Investigating pathogen biology at the level of the proteome

Bacterial infections are a major cause of morbidity and mortality throughout the world. By extending our understanding of the process of bacterial pathogenesis at the molecular level new strategies for their treatment and prevention can be developed. Proteomic technologies, along with other methods for global gene expression analysis, play an important role in understanding the mechanism(s) of bacterial pathogenesis. This review highlights the use of proteomics to identify protein biomarkers for virulent bacterial isolates and how these biomarkers can be correlated with the outcome of bacterial infection. Biomarker identification typically looks at the proteomes of bacteria grown under laboratory conditions. It is, however, the characterisation of the bacterial proteome during in vivo infection of its host that will eventually provide the most significant insights into bacterial pathogenesis. Although this area of research has significant technical challenges, a number of complementary proteome analytical approaches are being developed to identify and characterise the bacterial genes specifically expressed in vivo. Ultimately, the development of newly targeted therapies and vaccines using specific protein targets identified through proteomic analyses will be one of the major practical benefits arising from the proteomic analysis of bacterial pathogens.     

The Ferrier Lecture 1998. The molecular biology of consciousness investigated with genetically modified mice

The question is raised of the relevance of experimental work with the mouse and some of its genetically modified individuals in the study of consciousness. Even if this species does not go far beyond the level of 'minimal consciousness', it may be a useful animal model to examine the elementary building blocks of consciousness using the methods of molecular biology jointly with investigations at the physiological and behavioural levels. These building blocks which are anticipated to be universally shared by higher organisms (from birds to humans) may include: (i) the access to multiple states of vigilance, like wakefulness, sleep, general anaesthesia, etc.; (ii) the capacity for global integration of several sensory and cognitive functions, together with behavioural flexibility resulting in what is referred to as exploratory behaviour, and possibly a minimal form of intentionality. In addition, the contribution of defined neuronal nicotinic receptors species to some of these processes is demonstrated and the data discussed within the framework of recent neurocomputational models for access to consciousness.     

Evolution of consciousness.

The evolution of codification within the increasing complexity and diversity of relations is examined within a triadic architectural frame of filiated hierarchical levels of both material organization and consciousness. Inertia and entropy are understood as basic forces within codal organization, and evolution is examined as a force of mediation between these two forces, operating to move energy to more complex and diverse codal relations.     

The asynchrony of consciousness.

We present below a simple hypothesis on what we believe is a characteristic of visual consciousness. It is derived from facts about the visual brain revealed in the past quarter of a century, but it relies most especially on psychophysical evidence which shows that different attributes of the visual scene are consciously perceived at different times. This temporal asynchrony in visual perception reveals, we believe, a plurality of visual consciousnesses that are asynchronous with respect to each other, reflecting the modular organization of the visual brain. We further hypothesize that when two attributes (e.g. colour and motion) are presented simultaneously, the activity of cells in a given processing system is sufficient to create a conscious experience of the corresponding attribute (e.g. colour), without the necessity for interaction with the activities of cells in other processing systems (e.g. motion). Thus, any binding of the activity of cells in different systems should be more properly thought of as a binding of the conscious experiences generated in each system.     

Investigating the properties of Bacillus thuringiensis Cry proteins with novel loop replacements created using combinatorial molecular biology

Cry proteins are a large family of crystalline toxins produced by Bacillus thuringiensis. Individually, the family members are highly specific, but collectively, they target a diverse range of insects and nematodes. Domain II of the toxins is important for target specificity, and three loops at its apex have been studied extensively. There is considerable interest in determining whether modifications in this region may lead to toxins with novel specificity or potency. In this work, we studied the effect of loop substitution on toxin stability and specificity. For this purpose, sequences derived from antibody complementarity-determining regions (CDR) were used to replace native domain II apical loops to create "Crybodies." Each apical loop was substituted either individually or in combination with a library of third heavy-chain CDR (CDR-H3) sequences to create seven distinct Crybody types. An analysis of variants from each library indicated that the Cry1Aa framework can tolerate considerable sequence diversity at all loop positions but that some sequence combinations negatively affect structural stability and protease sensitivity. CDR-H3 substitution showed that loop position was an important determinant of insect toxicity: loop 2 was essential for activity, whereas the effects of substitutions at loop 1 and loop 3 were sequence dependent. Unexpectedly, differences in toxicity did not correlate with binding to cadherins--a major class of toxin receptors--since all Crybodies retained binding specificity. Collectively, these results serve to better define the role of the domain II apical loops as determinants of specificity and establish guidelines for their modification.     

Time of consciousness, consciousness of time

Time shapes our behavior: we must estimate the duration of events in our environment in order to anticipate changes and time our activity in function of these changes. However, there is no sensory modality devoted to the perception of time, therefore the question is to know which mechanisms underlie the consciousness that time flows and allow us to estimate time precisely. This article proposes a brief overview of psychological, neuropsychological and brain imaging studies which rely on theoretical models postulating the existence of an internal timer. These studies examine the different components--time base, counter and memory--of this timer: particularly they are aimed at characterising the relationships between the evolution of these components with age or their pathological alterations and changes in temporal judgements. They also attempt to specify the neural bases of these components. From this brief overview comes the idea that, if an internal timer exits, it does not mark objective time but a multitude of subjective times.     

Memory,consciousness and neuroimaging.

Neuroimaging techniques that allow the assessment of memory performance in healthy human volunteers while simultaneously obtaining measurements of brain activity in vivo may offer new information on the neural correlates of particular forms of memory retrieval and their association with consciousness and intention. We consider evidence from studies with positron emission tomography and functional magnetic resonance imaging indicating that priming, a form of implicit retrieval, is associated with decreased activity in various cortical regions. We also consider evidence concerning the question of whether two components of explicit retrieval--intentional or effortful search and successful conscious recollection--are preferentially associated with increased activity in prefrontal and medial temporal regions, respectively. Last, we consider recent efforts to probe the relation between the phenomenological character of remembering and neural activity. In this instance we broaden our scope to include studies employing event-related potentials and consider evidence concerning the neural correlates of qualitatively different forms of memory, including memory that is specifically associated with a sense of self, and the recollection of particular temporal or perceptual features that might contribute to a rich and vivid experience of the past.     

How to study consciousness scientifically.

The neurosciences have advanced to the point that we can now treat consciousness as a scientific problem like any other. The problem is to explain how brain processes cause consciousness and how consciousness is realized in the brain. Progress is impeded by a number of philosophical mistakes, and the aim of this paper is to remove nine of those mistakes: (i) consciousness cannot be defined; (ii) consciousness is subjective but science is objective; (iii) brain processes cannot explain consciousness; (iv) the problem of ''qualia'' should be set aside; (v) consciousness is epiphenomenal; (vi) consciousness has no evolutionary function; (vii) a causal account of consciousness is necessarily dualistic; (viii) science is reductionistic, so a scientific account of consciousness would show it reducible to something else; and (ix) an account of consciousness must be an information processing account.     

The neuronal basis for consciousness.

Attempting to understand how the brain, as a whole, might be organized seems, for the first time, to be a serious topic of inquiry. One aspect of its neuronal organization that seems particularly central to global function is the rich thalamocortical interconnectivity, and most particularly the reciprocal nature of the thalamocortical neuronal loop function. Moreover, the interaction between the specific and non-specific thalamic loops suggests that rather than a gate into the brain, the thalamus represents a hub from which any site in the cortex can communicate with any other such site or sites. The goal of this paper is to explore the basic assumption that large-scale, temporal coincidence of specific and non-specific thalamic activity generates the functional states that characterize human cognition.