Theoretical studies of Membrane Proteins : Properties, Prediction Methods and Genome-wide analysis

Membrane proteins are a large and important class of proteins. They are responsible for several of the key functions in a living cell, e.g. transport of nutrients and ions, cell-cell signaling, and cell-cell adhesion. Despite their importance it has not been possible to study their structure and organization in much detail because of the difficulty to obtain 3D structures. In this thesis theoretical studies of membrane protein sequences and structures have been carried out by analyzing existing experimental data. The data comes from several sources including sequence databases, genome sequencing projects, and 3D structures. Prediction of the membrane spanning regions by hydrophobicity analysis is a key technique used in several of the studies. A novel method for this is also presented and compared to other methods. The primary questions addressed in the thesis are: What properties are common to all membrane proteins? What is the overall architecture of a membrane protein? What properties govern the integration into the membrane? How many membrane proteins are there and how are they distributed in different organisms? Several of the findings have now been backed up by experiments. An analysis of the large family of G-protein coupled receptors pinpoints differences in length and amino acid composition of loops between proteins with and without a signal peptide and also differences between extra- and intracellular loops. Known 3D structures of membrane proteins have been studied in terms of hydrophobicity, distribution of secondary structure and amino acid types, position specific residue variability, and differences between loops and membrane spanning regions. An analysis of several fully and partially sequenced genomes from eukaryotes, prokaryotes, and archaea has been carried out. Several differences in the membrane protein content between organisms were found, the most important being the total number of membrane proteins and the distribution of membrane proteins with a given number of transmembrane segments. Of the properties that were found to be similar in all organisms, the most obvious is the bias in the distribution of positive charges between the extra- and intracellular loops. Finally, an analysis of homologues to membrane proteins with known topology uncovered two related, multi-spanning proteins with opposite predicted orientations. The predicted topologies were verified experimentally, providing a first example of "divergent topology evolution".

Subliminal or not? : An appraisal of semantic processing in the near absence of visual awareness

Stimuli that cannot be perceived (i.e., that are subliminal) can still elicit neural responses in an observer, but can such stimuli influence behavior and higher-order cognition? Empirical evidence for such effects has periodically been accepted and rejected over the last six decades. Today, many psychologists seem to consider such effects well-established and recent studies have extended the power of subliminal processing to new limits. In this thesis, I examine whether this shift in zeitgeist is matched by a shift in evidential strength for the phenomenon. This thesis consists of three empirical studies involving more than 250 participants, a simulation study, and a quantitative review. The conclusion based on these efforts is that several methodological, statistical, and theoretical issues remain in studies of subliminal processing. These issues mean that claimed subliminal effects might be caused by occasional or weak percepts (given the experimenters’ own definitions of perception) and that it is still unclear what evidence there is for the cognitive processing of subliminal stimuli. New data are presented suggesting that even in conditions traditionally claimed as “subliminal”, occasional or weak percepts may in fact influence cognitive processing more strongly than do the physical stimuli, possibly leading to reversed priming effects. I also summarize and provide methodological, statistical, and theoretical recommendations that could benefit future research aspiring to provide solid evidence for subliminal cognitive processing.