A Practical Approach, Second Edition=Ronald D. Ho.pdf

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FUNCTIONAL GENOMICS AND PROTEOMICS 637Control EmbryoTreated EmbryoIIIIIIIIIIIIIVFigure 15.4Outline of protein expression analysis with two-dimensional gel electrophoresis. (a) Extraction ofproteins from tissues of interest, (b) separation of proteins by isoelectric focusing, (c) separationof proteins by mass, and (d) extraction and purification of differentially expressed proteins, followedby mass-spectrometry analysis.is not able to provide additional information on the identity of the proteins, and thus, supplementaltechnologies for protein identification, such as mass spectrometry, must be used in conjunctionwith 2DE. See Figure 15.4 for an outline of the 2DE process.© 2006 by Taylor & Francis Group, LLC
638 DEVELOPMENTAL REPRODUCTIVE TOXICOLOGY: A PRACTICAL APPROACH, SECOND EDITIONThe basis for the separation of the hundreds of proteins within a sample is primarily the protein’sisoelectric point (IP), but separation is also based on molecular weight, solubility, and abundance.88,89 Briefly, the IP of a protein is the pH at which no net charge is exhibited by the protein.Protein extracts are placed onto an immobilized IP gradient (IIPG) strip, and an electric field isapplied. The IP of a protein is based upon the amino acid content; therefore, according to the pHrange used, different proteins can be resolved. After this primary one-dimensional separation, theIIPG strips are loaded onto an SDS polyacrylamide gel for electrophoresis. This second dimensionalseparation is thus based on the molecular weight of each protein, so that those proteins with similarIP’s now become resolved according to their molecular weights. 90–92 Following 2DE, the proteinsare visualized by the traditional Coomassie Blue or silver staining, although the dynamic range ofthese detection methods is limited. Recently, new methods of detection with fluorescent dyes, whichincrease the dynamic range in which proteins can be distinguished and quantified, have beenintroduced. For instance, the use of SYPRO orange and SYPRO red (Molecular Probes, Eugene,OR) enable increased sensitivity and reproducibility. 93–96Although 2DE is regarded as a standard method in proteomics, there are several aspects of itsapplication that limit its use. Proteins expressed at low levels often cannot be visualized becauseof the detection limits of this technology. 97 The difficulty in detecting low abundance proteins isfurther exacerbated because of masking by other, more highly expressed proteins. 98 Additionaltechnological limitations include the minimal solubility of membrane proteins, which often haveimportant roles in transporting chemicals across the cell membrane. 97,99 It is estimated that membraneproteins make up approximately 30% of the total cellular protein content, and resolving thisparticular problem is still a major challenge facing proteomics research.In order to better facilitate the use of 2DE and address some of the previously mentionedlimitations, fractionation is now often performed prior to isoelectric focusing. Fractionations areperformed with respect to different biochemical properties such as isolation according to cellularcompartments and gradients of aqueous solubility. Chromatography and free flow electrophoresisdevices have also been applied, not only to reduce protein mixture complexity but also to enrichthe presence of low expression proteins. 100b. Multidimensional Liquid ChromatographyAlthough the majority of proteomic studies utilize 2DE, alternatives have been under development.One such method incorporates the use of multidimensional liquid chromatography to separate theproteins prior to employing protein identification steps, such as mass spectrometry. 101,102 Liquidchromatography is more adaptable to high throughput and robotics, and more importantly, it offersseveral advantages in terms of protein separation. As previously discussed, some of the limitationsof 2DE relate to the inability to detect some proteins. Liquid chromatography, on the other hand,has better capabilities to separate protein mixtures and thus may be more informative than 2DE.Separation may be performed based on the molecular charge by use of an ion-exchange column.It is also possible to separate proteins on the basis of their hydrophobic interactions with thestationary phase or by specific affinity. The eluted protein fractions are subsequently identified,primarily by mass spectrometry.2. Protein Identificationa. Mass SpectrometryOnce differentially expressed proteins have been visualized, the next step involves protein identification.This is accomplished with mass spectrometry (MS), an approach that has lead to majoradvancements in proteomics research. Briefly, MS is a method that identifies molecules based ontheir molecular mass and charge signature (m/z) after they have been ionized and fragmented. The© 2006 by Taylor & Francis Group, LLC
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Second EditionDEVELOPMENTALandREPRO
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Published in 2006 byCRC PressTaylor
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Chapter 12Chapter 13Chapter 14Chapt
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The EditorRonald D. Hood, Ph.D., is
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Alan M. HobermanArgus ResearchHorsh
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APPENDIX ATerminology of Anatomical
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TERMINOLOGY OF ANATOMICAL DEFECTS 9
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Organ/StructureCodeNumberObservatio
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Organ/Structure10145 Ocular colobom
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Organ/StructurePulmonaryarteryPulmo
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Terminology of developmental abnorm
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Organ/StructureCervicalcentrumCodeN
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Organ/Structure10689 Misshapen thor
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Organ/StructureSacralcentrumSacralv
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968 DEVELOPMENTAL REPRODUCTIVE TOXI
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1000 DEVELOPMENTAL REPRODUCTIVE TOX
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Table 1Human Non-human Primate Rat
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Table 1 (continued)Sertoli CellsHum
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Table 2 (continued) Landmarks in th
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Table 2 (continued) Landmarks in th
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POSTNATAL DEVELOPMENTAL MILESTONES
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PART IPrinciples and Mechanisms© 2
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4 DEVELOPMENTAL REPRODUCTIVE TOXICO
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10 DEVELOPMENTAL REPRODUCTIVE TOXIC
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Table 2.6Receptor(Official Name a )
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Clearly, more research needs to be
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CHAPTER 6Comparative Features of Ve
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COMPARATIVE FEATURES OF VERTEBRATE
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Table 6.2Comparative reproductive a
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Maturation andRelease ofGametesSper
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Amniotic cavity 9.5 1.5 1-4 1-4,6,9
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Posteriorcardinal veinsestablishedT
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PosteriorcardinaldegenerationRight
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StomachappearsThirdpharyngealpouch;
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Table 6.6DescriptionComparative ges
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ParathyroidParathyroids 12.5 6.2 41
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Table 6.8DescriptionComparative ges
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Formation ofchoroid plexusof latera
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Optic nervefibers presentDifferenti
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Table 6.10DescriptionMuscular Syste
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Distalphalanges offingersseparatedF
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Table 6.11DescriptionIntermediateme
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Table 6.12DescriptionComparative ge
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CHAPTER 7Developmental Toxicity Tes
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DEVELOPMENTAL TOXICITY TESTING —
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Female 0.00-0.69 0.004-0.39 0.00-0.
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Figure 8.11775Pott DescribesScrotal
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The underlying physiology of juveni
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Table 8.5Total body composition by
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Table 8.6Serum chemistry values for
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Table 8.7Parameter bHematology valu
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CHAPTER 9Significance, Reliability,
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DEVELOPMENTAL AND REPRODUCTIVE TOXI
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Prior to the early 1980s, numerous
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Figure 9.51906Food andDrugs Act2000
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Table 9.18Selected comparison point
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Table 9.33Selected comparison point
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Table 9.48What do regulatorswant to
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CHAPTER 10Testing for Reproductive
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TESTING FOR REPRODUCTIVE TOXICITY 4
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We would like to acknowledge the ef
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CHAPTER 12Role of Xenobiotic Metabo
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ROLE OF XENOBIOTIC METABOLISM IN DE
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y ESR spectrometry. 122 Further ESR
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CHAPTER 13Use of Toxicokinetics in
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USE OF TOXICOKINETICS IN DEVELOPMEN
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CHAPTER 17Statistical Analysis for
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STATISTICAL ANALYSIS FOR DEVELOPMEN
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CHAPTER 19Perspectives on the Devel
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PERSPECTIVES ON THE DEVELOPMENTAL A
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Guideline OECD 415 (One Generation)
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The Office of Prevention, Pesticide
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CHAPTER 20Human Studies — Epidemi
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HUMAN STUDIES 801I. INTRODUCTIONEpi
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HUMAN STUDIES 803is actively trying
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HUMAN STUDIES 823are used, but the
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HUMAN STUDIES 829B. The Formation o
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HUMAN STUDIES 835of the number of s
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HUMAN STUDIES 837with spina bifida
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HUMAN STUDIES 83926. Haglund, B. an
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CHAPTER 21Developmental and Reprodu
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