Cytochrome P450 3A (CYP3A) enzymes catalyze the metabolism of a wide range of endogenous and exogenous compounds. Genetic variations in the 3 CYP3A isoforms (CYP3A28, CYP3A74, and CYP3A76) may influence their expression and activity, leading to inter-individual differences in xenobiotic metabolism. In domestic cattle, understanding how genetic variations modulate CYP3A activity is crucial for both its therapeutic implications (clinical efficacy and adverse drug effects) and food safety (residues in foodstuff). Here, we updated the variant calling of CYP3As in 300 previously sequenced Piedmontese beef cattle, using the most recent reference genome, which contains an updated, longer sequence for CYP3A28. All but one previously identified missense variants were confirmed and a new variant, R105W in CYP3A28, was discovered. Through computational mutagenesis and molecular docking, we computationally predicted the impact of all identified CYP3A variant enzymes on protein stability and their affinity for aflatoxin B1 (AFB1), a potent carcinogen and food contaminant. For CYP3A28, we also computationally predicted its affinity for the probe substrate nifedipine (NIF). We found that CYP3A28 with R105W variant cannot accommodate NIF nor AFB1 in the binding pocket, thus affecting their metabolism. Our work provides computational foundation and prioritized ranking of CYP3A variants for future experimental validations.

While traditional nutrition science is focusing on nourishing population, modern nutrition is aiming at benefiting individual people. The goal of modern nutritional research is to promote health, prevent diseases, and improve performance. With the development of modern technologies like bioinformatics, metabolomics, and molecular genetics, this goal is becoming more attainable. In this chapter, we will discuss the new concepts and technologies especially in informatics and molecular genetics and genomics, and how they have been implemented to change the nutrition science and lead to the emergence of new branches like nutrigenomics, nutrigenetics, and nutritional metabolomics.

Understanding the interactions between food and human biology is of utmost importance to facilitate the development of more efficient nutritional interventions that might improve our wellness status and future health outcomes by reducing risk factors for non-transmittable chronic diseases, such as cardiovascular diseases, cancer, obesity and metabolic syndrome. Dissection of the molecular mechanisms that mediate the physiological effects of diets and bioactive compounds is one of the main goals of current nutritional investigation and the food industry as might lead to the discovery of novel biomarkers. It is widely recognized that the availability of robust nutritional biomarkers represents a bottleneck that delays the innovation process of the food industry. In this regard, omics sciences have opened up new avenues of research and opportunities in nutrition. Advances in mass spectrometry, nuclear magnetic resonance, next generation sequencing and microarray technologies allow massive genome, gene expression, proteomic and metabolomic profiling, obtaining a global and in-depth analysis of physiological/pathological scenarios. For this reason, omics platforms are most suitable for the discovery and characterization of novel nutritional markers that will define the nutritional status of both individuals and populations in the near future, and to identify the nutritional bioactive compounds responsible for the health outcomes.

The aim of the present study was to establish the role of ACE gene polymorphisms in the risk of developing in-stent restenosis and/or coronary artery disease (CAD). Eight ACE gene polymorphisms were genotyped by 5' exonuclease TaqMan genotyping assays in 236 patients with CAD who underwent coronary artery stenting. Basal and procedure coronary angiographies were analyzed searching for angiographic predictors of restenosis and follow-up angiography was analyzed looking for binary restenosis. A group of 455 individuals without clinical and familial antecedents of cardiovascular diseases were included as controls. Haplotypes were constructed after linkage disequilibrium analysis. Distribution of ACE polymorphisms was similar in patients with and without restenosis. Similar results were observed when the analysis was made comparing the whole group of patients (with and without restenosis) and healthy controls. Six out of eight polymorphisms were in high linkage disequilibrium and were included in five haplotypes (AAAGCA, GGGATG, GAGATG, AGAGCA and AAGACA). The distribution of these haplotypes was similar in patients with and without restenosis. However, CAD patients showed an increased frequency of the AAAGCA haplotype (OR=1.31, 95% CI: 1.04-1.66, P=0.018) and decreased frequencies of GAGATG (OR=0.47, 95% CI: 0.25-0.88, P=0.011) and AGAGCA (OR=0.15, 95% CI: 0.02-0.65, P=0.002) haplotypes when compared to healthy controls. Haplotypes of the ACE gene could be a genetic factor related to coronary artery disease in the Mexican individuals, but do not support its role as a risk factor for developing restenosis after coronary stenting.

To test for an association with risk for restenosis after coronary stent placement, the TNF-alpha and IL-10 polymorphisms were analyzed by 5' exonuclease TaqMan assays in 162 patients who initially underwent coronary stenting. Analysis of basal and procedure coronary angiographies revealed a higher proportion of restenosis in lesions treated with bare metal stents compared with those treated with drug-eluting stents (P < 0.001). Distribution of TNF-alpha genotypes was similar in patients with and without restenosis. The IL-10 polymorphisms showed a moderate protective trend of the -819 TT genotype against restenosis when the lesions were analyzed (P = 0.071, OR = 0.471). Multivariate analysis confirmed a protective role for drug-eluting stents (P < 0.001, OR = 0.199) and the -819 TT genotype (P = 0.037, OR = 0.391). These results suggest the IL-10 -819 TT genotype has a protective role against in-stent restenosis.

Inflammation is the primary response to vessel wall injury caused by stent placement in coronary arteries. Cytokines of the interleukin-1 family are central regulators in immunoinflammatory mechanisms. The objective of this study was to test for association between IL-1 family gene polymorphisms and risk for restenosis after coronary stent placement. The IL-1B-511, IL-1F10.3, RN.4T>C, RN.6/1C>T, RN.6/2C>G, and IL-1RN VNTR polymorphisms were analyzed by 5' exonuclease TaqMan genotyping assays and polymerase chain reaction in a group of 165 patients who underwent coronary artery stenting. Basal and procedure coronary angiography were analyzed in search of angiographic predictors of restenosis and follow-up angiography was analyzed in search of binary restenosis. Patients with IL-1B-511 TT genotype had a 1.89-fold increased risk of developing restenosis. The analysis considering the lesions treated demonstrated that the lesions of patients with IL-1B-511 TT genotype had a 3.44-fold increased risk of developing restenosis. When the analysis considered the type of stent, the risk of developing restenosis was increased in lesions of patients with TT genotype (odds ratio = 4.50) who underwent coronary bare-metal stent implantation. Multiple logistic analysis identified IL-1B-511 TT genotype as an independent predictor for restenosis. The results suggest that IL-1B-511 polymorphism could be involved in the risk of developing restenosis after coronary stent placement.

Nowadays, nutrition focuses on improving health of individuals through diet. Current nutritional research aims at health promotion, disease prevention, and performance improvement. Modern analytical platforms allow the simultaneous measurement of multiple metabolites providing new insights in the understanding of the functionalities of cells and whole organisms. Metabonomics, "the quantitative measurement of the dynamic multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modifications", provides a systems approach to understanding global metabolic regulations of organisms. This concept has arisen from various applications of NMR and MS spectroscopies to study the multicomponent metabolic composition of biological fluids, cells, and tissues. The generated metabolic profiles are processed by multivariate statistics to maximize the recovery of information to be correlated with well-determined stimuli such as dietary intervention or with any phenotypic data or diet habits. Metabonomics is thus uniquely suited to assess metabolic responses to deficiencies or excesses of nutrients and bioactive components. Furthermore, metabonomics is used to characterize the metabolic phenotype of individuals integrating genetic polymorphism, metabolic interactions with commensal and symbiotic partners such as gut microflora, as well as environmental and behavioral factors including dietary preferences. This paper reports several experimental key aspects in nutritional metabonomics, reviews its applications employing targeted and holistic approach analysis for the study of the metabolic responses following dietary interventions. It also reports the assessment of intra- and inter-individual variability in animal and human populations. The potentialities of nutritional metabonomics for the discovery of new biomarkers and the characterization of metabolic phenotypes are discussed in a context of their possible utilizations for personalized nutrition to provide health maintenance at the individual level.

Three conformational polymorphs of N-(4'-methoxyphenyl)-3-bromothiobenzamide, yellow alpha, orange beta, and yellow gamma, have been identified by single-crystal X-ray diffraction. The properties and structure of the polymorphs were examined with FT Raman, FTIR (ATR), and UV/Vis spectroscopy, as well as differential scanning calorimetry. Computational data on rotational barriers in the isolated gas-phase molecule indicate that the molecular conformation found in the alpha form is energetically preferred, but only by around 2 kJ mol(-1) over the gamma conformation. The planar molecular structure found in the beta form is destabilized by 10-14 kJ mol(-1), depending on the calculation method. However, experimental evidence suggests that the beta polymorph is the most stable crystalline phase at room temperature. This is attributed to the relative planarity of this structure, which allows more and stronger intermolecular interactions, that is, more energetically effective packing. Calculated electronic-absorption maxima were in agreement with experimental spectra.

While traditional nutrition research has dealt with providing nutrients to nourish populations, it nowadays focuses on improving health of individuals through diet. Modern nutritional research is aiming at health promotion and disease prevention and on performance improvement. As a consequence of these ambitious objectives, the disciplines "nutrigenetics" and "nutrigenomics" have evolved. Nutrigenetics asks the question how individual genetic disposition, manifesting as single nucleotide polymorphisms, copy-number polymorphisms and epigenetic phenomena, affects susceptibility to diet. Nutrigenomics addresses the inverse relationship, that is how diet influences gene transcription, protein expression and metabolism. A major methodological challenge and first pre-requisite of nutrigenomics is integrating genomics (gene analysis), transcriptomics (gene expression analysis), proteomics (protein expression analysis) and metabonomics (metabolite profiling) to define a "healthy" phenotype. The long-term deliverable of nutrigenomics is personalised nutrition for maintenance of individual health and prevention of disease. Transcriptomics serves to put proteomic and metabolomic markers into a larger biological perspective and is suitable for a first "round of discovery" in regulatory networks. Metabonomics is a diagnostic tool for metabolic classification of individuals. The great asset of this platform is the quantitative, non-invasive analysis of easily accessible human body fluids like urine, blood and saliva. This feature also holds true to some extent for proteomics, with the constraint that proteomics is more complex in terms of absolute number, chemical properties and dynamic range of compounds present. Apart from addressing the most complex "-ome", proteomics represents the only platform that delivers not only markers for disposition and efficacy but also targets of intervention. The Omics disciplines applied in the context of nutrition and health have the potential to deliver biomarkers for health and comfort, reveal early indicators for disease disposition, assist in differentiating dietary responders from non-responders, and, last but not least, discover bioactive, beneficial food components. This paper reviews the state-of-the-art of the three Omics platforms, discusses their implication in nutrigenomics and elaborates on applications in nutrition and health such as digestive health, allergy, diabetes and obesity, nutritional intervention and nutrient bioavailability. Proteomic developments, applications and potential in the field of nutrition have been specifically addressed in another review issued by our group.

This paper described the efforts of scientists at the National Institute of Environmental Health Sciences (NIEHS) and their allies in the National Toxicology Program to molecularize toxicology by fostering the emergence of a new discipline: toxicogenomics. I demonstrate that the molecularization of toxicology at the NIEHS began in a process of 'co-construction'. However, the subsequent emergence of the discipline of toxicogenomics has required the deliberate development of communication across the myriad disciplines necessary to produce toxicogenomic knowledge; articulation of emergent forms, standards, and practices with extant ones; management of the tensions generated by grounding toxicogenomics in traditional toxicological standards and work practices even it transforms those standards and practices; and identification and stabilization of roles for toxicogenomic knowledge in markets and service sites, such as environmental health risk assessment and regulation. This paper describes the technological, institutional, and inter-sectoral strategies that scientists have pursued in order to meet these challenges. In so doing, this analysis offers a vista into both the means and meanings of molecularization.

Microinjecting the acetylcholinesterase inhibitor neostigmine into the pontine reticular formation of C57BL/6J (B6) mouse causes a rapid eye movement (REM) sleep-like state. This finding is consistent with similar studies in cat and both sets of data indicate that the REM sleep-like state is caused by increasing levels of endogenous acetylcholine (ACh). Muscarinic cholinergic receptors have been localized to the pontine reticular formation of B6 mouse but no previous studies have examined which of the five muscarinic receptor subtypes participate in cholinergic REM sleep enhancement. This study examined the hypothesis that M2 receptors in pontine reticular formation of B6 mouse contribute to the REM sleep-like state caused by pontine reticular formation administration of neostigmine. B6 mice (n=13) were implanted with electrodes for recording states of sleep and wakefulness and with microinjection cannulae aimed for the pontine reticular formation. States of sleep and wakefulness were recorded for 4 h following pontine reticular formation injection of saline (control) or neostigmine. Experiments designed to gain insight into the muscarinic receptor subtypes mediating REM sleep enhancement involved pontine reticular formation administration of neostigmine after pertussis toxin, neostigmine after methoctramine, and neostigmine after pirenzepine. Pertussis toxin was used to block effects mediated by M2 and M4 receptors. Methoctramine was used to block M2 and M4 receptors, and pirenzepine was used to block M1 and M4 receptors. Pertussis toxin and methoctramine significantly decreased the neostigmine-induced REM sleep-like state. In contrast, pretreatment with pirenzepine did not significantly decrease the REM sleep-like state caused by neostigmine. These results support the interpretation that M2 receptors in the pontine reticular formation of B6 mouse contribute to the generation of REM sleep.

This article examines one particular set of technologies arising from developments in human genetics, those aimed at improving the targeting, design and use of conventional small molecule drugs-pharmacogenetics. Much of the debate about the applications and consequences of pharmacogenetics has been highly speculative, since little or no working technology is yet on the market. This article provides a novel analysis of the development of pharmacogenetics, and the social and ethical issues it raises, based on the sociology of technological expectations. In particular, it outlines how two alternative visions for the development of the technology are being articulated and embedded in a range of heterogeneous discourses, artefacts, actor strategies and practices, including: competing scientific research agendas, experimental technologies, emerging industrial structures and new ethical discourses. Expectations of how pharmacogenetics might emerge in each of these arenas are actively shaping the trajectory of this nascent technology and its potential socio-economic consequences.

Pharmacogenetic capabilities have changed markedly since The SNP Consortium made a dense single-nucleotide polymorphism (SNP) map freely available in 2001. For more than 40 years, pharmacokinetics and pharmacodynamics of drug-metabolizing molecules were the focus of practical applications. Today, it is possible to use SNP-mapping technologies to create a genetic profile of each individual that can be used to identify patterns of susceptibility genes for common diseases as well as genetic risk/efficacy factors that are related to the effects of drugs.

The advent of the genomic era has brought about several new fields of study, one of them being pharmacogenomics, which seeks to link drug treatment (pharmaco-) with the individual's genetic make-up (genomics). Pharmacogenomics holds many promises for improved treatment of a large variety of medical conditions, including immunosuppression for organ transplantation and autoimmune disease. Many of these promises have, however, not yet been fulfilled. In this brief overview of the subject, we attempt to provide insights into the evolving field of pharmacogenomics and discuss some of its potential benefits and promises, technological tools used by pharmacogenomics, the reasons for delays in breakthroughs in the field, and the relevance of pharmacogenornics to immunosuppression.

The development of safe and effective new therapeutics is a long, difficult, and expensive process. Over the last 20-30 years, recombinant DNA (rDNA) technology has provided a multiple of new methods, molecular targets and DNA-based diagnostics to pharmaceutical research that can be utilized in assays for screening and developing potential biopharmaceutical drugs. In parallel, new innovative approaches to drug delivery systems were discovered and reached the market. Pharmaceutical biotechnology, pharmacogenomics, combinatorial chemistry, in close relation to high-throughput screening technologies, and bioinformatics are major advances that give a new direction to pharmaceutical sciences. To meet with the needs of this new dynamic era of pharmaceutical research and health care environment, pharmaceutical education has to set new priorities to keep pace with the challenges related to genomic technologies. The development of new initiative education programs, for both undergraduate and graduate curricula, in pharmacy has to be focused on preparing pharmacists oriented for both pharmacy practice and drug research and development. This can be achieved by providing future pharmacists with knowledge, skills and attitudes to be more competitive in the health care system, pharmacy practice-related fields, pharmaceutical industry and drug research and development areas, or finally in academia. Educators and pharmacy school members have the responsibility of deciding how, to what extent, by which methods, and/or in which way these changes and new directions in the education programs should be developed.

The ability to perform analyses for single-nucleotide polymorphisms (SNPs) has become routine in many molecular diagnostic laboratories. While various procedures and technologies are available to do so, we evaluated a novel technology for SNP analysis using the Factor V Leiden polymorphism as an example. The Factor V Leiden polymorphism G1691A is the most common genetic abnormality associated with hereditary thrombophilia. Current testing methods remain highly accurate yet their main disadvantage is gel-based detection. The READIT System (Promega Corp., Madison, WI) is a novel approach to SNP analysis that utilizes DNA polymerase-mediated pyrophosphorolysis to release dNTPs, which are converted to ATP and used in a luciferase detection reaction. We screened 280 DNA specimens, previously analyzed using the PCR/MnlI restriction digest assay, to evaluate READIT System capabilities along with the KingFisher robotic magnetic particle processor (ThermoLabsystems). Concordant results were obtained for 278/280 (99%) specimens. One discordant result was due to an equivocal relative light unit while the other was indeterminate. Both specimens gave correct results upon repeat analysis. The READIT System offers several advantages including: (1) rapid SNP analysis, (2) accuracy and precision, (3) cost effectiveness, (4) decreased turn-around times, (5) high throughput, and (6) excellent analysis software.

Differences in response to treatment or the incidence of adverse drug effects are quite common in clinical psychopharmacotherapy. Although several factors may account for these discrepancies, there is increasing knowledge that genetic factors play a major role. The aim of pharmacogenetics, a new and rapidly growing field in research, is to elucidate the variability in drug response and metabolism due to hereditary differences. According to the hypotheses on the mechanisms of drug action, several mutations in genes coding for neurotransmitter receptors, degrading enzymes, transport proteins or enzymes of the drug metabolizing system (P-450 isoenzymes) have been identified and investigated in psychiatric disorders over the last years. Although some controversy exists among the results, many studies are supportive of the hypothesis that psychopharmacogenetics will be helpful in predicting an individual patient's drug response while minimising the rate of side effects.