Mesolimbic Dopamine Involvement in Pavlovian and Operant Approach Behaviors

Thesis advisor: Jon C. HorvitzPrevious research has yielded conflicting results regarding the involvement of mesolimbic dopamine in Pavlovian and operant tasks. While there is abundant evidence that an operant lever press requires intact dopamine (DA) D1 transmission in the nucleus accumbens (ACB) and in the basolateral amygdala (BLA), there is conflicting evidence regarding the specific brain sites at which DA mediates a Pavlovian approach response. The present study was designed to compare the effects of ACB and BLA D1 receptor-blockade on an operant and Pavlovian task, while minimizing differences in behavioral response topography. Animals were trained on either a Pavlovian cued approach task or an operant cued nosepoke task. In the Pavlovian approach task, a tone signaled a pellet delivery to which animals responded with a head entry into a food compartment. In the operant nosepoke task, animals were trained to emit a nosepoke in response to the same tone, in order to trigger a pellet delivery. Bilateral microinfusions of the D1 antagonist SCH 23390 (0, 1 or 2 microgram/side) into either the ACB or the BLA produced a dose-dependent disruption of the operant nosepoke. In contrast, the Pavlovian cued approach response was unaffected by D1 antagonist microinfusions into either the ACB or the BLA. In addition, infusion of SCH 23390 into either site suppressed general locomotion. The results suggest a dissociation of the anatomical substrates mediating an operant nosepoke and a Pavlovian approach, despite similar response topographies. These findings are consistent with the notion that D1 activity at the ACB and BLA plays a role in the expression of operant responses, but not in the expression of Pavlovian approach responses.Thesis (PhD) — Boston College, 2010.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Psychology

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations

Protein Kinases

Proteins are the work horses of the cell. As regulators of protein function, protein kinases are involved in the control of cellular functions via intricate signalling pathways, allowing for fine tuning of physiological functions. This book is a collaborative effort, with contribution from experts in their respective fields, reflecting the spirit of collaboration - across disciplines and borders - that exists in modern science. Here, we review the existing literature and, on occasions, provide novel data on the function of protein kinases in various systems. We also discuss the implications of these findings in the context of disease, treatment, and drug development

Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria.

Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1H)-ones, exemplified by 34, that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that 34 occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region

Multiscale Mathematical Modeling of the Absorptive and Mucociliary Pathophysiology of Cystic Fibrosis Lung Disease

Airway disease is the primary cause of mortality for the over 70,000 patients with Cystic Fibrosis (CF) worldwide. It is characterized by lung infection, inflammation, and impaired mucociliary clearance (MCC) arising from depletion of the airway surface liquid (ASL) at the organ-scale. Dysfunction in the CF transmembrane conductance regulator protein causes dysregulation in ion and liquid transport alone and via other transport-related proteins. Analysis of cell-system interactions is experimentally complex, however, and motivates the use of mechanistic mathematical models that can also be used to design and optimize treatments for the disease. Tc99m or In111-labeled DTPA (DTPA) are small-molecule radiological probes that allow for observation of paracellular liquid convection and solute transport at cellular and organ scales, respectively. Previous work has shown that DTPA is hyperabsorbed in CF in a manner that strongly correlates with ASL hyperabsorption. The models of this dissertation describe, in part, the mechanisms that underlie this correlation. At the lung-scale, a physiologically motivated pharmacokinetic model was developed to describe the action of hypertonic saline (HS) as an inhaled therapy in CF. This model predicts that MCC is reduced in patients with CF because they have a reduced fraction of functional ciliated airway -- a model parameter -- that is increased via HS-induced airway rehydration. This prediction was verified \textit{in vitro} in human bronchial epithelial (HBE) cultures. A separate, cell-scale model accurately characterizes transcellular liquid transport in HBE cultures using transport parameters that agree well with previously reported values, producing ion flux estimates from the model fit to ASL and DTPA absorption that were similar to known physiological values. It also implicates diminished constitutive Cl¬- secretion in ASL dehydration but suggests that reduced paracellular integrity is the predominant factor leading to hyperabsorption in CF. The cell- and lung-scale models were then used to analyze treatment failure and suggest modifications of a clinical trial, which is the first indication of the utility of airway transport models in designing treatments for patients with CF

Reconsolidation of appetitive memory and sleep: functional connectomics and plasticity

Introduzione: La dipendenza da cibo \ue8 un disturbo comportamentale caratterizzato da modelli maladattativi di consumo alimentare, in cui alimenti ricchi in zuccheri, sale e/o grassi possono indurre una dipendenza tale da essere paragonata ai disturbi relativi all\u2019abuso di sostanze. Alla base di questo processo vi \ue8 l\u2019associazione tra questi cibi altamente palatabili e la sensazione piacevole e rinforzante indotta dal loro consumo, che pu\uf2 essere codificata in una nuova memoria maladattativa sottostante il disturbo di dipendenza. Infatti, le nuove informazioni che riceviamo quotidianamente dall\u2019esterno vengono processate dal nostro cervello tramite un primo stadio di codifica e un secondo stadio di consolidamento, durante il quale vengono stabilizzate in una nuova memoria e integrate nella rete cerebrale di conoscenze preesistenti. Tuttavia, dopo il suo consolidamento, una memoria pu\uf2 essere destabilizzata e riportata ad uno stato di labilit\ue0 che ne permette la modifica e l\u2019eventuale integrazione con nuove informazioni. Infine, un nuovo processo di stabilizzazione chiamato riconsolidamento \ue8 necessario affinch\ue9 la traccia mnemonica aggiornata sia nuovamente stabilizzata. Da recenti studi, \ue8 noto come il sonno sia rilevante sia per il consolidamento che per il riconsolidamento della memoria. Tuttavia, mentre \ue8 chiaro come il consolidamento che avviene durante il sonno permetta la stabilizzazione a lungo termine delle tracce mnemoniche, non \ue8 ancora stato del tutto chiarito il ruolo del sonno nel processo di riconsolidamento. Scopo: Date queste premesse, e nota l\u2019importanza dell\u2019interazione tra amigdala basolaterale (BLA) e ippocampo nel riconsolidamento delle memorie appetitive, gli obiettivi della presente tesi erano: i) valutare come l\u2019amigdala BLA e ippocampo interagiscono in termini di potenziali locali durante la riattivazione della memoria strumentale effettuata o durante la fase di attivit\ue0 o durante la fase di inattivit\ue0 del ciclo circadiano dei roditori; ii) valutare come il richiamo della memoria effettuato durante la fase attiva o quella inattiva possa influenzare il successivo processo di riconsolidamento, e iii) trovare, in-vivo, un marker di riattivazione della memoria appetitiva. Metodi: Sono stati utilizzati 32 ratti maschi, ceppo Sprague Dawley, a cui sono stati impiantati due elettrodi profondi: uno in BLA e uno in ippocampo, per la registrazione dei potenziali locali. I ratti sono stati sottoposti ad un protocollo comportamentale in gabbia operante di auto-somministrazione di saccarosio, composto da quattro stadi: addestramento (i), in cui i ratti imparavano l\u2019associazione tra la pressione di una leva e l\u2019emissione di un pellet di saccarosio; astinenza (ii), durante la quale i soggetti non venivano esposti al contesto di addestramento; riattivazione o non riattivazione (iii) della memoria strumentale in gabbia operante, svolta o durante la fase di attivit\ue0, o durante la fase di inattivit\ue0; test di ricaduta (iv). I potenziali locali sono stati analizzati per lo stadio (iii) in modo da ottenere la potenza delle oscillazioni theta e gamma per i due elettrodi profondi; tali frequenze sono state scelte in quanto rilevanti per i processi mnemonici. Infatti, il richiamo della memoria \ue8 correlato alla sincronizzazione delle onde theta (4-12 Hz) tra BLA e altre aree cerebrali quali l\u2019area CA1 dell\u2019ippocampo, ed \ue8 inoltre correlato alle basse gamma (30-60 Hz) nell\u2019ippocampo. Infine, l\u2019accoppiamento tra le onde theta e gamma nell\u2019ippocampo \ue8 un noto metodo di comunicazione tra sotto-aree ippocampali nel corso dei processi di memoria. Risultati: I risultati hanno mostrato la presenza di una correlazione inversa tra la potenza delle basse gamma nell\u2019area CA1 ippocampale e il tasso di risposta durante lo stadio di richiamo della memoria nella fase di attivit\ue0, indipendentemente dal fatto che i soggetti stessero o meno premendo la leva. Le basse gamma potrebbero quindi rappresentare un marker di correlazione per il richiamo della memoria appetitiva. Inoltre, la potenza di basse e alte gamma ippocampali aumenta durante le epoche di pressione di leva quando il richiamo della memoria viene effettuato nella fase di inattivit\ue0, suggerendo che le onde gamma potrebbero essere dei marker correlazionali specifici per la componente strumentale del richiamo della memoria effettuato durante la fase di inattivit\ue0. Conclusioni e limitazioni: Per concludere, i risultati hanno mostrato l\u2019importanza delle frequenze basse gamma nel richiamo delle memorie appetitive, tuttavia non hanno mostrato alcuna differenza a livello delle onde theta, n\ue9 a livello della BLA. Di conseguenza, si conclude che il protocollo utilizzato nella presente tesi non ha mostrato una sensibilit\ue0 sufficientemente elevata nell\u2019evidenziare i cambiamenti ipotizzati a livello dei potenziali locali. Lo svolgimento di ulteriori esperimenti che andranno a determinare misure di connettomica quali coerenza e accoppiamento, sia intra- che inter- area, aiuter\ue0 a determinare se e come le due aree comunicano tra di loro.Introduction: Food addiction is a behavioural disorder in which individuals develop maladaptive patterns of food consumption. Particularly, food containing processed sugars, salt, fat etc. can be addictive, and refined food consumption behaviours may meet the criteria for substance use disorders. For these characteristics, food addiction can also be considered a memory disorder. Memories in the brain are processed as follows: new information is encoded and then long-term consolidated through a process allowing its integration into already existing knowledge networks. After a memory has been consolidated, it can be destabilized and brought back to a labile state, requiring a new re-stabilization process called reconsolidation. Memory consolidation is known to require sleep. In fact, sleep allows new memory traces to long-term stabilize. Sleep also seems to influence memory reconsolidation; however, its involvement in this process is not yet clear. Aim: Given these premises, the goals of the project were: to evaluate how basolateral amygdala (BLA) and hippocampus interact in terms of local field potentials (LFPs) when appetitive instrumental memory is retrieved either during active or inactive phase of rats circadian rhythm; to evaluate how retrieving the memory in the activity vs inactivity phase influences following memory reconsolidation; and to find an in vivo electrophysiological marker of appetitive memory retrieval. In fact, it has been shown that BLA and dorsal hippocampus interaction is crucial for appetitive memory reconsolidation. Methods: Thirty-two male Sprague Dawley rats were implanted with in-depth electrodes for LFPs recordings in BLA and dorsal hippocampal CA1 and subject to a behavioural protocol apt to induce appetitive memory retrieval. The behavioural procedure consisted of four stages: training (i), in which animals learned lever pressing \u2013 sucrose reward association; abstinence (ii), during which subjects were not exposed to the training context; memory retrieval or no retrieval (iii): instrumental memory reactivation or no reactivation, performed either during active or inactive phase; and relapse test (iv), during which sucrose-seeking behaviour was analysed. Theta and gamma oscillations powers were analysed during stage (iii). In fact, they are known to be involved in memory processes. Memory retrieval has been shown to correlate with theta (4-12 Hz) synchronization between BLA and other brain areas (such as hippocampal CA1) and with low gamma (30-60 Hz) in hippocampus. Particularly, theta-gamma cross-frequency coupling has been shown to be used as a mean of communication between hippocampal sub-areas during memory processing. Results: Results showed an inverse correlation between hippocampal CA1 low gamma power and reactivation rate of responding (either when rats were lever pressing or not) when reactivation was performed during the active phase. This suggests that low gamma may be a correlational marker of instrumental sucrose memory retrieval, independent of whether rats were lever-pressing or not. Moreover, hippocampal CA1 gamma bands increased when lever pressing during instrumental memory reactivation while in the inactive phase, suggesting that both low and high gamma bands may be correlational markers to actual instrumental responding retrieval during the inactive phase. Conclusions and limitations: In conclusion, results showed that low gamma is relevant in sucrose appetitive memory retrieval. However, no difference was observed in the theta frequency band, nor at the level of BLA. Therefore, the current protocol did not have the sensitivity to detect predicted changes in LFPs. Further experiments would help investigating if and how the two areas interact, by determining connectomics measures such as coherence and coupling within and between areas

Manipulating Maladaptive Motivational Memories via Reconsolidation

Substance Use Disorders (SUDs), are generally viewed as disorders of maladaptive reward memory and motivation. In SUDs, memories formed during drug use associate environmental stimuli with the rewarding effects of drugs. These stimuli can subsequently trigger craving, highly motivated drug-seeking and relapse, even after years of abstinence. An exciting new approach to combatting these maladaptive memories is via reconsolidation, the process by which memories become briefly unstable upon recall in order to strengthen or update before restabilising. In Chapter 1, I review reward memory mechanisms in SUDs along with pharmacological and behavioural determinants of memory reconsolidation to identify potential drug targets for interfering with reconsolidation. In Chapter 2, I use meta-analysis to assess the effects of two classes of drugs; N-methyl D-aspartate (NMDAR) antagonists and β-Blockers on blocking reconsolidation of reward memory in rats and show that NMDAR antagonism is far more effective. Building on this knowledge, in Chapter 3, I show that 10mg of the NMDAR antagonist memantine in combination with the retrieval of smoking cue-drug memory does not affect relapse or craving in a group of quitting smokers. As this null finding may have represented either a failure to destabilise memories or inefficacy of memantine, in Chapter 4 I use a reward conditioning paradigm in hazardous drinkers to show that NMDAR antagonist Nitrous Oxide can interfere with reconsolidation of cue-alcohol memory, when administered after a reminder of learning that induces a negative prediction error. Chapter 5 builds on emerging evidence of the necessity of prediction error to destabilise memory, using guided expectancy violation to destabilise naturalistic cue-alcohol memories in hazardous drinkers. Subsequent disgust counterconditioning updated these memories, reducing motivational salience and liking of alcohol stimuli, with associated reduction in drinking. In Chapter 6 I discuss the research reported and suggest directions for further study