Imagining 'reactivity': allergy within the history of immunology

An allergy is commonly understood to be an overreaction of the immune system to harmless substances that are misrecognised as foreign. This concept of allergy as an abnormal, misdirected immune response-a biological fault-stems from the idea that the immune system is an inherently defensive operation designed to protect the individual through an innate capacity to discriminate between the benign and toxic, or self and nonself. However, this definition of allergy represents a radical departure from its original formulation. Literally meaning 'altered reactivity', the term was coined in 1906 by Austrian paediatrician Clemens von Pirquet, to describe the fundamentally mutable nature of the immune response. This paper argues that the conventional interpretation of allergy-as-pathology derives from specific concepts of 'organism', 'response', and 'normal' immune function that have-for over a century-governed the perception and study of immune phenomena within immunology. Through an examination of Louis Pasteur's conceptualisation of the host body/microorganism relationship, I argue that immunology is founded on a view of the organism as a discrete, autonomous entity, and on a concomitant notion of the immune response as essentially reactive. Revisiting the concept of 'altered reactivity', this paper points to the fact that allergy was initially posited as a general theory of immune responsiveness and, importantly, one that poses a significant challenge to orthodox notions of immunopathology. It suggests that Pirquet's unique view of immune responsiveness presents an account of organismic or biological identity that encapsulates, rather than reduces, its ecological complexity.     

On the cyclic nature of perception in vision versus audition

Does our perceptual awareness consist of a continuous stream, or a discrete sequence of perceptual cycles, possibly associated with the rhythmic structure of brain activity? This has been a long-standing question in neuroscience. We review recent psychophysical and electrophysiological studies indicating that part of our visual awareness proceeds in approximately 7–13 Hz cycles rather than continuously. On the other hand, experimental attempts at applying similar tools to demonstrate the discreteness of auditory awareness have been largely unsuccessful. We argue and demonstrate experimentally that visual and auditory perception are not equally affected by temporal subsampling of their respective input streams: video sequences remain intelligible at sampling rates of two to three frames per second, whereas audio inputs lose their fine temporal structure, and thus all significance, below 20–30 samples per second. This does not mean, however, that our auditory perception must proceed continuously. Instead, we propose that audition could still involve perceptual cycles, but the periodic sampling should happen only after the stage of auditory feature extraction. In addition, although visual perceptual cycles can follow one another at a spontaneous pace largely independent of the visual input, auditory cycles may need to sample the input stream more flexibly, by adapting to the temporal structure of the auditory inputs.     

On the forces that govern clonality versus sexuality in plant communities

Although sexuality is considered evolutionarily progressive, clonality is very common in plants and the prevailing means of reproduction in several community types. I discuss what could be the forces that have influenced the selection among sexual versus non-sexual reproduction at community level. I propose that, among others, the probability of self-competition must have been one of the key factors. The probability of meeting one’s own genes for wasteful competition is higher in communities where clonality prevails (and relatively high mean intra-species relatedness is expected), and higher in communities with low species diversity. On the other hand, lower diversity indicates a higher average fitness of species since the (finite) total pool of resources is distributed among fewer population with high density. I show, using four community types with contrasting diversity and clonality that community fitness (average fitness in the assemblage of species) can be expressed as the product of two variables––anti-diversity and degree of sexuality.     

Ployandry versus polygyny versus parasites

Although social insect colonies are most easily conceptualized as consisting of a single, once-mated queen and her worker progeny, the number of queens per colony and the number of times queens mate varies broadly in ants and other social insects. Various hypotheses have been suggested for the resulting range of breeding systems and social organizations, respectively; one set of hypotheses relating to both queen number and mate number at the same time is a need for genetic variation, especially in relation to disease resistance. We here carry out a comparative analysis using phylogenetic information and, contrary to one non-phylogenetic previous study, we find that polyandry and polygyny are not significantly associated. However, the level of relatedness within colonies, a quantity affected by both polyandry and polygyny, is significantly associated with parasite loads: species with colonies with low relatedness levels have lower parasite loads. Given that, under the variance-reduction principle, selection on queens for mating frequency ought to continue even in polygynous colonies, we suggest that while parasite loads indeed seem to correlate with intra-colony genetic variability, the relationship to polyandry and polygyny may be complex and requires considerably more experimental investigation.     

Indifferent Philosophy versus Almighty Authority: On consistency,consensus and unitary taxonomy

The ability of the taxonomic community to heed Charles Godfray's wake‐up call to create ‘unitary’ taxonomic systems and make them available on the internet is hampered by real difficulties over achieving taxonomic consistency, and a cultural reluctance amongst systematists to embrace consensus. This paper explores these issues by examining the taxonomic history of an African milkweed butterfly, Amauris damocles sensu lato. Recent differences of opinion over the classification of this insect relate to fundamental differences in the theory and practice of systematics, from creationism through authoritarianism to cladistics, differences of a kind that will forever bedevil the distributed taxonomic system. If practical unitary schemes are to emerge, then the taxonomic community will need to adopt new ways of managing and recording taxonomic change, and develop a more responsible attitude towards the needs of others who are dependent of the primary products of systematics ‐names, and the classification schemes they symbolize.     

Axial versus Appendicular: Constraint versus Selection

SYNOPSIS.Constraint theory has suffered from its many and varyingdefinitions and from repeated confusion with the action of selection.Constraints are difficult to isolate, more difficult to quantify,and their consequences may be simulated by the action of agentssuch as stabilizing selection. This paper presents an alternativemethod of constraint analysis using a simple one-dimensionalmeasurement. A total of 29 skeletal elements from 15 speciesrepresenting 11 orders of mammals were measured for length andnormalized for body mass, after which means, standard deviations,and variances were generated. A coefficient of variation analysiswas performed to normalize for mean element length. The axialskeleton was found to be less variable than the appendicular.The appendicular demonstrated a trend where the more distalelements were the most variable, and variation decreased withmore proximal positions. The three most variable of the 29 elementswere finger V, toe V, and metacarpal V. In summary, the axialskeleton was found to be more conservative in the lengths ofits elements, the more distal appendicular elements were lessconstrained than proximal ones and these constraints were probablythe results of genetic, developmental, and mechanical factors.It is also proposed that stabilizing selection played some rolein maintaining the curb on length variance in these structures,based on mechanical performance. The results of this study areintended to promote discussion of alternative methods of constraintanalysis.     

On the role of APC-activation for in vitro versus in vivo T cell priming

Professional antigen-presenting cells take up antigens for processing and presentation in association with MHC class I and II molecules. When APCs receive the right stimuli, they undergo a maturation process and migrate to secondary lymphoid organs to trigger T cell activation. In this study, we compared side-by-side in vivo and in vitro activation of T cells. Transgenic CD8(+) T cells specific for the p33 epitope, derived from the lymphocytic choriomeningitis virus glycoprotein, were labeled with CFSE and injected into syngeneic mice or alternatively, co-cultured in vitro with APCs. The p33 epitope was delivered as free peptide or genetically fused to virus-like particles. Whereas proliferation of specific T cells was comparable in both systems, the production of IFN-gamma and the expression of CD25 showed important differences. Induction of effector function and expression of activation markers were strongly enhanced in vitro by both the free peptide and VLPs. Surprisingly, addition of CpG-containing immune-stimulating DNA for activation of APCs dramatically increased effector T cell differentiation in vitro, whereas no enhancement could be observed in vitro. Thus, activation of professional APCs was mandatory for induction of effector CD8(+) T cell responses in vivo, while this step was largely dispensable in vitro.     

On the functional interchangeability, oxidant versus reductant, of members of the thioredoxin superfamily

Escherichia coli thioredoxin 1 has been characterized in vivo and in vitro as one of the most efficient reductants of disulfide bonds. Nevertheless, under some conditions, thioredoxin 1 can also act in vivo as an oxidant, promoting formation of disulfide bonds in the cytoplasm (E. J. Stewart, F. Aslund, and J. Beckwith, EMBO J. 17:5543-5550, 1998). We recently showed that when a signal sequence is attached to thioredoxin 1 it is exported to the periplasm, where it can also act as an oxidant, replacing the normal periplasmic catalyst of disulfide bond formation, DsbA, in oxidizing cell envelope proteins (L. Debarbieux and J. Beckwith, Proc. Natl. Acad. Sci. USA 95:10751-10756, 1998). Here we report pulse-chase studies of the efficiency of disulfide bond formation in strains exporting thioredoxin 1 and more-oxidizing variants of it. While the exported thioredoxin 1 itself substantially speeds up the kinetics of disulfide bond formation, a version of this protein containing the DsbA active site exhibits kinetics that are indistinguishable from those of the DsbA protein itself. Further, we confirm the findings of Jonda et al. (S. Jonda, M. Huber-Wunderlich, R. Glockshuber, and E. M?ssner, EMBO J. 18:3271-3281, 1999), who found that DsbB is responsible for the oxidation of exported thioredoxin 1, and we report the detection of a disulfide-bonded DsbB-thioredoxin 1 complex. Finally, we have found that under conditions of high-level expression of exported thioredoxin 1, the protein can act as both an oxidant and a reductant.     

On divide-and-conquer strategies for parsimony analysis of large data sets: Rec-I-DCM3 versus TNT

Roshan et al. recently described a divide-and-conquer technique for parsimony analysis of large data sets, Rec-I-DCM3, and stated that it compares very favorably to results using the program TNT. Their technique is based on selecting subsets of taxa to create reduced data sets or subproblems, finding most-parsimonious trees for each reduced data set, recombining all parts together, and then performing global TBR swapping on the combined tree. Here, we contrast this approach to sectorial searches, a divide-and-conquer algorithm implemented in TNT. This algorithm also uses a guide tree to create subproblems, with the first-pass state sets of the nodes that join the selected sectors with the rest of the topology; this allows exact length calculations for the entire topology (that is, any solution N steps shorter than the original, for the reduced subproblem, must also be N steps shorter for the entire topology). We show here that, for sectors of similar size analyzed with the same search algorithms, subdividing data sets with sectorial searches produces better results than subdividing with Rec-I-DCM3. Roshan et al.'s claim that Rec-I-DCM3 outperforms the techniques in TNT was caused by a poor experimental design and algorithmic settings used for the runs in TNT. In particular, for finding trees at or very close to the minimum known length of the analyzed data sets, TNT clearly outperforms Rec-I-DCM3. Finally, we show that the performance of Rec-I-DCM3 is bound by the efficiency of TBR implementation for the complete data set, as this method behaves (after some number of iterations) as a technique for cyclic perturbations and improvements more than as a divide-and-conquer strategy.     

On RecA protein-mediated homologous alignment of two DNA molecules. Three strands versus four strands

The recA protein from Escherichia coli can homologously align two duplex DNA molecules; however, this interaction is much less efficient than the alignment of a single strand and a duplex. Three strand paranemic joints are readily detected. In contrast, duplex-duplex pairing is detected only when the incoming (second) duplex is negatively supercoiled, and even here the pairing is inefficient. The recA protein-promoted four strand exchange reaction is initiated in a three strand region, with efficiency increasing with the length of potential three strand pairing available for initiation. This indicates that a paranemic joint involving three DNA strands may be an important intermediate in all recA protein-mediated DNA strand exchange reactions and that the presence of three strands rather than four is a fundamental structural parameter of paranemic joints.     

Lymphocytes apoptosis: young versus aged and humans versus rats

This paper deals with a comparative study of lymphocyte apoptosis in young versus aged and humans versus rats. Apoptotic rate achieved by the use of different apoptogenic inducers, acting at different cellular levels, and cell surface modifications were analyzed. The results showed that aged human lymphocytes and freshly isolated rat lymphocytes were more prone to undergo apoptosis. Therefore, the same apoptotic signal is recognized by human and rat lymphocytes, but the extent of the answer is related to the species, to the intensity of the apoptotic stimulus and to the metabolic/developmental condition of the cells. Surface modifications (lipids and glycans), typical of apoptosis, were observed. Our data showed that cell surface changes are species and age dependent. They are early events, progressively achieved in the course of the apoptotic process involving lateral membrane movements of molecules.