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Visual-Near-Infra-Red (VIS/NIR) spectroscopy has led the revolution in high-throughput phenotyping methods used to determine chemical and structural elements of organic materials. In the current state of the art, spectrophotometers used for imaging techniques are either very expensive or too large to be used as a field-operable device. In this study we developed a Sparse NIR Optimization method (SNIRO) that selects a pre-determined number of wavelengths that enable quantification of analytes in a given sample using linear regression. We compared the computed complexity time and the accuracy of SNIRO to Marten's test, to forward selection test and to LASSO all applied to the determination of protein content in corn flour and meat and octane number in diesel using publicly available datasets. In addition, for the first time, we determined the glucose content in the green seaweed Ulva sp., an important feedstock for marine biorefinery. The SNIRO approach can be used as a first step in designing a spectrophotometer that can scan a small number of specific spectral regions, thus decreasing, potentially, production costs and scanner size and enabling the development of field-operable devices for content analysis of complex organic materials., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Traditional interpretation of GC-MS output involved the semi-quantitative estimation of outstanding low or high specific metabolites and the ratio between metabolites. Here, we utilize a systems biology approach to steroid metabolomics of a complex steroid-related disorder, using an all-inclusive analysis of the steroidal pathway in the form of a subject steroidal fingerprint and disease signature, providing novel methods of normalization and visualization. The study compares 324 normal children to pure enzymatic deficiency in 27 untreated 21-hydroxylase CAH patients and to complex disease in 70 children with obesity. Steroid profiles were created by quantitative data generated by GC-MS analyses. A novel peer-group normalization method defined each individual subject's control group in a multi-dimensional space of metadata parameters. Classical steroid pathway visualization was enhanced by adding urinary end-product sub-nodes and by color coding of semi-quantitative metabolic concentrations and enzymatic activities. Unbiased automated data analysis confirmed the common knowledge for CAH - the inferred 17-hydroxyprogesterone was up-regulated and the inferred 21-hydroxylase enzyme activity was down-regulated. In childhood obesity, we observe a general decrease of both glucocorticoid and mineralocorticoid metabolites, increased androgens, up-regulation of 17,20-lyase, 17-OHase and 11β-HSD1 activity and down-regulation of 21-OHase enzymatic activity. Our study proved novel normalization and visualization techniques are to be useful in identifying subject fingerprint and disease signature in enzymatic deficiency and insufficiency, while demonstrating hypothesis generation in a complex disease such as childhood obesity., (Copyright © 2014 Elsevier Inc. All rights reserved.)

While the definition of the 'genotype' has undergone dramatic changes in the transition from classical to molecular genetics, the definition of the 'phenotype' has remained for a long time within the classical framework. In addition, while the notion of the genotype has received significant attention from philosophers of biology, the notion of the phenotype has not. Recent developments in the technology of measuring gene-expression levels have made it possible to conceive of phenotypic traits in terms of levels of gene expression. We demonstrate that not only has this become possible but it has also become an actual practice. This suggests a significant change in our conception of the phenotype: as in the case of the 'genotype', phenotypes can now be conceived in quantitative and measurable terms on a comprehensive molecular level. We discuss in what sense gene expression profiles can be regarded as phenotypic traits and whether these traits are better described as a novel concept of phenotype or as an extension of the classical concept. We argue for an extension of the classical concept and call for an examination of the type of extension involved.