolic) phenotypes which have a whole-body or kinetically-discernible inter-organ tissue-directed metabolic signature are an ideal target for this directed tracer-based definition of the 'functional' genotype; (3) metabolism, probed with tracer tool kits suitable for measuring rates of turnover, change and conversion, becomes in the current sociology of the 'Net', like AOL, Yahoo. Alta Vista, Lycos or Ask Jeeves, the portal for an exploration of the metabolic characteristics of the 'Genomics Internet'.

Laboratory evaluation of urea cycle disorders

The urea cycle disorders (UCDs) represent a group of inherited metabolic diseases with hyperammonemia as the primary laboratory abnormality. Affected individuals may become comatose or die if not treated rapidly. Diagnosis of a UCD requires a high index of suspicion and judicious use of the laboratory. It is important to rule out other conditions causing hyperammonemia that may require different treatment. The astute clinician may suspect a specific UCD in the appropriate clinical setting, but only laboratory results can confirm a specific diagnosis. The importance of the laboratory in helping the clinician to differentiate among various causes of hyperammonemia, in confirming a specific UCD, in carrier testing, and in prenatal diagnostic testing is highlighted in this review.