Dissertations / Theses on the topic 'Brain development'

The development of fluent reading requires coordinated development of key fiber pathways. While several fiber pathways have been implicated in reading, including the recently re-identified vertical occipital fasciculus (VOF), inferior longitudinal fasciculus (ILF), arcuate fasciculus and its 3 components, and inferior fronto-occipital fasciculus (IFOF), whether these fiber pathways support reading in young children with little to no exposure to print remains poorly understood. Consequently, over the course of three studies, the current dissertation aimed to narrow this research gap by addressing the following research questions: 1) Which fiber pathways support early literacy skill in young children 5-10 years old? 2) Are microstructural properties of these tracts predictive of age-related changes in reading across an interval of two years? 3) Do different components of the recently identified VOF differentially support reading? To answer these questions, we used diffusion-weighted imaging to measure white-matter development and to relate the microstructural properties of each fiber pathway to early literacy and literacy development. We report several novel findings that contribute to our growing understanding of the white matter connections supporting early literacy and literacy. For the first time, these studies revealed that the re-identified VOF can be reliably tracked in young children, bilaterally and is composed of three main components, which project from occipital temporal sulcus to angular, and middle and superior occipital gyri. We also found that the left AF, bilateral ILF, and particular components of the VOF play a role in early literacy and literacy development. Implications for contemporary models of reading development are discussed.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2008.
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references.
The brain ventricles are a conserved system of fluid-filled cavities within the brain that form during the earliest stages of brain development. Abnormal brain ventricle development has been correlated with neurodevelopmental disorders including hydrocephalus and schizophrenia. The mechanisms which regulate formation of the brain ventricles and the embryonic cerebrospinal fluid are poorly understood. Using the zebrafish, I initiated a study of brain ventricle development to define the genes required for this process. The zebrafish neural tube expands into the forebrain, midbrain, and hindbrain ventricles rapidly, over a four-hour window during mid-somitogenesis. In order to determine the genetic mechanisms that affect brain ventricle development, I studied 17 mutants previously-identified as having embryonic brain morphology defects and identified 3 additional brain ventricle mutants in a retroviral-insertion shelf-screen. Characterization of these mutants highlighted several processes involved in brain ventricle development, including cell proliferation, neuroepithelial shape changes (requiring epithelial integrity, cytoskeletal dynamics, and extracellular matrix function), embryonic cerebrospinal fluid secretion, and neuronal development. In particular, I investigated the role of the Na+K+ATPase alpha subunit, Atp1a1, in brain ventricle formation, elucidating novel roles for its function during brain development. This study was facilitated by the snakehead mutant, which has a mutation in the atp1a1 gene and undergoes normal brain ventricle morphogenesis but lacks ventricle inflation. Analysis of the temporal and spatial requirements of atp1a1 revealed an early requirement during formation, but not maintenance, of the neuroepithelium. I also demonstrated a later neuroepithelial requirement for Atp1a1-driven ion pumping that leads to brain ventricle inflation, likely by forming an osmotic gradient that drives fluid flow into the ventricle space.
(cont) Moreover, I have discovered that the forebrain ventricle is particularly sensitive to Na+K+ATPase function, and reducing or increasing Atp1a1 levels leads to a corresponding decrease or increase in ventricle size. Intriguingly, the Na+K+ATPase beta subunit atp1b3a, expressed in the forebrain and midbrain, is specifically required for their inflation, and thus may highlight a distinct regulatory mechanism for the forebrain and midbrain ventricles. In conclusion, my work has begun to define the complex mechanisms governing brain ventricle development, and I suggest that these mechanisms are conserved throughout the vertebrates.
by Laura Anne Lowery.
Ph.D.

Introduction Fetal ventriculomegaly is the most common detectable central nervous system abnormality affecting 1% of fetuses and is associated with abnormal neurodevelopment in childhood. Neurodevelopmental outcome is partially predictable by the 2D size of the ventricles in the absence of other abnormalities while the aetiology of the dilatation remains unknown. The main aim of this study was to investigate brain development in the presence of isolated ventriculomegaly during fetal and neonatal life. Methods Fetal brain MRI (1.5T) was performed in 60 normal fetuses and 65 with isolated ventriculomegaly from 22-38 gestational weeks. Volumetric analysis of the ventricles and supratentorial brain structures was performed on 3D reconstructed datasets while cortical maturation was assessed using a detailed cortical scoring system. The metabolic profile of the fetal brain was assessed using magnetic resonance spectroscopy. During neonatal life, volumetric analysis of ventricular and supratentorial brain tissue was performed while white matter microstructure was assessed using Diffusion Tensor Imaging. The neurodevelopmental outcome of these children was evaluated at 1 and 2 years of age. Results Fetuses with isolated ventriculomegaly had significantly increased cortical volumes when compared to controls while cortical maturation of the calcarine sulcus and parieto-occipital fissure was delayed. NAA:Cho, MI:Cho and MI:Cr ratios were lower whilst Cho:Cr ratios were higher in fetuses with ventriculomegaly. Neonates with prenatally diagnosed ventriculomegaly had increased ventricular and supratentorial brain tissue volumes and reduced FA values in the splenium of the corpus callosum, sagittal striatum and corona radiata. At year 2 of age, only 37.5% of the children assessed had a normal neurodevelopment. Conclusions The presence of relative cortical overgrowth, delayed cortical maturation and aberrant white matter development in fetuses with ventriculomegaly may represent the neurobiological substrate for cognitive, language and behavioural deficits in these children.

Autism spectrum disorder is a lifelong neurodevelopmental condition accompanied by differences in brain anatomy and connectivity. Whilst the ASD brain has been widely studied under the lens of neuroimaging, results are both spatially and temporally heterogeneous. The most ubiquitous findings relate to global differences in the trajectory of early brain growth. Thus, there is a compelling need to characterize the neurodevelopmental trajectory of brain maturation in ASD beyond these early years and beneath the global level. Therefore, the present work conducts an investigation into brain development in ASD, utilizing a variety of magnetic resonance metrics in a broad sample of children and adolescents with ASD and typically developing controls. We examine age-related differences in structural connectivity - measured by diffusion tensor imaging and myelin mapping techniques - alongside vertex-based measures of cortical anatomy, including cortical thickness, surface area and gyrification. In addition, we dissect these differences within a developmental framework by investigating linear, quadratic, and cubic age effects on each neuroanatomical component in order to identify the most appropriate model for examining between-group differences in the presence of significant age effects and age ‘by’ group interactions. Finally, we extend our cross-sectional investigations by carrying out a longitudinal study of myelination in ASD, showing for the first time that the ASD is accompanied by altered myelin development. Our overarching finding is that ASD is characterised by age-related, region-specific brain differences. Importantly, these differences encompass the trajectories of both grey- and white-matter development, which we have dissected further into contributions from cortical-thickness, surface-area and gyrification, as well as white matter microstructure and myelination, respectively. Therefore, measures of grey- and white-matter morphology and connectivity should not be interpreted independently, but jointly as they jointly elicit the atypical patterns of brain development and connectivity typically observed in ASD.

Prolidase deficiency (PD) is a rare autosomal recessive disorder caused by mutations in the prolidase gene, the PEPD, causing the reduction or the loss of the prolidase enzyme activity. PD patients present a variable onset, and severe skin ulcers mainly characterize the pathology. However, PD has a broad spectrum of phenotypes including mental impairment and developmental delay of variable degrees. Prolidase is a member of the matrix metalloproteinase (MMP) family. MMPs together with their inhibitors (tissue inhibitor of metalloproteinases, TIMPs) regulate the extracellular matrix maturation and remodelling life-long. Among them, prolidase is able to cleave dipeptides when prolin or hydroxyprolin residues are located at the C-terminal end. According to prolidase activity, its function has an impact on the metabolism of many biologically important molecules, particularly during the biosynthesis and degradation of collagen and procollagen. Therefore, prolidase indirectly has a role in the ECM remodelling. In particular, the ECM adjustments are essential in the brain, especially during the critical period of development: from passive structural property, to a direct influence on cell proliferation, migration, axonal guidance, synaptogenesis, homeostatic plasticity, learning and memory processes, and angiogenesis. In particular, the basement membrane beside the pial meninx (pBM) is a specialized structure of ECM whose integrity and proper assembly is essential for a correct cortical development and the collagen IV plays an essential role in pBM stability. Ruptures, even localized, in the pBM are accompanied by changes in the morphology of radial glia cells, subsequent cortical dysplasia, overmigration of neurons, decrease in the proliferation and migration of granule cell precursors, and reduction in Purkinje neuron dendrites. Recently, a mutant mouse with reduced prolidase activity has been identified with a spontaneous 4 bp deletion in the exon 14 of Pepd gene. The mutant mouse was named dark-like (dal) because of its darkened-coat color in homozygosis. The dal/dal phenotype includes small body size, reproductive degeneration, vacuolated cells at the cortical medullary junction of the adrenal gland, mild hydrocephalus, dark urine and altered bone phenotype. The prolidase activity was strongly reduced in cerebrum and cerebellum in dal mice. Moreover, they develop hypertrophic cardiomyopathy, but neither skin lesions nor recurrent infections were reported (in contrast to the reported human cases). The aim of this thesis was the study the brain development of dal/+ and dal/dal mice. Since no information were available, the analysis started with a morphological evaluation of the cerebellum, neocortex and hippocampus, through histological stainings. Then, immunohistochemistry reactions and western blotting analysis helped the anomalies characterizations. In particular, the attention has been mainly focused on the cerebellum, since it is the structure in which the ontogenetic events occurred also postnatally. The neocortex and hippocampal results were not described in details. Our results suggested that the absence of a full functional prolidase enzyme in the dal/dal mice results in a damage of the integrity of the pBM with an altered collagen, laminin and reelin profile. Such damage, could affect as a cascade of developmental events the proper lamination process of the cerebellum, leading to a cortical dysplasia together with the presence of degenerating and ectopic cells, defects in cerebellar lobulation and in the excitation/inhibition pattern of the cerebellar circuit.

Background. Improvements in postnatal care provided in neonatal intensive care units have resulted in increasing survive percentage of children born at the limits of viability. A large number of premature infants experienced major impairment and/or minor neurodevelopmental disabilities, such as cognitive, psychiatric and motor disorders. The etiology of these developmental deficits still remains not completely understood, but they may be the result of neonatal brain injury as well of interruption of the normal process of brain maturation that occurs during the last trimester of pregnancy, a critical period of prenatal ontogenesis. Prediction of the outcome of individual preterm infants is difficult. Although a premature infant may be asymptomatic for abnormal clinical signs, he may exhibit subtle alterations in brain activity which often remain unrecognized. A neurophysiologic evaluation of brain activity in the third trimester of gestation would probably be of great benefit for early detection of pathological processes or subclinical alterations. Electroencephalogram and cortical auditory evoked potentials turned out to be simple and useful techniques in evaluation of brain maturation. Aims. We conducted cross-sectional and longitudinal investigations at early crucial phases of development (35 and 40 weeks post-conception) in order to identify differences in cerebral activity between premature infants born at different gestational ages and full-term neonates, using electroencephalogram (EEG) at rest and cortical auditory evoked potentials (CAEP). We further aimed to correlate the neonatal data with later neurodevelopment. Methods. The research is divided into three studies: Study 1: EEG spectral activity was recorded at 35 post-conception weeks in 40 premature infants and compared between groups of infants born at different gestational age (“extremely low gestational age”, ELGA: 23–27+6, ‘‘very low gestational age’’, VLGA: 28–31+6 and “low gestational age”, LGA: 34-35). The results were correlated with behavioral developmental scores obtained at 12 months corrected age from 20 infants. Study 2: a subgroup of 10 infants of Study 1 repeated the EEG recording at 40 post-conception age. EEG spectral activity of this subgroup was compared longitudinally and further the activity recorded at 40 GA were compared with those of a group of 10 full-term infants. Study 3: CAEP were recorded in active sleep at 35 post-conception weeks in response to an auditory stimulation in 36 premature infants and compared between groups of infants born at different gestational age (ELGA, VLGA, LGA). The results were correlated with behavioral developmental scores obtained at 12 months corrected age from 20 infants. Methodology Study 1 and 2. Electrical brain activity was recorded for 40 minutes on 5 bipolar channels. Data were transformed into the frequency domain using a Fast Fourier Transform algorithm. Frequency spectrum was divided into the following bands: δ (0.5-4 Hz, comprising δ1 0.5-1 Hz and δ2 1-4 Hz), θ (4-8 Hz), α (8-13 Hz) and β (13-20 Hz). Statistical analysis were performed on absolute and relative power values only on central sites (C3-C4, C3-T3, C4-T4). Methodology Study 3. 1000 Hz (paradigm 1) and 500 Hz (paradigm 2) auditory stimulations were performed on continuous EEG recording. Design consisted of 300 tones for each paradigm. Inter-stimulus interval randomly varied between 600 and 900 ms; 12 monopolar channels were recorded, referenced to the bilateral linked ear lobes. 600 ms epochs were divided for statistical analysis in time windows of 100 ms. Statistical analysis were performed only on central sites (Fz, Cz). Results. Study 1. On C3-C4, relative spectral power values differed significantly between ELGA and LGA groups. Infants born at lower gestational ages had a higher amount of power in the δ and a lower amount of α and β spectral power. The preliminary data on those infants attaining 12 months of corrected age showed that higher amount of δ and a lower amount of β and α resulted associated with poor relational skills and personal self autonomies. Study 2. At 40 post-conception age, premature infants showed on C3-C4 a decrease in δ activity and a mild, not significant, increase in higher frequencies; no significant differences in spectral power values were found with full-term neonates. Study 3. In response to 1000 Hz tones no waveforms became evident on Fz in ELGA infants, while LGA presented a wide and slow positive response; the groups differed significantly. VLGA’s grand average waveform resembled that of LGA group, but characterized by a high variability. Responses to 500 Hz resulted highly variable and not reliable. Conclusions. We found early subtle brain electrical alterations in premature infants experiencing different developmental pathways, suggesting a different cortical organization; these differences seem to be associated with later development. The potential of neurophysiological methodologies is to provide a useful indicator of good prognosis or poor developmental outcomes.
Premesse. Gli avanzamenti tecnologici che negli ultimi decenni hanno caratterizzato le cure perinatali e le tecniche di terapia intensiva neonatale hanno permesso la sopravvivenza di una percentuale sempre maggiore di neonati prematuri nati ad età gestazionali sempre più basse, ai limiti della sopravvivenza. Eppure, studi sullo sviluppo a breve e lungo termine hanno dimostrato che molti neonati prematuri riportano esiti maggiori e/o disordini evolutivi minori, come deficit cognitivi e neuropsicologici, disturbi psichiatrici/comportamentali e motori. La causa di tali disordini dello sviluppo rimane poco chiara, ma può essere il risultato di sofferenza cerebrale in epoca neonatale come anche dell’interruzione del normale processo di sviluppo che avviene nel terzo trimestre di gravidanza, un periodo estremamente critico per la maturazione cerebrale. Predire come sarà lo sviluppo di un neonato prematuro rimane attualmente molto difficile. Infatti, sebbene un neonato possa essere asintomatico per segni clinici indicativi di una condizione patologica in atto, possono essere presenti alterazioni subcliniche del funzionamento cerebrale che spesso non vengono riconosciute. Una valutazione neurofisiologica dell’attività cerebrale nel neonato prematuro può probabilmente essere di grande utilità nel precoce riconoscimento di processi patologici o di alterazioni subcliniche. L’elettroencefalogramma (EEG) e i potenziali evocati uditivi corticali (CAEP) si sono dimostrati tecniche semplici e valide nel valutare la maturazione cerebrale. Obiettivi dello studio. Abbiamo condotto delle valutazioni neurofisiologiche trasversali e longitudinali in due fasi precoci e cruciali dello sviluppo (35 e 40 settimane postconcezionali) allo scopo di identificare differenze nell’attività elettrica cerebrale fra prematuri nati ad età gestazionali diverse e neonati a termine, usando EEG a riposo e i CAEP. Tali indagini in epoca neonatale sono state poi correlate con lo sviluppo comportamentale a distanza. Metodi. La ricerca è stata articolata in tre studi: Studio 1: è stata eseguita l’analisi spettrale dell’EEG registrato a 35 settimane postconcezionali in 40 neonati prematuri; tale attività è stata comparata fra gruppi di neonati nati ad età gestazionali diverse (estremi prematuri, ELGA: 23–27+6, veri prematuri, VLGA: 28–31+6 e prematuri, LGA: 34-35). I risultati ottenuti in epoca neonatale sono stati correlati con l’indice di sviluppo comportamentale ottenuto ai 12 mesi di età corretta nei primi 20 bambini che hanno raggiunto tale età. Studio 2: un sottogruppo di 10 neonati dello Studio 1 ha ripetuto la registrazione EEG a 40 settimane postconcezionali; la potenza spettrale ottenuta dalle registrazioni EEG a 35 e 40 settimane postconcezionali è stata cofrontata longitudinalmente; successivamente l’attività spettrale ottenuta alle 40 settimane postconcezionali è stata confrontata con quella di 10 neonati a termine alla nascita. Studio 3: i CAEP sono stati registrati in sonno attivo a 35 settimane postconcezionali in 36 prematuri e comparati fra gruppi di neonati nati ad età gestazionali diverse (ELGA, VLGA, LGA). I risultati sono stati correlati con l’indice di sviluppo comportamentale ottenuto ai 12 mesi di età corretta nei primi 20 bambini che hanno raggiunto quest’età. Metodologia Studio 1 e 2. L’attività elettrica cerebrale è stata registrata per 40 minuti su 5 canali bipolari. I dati ottenuti sono stati trasformati nel dominio delle frequenze utilizzando una trasformazione Fast Fourier. Lo spettro di frequenza è stato diviso nelle seguenti bande: δ (0.5-4 Hz, composto da δ1 0.5-1 Hz e δ2 1-4 Hz), θ (4-8 Hz), α (8-13 Hz) e β (13-20 Hz). Le analisi statistiche sono state eseguite sui valori di potenza assoluti e relativi ottenute solo dai siti centrali (C3-C4, C3-T3, C4-T4). Metodologia Studio 3. Durante la registrazione continua dell’EEG i neonati sono stati stimolati con treni di toni a 1000 Hz (paradigma 1) e a 500 Hz (paradigma 2). Il disegno sperimentale prevedeva 300 toni per ciascun paradigma. L’intervallo inter-stimolo variava in maniera casuale fra 600 e 900 ms; sono stati registrati 12 canali monopolari, riferiti bilateralmente ai lobi degli orecchi. Le epoche di 600 ms sono state divise per l’analisi statistica in finestre temporali di 100 ms. Le analisi statistiche sono state eseguite solo sui siti centrali (Fz, Cz). Risultati. Studio 1. In C3-C4, i valori di potenza spettrale relativa differivano significativamente fra i gruppi di ELGA e LGA. I neonati nati alle età gestazionali più basse avevano una maggiore potenza relativa in δ e una minore in α e β. La correlazione di questi dati con lo sviluppo comportamentale dei primi bambini che hanno raggiunto i 12 mesi di età corretta ha mostrato come alte percentuali di potenza in δ e basse in β e α fossero associate ad abilità relazionali più povere ed autonomie personali meno mature. Studio 2. A 40 settimane postconcezionali i prematuri hanno mostrato in C3-C4 una riduzione di potenza δ relativa e un lieve, non significativo, aumento di potenza nelle alte frequenze; non sono state trovate differenze significative rispetto i neonati a termine. Studio 3. Nel paradigma a 1000 Hz non è stato possibile rilevare nessuna risposta ai suoni nei neonati ELGA, mentre nei LGA in Fz era evidente una lenta ed ampia onda positiva; la grande media dei due gruppi differiva significativamente in Fz. La grande media dei neonati VLGA assomigliava a quella dei LGA, ma era caratterizzata da un’alta variabilità. Le risposte a toni di 500 Hz sono risultate troppo variabili e non riproducibili. Conclusioni. Confrontando neonati prematuri che hanno sperimentato linee di sviluppo differenti, abbiamo trovato delle differenze sottili nell’attività elettrica cerebrale che suggeriscono un’alterazione dell’organizzazione corticale. Tali differenze sembrano inoltre associate allo sviluppo comportamentale nel primo anno di vita. Questi risultati suggeriscono che le tecniche neurofisiologiche possano essere molto utili nella prognosi dei neonati prematuri.

Background. Brain retraction plays an important role in the cranial surgery, but the problems that can arise from excessive retraction are not negligible. The major limitation to the use of brain retractors is their high possibility of parenchyma’s damage: this becomes particularly evident in interventions of many hours that require a long-lasting spatulation. Possible lesions from cerebral retraction can include contusions, hematomas and haemorrhages that can also affect patient's outcome. Project Objectives. The first our goal was to study the instruments currently present for cerebral retraction by analysing their advantages and disadvantages. After this, the main objective was to create a new brain retraction tool and validate its use in cranial surgery. Another objective was to exploit endoscopic vision also in transcranial surgery designing work chambers perfectly suitable for introducing the endoscope easily while providing safe retraction for the surrounding brain. To achieve these results, it was therefore necessary to carry out an accurate preclinical phase study which also benefits from collaboration of a multidisciplinary team. Research activity and novelty of the project. The careful study of this topic, the anatomical and engineering laboratory tests, have made it possible to create new technological tools with many advantages in the neurosurgical field. The dynamic mechanical characterization of the brain allows to predict the mechanical behaviour of the human brain in health and disease also being able to foresee and possibly avoid complications for patients. Due to the continuous technological progress in the neurosurgery field, today the need to understand the correlation between the material structure and related viscoelastic properties is becoming ever more crucial also in order to develop design guidelines for the next generation of biomaterials, to match tissue and extra cellular matrix mechanics for in vitro tissue models and applications in regenerative medicine. Conclusions and future perspectives. The knowledge of the behaviour of the brain parenchyma in response to a compression force is therefore important in order to understand the mechanisms underlying the damage, the dangerous thresholds and therefore the possible prevention of brain complications. This last aspect was fundamental to be able to create new "intelligent" surgical instruments that operate safely. We therefore performed tests on preclinical model, on specimens and then also on animals; we finally studied the brain parenchyma from the histological point of view, documenting the visible damage of the cerebral retraction. These phases were essential to then proceed with clinical phase on patients: the next steps will be to test the prototyped spatula on patient in the surgical theatre and finish the last preclinical tests of the chamber. We also hope to file the patent for the new spatula by the end of this year.
Background. La retrazione cerebrale svolge un ruolo importante nella chirurgia cranica, ma i problemi che possono derivare da un'eccessiva retrazione non sono trascurabili. Il principale limite all'uso dei divaricatori cerebrali è la loro elevata possibilità di danno del parenchima: questo diventa particolarmente evidente negli interventi di tante ore che richiedono una retrazione di lunga durata. Possibili lesioni da retrazione cerebrale possono includere contusioni, ematomi ed emorragie che possono anche influenzare l’outcome del paziente. Obiettivi del progetto. Il primo nostro obiettivo era quello di studiare gli strumenti attualmente presenti per la retrazione cerebrale analizzandone vantaggi e svantaggi. Successivamente, l'obiettivo principale era creare un nuovo strumento di retrazione cerebrale e convalidarne l'uso nella chirurgia cranica. Un altro obiettivo era quello di sfruttare la visione endoscopica anche nella chirurgia transcranica progettando camere di lavoro perfettamente adatte per introdurre facilmente l'endoscopio fornendo al contempo una retrazione sicura per il cervello circostante. Per raggiungere questi risultati è stato quindi necessario condurre un accurato studio in fase preclinica con la collaborazione di un team multidisciplinare. Attività di ricerca e novità del progetto. L'attento studio di questo argomento, i test eseguiti in laboratorio di anatomia e di ingegneria, hanno permesso di creare nuovi strumenti tecnologici con molti vantaggi in campo neurochirurgico. La caratterizzazione meccanica dinamica del cervello permette di predire il comportamento meccanico del cervello umano sano e malato potendo anche prevedere ed eventualmente evitare complicanze per i pazienti. Grazie al progresso tecnologico nel campo della neurochirurgia, oggi la necessità di comprendere la correlazione tra la struttura del materiale e le relative proprietà viscoelastiche sta diventando sempre più cruciale anche al fine di sviluppare linee guida progettuali per la prossima generazione di biomateriali, per abbinare tessuti ed extra meccanica della matrice cellulare per modelli tissutali in vitro e applicazioni nella medicina rigenerativa. Conclusioni e prospettive future. La conoscenza del comportamento del parenchima cerebrale in risposta ad una forza di compressione è quindi importante per comprendere i meccanismi alla base del danno, le soglie pericolose e quindi la possibile prevenzione delle complicanze cerebrali. Quest'ultimo aspetto è stato fondamentale per poter realizzare nuovi strumenti chirurgici “intelligenti” che operino in sicurezza. Abbiamo quindi eseguito test su modellino preclinico, su cadavere e poi anche su animale; abbiamo infine studiato il parenchima cerebrale dal punto di vista istologico documentando il danno visibile causato dalla retrazione cerebrale. Questi steps sono stati fondamentali per poi procedere con la fase clinica sui pazienti: i prossimi passi saranno testare il prototipo della spatola sul paziente in sala operatoria e terminare gli ultimi test preclinici della camera. Confidiamo anche di depositare il brevetto per la nuova spatola entro la fine di quest'anno

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Brain and Cognitive Sciences, 2012.
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. Page 125 blank.
Includes bibliographical references.
The integration of anatomical, functional, and developmental approaches in cognitive neuroscience is essential for generating mechanistic explanations of brain function. In this thesis, I first establish a proof-of-principle that neuroanatomical connectivity, as measured with diffusion weighted imaging (DWI), can be used to calculate connectional fingerprints that are sufficient to delineate fine anatomical distinctions in the human brain (Chapter 2). Next, I describe the maturation of structural connectivity patterns by applying these connectional fingerprints to over a hundred participants ranging from five to thirty years of age, and show that these connectional patterns have different developmental trajectories (Chapter 3). I then illustrate how anatomical connections may shape (or in turn be shaped by) function and behavior, within the framework of reading ability and describe how white matter tract integrity may predict future acquisition of reading ability in children (Chapter 4). I conclude by summarizing how these experiments offer testable hypotheses of the maturation of structure and function. Studying the complex interplay between structure, function, and development will get us closer to understanding both the constraints present at birth, and the effect of experience, on the biological mechanisms underlying brain function.
by Zeynep Mevhibe Saygin.
Ph.D.

Les connaissances des voies moléculaires et cellulaires régulant le développement neuronal dans le cerveau adulte peuvent être utilisées pour mettre au point des stratégies efficaces de thérapie de remplacement cellulaire. L’étude de la dynamique et des mécanismes nécessaires à la neurogenèse adulte, requiert des techniques d’imagerie en temps réel. En outre, il est important de développer des méthodes d'imagerie sans marqueurs. Mon travail vise, en partie, à relever ces défis. Les néo-neurones générés chez l’adulte migrent densément le long des vaisseaux sanguins et des tubes gliaux dans le courant de migration rostral (CMR). Cet alignement peut créer une anisotropie qui peut être détectée en lumière polarisée. J'ai d'abord essayé cette technique pour la détection sans marqueurs des cellules migratrices dans le CMR. Bien que l’imagerie avec la lumière polarisée suscite certaines espérances, elle a toutefois fait apparaître que l'anisotropie des cellules migratrices est très faible et que sa détection est entravée par des signaux de fortes intensités provenant des axones myélinisés se trouvant à proximité. Ensuite, j'ai étudié la migration des neuroblastes marqués viralement pour élucider certains mécanismes nécessaires à leur migration. La signalisation GABAergique joue un rôle important dans la migration neuronale, déterminée par le gradient chlorique trans-membranaire. Ce dernier est, à son tour, contrôlé par KCC2, un co-transporteur responsable de l'extrusion de Cl-. Il est connu que KCC2 est exprimé dans les stades de développement plus avancés. Toutefois, le rôle de KCC2 dans la migration neuronale est inconnu et mes expériences suggèrent que ce co-transporteur est impliqué dans la migration radiale, mais pas tangentielle, de neuroblastes. Enfin, j'ai exploré in vivo comment la plasticité structurelle des néo-neurones générés chez l’adulte dans le bulbe olfactif (BO) est modulée par les odeurs. On ne sait pas comment le fonctionnement du BO s’ajuste à l’environnement olfactif de facon rapide lorsque de nouvelles synapses de néo-neurones ne sont pas encore formées. Mes données in vivo d'imagerie à deux photons complètent les travaux antérieurs de notre laboratoire, révélant une nouvelle forme de plasticité structurale dans le cerveau adulte. Ainsi, en utilisant diverses méthodes d'imagerie j'ai essayé de mieux comprendre la migration et la plasticité des nouveaux neurones dans le cerveau adulte.
The knowledge about molecular and cellular pathways orchestrating neuronal development in the adult brain can be used to build up efficient strategies for cell replacement therapies. Adult neurogenesis is a very dynamic process, and it is crucial to monitor it directly to decipher mechanisms required for neuronal development. Furthermore, it is important to develop label-free imaging methods. My work is, in part, aimed at addressing these challenges. Adult-born neurons migrate densely along blood vessels and glial tubes in the rostral migratory stream (RMS). This alignment may create anisotropy which can be detected in polarized light. I first tried this technique for label-free detection of migratory cells in the RMS. While this imaging may have some promises, it showed that anisotropy in migrating cells is quite low and its detection is hampered by large signals deriving from nearby myelinated axons. I further studied the migration of virally labeled neuroblasts to elucidate some of the mechanisms required for their migration. GABAergic signaling plays an important role in neuronal migration and is defined by transmembrane Cl- gradient. This, in turn is controlled by the Cl- extruding co-transporter KCC2, known to have a late developmental expression. The role of KCC2 in neuronal migration is unknown and my experiments suggest that this co-transporter is involved in the radial, but not tangential migration of neuroblasts. Finally, I explored in vivo the odor-related structural plasticity of adult-born neurons in the olfactory bulb (OB). It remains unknown how OB functioning is adjusted to rapidly changing odor environment when new synapses of adult-born neurons have not yet been formed. My in vivo two-photon imaging data complements the previous work in our lab, revealing altogether a new form of structural plasticity in the adult OB. Thus, using diverse imaging methods I tried to better understand the migration and plasticity of new neurons in the adult brain.

Metabolic support was long considered to be the only developmental function of haematopoiesis. In this role, erythroblast are considered simple carriers that transfer and deliver heme-bound diatomic oxygen to various developing organs. Herein, we report an unexpected function of erythroblasts that occur in a brief temporal window from embryonic day (E) 8.5-E9.5 by donation of sacrificial yolk sac erythroblasts to neuroepithelial cells of developing neural tube. In this temporal window, neuroepithelial cells transiently merge with endothelial lining of yolk sac blood vessels, gain access to the luminal contents and eventually engulf that luminal erythroblasts. Subsequently, neuroepithelial cells deplete the heme contents of cannibalised erythroblasts via process of trans-endocytosis. In consequence, cannibalistic neuroepithelial cells differentiate precociously into neurons. The complementary in vitro experiments revealed that access to exogenous heme can accelerate neuronal differentiation via enhanced availability of the key Wnt pathway mediator, catenin-β1, by redox-dependent mechanisms. The coupling of haematopoiesis and neurogenesis provides a fail-safe developmental mechanism that calibrates the energetic demands of developing neural tube to density of blood vessels and also to hematopietic activity. The molecular basis for reprogrammability of developmental time and the potency of heme as a temporal reprogrammer of development are discussed in separate chapters of the thesis. We anticipate that the mechanism disclosed herein may provide a basis to explain the long-established but unresolved causal association of neural tube defects and deficiency of hematopoietic micronutrients including folate.

Metabolic support was long considered to be the only developmental function of haematopoiesis. In this role, erythroblast are considered simple carriers that transfer and deliver heme-bound diatomic oxygen to various developing organs. Herein, we report an unexpected function of erythroblasts that occur in a brief temporal window from embryonic day (E) 8.5-E9.5 by donation of sacrificial yolk sac erythroblasts to neuroepithelial cells of developing neural tube. In this temporal window, neuroepithelial cells transiently merge with endothelial lining of yolk sac blood vessels, gain access to the luminal contents and eventually engulf that luminal erythroblasts. Subsequently, neuroepithelial cells deplete the heme contents of cannibalised erythroblasts via process of trans-endocytosis. In consequence, cannibalistic neuroepithelial cells differentiate precociously into neurons. The complementary in vitro experiments revealed that access to exogenous heme can accelerate neuronal differentiation via enhanced availability of the key Wnt pathway mediator, catenin-β1, by redox-dependent mechanisms. The coupling of haematopoiesis and neurogenesis provides a fail-safe developmental mechanism that calibrates the energetic demands of developing neural tube to density of blood vessels and also to hematopietic activity. The molecular basis for reprogrammability of developmental time and the potency of heme as a temporal reprogrammer of development are discussed in separate chapters of the thesis. We anticipate that the mechanism disclosed herein may provide a basis to explain the long-established but unresolved causal association of neural tube defects and deficiency of hematopoietic micronutrients including folate.

MicroRNA (miRNA) function is required for normal animal development, in particular in stem cell and precursor populations. I hypothesize that miRNAs are similarly required for stem cell maintenance and appropriate fate commitment in the brain. To test the requirement for global microRNA production, I depleted the microRNA biosynthetic enzyme DICER in the developing mouse brain. I found that DICER loss in embryonic neural progenitor cells leads to embryonic lethality with microcephaly. By histological analysis, I found defects in both neural progenitor cell maintenance and cell differentiation. I also identified new candidate microRNAs for this phenotype by profiling miRNAs in DICER-depleted and control cells. Three microRNAs which are good candidates to modulate nervous differentiation are miR-23b, -182, and -34a. I describe the expression pattern and functional characterization of these candidates. In particular, miR-34a depletes neuron production after progenitor cell differentiation in culture, likely by modulating cell cycling and Notch pathway genes.

Machine collaboration with the biological body/brain by sending electrical information back and forth is one of the leading research areas in neuro-engineering during the twenty-first century. Hence, Brain-Machine-Brain Interface (BMBI) is a powerful tool for achieving such machine-brain/body collaboration. BMBI generally is a smart device (usually invasive) that can record, store, and analyze neural activities, and generate corresponding responses in the form of electrical pulses to stimulate specific brain regions. The Smart Brain-Machine-Brain-Interface (SBMBI) is a step forward with compared to the traditional BMBI by including smart functions, such as in-electrode local computing capabilities, and availability of cloud connectivity in the system to take the advantage of powerful cloud computation in decision making. In this dissertation work, we designed and developed an innovative form of Smart Brain-Machine-Brain Interface (SBMBI) and studied its feasibility in different biomedical applications. With respect to power management, the SBMBI is a semi-passive platform. The communication module is fully passive—powered by RF harvested energy; whereas, the signal processing core is battery-assisted. The efficiency of the implemented RF energy harvester was measured to be 0.005%. One of potential applications of SBMBI is to configure a Smart Deep-Brain-Stimulator (SDBS) based on the general SBMBI platform. The SDBS consists of brain-implantable smart electrodes and a wireless-connected external controller. The SDBS electrodes operate as completely autonomous electronic implants that are capable of sensing and recording neural activities in real time, performing local processing, and generating arbitrary waveforms for neuro-stimulation. A bidirectional, secure, fully-passive wireless communication backbone was designed and integrated into this smart electrode to maintain contact between the smart electrodes and the controller. The standard EPC-Global protocol has been modified and adopted as the communication protocol in this design. The proposed SDBS, by using a SBMBI platform, was demonstrated and tested through a hardware prototype. Additionally the SBMBI was employed to develop a low-power wireless ECG data acquisition device. This device captures cardiac pulses through a non-invasive magnetic resonance electrode, processes the signal and sends it to the backend computer through the SBMBI interface. Analysis was performed to verify the integrity of received ECG data.

Perinatal inflammation contributes to neurodevelopmental diseases, and animal models have revealed that the inflammatory response within the central nervous system is age dependent. It remains unclear what intrinsic and/or extrinsic factors are responsible for this variation. Here, my aim was to discover the mechanisms responsible for the age-dependent changes in the inflammatory response of the brain by injecting interleukin-1 (IL-1β) into the brain of mice at postnatal day (P)7, P14, P21 or into adult mice. A "window of susceptibility" was found at P14, which was associated with marked neutrophil recruitment and blood-brain barrier (BBB) breakdown, in response to a low dose of IL-1β. Evaluation of cytokine, chemokine, and adhesion molecule mRNA transcripts failed to reveal any specific increases in basal or reactive expression following the injection of IL-1β at P14. The extrinsic hepatic acute phase response (APR) was evaluated, but, once again, there was no evidence that an altered APR might account for the enhanced inflammatory response at P14. Indeed, an inverse relationship between the magnitude of the leukocyte recruitment to the brain and the APR was discovered. Enhancement of the APR with intravenous IL-1β after injection of a low dose of IL-1β into the brain was found to reduce the number of neutrophils and BBB permeability in the brain. While no molecular changes seem to account for the presence of the "window of susceptibility", a population of Iba-1⁺ large, flattened and irregular perivascular cells was discovered within the P14 brain, that may contribute to the increased leukocyte recruitment at P14. Although variations in the brain inflammatory response with development were not fully account for, my results highlight the importance of the systemic inflammatory response on the outcome of acute brain injury and suggest that the systemic APR might be manipulated therapeutically to protect the brain in the perinatal period.

Human genetics has identified essential roles for many centriole- and cilia-related proteins during human development. Mutations in centrosome-associated genes commonly cause microcephaly, or "small brain," and mutations in cilia-associated genes cause a diverse spectrum of diseases termed "ciliopathies." However, the functional relationships between these two crucial organelles are less well studied. The activities of centrosome-related proteins during mitosis and cytoskeletal remodeling are well-characterized, but their in vivo functions are incompletely understood. Here, we identify novel human mutations in a centrosomal gene which encodes a regulatory subunit of a microtubule interacting protein, and uncover unexpected pathways during vertebrate development. Human mutations cause severe microlissencephaly, reflecting defects in cerebral cortical neurogenesis, and loss of function in mice and zebrafish confirm essential roles in embryonic development, neurogenesis, and cell survival. Surprisingly, null mutant embryos display hallmarks of aberrant Sonic hedgehog signaling, including holoprosencephaly. Deficient induced pluripotent stem cells and lymphoblasts show defective proliferation and spindle structure, while deficient fibroblasts also demonstrate a remarkable excess of centrioles, including excessive maternal centrioles, with supernumerary cilia but deficient Hedgehog signaling. Our results reveal novel roles for this protein in regulating overall centriole number, mother centriole and cilia number, and as an essential gene for normal Hedgehog signaling during neocortical development.

Preterm birth can interfere with the intra-uterine mechanisms driving cerebral development during the third trimester of gestation and often results in severe neuro-developmental impairments. Characterizing normal/abnormal patterns of early brain maturation could be fundamental in devising and guiding early therapeutic strategies aimed at improving clinical outcome by exploiting the enhanced early neuroplasticity. Over the last decade the morphology and structure of the developing human brain has been vastly characterized; however the concurrent maturation of brain function is still poorly understood. Task-dependent fMRI studies of the preterm brain can directly probe the emergence of fundamental neuroscientific notions and also provide clinicians with much needed early diagnostic and prognostic information. To date, task-fMRI studies of the preterm population have however been hampered by methodological challenges leading to inconsistent and contradictory results. In this thesis I present a modular and flexible system to provide clinicians and researchers with a simple and reliable solution to deliver computer-controlled stimulation patterns to preterm infants during task-fMRI experiments. The system is primarily aimed at studying the developing sensori-motor system as preterm infants are often affected by neuro-motor dysfunctions such as cerebral palsy. Wrist and ankle robotic stimulators were developed and firstly used to study the emerging somatosensory 'homunculus'. The wrist robotic stimulator was then used to characterize the development of the sensori-motor system throughout the mid-to-late preterm period. An instrumented pacifier system was also developed to explore the potential sensorimotor modulation of early sucking activity; however, despite its clear potential to be employed in future fMRI studies, results have not yet been obtained on preterm infants. Functional difficulties associated with prematurity are likely to extend to multi-sensory integration, and the olfactory system currently remains under-investigated despite its clear developmental importance. A custom olfactometer was developed and used to assess its early functionality.

Thesis (Ph. D.)--University of California, San Diego, 2007.
Title from first page of PDF file (viewed January 14, 2008). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 100-118).

Left-right asymmetry is a highly conserved feature of the nervous system. However, it is not known how functional lateralisation is represented at the level of lateral differences in circuit microarchitecture. In this study, I identify asymmetric neuronal connectivity in the larval zebrafish brain, resolve L-R differences in the morphology and connectivity of individual projection neurons and investigate the molecular and cellular mechanisms by which lateralisation develops. The habenular nuclei form part of the highly conserved dorsal dien cephalic conduction system. I find that the habenulae display laterotopic ef ferent connectivity, wherein left and right-sided axons are segregated along the dorso-ventral axis of their target, the interpeduncular nucleus (IPN). Habenular neurons elaborate remarkable "spiralling" terminal arbors within the IPN. I have identified two sub-types of habenular neuron, defined by ax onal arbors with distinct morphology and targeting. Both sub-types are found in both the left and right habenula, but in substantially different ratios. Thus, the vast majority of left habenular neurons elaborate tall, crown-shaped arbors localised to the dorsal IPN, whereas almost all right- sided cells form flattened arbors restricted to the ventral IPN. This left- right asymmetry in cell-type composition, combined with the differential targeting of neuronal sub-types, underlies the laterotopic connectivity of the habenulae. This reveals a fundamental strategy that serves to differentiate functional circuitry on the two sides of the CNS: equivalent components are specified on both sides and lateralisation results from differences in the ratios of neuronal sub-types on the left and right. Left-sided Nodal signalling is essential for controlling the orientation, or laterality, of laterotopic connectivity, but is not required for asymmetry per se. The left-sided parapineal nucleus is required for the development of normal asymmetric phenotypes, including the development of both left and right-sided axon arbors with appropriate morphology and targeting. How ever, following laser-ablation of the parapineal, left and right-sided neurons continue to elaborate arbors with distinct lateralised morphologies, indicating that additional developmental mechanisms act to convey left-right identity information to this highly conserved circuit.

Radial glial cells play an important role during embryonic development in mammals. They are not only important for neural production but help to organise the architecture of the neocortex. Glial cells proliferate during the development of the brain in the embryo, before differentiating to produce neurons at a rate which increases towards the end of embryonic brain development. Glial cells communicate via Adenosine tri-phosphate (ATP) mediated calcium waves, which may have the effect of locally synchronising cell cycles, so that clusters of cells proliferate together, shedding cells in uniform sheets. Hence radial glial cells are not only responsible for the production of most neocortical neurons but also contribute to the architecture of the brain. It has been argued that human developmental disorders which are associated with cortical malfunctions such as infantile epilepsies and mental retardation may involve defects in neuronal production and/or architecture and mathematical modelling may shed some light upon these disorders. This thesis investigates, among other things, the conditions under which radial glial cells' cell cycles become `phase locked', radial glia proliferation and stochastic effects. There are various models for the cell cycle and for intracellular calcium dynamics. As part of our work, we marry two such models to form a model which incorporates the effect of calcium on the cell cycle of a single radial glial cell. Furthermore, with this achieved we consider populations of cells which communicate with each other via the secretion of ATP. Through bifurcation analysis, direct numerical simulation and the application of the theory of weakly coupled oscillators, we investigate and compare the behaviour of two models which differ from each other in the time during the cell cycle at which ATP is released. Our results from this suggest that cell cycle synchronisation is highly dependent upon the timing of ATP release. This in turn suggests that a malfunction in the timing of ATP release may be responsible for some cortical development disorders. We also show how the increase in radial glia proliferation may mostly be down to radial glial cells' ability to recruit quiescent cells onto the cell cycle. Furthermore, we consider models with an additive noise term and through the application of numerical techniques show that noise acts to advance the onset of oscillatory type solutions in both models. We build upon these results and show as a proof of concept how noise may act to enhance radial glia proliferation.

The glycine cleavage system (GCS) is a multi-enzyme complex localised in the mitochondria and serves as the main catabolic pathway for glycine. It contributes to supply of one-carbon units into folate one-carbon metabolism (FOCM) which utilises them for vital processes such as purines and thymidylate biosynthesis and methylation reactions. This thesis focuses on the role of glycine decarboxylase (Gldc), a member of the GCS, in embryonic development of the brain. It utilises two loss-of-function mouse models for Gldc which were found to exhibit two distinct disease phenotypes: non-ketotic hyperglycinemia (NKH) and neural tube defects (NTDs). The aims of this project are to investigate what effects GCS deficiency has on FOCM, the developmental mechanisms underlying NTDs caused by loss of Gldc expression, and suitability of the Gldc mice models as animal models for classical NKH. NKH is a rare metabolic disease caused by mutations of GCS genes (mainly GLDC) and characterised by accumulation of glycine in body fluids, resulting in severe neurological dysfunction and poor survival. Gldc-deficient mice exhibited features of NKH including elevated glycine, early post-natal lethality, and hydrocephalus. Enlargement of the brain ventricles was found to already be present at late-foetal stage, while glycine levels in whole embryos were already elevated shortly after neurulation. Gldc-deficient embryos also displayed NTDs, a common birth defect of the central nervous system that result from failure of the neural tube to close. Gldc-deficient embryos displayed abnormal folate metabolism, growth retardation and reduced cell proliferation. Supplementation with one-carbon units through dietary means was able to normalise folate profiles, completely rescue the NTDs, and normalise proliferation and growth in Gldc-deficient embryos. Diet-induced folate deficiency and interactions with the Mthfr mutation (which results in a methylation defect) did not exacerbate the NTDs caused by the Gldc mutation. This study provides the first mouse model for classical NKH and suggests that the pathology of NKH begins earlier in development than suspected. It also suggests that Gldc deficiency causes NTDs by reducing the supply of glycine-derived, mitochondrial one-carbon units for FOCM reactions.

Research has demonstrated that the human brain undergoes significant change in both structure and function during adolescence, but little is known about the role of puberty in this developmental process. The aim of this thesis is to investigate the relationship between puberty and brain development during adolescence. The first two chapters of this thesis summarise the current understanding of the behavioural and brain changes associated with both adolescence and puberty, and review the methods employed to assess puberty in research. Chapters 3 and 4 focus on the relationship between puberty and changes in brain structure. In Chapter 3, the influence of puberty on subcortical structural development is investigated in a large longitudinal MRI dataset, using a mixed effects modelling analysis method. Chapter 4 investigates the relationship between pubertal status, as measured by physical pubertal stage and levels of salivary sex steroid hormones, and white matter structural development in a cross-sectional sample of 12-16 year old boys, using diffusion tensor imaging. In Chapters 5-7, functional brain changes with puberty are explored. Chapters 5 and 6 focus on social emotion processing, where social emotions (e.g. embarrassment) are defined as emotions that require an awareness of other people’s mental states, while basic emotions (e.g. fear) are those which do not. In Chapter 5, the neural correlates of social and basic emotion processing are investigated in relation to pubertal status. In Chapter 6, the fMRI data are reanalysed using psycho-physiological interaction (PPI) analysis to investigate puberty-related changes in functional connectivity during the same task. Chapter 7 explores, in males, how developmental changes in brain function when performing a risk-taking task are related to puberty, independently of chronological age. Finally, in Chapter 8, the results of the empirical studies are summarised and the findings and implications of the thesis are discussed.

Yucatan minipigs have become increasingly common animal models in neuroscience where recent studies, investigating blast-induced traumatic brain injury, stroke, and glioblastoma, aim to uncover brain injury mechanisms [1-3]. Magnetic Resonance Imaging (MRI) has the potential to validate and optimize unknown parameters in controlled populations. The key to group-level MRI analysis within a species is to align (or register) subject scans to the same volumetric space using a brain template. However, large animal brain templates are lacking, which limits the use of MRI as an effective research tool to study group effects. The objective of this study was to create an MRI-based Yucatan minipig brain template allowing for uniform group-level analysis of this animal model in a standard volumetric space to characterize brain mechanisms. To do this, 5-7 month old, male Yucatan minipigs were scanned using a 3 Tesla whole-body scanner (Siemens AG, Erlangen) in accordance with IACUC. T1-weighted anatomical volumes (resolution = 1×1×1 mm3; TR = 2300 ms; TE= 2.89 ms; TI = 900 ms; FOV = 256 mm2 ; FA = 8 deg) were collected with a three-dimensional magnetization prepared rapid acquisition gradient echo (MPRAGE) pulse sequence [4]. The volumes were preprocessed, co-registered, and averaged using both linear and non-linear registration algorithms in AFNI [5] to create four templates (n=58): linear brain, non-linear brain, linear head, and non-linear head. To validate the templates, tissue probability maps (TPMs) and variance maps were created, and landmark variation was measured. TPMs computed in FSL [6] and AFNI show enhanced tissue probability and contrast in the non-linear template. Additionally, variance maps showed a more uniform spatial variance in the non-linear template compared to the linear. Registration variation within the brain template was within 1.5 mm and displayed improved landmark variation in the non-linear brain template. External evaluation subjects (n=12), not included in the template, were registered to the four templates to assess functionality. The results indicate that the developed templates provide acceptable registration accuracy to enable population comparisons. With these templates, researchers will be able to use MRI as a tool to further neurological discovery and collaborate in a uniform space.
M.S.
Magnetic resonance imaging (MRI) is commonly used in neuroscience as a non-invasive diagnostic tool with the potential to reveal unknown brain injury mechanisms. MRI is particularly useful in large animal models to validate and optimize unknown parameters in controlled populations. The key to group-level MRI analysis within a species is to align (or register) subject scans to the same volumetric space using a brain template. However, large animal brain templates are lacking, which limits the use of MRI as an effective research tool to study group effects. The objective of this study was to create an MRI-based Yucatan minipig brain template allowing for uniform group-level analysis of this animal model in a standard volumetric space to better characterize brain mechanisms. The neuroanatomy of the Yucatan minipig, which is characterized by an increased brain size and gyrencephalic intricacies similar to humans, has made it an increasingly common animal model in neuroscience. Linear and non-linear registration methods were performed in Analysis of Functional NeuroImages (AFNI) software to create both brain and head templates for 5-7 month old, male Yucatan minipigs (n=58). This study was validated looking at template variance, tissue probability maps (TPMs) of segmented grey matter, white matter, and cerebrospinal fluid, and landmark variation. The results indicate that the developed templates provide acceptable registration accuracy to enable population comparisons. With these templates, researchers will be able to use MRI as a tool to further neurological discovery and collaborate in a uniform space.

The period of life between puberty and adulthood, adolescence, has perplexed adults for millennia. Adolescence is marked by significant physical, cognitive, and social changes. Social lives become more complex during adolescence, and the teenage years are when we hone our skills at navigating the social world. The aim of my thesis was to examine brain development and social interactions during the period of adolescence. I conducted three brain imaging experiments to investigate typical developmental trajectories of brain structure between childhood and adulthood. These three studies used a large longitudinal dataset and mixed-effects modelling in order to account for individual differences. My first study found evidence that intracranial volume continues to develop through the second decade, and describes the consequences of intracranial volume correction procedures on developmental studies. The second study provided evidence for the hypothesis that subcortical brain regions involved in processing affect and reward structurally mature before prefrontal cortical regions involved in cognitive control to varying degrees across individuals. The third study found evidence for continued structural development regions of the brain involved in understanding other people between late childhood to early adulthood. My behavioural experiment showed that keeping track of non-social information impacts the ability to navigate social interactions in adolescents and adults. In addition to these four empirical studies, I conducted three reviews to synthesise and update our understanding of a) adolescence as a potential sensitive period for social learning, b) what longitudinal structural brain imaging studies can tell us about brain development, and c) the evidence for how using the Internet could impact brain development in adolescence. Overall, my findings shed new light, and challenge current theories, on brain development and social cognition during adolescence.

The incidence of preterm birth is increasing and has emerged as a leading cause of neurodevelopmental impairment in childhood. In early development, defined here as the period before and around birth, the brain undergoes significant morphological, functional and appearance changes. The scope and rate of change is arguably greater than at any other time in life, but quantitative markers of this period of development are limited. Improved understanding of cerebral changes during this critical period is important for mapping normal growth, and for investigating mechanisms of injury associated with risk factors for maldevelopment such as premature birth. The objective of this thesis is the development of methods for spatio-temporal modeling and quantitative measures of brain development that can assist understanding the patterns of normal growth and can guide interventions designed to reduce the burden of preterm brain injury. An approach for constructing high-definition spatio-temporal atlases of the developing brain is introduced. A novelty in the proposed approach is the use of a time-varying kernel width, to overcome the variations in the distribution of subjects at different ages. This leads to an atlas that retains a consistent level of detail at every time-point. The resulting 4D fetal and neonatal average atlases have greater anatomic definition than currently available 4D atlases, an important factor in improving registrations between the atlas and individual subjects with clear anatomical structures and atlas-based automatic segmentation. The fetal atlas provides a natural benchmark for assessing preterm born neonates and gives some insight into differences between the groups. Also, a novel framework for longitudinal registration which can accommodate large intra-subject anatomical variations is introduced. The framework exploits previously developed spatio-temporal atlases, which can aid the longitudinal registration process as it provides prior information about the missing anatomical evolution between two scans taken over large time-interval. Finally, a voxel-wise analysis framework is proposed which complements the analysis of changes in brain morphology by the study of spatio-temporal signal intensity changes in multi-modal MRI, which can offer a useful marker of neurodevelopmental changes.

The maintenance of a proper balance between excitatory and inhibitory neurotransmission (E/I ratio) is crucial for correct brain development, function and plasticity. Through its inhibitory action, GABA (gamma-aminobutyric acid) neurotransmitter is the principal regulator of E/I ratio, exerting a precise modulation of excitatory transmission. Conversely, at the early stages of neuronal maturation, GABA operates as an excitatory neurotransmitter directly evoking action potentials. Then, during development, it acquires its typical role of brake for neuronal activity through the fundamental process called “excitatory-to-inhibitory switch of GABA”, the postnatal transition of GABA transmission from excitatory to inhibitory, directly related to the action of the potassium-chloride co-transporter KCC2. Defects in GABA switch have been largely described in neurodevelopmental disorders such as epilepsy, autism and schizophrenia. In this context, we have recently unveiled a new role of ATM (Ataxia Telangiectasia Mutated), a protein kinase involved in DNA double strand breaks (DSB) repair, in orchestrating the maturation of GABAergic inhibition. Here we demonstrate that the exposure of wild-type neurons in a “critical window” during development to an inhibitor of ATM kinase activity (KU), a drug already exploited as therapeutic tool in oncology, accelerates the excitatory-to-inhibitory switch of GABA. We show that the molecular mechanism underlying KU effect involves the transcription factor Egr4 and the epigenetic regulator MeCP2, which independently and in parallel boost KCC2 expression both in vitro and in vivo. The resultant neuronal network exhibits a potentiated inhibitory synaptic transmission and appears resistant to a hyper-excitability paradigm. Surprisingly, we found an increased expression of ATM associated to low levels of KCC2 in Mecp2y/- mice, the genetic model of Rett syndrome (RTT), a neurodevelopmental disorder associated to mental retardation. Coherently, KU treatment in Mecp2y/- neurons, potentiating Egr4 activity on Kcc2b promoter and restoring proper KCC2 expression, rescues the delayed GABA switch and counteracts the pharmacologically-induced hyper-excitability, suggesting that increased ATM levels contribute to the generation of the altered neuronal phenotype in RTT. The results collected in this thesis provide new evidence and molecular mechanisms of ATM crucial role in the physiological development of central neurons and highlight ATM inhibition as a prospective therapeutic tool in neurodevelopmental disorders.

Success For Life (SFL) is a brain research-based program for children, birth through age six. This research examined the development and implementation of SFL in 13 early childhood settings. Participants were 24 female early childhood teachers and 146 (73 male) children. Teachers included seven infant, four toddler, nine preschool and four kindergarten teachers. Children included infants(n=29), toddlers(n=27), and prek/kindergartners (n=90). A Request for Proposals was disseminated to identify possible implementation sites. After participation was confirmed, teachers attended a full day's training which included a description of brain development/function, the latest brain research, how to implement SFL and other logistics of the study. Program implementation occurred over approximately four months. A field site coordinator visited each site bimonthly to provide on-going technical assistance. This was an intervention project with a pre and post implementation design. Four instruments were used: a teacher questionnaire, a classroom environment measure, a child measure and teacher journals. Results suggested that teachers became more knowledgeable about brain development research and about how children grow and learn. Teachers were better able to make connections between brain research findings and how to apply these findings to their programs and daily activities. Likewise, the environment measure indicated that teachers were better able to arrange environments for learning. They reported that children showed significant increases in skills development and performance in the following areas: physical mastery, social relations/interactions, cognitive development, and language/communications. Additionally, teachers reported improvements in emotional expression and well-being among infants and toddlers. Toddlers and preschoolers showed significant increases in creative/ artistic expression. Finally, teachers indicated that preschoolers showed increases in initiative, use of logic/mathematics skills, and musical coordination and movement. Research findings suggest that Success For Life is able to bridge the gap between theory and practice and benefits children, teachers and programs.

Hypoxic ischemic encephalopathy (HIE) is a relatively common and potentially devastating form of perinatal brain injury, associated with neurodevelopmental problems and mortality. HIE is an evolving process. There is a need for real-time, in-vivo measurements of brain oxygenation and metabolism for clinical assessment in the first days of life, to detect those at risk of further brain injury who may benefit from redirection of care. This thesis describes the development of a broadband near-infrared spectroscopy (NIRS) system to monitor changes in metabolism and haemodynamics in HIE infants at the cotside. This system uses multiple wavelengths (λ=136,770-905nm) to monitor changes in concentration of the oxidation state of cytochrome-c-oxidase (oxCCO) as well as haemoglobin oxygenation. Changes in oxCCO are indicative of CCO redox state changes within mitochondria and therefore represent oxygen utilization. The 2-channel system incorporates a broadband source, optical fibres, spectrograph and CCD. This set up is flexible and robustly monitors changes in haemoglobin and oxCCO. The system was developed specifically for the neonatal intensive care unit (NICU) and has been demonstrated on 38 brain-injured newborn infants (28 with HIE). Data was continuously collected over the frontal lobe simultaneously with systemic data for multimodal analysis. This allows the study of cerebral changes in response to global pathophysiological events. HIE was assessed by magnetic resonance spectroscopy measurement of lactate to NAA ratio (Lac/NAA), the gold standard for neurodevelopmental outcome. Initially the analysis focussed on spontaneous hypoxias. The relationship between haemoglobin oxygenation and oxCCO during hypoxic events was significantly associated with Lac/NAA (n=22,r=0.51,p=0.02). Further investigation of the dynamics of the cerebral changes during hypoxias found oxCCO differences with injury severity (not observed in haemoglobins). Finally, the relationship between cerebral signals and systemic physiology was investigated with a multivariate statistical technique. A strong relationship between oxCCO and systemic changes indicated severe brain injury (n=12,p=0.04).

Il gene Sox2 codifica per un fattore di trascrizione attivo nelle cellule staminali durante lo sviluppo del SNC nei vertebrati. Mutazioni eterozigoti di Sox2 nell'uomo causano uno spettro caratteristico di anomalie del SNC, che coinvolgono l'ippocampo e l'occhio, e che causano epilessia, disabilità di apprendimento e difettivo controllo motorio. Per comprendere il ruolo di Sox2 nello sviluppo neuronale, il nostro laboratorio ha generato KO condizionali di Sox2 nel topo. Le conseguenze della delezione di Sox2 in diversi momenti dello sviluppo producono importanti difetti cerebrali. Il KO condizionale permette di osservare una funzione importante di Sox2 anche nel mantenimento del self-renewal e delle colture a lungo termine di NSC in vitro. Sox2-mut NSC, coltivate come neurosfere, derivate dal prosencefalo di topi P0, si auto-rinnovano per diversi passaggi in coltura, ma poi vanno incontro a esaurimento della coltura. La formazione delle sfera viene recuperata da lentivirus Sox2. Questo rivela un ruolo essenziale per Sox2 nel mantenimento delle NSC. Per comprendere i meccanismi delle funzioni di Sox2, una questione centrale è quali geni Sox2 regola come un fattore di trascrizione, con quali meccanismi, e quali geni Sox2-regolati sono mediatori critici della sua funzione. Un nuovo modo in cui Sox2 regola i suoi targets è stato recentemente osservato nel nostro laboratorio: Sox2 mantiene un elevato numero di interazioni a lungo raggio tra geni ed enhancer distali, che regolano l'espressione genica. Abbiamo determinato mediante Chia-PET l’intero pattern di interazioni a lungo raggio in NSC wt e Sox2-mut. La delezione di Sox2 causa una vasta perdita di interazioni a lungo raggio e ridotta espressione di un sottogruppo di geni associati. L'espressione di uno di questi geni, SOCS3, recupera il difetto di self-renewal delle cellule mut. Il nostro lavoro identifica Sox2 come un importante regolatore della connettività funzionale cromatinica nelle NSC e dimostra il ruolo di geni associati con interazioni Sox2-dipendenti nel mantenimento delle NSC e, potenzialmente, in disturbi dello sviluppo neurologico. Abbiamo studiato il differenziamento delle cellule Sox2-mut in neuroni e glia, rispetto ai controlli: in stadio avanzato, poche cellule β-tub-positive sono state osservate nei mut differenziati, con scarsa morfologia differenziata. Questo risultato ha mostrato l'importanza di Sox2 nello sviluppo in neuroni maturi. Abbiamo anche analizzato i cambiamenti nell'espressione genica derivati dalla delezione di Sox2 mediante analisi RNA-seq di tre campioni per entrambe le cellule wt e Sox2-mut indifferenziate, e in due condizioni di differenziamento (giorno 4 e il giorno 11). Centinaia di geni sono deregolati in cellule mutanti. Il gene più down-regolato è SOCS3, quindi abbiamo trasdotto le cellule Sox2-mut con un lentivirus SOCS3. Le cellule mut trasdotte inizialmente crescono come le cellule non trasdotte (solo una parte delle cellule era stata trasdotta), ma continuano a crescere anche dopo che le cellule mut non trasdotte si sono completamente esaurite.Questi risultati suggeriscono che SOCS3 recupera parzialmente il difetto di proliferazione delle cellule mut. Ho anche provato se la reintroduzione di SOCS3 potrebbe recuperare il difetto nel differenziamento neuronale delle cellule mut e i miei esperimenti iniziali suggeriscono che potrebbe essere così: le cellule SOCS3-trasdotte erano tutte GFAP-negative e sembravano β-tub-positive, anche se sembravano avere una morfologia sofferente. Altro scopo è verificare il ruolo di alcuni degli altri geni più deregolati come mediatori della funzione di Sox2 nel self-renewal e nel differenziamento, con esperimenti di rescuing. Infine mi propongo di verificare se la reintroduzione di Sox2 nelle cellule mut potrebbe ripristinare le interazioni a lungo raggio, perse nei mutanti, di un piccolo numero di geni bersaglio identificati, con esperimenti di 3C.
The Sox2 gene encodes a transcription factor active in stem/progenitor cells during the development of central nervous system in vertebrates. Heterozygous Sox2 mutations in humans cause a characteristic spectrum of CNS abnormalities, involving the hippocampus and the eye, and causing epilepsy, learning disabilities and defective motor control. In order to understand the role of Sox2 in neural development, our laboratory generated Sox2 conditional KO mutations in mouse. The consequences of Sox2 ablation at different developmental time points produced important brain defects, more serious when the ablation was early. Sox2 conditional KO allowed to observe an important function for Sox2 also in the maintenance of NSC self-renewal in long-term in vitro NSC cultures. Sox2-mut NSC, cultured as neurospheres from P0 mouse forebrain, self-renewed for several passages in culture, but then underwent a decrease in growth, with progressive culture exhaustion. Sphere formation could be rescued by lentiviral Sox2. This reveled an essential role for Sox2 in the development of multiple CNS regions and in the maintenance of NSC. To understand the mechanisms of Sox2 function, a central question is which genes Sox2 regulates as a transcription factor, by what mechanisms Sox2 acts in regulating them, and which Sox2-regulated genes are critical mediators of its function. A new way in which Sox2 regulates its targets has been recently observed in our laboratory: Sox2 maintains a high number of long-range interactions between genes and distal enhancers, that regulate gene expression. We determined, by genome-wide chromatin interaction analysis (RNApolII ChIA-PET) the global pattern of long-range chromatin interactions in normal and Sox2-mut mouse NSC. Sox2 deletion caused extensive loss of long-range interactions and reduced expression of a subset of genes associated with Sox2-dependent interactions. Expression of one of these genes, Socs3, rescued the self-renewal defect of Sox2-mut NSC. Our work identifies Sox2 as a major regulator of functional chromatin connectivity in NSC, and demonstrates the role of genes associated with Sox2-dependent interactions in NSC maintenance and, potentially, in neurodevelopmental disorders. We studied the differentiation of Sox2-mut cells into neurons and glia, as compared to controls: at advanced stage, very few β-tub-positive cells were observed in Sox2-mut cells differentiated, with poor differentiated morphology. This result showed the importance of Sox2 in the development into mature neurons. We also analyzed the changes in gene expression resulting from Sox2 deletion by RNA-seq analysis of three samples for both wt and Sox2-mut cells in undifferentiated cells, and two differentiation conditions (day 4 and day 11). Hundreds of genes were deregulated in mutant cells. The most down-regulated gene was Socs3, so we transduced Sox2-mut cells with a lentiviral Socs3–vector, coexpressing GFP. Socs-3 transduced mut cells initially grew as the untransduced cells (only a proportion of the cells had been tranduced), but continued to grow even after the untransduced mut cells were completely exhausted, and transduced cells were positively selected. These results suggested that Socs3 partially rescued the proliferation defect of mut cells. I also tested if the reintroduction of Socs3 could rescue the neuronal differentiation defect of mut cells and my initial experiments suggest that this might be the case: Socs3-transduced cells were all GFAP-negative, and they all appeared β-tub-positive, though they seemed to have a suffering morphology. I aimed to test the role of some of the other most deregulated genes as mediators of Sox2 function in self-renewal and differentiation, by rescuing experiments of mut cells. I aim to test if Sox2 reintroduction in mut cells could rescue the long-range interactions of a small number of identified target genes, lost in Sox2-mut cells, by 3C experiments.

Thesis (Ph.D.)--Tufts University, 2000.
Adviser: David A. Boas. Submitted to the Dept. of Electrical Engineering and Computer Science. Includes bibliographical references (leaves 139-147). Access restricted to members of the Tufts University community. Also available via the World Wide Web;

This thesis establishes normal age-related changes in the magnetic resonance (MR) T1 and T2 relaxation time constants using data collected as part of the National Institutes of Health (NIH) MRI Study of Normal Brain Development. This ongoing multi-centre study of normal brain and behaviour development provides both longitudinal and cross-sectional data and has enabled us to investigate the relaxation time constant evolution in several brain regions for children within the range of 0-4.5 years. Due to the multi-centre nature of the study and the extended period of data collection, periodically scanned inanimate and human phantoms were used to assess intra and inter-site variability. The main finding of this thesis is the parametrization of the mono-exponential behaviour of both the T1 and T2 relaxation time constants from birth until 4.5 years of age. This behaviour is believed to reflect the rapid changes in water content as well as myelination processes observable during neonatal brain development. These results, comprising over 200 subject scans, represents a subset of a publicly available normative pediatric MRI database, providing a basis for comparison for studies assessing normal brain development and deviation due to various neurological disorders.

Les enképhalines (ENK), étant neuromodulateurs, ont un rôle prépondérant dans plusieurs circuits neuronaux tels que ceux de la récompense, la peur et l’anxiété. Dans cette étude, nous avons ciblé les ENK et atténué leur expression dans le noyau accumbens et l’amygdale centrale par le biais d’injections de vecteurs lentiviraux exprimant un shRNA spécifique à l’ENK. Les injections des lentivirus exprimant un shENK ont été comparées à des hémisphères intacts et à des injections du même vecteur exprimant un shRNA témoin, pour révéler des diminutions de l'ARNm des ENK de 62 %. Ces quantifications ont été validées in vivo par la comparaison du signal radioactif des sondes pour l’ARNm des ENK dans les régions infectées par le virus, ces régions ayant été identifiées par immunohistochimie. Nous démontrons une spécificité de l’atténuation de l’ARNm des ENK puisqu’aux sites des injections, il n'y a pas eu de diminution de l’ARNm de la GAD65.
Enkephalin (ENK), a prominent endogenous opioid mediator of the behavioural response, elicits its function in important circuits of the brain such as reward, fear and anxiety. In this study, we have targeted the downregulation of ENK expression by the delivery of a lentiviral vector with an expressing shRNA specific to ENK mRNA in ENK rich regions, such as the nucleus accumbens and central amygdala. By injecting a vector expressing an shENK and comparing it to non-injected hemispheres, as well as to injections of the same vector yet expressing a scrambled shRNA, we have observed an average downregulation of 62% ENK mRNA. Quantifications were performed in vivo, by collecting the in situ hybridization radioprobe signal for ENK mRNA of regions infected by the virus; the latter visualized immunohistochemically. Our results show a knockdown specificity of ENK mRNA and tissue integrity, as demonstrated by the lack of GAD65 mRNA disruption.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.
Cataloged from PDF version of thesis. Vita.
Includes bibliographical references.
The head is one of the most complex and important parts of the body. The shape of the head is largely determined by the size of the brain and morphology of the facial skeleton. These tissues consist of different cell types and undergo distinct developmental programs. However, development of the brain and various parts of the face may be coordinated so that tissues form in the correct order and scale to each other appropriately. Work presented here demonstrates that the Xenopus Extreme Anterior Domain (EAD), a group of 500 cells located at the anterior tip of the frog embryo, coordinates brain and craniofacial development through two distinct mechanisms. First, the EAD acts as a long range organizer for head development by regulating the size of both the brain and surrounding facial cartilage. Perturbing expression of frzb and crescent, genes encoding Wnt antagonists, in the EAD is sufficient to decrease cell proliferation in the brain and neural crest. Analysis of transgenic reporter embryos suggests that the EAD affects beta-catenin Wnt signaling over a range of 800 microns. By affecting the growth of both the brain and neural crest-derived cartilage, the EAD determines the overall size of the head. Second, the EAD synchronizes neural crest migration and the formation of two columns of cells, termed the pre-mouth array, that precede mouth opening. During this process, Kinin-Kallikrein signaling from the EAD is required to guide neural crest cells into the face. After their migration, neural crest cells signal back to the EAD to regulate pre-mouth array morphogenesis via Wnt/PCP signaling. Formation of the pre-mouth array involves convergent extension-like behavior where the EAD, originally a wide and short mass of cells, narrows and lengthens to form two columns of cells which later split down the middle during mouth opening. Reciprocal signaling between the EAD and neural crest ensures that mouth opening begins after the neural crest have completed migration. The organizing function of the EAD is likely conserved in vertebrates including humans. Understanding global coordination of brain and craniofacial development provides insight into the causes of facial abnormalities and microcephaly.
by Justin Chen.
Ph. D.