Health-related quality of life, pain, and fatigue in young adults with cerebral palsy.

AIM: To describe health-related quality of life (HRQoL), pain, fatigue, and other health variables in young adults with cerebral palsy (CP), and to explore associations with the Gross Motor Function Classification System - Expanded and Revised (GMFCS-ER) and physical activity. METHOD: This was a cross-sectional study of 61 young adults at a mean age of 21 years 2 months (standard deviation 8mo, range 20-22y) with CP, from a geographically defined area. Data collection included: Short Form 36 version 2 for HRQoL, Brief Pain Inventory - Short Form, Fatigue Severity Scale, level of physical activity, medical history, and physical examination. RESULTS: Overall HRQoL equalled that of population norms; however self-reported physical health was lower in GMFCS-ER levels III to V compared to GMFCS-ER levels I to II. Self-reported mental health was, inversely, lower in GMFCS-ER levels I to II compared to GMFCS-ER levels III to V. Pain prevalence was 49%, and pain was present across all GMFCS-ER levels. Fatigue, as well as sleep problems, had 41% prevalence, with fatigue severity decreasing with increasing level of physical activity. INTERPRETATION: General HRQoL in young adults with CP was comparable to population norms. Pain and fatigue are important to address in high motor-functioning individuals also. Physical activity could be a possible protective factor against fatigue. WHAT THIS PAPER ADDS: Health-related quality of life in young adults with cerebral palsy (CP) was comparable to population norms. Pain, fatigue, and sleep problems occurred at all Gross Motor Function Classification System levels. There is a possible protective effect of physical activity on fatigue.

Grapevine Plasticity in Response to an Altered Microclimate: Sauvignon Blanc Modulates Specific Metabolites in Response to Increased Berry Exposure.

In this study, the metabolic and physiological impacts of an altered microclimate on quality-associated primary and secondary metabolites in grape (Vitis vinifera) 'Sauvignon Blanc' berries was determined in a high-altitude vineyard. The leaf and lateral shoot removal in the bunch zones altered the microclimate by increasing the exposure of the berries. The physical parameters (berry diameter and weight), primary metabolites (sugars and organic acids), as well as bunch temperature and leaf water potential were predominantly not affected by the treatment. The increased exposure led to higher levels of specific carotenoids and volatile terpenoids in the exposed berries, with earlier berry stages reacting distinctly from the later developmental stages. Plastic/nonplastic metabolite responses could be further classified to identify metabolites that were developmentally controlled and/or responded to the treatment in a predictable fashion (assessed over two consecutive vintages). The study demonstrates that grapevine berries exhibit a degree of plasticity within their secondary metabolites and respond physiologically to the increased exposure by increasing metabolites with potential antioxidant activity. Taken together, the data provide evidence that the underlying physiological responses relate to the maintenance of stress pathways by modulating antioxidant molecules in the berries.

Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach.

BACKGROUND: Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. ß-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types of pathogens, including potato infected with Phytophthora infestans. However, the molecular mechanisms behind this are unclear and seem to be dependent on the system studied. To elucidate the defence responses activated by BABA in potato, a genome-wide transcript microarray analysis in combination with label-free quantitative proteomics analysis of the apoplast secretome were performed two days after treatment of the leaf canopy with BABA at two concentrations, 1 and 10 mM. RESULTS: Over 5000 transcripts were differentially expressed and over 90 secretome proteins changed in abundance indicating a massive activation of defence mechanisms with 10 mM BABA, the concentration effective against late blight disease. To aid analysis, we present a more comprehensive functional annotation of the microarray probes and gene models by retrieving information from orthologous gene families across 26 sequenced plant genomes. The new annotation provided GO terms to 8616 previously un-annotated probes. CONCLUSIONS: BABA at 10 mM affected several processes related to plant hormones and amino acid metabolism. A major accumulation of PR proteins was also evident, and in the mevalonate pathway, genes involved in sterol biosynthesis were down-regulated, whereas several enzymes involved in the sesquiterpene phytoalexin biosynthesis were up-regulated. Interestingly, abscisic acid (ABA) responsive genes were not as clearly regulated by BABA in potato as previously reported in Arabidopsis. Together these findings provide candidates and markers for improved resistance in potato, one of the most important crops in the world.

An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.

Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.

Genetic analysis of the metabolic pathways responsible for aroma metabolite production by Saccharomyces cerevisiae.

During alcoholic fermentation, higher alcohols, esters, and acids are formed from amino acids via the Ehrlich pathway by yeast, but many of the genes encoding the enzymes have not yet been identified. When the BAT1/2 genes, encoding transaminases that deaminate amino acids in the first step of the Ehrlich pathway are deleted, higher metabolite formation is significantly decreased. Screening yeast strains with deletions of genes encoding decarboxylases, dehydrogenases, and reductases revealed nine genes whose absence had the most significant impact on higher alcohol production. The seven most promising genes (AAD6, BAT2, HOM2, PAD1, PRO2, SPE1, and THI3) were further investigated by constructing double- and triple-deletion mutants. All double-deletion strains showed a greater decrease in isobutanol, isoamyl alcohol, isobutyric, and isovaleric acid production than the corresponding single deletion strains with the double-deletion strains in combination with ∆bat2 and the ∆hom2-∆aad6 strain revealing the greatest impact. BAT2 is the dominant gene in these deletion strains and this suggests the initial transaminase step of the Ehrlich pathway is rate-limiting. The triple-deletion strains in combination with BAT2 (∆bat2-∆thi3-∆aad6 and ∆bat2-∆thi3-∆hom2) had the greatest impact on the end metabolite production with the exception of isoamyl alcohol and isovaleric acid. The strain deleted for two dehydrogenases and a reductase (∆hom2-∆pro2-∆aad6) had a greater effect on the levels of these two compounds. This study contributes to the elucidation of the Ehrlich pathway and its significance for aroma production by fermenting yeast cells.

GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network.

BACKGROUND: Gene Set Analysis (GSA) has proven to be a useful approach to microarray analysis. However, most of the method development for GSA has focused on the statistical tests to be used rather than on the generation of sets that will be tested. Existing methods of set generation are often overly simplistic. The creation of sets from individual pathways (in isolation) is a poor reflection of the complexity of the underlying metabolic network. We have developed a novel approach to set generation via the use of Principal Component Analysis of the Laplacian matrix of a metabolic network. We have analysed a relatively simple data set to show the difference in results between our method and the current state-of-the-art pathway-based sets. RESULTS: The sets generated with this method are semi-exhaustive and capture much of the topological complexity of the metabolic network. The semi-exhaustive nature of this method has also allowed us to design a hypergeometric enrichment test to determine which genes are likely responsible for set significance. We show that our method finds significant aspects of biology that would be missed (i.e. false negatives) and addresses the false positive rates found with the use of simple pathway-based sets. CONCLUSIONS: The set generation step for GSA is often neglected but is a crucial part of the analysis as it defines the full context for the analysis. As such, set generation methods should be robust and yield as complete a representation of the extant biological knowledge as possible. The method reported here achieves this goal and is demonstrably superior to previous set analysis methods.

The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.

BACKGROUND: Carotenoids are a heterogeneous group of plant isoprenoids primarily involved in photosynthesis. In plants the cleavage of carotenoids leads to the formation of the phytohormones abscisic acid and strigolactone, and C13-norisoprenoids involved in the characteristic flavour and aroma compounds in flowers and fruits and are of specific importance in the varietal character of grapes and wine. This work extends the previous reports of carotenoid gene expression and photosynthetic pigment analysis by providing an up-to-date pathway analysis and an important framework for the analysis of carotenoid metabolic pathways in grapevine. RESULTS: Comparative genomics was used to identify 42 genes putatively involved in carotenoid biosynthesis/catabolism in grapevine. The genes are distributed on 16 of the 19 chromosomes and have been localised to the physical map of the heterozygous ENTAV115 grapevine sequence. Nine of the genes occur as single copies whereas the rest of the carotenoid metabolic genes have more than one paralogue. The cDNA copies of eleven corresponding genes from Vitis vinifera L. cv. Pinotage were characterised, and four where shown to be functional. Microarrays provided expression profiles of 39 accessions in the metabolic pathway during three berry developmental stages in Sauvignon blanc, whereas an optimised HPLC analysis provided the concentrations of individual carotenoids. This provides evidence of the functioning of the lutein epoxide cycle and the respective genes in grapevine. Similarly, orthologues of genes leading to the formation of strigolactone involved in shoot branching inhibition were identified: CCD7, CCD8 and MAX1. Moreover, the isoforms typically have different expression patterns, confirming the complex regulation of the pathway. Of particular interest is the expression pattern of the three VvNCEDs: Our results support previous findings that VvNCED3 is likely the isoform linked to ABA content in berries. CONCLUSIONS: The carotenoid metabolic pathway is well characterised, and the genes and enzymes have been studied in a number of plants. The study of the 42 carotenoid pathway genes of grapevine showed that they share a high degree of similarity with other eudicots. Expression and pigment profiling of developing berries provided insights into the most complete grapevine carotenoid pathway representation. This study represents an important reference study for further characterisation of carotenoid biosynthesis and catabolism in grapevine.

The effect of scale on gene expression: commercial versus laboratory wine fermentations.

Molecular and cellular processes that are responsible for industrially relevant phenotypes of fermenting microorganisms are a central focus of biotechnological research. Such research intends to generate insights and solutions for fermentation-based industries with regards to issues such as improving product yield or the quality of the final fermentation product. For logistical reasons, and to ensure data reproducibility, such research is mostly carried out in defined or synthetic media and in small-scale fermentation vessels. Two questions are frequently raised regarding the applicability of this approach to solve problems experienced in industrial fermentations: (1) Is synthetic medium a sufficiently accurate approximation of the generally more complex natural (and frequently highly variable) substrates that are employed in most fermentation-based industries, and (2) can results obtained in small-scale laboratory fermentations be extrapolated to large-scale industrial environments? Here, we address the second question through a comparative transcriptomic approach by assessing the response of an industrial wine yeast strain fermenting a natural grape juice in small-scale laboratory and large-scale industrial conditions. In yeast, transcriptome analysis is arguably the best available tool to holistically assess the physiological state of a population and its response to changing environmental conditions. The data suggest that scale does indeed impact on some environmental parameters such as oxygen availability. However, the data show that small-scale fermentations nevertheless accurately reflect general molecular processes and adaptations during large-scale fermentation and that extrapolation of laboratory datasets to real industrial processes can be justified.

Does loss of spasticity matter? A 10-year follow-up after selective dorsal rhizotomy in cerebral palsy.

AIM: The aim of this study was to evaluate the long-term effects of selective dorsal rhizotomy (SDR) in children with cerebral palsy (CP). METHOD: Nineteen children (four females, 15 males; mean age 4y 7mo, SD 1y 7mo) with bilateral spastic CP, were prospectively assessed at baseline and 18 months, 3 years, and 10 years after SDR. Assessments included the Modified Ashworth Scale for spasticity, the Gross Motor Function Measure 88 (GMFM-88) and the Wilson gait scale for ambulation, neurological investigations, and passive joint range of motion assessment. A 10-year retrospective chart review was added for orthopaedic surgery after SDR. RESULTS: Baseline muscle tone at the hip, knee, and ankle level displayed a high degree of spasticity that normalized after SDR. After 10 years there was a slight recurrence of spasticity at the knee and ankle. Joint range of motion declined from a maximum at 3 years after SDR to the 10-year follow-up. Median ambulatory status was best 3 years after SDR and then declined. The GMFM-88 score increased from the median baseline value of 51 to 66 (p=0.002) and 76 (p<0.001) at the initial follow-ups. After 10 years there was a decline in gross motor function with a reduction in the GMFM-88 score to 62 (p=0.022). Within 10 years, 16 out of 19 patients had a mean of three orthopaedic surgeries (SD 2.8), soft tissue surgery being the most common. INTERPRETATION: The spasticity-reducing effect of SDR, although pronounced, did not seem to improve long-term functioning or prevent contractures. This suggests that contracture development in CP is not mediated by spasticity alone.

Identifying genes that impact on aroma profiles produced by Saccharomyces cerevisiae and the production of higher alcohols.

During alcoholic fermentation, many volatile aroma compounds are formed by Saccharomyces cerevisiae, including esters, fatty acids, and higher alcohols. While the metabolic network that leads to the formation of these compounds is reasonably well mapped, surprisingly little is known about specific enzymes involved in specific reactions, the regulation of the network, and the physiological roles of individual pathways within the network. Furthermore, different yeast strains tend to produce significantly different aroma profiles. These differences are of tremendous biotechnological interest, since producers of alcoholic beverages such as wine and beer are searching for means to diversify and improve their product range. Various factors such as the redox, energy, and nutritional balance of a cell have previously been suggested to directly or indirectly affect and regulate the network. To gain a better understanding of the regulations and physiological role of this network, we screened a subset of the EUROSCARF strain deletion library for genes that, when deleted, would impact most significantly on the aroma profile produced under fermentative conditions. The 10 genes whose deletion impacted most significantly on higher alcohol production were selected and further characterized to assess their mode of action within or on this metabolic network. This is the first description of a large-scale screening approach using aroma production as the primary selection criteria, and the data suggest that many of the identified genes indeed play central and direct roles within the aroma production network of S. cerevisiae.

A First Clinical Trial on Botulinum Toxin-A for Chronic Muscle-Related Pain in Cerebral Palsy.

Objective: To test if botulinum toxin-A (BoNT-A) is effective in reducing chronic muscle-related pain in adults with spastic cerebral palsy (CP), as compared to placebo. Design: A single-center, double-blind, parallel, randomized placebo-controlled trial. The design included an interim analysis to allow for confirmatory analysis, as well as pilot study outcomes. Setting: Tertiary university hospital. Participants: Adults with spastic CP and chronic pain associated with spastic muscle(s). Intervention: Treatment was one session of electromyographically guided intramuscular injections of either BoNT-A or placebo normosaline. Main Study Outcomes: The primary outcome was the proportion who achieved a reduction of pain intensity of two or more steps on the Numerical Rating Scale 6 weeks after treatment. Results: Fifty individuals were screened for eligibility, of whom 16 were included (10 female, 6 male, mean age = 32 years, SD = 13.3 years). The randomization yielded eight participants per treatment arm, and all completed the study as randomized. The study was stopped at the interim analysis due to a low probability, under a preset threshold, of a positive primary outcome. Four individuals were treatment responders in the BoNT-A group for the primary outcome compared to five responders in the placebo group (p = 1.000). Adverse events were mild to moderate. In exploratory analysis, the BoNT-A group had a trend of continuing reduction of pain at the last follow-up, after the primary endpoint. Conclusions: This study did not find evidence that BoNT-A was superior to placebo at the desired effect size (number needed to treat of 2.5) at 6 weeks after treatment. Trial registration:ClinicalTrials.gov: NCT02434549.

Comparative transcriptomic and proteomic profiling of industrial wine yeast strains.

The geno- and phenotypic diversity of commercial Saccharomyces cerevisiae wine yeast strains provides an opportunity to apply the system-wide approaches that are reasonably well established for laboratory strains to generate insight into the functioning of complex cellular networks in industrial environments. We have previously analyzed the transcriptomes of five industrial wine yeast strains at three time points during alcoholic fermentation. Here, we extend the comparative approach to include an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis of two of the previously analyzed wine yeast strains at the same three time points during fermentation in synthetic wine must. The data show that differences in the transcriptomes of the two strains at a given time point rather accurately reflect differences in the corresponding proteomes independently of the gene ontology (GO) category, providing strong support for the biological relevance of comparative transcriptomic data sets in yeast. In line with previous observations, the alignment proves to be less accurate when assessing intrastrain changes at different time points. In this case, differences between the transcriptome and proteome appear to be strongly dependent on the GO category of the corresponding genes. The data in particular suggest that metabolic enzymes and the corresponding genes appear to be strongly correlated over time and between strains, suggesting a strong transcriptional control of such enzymes. The data also allow the generation of hypotheses regarding the molecular origin of significant differences in phenotypic traits between the two strains.

Cognition in Children with Arachnoid Cysts.

BACKGROUND: This study aims to evaluate if children with temporal arachnoid cysts (AC) have cognitive symptoms and if neurosurgery improves these. METHODS: A prospective case series study including consecutive pediatric patients with temporal AC. The children underwent neuroradiology, neuroopthalmologic evaluation, and a standard electroencephalography (EEG). Additionally, a neuropsychologist performed a standardized set of evaluations, with a one-year follow-up consisting of Weschler Intelligence Scale for Children version IV (WISC-IV), FAS (for verbal fluency), Boston Naming Test (BNT, for visual naming ability) and NEPSY-II (Developmental NEuroPSYchological Assessment) for verbal memory. RESULTS: Fifteen children, 9 boys and 6 girls, were evaluated and 11 underwent surgery. The Full Scale IQ subscore (FSIQ) improved from M = 84.8 to M = 93.0 (p = 0.005). The preoperative Verbal Comprehension Index (VCI) was in the low average range (M = 86.7), improving to a level within the average range (M = 94.7, p = 0.001). Preoperative Perceptual Speed Index (PSI) was in the below average range (M = 81.5), improving to a level within the average range (M = 92.5, p = 0.004). CONCLUSION: ACs are a common finding in a pediatric neurosurgical setting. Our data suggest that some temporal AC have a negative effect on general cognitive ability and that this impairment can be improved by surgery. We suggest a standardized evaluation, including comprehensive and validated neuropsychological assessment tools, to thoroughly assess symptoms as well as the postoperative outcome.

Exploring social participation in young adults with cerebral palsy.

OBJECTIVES: To describe social outcomes for young adults with cerebral palsy, and to explore associations of social outcomes with their classification levels within the Gross Motor Function, Manual Ability and Communication Function Classification Systems, and with the presence of intellectual disability. DESIGN: A cross-sectional study with a population-based inclusion approach at a neuropaediatric referral centre in Sweden. SUBJECTS: Sixty-one young adults with cerebral palsy, age 20-22 years. METHODS: Physical examination and questionnaires on social outcomes including living arrangements, relationships, occupation, personal finances, extent of family support with personal care, and physical examination. RESULTS: Twenty percent of the young adults with cerebral palsy had moved out of the parental home. Forty-three percent were dependent on family support for basic activities of daily living. Seventy-nine percent of those without intellectual disability were employed or studying. The Communication Function Classification Systems, and presence of intellectual disability, demonstrated associations with most social outcomes, followed in significance by Manual Ability Classification System. CONCLUSION: In this study young adults with cerebral palsy to a high extent lived in the parental home, and more often without employment, compared with their peers. Many were dependent on parental support, financially, and with activities of daily living. Intellectual disability and communication function were important determinants of social participation. Interventions aimed at alleviating the impact of these particular disabilities should be prioritized.

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.

BACKGROUND: Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms. RESULTS: OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions. CONCLUSION: OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at http://ontodas.nbn.ac.za.

Isolation and Whole-Genome Sequencing of Environmental Campylobacter.

As a leading cause of bacterial-derived gastroenteritis worldwide, Campylobacter has a significant impact on human health. In the developed world, most campylobacteriosis cases are attributed to the consumption of undercooked, contaminated poultry; however, it has been shown that Campylobacter can be transmitted to humans through contaminated water and other types of food, including beef and milk. As such, high-resolution microbial source-tracking is essential for health department officials to determine the source(s) of Campylobacter outbreaks. For these reasons, this protocol provides the techniques needed for isolation of Campylobacter from agricultural and environmental sources, as well as human clinical specimens. Additionally, we describe a simple method for preparing high-quality genomic DNA that can be used for whole-genome sequencing and downstream bioinformatics analyses of Campylobacter genotypes. © 2018 by John Wiley & Sons, Inc.

Mitochondrial variant G4132A is associated with familial non-arteritic anterior ischemic optic neuropathy in one large pedigree.

OBJECTIVE: To identify the genetic factors associated with familial non-arteritic anterior ischemic optic neuropathy (NA-AION) in a large pedigree. METHODS: Eleven family members of a single pedigree, including six affected with NA-AION, underwent detailed clinical examinations. The mitochondrial DNA of the proband was sequenced in its entirety in search of disease-causing mutations associated with NA-AION in the pedigree. A control panel comprising 1488 patients suspected of having Leber hereditary optic neuropathy (LHON) and 97 general-population control subjects was screened for the mitochondrial sequence variant identified in the family. RESULTS: Affected family members were all male and exhibited classic features of NA-AION. Their mean age was 50.2 +/- 5.0 years. A total of 23 sequence variations were detected in the mitochondrial genome of the proband, including one novel sequence variation (G4132A, Ala276Thr) in the NADH dehydrogenase subunit 1 gene (ND1). The G4132A mitochondrial variant was detected in six members of a single pedigree with NA-AION. The G4132A variation was not observed in any of the 1585 subjects in the control panel. Moreover, this variant was not identified in over 2469 ethnically diverse individuals previously evaluated through the Human Mitochondrial Genome Database. None of the three major mutations associated with LHON (G3460A, G11778A, T14484C) were identified in the family. CONCLUSION: The G4132A mitochondrial variation is associated with familial NA-AION in our pedigree.

Chemiomics: network reconstruction and kinetics of port wine aging.

Network reconstruction (NR) has proven to be useful in the detection and visualization of relationships among the compounds present in a Port wine aging data set. This view of the data provides a considerable amount of information with which to understand the kinetic contexts of the molecules represented by peaks in each chromatogram. The aim of this study was to use NR together with the determination of kinetic parameters to extract more information about the mechanisms involved in Port wine aging. The volatile compounds present in samples of Port wines spanning 128 years in age were measured with the use of GC-MS. After chromatogram alignment, a peak matrix was created, and all peak vectors were compared to one another to determine their Pearson correlations over time. A correlation network was created and filtered on the basis of the resulting correlation values. Some nodes in the network were further studied in experiments on Port wines stored under different conditions of oxygen and temperature in order to determine their kinetic parameters. The resulting network can be divided into three main branches. The first branch is related to compounds that do not directly correlate to age, the second branch contains compounds affected by temperature, and the third branch contains compounds associated with oxygen. Compounds clustered in the same branch of the network have similar expression patterns over time as well as the same kinetic order, thus are likely to be dependent on the same technological parameters. Network construction and visualization provides more information with which to understand the probable kinetic contexts of the molecules represented by peaks in each chromatogram. The approach described here is a powerful tool for the study of mechanisms and kinetics in complex systems and should aid in the understanding and monitoring of wine quality.

Field-omics-understanding large-scale molecular data from field crops.

The recent advances in gene expression analysis as well as protein and metabolite quantification enable genome-scale capturing of complex biological processes at the molecular level in crop field trials. This opens up new possibilities for understanding the molecular and environmental complexity of field-based systems and thus shedding light on the black box between genotype and environment, which in agriculture always is influenced by a multi-stress environment and includes management interventions. Nevertheless, combining different types of data obtained from the field and making biological sense out of large datasets remain challenging. Here we highlight the need to create a cross-disciplinary platform for innovative experimental design, sampling and subsequent analysis of large-scale molecular data obtained in field trials. For these reasons we put forward the term field-omics: "Field-omics strives to couple information from genomes, transcriptomes, proteomes, metabolomes and metagenomes to the long-established practice in crop science of conducting field trials as well as to adapt current strategies for recording and analysing field data to facilitate integration with '-omics' data."

Untangling the chemistry of port wine aging with the use of GC-FID, multivariate statistics, and network reconstruction.

Chromatography separates the different components of complex mixtures and generates a fingerprint representing the chemical composition of the sample. The resulting data structure depends on the characteristics of the detector used, univariate for devices such as a flame ionization detector (FID) or multivariate for mass spectroscopy (MS). This study addresses the potential use of a univariate signal for a nontargeted approach to (i) classify samples according to a given process or perturbation, (ii) evaluate the feasibility of developing a screening procedure to select candidates related to the process, and (iii) provide insight into the chemical mechanisms that are affected by the perturbation. To achieve this, it was necessary to use and develop methods for data preprocessing and visualization tools to assist an analytical chemist to view and interpret complex multidimensional data sets. Dichloromethane Port wine extracts were collected using GC-FID; the chromatograms were then aligned with correlation optimized warping (COW) and subsequently analyzed with multivariate statistics (MVA) by principal component analysis (PCA) and partial least-squares regression (PLS-R). Furthermore, wavelets were used for peak calling and alignment refinement, and the resulting matrix was used to perform kinetic network reconstruction via correlation networks and maximum spanning trees. Network-target correlation projections were used to screen for potential chromatographic regions/peaks related to aging mechanisms. Results from PLS between aligned chromatograms and target molecules showed high X to Y correlations of 0.91, 092, and 0.89 with 5-hydroxymethylfurfural (HMF) (Maillard), acetaldehyde (oxidation), and 4,5-dimethyl-(5H)-3-hydroxy-2-furanone, respectively. The context of the correlation (and therefore likely kinetic) relationships among compounds detected by GC-FID and the relationships between target compounds within different regions of the network can be clearly seen.