Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The field of neuroscience has the potential to address profound questions including explaining how neural activity enables complex behaviors and conscious experience. However, currently the field is a long way from understanding these issues, and progress has been slow. One of the main problems holding back the pace of discovery is that it is still unclear how to interpret neural activity once it has been recorded. This lack of understanding has led to many different data analysis methods, which makes it difficult to evaluate the validity and importance of many reported results. If a clearer understanding of how to interpret neural data existed, it should be much easier to answer other questions about how the brain functions. In this thesis I describe how to use a data analysis method called 'neural population decoding' to analyze data in a way that is potentially more relevant for understanding neural information processing. By applying this method in novel ways to data from several vision experiments, I am able to make several new discoveries, including the fact that abstract category information is coded in the inferior temporal cortex (ITC) and prefrontal cortex (PFC) by dynamic patterns of neural activity, and that when a monkey attends to an object in a cluttered display, the pattern of ITC activity returns to a state that is similar to when the attended object is presented alone. These findings are not only interesting for insights that they give into the content and coding of information in high level visual areas, but they also demonstrate the benefits of using neural population decoding to analyze data. Thus, the methods developed in this thesis should enable more rapid progress toward an algorithmic level understanding of vision and information processing in other neural systems. / by Ethan M. Meyers. / Ph.D.

Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 1999. / Includes bibliographical references (leaves 181-193). / by Carsten Dietrich Hohnke. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 1995. / Includes bibliographical references (leaves 107-110). / by Karl Zipser. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 2013. / Cataloged from PDF version of thesis. Vita. / Includes bibliographical references (p. 153-184). / Autism spectrum disorder (ASD) is a complex and heterogeneous disorder, and in the vast majority of cases the etiology is unknown. However, there are many syndromes of known genetic origin that have a high incidence of autism. These highly penetrant syndromic forms of autism offer a unique opportunity for the study of ASD because animal models can be readily engineered to carry the same genetic disruption. Animal models are crucial for understanding neurological disorders at the biological level, and while these monogenic disorders are relatively rare, their animal models are likely to prove indispensable in identifying common pathogenic pathways in ASD and associated intellectual disability (ID). As evidence accumulates from genetic and molecular studies, autism is increasingly being regarded as a disease of the synapse. In particular, a preponderance of genes associated with ASD appear to regulate the synaptic signaling pathways necessary for the proper control of neuronal protein synthesis. Here, we test the hypothesis that many ASDs may result from alterations in synaptic protein synthesis by examining neuronal translation in the mouse models of fragile X (FX) and tuberous sclerosis (TSC), the two leading inherited causes of ASD. Specifically, we determined if altered synaptic protein synthesis downstream of metabotropic glutamate receptor 5 (mGluR5) is a shared disruption in these disorders, and therefore may ultimately contribute to the pathophysiology of ASD in general. First, we show that multiple aspects of mGluR-mediated protein synthesis are altered in the mouse model of FX, suggesting that exaggeration of these processes may account for the diverse phenotypes associated with the disorder. Next, we demonstrate that disruptions in the mGluR pathway do not appear to be limited to this FX, as there is diminished synaptic protein synthesis and mGluR-LTD in a mouse model of TSC as well. This suggests that genetically heterogeneous causes of ASD and ID may produce similar deficits through bidirectional deviations in mGluR-mediated protein synthesis. Finally, we address the mechanisms by which mGluR activation is coupled to protein synthesis, which may elucidate novel avenues for the next generation of mGluR-based therapies for the treatment of ASD. / by Benjamin D. Auerbach. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 1996. / Includes bibliographical references (p. 171-177). / by Philip N. Sabes. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2015. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (pages 123-131). / Magnetoencephalography (MEG) and electroencephalography (EEG) are noninvasive functional neuroimaging techniques that provide high temporal resolution recordings of brain activity, offering a unique means to study fast neural dynamics in humans. Localizing the sources of brain activity from MEG/EEG is an ill-posed inverse problem, with no unique solution in the absence of additional information. In this dissertation I analyze how solutions to the MEG/EEG inverse problem can be improved by including information about temporal dynamics of brain activity and connectivity within and among brain regions. The contributions of my thesis are: 1) I develop a dynamic algorithm for source localization that uses local connectivity information and Empirical Bayes estimates to improve source localization performance (Chapter 1). This result led me to investigate the underlying theoretical principles that might explain the performance improvement observed in simulations and by analyzing experimental data. In my analysis, 2) I demonstrate theoretically how the inclusion of local connectivity information and basic source dynamics can greatly increase the number of sources that can be recovered from MEG/EEG data (Chapter 2). Finally, in order to include long distance connectivity information, 3) I develop a fast multi-scale dynamic source estimation algorithm based on the Subspace Pursuit and Kalman Filter algorithms that incorporates brain connectivity information derived from diffusion MRI (Chapter 3). Overall, I illustrate how dynamic models informed by neurophysiology and neuroanatomy can be used alongside advanced statistical and signal processing methods to greatly improve MEG/EEG source localization. More broadly, this work provides an example of how advanced modeling and algorithm development can be used to address difficult problems in neuroscience and neuroimaging. / by Camilo Lamus Garcia Herreros. / Ph. D.

Thesis: Ph. D. in Neuroscience, Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 119-128). / Gene expression is dynamic in living systems, enabling environmental adaptation and homeostasis. Transcript levels may change temporarily during distinct phases of biological processes, while longer lasting modifications to their regulatory machinery can lead to specific cell states or disease phenotypes. However, versatile and robust methods to investigate causal relationships between gene expression states and biological phenotypes remain elusive. My thesis work - divided into two main parts - has focused on the development of technologies to enable efficient, generalizable, and precise perturbation of mammalian gene expression. The first part of my research focused on the development of light-inducible transcriptional effectors (LITEs) to mediate positive and negative regulation of endogenous mammalian gene expression (Konermann et al. Nature 2013). Optical stimulation enables precise spatiotemporal control to closely match endogenous transcriptional dynamics. I engineered the LITE system based on the programmable TALE DNA binding proteins from plant pathogens in combination with the light-inducible dimer cryptochrome 2 - cibi from Arabidopsis thaliana. Light enables fast and reversible recruitment of transcriptional effector domains to the TALE bound to the endogenous target promoter through dimerization of cryptochrome 2 - cibi. I applied LITEs to control gene expression in primary neurons as well as in the mouse brain in vivo, demonstrating their potential to dissect genetic contributions to dynamic behaviors such as learning. Epigenetic regulation of transcriptional state is an additional layer of endogenous control exerted by the cell to store more permanent states such as memories. To interrogate epigenetic in addition to transcriptional dynamics, I next developed TALE-mediated targeting of 32 repressive histone effectors to alter epigenetic states in a locus-specific manner. The LITE system establishes a novel mode of optogenetic control of endogenous cellular processes and enables direct testing of the causal roles of genetic and epigenetic regulation in normal biological processes and disease states. One major limiting aspect of TALE-based transcriptional activators is the costly and labor-intensive construction of their repetitive DNA binding domains. As a result, the utility of TALEs for higher-throughput gene targeting experiments remains limited. The CRISPR nuclease Cas9, however, can be easily programmed using a short guide RNA homologous to the target genomic DNA of interest. Additionally, Cas9 can be easily converted into an RNA-guided DNA binding protein (dCas9) via inactivation of its two catalytic domains. The ease and scalability of the CRISPR-Cas9 system potentially enables systematic, genome-scale perturbation, but the magnitude of transcriptional upregulation achieved by the current generation of Cas9 transcriptional activators typically ranges from low to ineffective. In order to achieve a system where the majority of Cas9 activators are highly functional, I undertook structure-guided engineering to generate a potent, sjynergistic Cas9 activation complex (SAM) capable of mediating robust upregulation with a single sgRNA (Konermann et al., Nature, 2015) which outperforms current systems by more than two orders of magnitude. I demonstrated that these transcriptional effectors are capable of activating up to 10 genes simultaneously, allowing for understanding of complex genetic and regulatory networks. Genome-scale GOF screening approaches have largely remained limited to the use of cDNA library systems, which are costly and challenging to use in a pooled format. To overcome this limitation, I designed a genome-scale sgRNA library targeting every coding isoform from the RefSeq database (23,430 isoforms) for a final library of 70,290 guides. I next aimed to identify gain-of-function changes that can lead to the development of BRAF inhibitor resistance in BRAFV 600 mutant melanoma cells. The screen results highlighted a number of gene candidates that both confirm known BRAF inhibitor-resistance pathways and suggest novel mechanisms of action. SAM activators present a highly reliable and generalizable tool for genome-wide interrogation of gene function and interaction in diverse biological processes. Recently, we have extended the utility of the SAM system to enable bimodal control through the use of modified, truncated deadRNAs (dRNAs) (Dahlman, et al., Nature Biotechnology 2015). These dRNAs prevent nucleolytic activity of an active Cas9 nuclease and transform the wildtype enzyme into an efficient transcriptional activator when combined with the SAM activator-components. This system enables simultaneous knock-out of gene A and activation of gene B in the same cell population, enabling bidirectional interrogation of gene interaction and regulatory networks. / by Silvana Konermann. / Ph. D. in Neuroscience

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 2009. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references. / Alterations in sensory experience can persistently modify the responses of cortical neurons. Ocular dominance (OD) plasticity, a process in which alternation of visual input induces a shift in cortical responsiveness, is an extensively studied model of such experience-dependent plasticity. However, the synaptic mechanisms underlying OD plasticity are not well understood. Recent studies revealed that both Hebbian and homeostatic mechanisms play a role in OD plasticity. Therefore, we were interested in monitoring the process of rapid plasticity at individual synapses in vivo to gain insight into the interplay of these two mechanisms. Ca2+/calmodulin dependent protein kinase II (CaMKII) is a major component of the postsynaptic density. Activation of CaMKII is necessary and sufficient for LTP induction, is required for OD plasticity, and its expression pattern coincides with the site of rapid plasticity in the supragranular layers II/III of the visual cortex. Moreover, CaMKII can convert transient Ca2+ influx into a prolonged biochemical process via autophosphorylation that renders CaMKII activity Ca2+ independent. Hence, CaMKII is well suited as a reporter of synaptic activity. We previously engineered a probe, Camui, which utilizes the optical phenomenon of fluorescence resonance energy transfer (FRET), to monitor CaMKII activation. This thesis embodies the work done to improve Camui to be a better tool for in vivo reporting of CaMKII activity, as well as the use of this improved probe for in vivo detection of CaMKII activity in single spines before and after 4 hrs of monocular deprivation (MD) in the ferret visual cortex. / (cont.) We found that after only 4 hrs of MD, the overall CaMKII activity in spines, and adjacent dendritic regions, of neurons in the deprived eye domain increased significantly. This increase was also seen in the binocular eye domain. In the open eye domain, however, this overall increase in CaMKII activity was absent. These observations were specific to MD as control experiments did not show such changes. Moreover, detailed analysis revealed that spines that were eliminated after 4 hrs of MD had a low level of basal CaMKII activity. Our results lend support to the model that both Hebbian, as well as homeostatic compensatory mechanism can subserve OD plasticity. / by Show Ming Kwok. / Ph.D.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 129-170). / Adults greatly impact children's learning: they serve as models of how to behave, and as parents, provide the larger social context in which children grow up. This thesis explores how adults impact children's learning across two time scales. Chapters 2 and 3 ask how a brief exposure to an adult model impacts children's moment-to-moment approach towards learning, and Chapters 4 and 5 look at how children's long-term social context impacts their brain development and capacity to learn. In Chapter 2, I show that preschool-age children integrate information from adults' actions, outcomes, and testimony to decide how hard to try on novel tasks. Children persist the longest when adults practice what they preach: saying they value effort, or giving children a pep talk, in conjunction with demonstrating effortful success on their own task. Chapter 3 demonstrates that social learning about effort is present in the first year of life and generalizes across tasks. In Chapter 4, I find that adolescents' long-term social environments have a selective impact on neural structure and function: socioeconomic-status (SES) relates to hippocampal-prefrontal declarative memory, but not striatal-dependent procedural memory. Finally, in Chapter 5 I demonstrate that the neural correlates of fluid reasoning differ by SES, suggesting that positive brain development varies by early life environment. Collectively, this work elucidates both the malleable social factors that positively impact children's learning and the unique neural and cognitive adaptations that children develop in response to adverse environments. / by Julia Anne Leonard. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 1993. / Includes bibliographical references (leaves 156-168). / by Hiroshi Ando. / Ph.D.