The challenges for molecular nutrition research 2: quantification of the nutritional phenotype

In quantifying the beneficial effect of dietary interventions in healthy subjects, nutrition research meets a number of new challenges. Inter individual variation in biomarker values often is larger than the effect related to the intervention. Healthy subjects have a remarkable capacity to maintain homeostasis, both through direct metabolic regulation, metabolic compensation of altered diets, and effective defence and repair mechanisms in oxidative and inflammatory stress. Processes involved in these regulatory activities essentially different from processes involved in early onset of diet related diseases. So, new concepts and approaches are needed to better quantify the subtle effects possibly achieved by dietary interventions in healthy subjects. Apart from quantification of the genotype and food intake (these are discussed in separate reviews in this series), four major areas of innovation are discussed: the biomarker profile concept, perturbation of homeostasis combined with omics analysis, imaging, modelling and fluxes. All of these areas contribute to a better understanding and quantification of the nutritional phenotype.     

The challenges for molecular nutrition research 1: linking genotype to healthy nutrition

Nutrition science finds itself at a major crossroad. On the one hand we can continue the current path, which has resulted in some substantial advances, but also many conflicting messages which impair the trust of the general population, especially those who are motivated to improve their health through diet. The other road is uncharted and is being built over the many exciting new developments in life sciences. This new era of nutrition recognizes the complex relation between the health of the individual, its genome, and the life-long dietary exposure, and has lead to the realisation that nutrition is essentially a gene-environment interaction science. This review on the relation between genotype, diet and health is the first of a series dealing with the major challenges in molecular nutrition, analyzing the foundations of nutrition research. With the unravelling of the human genome and the linking of its variability to a multitude of phenotypes from "healthy" to an enormously complex range of predispositions, the dietary modulation of these propensities has become an area of active research. Classical genetic approaches applied so far in medical genetics have steered away from incorporating dietary effects in their models and paradoxically, most genetic studies analyzing diet-associated phenotypes and diseases simply ignore diet. Yet, a modest but increasing number of studies are accounting for diet as a modulator of genetic associations. These range from observational cohorts to intervention studies with prospectively selected genotypes. New statistical and bioinformatics approaches are becoming available to aid in design and evaluation of these studies. This review discusses the various approaches used and provides concrete recommendations for future research.     

Psychiatric research: psychoproteomics,degradomics and systems biology

While proteomics has excelled in several disciplines in biology (cancer, injury and aging), neuroscience and psychiatryproteomic studies are still in their infancy. Several proteomic studies have been conducted in different areas of psychiatric disorders, including drug abuse (morphine, alcohol and methamphetamine) and other psychiatric disorders (depression, schizophrenia and psychosis). However, the exact cellular and molecular mechanisms underlying these conditions have not been fully investigated. Thus, one of the primary objectives of this review is to discuss psychoproteomic application in the area of psychiatric disorders, with special focus on substance- and drug-abuse research. In addition, we illustrate the potential role of degradomic utility in the area of psychiatric research and its application in establishing and identifying biomarkers relevant to neurotoxicity as a consequence of drug abuse. Finally, we will discuss the emerging role of systems biology and its current use in the field of neuroscience and its integral role in establishing a comprehensive understanding of specific brain disorders and brain function in general.     

Observational study to assess the relationship between enteral nutrition delivery and nutritional biomarkers among mechanically ventilated critically ill patients

BackgroundBiochemical assessment is considered a useful tool in assessing the patient’s nutritional status and intake. However, during critical illness, nutritional biomarkers, such as albumin, and haemoglobin (HB) may reflect the severity of acute illness. The aim of this study is to assess the relationship between energy and protein delivery with the change in albumin, HB, “mean corpuscular volume”(MCV), and “mean corpuscular haemoglobin concentration” (MCHC) levels in critically ill patients.MethodIn this prospective observational study we monitored the intake of energy and protein in a group critically ill patients for 6 consecutive days. Biochemical data including albumin, HB, MCV and MCHC was measured on admission and on day 6 of the follow-up. The variation in the biomarkers between admission and day 6 was calculated as the follow-up reading minus the reading obtained upon admission to (Intensive Care Unit) ICU.ResultsThis study included 43 patients. There was a significant difference in the albumin and HB levels between admission and follow up readings. No statistical association was recorded between the intake and the changes in albumin, MCV and MCHC level during ICU stay. The results showed a significant association between the intake of energy (R = 0.393), and protein (R = 0.385), with the increase in HB level during hospitalisation.ConclusionOverall, this study showed that most nutritional biomarkers were not influenced by nutritional therapy during the acute phase of illness. These findings may directly undermine the usefulness of the serial measurements of these biomarkers in the early phase of ICU admission.     

Disciplinary baptisms: a comparison of the naming stories of genetics, molecular biology, genomics, and systems biology

Understanding how scientific activities use naming stories to achieve disciplinary status is important not only for insight into the past, but for evaluating current claims that new disciplines are emerging. In order to gain a historical understanding of how new disciplines develop in relation to these baptismal narratives, we compare two recently formed disciplines, systems biology and genomics, with two earlier related life sciences, genetics and molecular biology. These four disciplines span the twentieth century, a period in which the processes of disciplinary demarcation fundamentally changed from those characteristic of the nineteenth century. We outline how the establishment of each discipline relies upon an interplay of factors that include paradigmatic achievements, technological innovation, and social formations. Our focus, however, is the baptism stories that give the new discipline a founding narrative and articulate core problems, general approaches and constitutive methods. The highly plastic process of achieving disciplinary identity is further marked by the openness of disciplinary definition, tension between technological possibilities and the ways in which scientific issues are conceived and approached, synthesis of reductive and integrative strategies, and complex social interactions. The importance--albeit highly variable--of naming stories in these four cases indicates the scope for future studies that focus on failed disciplines or competing names. Further attention to disciplinary histories could, we suggest, give us richer insight into scientific development.     

PROTICdb: a web-based application to store, track, query, and compare plant proteome data

PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The purposes of PROTICdb are (i) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements, and (ii) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of post-translational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs of image analysis and MS identification software, or by filling web forms. 2-D PAGE annotated maps can be displayed, queried, and compared through a graphical interface. Links to external databases are also available. Quantitative data can be easily exported in a tabulated format for statistical analyses. PROTICdb is based on the Oracle or the PostgreSQL Database Management System and is freely available upon request at the following URL: http://moulon.inra.fr/ bioinfo/PROTICdb.     

dbVOR: a database system for importing pedigree,phenotype and genotype data and exporting selected subsets

Background

When studying the genetics of a human trait, we typically have to manage both genome-wide and targeted genotype data. There can be overlap of both people and markers from different genotyping experiments; the overlap can introduce several kinds of problems. Most times the overlapping genotypes are the same, but sometimes they are different. Occasionally, the lab will return genotypes using a different allele labeling scheme (for example 1/2 vs A/C). Sometimes, the genotype for a person/marker index is unreliable or missing. Further, over time some markers are merged and bad samples are re-run under a different sample name. We need a consistent picture of the subset of data we have chosen to work with even though there might possibly be conflicting measurements from multiple data sources.

Results

We have developed the dbVOR database, which is designed to hold data efficiently for both genome-wide and targeted experiments. The data are indexed for fast retrieval by person and marker. In addition, we store pedigree and phenotype data for our subjects. The dbVOR database allows us to select subsets of the data by several different criteria and to merge their results into a coherent and consistent whole. Data may be filtered by: family, person, trait value, markers, chromosomes, and chromosome ranges. The results can be presented in columnar, Mega2, or PLINK format.

Conclusions

dbVOR serves our needs well. It is freely available from https://watson.hgen.pitt.edu/register. Documentation for dbVOR can be found at https://watson.hgen.pitt.edu/register/docs/dbvor.html.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0505-4) contains supplementary material, which is available to authorized users.     

Challenges in studies on flowering time: interfaces between phenological research and the molecular network of flowering genes

Flowering time is a well-studied subject in ecology, evolution and molecular biology. Long-term phenological studies have shown relationships between flowering time and environmental and endogenous factors in many species. In contrast, molecular studies using model plants have revealed a complex regulatory network of flowering. We propose that flowering would be a model trait for the integrated study of ecology, evolution and molecular biology. We introduce briefly the flowering regulatory pathways of Arabidopsis thaliana, followed by molecular techniques such as transgenic manipulation, quantitative real-time PCR and detection of differentially expressed genes that could facilitate the study of ‘nonmodel’ species of ecological interest but with little available genome information. Application of the flowering gene network to wild species will be illustrated by two examples: modeling and prediction of the expression of flowering genes in Arabidopsis halleri, and the latitudinal cline of bud set and cessation in Populus. Finally, we discuss the challenges in integrating knowledge of the regulatory network on flowering into ecologically unique flowering phenomena such as synchronous intermittent mass flowering—the topic of this special issue.     

Mini-review to analyse the phenotype, genotype, and alloantibody titre against Diego antigens in the Chinese population

Diego blood antigens are important antigens in Mongoloid people and native South Americans owing to the Dia positivity rate found in these populations. However, the prevalence of Di^a+ is different among native populations of America and China. Our study reviewed the genotype, phenotype, and alloantibody titre of Diego blood group antigens to explain the existence of the dosage effect for Diego antigens. The prevalence of Di^a+ varied from 2.26% to 10.43% in the Chinese population was lower than that observed in Native Americans living in USA, Brazil, and Venezuela. The Di(a+b-)/Di(a+b+) ratio in the Chinese was 0.0044~0.0268, which was also lower than that observed in native Americans at 0.0203–0.1628, indicating that the major allele was Di(a+b+) in Di^a+Chinese or Asians. We also collected Di(a+b-), Di(a+b+), and Di(a-b+) samples from Chinese samples to examine the agglutinin titres with anti-Di^a and anti-Di^b and the results supported the existence of the dosage effect for Diego antigens. The agglutinin titres of anti-Di^a in Di(a+b+) specimens were lower than those in Di(a+b-) specimens, and agglutinin titres of anti-Di^b in Di(a+b+) specimens were lower than those in Di(a-b+) specimens. Alloantibodies against Di^a and Di^b antigen are majorly responsible for haemolytic disease of the new-born and anti-Di^a reactions resulting in stillborn foetus and transfusion reactions, such as fever and rash,were also reported in the Chinese population.     

Bone and the kidney: a systems biology approach to the molecular mechanisms of renal osteodystrophy

Despite its apparent static condition, the skeleton undergoes a permanent process of remodeling mediated by osteoblasts and osteoclasts. The activity of these cells is regulated by a plethora of factors, ranging from mechanical stress to the effects of hormones to the immune system. One well-studied regulatory system involves the maintenance of calcium homeostasis through a network whose main regulatory components include ionized calcium, phosphate, parathyroid hormone and active vitamin D. This system establishes the link between bone and kidney, as one of the kidney's endocrine functions is the activation of vitamin D, while electrolyte homeostasis is one of its excretory functions. Impaired renal function leads to disturbances in this regulatory system, resulting in the complex syndrome of renal osteodystrophy that affects the majority of patients with chronic renal failure. This review summarizes the current understanding of bone physiology on a molecular level, examines some of the pathological pathways related to renal disease, and concludes with an outlook on how the emerging field of systems biology may contribute to a more dynamic and quantitative understanding of the physiology and pathophysiology of renal bone disease.     

Separate and combined effects of nutrition during juvenile and sexual development on female life-history trajectories: the thrifty phenotype in a cockroach

We have yet to understand fully how conditions during different periods of development interact to influence life-history structure. Can the negative effects of poor juvenile nutrition be overcome by a good adult diet, or are life-history strategies set by early experience? Here, we tested the influence and interaction of different nutritional quality during juvenile and sexual development on female resource allocation physiology, life history and courtship behaviour in the cockroach, Nauphoeta cinerea. Nymphs were raised on either a good-quality or poor-quality diet. After adult eclosion, females were either switched to the opposite diet or remained on their original diet. We assessed mating behaviour and lifetime reproductive success for half of the females from each treatment. We evaluated reproductive investment, somatic investment and resource reallocation from reproduction to the soma via oocyte apoptosis in the remaining females. We found that poor juvenile conditions resulted in a fat phenotype with slow juvenile growth and short reproductive lifespan that could not be retrieved with a change in diet. Good juvenile conditions resulted in the converse, but again fixed, phenotype in adulthood. Thus, juvenile nutrition sets adult patterns of resource allocation.     

How generalists coexist: the role of floral phenotype and spatial factors in the pollination systems of two Ranunculus species

Aims Competition for pollinators between phenotypically similar flowers is believed to play an important role in floral trait diversification in the angiosperms. However, in many plant communities, species with apparently similar floral phenotypes and generalist pollination systems co-flower. Here, the pollination systems of Ranunculus acris L. and Ranunculus repens L. were investigated to determine the factors enabling the species to coexist within apparently overlapping pollination niches.Methods Sympatrically flowering populations of R. acris and R. repens were investigated at three study sites in West Wales. The floral phenotypes of the two species were compared using measurements of floral morphology and spectral analyses of petal reflectance, using principal component analysis and bee and fly colour-space models. Evidence of inter-specific discrimination by foraging insects was tested for in the field and using floral arrays. The relative roles of behavioural constancy and spatial patchiness in maintaining pollinator fidelity were estimated.Important findings The floral phenotypes of R. acris and R. repens differed significantly. Social bees were highly constant when foraging at flowers of the two species and patchy floral distribution explained some of the observed fidelity. Dipterans visiting mixed floral arrays appeared to discriminate between the species, visiting more R. acris than R. repens flowers, but there was no difference in the number of visits to single-species arrays. Social bees were more likely to display constancy to flowers of R. repens in the field. Patchiness in floral distribution, subtle differences in floral phenotype, pollinator preferences and behavioural constancy are all likely to contribute to the continued coexistence of R. acris and R. repens, despite apparent overlap in their pollination niches. Such differences have the potential to facilitate the maintenance of species diversity in plant communities, even where plants appear to share similar floral phenotypes.     

Introduction to the DISRUPT postprandial database: subjects, studies and methodologies

Dysregulation of lipid and glucose metabolism in the postprandial state are recognised as important risk factors for the development of cardiovascular disease and type 2 diabetes. Our objective was to create a comprehensive, standardised database of postprandial studies to provide insights into the physiological factors that influence postprandial lipid and glucose responses. Data were collated from subjects (n = 467) taking part in single and sequential meal postprandial studies conducted by researchers at the University of Reading, to form the DISRUPT (DIetary Studies: Reading Unilever Postprandial Trials) database. Subject attributes including age, gender, genotype, menopausal status, body mass index, blood pressure and a fasting biochemical profile, together with postprandial measurements of triacylglycerol (TAG), non-esterified fatty acids, glucose, insulin and TAG-rich lipoprotein composition are recorded. A particular strength of the studies is the frequency of blood sampling, with on average 10–13 blood samples taken during each postprandial assessment, and the fact that identical test meal protocols were used in a number of studies, allowing pooling of data to increase statistical power. The DISRUPT database is the most comprehensive postprandial metabolism database that exists worldwide and preliminary analysis of the pooled sequential meal postprandial dataset has revealed both confirmatory and novel observations with respect to the impact of gender and age on the postprandial TAG response. Further analysis of the dataset using conventional statistical techniques along with integrated mathematical models and clustering analysis will provide a unique opportunity to greatly expand current knowledge of the aetiology of inter-individual variability in postprandial lipid and glucose responses.     

Design and analysis of mixture systems: Applications in hydroponic,plant nutrition research

This study demonstrates that nutrient solutions can be defined as mixture systems. A general methodology for design and analysis of mixture optimization experiments is developed. The emphasis is centered on multivariate investigation of the zone of optimal solution properties as a function of the ion composition and the total ionic strength of the solution. The study of the effects of ion interaction on well-defined solution properties is also possible by this multivariate approach. This work is a valuable tool in mineral nutritional research, because for the first time the chemical feasibility conditions of such solution, combined with additional chemical, physiological or economical constraints, form the foundation of the statistical experimental design theory, which makes the optimization of complex mixtures of ions in relation to well-defined response variables possible.     

The portable dictionary of the mouse genome: a personal database for gene mapping and molecular biology

The Portable Dictionary of the Mouse Genome is a database for personal computers that contains information on approximately 10,000 loci in the mouse, along with data on homologs in several other mammalian species, including human, rat, cat, cow, and pig. Key features of the dictionary are its compact size, its network independence, and the ability to convert the entire dictionary to a wide variety of common application programs. Another significant feature is the integration of DNA sequence accession data. Loci in the dictionary can be rapidly resorted by chromosomal position, by type, by human homology, or by gene effect. The dictionary provides an accessible, easily manipulated set of data that has many uses—from a quick review of loci and gene nomenclature to the design of experiments and analysis of results. The Portable Dictionary is available in several formats suitable for conversion to different programs and computer systems. It can be obtained on disk or from Internet Gopher servers (mickey.utmem.edu or anat4.utmem.edu), an anonymous FTP site (nb.utmem.edu in the directory pub/genedict), and a World Wide Web server (http://mickey.utmem.edu/front.html).