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This chapter discusses several classes of cyclic isoprenoids and their respective derivatives, which have proven to be important biomarkers that can be used to estimate algal and vascular plant contributions as well as diagenetic proxies. Sterols are a group of cyclic alcohols (typically between C₂₆ and C₃₀) that vary structurally in the number, stereochemistry, and position of double bonds as well as methyland ethyl-group substitutions on the side chain. Sterols are biosynthesized from isoprene units using the mevalonate pathway and are classified as triterpenes (i.e., consisting of six isoprene units). Marine organisms such as phytoplankton and zooplankton tend to be dominated by C₂₇ and C₂₈ sterols, while vascular plants have been shown to have a relatively high abundance of C₂₉ sterols. The chapter shows that although C₂₉ sterols are considered to be the dominant sterols found in vascular plants, these compounds may be present in certain epibenthic cyanobacteria and phytoplanktonic species, indicating that these compounds represent a very diverse and powerful suite of chemical biomarkers in aquatic ecosystems.

This chapter examines hydrocarbons present in the environment and derived from natural and anthropogenic sources. Since the industrial revolution, the abundance of hydrocarbons derived from anthropogenic sources (petroleum hydrocarbons) has increased significantly in aquatic systems. Natural oil seeps and erosion of bitumen deposits can also contribute to hydrocarbon abundance and composition in systems. These petroleum hydrocarbons can be distinguished from biological hydrocarbons by their absence of odd-carbon chain lengths commonly found in biological hydrocarbons and the greater structural diversity found in petroleum hydrocarbons. The chapter focuses on naturally produced hydrocarbons. It provides examples of how aliphatic and isoprenoid hydrocarbons have been successfully used to distinguish between algal, bacterial, and terrigenous vascular plant sources of carbon in aquatic systems. It discusses how pristine and phytane are formed from phytol under oxic vs. anoxic conditions, respectively. It also introduces highly branched isoprenoids and their use as algal biomarkers.

This chapter examines lignin, which has proven to be a useful chemical biomarker for tracing vascular-plant inputs to aquatic systems. Cellulose, hemicellulose, and lignin generally make up >75% of the biomass of woody plant materials. Lignins are a group of macromolecular heteropolymers found in the cell wall of vascular plants that are made up of phenylpropanoid units. The shikimic acid pathway, which is common in plants, bacteria, and fungi, is the pathway for synthesis of aromatic amino acids (e.g., tryptophan, phenylalanine, and tyrosine), thereby providing the parent compounds for the synthesis of the phenylpropanoid units in lignins. The chapter also examines cutins and suberins, which are lipid polymers in vascular plant tissues and serve as a protective layer (cuticle) and as cell wall components of cork cells, respectively. It describes how cutins have been shown to be an effective biomarker for vascular plants in aquatic systems.

This chapter examines the primary photosynthetic pigments used in absorbing photosynthetically active radiation, which include chlorophylls, carotenoids, and phycobilins—with chlorophyll representing the dominant photosynthetic pigment. Although a greater amount of chlorophyll is found on land, 75% of the annual global turnover occurs in oceans, lakes, and rivers/estuaries. All of the light-harvesting pigments are bound to proteins making up distinct carotenoid and chlorophyll-protein complexes. The chapter considers the chemistry and application of these very important chemical biomarkers and discusses their limitations in aquatic systems. The matrix factorization program CHEMical TAXonomy (CHEMTAX) was introduced to calculate the relative abundance of major algal groups based on concentrations of diagnostic pigments and is also discussed.

This chapter looks at the adoption in the 1980s of the clinical diagnosis known as “mild cognitive impairment” (MCI). Formal recognition of MCI, the value of which continues to be debated in some circles, is the result of an exerted effort to systematically identify incipient Alzheimer disease (AD) in the clinic and is closely associated with the founding of specialist memory clinics. The chapter presents ethnographic findings of interviews with individuals who have been diagnosed with MCI. The move toward the prevention of AD represents a shift in which it is assumed that embodied risk can be made manifest in the form of biomarkers. This shift is to be accomplished by researching, standardizing, and gradually routinizing the use of several biomarkers believed to put individuals at increased risk for AD.

This chapter illustrates an account of the shift, commencing in the late 1980s, to the molecularization of Alzheimer disease (AD), and the attempt to identify significant bodily changes as much as 20 years before behavioral changes can be diagnosed in individuals. It considers the rationale for efforts to formulate a “prodromal” diagnosis before behavioral symptoms or memory loss are detected, followed by a presentation of the involved molecular diagnostic tools (biomarkers) with emphasis on spinal taps, neuroimaging, and genetic testing. The significance of the first two of these biomarkers is attributed to their apparent ability to detect the onset of the amyloid cascade process. The chapter also discusses the anomalies and uncertainties associated with biomarker testing.

In this chapter we present two examples of longitudinal studies. Both studies utilize an etic–emic approach and both are underway in urban, cosmopolitan areas. In both studies the etic approach stems from the use of standardized, previously validated instruments and a design that called for a specific research protocol. We describe how the emic perspective was incorporated into the respective projects through a detailed discussion of how positive working partnerships were formed and maintained and the ways by which the questionnaires were constructed, pilot tested, and revised. We note that for both projects being culturally sensitive to the populations had more to do with our paying attention and being sensitive to language, gender, age, race and ethnicity, and poverty. In this chapter we also provide a brief conceptual discussion of data analytic considerations for longitudinal data.

This chapter describes the emerging roles of brain imaging and other biomarker measurements of Alzheimer's disease (AD) progression and pathology in the evaluation of putative AD-slowing, risk—reducing, and prevention therapies. It discusses the advantages, disadvantages, and complementary roles of structural magnetic resonance imaging (MRI), fluorodeoxyglucose positron emission tomography (FDG PET), and fibrillar amyloid-β (Aβ) PET in clinical trials of AD patients, patients with mild cognitive impairment (MCI), and cognitively normal people at increased genetic risk for AD. It proposes strategies to optimize these methods’ statistical power, address potentially confounding treatment effects, and develop reasonably likely surrogate endpoints for the rapid and rigorous evaluation of promising pre-symptomatic treatments. Finally, it recommends scientific strategies and new public policies to accelerate the identification of demonstrably effective pre-symptomatic AD treatments without losing a generation.

This chapter provides a general background on the synthesis of chemical biomarkers and their association with key metabolic pathways in organisms, as related to differences in cellular structure and function across the three domains of life. It discusses photosynthesis, the dominant pathway by which biomass is synthesized. It also presents information about chemoautotrophic and microbial heterotrophic processes. The holistic view of biosynthetic pathways of chemical biomarkers provides a roadmap for other chapters in the book, where more specific details on chemical pathways are presented for each of the respective biomarker groups. While other organic geochemistry books have generally introduced the concepts of chemical biomarkers in the context of physical and chemical gradients found in natural ecosystems (e.g., anaerobic, aerobic), this book begins by examining biosynthetic pathways at the cellular level of differentiation.

This chapter provides a brief historical account of the success and limitations of using chemical biomarkers in aquatic ecosystems. It also introduces the general concepts of chemical biomarkers as they relate to global biogeochemical cycling. The application of chemical biomarkers in modern and/or ancient ecosystems is largely a function of the inherent structure and stability of the molecule, as well as the physicochemical environment of the system wherein it exists. In some cases, redox changes in sediments have allowed for greater preservation of biomarker compounds; in well-defined laminated sediments; for example, a strong case can be made for paleo-reconstruction of past organic matter composition sources. However, many of the labile chemical biomarkers may be lost or transformed within minutes to hours of being released from the cell from processes such as bacterial and/or metazoan grazing, cell lysis, and photochemical breakdown. The role of trophic effects versus large-scale physiochemical gradients in preserving or destroying the integrity of chemical biomarkers varies greatly across different ecosystems. These effects are discussed as they relate to aquatic systems such as lakes, estuaries, and oceans.

This chapter provides a background on the important role technology has played in the study of chemical biomarkers, and the many advances in the field that have resulted from the development of new analytical tools. It introduces some of the classic analytical tools used in organic geochemistry, including gas chromatography-mass spectrometry (GC-MS), pyrolysis GC-MS, direct temperature-resolved MS, compound-specific isotope analysis, high-performance liquid chromatography, and nuclear magnetic resonance (NMR) spectroscopy. Additionally, characterization of dissolved organic matter (DOM) and chromophoric DOM by fluorescence, use of pulsed amperometric detector (PAD) detectors in the analysis of sugars, and capillary electrophoresis are introduced. Recent advances in the following areas are also covered: (1) analysis of polar organic compounds utilizing liquid chromatography mass spectrometry, (2) multidimensional NMR, and (3) Fourier transform ion cyclotron resonance MS.

This chapter examines nucleic acids, polymers of RNA and DNA, which act as the templates for protein synthesis. High levels of nucleic acids in microbes contribute to their elevated nitrogen and phosphorus contents. In recent years, isotopic signatures of nucleic acids have provided new insights about the sources of carbon-supporting bacterial activity. The chapter discusses recent efforts to bridge the fields of organic geochemistry and molecular ecology. The coupling of biomarker information to molecular (genetic) data has the potential to provide new insights about specific sediment microbial communities and their effects on sediment organic matter. Recent studies have provided information about the evolutionary basis of biosynthetic pathways, which influence the capabilities of microorganisms to utilize specific substrates and the synthesis of unique biomarkers. Such efforts demonstrate the impact that microorganisms have on organic geochemistry.

This chapter discusses fatty acids, the building blocks of lipids, which represent a significant fraction of the total lipid pool in aquatic organisms. It explores how chain length and levels of unsaturation (number of double bonds) have been shown to be correlated to decomposition, indicating a pre- and postdepositional selective loss of short-chain and polyunsaturated fatty acids. In contrast, saturated fatty acids are more stable and typically increase in relative proportion to total fatty acids with increasing sediment depth. Polyunsaturated fatty acids (PUFAs) are predominantly used as proxies for the presence of “fresh” algal sources, although some PUFAs also occur in vascular plants and deep-sea bacteria. Thus, these biomarkers represent a very diverse group of compounds present in aquatic systems. The numerous applications of fatty acid biomarkers to identifying the sources of organic matter in lakes, rivers, estuaries, and marine ecosystems are discussed.

This chapter focuses on several classes of polar lipids, including alkenones, which are di-, tri-, and tetra-unsaturated long-chain ketones. These compounds are produced by a restricted number of species of prymnesiophyte algae (coccolithophorid alga Emiliania huxleyi), living over a wide temperature range. Prymnesiophytes are able to live under different temperature regimes because they are able to regulate the degree of unsaturation of these compounds; as ambient water temperature decreases, unsaturation increases. Long-chain ketones are more stable than most unsaturated lipids and can survive diagenesis. Because of these properties, alkenones have been used widely as paleothermometers. Paleoclimate studies of continental environments have been hampered by the lack of a useful temperature proxy. Glycerol dialkyl glycerol tetraethers (GDGTs) occur ubiquitously, including sites where alkenones are not produced due to the absence/low abundance of alkenone-producing algae. The TEX86 index, based on the number of cyclopentane rings in the GDGTs, provides a useful paleotemperature index for lakes and other sites where alkenones are not produced. The analysis of intact polar molecules is also becoming more widespread with the advent of liquid chromatography mass spectrometry techniques.

This chapter examines the application of anthropogenic compounds as biomarkers. Since World War II, human activities have introduced a wide array of compounds into the environment, including insecticides such as dichloro-diphenyl-trichloroethane and pesticides, halocarbons (chlorofluorocarbons), sewage products (coprostanol), and polycyclic aromatic hydrocarbons (PAHs). The chapter introduces structural features of these compounds, their distribution and transformation in the environment, and their potential use(s) as tracers. It presents examples of how relationships between anthropogenic markers and biomarkers can be used to provide information about the sources, delivery, and fate of natural organic matter in aquatic ecosystems. It introduces various emerging contaminants (personal care pharmaceutical products, caffeine, and flame retardants) and their potential use as tracers for anthropogenic organic matter in aquatic ecosystems. It describes how δ‎¹³C, stable isotopes of Cl and Br, and radiocarbon can be used to apportion sources of organic contaminants (e.g., PAHs and PCBs).

This chapter discusses the potential for personalized medicine as it applies to schizophrenia, one of the most severe mental disorders. The first half of this chapter will address the genetics of schizophrenia, and in particular what is known about the pharmacogenomics of treatment response and side effects. The second half will focus on the neurobiology and physical abnormalities of schizophrenia, and discuss these in the context of endophenotypes and biomarkers of the illness. Finally, this chapter will conclude with a synthesis of the previously discussed genetic and neurobiological findings in schizophrenia and ideas on how this knowledge can be translated into the framework of personalized medicine.

There is a clear need for biomarkers in neuro-degenerative and psychiatric disorders for both early and differential diagnosis, personalized prediction of treatment response, and in drug discovery. Non-invasive neuroimaging is a key area for biomarker development because it connects behavioural outcomes with structural, functional, and molecular mechanisms. This chapter discusses neuroimaging biomarkers in relation to dementia, schizophrenia, and mood disorders (bipolar and major depressive disorders). The current candidate biomarkers for each disorder are reviewed, across the full range of imaging modalities, followed by an evaluation of their future prospects. The chapter concludes that there has been substantial progress towards personalized neuroimaging-based biomarkers but much remains to be done. Such biomarkers must be validated for specific disorders and may include neuroimaging and non-neuroimaging components.

This chapter explores the use of autonomic nervous system (ANS) measures as potential biomarkers for medically unexplained disorders. It is proposed that these disorders are better classified and treated as related symptom clusters with logical physiological and psychophysiological involving the sympathetic and parasympathetic branches of the ANS. Heart rate variability is described and several examples are given of how specific autonomic biomarkers are related to mental and physical function. Some examples from the worlds of chronic pain and gastroenterology are presented as exemplars using of a simple marker (HRV) that reflects imbalance between the body’s primary excitatory and inhibitory systems, that can readily be linked to gene-brain personalized medicine markers underlying excitation-inhibitory imbalances in brain-based disorders.