Phylogenetic diversification of immunoglobulin genes and the antibody repertoire

Immunoglobulins are encoded by a large multigene system that undergoes somatic rearrangement and additional genetic change during the development of immunoglobulin-producing cells. Inducible antibody and antibody-like responses are found in all vertebrates. However, immunoglobulin possessing disulfide-bonded heavy and light chains and domain-type organization has been described only in representatives of the jawed vertebrates. High degrees of nucleotide and predicted amino acid sequence identity are evident when the segmental elements that constitute the immunoglobulin gene loci in phylogenetically divergent vertebrates are compared. However, the organization of gene loci and the manner in which the independent elements recombine (and diversify) vary markedly among different taxa. One striking pattern of gene organization is the "cluster type" that appears to be restricted to the chondrichthyes (cartilaginous fishes) and limits segmental rearrangement to closely linked elements. This type of gene organization is associated with both heavy- and light-chain gene loci. In some cases, the clusters are "joined" or "partially joined" in the germ line, in effect predetermining or partially predetermining, respectively, the encoded specificities (the assumption being that these are expressed) of the individual loci. By relating the sequences of transcribed gene products to their respective germ-line genes, it is evident that, in some cases, joined-type genes are expressed. This raises a question about the existence and/or nature of allelic exclusion in these species. The extensive variation in gene organization found throughout the vertebrate species may relate directly to the role of intersegmental (V<==>D<==>J) distances in the commitment of the individual antibody-producing cell to a particular genetic specificity. Thus, the evolution of this locus, perhaps more so than that of others, may reflect the interrelationships between genetic organization and function.      

Conformational Sampling and Binding Site Assessment of Suppression of Tumorigenicity 2 Ectodomain

Suppression of Tumorigenicity 2 (ST2), a member of the interleukin-1 receptor (IL-1R) family, activates type 2 immune responses to pathogens and tissue damage via binding to IL-33. Dysregulated responses contribute to asthma, graft-versus-host and autoinflammatory diseases and disorders. To study ST2 structure for inhibitor development, we performed the principal component (PC) analysis on the crystal structures of IL1-1R1, IL1-1R2, ST2 and the refined ST2 ectodomain (ST2^ECD) models, constructed from previously reported small-angle X-ray scattering data. The analysis facilitates mapping of the ST2^ECD conformations to PC subspace for characterizing structural changes. Extensive coverage of ST2^ECD conformations was then obtained using the accelerated molecular dynamics simulations started with the IL-33 bound ST2^ECD structure as instructed by their projected locations on the PC subspace. Cluster analysis of all conformations further determined representative conformations of ST2^ECD ensemble in solution. Alignment of the representative conformations with the ST2/IL-33 structure showed that the D3 domain of ST2^ECD (containing D1-D3 domains) in most conformations exhibits no clashes with IL-33 in the crystal structure. Our experimental binding data informed that the D1-D2 domain of ST2^ECD contributes predominantly to the interaction between ST2^ECD and IL-33 underscoring the importance of the D1-D2 domain in binding. Computational binding site assessment revealed one third of the total detected binding sites in the representative conformations may be suitable for binding to potent small molecules. Locations of these sites include the D1-D2 domain ST2^ECD and modulation sites conformed to ST2^ECD conformations. Our study provides structural models and analyses of ST2^ECD that could be useful for inhibitor discovery.     

Production of Diamino propionic acid ammonia lyase by a new strain of Salmonella typhimurium PU011

Background  

Seeds of the legume plant Lathyrus sativus, which is grown in arid and semi arid tropical regions, contain Diamino Propionic acid (DAP). DAP is a neurotoxin, which, when consumed, causes a disease called Lathyrism. Lathryrism may manifest as Neurolathyrism or Osteolathyrism, in which the nervous system, and bone formation respectively, are affected. DAP ammonia lyase is produced by a few microorganisms such as Salmonella typhi, Salmonella typhimurium and Pseudomonas, and is capable of detoxifying DAP.     

Modelling the transition from simple to complex Ca2+oscillations in pancreatic acinar cells

A mathematical model is proposed which systematically investigates complex calcium oscillations in pancreatic acinar cells. This model is based on calcium-induced calcium release via inositol trisphosphate receptors (IPR) and ryanodine receptors (RyR) and includes calcium modulation of inositol (1,4,5) trisphosphate (IP₃) levels through feedback regulation of degradation and production. In our model, the apical and the basal regions are separated by a region containing mitochondria, which is capable of restricting Ca²⁺ responses to the apical region. We were able to reproduce the observed oscillatory patterns, from baseline spikes to sinusoidal oscillations. The model predicts that calcium-dependent production and degradation of IP₃ is a key mechanism for complex calcium oscillations in pancreatic acinar cells. A partial bifurcation analysis is performed which explores the dynamic behaviour of the model in both apical and basal regions.     

Root carboxylate exudation capacity under phosphorus stress does not improve grain yield in green gram

Key message

Genetic variability in carboxylate exudation capacity along with improved root traits was a key mechanism for P-efficient green gram genotype to cope with P-stress but it did not increase grain yield.

Abstract

This study evaluates genotypic variability in green gram for total root carbon exudation under low phosphorus (P) using ¹⁴C and its relationship with root exuded carboxylates, growth and yield potential in contrasting genotypes. Forty-four genotypes grown hydroponically with low (2 μM) and sufficient (100 μM) P concentrations were exposed to ¹⁴CO₂ to screen for total root carbon exudation. Contrasting genotypes were employed to study carboxylate exudation and their performance in soil at two P levels. Based on relative ¹⁴C exudation and biomass, genotypes were categorized. Carboxylic acids were measured in exudates and root apices of contrasting genotypes belonging to efficient and inefficient categories. Oxalic and citric acids were released into the medium under low-P. PDM-139 (efficient) was highly efficient in carboxylate exudation as compared to ML-818 (inefficient). In low soil P, the reduction in biomass was higher in ML-818 as compared to PDM-139. Total leaf area and photosynthetic rate averaged for genotypes increased by 71 and 41 %, respectively, with P fertilization. Significantly, higher root surface area and volume were observed in PDM-139 under low soil P. Though the grain yield was higher in ML-818, the total plant biomass was significantly higher in PDM-139 indicating improved P uptake and its efficient translation into biomass. The higher carboxylate exudation capacity and improved root traits in the later genotype might be the possible adaptive mechanisms to cope with P-stress. However, it is not necessary that higher root exudation would result in higher grain yield.     

Regeneration in the auditory system of nymphal and adult bush crickets Tettigonia viridissima

Regeneration and reestablishment of synaptic connections is an important topic in neurobiological research. In the present study, the regeneration of auditory afferents and the accompanying effects in the central nervous system are investigated in nymphs and adults of the bush cricket Tettigonia viridissima L. (Orthoptera: Tettigoniidae). In all animals in which the tympanal nerve is crushed, neuronal tracing shows a regrowth of the afferents into the prothoracic ganglion. This regeneration is seen in both adult and nymphal stages and starts 10–15 days after nerve crushing. Physiological recordings from the leg nerve indicate a recovery of tympanal fibres and a formation of functional connections to interneurones in the same time range. Electrophysiological recordings from the neck connective suggest additional contralateral sprouting of interneurones and the formation of aberrant connections. The regeneration processes of the tympanal nerve in nymphal stages and adults appear to be similar.     

Pollination strategies in Cretan Arum lilies

Flowers of the genus Arum are known to attract dung‐breeding flies and beetles through olfactory deceit. In addition to this strategy, the genus has evolved several other pollination mechanisms. The present study aimed to characterize the pollination strategies of the Cretan Arum species by investigating the flowering phenology, thermogeny, inflorescence odours, and the pollinating fauna. The results obtained show that Arum cyrenaicum and Arum concinnatum emit a strong dung smell and exhibit the distinctive features associated with this pollination syndrome. Both species are highly thermogenic, have a similar odour profile and attract small‐bodied Diptera. Although sharing the same habitat, these two plant species are never found growing sympatrically as a result of the early blooming period of A. cyrenaicum. By contrast, Arum creticum and Arum idaeum have evolved a more traditional and mutually beneficial pollination mechanism. The stinking smell has been replaced by a more flower‐like odour that attracts bees (Lasioglossum sp.) and, occasionally, bugs (Dionconotus cruentatus). Although attracting the same pollinator, the main compound present in the odour of A. creticum is different from that of A. idaeum. Principal component analysis (PCA), based on physiologically active components of the flower odours determined by testing on the antenna of the Lasioglossum bee, revealed two different clusters, indicating that pollinators can potentially discriminate between the odours of the two species. A further PCA on the main floral odour volatiles as identified by gas chroatography‐mass spectroscopy from all the Arum species under investigation displayed odour‐based similarities and differences among the species. The PCA‐gas chomotography‐electroantennographic detection active peaks analysis showed that the two species, A. creticum and A. idaeum, form two groups and are clearly separated from A. cyrenaicum and A. concinnatum, which, conversely, cluster together. The evolutionary forces and selective pressures leading to diversification of pollination mechanisms in the Cretan Arum spp. are discussed. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 991–1001.     

Responses of the blister beetle Hycleus apicicornis to visual stimuli

Insect attraction to host plants may be partly mediated by visual stimuli. In the present study, the responses of adult Hycleus apicicornis (Guér.) (Coleoptera: Meloidae) to plant models of different colours, different combinations of two colours, or three hues of blue of different shapes are compared. Single‐colour models comprised the colours sky blue, bright green, yellow, red, white and black. Sky blue (reflecting light in the 440–500 nm region) is the most attractive, followed by white, which reflects light over a broader range (400–700 nm). On landing on sky blue targets, beetles exhibit feeding behaviour immediately. When different hues of blue (of different shapes) are compared, sky blue is preferred over turquoise, followed by dark blue, indicating that H. apicicornis is more attracted to lighter hues of blue than to darker ones. No significant differences are found between the three shapes (circle, square and triangle) tested, suggesting that reflectance associated with colour could be a more important visual cue than shape for host location by H. apicicornis. The preference of H. apicicornis for sky blue can be exploited in designing an attractive trap for its management.