Psychobiophysics of transcranial magnetic stimulation

Transcranial magnetic stimulation (TMS) is a technique that stimulates the brain using a magnetic coil placed on the scalp. Since it is applicable to humans non-invasively, directly interfering with neural electrical activity, it is potentially a good tool to study the direct relationship between perceptual experience and neural activity. However, it has been difficult to produce a clear perceptible phenomenon with TMS of sensory areas, especially using a single magnetic pulse. Also, the biophysical mechanisms of magnetic stimulation of single neurons have been poorly understood.

In the psychophysical part of this thesis, perceptual phenomena induced by TMS of the human visual cortex are demonstrated as results of the interactions with visual inputs. We first introduce a method to create a hole, or a scotoma, in a flashed, large-field visual pattern using single-pulse TMS. Spatial aspects of the interactions are explored using the distortion effect of the scotoma depending on the visual pattern, which can be luminance-defined or illusory. Its similarity to the distortion of afterimages is also discussed. Temporal interactions are demonstrated in the filling-in of the scotoma with temporally adjacent visual features, as well as in the effective suppression of transient visual features. Also, paired-pulse TMS is shown to lead to different brightness modulations in transient and sustained visual stimuli.

In the biophysical part, we first develop a biophysical theory to simulate the effect of magnetic stimulation on arbitrary neuronal structure. Computer simulations are performed on cortical neuron models with realistic structure and channels, combined with the current injection that simulates magnetic stimulation. The simulation results account for general and basic characteristics of the macroscopic effects of TMS including our psychophysical findings, such as a long inhibitory effect, dependence on the background activity, and dependence on the direction of the induced electric field.

The perceptual effects and the cortical neuron model presented here provide foundations for the study of the relationship between perception and neural activity. Further insights would be obtained from extension of our model to neuronal networks and psychophysical studies based on predictions of the biophysical model.

Neural representation of auditory temporal structure

Neurons in the songbird forebrain nucleus HVc are highly sensitive to auditory temporal context and have some of the most complex auditory tuning properties yet discovered. HVc is crucial for learning, perceiving, and producing song, thus it is important to understand the neural circuitry and mechanisms that give rise to these remarkable auditory response properties. This thesis investigates these issues experimentally and computationally.

Extracellular studies reported here compare the auditory context sensitivity of neurons in HV c with neurons in the afferent areas of field L. These demonstrate that there is a substantial increase in the auditory temporal context sensitivity from the areas of field L to HVc. Whole-cell recordings of HVc neurons from acute brain slices are described which show that excitatory synaptic transmission between HVc neurons involve the release of glutamate and the activation of both AMPA/kainate and NMDA-type glutamate receptors. Additionally, widespread inhibitory interactions exist between HVc neurons that are mediated by postsynaptic GABA_A receptors. Intracellular recordings of HVc auditory neurons in vivo provides evidence that HV c neurons encode information about temporal structure using a variety of cellular and synaptic mechanisms including syllable-specific inhibition, excitatory post-synaptic potentials with a range of different time courses, and burst-firing, and song-specific hyperpolarization.

The final part of this thesis presents two computational approaches for representing and learning temporal structure. The first method utilizes comput ational elements that are analogous to temporal combination sensitive neurons in HVc. A network of these elements can learn using local information and lateral inhibition. The second method presents a more general framework which allows a network to discover mixtures of temporal features in a continuous stream of input.

A model of the olfactory bulb and beyond

The olfactory bulb of mammals aids in the discrimination of odors. A mathematical model based on the bulbar anatomy and electrophysiology is described. Simulations of the highly non-linear model produce a 35-60 Hz modulated activity, which is coherent across the bulb. The decision states (for the odor information) in this system can be thought of as stable cycles, rather than as point stable states typical of simpler neuro-computing models. Analysis shows that a group of coupled non-linear oscillators are responsible for the oscillatory activities. The output oscillation pattern of the bulb is determined by the odor input. The model provides a framework in which to understand the transformation between odor input and bulbar output to the olfactory cortex. This model can also be extended to other brain areas such as the hippocampus, thalamus, and neocortex, which show oscillatory neural activities. There is significant correspondence between the model behavior and observed electrophysiology.

It has also been suggested that the olfactory bulb, the first processing center after the sensory cells in the olfactory pathway, plays a role in olfactory adaptation, odor sensitivity enhancement by motivation, and other olfactory psychophysical phenomena. The input from the higher olfactory centers to the inhibitory cells in the bulb are shown to be able to modulate the response, and thus the sensitivity, of the bulb to odor input. It follows that the bulb can decrease its sensitivity to a pre-existing and detected odor (adaptation) while remaining sensitive to new odors, or can increase its sensitivity to discover interesting new odors. Other olfactory psychophysical phenomena such as cross-adaptation are also discussed.

Signal transduction, regulation, and developmental logic of EGFR signalling in C. elegans

RTKs-mediated signaling systems and the pathways with which they interact (e.g., those initiated by G protein-mediated signaling) involve a highly cooperative network that sense a large number of cellular inputs and then integrate, amplify, and process this information to orchestrate an appropriate set of cellular responses. The responses include virtually all aspects of cell function, from the most fundamental (proliferation, differentiation) to the most specialized (movement, metabolism, chemosensation). The basic tenets of RTK signaling system seem rather well established. Yet, new pathways and even new molecular players continue to be discovered. Although we believe that many of the essential modules of RTK signaling system are rather well understood, we have relatively little knowledge of the extent of interaction among these modules and their overall quantitative importance.

My research has encompassed the study of both positive and negative signaling by RTKs in C. elegans. I identified the C. elegans S0S-1 gene and showed that it is necessary for multiple RAS-mediated developmental signals. In addition, I demonstrated that there is a SOS-1-independent signaling during RAS-mediated vulval differentiation. By assessing signal outputs from various triple mutants, I have concluded that this SOS-1-independent signaling is not mediated by PTP-2/SHP-2 or the removal of inhibition by GAP-1/ RasGAP and it is not under regulation by SLI-1/Cb1. I speculate that there is either another exchange factor for RASor an as yet unidentified signaling pathway operating during RAS-mediated vulval induction in C. elegans.

In an attempt to uncover the molecular mechanisms of negative regulation of EGFR signaling by SLI-1/Cb1, I and two other colleagues codiscovered that RING finger domain of SLI-1 is partially dispensable for activity. This structure-function analysis shows that there is an ubiquitin protein ligase-independent activity for SLI-1 in regulating EGFR signaling. Further, we identified an inhibitory tyrosine of LET-23/ EGFR requiring sli-1(+)for its effects: removal of this tyrosine closely mimics loss of sli-1 but not loss of other negative regulator function.

By comparative analysis of two RTK pathways with similar signaling mechanisms, I have found that clr-1, a previously identified negative regulator of egl-15 mediated FGFR signaling, is also involved in let-23 EGFR signaling. The success of this approach promises a similar reciprocal test and could potentially extend to the study of other signaling pathways with similar signaling logic.

Finally, by correlating the developmental expression of lin-3 EGF to let-23 EGFR signaling activity, I demonstrated the existence of reciprocal EGF signaling in coordinating the morphogenesis of epithelia. This developmental logic of EGF signaling could provide a basis to understand a universal mechanism for organogenesis.

Studies of the serotonin type 3A receptor and the chemical preparation of tRNA

This thesis describes studies surrounding a ligand-gated ion channel (LGIC): the serotonin type 3A receptor (5-HT₃AR). Structure-function experiments using unnatural amino acid mutagenesis are described, as well as experiments on the methodology of unnatural amino acid mutagenesis. Chapter 1 introduces LGICs, experimental methods, and an overview of the unnatural amino acid mutagenesis.

In Chapter 2, the binding orientation of the clinically available drugs ondansetron and granisetron within 5-HT₃A is determined through a combination of unnatural amino acid mutagenesis and an inhibition based assay. A cation-π interaction is found for both ondansetron and granisetron with a specific tryptophan residue (Trp183, TrpB) of the mouse 5-HT₃AR, which establishes a binding orientation for these drugs.

In Chapter 3, further studies were performed with ondansetron and granisetron with 5-HT₃A. The primary determinant of binding for these drugs was determined to not include interactions with a specific tyrosine residue (Tyr234, TyrC2). In completing these studies, evidence supporting a cation-π interaction of a synthetic agonist, meta-chlorophenylbiguanide, was found with TyrC2.

In Chapter 4, a direct chemical acylation strategy was implemented to prepare full-length suppressor tRNA mediated by lanthanum(III) and amino acid phosphate esters. The derived aminoacyl-tRNA is shown to be translationally competent in Xenopus oocytes.

Appendix A.1 gives details of a pharmacological method for determining the equilibrium dissociation constant, K_B, of a competitive antagonist with a receptor, known as Schild analysis. Appendix A.2 describes an examination of the inhibitory activity of new chemical analogs of the 5-HT₃A antagonist ondansetron. Appendix A.3 reports an organic synthesis of an intermediate for a new unnatural amino acid. Appendix A.4 covers an additional methodological examination for the preparation of amino-acyl tRNA.

Targeting DNA repeat sequences with Py-Im polyamides

Hairpin pyrrole-imdazole polyamides are cell-permeable, sequence-programmable oligomers that bind in the minor groove of DNA. This thesis describes studies of Py-Im polyamides targeted to biologically important DNA repeat sequences for the purpose of modulating disease states. Design of a hairpin polyamide that binds the CG dyad, a site of DNA methylation that can become dysregulated in cancer, is described. We report the synthesis of a DNA methylation antagonist, its sequence specificity and affinity informed by Bind-n-Seq and iteratively designed, which improves inhibitory activity in a cell-free assay by 1000-fold to low nanomolar IC50. Additionally, a hairpin polyamide targeted to the telomeric sequence is found to trigger a slow necrotic-type cell death with the release of inflammatory molecules in a model of B cell lymphoma. The effects of the polyamide are unique in this class of oligomers; its effects are characterized and a functional assay of phagocytosis by macrophages is described. Additionally, hairpin polyamides targeted to pathologically expanded CTG•CAG triplet repeat DNA sequences, the molecular cause of myotonic dystrophy type 1, are synthesized and assessed for toxicity. Lastly, ChIP-seq of Hypoxia-Inducible Factor is performed under hypoxia-induced conditions. The study results show that ChIP-seq can be employed to understand the genome-wide perturbation of Hypoxia-Inducible Factor occupancy by a Py-Im polyamide.

Contribution of the temporoammonic pathway to hippocampal processing

The temporoammonic (TA) pathway is the direct, monosynaptic projection from layer III of entorhinal cortex to the distal dendritic region of area CA1 of the hippo­ campus. Although this pathway has been implicated in various functions, such as memory encoding and retrieval, spatial navigation, generation of oscillatory activity, and control of hippocampal excitability, the details of its physiology are not well understood. In this thesis, I examine the contribution of the TA pathway to hippocampal processing. I find that, as has been previously reported, the TA pathway includes both excitatory, glutamatergic components and inhibitory, GABAergic components. Several new discoveries are reported in this thesis. I show that the TA pathway is subject to forms of short-term activity-dependent regulation, including paired-pulse and frequency­ dependent plasticity, similar to other hippocampal pathways such as the Schaffer collateral (SC) input from CA3 to CA1. The TA pathway provides a strongly excitatory input to stratum radiatum giant cells of CA1. The excitatory component of the TA pathway undergoes a long-lasting decrease in synaptic strength following low-frequency stimulation in a manner partially dependent on the activation of NMDA receptors. High­ frequency activation of the TA pathway recruits a feedforward inhibition that can prevent CA1 pyramidal cells from spiking in response to SC input; this spike-blocking effect shows that the TA pathway can act to regulate information flow through the hippocampal trisynaptic pathway.

On the interaction of actinomycin and DNA

Experiments have been accomplished that (a) further define the nature of the strong, G-containing DNA binding sites for actinomycin D (AMD), and (b) quantitate the in vitro inhibition of E. coli RNA polymerase activity by T7 DNA-bound AMD.

Twenty-five to forty percent of the G's of crab dAT are disallowed as strong AMD binding sites. The G's are measured to be randomly distributed, and, therefore, this datum cannot be explained on the basis of steric interference alone. Poly dAC:TG binds as much AMD and as strongly as any natural DNA, so the hypothesis that the unique strong AMD binding sites are G and a neighboring purine is incorrect. The datum can be explained on the basis of both steric interference and the fact that TGA is a disallowed sequence for strong AMD binding.

Using carefully defined in vitro conditions, there is one RNA synthesized per T7 DNA by E. coli RNA polymerase. The rate of the RNA polymerase-catalyzed reaction conforms to the equation 1/rate = 1/k_A(ATP) + 1/K_G(GTP) + 1/K_C(CTP) + 1/K_U(UTP) T7 DNA-bound AMD has only modest effects on initiation and termination of the polymerase-catalyzed reaction, but a large inhibitory effect on propagation. In the presence of bound AMD, k_G and k_C are decreased, whereas k_A and k_U are unaffected. These facts are interpreted to mean that on the microscopic level, on the average, the rates of incorporation of ATP and UTP are the same in the absence or presence of bound AMD, but that the rates of incorporation of GTP and CTP are decreased in the presence of AMD.

Part I. Synthesis of L-amino acid oxidase by a serine- or glycine-requiring strain of neurospora. Part II. Studies concerning multiple electrophoretic forms of tyrosinase in neurospora

Part I: Synthesis of L-Amino Acid Oxidase by a Serine- or Glycine-Requiring Strain of Neurospora

Wild-type cultures of Neurospora crassa growing on minimal medium contain low levels of L-amino acid oxidase, tyrosinase, and nicotinarnide adenine dinucleotide glycohydrase (NADase). The enzymes are derepressed by starvation and by a number of other conditions which are inhibitory to growth. L-amino acid oxidase is, in addition, induced by growth on amino acids. A mutant which produces large quantities of both L-amino acid oxidase and NADase when growing on minimal medium was investigated. Constitutive synthesis of L-amino acid oxidase was shown to be inherited as a single gene, called P110, which is separable from constitutive synthesis of NADase. P110 maps near the centromere on linkage group IV.

L-amino acid oxidase produced constitutively by P110 was partially purified and compared to partially purified L-amino acid oxidase produced by derepressed wild-type cultures. The enzymes are identical with respect to thermostability and molecular weight as judged by gel filtration.

The mutant P110 was shown to be an incompletely blocked auxotroph which requires serine or glycine. None of the enzymes involved in the synthesis of serine from 3-phosphoglyceric acid or glyceric acid was found to be deficient in the mutant, however. An investigation of the free intracellular amino acid pools of P110 indicated that the mutant is deficient in serine, glycine, and alanine, and accumulates threonine and homoserine.

The relationship between the amino acid requirement of P110 and its synthesis of L-amino acid oxidase is discussed.

Part II: Studies Concerning Multiple Electrophoretic Forms of Tyrosinase in Neurospora

Supernumerary bands shown by some crude tyrosinase preparations in paper electrophoresis were investigated. Genetic analysis indicated that the location of the extra bands is determined by the particular T allele present. The presence of supernumerary bands varies with the method used to derepress tyrosinase production, and with the duration of derepression. The extra bands are unstable and may convert to the major electrophoretic band, suggesting that they result from modification of a single protein. Attempts to isolate the supernumerary bands by continuous flow paper electrophoresis or density gradient zonal electrophoresis were unsuccessful.

A computer-aided investigation of motion detection units in the fly

This work deals with two related areas: processing of visual information in the central nervous system, and the application of computer systems to research in neurophysiology.

Certain classes of interneurons in the brain and optic lobes of the blowfly Calliphora phaenicia were previously shown to be sensitive to the direction of motion of visual stimuli. These units were identified by visual field, preferred direction of motion, and anatomical location from which recorded. The present work is addressed to the questions: (1) is there interaction between pairs of these units, and (2) if such relationships can be found, what is their nature. To answer these questions, it is essential to record from two or more units simultaneously, and to use more than a single recording electrode if recording points are to be chosen independently. Accordingly, such techniques were developed and are described.

One must also have practical, convenient means for analyzing the large volumes of data so obtained. It is shown that use of an appropriately designed computer system is a profitable approach to this problem. Both hardware and software requirements for a suitable system are discussed and an approach to computer-aided data analysis developed. A description is given of members of a collection of application programs developed for analysis of neuro-physiological data and operated in the environment of and with support from an appropriate computer system. In particular, techniques developed for classification of multiple units recorded on the same electrode are illustrated as are methods for convenient graphical manipulation of data via a computer-driven display.

By means of multiple electrode techniques and the computer-aided data acquisition and analysis system, the path followed by one of the motion detection units was traced from open optic lobe through the brain and into the opposite lobe. It is further shown that this unit and its mirror image in the opposite lobe have a mutually inhibitory relationship. This relationship is investigated. The existence of interaction between other pairs of units is also shown. For pairs of units responding to motion in the same direction, the relationship is of an excitatory nature; for those responding to motion in opposed directions, it is inhibitory.

Experience gained from use of the computer system is discussed and a critical review of the current system is given. The most useful features of the system were found to be the fast response, the ability to go from one analysis technique to another rapidly and conveniently, and the interactive nature of the display system. The shortcomings of the system were problems in real-time use and the programming barrier—the fact that building new analysis techniques requires a high degree of programming knowledge and skill. It is concluded that computer system of the kind discussed will play an increasingly important role in studies of the central nervous system.

The Molecular Basis of Lysine Acetylation: Addition, Removal, and Recognition

Acetyltransferases and deacetylases catalyze the addition and removal, respectively, of acetyl groups to the epsilon-amino group of protein lysine residues. This modification can affect the function of a protein through several means, including the recruitment of specific binding partners called acetyl-lysine readers. Acetyltransferases, deacetylases, and acetyl-lysine readers have emerged as crucial regulators of biological processes and prominent targets for the treatment of human disease. This work describes a combination of structural, biochemical, biophysical, cell-biological, and organismal studies undertaken on a set of proteins that cumulatively include all steps of the acetylation process: the acetyltransferase MEC-17, the deacetylase SIRT1, and the acetyl-lysine reader DPF2. Tubulin acetylation by MEC-17 is associated with stable, long-lived microtubule structures. We determined the crystal structure of the catalytic domain of human MEC-17 in complex with the cofactor acetyl-CoA. The structure in combination with an extensive enzymatic analysis of MEC-17 mutants identified residues for cofactor and substrate recognition and activity. A large, evolutionarily conserved hydrophobic surface patch distal to the active site was shown to be necessary for catalysis, suggesting that specificity is achieved by interactions with the alpha-tubulin substrate that extend outside of the modified surface loop. Experiments in C. elegans showed that while MEC-17 is required for touch sensitivity, MEC-17 enzymatic activity is dispensible for this behavior. SIRT1 deacetylates a wide range of substrates, including p53, NF-kappaB, FOXO transcription factors, and PGC-1-alpha, with roles in cellular processes ranging from energy metabolism to cell survival. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an apo form and in complex with a cofactor and a pseudo-substrate peptide. The catalytic domain adopts the canonical sirtuin fold. The CTR forms a beta-hairpin structure that complements the beta-sheet of the NAD^+-binding domain, covering an essentially invariant, hydrophobic surface. A comparison of the apo and cofactor bound structures revealed conformational changes throughout catalysis, including a rotation of a smaller subdomain with respect to the larger NAD^+-binding subdomain. A biochemical analysis identified key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain. DPF2 represses myeloid differentiation in acute myelogenous leukemia. Finally, we solved the crystal structure of the tandem PHD domain of human DPF2. We showed that DPF2 preferentially binds H3 tail peptides acetylated at Lys14, and binds H4 tail peptides with no preference for acetylation state. Through a structural and mutational analysis we identify the molecular basis of histone recognition. We propose a model for the role of DPF2 in AML and identify the DPF2 tandem PHD finger domain as a promising novel target for anti-leukemia therapeutics.