T because the system is `physiologic.’ However, the milieu of the human body is undefined. It is too complex to understand with the scientific tools currently available. This is the reason we turn to in vitro systems, which reduce questions to forms answerable using the scientific method. The problem then becomes one of establishing the true value of inferences obtained in our simple, yet profoundly incomplete (vis-?vis the brain in the case of AD), experimental systems. I argue that the milieu of A in situ in vivo cannot be defined precisely, and if we cannot do so, then what constant of proportionality can be employed to relate our in vitro findings to the structure and behavior of A in the human brain? How does the milieu change between different sub-cellular, cellular, or anatomical locations? How do purification procedures designed to yield A assemblies alter the native states of such assemblies? It has been argued, for example, that when fibrillar A is isolated, a native proteoglycan component is lost [86]. `Native state’ assemblies could comprise such complexes, or order PXD101 complexes involving other biomolecules. Importantly, these states could display unique primary, secondary, tertiary, or quaternary structures of the A component. These arguments apply both to studies of A pre-existent in biological milieus and to studies in which A is introduced exogenously. We also are faced with the dilemma of time. How do A assemblies change over time in a particular milieu? What are the equilibrium relationships involved? Work by Bateman and colleagues [87] has shown that biological half-lives for newly produced A measured in CSF are of the order of 6 hours. From where do the A species we seek to study come? Do subsets of these species traffic to different cell types, organelles, or extra-cellular sitesWhat may be the most intractable issue is that of `iatrogenesis’; that is, how do we, in the process of isolating and studying A derived from cellular or organismal sources, alter the native state of the peptide? Such alteration(s) has the capacity to invalidate the determination of structure ctivity relationships (SARs). We may know that a particular assembly that we have isolated from the brain, characterized structurally, and studied in vitro has certain activities, but we do not know that this assembly actually existed in the biological milieu prior to its isolation. The most obvious examples of iatrogenesis are the use of SDS in A isolation procedures and in SDS-PAGE. The theory of SDS-PAGE requires the presence of SDS to denature proteins. Oligomers are predominately noncovalent A complexes. SDS dissociates such complexes well. In addition, and less well understood, there is the ability of SDS to induce A self-association [88], especially into the trimer and tetramer states [64,89]. The use of SDS is but one caveat in our approaches to establishing SARs. Other compounds that can affect oligomerization state and that have been used in A isolation procedures from human brains include 1 Triton X-100, 5 M guanidine HCl, and 70 or 88 formic acid [90-94].Conclusions The prior discussion has emphasized the complexity of the A system, both in vitro and in PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27385778 vivo. It has focused on principles governing our study of A oligomers, on weaknesses and caveats in our approaches to these studies, on the nebulous nature of our conception of oligomers and our use of the term itself, and on the problems of establishing the biological relevance of our work. It wou.