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.     

Towards welfare biology: Evolutionary economics of animal consciousness and suffering

Welfare biology is the study of living things and their environment with respect to their welfare (defined as net happiness, or enjoyment minus suffering). Despite difficulties of ascertaining and measuring welfare and relevancy to normative issues, welfare biology is a positive science. Evolutionary economics and population dynamics are used to help answer basic questions in welfare biology: Which species are affective sentients capable of welfare? Do they enjoy positive or negative welfare? Can their welfare be dramatically increased? Under plausible axioms, all conscious species are plastic and all plastic species are conscious (and, with a stronger axiom, capable of welfare). More complex niches favour the evolution of more rational species. Evolutionary economics also supports the common-sense view that individual sentients failing to survive to mate suffer negative welfare. A kind of God-made (or evolution-created) fairness between species is also unexpectedly found. The contrast between growth maximization (as may be favoured by natural selection), average welfare, and total welfare maximization is discussed. It is shown that welfare could be increased without even sacrificing numbers (at equilibrium). Since the long-term reduction in animal suffering depends on scientific advances, strict restrictions on animal experimentation may be counter-productive to animal welfare.     

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.     

Backyard evolutionary biology: Investigating local flowers brings learning to life

Inquiry‐based learning allows students to actively engage in and appreciate the process of science. As college courses transition to online instruction in response to COVID‐19, incorporating inquiry‐based learning is all the more essential for student engagement. However, with the cancelation of in‐person laboratory courses, implementing inquiry can prove challenging for instructors. Here, I describe a case that exemplifies a strategy for inquiry‐based learning and can be adapted for use in various course modalities, from traditional face‐to‐face laboratory courses to asynchronous and synchronous online courses. I detail an assignment where students explore the developmental basis of morphological evolution. Flowers offer an excellent example to address this concept and are easy for students to access and describe. Students research local flowering plants, collect and dissect flower specimens to determine their whorl patterns, and generate hypotheses to explain the developmental genetic basis of the patterns identified. This task allows students to apply their scientific thinking skills, conduct guided exploration in nature, and connect their understanding of the developmental basis of evolutionary change to everyday life. Incorporating inquiry using readily available, tangible, tractable real‐world examples represents a pragmatic and effective model that can be applied in a variety of disciplines during and beyond COVID‐19.     

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.     

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.     

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.     

Attention,self-regulation and consciousness.

Consciousness has many aspects. These include awareness of the world, feelings of control over one''s behaviour and mental state (volition), and the notion of continuing self. Focal (executive) attention is used to control details of our awareness and is thus closely related to volition. Experiments suggest an integrated network of neural areas involved in executive attention. This network is associated with our voluntary ability to select among competing items, to correct error and to regulate our emotions. Recent neuroimaging studies suggest that these various functions involve separate areas of the anterior cingulate. We have adopted a strategy of using marker tasks, shown to activate the brain area by imaging studies, as a means of tracing the development of attentional networks. Executive attention appears to develop first to regulate distress during the first year of life. During later childhood the ability to regulate conflict among competing stimuli builds upon the earlier cingulate anatomy to provide a means of cognitive control. During childhood the activation of cingulate structures relates both to the child''s success on laboratory tasks involving conflict and to parental reports of self-regulation and emotional control. These studies indicate a start in understanding the anatomy, circuitry and development of executive attention networks that serve to regulate both cognition and emotion.     

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.