Revealing local information : Identification of salient functional brain links in resating state brain

Communication amongst various regions of our brain makes it possible for us to perform a wide array of cognitive tasks. To capture these communications at a local level has remained challenging in the field of neuroimaging due to the sheer number of functional brain links that is needed to be explored. Different methods aimed at investigating these links either focuses on selection biases or increases the complexity of the method. The current thesis addresses this issue, by introducing a new simple method, namely Link Wise Median Splitting, which remains free of any selection biases. With the aid of simulations, we first demonstrated the higher sensitivity of this method over traditional approaches. Furthering the versatility of the method, we applied it to three different study designs involving resting state functional connectivity. The three study designs aimed to understand three distinct cognitive processes, revealed crucial information about the resting state brain. In sum, this thesis concluded by showing the benefits of using Link Wise Median Splitting over traditional methods to investigate functional brain links.La comunicació entre diverses regions del nostre cervell fa possible que fem una àmplia gamma de tasques cognitives. Capturar aquestes comunicacions a nivell local és encara un repte en el camp de la neuroimatge degut a la gran quantitat de connexions cerebrals funcionals que cal explorar. Els diferents mètodes destinats a investigar aquestes connexions es centren o bé en els biaixos de selecció o bé en augmentar la complexitat del mètode. La tesi actual aborda aquest assumpte introduint un nou mètode senzill, l’anomenat Link Wise Median Splitting, que queda lliure de biaixos de selecció. Amb l'ajuda de simulacions, primer hem demostrat la major sensibilitat d'aquest mètode respecte als enfocaments tradicionals. Aprofundint en la versatilitat del mètode, l'hem aplicat a tres dissenys d'estudi diferents de connectivitat funcional en l'estat de repòs. Els tres dissenys d'estudi, adreçats a comprendre tres processos cognitius diferents, han revelat informació crucial sobre el cervell en l'estat de repòs. En resum, aquesta tesi mostra els beneficis de l'ús de Link Wise Median Splitting sobre mètodes tradicionals per investigar connexions funcionals del cervell.Programa de doctorat en Biomedicin

A beginner's handbook to identify and characterize i-motif DNA

Genomic DNA exhibits an innate ability to manifest diverse sequence-dependent secondary structures, serving crucial functions in gene regulation and cellular equilibrium. While extensive research has confirmed the formation of G-quadruplex structures by guanine-rich sequences in vitro and in cells, recent investigations have turned the quadruplex community's attention to the cytosine (C)-rich complementary strands that can adopt unique tetra-stranded conformation, termed as intercalated motif or i-motif. I-motifs are stabilized by hemi-protonated C:CH+ base pairs under acidic conditions. Initially, the in vivo occurrence of i-motifs was underestimated because their formation is favored at non-physiological pH. However, groundbreaking research utilizing the structure-specific iMab antibody and high-throughput sequencing have recently detected their conserved dispersion throughout the genome, challenging previous assumptions. Given the evolving nature of this research field, it becomes imperative to conduct independent in vitro experiments aimed at identifying potential i-motif formation in C-rich sequences and consolidating the findings to address the properties of i-motifs. This chapter serves as an introductory guide for the swift identification of novel i-motifs, where we present an experimental framework for investigating and characterizing i-motif sequences in vitro. In this chapter, we selected a synthetic oligonucleotide (C7T3) sequence and outlined appropriate methodologies for annealing the i-motif structure into suitable buffers. Then, we validated its formation by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopy. Finally, we provided a thorough account of the step-by-step procedures to investigate the effect of i-motif formation on the stalling or retardation of DNA replication using high resolution primer extension assays.</p