# Metabolomics/Printable version

The current, editable version of this book is available in Wikibooks, the open-content textbooks collection, at
https://en.wikibooks.org/wiki/Metabolomics

# Introduction to Metabolomics

Back to Book Table of Contents: Metabolomics Next chapter: Metabolites
* History
* Relationship to Traditional Metabolism

## The New World of Metabolomics

In the world of biology and biochemistry there are many tiers of function. There is the genome, which is the underlying blueprint for the workings of our cells. From the genome arises the proteome; the factories, building blocks and workhorses of the cell and the organism. But neither of these is enough to truly understand the workings of biological systems.
Cells and organisms have far more in them than just proteins and DNA. Metabolites are the organic chemical compounds that either start off the reactions within biology or act as intermediates, changing or being incorporated into each reaction along a metabolic pathway. The grand total of these compounds and their interactions throughout a cell or a species is the Metabolome. Traditionally metabolism was our way of understanding the Metabolome. It was measured in small-scale pathways through a reductionist approach. The idea was that the sum of the parts could be used to truly understand the whole. But the Metabolome can’t effectively be found through the sum of the parts, especially in the context of systems biology and metabolic engineering.
Newer tiers like Phenomics (the study of the set of phenotypes expressed by a cell) and new disciplines like Nutrigenomics (the study of relationship between nutrition and genetic function) depend heavily on comprehending the Metabolome in a large-scale fashion.
Metabolomics is the solution to this problem. A comprehensive, systems biology conscious approach to understanding the Metabolome in its full scope. Metabolomics seeks to avoid reductionism and apply high throughput analysis methods on metabolic levels in the cell. It will revolutionize fields like metabolic engineering and increase our knowledge of biological function phenomenally.

## Recommended Reading & Sources

Introduction: Metabolomics

## Articles and Web Pages for Review and Inclusion
## Peer-Reviewed Article #1:

What is metabolomics all about?
Roessner U, Bowne J. BioTechniques Special Issue (2009) 46:363–365
Reviewer: Arooj I

#### Main Focus

       The main focus of “What is metabolic all about?” by Ute Roessner and Jairus Bowne, is to describe various techniques (pathway mapping, metabolite fingerprinting, comparative overlays and etc.) which develop metabolomics to better understand the organization and roles of organisms in the environment. There were four species used in a study to determine the metabolite profiles. These species were; moss Physcomitrella patens, the model plant Arabidopsis thaliana, and the crop plants Hordeum vulgare L. and Triticum aestivum L. These comparisons were done with techniques such as cluster analysis, DiMS, and target analysis.

#### New Terms
##### New Term 1

    Multi-variant Method: This is a statistical method based on multivariate statistics. Multivariate statistics is a statistical analysis of more than one statistical variable at a time. This technique can be used to detect the effects of all the variables in a trade study.
http://www.ajronline.org/cgi/content/full/185/2/299,http://en.wikipedia.org/wiki/Multivariate_statistics

##### New Term 2

    Genetic Perturbation: This is a small change in a physical system. In a genetic perturbation is a biological change such as a mutation in an organism. http://www.ask.com/web?q=dictionary%3A+perturbation&content=ahdict%7C61997&o=10616&l=dir

##### New Term 3

    Metabolome: A metabolome is a complete set of small-molecule metabolites such as metabolic intermediates, hormones and other signaling molecules, and secondary metabolites which can be found within a biological sample, such as a single organism.
< http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-3TVXPC7-3&_user=47004&_coverDate=09%2F01%2F1998&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000005018&_version=1&_urlVersion=0&_userid=47004&md5=6ad860575d4269aa5de1da98a652c927>

##### New Term 4

    Transcriptomics: This is the study of a transcriptome. A transcriptome is the complete set of RNA transcripts produced by the genome at any one time. http://www.ask.com/bar?q=What+is+Transcriptomics&page=1&qsrc=2417&dm=all&ab=0&u=http%3A%2F%2Fgenome.wellcome.ac.uk%2Fdoc_WTD020758.html&sg=M6I18%2Fh0XH0FoWssUi2tSOVf6%2FiU%2Fnjmbi36hiDRfOM%3D&tsp=1265598042743

##### New Term 5

    Target Analysis: This analysis involves using one particular analytical technique for the determining and quantifying a small set of known metabolites. http://www.jointcommission.org/NR/rdonlyres/2B5D26DA-6BD1-48FD-A7FA-F9BBCBA49A9D/0/ORYX_Target_Analysis.pdf

##### New Term 6

    Metabolic Fingerprinting: A mass profile of the sample of interest is generated and then compared in a large sample population to screen for differences between the samples. http://www.biotechniques.com/multimedia/archive/00044/BTN_A_000113133_O_44653a.pdf

##### New Term 7

    Direct Infusion Electrospray Mass Spectrometry (DiMS): In this technique, crude extracts of subspecies are taken and directly injected to a mass spectrometer to obtain mass profiles. These mass profiles can then be used to study the metabolite differences between the subspecies of a class. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC92589/

##### New Term 8

    Hierarchical Cluster Analysis: This is a cluster analysis technique which arranges the clusters in an order of hierarchy. The two main categories for the hierarchical arrangements are agglomerative and divisive. Cluster analysis is the assignment of a set of observations into clusters in which the observations have some relevance in relation. http://www.statistics.com/resources/glossary/h/hclusteran.php, http://www.clustan.com/hierarchical_cluster_analysis.html

#### Summary

Metabolomics in the last twenty years has made gigantic progress in sequencing a number of different organisms and has made large investments in developing analytical approaches for the study of different cell products. These ‘omics approaches such as transcriptomics, metabolomics and etc. are essential in the study of organisms responding to their environments. Metabolomics helps understand the physiological state of an organism. Metabolites act as the language of metabolomics. Only a few technologies have been employed such as mass spectrometry with chromatographic techniques like NMR to analyze these metabolites. Due to the complexity of a metabolome, it is difficult to employ a single technique for analysis. Therefore a number of approaches have to be established for extraction of the information and interpreting it in a biological context. Detection, quantification and identification can be accomplished through cluster analysis, pathway mapping and etc.
One application used in the study of metabolomics is target analysis, which helps in determination and quantification of a few known metabolites. Another application is metabolite profiling which analyzes large set of compounds using important tools like GC-MS. Metabolomics helps quantify as many metabolites as possible and metabolic fingerprinting helps differentiate between these samples.
Most of the research in metabolomics is based on the construction of phylogenetic trees. Primary metabolites are used to determine nutritional and growth status. Secondary metabolites function as markers for taxonomy and phylogenetics. Direct infusion ectecrospray mass spectrometry was a very helpful tool in determining different fungal species. When compared to the phenotypic tree, more than 80% of the species could be classified based on their mass profile. To determine mechanisms for adaptation and tolerance of plants to abiotic stresses revealed that a number of responses are plant specific or are common between stresses and/or plants.
A study to compare levels of metabolites in four different species using metabolomic techniques demonstrated that the metabolite profiles of the species were very different. Classifications such as these demonstrate metabolomics as an important tool for the identification and classification or organisms. Studies in metabolomics would be pretty helpful for the basic principle of life and its evolution. The drawbacks of metabolomics could be that it only measures a small portion of all elements in a biological system. In the future, study of metabolomics such as the response of various organisms to different environments at the genetic, transcript, protein and metabolite levels would strengthen are knowledge of the biology framework in different life systems. It would also help us understand the function, organization and roles of organisms in nature.

#### Relevance to a Traditional Metabolism Course

The course about metabolism, teaches students about the chemical reactions occurring in an organism such as citric acid cycle, glycolysis and gluconeogenesis. From reading this article, it was found that metabolomics is a study of the chemical footprints left behind by the cellular processes organisms carry out in everyday life. Metabolomics in the article is described by various techniques used to statistically analyze these footprints. The footprints in the article are believed to be called metabolites. These metabolites are studied in subspecies of a class using techniques such as metabolic fingerprinting, DiMS and hierarchical cluster analysis. Most of these techniques are new analytical approaches, allowing biochemists broaden there research goals in metabolism.

## Web Resource: Introduction to Metabolomics

Introduction to Metabolomics
Barrett D. Introduction to Metabolomics Powerpoint File. Centre for Analytical Bioscience School of Pharmacy, The University of Nottingam
Reviewer: Steve S.

#### Main Focus

A summary of the basic principles of Metabolomics. Serves as a basic introduction to various experimental and analytical techniques of use in the field.

#### New Terms
##### Genomics

    The Study of whole genomes of organisms. Focuses on sequencing and analyzing entire genomes of organisms. (source: http://epa.gov/osa/spc/pdfs/genomics.pdf)

##### Transcriptomics

    The Study of gene transcripts. This science involves the study of all types of RNA produced from DNA, mRNA, rRNA, tRNA, and non-coding RNA. The transcript can be from one, or a whole population of cells. (source: http://www.systemsbiology.nl/datgen/transcriptomics/transcriptomics.html)

##### Proteomics

    The Study of the final protein products of an organism, population of cells, or individual cell. Various techniques are used to isolate, identify, and study the proteins in a proteome.(source: http://www.ncbi.nlm.nih.gov/pubmed/9740045)

##### Metabolomics

    A field of study regarding the various products and reactions that take place within an organism to achieve its various needs. Involves the study of both metabolites, as well as metabolic pathways. Closely associated with the field of proteomics. (source: http://www.bmrb.wisc.edu/metabolomics/)

##### Metabolites

    Products, as well as intermediate molecules, involved in metabolism. (source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1904337/?tool=pubmed)

##### Metabolic Pathway

    A set of chemical reactions inside a cell. Through series of intermediate steps,a metabolic pathway provides needed metabolic products. (source: http://www2.ufp.pt/~pedros/bq/integration.htm)

##### Chromatography

    Various laboratory techniqes which involve separating components of a mixture. Include Adsorption, Partition, Ion-exchange, Exclusion, and Affinity chromatography techniques. (source: http://www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf)

##### NMR analysis

    Analysis of data aquired through measurement of Nuclear Magnetic Resonance. NMR is a phenomenon that certain nuclei in molecules aquire when exposed to a static magnetic field. This effect is only observed in nuclei that have a property called spin. Through analysis of the level of NMR, information about the contents of a sample can be obtained. (source: http://www.cis.rit.edu/htbooks/nmr/inside.htm)

##### Metabolomic Fingerprinting

    A metabolomic fingerprint is an instantaneous measurement of the biochemistry of a cell under certain conditions. By observing the changes in metabolome under different conditions, these conditions can be diagnosed before typical symptoms occur. (source: http://dbkgroup.org/dave_files/Pharmacogenomics.pdf)

##### Mass Spectrometry

    The determination of chemistry of a molecule by breaking the molecule down into component ions. These ions are then separated according to their mass, and their charge. The output of mass spectometry is a count of ions of certain masses/charges. (source: http://www.cem.msu.edu/~reusch/VirtualText/Spectrpy/MassSpec/masspec1.htm)

#### Summary

Biology can be viewed as information processing on four interconnected levels. Each of these levels of information has an associated field of study. The flow of information starts at DNA, to RNA, to proteins, and finally metabolites. These are studied as the fields of Genomics, Transcriptomics, Proteomics, and Metabolomics. Metabolic Pathways are interconnected sets of chemical reactions. These pathways are complex, and difficult to study. However, many benefits can be gleaned from the study of metabolomics, and metabolites. Many metabolites are very highly conserved molecules. This means that the study of one organism can often yield results applicable to a wide range of organisms. Metabolomes can show influences of both genetics and environmental impacts. This allows metabolic diagnostics to have great power, as regardless of the source of a disease, it can be detected. Metabolites can be analyzed and measured through many techniqes. The main techniques include Mass Spectometry, NMR analysis, and chromatography. There are four levels on which metabolomes can be viewed. From most to least specific, these are Metabolite Target Analysis - measuring specific amounts of a single metabolite, Metabolic Profiling - viewing the abundance of related groups of compounds, metabolomics - the study of all metabolites in a cell, and Metabolic Fingerprinting - simple classification of metabolomes into important categories. There are many contributing factors to the difficulty in studying metabolomes. Rather than processing static information, of specific bits, such as genetics - which are made up of 4 base pairs, or proteins - made up of 20 Amino Acids. In contract, metabolism involves the interactions, over time, of thousands and thousands of different molecules. The products measured for metabolomes can vary in concentration from as low as nanomolar, to micromolar concentrations. Data from metabolomic analysis requires further analysis in order to interpret. The two main forms of these analysis is Principal Component Analysis. Despite these drawbacks, the benefits available from this analysis make it a productive field of study.

#### Relevance to a Traditional Metabolism Course

This article is a power point presentation, which provides an overview of Metabolomics. It serves nicely as a broad introduction to the techniques available for Metabolomics, as well as the purpose behind these techniques, their strengths, and weaknesses. There is a brief overview as to the role of metabolites, and their position in metabolic pathways - this is mostly presented as a review, however, and is most helpful to one already familiar with the concepts. This article is appropriate for giving an overview, or for a broad review, and does not go in depth in any given topic.

# Metabolites

Back to Previous Chapter: Introduction to Metabolomics Next chapter: Hormones
* Carbohydrates
* Lipids
* Amino Acids
* Nucleotides

### Table of Contents

* Carbohydrates
* Lipids
* Amino Acids
* Nucleotides

## Metabolites

Metabolites are organic compounds that are starting materials/intermediates in metabolism pathways. Metabolites are small simple structures absorbed in a diet. They include vitamins and essential amino acids. They can be used to construct more complex molecules, or they can be broken down into simpler ones. Intermediary metabolites may be synthesized from other metabolites and often release chemical energy. For example, glucose, can be synthesized via gluconeogenesis (an anabolic reaction) to form starch or glycogen, and can be broken down during glycolysis (catabolic reaction) to obtain chemical energy. End products of metabolism are excreted from the organism. Urea, for example, is an end product of protein degradation in man. Carbon dioxide is usually thought of as an end product of carbohydrate, protein, and fat degradation in aerobic organisms, although technically, carbon dioxide, as carbonic acid, can also participate in the biosynthesis of some substances, particularly in plants. Catabolism and Anabolism Catabolism: degradative metabolism involving the release of energy and resulting in the breakdown of complex materials (as proteins or lipids) within the organism. Anabolism: the constructive part of metabolism concerned especially with macromolecular synthesis.
Catabolism: File:Http://www.merriam-webster.com/dictionary/catabolism. Anabolism: File:Http://www.merriam-webster.com/dictionary/anabolism.

### Metabolites and their pathways
#### KEGG Pathways

GenomeNet is a resource database developed by the Kyoto University Bioinformatics Center dedicated to provide computational devices to aid the study on the genome are various areas in biomedical sciences. The database provide tons of diversified maps of various metabolic pathways in humans and in plants. In addition, topics such as disease and drugs research are also mentioned and discussed in details with visual aids. Gene sequencing and analysis are also hugely emphasized at GenomeNet that provides many bioinformatic tools to in studying the genome sequence motif, phylogenetic research, and everything else you want to know about genes. One of the huge contribution from GenomeNet is providing KEGG maps and pathways that served as visual aids for studying of Matabolomics.
Kyoto Encyclopedia of Genes and Genomes or KEGG, is a database of biological systems which consists of genes, proteins, chemical building blocks, molecular pathways, hierarchies and relationships between various biological objects. KEGG links genomes to biological systems and maps pathways together to see the interactive cycle and the metabolites involved. You can also search through the KEGG website by entering a specific organism.
Primary Metabolites: Below are links that show the different pathways of all Primary metabolites. Primary metabolites encompass reactions involving compounds which are formed as part of the normal anabolic and catabolic processes. These processes take in the cells of the organism.
KEGG Maps of Some Primary Metabolites :
* Carbohydrate Secondary Metabolite Pathway
* Lipid Metabolite Pathway
* Nucleotide Metabolism Pathway
* Energy Synthesizing Pathway
* Other Primary Metabolites Pathways
* Amino Acid Metabolite Pathways
* Glycan Biosynthesis Metabolite Pathway
* Cofactors and Vitamins Metabolite Pathways
New Vocabulary: 1. Orthologs, or orthologous genes, are genes in different species that are similar to each other because they originated from a common ancestor. 2. Ohnologous genes are paralogous genes that have originated by a process of whole-genome duplication. 3. Paralogs: a gene in an organism that is duplicated to occupy two different positions in the same genome, making the two copies paralogous. 4. Xenologs: Homologs resulting from horizontal gene transfer between two. Xenologs can have different functions, if the new environment is vastly different for the horizontally moving gene. In general, though, xenologs typically have similar function in both organism 5. Gametology: term which denotes the relationship between homologous genes on nonrecombining, opposite sex chromosomes. Gametologs result from the origination of genetic sex determination and barriers to recombination between sex chromosomes
Relevance: This website database relates to our course work and text book by compiling all of the metabolism pathways. It defines metabolites, characterizes them in their role they play in any pathway and gives us a clear view on the relationship it has with organism as a whole. This database can be used for research to further develop our understanding in the world of Metabolomics which will in turn help us understand and maybe even cure different illnesses.

#### MetaCyc

MetaCyc is a database for over 900 primary and secondary metabolic pathways from various organisms; it also contains associated compounds, enzymes, and genes. Similary to KEGG, MetaCryc database aid the studying of Metabolomics by providing visual aid of many metabolic pathways.
The exciting aspect of MetaCyc pathways is the detail explanation of the pathways. You can view all metabolites and their subclasses. (It also allows you to see all metabolites in relationship to each other and their hierarchy.)
New vocabulary: 1. Prostaglandin is any member of a group of lipid compounds that are derived enzymatically from fatty acids and have important functions in the animal body. Every prostaglandin contains 20 carbon atoms, including a 5-carbon ring. They are mediators and have a variety of strong physiological effects; although they are technically hormones, they are rarely classified as such. 2. Cyclooxygenases: Prostaglandins are produced following the sequential oxidation of AA, DGLA or EPA by cyclooxygenases (COX-1 and COX-2) and terminal prostaglandin synthesis. 3. Pseudo compound: is not necessarily a physical compound. For example light, or a mis match of DNA base pairs, could be considered pseudo compounds.
4. Superatoms: are clusters of atoms that seem to exhibit some of the properties of elemental atoms. 5. Taxon (plural taxa), or taxonomic unit, is a name designating an organism or group of organisms.
Relevance: This web site database relates to our course work and textbook in the same way the KEGG web page is. MetaCyc however allows for a user friendly specific search based on the organism. It also looks for closely on the genome.

#### The Human Metabolome Database

Human Metabolome Database is the most complete collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 metabolites. It contains every metabolite and where you can find them (biofluids, tissue etc) it gives the molecular structure, weight and IUPC. The HMDB also contains a collection of experimental metabolite concentration data compiled from hundreds of mass spectra and Nuclear Magnetic resonance metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. The HMDB contains compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Another aspect of the HMDB is Biofluid search which allows you to look at normal and abnormal concentrations of different metabolites for 7 different biofluids.
Universe-review.ca is a link that gives a brief summary on different essential metabolites. It goes through the structure of the molecule and their role in various metabolic pathways. Biosynth Chemistry & Biology is another site with specific information on Lipids. New Vocabulary: 1. CAS registry numbers are unique numerical identifiers for chemical compounds, polymers, biological sequences, mixtures and alloys. They are also referred to as CAS numbers, CAS RNs or CAS #s 2. Biofluid: encompasses any fluid found in the body, HMDB includes: Amniotic Fluid, Bile, Blood, Breast Milk, CSF, Feces, Lymph, Menses, Mucus, Saliva, Sebum, Semen, Sweat, Synovial Fluid, Urine, Vitreous Humour and Vomit. 3. Sebum: oily substances are secreted by Sebaceous glands called sebum and the debris of dead fat-producing cells. 4. Simplified molecular input line entry specification or SMILES: is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. 5. American Standard Code for Information Interchange (ASCII), character encoding based on the English alphabet. ASCII codes represent text in computers, communications equipment, and other devices that work with text Relevance: While the past two data base are more specific for metabolite pathways, HMDB focuses on the metabolite composition and chemistry/ chemical interaction. This is relevant because HMDB really breaks down each metabolite to the molecular level. HMDB also allows for purchasing of these compounds.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1694820.com
Summary: The main point of this peer review article is to discuss the glycolysis process, which results in the formation of ATP as the main fuel in the anaerobic eukaryote, Monocercomonoides. Both ATP and Glucose are metabolites that relate directly to glycolysis and would be included in the organism's metabalome. Since anaerobic eukaryotes lack a complete tricarboxylic acid cycle, they can only extract few molecule of ATP per molecule of glucose. This is opposite of human cells, which makes this article important as it discusses alternate versions of enzymes in glycolysis. In anaerobic eukaryotes, enzymes such as pyruvate orthophosphate dikinase and pyrophosphate-fructose 6-phosphate phosphotransferase were examined through horizontal gene transfers from the bacteria in question to other eukaryotes. Horizontal gene transfers are processes in which an organism transfers genetic material to another cell that is not its offspring. Analysis of the glycolytic pathway of Monocercomonoides resulted in identification of both single-gene trees and conserved HGT events that provide evidence for the monophyly of protists known as Ecavata. Shared horizontal gene transfer events between oxymonads and both Giardia and Trichomonas further supported this relationship. This relationship becomes an important resource as it focuses on using glucose metabolites of Monocercomonoides to determine its lineage.
Terms: Horizontal Gene Transfer- process in which an organism transfers genetic material to another cell that is not its offspring Monophyly- a group of organisms that includes an ancestral species and all of its descendants. Oxymonad- a group of flagellated protozoa found exclusively in the intestines of termites and other wood-eating insects. Diplomonads- a group of flagellates, most of which are parasitic. Also classified as Protists. Walking primers-is a sequencing method for sequencing large DNA fragments (between 1,3 and 7 kilobases) that works by dividing long sequences into several consecutive short ones. Phylogenetic analyses- Analysis of the evolutionary connections between traits (for example, sequences) Taxa- Any organism or group of organisms of the same taxonomic rank; for example, members of an order, family, genus, or species.
Relevance: How does this information relate to the information that you have studied in this course to date? This resource is very closely related to our current coursework. As one would recall we had to memorize the complete glycolysis pathway, which is exactly what this article covered. It focused on the enzymes involved in the pathway, which are some that I have memorized. It also reviewed the process through an anaerobic prospective, which sheds light on how glycolysis can be altered but still produce ATP. This is very interesting as we mainly focused on just the one type of glycolysis.

#### Institute for Analytical Sciences

http://www.isas.de/english/menu-top/research/research-departments/metabolomics/
Summary: ISAS’s main focus is to create analytical methods that will be able to answer questions about a metabolites specificity, selectivity, and dynamic range. They want to be able to identify a metabolom in a single step (ex: from a sample of air breathed out by a person being able to identify dangerous metabolites that would signal cancer was present in the lungs). Another goal of ISAS is to detect differences at the single cell level that come from mutations and the varying environments that each cell is in.
Terms: Biogenic- necessary for the maintenance of life processes (http://www.thefreedictionary.com/biogenic) Mycotoxins-A toxin produced by a fungus. The term is usually reserved for fungal metabolites that are toxic to man and/or animals and are produced by molds growing on foodstuffs (e.g., aflatoxins, ergot alkaloids). (http://www.plantpath.cornell.edu/glossary/Defs_M.htm)
Microfluidics- Microfluidics is the science of designing, manufacturing, and formulating devices and processes that deal with volumes of fluid on the order of nanoliters or picoliters. The devices themselves have dimensions ranging from millimeters down to micrometers. (http://whatis.techtarget.com/definition/0,,sid9_gci526632,00.html)
Hyphal- a long, branching filamentous cell of a fungus, and also of Actinobacteria. In fungi, hyphae are the main mode of vegetative growth, and are collectively called a mycelium. (http://en.wikipedia.org/wiki/Hyphal)
Amperometric- relating to or being a chemical titration in which the measurement of the electric current flowing under an applied potential difference between two electrodes in a solution is used for detecting the end point (http://www.webster.com/dictionary/amperometric)
Voltammetry- is a category of electroanalytical methods used in analytical chemistry and various industrial processes. In voltammetry, information about an analyte is obtained by measuring the current as the potential is varied. (http://en.wikipedia.org/wiki/Voltammetry)
Chronocoulometry- The study of electrode surface properties, such as surface area. (http://www.answers.com/topic/chronocoulometry?cat=technology)
Cytostatic- inhibiting or suppressing cellular growth and multiplication (http://medical-dictionary.thefreedictionary.com/cytostatic)
Relevance: A lot of the techniques that ISAS uses so far are similar to subjects we have studied in the course. ISAS uses nuclear magnetic resonance spectrometry to evaluate intracellular and extracellular metabolites in human bowel tissues in an attempt to identify metabolites created by cancer cells. In Chapter 4 we learned that NMR can show the dynamic part of a components structure (folding, conformational alterations, and interactions with different molecules). Through the use of this method people could diagnosed with colorectal cancer earlier and through a less invasive method than before. Since cancer cells have mutated genes and create different metabolites than the colorectal cells normally would, a method being able to identify these products would be very helpful. In chapter 3 we learned about Mass Spec methods including MALDI MS, ESI MS, and MS/MS. ISAS uses ion mobility mass spectrometry in a lot of their projects including mold identification, analysis of breath to check for diabetes and lung cancer. Ion Mass Spec (IMS) detects low amounts of chemicals by using a homogenous electric field to see differences in migration of the gas phase ions. Where proteomics and genomics can show general drug treatments for problems, the Single Cell Laboratory research could be used to create specific drugs for each individual person’s unique cells and how their metabolome might be different.

#### Learn More

Additional Articles:
1)A metabolome study of the steady-state relation between central metabolism, amino acid biosynthesis and penicillin production in Penicillium chrysogenum
2)A critique of the molecular target-based drug discovery paradigm based on principles of metabolic control: Advantages of pathway-based discovery
3)Metabolomics - the way Forward
Images The following links are images, structures and diagrams of each previously mentioned metabolite. File:Http://www.brynmawr.edu/Acads/Chem/mnerzsto/carb-1.htm - Carbohydrate structures. File:Http://www.ncbi.nlm.nih.gov/sites/entrez?db=pccompound&term=carbohydrate – PubChem images for Carbohydrate. File:Http://www.ncbi.nlm.nih.gov/sites/entrez - PubChem images for Lipids. File:Http://www.chemistryland.com/ElementarySchool/BuildingBlocks/Lipids.jpg - Lipid File:Http://www.ncbi.nlm.nih.gov/sites/entrez - PubChem Amino Acids File:Http://www-jmg.ch.cam.ac.uk/data/molecules/amino/ - All Amino Acids (formula and diagram) File:Http://www.ncbi.nlm.nih.gov/sites/entrez - Nucleotide PubChem File:Http://publications.nigms.nih.gov/thenewgenetics/images/ch1 nucleotide.jpg - The big picture - Nucleotides File:Http://www.nvo.com/jin/nss-folder/scrapbookcell/4 nucleotide.jpg – 4 Nucleotides File:Http://www.ncbi.nlm.nih.gov/sites/entrez - Co-factors PubChem File:Http://www.ncbi.nlm.nih.gov/sites/entrez PubChem Glycan

## Metabolites Index
# Hormones

Back to Previous Chapter: Metabolites Next chapter: Analytical Methods

# Hormones

Hormones are defined as chemical signals that affect one or more cells in an organism. Hormones can have an amplification effect where a small signal causes a large response.

## Table of Contents

* Insulin
* Glucagon
* Somatostatin
* Corticosteroids
* Mineralocorticoids
* Leptin
* Adiponectin
* Ghrelin

# Analytical Methods

Back to Previous Chapter: Hormones Next chapter: Computational Modeling of Metabolic Control
* NMR
* Mass Spectrometry
* Sample Preparation
* Fluids
* Tissues
* Statistical Methods

## Analytical Methods Introduction

Metabolomics is a field where the discovery of specific cellular metabolites is essential to the field. Without the tools and methods to discover the metabolites, metabolite profiles and cellular processes unique to organisms cannot be discovered. Methods for discovering metabolomes range from technical chemical methods such as NMR to statistical analysis.

## The Sumner Group

The Sumner Group is involved in the research of plant metabolomics. This is challenging because of 3 primary limitations. Profiling the metabolome is difficult because of its chemical diversity. Genomic and proteomic variance are limited by the basic components (nucleotides and amino acids), whereas metabolomes lack any sort of consistency. Another problem is dynamic range, which deals with measurement tolerance and sensitivity. The third problem is analytical and biological variance, which deals with deviations in measurement and in composition. The Sumner group is developing a way to get around these problems by dividing metabolites into different groups for analysis. The analytical techniques they develop are used to research disease in plants, and also to develop computational model organisms of plants.
Terms
transcriptome – the set of all transcripts produced by either a single cell or an entire organism principal component analysis – a statistical technique used to separate data into classes hierarchical clustering – a method to determine relationships or similarity between data sets. GC/MS (gas chromatography coupled to mass spectrometry ) - a way to profile large numbers of metabolites by separation (GS) and then measurement (MS) HPLC (high performance liquid chromatography) – a technique to separate both volatile and nonvolatile elements. Coupled to MS, it is another way to profile a large number of metabolites.
Relevance
The research of this group looks at metabolic regulation and its relationship to diseases in plants. This course looks at metabolic regulation, and problems within a pathway that can lead to disease. The area that is more relevant is the group's efforts at creating a model organism. The comprehensive understanding of an organism's metabolic regulation, depending on environmental conditions, relates to the regulatory mechanisms covered in class thus far.

## Three Dimensional Cellular Microarray for High-Throughput Toxicology Assays

Three-dimensional cellular microarray for high-throughput toxicology assays
The main purpose of this paper was to develop a miniaturized 3D cell-culture array (DataChip) that would screen drug candidates for toxicity of a particular drug at the early stages of drug development. This is important due to amount of research put into drug development in today's world. The DataChip will hopefully select for drugs that cause adverse effects, remove them from development and help bring more drugs into the development process. This DataChip will be able to rapidly identify metabolic activation or deactivation of xenobiotics before they ever enter a human being. Xenobiotics are metabolized in the liver and in most cases, the liver is adversely affected by drugs. The DataChip’s aim is to significantly reduce the number of cases of liver failure due to xenobiotic metabolism, which is the leading cause of liver failure.
Terms:
Xenobiotics – chemical which is found in an organism but which is not normally produced or expected to be present in it
Microarray – biological assay
Alginate - viscous gum that is abundant in the cell walls of brown algae
P450 isoforms – (CYP1A2, CYP2D6, and CYP3A4) enzymes that are a part of the mixed-function oxidase system
IC50 values - or the half maximal inhibitory concentration
Hep3B cells – Human hepatoma cells
Fluorogenic - a process in which fluorescence is generated
Ketoconazole - synthetic antifungal drug used to prevent and treat skin and fungal infections
Relevance: In class, we were discussing different metabolic pathways in the human body and the different products they produce. We were also learning how all these processes are linked to one another. This paper talks about new ways to detect harmful side effects caused by the metabolism of a substance. Xenobiotics are broken down in the liver. Glycolysis and gluconeogenesis both take place in the liver as well. If the liver if damaged by xenobiotic metabolism, then glycolysis and gluconeogenesis would also be disrupted. This paper describes other metabolic process that occurs in the body and the possible side effects of the metabolites.

## Recommended Reading

High Resolution Separations and Improved Ion Production and Transmission in Metabolomics
Metabolomics involves the detection and quantification of as many sample components as reasonably possible in order to identify compounds that can be used to characterize the samples under study. In electrospray ionization, ions are produced for analysis my mass spectrometry (MS). When applying this technique to metabolomics, it is important that metabolome sample constituents are efficiently separated prior to ion production, so that ionization suppression is minimized. This will ensure an extensive dynamic range of the measurement, as well as coverage of the metabolome. Measurement sensitivity may be increased by optimizing the MS inlet and interface.
Advancements in front end liquid chromatography (LC) separations, electrospray ionization and ion transmission efficiency have increased the sensitivity of liquid chromatography-mass spectrometry (LC-MS)-based measurements. An extended and more reproducible coverage of the metabolome has resulted in the detection of larger numbers of features characterized by accurately measured masses and retention times. Ionization efficiency has been improved with small i.d. columns that provide lower flow rates. This has led to greater sensitivity and better quantification. However, longer columns that provide high separation peak capacities produce lengthy analysis times that are not amenable in the analysis of large numbers of samples, which are required for statistically significant metabolomics studies. Alternative and complementary approaches, such as ionization electrospray-mass spectrometry (IMS-MS) or liquid chromatography-ionization microspray-mass spectrometry (LC-IMS-MS) are in development. These methods would provide higher throughput, which would allow for a moderately high coverage analysis of several hundred samples over the duration of a few days.
Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS
In an effort to simplify and streamline compound identification from metabolomics data generated by liquid chromatography time-of-flight mass spectrometry, software has been developed for constructing Personalized Metabolite Databases with content from over 15,000 compounds pulled from the public METLIN database. Extra functionalities have been added that permit the addition of user-defined retention times as an orthogonal searchable parameter; and allow interfacing to separate software, a Molecular Formula Generator (MFG), that facilitates reliable interpretation of any database matches from the accurate mass spectral data. In an effort to assess the utility of this identification strategy, retention times have been added to a subset of masses in this database that represent a mixture of 78 synthetic urine standards. The mixture was analyzed and screened against this METLIN urine database, which resulted in 46 accurate mass and retention time matches. Human urine samples had been analyzed under the same analytical conditions and were screened against this database. Another 374 had an accurate mass match to the database, where 163 of those masses had the highest MFG score. What’s more, MFG calculated a formula for an additional 849 ions that had no database matches. These results indicate that the METLIN Personal Metabolite database and MFG software offer an exemplary strategy for confirming the formula of database matches. If no database match is found, possible formulas are suggested.
Since a mass determination cannot assign elemental composition with absolute certainty, it has been suggested to complement database assignment of high mass accuracy data with other techniques such as isotope ratios and RT. It has been demonstrated that the METLIN Personal Metabolite Database software can be used to assign the correct elemental compositions for a set of urine metabolite standards. Including RT as a separate, orthogonal variable will allow for rapid, positive identification of the temporally resolved masses. Combining MFG capacity with mass and RT database matching is expected to increase the confidence with which both known and unknown compounds are assigned a correct elemental composition.
Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry
Fourier Transform Cyclotron Resonance Mass Spectrometry (FTICR-MS) offers unparalleled mass resolution, mass accuracy, and superb detection sensitivity. With these features, FTICR-MS is capable of becoming a powerful technique for high-throughput metabolomics analysis. This study examines properties of ultrahigh-field 12-Tesla (12T) in order to identify and quantify human plasma metabolites, and for the untargeted metabolic fingerprinting of inbred-strain mouse serum by direct infusion (DI). Rational elemental compositions (incorporated unlimited C, H, N and O, and a maximum of two S, three P, two Na, and one K per formula) of approximately 250 out of 570 metabolite features were detected in a 3-min infusion analysis of aqueous extract of human plasma, and were able to identify more than 100 metabolites. Isotopically-labeled internal standards were used to obtain high-quality calibration curves for the absolute quantitation of choline with sub-pmol sensitivity. This required 500 times less sample than previous LC/MS analyses. Optimal serum dilution conditions allowed for chemical compounds that were spiked into mouse serum as metabolite mimics to produce a linear response that spanned over a 600-fold concentration range. DI/FTICR-MS analysis was conducted on serum from 26 mice from 2 inbred strains, with and without acute trichloroethylene (TCE) treatment. This method had also been extended to the metabolomic fingerprinting of serum samples from 49 mice from 5 inbred strains that were involved in an acute alcohol toxicity study, with positive and negative electrospray ionization (ESI). It was demonstrated that more upwards of 400 metabolites could be profiled within 24 hrs, when applying DI/FTICR-MS to these samples.
Ultrahigh-field FTICR-MS has proven to be a potentially invaluable tool for qualitative metabolomics. The superior mass resolution facilitates the detection of hundreds of metabolites in complex samples in the DI mode. The mass accuracy frequently allows the identification of low-mass metabolites that are based solely on mass. This is accomplished by generating elemental compositions and then searching available metabolome databases.
Ultrahigh-field FTICR-MS can also be used to rapidly generate differential metabolite profiles in samples taken from large studies. However, DI/FTICR-MS is not comprehensive and therefore will not likely eliminate the need for chromatographic separations to achieve thorough metabolome coverage and to differentiate metabolite isomers. Software is currently being developed to enhance the potential of FTICR-MS for high-throughput metabolomics. This software would facilitate analyses by automatic detection of differentially-abundant metabolites, followed by their automated identification via elemental composition determination and metabolome database searching.

# Articles and Web Pages for Review and Inclusion

Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometry
LC-MS-based metabolomics in drug metabolism

# Computational Modeling of Metabolic Control

Back to Previous Chapter: Analytical Methods Next chapter: Databases

# Computational Modeling of Metabolic Control

Metabolomics is a systems biology look at the interactions of metabolic pathways within an organism.
Computational tools are useful and necessary to model these complex interactions and predict outcomes of perturbations of the system. A computational model of mitochondria and electrophysiological metabolism has been established, and applied to data collected from analyses conducted on cardiac mitochondria and phosphate metabolites in striated muscle, in vivo. The model is based on kinetic and thermodynamic details of reaction mechanisms of biochemical species. Building such an elaborate and kinetically encompassing model necessitated a vast collection of quantitative data from respiring mitochondria under specific closely monitored conditions. These details were then catalogued along with their results. Further validation of the model resulted from in vitro data measurements from cardiac muscle and in vivo measurements from skeletal muscle. The model was capable of predicting the roles of NAD and ADP in tricarboxylic acid cycle dehydrogenase regulation, and determined that NAD was a more significant regulator. The model was also capable predicting the effects of cytosolic pH fluctuation. Specifically, the model determined that decreases in the pH resulted in mitochondrial membrane potential reduction, which in turn decreased the rate of ATP synthesis.
Current research suggests that a vast quantity of independent data collected from experiments on in vivo and ex vivo systems would provide a comprehensive model of mitochondria metabolism. Established predictions based upon this model indicated the mitochondrial redox state as a primary regulator of tricarboxylic acid cycle flux. This model also reinforces results from similarly conducted research supporting the determination of inorganic phosphate strongly affecting the mitochondria redox state. Specifically, it was determined that inorganic phosphate influences the tricarboxylic acid cycle as a substrate and a cofactor. The current model also determined that mitochondrial ATP synthesis is directly dependent upon ADP and inorganic phosphate activation of oxidative phosphorylation, as well as NAD and inorganic phosphate activation of the tricarboxylic acid cycle.
A future prospect for this model is expected to involve analyzing calcium regulation of mitochondrial energetics. This will require including the established roles of Ca2+ in regulating pyruvate dehydrogenase, isocitrate dehydrogenase, and -ketoglutarate dehydrogenase within the model.
References: http://www.jbc.org/cgi/content/full/282/34/24525

## E-Cell2 Simulation System

Available for download at http://www.e-cell.org
Main Focus:
The E-Cell2 simulation system is a publicly available simulation system for modeling, simulation and analysis of complex, heterogeneous and multi-scale systems like the cell. Within this package, a computational tool for mitochondrial systems biology has been included. The model was developed by integrating enzyme kinetics studies previously published in the literature. Instead of looking at pathways individually, the model integrates the respiratory chain, the TCA cycle, fatty acid B-oxidation, and metabolite transport systems to allow an observation of the dynamic behavior of the mitochondria as a whole. The model should allow investigators to evaluate the influence of metabolite treatments on the organelle as a whole.
This model is flexible and allows the incorporation of other models created by independent researchers. E-Cell is implemented in C++ computer language.
Additional literature about the model: http://bioinformatics.oxfordjournals.org/cgi/reprint/20/11/1795
New Terms:

### Lineweaver-Burk plots

    Also known as a double reciprocal plot, this is a graphical representation of the Lineweaver-Burk equation of enzyme kinetics. This method was developed before nonlinear regression was available to fit curve data into straight lines. The plot is used to provide a graphical analysis of the Michaelis-Menten equation and describe values for Vmax and KM.

### Michaelis-Menten equation

    This equation describes the relationship between the rate of substrate conversion by an enzyme to the concentration of the substrate. The equation is given below, where Km is the Michaelis constant, V is the rate of conversion, Vmax is the maximum rate of conversion, and [S] is the substrate concentration.

### Fourth-order Runge-Kutta method

    This is a method of numerically (approximately) integrating ordinary differential equations. It uses a trial step at the midpoint of an interval to cancel our lower-order error terms. The method is reasonably simple and robust, making it a good candidate for numerical solutions of differential equations. The method was developed by the German mathematicians C. Rung and M.W.Kutta.

### TCA Cycle

    Abbreviation for the tricarboxylic acid cycle. This is also commonly referred to as the citric acid cycle or the Krebs cycle (for its discovered Hans Krebs).

### Quantitative Modeling

    As opposed to experimental modeling which shows the general interactions of systems, quantitative modeling describes the precise concentrations of metabolite flux in and out of systems. Quantitative modeling has been made possible through mathematical analysis of biochemical models and has become essential to understand the cell at a systems level.

### Bifurcation

    In general, bifurcation is the splitting of a main body into two parts. In a dynamic system bifurcation is a period of doubling, quadrupling etc.
Connection to Biochemistry Metabolism Course:
The mitochondrial model includes processes we have studied in depth, including fatty acid B-oxidation (chapter 17) and the respiratory chain (chapter 20). It also includes inner-membrane transport system. We have looked at several transport systems, for example the citrate shuttle for acetate out of the mitochondria (chapter21). Another cycle included in the model, the TCA cycle or Citric Acid Cycle (chapter 16) was a large focus of our studies.

## Computer Simulation of Metabolism:

Available at: http://www.hort.purdue.edu/cfpesp/models/models.htm
Main Focus:
The site has a good introduction to the utility of computational models for quantitatively analyzing traditional isotopic tracer methods and isotopic kinetic data. Experimental methods using stable isotope and radioisotope tracers to monitor kinetics of intermediates in metabolic pathways can be interpreted using computer routines to give insight into the fluxes and compartmentation of the pools of these metabolites. The site provides a breakdown of an example of a basic iterative computer model used to simulate labeling behavior of non-steady state intermediates. The important distinction is that iterative model can be applied to non-steady-state situations or to a situation with multiple pools of intermediates with different turnover rates, basic kinetic equations cannot.
New Terms:

### Steady-state

    Pools of intermediates and rates of reactions remain constant with time.

### Non-steady state

    Pools of intermediates expand and deplete with time.

### Pulse-chase labeling kinetics

    In this commonly used protocol, a cell sample is exposed to a radio-labeled compound for a brief period of time, referred to as a ‘pulse’. The quantity of labeling can be shown to be a function of the length of exposure time. After exposure, the sample is washed with a buffer solution. This removes the isotope. Next, there is a ‘chase’ step where the sample is incubated with a non-labeled form of the compound. These experiments are useful for following intra-cellular location of proteins or the transformation of a metabolite into others over a period of time/ through a biological pathway.

### Effluxes

    Refers to the movement of metabolites out of a cell or compartment.

### Hill Coefficient

    This is a measure of cooperativity in a binding process. It was originally worked out for the binding of oxygen to hemoglobin. A hill coefficient of 1 indicates independent binding, a hill coefficient greater than 1 indicates a positive cooperative binding of one ligand facilitates binding of subsequent ligands at other sites on the multimeric receptor complex.

### GS/GOGAT Cycle

    Responsible for glutamate synthesis. Within this process ammonia is assimilated and recycled. The GS stands for glutamine synthase and GOGAT stands for an NADPH-dependent glutamine:2-oxoglutarate amidotransferase (or glutamate synthase).
Connection to Biochemistry Metabolism Course:
Within this site pools of metabolic intermediates and multiple compartments are considered. We have explored the impact of compartmentalization as a form of regulation. For example in the regulation of hexokinase IV (glucokinase) when fructose 6-phosphate concentration in the liver is high, a nuclear binding protein draws hexokinase IV into the nucleus. This prevents it from acting in glycolysis. We have also looked at the significance of pools of activated intermediates (such as Acetly-CoA and succcinly-CoA) and reduced intermediates (such as NADH and NADPH) and the role their transport and availability plays in metabolic reactions.

## JWS Online Cellular Systems Modeling

Available at http://jjj.biochem.sun.ac.za/index.html
Query for all organisms metabolic pathway simulations: http://jjj.biochem.sun.ac.za/cgi-bin/processModelSelection.py?organism=All&category=metabolism
Main Focus:
JWS Online is a systems biology tool for simulation of kinetic models from a curated model database. It provides access to a collection of published kinetics models divided into the categories of metabolism, gene expression, translation, cell cycle, enzymology, single transduction, and unknown. The models can be queried by this category and/or by the organism being modeled. Organisms available range from Homo Sapien to Dictyostelium. The models have been compiled from various authors (another query option), and are available for download or can be run within the website. Manuscript details (author, source, description, etc.) are also provided. Java applets are required to run the models. Within the models users can change enzyme parameters, run time simulations or do steady state analysis.
New Terms:

### Curated Database

    A curated database refers to a database that has been created and is maintained with a significant amount of ‘manual’ labor. Its creators typically monitor and update the content of the sight as appropriate.

### Enzymology

    The branch of chemistry concerned with the properties and actions of enzymes.

### The Silicon Cell Project

    Research initiative that JWS Online is a part of. The long term goal of this project is “the computation of Life at the cellular level on the basis of the complete genomic, transcriptomic, proteomic, metabolomic and cell-physiomic information that will become available in the forthcoming years”. Those involved predicted the initiative would take a decade to complete, and it began in 2000. (No word available as to how close they feel they are to completion).

### Armoracia rausticana

    Misspelled within the site (actual spelling Armoracia rusticana), this is the scientific name for the plant horseradish.

### Entamoeba histolytica

    This is a type of anaerobic parasitic protozoan. It infects primarily humans and other primates, leading to amoebic dysentery or amoebic liver abscess.

### Leishmania infantum

    This parasite is an intracellular pathogen of the immune system. It targets macrophages and dendritic cells, causing the disease Leishmaniasis which affects millions of people worldwide. A more severe and life-threatening form of the illness is caused by a different species, L. donovani.

### Lactococcus lactic

    This is a mesophilic fermentative bacterium which produces lactic acid from sugar (hexose) fermentation. Strains of this bacterium are used in the production of fermented milk products.
Connection to Biochemistry Metabolism Course:
Within this database many different models of metabolic pathways are available. For example, glycolysis pathways from many different authors are offered for E. coli, H. sapiens, L. lactis, S. cerevisiae, sugar cane, and more. By clicking ‘run’ we can see the pathway, for example for glycolysis in S. cervisiae. For our studies it is interesting to then compare that to the glycolysis pathway in humans. The ability to perturb any cofactor, intermediate, or enzyme in the system and see its affect on the entire system reinforces the connections we have been studying all year. For example, increasing ATP will decrease formation of Fructose 1,6-bisphosphate.

## GEM System: Automatic Prototyping of Cell-wide Metabolic Pathway Models From Genomes

By: Kazuharu Arakawa,1 Yohei Yamada,1 Kosaku Shinoda,1 Yoichi Nakayama,1 and Masaru Tomita BMC Bioinformatics. 2006; 7: 168. Published online 2006 March 23. doi: 10.1186/1471-2105-7-168. Copyright © 2006 Arakawa et al; licensee BioMed Central Ltd.
Available at: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1435936%20-%20peer%20review%20article
Main Focus:
Being able to model cellular processes on a systems wide level is a labor intensive process. This article introduces a new tool, the Genome-based Modeling (GEM) System, which makes this task accessible. It is a tool that simulates cell-wide metabolic pathways using genomic sequence data and other biological information from public repositories. The genomic sequence data (annotated or unannotated) is used to create a rough metabolic network from publicly available databases and allows for more specific information to be added retrospectively. The system works by matching coding regions of the genome sequence with reaction stoichiometry for qualitative modeling. Next, a cell-wide simulation is created using these reactions quantitatively modeled through kinetic equations. The computer-based model produced allows researchers to simulate and study complex dynamic biological systems, analyzing system-level behavior and testing experimental hypotheses. Most previous models are developed manually and/or focus on small pathways when dealing with dynamic modeling. An Escherichia coli metabolism model developed by the GEM system achieved 100% coverage of the KEGG database model, 92.38% when compared with the EcoCyc database, and 95.06% when compared with the iJR904 genome-scale model.
New Terms:

### Systems Biology

    The study of the integrated and interacting network of genes, proteins, and biochemical reactions in an organism as a whole.

### Bottom-up Approach

    In this context, refers to beginning the process of molecular modeling with a great amount of expert knowledge and experimental data. This information is combined to create a coherent model.

### Top-Down Approach

    Beginning with a complete model and using it to produce specific information. This is the approach taken by GEM by using genomic data to create a basic metabolic network, adding more specific information later.

### Bottleneck

    This is a process or event which creates a large backup in a system. Manual modeling of cellular networks has been referred to as a bottleneck in systems biology because it is a slow process that causes a backup in the large amount of information which goes into it.

### Systems Biology Markup Language (SMBL)

    A standard format for systems biology information which is computer-readable. This format is required for input data in to many different simulation software packages. The automated output of GEM can be concerted to SBML.

### GLIMMER

    This is a system for identifying genes in microbial DNA. It is used within GEM to annotate genome data when unannotated data is given

### MetaCyc Database

    A database of non-redundant, experimentally elucidated metabolic pathways, containing over 900 pathways from more than 900 different organisms. The pathways are involved in bot primary and secondary metabolisms, as well as associated compounds, enzymes, and genes. This database is used to check pathways generated using GEM. http://metacyc.org/

### COG

    A database tool for genome-scale analysis of protein functions and evolution. GEM uses this resource to help annotate genomic data.

### EcoCyc

    This is a scientific database for the bacterium Escherichia coli K-12 MG 1655. The project performs a literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. http://ecocyc.org/

### iJR904 genome-scale model

    A complete, chemical description of E. coli metabolism. It includes 904 genes and 931 unique biochemical reactions.
Connection to Biochemistry Metabolism Course:
We have discussed how homeostasis within living cells is maintained in a “steady state dynamic”. This refers to the idea that while the gross composition of the cell stays the same over time, the concentrations of materials in the cell are constantly changing in response to changes in the environment and the needs of the organism. The GEM systems tool is a way of modeling the dynamic interactions within the cell which correspond to these changes. This is powerful because, while understanding metabolic pathways is helpful, being able to simulate them and experimentally model their actions under set conditions is extremely useful in research.
In class and the text we have also been exposed to the KEGG pathway database. This database models an integrated system of pathways, including the relationships of these pathways to genomic data, chemical building blocks of substances, and networks of interactions and relationships. GEM uses KEGG as a standard reference. By stating that their tool achieves 100% coverage when compared with KEGG, they are stating that their tool was able to identify all of the relationships that the KEGG database dose. Since KEGG is a well accepted resource for this type of information, this comparison signifies that their tools produces significant results.

## Computational Model of In Vivo Human Energy Metabolism During Semistarvation and Refeeding

By: Kevin D. Hall Am J Physiol Endocrinol Metab 291: E23-E37, 2006. First published January 31, 2006; doi:10.1152/ajpendo.00523.2005 0193-1849/06
Available at http://ajpendo.physiology.org/cgi/content/full/291/1/E23
Main Focus:
This paper describes a mathematical model that relates dietary marco-nutrient intake to computed whole body expenditure, de novo lipogenesis, gluconeogenesis, and turnover and oxidation of carbohydrate, fat, and protein. Using the classic Minnesota human starvation experiment and published in vivo human data the model simulates measured body weight and fat mass changes during semi-starvation and refeeding. In conjunction with this, unmeasured metabolic fluxes underlying these body composition changes were predicted. The study also looks at body composition in terms of fat and lean tissue in relation to the in vivo metabolic fluxes that regulate this composition.
New Terms:

### Minnesota Human Starvation Experiment

    Performed at the University of Minnesota from November 1944 to December 1945, this experiment is renowned for its comprehensive set of careful measurements taken over an extended duration of precisely controlled feeding. The goal of the experiment was to investigate the physiological and physiological effects of severe and prolonged dietary restriction and the effectiveness of dietary rehabilitation strategies.

### Lipolysis

    The breakdown of lipids stored in the cell, or the hydrolysis of triacylglycereides to free fatty acids from fats.

### Proteolysis

    The breakdown of proteins in the cell.

### PI

    Protein intake rate in kcal/day

### ProtOx

    Rate of protein oxidation in kcal/day

### FI

    Fat intake rate in kcal/day

### FatOx

    Rate of fat oxidation in kcal/day

### BCM

    Body Cell Mass (in grams)

### CI

    Carbohydrate intake rate in kcal/day

### CarbOx

    Rate of carbohydrate oxidation in kcal/day

### RMR

    Resting metabolic rate in kcal/day

### ProtOx

    Rate of protein oxidation in kcal/day

### Basal metabolic rate (BMR)

    The amount of energy normally required by an individual at rest in a neutrally temperature environment.
Connection to Biochemistry Metabolism Course:
As we have studied, the model showed connections between the daily content of body protein, glycogen, and fat and the daily average rates of proteolysis, glycolysis/ gluconeogenesis, and lipolysis, respectively. Based on what we have learned, in the starved state with a lack of these inputs (protein, glycogen, fat) we would expect a increase in proteolysis, a decrease in gluconeogenesis and an increase in glylcolysis, and an increase in lipolysis. This is exactly what the model showed in the semi-starved state. In the fed state, or refeeding state of the model, we see the opposite of these conditions.

## An Enzyme Mechanism Language for the Mathematical Modeling of Metabolic Pathways

By: Chin-Rang Yang 1,3, Bruce E. Shapiro 4, Eric D. Mjolsness 2,3 and G. Wesley Hatfield 1,3,* Bioinformatics 2005 21(6):774-780; doi:10.1093/bioinformatics/bti068 Available at http://bioinformatics.oxfordjournals.org/cgi/content/full/21/6/774
Main Focus:
The goal of this project was to create mathematical models of common mechanisms that occur in metabolic pathways and other biological processes. The authors have developed kMech, a language extension of Cellerator, that models a suite of enzyme mechanisms. These enzyme mechanisms can be used within mathematical modeling of enzyme-related pathways. The reaction mechanisms are based on mass action kinetics and each generates a set of elementary reactions that are then translated into ordinary differential equations and association-dissociation reactions that can be solved by Mathematica. The simulations modeled by kMech procude graphic outputs. The program can be executed by Mathematica software installed in a Microssoft Windows, MacOS or Linux operating system. The advantage of kMech over traditional enzyme modeling approaches is that its reaction mechanisms incorporate multiple substrates, products, and regulatory mechanisms. It is a user-friendly tool which allows biologists to model biochemical pathway without knowledge of the underlying mathematics.
New Terms:

### Cellerator

    A tool for generating reaction network models of cellular processes

### Mathematica

    A widely used commercial computer algebra system that integrates numeric and symbolic computational engines with a graphical output and a programming language.

### Mass Action Kinetics

    Mass action kinetics states that the rate of a reaction if equal to the product of a rate constant (k) times the concentration of the substrate (S), also referred to as the mass.

### Systems Biology Markup Language (SBML)

    A standard format for systems biology information that is computer-readable. This format is required for input data in to many different simulation software packages.

### Steady-state Velocity Equations

    Equations for enzyme modeling that set the derivatives of the concentrations of each reactant in the model to zero over time. This simplifies a set of non-linear differential equations to linear algebraic equations.
Connection to Biochemistry Metabolism Course:
The design of kMech allows it to model many single and multiple substrate enzyme mechanisms such as those we have studied in class, including feedback inhibition by allosteric, competitive and non-competitive mechanisms. These regulation mechanisms have been a focus of our course. One example of a model we have studied that falls into the category of allosteric inhibition is fructose 1,6-bisphosphatases inhibition by fructose 2,6-bisphossphate and AMP.

## Articles and Web Pages for Review and Inclusion

Peer-Reviewed Article #1:
Computational Modeling of Cancer Cachexia
Curr Opin Clin Nutr Metab Care. 2008 May; 11(3): 214–221.
Main Focus
       Identify the main focus of the resource. Possible answers include specific organisms, database design, intergration of information, but there are many more possibilities as well.
New Terms

### New Term 1

    Definition. (source: http://)

### New Term 2

    Definition. (source: http://)

### New Term 3

    Definition. (source: http://)

### New Term 4

    Definition. (source: http://)

### New Term 5

    Definition. (source: http://)

### New Term 6

    Definition. (source: http://)

### New Term 7

    Definition. (source: http://)

### New Term 8

    Definition. (source: http://)

### New Term 9

    Definition. (source: http://)

### New Term 10

    Definition. (source: http://)
Summary
       Enter your article summary here. Please note that the punctuation is critical at the start (and sometimes at the end) of each entry. It should be 300-500 words. What are the main points of the article? What questions were they trying to answer? Did they find a clear answer? If so, what was it? If not, what did they find or what ideas are in tension in their findings?
Relevance to a Traditional Metabolism Course
       Enter a 100-150 word description of how the material in this article connects to a traditional metabolism course. Does the article relate to particular pathways (e.g., glycolysis, the citric acid cycle, steroid synthesis, etc.) or to regulatory mechanisms, energetics, location, integration of pathways? Does it talk about new analytical approaches or ideas? Does the article show connections to the human genome project (or other genome projects)?

# Nutrition

Back to Previous Chapter: Computational Modeling of Metabolic Control Next Chapter: Databases

## Introduction to Nutrition and Metabolomics

Metabolomics has been widely adopted in pharmacology and toxicology but is relatively new in human nutrition. The ultimate goal, to understand the effects of exogenous compounds on human metabolic regulation, is similar in all 3 fields. However, the application of metabolomics to nutritional research will be met with unique challenges. Little is known of the extent to which changes in the nutrient content of the human diet elicit changes in metabolic profiles. Moreover, the metabolomic signal from nutrients absorbed from the diet must compete with the myriad of nonnutrient signals that are absorbed, metabolized, and secreted in both urine and saliva. The large-bowel microflora also produces significant metabolic signals that can contribute to and alter the metabolome of biofluids in human nutrition. Notwithstanding these possible confounding effects, every reason exists to be optimistic about the potential of metabolomics for the assessment of various biofluids in nutrition research. This potential lies both in metabolic profiling through the use of pattern-recognition statistics on assigned and unassigned metabolite signals and in the collection of comprehensive data sets of identified metabolites; both objectives have the potential to distinguish between different dietary treatments, which would not have been targeted with conventional techniques. The latter objective sets out a well-recognized challenge to modern biology: the development of libraries of small molecules to aid in metabolite identification. The purpose of the present review was to highlight some early challenges that need to be addressed if metabolomics is to realize its great potential in human nutrition.
American Journal of Clinical Nutrition, Vol. 82, No. 3, 497-503, September 2005 © 2005 American Society for Clinical Nutrition

### What is Metabolomics?

Metabolomics is newly developing field studying the products and effects of the metabolism on the pathological and physiological states within biological samples. Metabolomics offers the possibility of discovering the reasons and causes of certain phenotypes. Another discovery from Metabolomics is the discovery of biomarkers, which reveal changes in health and disease, and can reflect dietary habits. Metabolomics is essential in the study of how specific diets interact with the human body, one of the most important aspects of nutrition.
Koulman, A., and D. A. Volmer. "Perspectives for metabolomics in human nutrition: an overview." Nutrition Bulletin 33.4 (2008)
Small molecule metabolites, the end product of cellular processes, are the most accurate marker of the responses of biological systems resulting from changes either genetic or environmental. There are approximately 2,900 biochemicals (metabolites) that are the key to cellular phenotypes.
Milburn, Michael. "Using Metabolic Profiling Technology to Advance Cell Culture Development." BioPharm International June 2009, p.28-34

### Limitations of Metabolomics

Metabolic profiling has been conducted for over 50 years, which has provided a lot of very helpful information but currently there is not enough data nor a standard way to collect and record data for the study of metabolomics to really be helpful now. Metabolomics has the potential to discover early warning signs of certain diseases as well as determine the effects of certain foods and drugs on the body. This potential could be much greater if more data is collected and recorded accurately and precisely into a database. By recording the effects of age, gender, race, ethnicity, body composition, health, dietary intake, physical activity, stress, and many more factors, people would be able to better interpret their new metabolomic data and advance the general metabolomic knowledge. Without this there is no baseline or control group with which to compare data which greatly hinders proper research and theory creation.
Walsh, M. C. and A. Nugent, L. Brennan and M. J. Gibney. "Understanding the metabolome – challenges for metabolomics." UCD Institute of Food and Health, University College Dublin, Ireland. The British Nutrition Foundation. The Nutrition Bulletin, December 2008. URL: http://web.ebscohost.com/ehost/pdfviewer/pdfviewer?vid=6&hid=109&sid=bd42c8d7-0cb2-4f8b-954e-d93dc1b131df%40sessionmgr111

### Future Of Metabolomics

The future of Metabolomics seems to be coming ever clearer in the wake of increasing scientific innovation in the area of the genome. Through the use and study of various aspects of the genome there has been great scientific improvement which has laid the groundwork for more relevant innovations. Such innovations would include proteome (the study of entire protein complements of cells tissues or fluid compartments), and the metabolome (the study of entire metabolite complements in cells, tissues or fluids) which will support modern nutrition (1). With these scientific leaps in genomic research, Metabolomics, lead by Nutrition, has the potential to reduce disease in both individuals and entire populations. This is all made possible by several innovative and relatively new technologies such as the gene array which performs global gene expression analysis (1). This is just one of the many feats of engineering which have made it possible for us to quantify and understand the human gene and how it relates to Nutrition.
J. B. German, M. A. (2002). Metabolomics and Individual Metabolic Assessment: The Next Great Challenge for Nutrition. The Journal Of Nutrition , URL: http://jn.nutrition.org/cgi/content/full/132/9/2486#BIBL.

## Nutrition, Metabolomics, and Disease

Dysregulation at the level of primary metabolic organs and tissues form the foundation of many diseases. Some primary tissues of current interest include adipose tissue, skeletal muscle, the intestine and liver. The metabolic syndrome, type 2 diabetes and obesity may all be understood as ecological phenomena where metabolism is the primary intermediary between diet and health outcomes. The assessment of essential nutrient status and a comprehensive understanding of metabolic response (e.g. metabolic phenotype) to ecological risk factors is necessary for the identification of effective disease prevention strategies as well as interventions in the clinical treatment of metabolic disease.

### Nutrition and Oral Disease

The below is not medical advice, and is not (as prohibited by government regulation) designed to treat, or prevent any illnesses. The information is currently under review for quality and accuracy.
Nutrition plays a key role in the prevention of many oral diseases, dental caries, dental erosion, developmental defects, oral mucosal diseases and periodontal disease. Poor nutrition can lead to a breakdown in tooth enamel and an increase in oral mucosal. The consumption of soft drinks, which are heavy with acid, has been shown to lead to significant dental erosion. A balanced diet and proper nutrition are essential to the maintaining of a healthy oral system, as well as the rest of the body. Bacteria can also cause periodontal disease, gum disease, and erosion. Chewing antibiotics is one way to prevent periodontal disease.
Periodontal disease, an oral infectious disease involving inflammation and loss of bone and supporting tissues, progresses more rapidly in undernourished developing populations around the world. Many local and systematic factors influence the severity and longevity of progression of the common yet preventable disease.
Malnutrition however exacerbates the severity of oral infections, which are contributing factors to other life-threatening diseases. Deficiencies in vitamin C lead to scurvy, while deficiencies in vitamin A, D and other protein-energy components are associated with enamel hyplosia and salivary gland atrophy. Antioxidant intake in foods, such as pomegranate seeds, green or black teas, have been used as buffers of reactive oxygen species that lead to tooth decay. Antioxidants are found in high fruit and vegetable diets and have been determined to contain anti carcinogenic properties. Diet plays an important role in the dynamic equilibrium of dimineralization-remineralization of the tooth surface. Therefore, food's form, frequency of sugar and alcohol intake, and combination of vital nutrients and minerals play an important role in maintaining a healthy oral system.
Moynihan, Paula J. "The role of diet and nutrition in the etiology and prevention of oral diseases." Bulletin of the World Health Organization 83.9 (2005)
Position of the American Dietetic Association: Liberalization of the Diet Prescription Improves Quality of Life for Older Adults in Long-Term Care Journal of the American Dietetic Association - December 2005 (Vol. 105, Issue 12, Pages 1955-1965, DOI: 10.1016/j.jada.2005.10.004)
Rugg-gunn A. Nutrition, diet and oral health. Journal of the Royal College of Surgeons of Edinburgh [serial online]. December 2001;46(6):320. Available from: Academic Search Complete, Ipswich, MA. Accessed June 3, 2010.

### Nutrition and Celiac disease

Celiac disease (CD) is an inflammatory small intestinal disorder that can lead to severe villous atrophy, malabsorption, and malignancy. It is triggered by the gluten proteins of wheat, barley, and rye. All patients express the antigen presenting molecules human leukocyte antigen-DQ2 (HLA-DQ2) and/or HLA-DQ8, which bind gluten peptides and thus activate destructive intestinal T cells. Patients with untreated CD have circulating IgA autoantibodies to the enzyme tissue transglutaminase (tTG), a component of endomysium. Testing for serum IgA tTG has a high predictive value. Therapy of CD is a lifelong gluten-free diet. Counseling by an expert dietitian and association with a celiac support group are important in helping the patient embark on a healthy gluten-free diet. Current research focuses on non-dietary therapies and treatment of refractory (diet-unresponsive) CD.
Kelly, Ciaran P., Dennis, Melinda D., Schuppan, Detlef. “Celiac Disease: Epidemiology, Pathogenesis, Diagnosis, and Nutritional Management”. Nutrition in Clinical Care (April 2005).
There is an estimated prevalence of 1% in North America. Typically symptoms become present in early childhood and consist of abdominal cramps, diarrhea, malabsorption and nutrient deficiencies. A link has been found with giving infant cereal, which contains gluten, too young and developing Celiac disease. Parents are advised to wait until 4-6 months of age before giving babies infant cereal. In a study of over 1500 children 51 developed the disease and those who were exposed to infant cereal before 3 months were at 5 times more likely to develop the disease.
Belanger, Jeanette E.; Wooltorton, Eric; "Is the timing of infant cereal introduction a risk factor for celiac disease autoimmunity?" Canadian Medical Association Journal p.1374, November 22, 2005

### Nutrition and Childhood Obesity

The rapid increase in the prevalence of obesity in children and adolescents is alarming, particularly in light of its many medical and psychosocial consequences.Due to the multifactorial etiology of overweight and obesity, action is needed concurrently at many levels. Physicians should screen for overweight and obesity regularly in order to address the problem at an early stage. One promising approach is to introduce healthy eating habits, focusing on portion control and a diet rich innon-starchy vegetables, fruits, and legumes, and sufficient in moderate-glycemic index/load foods, protein, healthy types of fat, and reduced-fat dairy foods. In addition, it is important to decrease sedentary behaviors and increase physical activity. The earlier a healthy lifestyle is introduced into a child's life, the more likely it is to become a way of life. Parents have a major role to play in controlling what their young child eats and in reinforcing healthy eating at an early age, serving as role models themselves. Interventions that include the whole family in the process are likely to have the most success in the prevention and treatment of childhood overweight and obesity.
Philippas, Niki G, Lo, Clifford W. “Childhood Obesity: Etiology, Prevention, and Treatment”. Nutrition in Clinical Care. (April 2005).

### Nutrition and the link between Childhood Obesity and Severe Adult Obesity

Childhood obesity not only affects the health and nutrition of a child’s life, but also puts them at a higher risk of having severe adult obesity. In a study done by Ilonna and Alfred Rimm where they conducted a questionnaire completed by 73,532 women, they found that a large portion of severely obese women were also obese children. The data found from their study also suggests that the risk of an overweight child developing severe adult obesity is significantly greater than that of non-obese children. Since adult obesity can be linked to so many health problems and adult diseases, this study shows the importance of weight control through childhood.
Rimm, Ilonna J., and Alfred A. Rimm, PHD. "Association between Juvenile Onset Obesity and Severe Adult Obesity in 73,532 Women." Public Health Briefs66.5 (1976): 479-81. Print.

## Obesity and the Link to Malignant Cancer

Not only does being obese contribute to things like cardiovascular disease and diabetes, research has shown that it can also be linked to an increased risk of cancer. Researchers estimate that excess weight may account for 14 percent of cancer death in men and 20 percent of cancer deaths in women. As far as preventable risk factors for cancer go, only smoking rates higher. There is a major connection between cancer and insulin, which happens to be one of the main hormones that responds to obesity. The more obese the individual, then typically the more insulin they will have in their system. Also, concentrations of hormones that cause inflammation may rise with fat concentrations, which also may set cancer in motion Any of these fluctuations in hormone levels could work together to initiate carcinogenesis.
Nutrition Health Review: The Consumer's Medical Journal; 2009, Issue 100, p8-8, 1/2p

## Maternal Influence on Nutrition

Adequate nutrition and balance of vitamins has a huge effect on human growth before we are even born. During pregnancy, it is important for mother’s to maintain proper balances of vitamins and minerals in order to support the long term develop and health of the metabolism in her child. A recent study published in The New England Journal of Medicine indicated the importance of Vitamin A, for example. The article notes that “vitamin A deficiency in a mother during pregnancy could have lasting adverse effects on the lung health of her offspring” by not providing the child with the support it is needs to build healthy alveoli of the lungs (West et. Al 2010). Properly developed lungs, help contribute to the overall health of an infant. Other research has also determined the importance of micronutrients in a mother’s diet that help support a healthy baby. Mother’s who maintained diets high in micronutrients and vitamins found in green leafy vegetables, fruit and milk tended to have larger and healthier babies. The study also notes that mother’s who had high levels of glucose; insulin, cholesterol, and triglycerides during pregnancy increased the chances that their child would develop higher insulin resistance, which is one of the main causes of diabetes (Yajnik 2006).
Checklye W, West KP Jr, Wise RA, Baldwin MR, Wu L, LeClerg SC, Christian P, Katz J, Tielsch JM, Khatry S, Sommer A. 2010. Mineral Vitamin A Supplementation and Lung Function in Offspring. New England Journal of Medicine. 13:362(19): 1784-94.
Yajnik, Chittarani. 2006. Nutritional Control of Fetal Growth. Nutrition Reviews. 64(5): 49-51.

### Iodine Deficiency in Pregnancy

Iodine is necessary for the synthesis of the thyroid hormones. Nearly 80 percent of the iodine in the body is found in the thyroid gland, most of it is the thyroid hormones. The amount of iodide, a form of iodine, in drinking water generally depends on the iodine content of local soil. Some 10 percent of the world population is at risk of developing iodine deficiency because they live at high altitudes where the drinking water is low in iodide. To counteract low iodine levels iodide is sometimes added to commercial table salt.
In iodine deficiency, the thyroid gland attempts to capture more iodide for the synthesis of thyroid hormones and enlarges. The iodide level in the blood and urine is very low. A pregnant woman who is deficient in iodine may have a baby whose brain is improperly developed because of iodine deficiency. This condition is called cretinism (Beers: 1999). Cretinism is marked by irreversible mental and growth retardation (Tatsumi: 1992).
The Merck Manual, 17th ed. Mark H. Beers, MD, Robert Berkow, MD, eds. Whitehouse Station, NJ: Merck Research Labs, 1999.
Ke-ita Tatsumi1, Kiyoshi Miyai1, Tsugunori Notomi1, Kyoko Kaibe1, Nobuyuki Amino1, Yuji Mizuno2 & Hitoshi Kohno.3 “Cretinism with combined hormone deficiency caused by a mutation In the PIT1 gene” Nature Genetics 1, 56–58 (1992) doi: 10.1038/ng0492-56

## Nutrient specific sections

The are many types of vitamins classified by the materials in which they will dissolve, two of which are: Fat Soluble and Water Soluble. Others are Calcium, Fish Oil, Flax Seed, Iron, Vitamin K, Vitamin E, and Vitamin D.

### Calcium

Calcium is mineral that is the most likely to be deficient in the human diet. 99% of the calcium in the human body is stored in the bones and teeth. It is the most supportive element in bones and teeth and makes up 70% of bone weight and accounts for bone strength. The last 1% floats in the bloodstream and performs a variety of functions throughout the body. It also helps in contracting muscles and regulating the contractions of the heart. It also plays a key role in the transmission of nerve impulses and in blood clotting. It is also involved in the stimulation of contractions during childbirth as well as milk production. In order for the body to absorb calcium, there needs to be Vitamin D in the blood. Vitamin D is a key ingredient that enables calcium to pass from the digestive system into the bones or blood. Even though everyone knows that calcium is important in a healthy adult diet, some people still don’t get enough and end up being deficient. Calcium deficiency causes the bones to weaken and thin out and can even cause them to be brittle. It also causes osteoporosis which means that the bones have developed tiny holes and increases risk of fracture. Osteoporosis seems to affect women more often than men. So, for the average adult, ingest 1000mg of calcium and you will continue to grow up big and strong.
References: http://www.thedietchannel.com/What-You-Should-Know-About-Calcium-Deficiency.htm; http://www.vitamins-nutrition.org/vitamins/calcium.html
At the other end of the spectrum, a study was done by Taru K Pilvi et al. to investigate energy restriction and its effect on weight loss. As a further investigation, this study also aimed to explain "whether the [weight-loss] effect of energy restriction can be further enhanced by modification of dietary protein source and calcium." They found that the increased levels of dairy protein and calcium had a "significant effect on hepatic lipid changes." The mice of this study that were fed a diet with increased levels of whey protein and calcium exhibited a reduction in "the relative level of potentially diabetogenic ceramides and diacylglycerols to the level observed in lean animals." Another study showed similar effects of increased dairy in the diet of obese subjects. This study done by Zemel MB et al. showed a direct association between increased dietary calcium and lipid utilization. Both of these studies concluded that increased calcium consumption during energy restriction results in augmented weight loss in obese individuals.
References: Taru K Pilvi et al. 2008. Metabolomic changes in fatty liver can be modified by dietary protein and calcium during energy restriction, World J Gastroenterol, 14(28): 4462–4472. Zemel MB et al. 2005. Dairy augmentation of total and central fat loss in obese subjects, International journal of obesity, 29(4):391-397.

### Fat Soluble Vitamins

Fat soluble vitamins can be very important to some people more than others for many reasons. The American Society for Nutrition claims that, "fat-soluble vitamins are needed for maintaining optimal function of innate and adaptive immune cells." In that case, fat soluble vitamins can help improve immune response to tumors. However, that is not the only thing that fat soluble vitamins can help improve. There are a variety of fat soluble vitamins that can improve health. The beneficial effects can vary considering that they can improve different aspects of the human body. Fat-soluble vitamins -- vitamins A, D, E and K -- dissolve in fat before they are absorbed in the blood stream to carry out their functions. Excesses of these vitamins are stored in the liver. Because they are stored, they are not needed every day in the diet.
Meydani, Simin (2005), Are Fat-Soluble Vitamins Effective in Enhancing Tumoricidal Cell Activity?, The Journal of Nutrition
* Vitamin A
* Vitamin K

### Fish Oil

Fish oil is found in omega 3 and is part of long-chain polyunsaturated fatty acids. It a natural oil usually produced from the body of cold-water fish. The generic name is vitamin A and the brand names are A-25, A/Fish Oil, Aquasol A which comes in a capsule form with soft gel liquid inside. It is known as the marine oils and is essential fatty acids that are found in fish. There are two main ingredients to fish oil. One is the 20 carbon eicosapentaenoic acid (EPA). The other is the 22-carbon docosahexaenoic acid (DHA). The average fish oil supplement is 20 EPA and 10 DHA for a total of 30 omega-3, which may help to keep block triglycerides in check and help protect against atherosclerosis. Studies have found that fish oil may help prevent Crohn's disease, high blood pressure, high triglycerides and rheumatoid arthritis. Fish oil is also good for the brain because the brain is one of the largest consumers of DHA. It can be known as brain food.
Reference: http://www.nutrasanus.com/fish-oil.html, http://vvv.com/healthnews/fishoils.html
In one Australian study, fish oil supplements taken by women during pregnancy were associated with improved hand-eye coordination of their children. It is also suggested that high doses of fish oil are beneficial in the last weeks of pregnancy and further research is being done to determine the ways in which it is.
Reference: http://www.nytimes.com/2007/01/02/health/nutrition/02nutr.html?scp=3&sq=fish+oil+supplements&st=nyt
Populations that consume large amounts of fish have been associated with reduced incidences of breast cancer. LIke it has been said, fish oil is high in omega-3 fatty acids (EPA and DHA), and research is being done to determine whether it is that aspect of fish that seems to contribute to protection against breast cancer.
Reference: http://escholarship.org/uc/item/12g6398b?query=fish%20oil

### Flax Seed

According to health experts, the seed of the blue-flowering flax plant that can be easily found on Canadian and Mesopotamian soil, is packed with disease-fighting nutrients and fiber. It is also loaded with two fatty acids that are necessary for our bodies: omega-3s and lingans, which also work as natural antioxidants. The omega-3s in the flax seed help remove toxins from the human body, as well as helping with the prevention of heart disease and inflammation. The lignans aid with the prevention of cancers and provides 700 times the amount of fiber that can be found in legumes or whole grains. This fiber is also great for fighting bad cholesterol and type 2 diabetes. Omega-3 and lignan are essential to every membrane and cell in the human body, making them extremely beneficial. Flax seed has the ability to fix radical oxygen atoms. Radical oxygen molecules can cause molecular damage to DNA, shortening and damaging it. They are associated with the deterioration of the body often associated with aging.
Flax seed also has notable effects on the menstrual cycle. It prolonges the fertile stage of the menstrual cycle, the luteal phase. It also helps regulate the release of an ovum. Women that regularly consume flax seed are more likely to release an egg for every menstrual cycle they have than women who have a low fiber diet withno flax seed supplements. Two phytochemicals in flax seed are linked to changes in the female hormonal cycle associated with these changes in the menstrual cycle. They are absorbed in the intestines and affect the ratios of estrogen, progesterone, and testosterone during different times in the menstrual cycle. A study at Duke University found that men scheduled for prostate cancer surgery who began eating two teaspoons of flaxseed oil daily, showed that within 30 days the flax seed halted tumor growth and many of the cancer cells had self-destructed. Although all parts of the flax seed including the seed, oil, or both would benefit our diets, shopping for flaxseed can prove difficult as there are so many processed variations of the plant, each of which with its own care instructions. Be sure to read the back of all packaging’s to make sure you choose the best one for you.
Reference: Rubin, Tina. "The Flax of Life." Better Nutrition Apr. 2010: 54. Print.
Prasad, Kailash. "Hydroxyl radical-scavenging property of secoisolariciresinol diglucoside (SDG) isolated from flax-seed ." Molecular and Cellular Biochemistry Mar. 1997: 168. Print.
WR Phipps, MC Martini. "Effect of flax seed ingestion on the menstrual cycle." Journal of Clinical Endocrinology & Metabolism 1993: 77. Print.

### Iron

Iron is split into two categories. HEME iron can be obtained only from meat, fish and poultry and is an easier type of iron for the body to break down and use as a nutrient. NON-HEME iron can be obtained from fruits, vegetables, beans, nuts and grains and is more difficult for the body to absorb. The Recommended Dietary Allowance (RDA) for males aged 19 to 50 is 8mg/day. Females in the same age range are suggested to consume 18mg of iron per day. Iron deficiency is the number one nutritional disorder in the world. It can be caused by a low dietary intake of iron or the inability to absorb the iron consumed. Also, excessive blood loss is another factor. Women are at a higher risk for iron deficiency because of the consistent menstrual blood loss experienced during their menstrual cycle. To help fight iron deficiency many breakfast cereals are iron-fortified shown on the nutrition label.
Reference: http://ods.od.nih.gov/factsheets/iron.asp#h4 http://www.mckinley.illinois.edu/Handouts/dietary_sources_iron.html
Iron is both an essential nutrient and a potential toxicant to cells, requiring a highly sophisticated and complex set of regulatory approaches to meet the demands of cells as well as to prevent excess accumulation. For humans, iron plays a central role in oxygen transport and the synthesis of haemoglobin, myoglobin, and some important enzymes to energy production. Many studies have demonstrated that iron deficiency may impair the performance of athletes, so normal iron status in athletes is especially important. Exercise alone may not lead to a true iron deficiency, but probably results from dietary choices, inadequate iron intake, and menstruation. Iron deficiency affects particularly pregnant women, young children, and adolescents. Iron is a micro-nutrient and is required for regulation of brain neurotransmitters by altering the pathway enzymatic system. Studies have shown that iron deficiency in infants can negatively impact neurological development necessary later in life. It is thought that early iron deficiency can possibly impair the development and function of the hippocampus in the brain, which plays an important role in developing and retaining long-term memories. Iron deficiency in infants might also impair the dopamine system. It is possible that those adolescents who were exposed to chronic and sever iron deficiency in their infant stages may exhibit deficits on tests in things like Spatial Working Memory, Rapid VIsual Information Processing, Pattern Recognition Memory, and Spatial Recognition Memory.
Reference: Qian, Zhong Ming. "Nitric Oxide and Changes of Iron Metabolism in Exercise". Cambridge Journals.
Agarwal, Kailash N. "Iron and the Brain: Neurotransmitter receptors and Magnetic Resonance Spectroscopy". British Journal of Nutrition.
Lukowski, Angela F. "Iron deficiency in infancy and neurocognitive functioning at 19 years: evidence of long-term deficits in executive function and recognition memory."

#### Vitamin K and Vitamin E Interactions

As noted above each vitamin is necessary "for maintaining optimal function of innate and adaptive immune cells" yet it is important to remember that each vitamin also interacts with the others. Interestingly, some studies have indicated that Vitamin E may decrease Vitamin K's addition to the immune system. Though the connection has not been proven, preliminary clinical trials have reflected that Vitamin K's metabolism is slowed with an excess of Vitamin E. One hypothesis is that Vitamin K and E compete for the enzyme. So far only rats have been tested, though it has been observed with statistical significance that when an excess of Vitamin E is present there are far fewer MK-4's (the metabolized Vitamin K).
Vitamin A is a vitamin that is needed by the retina of the eye in the form of a specific metabolite, the light-absorbing molecule retinal. This molecule is necessary for both scotopic and color vision. Vitamin A also functions in a very different role, as an irreversibly oxidized form of retinoic acid, which is an important hormone-like growth factor for epithelial and other cells. Vitamin A can be found in two principal forms in foods: Retinol which is the form of vitamin A absorbed when eating animal food sources. The carotenes alpha-carotene, beta-carotene, gamma-carotene; and the xanthophyll beta-cryptoxanthin (all ofwhich contain beta-ionone rings), function as vitamin A in herbivores and omnivore animals. The discovery of vitamin A may have stemmed from research dating back to 1906, indicating that factors other than carbohydrates, proteins, and fats were necessary to keep cattle healthy. Adequate supply of Vitamin A is especially important for pregnant and breastfeeding women, since deficiencies cannot be compensated by postnatal supplementation. However, excess Vitamin A, especially through vitamin supplementation, can cause birth defects and should not exceed recommended daily values. Since vitamin A is fat-soluble, disposing of any excesses taken in through diet is much harder than with water-soluble vitamins B and C, thus vitamin A toxicity may result. This can lead to nausea, jaundice, irritability, anorexia vomiting, blurry vision, headaches, hairloss, muscle and abdominal pain and weakness, drowsiness, and altered mental status. Toxic effects of vitamin A have been shown to significantly affect developing fetuses. Therapeutic doses used for acne treatment have been shown to disrupt cephalic neural cell activity. The fetus is particularly sensitive to vitamin A toxicity during the period of organogenesis.
Reference: Traber, Maret G. (2008). "Vitamin K Interactions a 50-year Problem." Nutrition Reviews, 66(11):624-629, doi: 10.1111/j.1753-4887.2008.00123.x.

## Vitamin D

Vitamin D is sometimes known as the “sun-shine vitamin” due to it's ability to fight off infections. It is also important for bone health. It can protect against osteoporosis, arthritis and other bone problems. In the study of Osteoporotic fractures in men study, researchers found that low vitamin D levels were connected to a greater possibility for arthritis, whereas men with higher vitamin D levels had reduced chances of developing arthritis. With a sufficient intake of Vitamin D, it is possible to build a defense against arthritis, as the vitamin D helps to regulate the development and maintenance of bone and cartilage.
Vitamin D has been recently found to have many additional health benefits outside of bone health. People with sufficient vitamin D levels have been found to have increased testosterone and muscle mass. Gaining your vitamin D solely through sunshine is generally not enough to maintain a healthy level.
Vitamin D supplements are widely recommended for people who live in environments that don’t receive an adequate amount of sunshine. Vitamin D is one of the body’s essential vitamins and a 2010 study by Japanese researchers suggest there might be a link between vitamin D and flu prevention. Although more studies will be necessary to make a conclusive link, there was an 8% decrease in flu diagnoses among children who received the recommended 700-1000 IU a day as compared to those receiving a placebo.
Vitamin D is one of many important body essential vitamins that help balance the body. It is known to be an immune system regulator. Researchers states that, “the active form of vitamin D, 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], has been shown to inhibit the development of autoimmune diseases, including inflammatory bowel disease (IBD).” In total reverse of proper Vitamin D intake and low counts of Vitamin D receptors, it can result in accelerated inflammatory bowel disease. Dietary calcium can help trigger the effects of Vitamin D on the immune system because it has its own independent effects on inflammatory bowel disease. Therefore 1,25(OH)2D3 treatment of mice on low-calcium diets can improve the symptoms of inflammatory bowel disease.
Vitamin D is a group of fat-soluble secosteroids, the two major physiologically relevant forms of which are vitamin D2 (ergocalciferol) and vitamin D3 (cholecalciferol). Vitamin D without a subscript refers to either D2 or D3 or both. Vitamin D is produced in the skin of vertebrates after exposure to ultraviolet B light, and occurs naturally in a small range of foods. In some countries staples such as milk, flour and margarine are artificially fortified with vitamin D, and it is also available as a supplement in pill form. Vitamin D is carried in the bloodstream to the liver, where it is converted into the prohormone calcidiol. Circulating calcidiol may then be converted into calcitriol, the biologically active form of vitamin D, either in the kidneys or by monocyte-macrophages in the immune system. When synthesized by monocyte-macrophages, calcitriol acts locally as a cytokine, defending the body against microbial invaders. When synthesized in the kidneys, calcitriol circulates as a hormone, regulating, among other things, the concentration of calcium and phosphate in the bloodstream, promoting the healthy mineralization, growth and remodeling of bone, and the prevention of hypocalcemic tetany. Vitamin D insufficiency can result in thin, brittle, or misshapen bones, while sufficiency prevents rickets in children and osteomalacia in adults, and, together with calcium, helps to protect older adults from osteoporosis. Vitamin D also modulates neuromuscular function, reduces inflammation, and influences the action of many genes that regulate the proliferation, differentiation and apoptosis of cells. Important that Washington citizens try to find time to get out in the sun and get there vitamin D. there are a vast array of consequences for the human body that does no obtain enough vitamin D. So get out there and get your sunshine.
Cantorna, M.T, Zhu, Yan, Froicu, Monica and Wittke, Anja (2004), Vitamin D status, 1,25-dihydroxyvitamin D3, and the immune system, The American Journal of Clinical Nutrition
There was a study done about the correlation between milk consumption and prostate cancer. The study, although far from having definite answers seemed to find a pattern in the decreased rates of prostate cancer in men who take in lots of vitamin D. The vitamin D seems to have some sort of preventative effect on prostate cancer. It was certainly found that men who take in less vitamin D have a greater chance of getting and dying from prostate cancer. The study did find that the calcium in milk decreases the production of vitamin D3 which in turn cancels out the beneficial effects of the vitamin. In other words vitamin D from milk, although still good for you, does not have to preventative effect on prostate cancer as a healthy does of pure vitamin D does. Givens, D. I. and R. Morgan and P. C. Elwood. "Relationship between milk consumption and prostate cancer: a short review." Animal Science Research Group, School of Agriculture, Policy and Development, Faculty of Life Sciences, University of Reading, Reading, UK; Department of Primary Care and Public Health Centre for Health Sciences Research, Cardiff University, Neuadd Meirionnydd, Heath Park, Cardiff, UK. December 2008 http://web.ebscohost.com/ehost/pdfviewer/pdfviewer?vid=6&hid=109&sid=c363fced-4af5-4cc1-8834-e7cbab5d40a6%40sessionmgr113
Brown, Jordana, Doing the D, Joe Weider's Muscle and Fitness, 2010 Weir, Kirsten, D Plus, Current Science, 2010 Can D Fight Off the Flu?, Nutrition Action Health Letter, 2010
Vitamin D Signals Immune System to Fight Infections, Tufts University Health & Nutrition Letter, 2010
* Vitamin E

### Water Soluble Vitamins

B-complex vitamins and vitamin C are water-soluble vitamins that are not stored in the body and must be replaced each day.These vitamins are easily destroyed or washed out during food storage and preparation.The B-complex group is found in a variety of foods: cereal grains, meat, poultry, eggs, fish, milk, legumes and fresh vegetables. Citrus fruits are good sources of vitamin C. The use of megadoses of vitamins is not recommended and in some cases can have undesirable results. In 2010, Canadian researches studied 238 people with chronic kidney disease, challenging earlier studies that had suggested B vitamins could protect the kidneys because they lower blood levels of homocysteine, an amino acid that is linked to a higher risk of kidney damage. Yet after three years of studies it was found that those who got the high-dose B vitamins had a greater decrease in kidney function that those who received the placebo. Vitamins are essential nutrients found in foods. The requirements are small but they perform specific and vital functions essential for maintaining health. Water-soluble vitamins dissolve in water and are not stored; they are eliminated in urine. We need a continuous supply of them in our diets. The water-soluble vitamins are the B-complex group and vitamin C.
Water-soluble vitamins are easily destroyed or washed out during food storage or preparation. Proper storage and preparation of food can minimize vitamin loss. To reduce vitamin loss, refrigerate fresh produce, keep milk and grains away from strong light, and use the cooking water from vegetables to prepare soups N, J (Jun 2010), B Vitamins Harm Kidneys, Nutrition Action Health Letter
Anderson, J (2008), Water Soluble Vitamins, Colorado State University
* Vitamin C
* Folate
* Dietary fiber

# Databases

Back to Previous Chapter: Computational Modeling of Metabolic Control Next chapter: Applications

# Overview

The vast amount of metabolomic information harvested using high-throughput techniques has necessitated an effective means of storage to organize, disseminate, and facilitate analysis and annotation. This need has driven the development of databases as a repository of metabolomic data being produced. Data housed in these databases covers the wide-spectrum of research being done in the metabolomic world from NMR spectra to metabolic pathway substrates and products.
Metabolomic database serve a primary purpose or organizing information on the large catalog of metabolites that are encountered in metabolism pathways. There are many different databases that exist on the World Wide Web and house a wide variety of information covering a large variety of organisms.

## Example Databases
### Biological Magnetic Resonance Data Bank

The Biological Magnetic Resonance Data Bank (BMRB) focuses on quantitative data generated by spectroscopic investigations of biological macromolecules. It has links to search engines such as PubChem, that connect to recent articles and new data. It also links to projects and other databases that are all related to Metabolomics and Metabonomics. This database focuses on the NMR research aspect of metabolites discovery and what roles they play in metabolism. BMRB offers a large list of different known compounds and the information associated to it.
Terms:
* Metabonomics (verses Metabolomics): The words 'Metabolomics' and 'Metabonomics' are often used interchangeably, though a consensus is beginning to develop as to the specific meaning of each. The goals of Metabolomics are to catalog and quantify the myriad small molecules found in biological fluids under different conditions. Metabonomics is the study of how the metabolic profile of a complex biological system changes in response to stresses like disease, toxic exposure, or dietary change
* Metabolites: low molecular weight molecules.
* Diamagnetism: A weak repulsion from a magnetic field. It is a form of magnetism that is only exhibited by a substance in the presence of an externally applied magnetic field. It results from changes in the orbital motion of electrons. Applying a magnetic field creates a magnetic force on a moving electron in the form of F = Qv × B. This force changes the centripetal force on the electron, causing it to either speed up or slow down in its orbital motion. This changed electron speed modifies the magnetic moment of the orbital in a direction opposing the external field
* Calmodulin: An example of calcium binding regulatory proteins in intracellular signaling pathways. It is highly conserved and abundant in all eukaryotic cells. As a signaling protein, Calmodulin's function is to bind calcium ions and then bind a target protein, affecting its activity. It affects processes ranging from neurotransmitter release to membrane protein organization
* Heuristic: A method to help solve a problem, commonly informal. It is particularly used for a method that often rapidly leads to a solution that is usually reasonably close to the best possible answer.
Relevance: This information relates to what we have studied in class because we have been studying metabolism and the metabolites involved. This resource is simply a collection of all the accountable knowledge that exists. The field of metabolomics is growing and with the help of NMR spectroscopy more compounds and metabolites will be discovered along with their functionality. The information studied in class forms the foundation for this knowledge

### Metabolomics: Resources, Reagents, and Kits for Metabolomic Analysis

The Sigma-Alderich database provides access to a number of metabolomic kits and reagents, as well as a number of resources, including information on cell signaling pathways, enzyme structures/functions/specificities, animations, charts, and an online library. This site also provides links to other resources.
Terms:
* Cytokines: a group of proteins and peptides used in organisms as signaling compounds. Consists mainly of small water-soluble proteins and glycoproteins. Also play a central role in the immune system.
* Metabolome: a collection of all the metabolic products and intermediates found in an organism.
* Angiopoietin: protein growth factors that promote the formation of new blood vessels. Only four identified angiopoietins: Ang1, Ang2, Ang3, and Ang4.
* Phosphoproteomics: a type of proteomics involved in identifying, cataloging, and characterizing proteins containing a phosphate group as post-translational modification.
Relevance: This website shows cell signaling and other metabolic pathways (including glycolysis) in an animated, in-depth way. This site also provides a search feature to find pathways related to molecules of your choosing.

### Madison Metabolomics Consortium Database

The Madison Metabolomics Consortium Database contains metabolites determined through NMR and MS. It contains information with the main focus on Arabidopsis thaliana, but also refers to many different species. The database also contains information on the presence of metabolites under several different physiological conditions, their structures in 2D and 3D, and links to related resource sources and other databases.
Terms:
* Nuclear magnetic resonance spectroscopy (NMR): technique using nuclear magnetic resonance to determine structural information about a molecule.
* Mass spectroscopy (MS): technique that uses the mass-to-charge ratio of ions to determine the composition of a sample.
* Arabidopsis thaliana: the thale cress, a species of plant with a small genome and rapid life cycle that is a model organism in the lab.
* chemoinformatics: the use of computer and informational techniques, applied to a range of problems in the field of chemistry
* Chemical shift: relevant to NMR, chemical shift describes the dependence of nuclear magnetic energy levels on the electronic environment of a molecule.
Relevance: How does this information relate to the information that has been studied in this course to date? Using this website, it is possible to enter a molecule of interest into the search engine and obtain links that will lead to a list of pathways in which that molecule participates. Doing this for glucose, two pathways with which were covered in class: starch degradation (aka glycolysis) and glycogen degradation were displayed.

### MetaCyc

The main focus of the MetaCyc Database is to collect and display information on experimentally studied pathways from a variety of organisms. Pathways are divided into five categories: biosynthesis, degradation/utilization/assimilation, detoxification, generation of precursor metabolites and energy, and Super-Pathways. Clicking on any of these will open, in outline format, more specific categories. This eventually leads to individual Metabolomes that are described graphically. There is also descriptions with details about their history and connected pathways. The database can also be browsed by compounds and reactions, though these sections tend to be less detailed.
MetaCyc allows anyone to submit newly identified pathways, but they unsurprisingly demand detailed, experimentally proven data which is closely examined before any additions are curated.
Terms:
* Superatom: A cluster of atoms that has the same behavior as elemental atoms.
* Prostaglandins: A group of lipid compounds found in a wide variety of tissues that are synthesized from essential fatty acids. Cells have several receptors for prostaglandins that lead to actions ranging from smooth muscle constriction to increasing spinal neurons' sensitivity to pain.
Relevance: MetaCyc is closely related to the material that we have been learning about in class because it is a comprehensive database that covers many of the same pathways, such as glycolysis I (http://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=GLYCOLYSIS)

### The Scripps Center for Mass Spectrometry: Metabolomics Science Webpage

The main focus of the Scripps Center for Mass Spectrometry is to provide a user-friendly websites for scientist in the field of Metabolomics. They provide general information on analytical tools, timelines of Metabolomics history, Metabolomic events held around the world, databases of metabolic systems, as well as bioinformatics software.
Terms:
* Pathophysiology: the physiology of abnormal or diseased organisms or their parts; the functional changes associated with a disease or syndrome.
* Lipidomics: deals with Lipids studying not only their structures, but also functions and modifications occurring during physiological and pathological conditions.
* Exdogenous: of or noting the metabolic assimilation of proteins or other metabolites, the elimination of nitrogenous catabolites being in direct proportion to the amount of metabolites taken in.
* Ernobiotic: a chemical or substance that is foreign to an organism or biological system.
* Paraccetamol: The generic name for a common nonprescription medication useful in the treatment of mild pain or fever.
* GC-MS: gas chromatography mass spectrometry
* CE-MS: capillary electrophoresis mass spectrometry
* FT-IR: Fourier transform infrared spectrometry
Relevance: This Website relates to the information that we have been studying in class because it is it full of information about pathways and numerous databases. One such database is the KEGG Pathway Database, which contains all the pathways that are involved in metabolism. It shows such pathways as Glycolysis, Gluconeogenesis, Citrate cycle, pentose phosphate pathway, glactose metabolism, pyruvate metabolism, and hundreds more. Click here to check out they glycolysis pathway -> http://www.genome.jp/kegg/pathway/map/map00010.html This website does a good job of showing how all the pathways are interconnected into one another.

### The Human Metabolome Database

The Human Metabolome Database is an extremely comprehensive, free electronic database that gives a detailed overview of human metabolites divided into chemical, clinical, and molecular biology/biochemistry data.
Terms:
* Human Metabolome Project: The HMB is an ambitious Canadian project begun over 3 years ago with the ultimate goal of “identifying, quantifying and cataloging” every metabolite detectable in human tissue at concentrations greater than 1 micromolar.
* Biofluids: A biological fluid such as urine, blood or sweat. In this database, metabolites can be categorized by their biofluid localization.
* Chemical Class: A broad term used to categorize organic and inorganic chemicals based on common characteristics into groups such as amines and carbohydrates. The database can be browsed by chemical class.
* Metabocard: The individual datasheets for metabolites in this database are called metabocards. Each one contains a detailed description, over 90 categories of data, and cited sources. An example metabocard for citric acid can be found at: http://hmdb.ca/scripts/show_card.cgi?METABOCARD=HMDB00094.txt
* TOCSY: Total correlation spectroscopy in which magnetization through chemical bonds of adjacent protons and protons connected by adjacent protons is visualized. An
Relevance: The Human Metabolome Database is connected to our coursework by its extremely thorough amount of data on all of the metabolites that we've been studying. Reaction intermediates and products such as glucose, 3-phosphoglycerate, and citrate can all be looked up and everything from the 3d structure to associated disorders are provided.

### KNApSAcK

KNApSAcK is a Java application that presents an interactive display of biochemical information that can be searched by organism or metabolite name. KNApSAcK focuses primarily on the origin and mass spectra of particular metabolites.
Terms:
* JRE: The Java Runtime Environment is a set of free software programs that are used by many internet developers to run java programs and scripts on users' computers.
* Mw +- margin: A search parameter of KNApSAcK that allows a user to search for metabolites within a gram range of a set number. For example, searching for MW: 100 with a margin of 2 would return all metabolites with a molecular weight between 98 and 102 grams.
* Phylum: The fourth taxonomic rank for classifying organisms, between kingdom and class. Cyanobacteria is one phylum. The database allows searches based on any specifying any taxonomic rank, although the higher ones take significant time to load.
* m/z: The mass-to-charge ratio, a physical quantity that is used in the detailed examination of charged particles. It is a key aspect of mass spectrometry studies and the database focuses heavily on this data.
Relevance: KNApsAcK connects to our coursework because it allows for comparison of metabolites important to different organisms. One example search that was attempted was to see the metabolites shared by cyanobacteria and plants for photosynthesis.

### BRENDA

The BRENDA developers boast that it is the main internet repository of functional enzyme data of the scientific community. An extremely robust system, it allows for searching of more than 4000 enzymes and provides comprehensive information on each of them, including indispensable reaction diagrams.
Terms:
* ECTree: A term for the outline organization BRENDA uses to characterize related enzymes. An example image of an ECTree for Oxidoreductases from the user manual:
* TaxTree: TaxTree is the interactive display used by BRENDA to search for organisms by taxonomy. Once an organism or taxonomy designation is chosen, all of the enzymes in the database linked to it are displayed.
* Substructure Search: The substructure search function allows a user to actually draw part of the enzyme structure in skeletal formula. All enzymes containing the component drawn are returned.
* EC Explorer: A search function that allows the user to access enzyme information by a several criteria including common name, reaction, and even history.
* Systematic Name: A style of naming enzymes controlled by the Enzyme condition. The enzyme is categorized by four numbers classifying its main class, subclass, sub-subclass and serial number which are all separated by periods.
Relevance: Information on this database is reinforces what was covered in class. Material covered in class also is the foundation for the material on this database

### Reactome

The Reactome is a collaboration between Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and the Gene Oncology Consortium to provide a curated database that catalogs core pathways and reactions in human biology. The Reactome obtains information from researchers with expertise in their fields and is cross-validated by an Reactome editorial team which references other databases such as the NCBI, Ensembl, and UniProt. Alongside the human pathways and reactions the Reactome also contains inferred data from 22 non-human species including mouse, rat, chicken, puffer fish, worm, fly, yeast, two plants and E.coli.
Current versions of the Reactome allow for searching by keyword but also allow a more visual approach by allowing researchers to view a map of much of the data being housed in the database and allowing reactions to be selected and zoomed in on from the top level.
Terms
* Skypainter tool: A tool provided by the Reactome which allows a list of proteins or gene identifiers to be uploaded to color one of the reaction or pathway maps generated by the database.
* Morbid map: A diagram showing chromosome location of genes that are known to be associated with disease.
* Reactome Author Tool: Desktop application written in Java that is utilized to enter new data into the Reactome. Use a graphical interface to allow for ease in expanding or adding reactions and pathways.
* BioPAX: an attempt at a common exchange format for biological pathway data.
* SBML: Systems Biology Markup Language; a computer-readable format representing biochemical reaction networks.
* PSI-MI: Proteomics Standards Initiative - Molecular Interactions; A standardized format which described molecular interactions.
Relevance: Much of the data housed in the Reactome database covers many of the pathways and reactions we have covered in the course such as the intermediary metabolism and regulator pathways. Like many of the other metabolomics database it can be thought of almost like a textbook containing thousands of entries on metabolism and its associated events.

### KEGG Pathway DB

The KEGG Pathway Database is a large part of a collection of smaller databases which comprise the Kyoto Encyclopedia of Genes and Genomes. The Pathway database is known for its extensive collection of metabolic pathways and its handling of their interconnections, as well as other non metabolic cellular interactions. The database does an excellent job of integrating genomic, chemical and systemic functional information into an easily readable format.
Instead of new terms, enjoy this list of subsections of the database.
* 1.1 Carbohydrate Metabolism
* 1.2 Energy Metabolism
* 1.3 Lipid Metabolism
* 1.4 Nucleotide Metabolism
* 1.5 Amino Acid Metabolism
* 1.6 Metabolism of Other Amino Acids
* 1.7 Glycan Biosynthesis and Metabolism
* 1.8 Biosynthesis of Polyketides and Nonribosomal Peptides
* 1.9 Metabolism of Cofactors and Vitamins
* 1.10 Biosynthesis of Secondary Metabolites
* 1.11 Xenobiotics Biodegradation and Metabolism

### BMRB, MMCD and the Sesame laboratory module

Databases have been recently developed as metabolomics resources. Some of the databases that have been designed as metabolomics resources are intended to assist in MS and NMR analyses of relevant research. Among these particular databases are the BioMagResBank (BMRB), Madison Metabolomics Consortium Database (MMCD) and a module for the Sesame laboratory information management system.
The BMRB comprises of experimental spectral data for over 270 pure compounds. Each molecule entry includes five or six one- and two-dimensional NMR data sets, as well as compound source information, solution conditions, data collection protocol and the NMR pulse sequences. Database entries can be accessed by name, monoisotopic mass and chemical shift. Currently in development is an open access feature to this database that will allow users to contribute their own data, and substantiate the BMRB.
The MMCD consists of information on over 10,000 metabolites that primarily consists of data collected from Arabidopsis metabolites. Users may make queries comprising of MS and/or NMR spectra.
The Sesame laboratory module collects all metabolomics based experimental protocols, background information, and data for a particular study.
Link to article:
http://psb.stanford.edu/psb-online/proceedings/psb07/markley.pdf

## References
### CellCircuits: a database of protein network models

General Overview: This article provides a rationale for the development of CellCircuits, an open- access database that focuses on molecular network models. The database covers models that have been derived computationally and posted in published journal articles. The article explains that the ultimate goal of the project is to bridge the gap between molecular databases, even those with unconfirmed data, and strictly regulated pathway databases. The body of the article explores not only the rationale of CellCircuits, but the computational process that went into developing it and some example results of molecular networks models.
Terms:
* GO Annotation: GO refers to the Gene Ontology project, which is a system of universal descriptions of genes across a broad variety of databases. The developers of CellCircuits have used GO to score genes in comparisons across databases.
* Data Processing Pipeline: A pipeline is a construct used to carry data through threads, scripts, and processes through a chain of software elements. CellCircuits uses pipelines to draw text information from input models for processing.
* MySQL: MySQL is a database management system that allows users to easily set up multi- platform systems of data control and is very popular for internet applications, Wikipedia being one example. CellCircuits is built with MySQL.
* Scoring models: Scoring models is a concept that refers to a system for comparison of two sets of data. In CellCircuits, scoring models are used in conjunction with the GO database to compare sets of genes from input models.
* Perl: Perl is a popular procedural programming language heavily derived from C. The primary graphical interface of CellCircuits is written in Perl.
Relevance: This article relates to our coursework because it shows some of the dizzying heights of complexity involved in trying to collate the growing body of metabolomics data into a usable form for the general science community.

### ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites

General Overview – This article explains the development and use of the ProMEX mass spectral library database. The goal of the expanding database is to allow users to compare an unknown sample to a body of confirmed mass spectra for known proteins. The article explores some of the theory and algorithms that go into making that possible.
Terms
* Metadata: A common database term that refers to the overlying information on an object rather than discrete points. The ProMEX developers use it to refer to the consensus of experimental results and mass spectrometric parameters.
* AGI Codes: A uniform system of nomenclature to classify genes that was developed in 1999. AGI codes reference the organism, chromosome number, gene, and gene ID. The announcement of the original decision to create the system for Arabidopsis genes can be found at: http://mips.gsf.de/proj/thal/db/about/agicodes.html
* LC-MS: Liquid chromatography- mass spectrometry is an uncreatively named data gathering process that combines the two techniques to allow for highly sensitive detection of specific chemicals. The ProMEX developers use LC-MS to distinguish even closely related samples.
* CLR: Common Language Runtime is a virtual machine developed by Microsoft. It provides an execution environment for software programs on a variety of platforms. The ProMEX's algorithms for comparing spectra run within the CLR.
Threshold: In comparing the mass spectra of an unknown, user provided sample against those in the database, the threshold value is point at which mass spectra hits are ignored because they are not considered matching.
Relevance – ProMEX is a relevant resource to our coursework because it shows how quickly the field of metabolomics is advancing. Using the search algorithms described in this article, users can now identify unknown proteins from experimental data in a quick and highly automated process.

### Correcting ligands, metabolites, and pathways

General Overview – The authors of this article explain that the goal of their database, Biometa, is to provide an example of the need to correct inaccurate pathways and chemical structures. After originally developing this database, they came up with tools to validate the data it contained by stereochemistry and stoichiometric outcomes only to find that they had a high error rate. The article explains the creation of the database and validation tools and the steps they took to make corrections.
Terms
* Xenobiotics: Chemicals that can be experimentally or clinically detected in an organism that is not capable of normally producing them, either at all or at the concentration that they appear. The authors of the article use xenobiotics as an example of the staggering intricacy of metabolomics.
* Reactants and Products: Although these are not new terms, their use in BioMeta is significant because the authors deliberately eschewed use of “substrate,” feeling that it was inappropriate for their purposes on the grounds that it can refer to either reactant or product of an enzyme and they are only interested in catalyzed reactions.
* “Fuzzy” Synonyms: To deal with a lack of uniform nomenclature, BioMeta contains synonym tables that recognize many common names for compounds or pathways. If an initial search can't locate a synonym, it is referred to a table of fuzzy synonyms that strips out non- alphanumeric characters and capitalizes all letters for a looser, but still automated, comparison.
* ElemCount: ElemCount is one field used by the BioMeta Compounds data table that covers the raw quantity of each element in a compound. Searches can be made with it specifying a minimum or maximum number
* Molfiles: Molfiles are minute structure descriptions of small compounds that can be quickly analyzed and validated by the developers' chemical structure software.
* Canonicalization: The concept of recognizing several synonymous data references as a single reference. The validation tools used by the developers make heavy use of canonicalization at most steps to reduce repetitive comparisons and false error reports.
Relevance – This article is relevant to our coursework because it explains the logical eventuality that with the incredibly vast amount of metabolomics data and speed at which it is growing, errors are inevitable. The authors offer some insight into how this problem can be corrected and the necessity of doing so. The compound query window from the BioMeta database.

### HMDB: The Human Metabolome Database

The Human Metabolome Database (HMDB) was established in 2004 with the explicit aim to catalog the whole metabolome in humans just as the Human Genome project unraveled the mysteries behind our genetic code. This paper covers the information contained in the database, which includes compound description, synonyms, physo-chemical structure, disease association, pathways information, and NMR Spectra and MS spectra among other things; each entry in the database contains 90 entries filled with relevant information. The paper also serves as a design documentation for the database, detailing how it was built with care to allow for efficient searching as well as explaining the quality control and curation of the database.
The HMDB is built upon a MySQL database that serves as the backend to to the graphical web-page interface. Raw text found in the database is translated to HTML via special Perl scripts that also generate links and graphics. The MySQL database is part of a generalized metabolomic LIMS system called MetaboLIMS that utilizes Java to handle input and queries.
The robustness of the database allows researchers to search from many different angles including by chemical structure, BLAST, single and multiple sequences, MS and NMR spectra, and boolean text searches via GLIMPSE.
Terms
* Biomarker: A biochemical feature that can be used to detect or measure a disease or the effects of a treatment.
* Medical Informatics: A field of information science that primarily deals with the analysis and distribution of medical data through the use of computers. This data can be applied to different areas of health care and medicine.
* GLIMPSE: Global Implicit Search; an indexing and query scheme for searching file systems.
* SimCell: A metabolic simulation software package which models complex metabolic pathways at the cellular level with real-time movies of the enzymatic process. These movies can also be graphed by the package.
* Nutrigenomics: The study of how foods interact with genes as to increase the risk factor of chronic disease.
Relevance: The information housed in the HMDB can be traced through all of the coursework that has been covered so far. Many of the metabolites housed in the HMDB were directly discussed in both the textbook and the lectures covered in class. Of course this is a surface connection between the information the text and this paper as the HMDB and other metabolic databases really encompass the majority of the metabolism world as they serve as as a repository under which all past and future research data can be stored.

### Toward Pathway Engineering: A New Database of Genetic and Molecular Pathways

The KEGG database was created with the sole purpose of providing a diagram of molecular and genetic interactions to aid in the understanding of biological systems. Its creation was fueled in part by the completion of the Human Genome Project as a way to take this massive amount of information and place it in the proper locations in a system. KEGG is connected to DNA and Protein databases by integration with the tool DBGET, which acts to search across databases.
Terms
* DBGET: An integrated database retrieval tool to search across databases.
* GenomeNet: A network that establishes a informatics framework for genome research and related areas.
* Φx174: Small virus genome consisting of 11 genes; one of the first viruses sequenced.
* Superfamilies: A classification scheme to group proteins.
* Boehringer wall chart: A classic biological pathway chart.
Relevance: The KEGG database is just another entry in the long line of databases which sum up much of the metabolic pathway information we have learned in class.

# Articles and Web Pages for Review and Inclusion

Nutritional Metabolomics Database
A Liquid Chromatography-Mass Spectrometry-Based Metabolome Database for Tomato
Plant Physiology 141:1205-1218 (2006)

# Applications

Back to Previous Chapter: Databases Next chapter: Contributors

# Applications
### Introduction to Applications

The field of metabolomics has been growing in recent years. The expanding field has encompassed and helped in disease research, pharmaceuticals and nutrition. Metabolomics could potentially become a standard dianostic tool to maintain health, diagnose ailments as well as provide us an accurate model of biochemical processes within organisms.

### Applications
# Contributors

Back to Previous Chapter: Applications Go to First Chapter: Introduction to Metabolomics
* Tung Luong Guiltyblade (talk)
* Katie Grimshaw
* Sophia Lafergola DieselSandwich (talk)
* Kevin King
* Lindsay Littman