Wing serial homologs and the origin and evolution of the insect wing

The origin and evolution of insect wings has been the subject of extensive debate. The issue has remained controversial largely because of the absence of definitive fossil evidence or direct developmental evidence of homology between wings and a putative wing origin. Recent identification of wing serial homologs (WSHs) has provided researchers with a potential strategy for identifying WSHs in other species. Future comparative developmental analyses between wings and WSHs may clarify the important steps underlying the evolution of insect wings.     

The "eyespot module" and eyespots as modules: development, evolution, and integration of a complex phenotype

Organisms are inherently modular, yet modules also evolve in response to selection for functional integration or functional specialization of traits. For serially repeated homologous traits, there is a clear expectation that selection on the function of individual traits will reduce the integration between traits and subdivide a single ancestral module. The eyespots on butterfly wings are one example of serially repeated morphological traits that share a common developmental mechanism but are subject to natural and sexual selection for divergent functions. Here, I test two hypotheses about the organization of the eyespot pattern into independent dorsal-ventral and anterior-posterior modules, using a graphical modeling technique to examine patterns of eyespot covariation among and within wing surfaces in the butterfly Bicyclus anynana. Although there is a hierarchical and complex pattern of integration among eyespots, the results show a surprising mismatch between patterns of eyespot integration and the developmental and evolutionary eyespot units identified in previous empirical studies. These results are discussed in light of the relationships between developmental, functional, and evolutionary modules, and they suggest that developmental sources of independent trait variation are often masked by developmental sources of trait integration.     

Perspective: network-guided pattern formation of neural dynamics

The understanding of neural activity patterns is fundamentally linked to an understanding of how the brain''s network architecture shapes dynamical processes. Established approaches rely mostly on deviations of a given network from certain classes of random graphs. Hypotheses about the supposed role of prominent topological features (for instance, the roles of modularity, network motifs or hierarchical network organization) are derived from these deviations. An alternative strategy could be to study deviations of network architectures from regular graphs (rings and lattices) and consider the implications of such deviations for self-organized dynamic patterns on the network. Following this strategy, we draw on the theory of spatio-temporal pattern formation and propose a novel perspective for analysing dynamics on networks, by evaluating how the self-organized dynamics are confined by network architecture to a small set of permissible collective states. In particular, we discuss the role of prominent topological features of brain connectivity, such as hubs, modules and hierarchy, in shaping activity patterns. We illustrate the notion of network-guided pattern formation with numerical simulations and outline how it can facilitate the understanding of neural dynamics.     

Linear patterns of Alzheimer's disease mutations along alpha-helices of presenilins as a tool for PS-1 model construction

We performed an analysis of mutation patterns in all 10 hydrophobic regions (HRs) of presenilin-1 (PS-1) and PS-2 using a recent database of Alzheimer's disease (AD) mutations. The linear patterns were confirmed and extended to areas spanning as many as three faces of a given HR. The complementary areas of residues free of AD mutations were identified based on the location of non-pathogenic polymorphisms and PS-1 versus PS-2 amino acid discordances. Taking into account the location of areas of AD mutations and mutation-free areas/regions, we proposed a preliminary model of PS-1 structure using a general stick-out-mutation rule. To build a molecular structure of PS-1 and preserve features of the preliminary model, we used bacteriorhodopsin template in homology/comparative modelling. Two molecular models were built differing in the location of C-terminal fragment helices. The models properly distinguish residues belonging to AD-affected sites and non-pathogenic areas, and may be used for classification purposes. They also comply with experimental results, such as differences in accessibility of the catalytic residues in uncleaved PS-1, and binding of PEN-2 by the PS-1 NF motif.     

The result of evolutionary limb loss on the complement of motor neurons in a crayfish limb nerve revealed by serial homology

Many macruran decapod crustaceans show sexual dimorphism of abdominal appendages adapted for use as secondary reproductive organs. Not only does the Australian crayfish, Cherax destructor, show no external, abdominal dimorphism, but both males and females have lost the pleopods of the first abdominal segment entirely. The first nerves of the abdominal ganglia of crayfish and lobsters carry the axons of the pleopod motor neurons. We used intracellular cobalt infusion into the first nerves of the first and second abdominal ganglia to reveal the motor neuron complement of these ganglia in males and females. The first nerves of the second abdominal ganglia of both males and females have approximately 37 motor neurons associated with them. The homologous nerves in the first abdominal segment, where there are no pleopods, have only 8 or 9 motor neurons associated with them. The evolutionary implications of this difference are discussed.     

The diapause decision as a cascade switch for adaptive developmental plasticity in body mass in a butterfly

Switch‐induced developmental plasticity, such as the diapause decision in insects, is a major form of adaptation to variable environments. As individuals that follow alternative developmental pathways will experience different selective environments the diapause decision may evolve to a cascade switch that induces additional adaptive developmental differences downstream of the diapause decision. Here, we show that individuals following alternative developmental pathways in a Swedish population of the butterfly, Pararge aegeria, display differential optimization of adult body mass as a likely response to predictable differences in thermal conditions during reproduction. In a more northern population where this type of selection is absent no similar difference in adult mass among pathways was found. We conclude that the diapause decision in the southern population appears to act as a cascade switch, coordinating development downstream of the diapause decision, to produce adult phenotypes adapted to the typical thermal conditions of their expected reproductive period.     

From Caenorhabditis elegans to the human connectome: a specific modular organization increases metabolic,functional and developmental efficiency

The connectome, or the entire connectivity of a neural system represented by a network, ranges across various scales from synaptic connections between individual neurons to fibre tract connections between brain regions. Although the modularity they commonly show has been extensively studied, it is unclear whether the connection specificity of such networks can already be fully explained by the modularity alone. To answer this question, we study two networks, the neuronal network of Caenorhabditis elegans and the fibre tract network of human brains obtained through diffusion spectrum imaging. We compare them to their respective benchmark networks with varying modularities, which are generated by link swapping to have desired modularity values. We find several network properties that are specific to the neural networks and cannot be fully explained by the modularity alone. First, the clustering coefficient and the characteristic path length of both C. elegans and human connectomes are higher than those of the benchmark networks with similar modularity. High clustering coefficient indicates efficient local information distribution, and high characteristic path length suggests reduced global integration. Second, the total wiring length is smaller than for the alternative configurations with similar modularity. This is due to lower dispersion of connections, which means each neuron in the C. elegans connectome or each region of interest in the human connectome reaches fewer ganglia or cortical areas, respectively. Third, both neural networks show lower algorithmic entropy compared with the alternative arrangements. This implies that fewer genes are needed to encode for the organization of neural systems. While the first two findings show that the neural topologies are efficient in information processing, this suggests that they are also efficient from a developmental point of view. Together, these results show that neural systems are organized in such a way as to yield efficient features beyond those given by their modularity alone.     

Evidence for the classification of a crayfish pathogen as a member of the genus Coxiella

AIMS: The study aimed to provide characterization of a potential new species of Coxiella, identified following a series of outbreaks of disease in Australian native freshwater crayfish. METHODS AND RESULTS: PCR primers designed for amplification of Coxiella burnetii genes including 16S rDNA, com1 and sodB were used to amplify homologues in the Coxiella-like crayfish pathogen. Products were then cloned and sequenced. The organism demonstrated a high degree of sequence homology in the highly conserved 16S rDNA (96%) and sodB (99%) genes, as well as the Coxiella sp. specific com1 (100%) gene. Regions flanking the sodB coding sequence demonstrated homology to C. burnetii antioxidant AhpC/Tsa family protein and dihydrodipicolinate reductase gene. CONCLUSIONS: The degree of homology between the genes selected and flanking regions suggested the two organisms were sufficiently closely related to belong to the same genus. SIGNIFICANCE AND IMPACT OF THE STUDY: This study provided evidence for a potential new species in the currently monospecific genus Coxiella, with the only described member being C. burnetii, a category B biological warfare agent.     

Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology

In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework-natural selection and inheritance-the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification.     

Juvenile hormone as a mediator of plasticity in insect life histories

Insects display much variation in life histories mediated by juvenile hormone. We focus on the contribution of JH to variations in migratory life histories. In many migrants such as the large milkweed bug and the monarch butterfly, JH directly influences migratory flight and the relation between flight and reproduction (oogenesis-flight syndrome). In the true armyworm, JH regulates interactions among female calling, pheromone production, ovarian development, and migration with varying blends of structurally related forms of JH and JH acid. A role for JH also occurs in wing polymorphisms. Aphids regulate wing production via JH-mediated maternal effects; and in crickets, JH esterase modulates the JH influence on wing form. In addition, JH is implicated in wing muscle histolysis. The comprehensive Fairbairn model for JH regulation of wing polymorphisms in flight behavior predicts that JH action will depend on the mode of genetic control, whether single locus or polygenic. Our own studies of the soapberry bug, Jadera haematoloma, reveal a four-morph wing polymorphism in a species rapidly evolving on a new host plant. There are long- and short-winged forms, and the long-winged form displays three degrees of flight muscle histolysis. The polymorphism is subject to both genetic and environmental variations that are mediated by JH. Application of methoprene increases the frequency of the short-winged forms, but there is both within- and between-population genetic variation and genotype by environment interaction (plasticity) in the response to JH. Arch. Insect Biochem. Physiol. 35:359–373, 1997. © 1997 Wiley-Liss, Inc.     

Analysis of a summary network of co-infection in humans reveals that parasites interact most via shared resources

Simultaneous infection by multiple parasite species (viruses, bacteria, helminths, protozoa or fungi) is commonplace. Most reports show co-infected humans to have worse health than those with single infections. However, we have little understanding of how co-infecting parasites interact within human hosts. We used data from over 300 published studies to construct a network that offers the first broad indications of how groups of co-infecting parasites tend to interact. The network had three levels comprising parasites, the resources they consume and the immune responses they elicit, connected by potential, observed and experimentally proved links. Pairs of parasite species had most potential to interact indirectly through shared resources, rather than through immune responses or other parasites. In addition, the network comprised 10 tightly knit groups, eight of which were associated with particular body parts, and seven of which were dominated by parasite–resource links. Reported co-infection in humans is therefore structured by physical location within the body, with bottom-up, resource-mediated processes most often influencing how, where and which co-infecting parasites interact. The many indirect interactions show how treating an infection could affect other infections in co-infected patients, but the compartmentalized structure of the network will limit how far these indirect effects are likely to spread.     

Structural relationships of homologous proteins as a fundamental principle in homology modeling

Protein structure prediction is based mainly on the modeling of proteins by homology to known structures; this knowledgebased approach is the most promising method to date. Although it is used in the whole area of protein research, no general rules concerning the quality and applicability of concepts and procedures used in homology modeling have been put forward yet. Therefore, the main goal of the present work is to provide tools for the assessment of accuracy of modeling at a given level of sequence homology. A large set of known structures from different conformational and functional classes, but various degrees of homology was selected. Pairwise structure superpositions were performed. Starting with the definition of the structurally conserved regions and determination of topologically correct sequence alignments, we correlated geometrical properties with sequence homology (defined by the 250 PAM Dayhoff Matrix) and identity. It is shown that both the topological differences of the protein backbones and the relative positions of corresponding side chains diverge with decreasing sequence identity. Below 50% identity, the deviation in regions that are structurally not conserved continually increases, thus implying that with decreasing sequence identity modeling has to take into account more and more structurally diverging loop regions that are difficult to predict. © 1993 Wiley-Liss, Inc.     

Cell signaling as a cognitive process

Cellular identity as defined through morphology and function emerges from intracellular signaling networks that communicate between cells. Based on recursive interactions within and among these intracellular networks, dynamical solutions in terms of biochemical behavior are generated that can differ from those in isolated cells. In this way, cellular heterogeneity in tissues can be established, implying that cell identity is not intrinsically predetermined by the genetic code but is rather dynamically maintained in a cognitive manner. We address how to experimentally measure the flow of information in intracellular biochemical networks and demonstrate that even simple causality motifs can give rise to rich, context‐dependent dynamic behavior. The concept how intercellular communication can result in novel dynamical solutions is applied to provide a contextual perspective on cell differentiation and tumorigenesis.     

用距离几何算法和同源建模法对水稻类金属硫蛋白（rgMT）的三维结构建模

水稻类金属硫蛋白(rgMT)的两端是高度保守的半胱氨酸富含区的结构域(CR区),中间是不含半胱氨酸的间隔区,呈典型的三段式结构。本研究分别采用距离几何算法和同源建模相结合的方法对水稻类金属硫蛋白进行三级结构建模。在排列出CR区的所有可能的半胱氨酸-金属硫络合的组合方式,并对每一种组合方式给出一定的限制条件后各生成20个随机构象。根据生成的随机构象足否能形成金属硫络合结构,从900个随机构象中最终选出6个构象(N端4种,C端2种组合)作为可能的结构模型。另一方面,采用GOR方法对间隔区进行了二级结构预测,随后用同源建模法对其建模。将上述建成的三部分模型连接起来后形成rgMT的整体三维构象。结果表明rgMT能像哺乳动物MT蛋白一样,可形成两个独立的、在结构和能量上均没有障碍的金属-硫络合结构。介于所有植物类金属硫蛋白都具有典型的三段式结构,其中的一部分还具有与rgMT相同的半胱氨酸排列方式,所以rgMT三维结构模型的建立对于其他植物类金属硫蛋白的结构研究具有重要的参考价值。     

Rearrangement of light harvesting bacteriochlorophyll homologues as a response of green sulfur bacteria to low light intensities

The pigment composition of two species of green-colored BChl c-containing green sulfur bacteria (Chlorobium limicola and C. chlorovibrioides) and two species of brown-colored BChl e-containing ones (C. phaeobacteroides and C. phaeovibrioides) incubated at different light intensities have been studied. All species responded to the reduction of light intensity from 50 to 1 Einstein(E) m^–2 s^–1 by an increase in the specific content of light harvesting pigments, bacteriochlorophylls and carotenoids. At critical light intensities (0.5 to 0.1 E m^–2 s^–1) only brown-colored chlorobia were able to grow, though at low specific rates (0.002 days^–1 mg prot^–1). High variations in the relative content of farnesyl-bacteriochlorophyll homologues were found, in particular BChl e ₁ and BChl e ₄, which were tentatively identified as [M, E] and [I, E] BChl_F e, respectively. The former was almost completely lost upon reduction of light intensity from 50 to 0.1 E m^–2 s^–1, whereas the latter increased from 7.2 to 38.4% and from 13.6 to 42.0% in C. phaeobacteroides and C. phaeovibrioides, respectively. This increase in the content of highly alkylated pigment molecules inside the chlorosomes of brown species is interpreted as a physiological mechanism to improve the efficiency of energy transfer towards the reaction center. This study provides some clues for understanding the physiological basis of the adaptation of brown species to extremely low light intensities.Abbreviations BChl bacteriochlorophyll - [M, E] BChl_F e 8-methyl, 12-ethyl BChl e, esterified with farnesol (F). Analogously: I - isobutyl - Pr propyl - Car carotenoids - Chlb chlorobactene - HPLC high performance liquid chromatography - Isr isorenieratene - LHP light harvesting pigments - PDA photodiode array detector - RC reaction center - RCH relative content of homologues     

Properties of a unique mutant of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus that exhibits a partial many polyhedra and few polyhedra phenotype on extended serial passaging in suspension cell cultures

Summary Serial passaging of wild-type Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HaSNPV) in H. zea (Hz-AM1) insect cell cultures results in rapid selection for the few polyhedra (FP) phenotype. A unique HaSNPV mutant (ppC19) was isolated through plaque purification that exhibited a partial many polyhedra (MP) and FP phenotype. On serial passaging in suspension cell cultures, ppC19 produced fivefold more polyhedra than a typical FP mutant (FP8AS) but threefold less polyhedra than the wild-type virus. Most importantly, the polyhedra of ppC19 exhibited MP-like virion occlusion. Furthermore, ppC19 produced the same amount of budded virus (BV) as the FP mutant, which was fivefold higher than that of the wild-type virus. This selective advantage was likely to explain its relative stability in polyhedra production for six passages when compared with the wild-type virus. However, subsequent passaging of ppC19 resulted in a steep decline in both BV and polyhedra yields, which was also experienced by FP8AS and the wild-type virus at high passage numbers. Genomic deoxyribonucleic acid profiling of the latter suggested that defective interfering particles (DIPs) were implicated in this phenomenon and represented another undesirable mutation during serial passaging of HaSNPV. Hence, a strategy to isolate HaSNPV clones that exhibited MP-like polyhedra production but FP-like BV production, coupled with low multiplicities of infection during scale-up to avoid accumulation of DIPs, could prove commercially invaluable.     

From phenotype to gene: Detecting disease-specific gene functional modules via a text-based human disease phenotype network construction

Currently, some efforts have been devoted to the text analysis of disease phenotype data, and their results indicated that similar disease phenotypes arise from functionally related genes. These related genes work together, as a functional module, to perform a desired cellular function. We constructed a text-based human disease phenotype network and detected 82 disease-specific gene functional modules, each corresponding to a different phenotype cluster, by means of graph-based clustering and mapping from disease phenotype to gene. Since genes in such gene functional modules are functionally related and cause clinically similar diseases, they may share common genetic origin of their associated disease phenotypes. We believe the investigation may facilitate the ultimate understanding of the common pathophysiologic basis of associated diseases.     

Identification of Drosophila melanogaster RECQE as a member of a new family of RecQ homologues that is preferentially expressed in early embryos

We describe the isolation of a new type of RecQ homologue in Drosophila melanogaster, RECQE. The Recqe gene consists of five exons and four introns, and encodes a protein of 1058 amino acids with a predicted molecular weight of 120,000 Da. The RECQE protein has seven helicase motifs. The helicase domain shows 42% identity overall to that of Escherichia coli RecQ DNA helicase, and is most closely related to Homo sapiens RecQL5 and Caenorhabditis elegans E03A3.2. The C-terminal region of RECQE protein is unique and the longest known among members of the RecQ superfamily. We demonstrate that the RECQE protein has DNA helicase activity and that the C-terminal region is dispensable for this activity. The RECQE mRNA accumulates in oocytes and is expressed at high levels in early embryos. We show for the first time that the expression of a RecQ homologue is developmentally regulated in embryos. These data suggest that the DNA helicase activity of RECQE might be involved in the DNA metabolism of early embryos. Received: 10 September 1999 / Accepted: 30 November 1999