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PubMed1993

Developmental analysis reveals labial and subradular ganglia and the primary framework of the nervous system in nudibranch gastropods.

Previous ultrastructural observations on late stage larvae of dorid nudibranchs (Gastropoda, Opisthobranchia) revealed two pairs of ganglia within the base of the foot that do not have obvious counterparts in existing descriptions of other gastropod larvae [Chia and Koss (1989). Cell Tiss. Res. 256:17-26.] One of these ganglionic pairs has been implicated in the initiation of settlement preceding metamorphosis [Arkett et al. (1989). Biol. Bull. 176:155-160.] By examining neurogenesis in sequential larval stages, I have found that the pattern of connectives and commissures associated with these enigmatic ganglia is comparable to patterns found in less consolidated adult nervous systems of chitons, monoplacophorans, and archaeogastropods. These comparative data suggest that the two pairs of ganglia in dorid nudibranch larvae are homologues of labial and subradular ganglia. The labial ganglia become incorporated into the cerebral ganglia at metamorphosis. In an attempt to integrate anatomical and developmental observations with behavioral and neurophysiological results, I suggest that receptor cells of the larval labial ganglia may become postmetamorphic primary mechanoreceptors of the oral tube, which have central cell bodies within the "cerebral" ganglia and which help coordinate feeding. Results of this study also address a larger evolutionary issue by questioning the traditional model of an ancestral molluscan nervous system that consists of four longitudinal nerve cords that arise from separate sites along a circumesophageal nerve ring. This pattern results from secondary connections in nudibranchs and possibly other molluscs. The primary condition of a single axon bundle emerging from each cerebral ganglion is more similar to the developing nervous system in polychaete annelids than what has been recognized previously.

Animals↗
PubMed2006

Sec2 is a highly efficient exchange factor for the Rab protein Sec4.

Sec2 is a reversibly membrane associated multi-domain protein with guanine nucleotide exchange activity towards the yeast Rab-protein Sec4. Both proteins are localized to secretory vesicles destined for exocytosis. We have used transient kinetic methods to show that Sec2 is a highly active exchange factor, in contrast to other proteins previously characterized as Rab exchange factors. With a K(d) value for the Sec2:Sec4.GDP interaction of ca 70 microM and a maximal rate of GDP displacement of ca 15 s(-1), it is 100-1000-fold more effective than other proteins showing exchange activity towards Rabs (MSS4, DSS4, Vps9) and ca tenfold faster than Cdc25 as a Ras specific exchanger, although still 100-fold slower than the fastest systems studied so far, EF-Tu/Ef-Ts and Ran/RCC1. A comparison with other proteins showing Rab exchange activity shows that maximal rates of GDP dissociation catalyzed by Sec2 are orders of magnitude faster. When comparing Sec2 with DSS4, which also acts on Sec4, the difference was particularly dramatic. Another difference is seen in the kinetics of association of GTP with the Sec4:Sec2 complex, a process which is extremely slow for DSS4/MSS4 complexes with cognate Rabs but in the range observed for other GTPase:exchanger complexes for Sec4:Sec2., It is suggested that systems such as Ef-Tu/Ef-Ts and Ran/RCC1 have evolved for maximal possible activity for the interaction between two soluble proteins, whereas other evolutionary constraints which are connected to the spatial and temporal coordination of events in vesicular transport and other regulatory networks have determined the detailed kinetic properties of the other systems.

GTP-Binding Proteins↗
PubMed2005

Structural evidence for a two-metal-ion mechanism of group I intron splicing.

We report the 3.4 angstrom crystal structure of a catalytically active group I intron splicing intermediate containing the complete intron, both exons, the scissile phosphate, and all of the functional groups implicated in catalytic metal ion coordination, including the 2'-OH of the terminal guanosine. This structure suggests that, like protein phosphoryltransferases, an RNA phosphoryltransferase can use a two-metal-ion mechanism. Two Mg2+ ions are positioned 3.9 angstroms apart and are directly coordinated by all six of the biochemically predicted ligands. The evolutionary convergence of RNA and protein active sites on the same inorganic architecture highlights the intrinsic chemical capacity of the two-metal-ion catalytic mechanism for phosphoryl transfer.

Cations, Divalent↗
PubMed2006

Evolutionary origins of leadership and followership.

Drawing upon evolutionary logic, leadership is reconceptualized in terms of the outcome of strategic interactions among individuals who are following different, yet complementary, decision rules to solve recurrent coordination problems. This article uses the vast psychological literature on leadership as a database to test several evolutionary hypotheses about the origins of leadership and followership in humans. As expected, leadership correlates with initiative taking, trait measures of intelligence, specific task competencies, and several indicators of generosity. The review finds no link between leadership and dominance. The evolutionary analysis accounts for reliable age, health, and sex differences in leadership emergence. In general, evolutionary theory provides a useful, integrative framework for studying leader-follower relationships and generates various novel research hypotheses.

Biological Evolution↗
PubMed2026

A spatiotemporal resolution to genetic redundancy: MIR164 diversification coordinates development and metabolism in Brassica.

Whole-genome duplication (WGD) events create genetic redundancy, posing the evolutionary challenge of how paralogs escape functional overlap to drive innovation. Here, we demonstrate that the MIR164 family in Brassica oleracea resolves this redundancy through spatiotemporal niche partitioning. Following WGD, the family expanded to eight members, which subsequently underwent divergent selection-some preserved under purifying selection, while others showed signals of positive selection. This led to expression divergence, with Bol-MIR164a1 emerging as a key universally expressed paralog. CRISPR-Cas9 mutagenesis of Bol-MIR164a1 revealed its essential role in coordinating two pivotal traits: leaf serration and leaf coloration. Mutants exhibited enhanced leaf serration due to spatial deregulation of CUC2 at organ boundaries, concurrently with yellow-green leaves and elevated flavonoid accumulation. We mechanistically linked the metabolic phenotype to direct transactivation of the anthocyanidin reductase (ANR) promoter by NAC100, alongside its upregulation of chlorophyll catabolism genes. Our findings establish a paradigm in which spatial segregation of target gene expression domains enables a single, widely expressed miRNA paralog to resolve genetic redundancy by independently orchestrating distinct regulatory programs. This provides a fundamental framework for understanding complex trait evolution in polyploids. This allows a single miRNA locus to independently orchestrate both morphological patterning and metabolic programming, providing a fundamental framework for understanding complex trait evolution in polyploid crops.

MicroRNAs↗
PubMedDate not supplied

[MtDNA-like sequences and the coordination of the functioning of mammalian nuclear and mitochondrial genomes].

Mitochondrial DNA-like sequences in the nuclear genome of mammals are classified in two types: ontogenetic and evolutionary. Mechanisms of the transfer of DNA from mitochondria into nucleus and transformation of the ontogenetic mtDNA-like sequences to evolutionary ones are discussed. The origin of short sequences of DNA common to nuclear and mitochondrial genome and the role of these sequences in the coordination of gene expression have received much attention.

Animals↗
PubMed2002

ECVAM-ICCVAM: prospects for future collaboration.

The level and complexity of testing for hazard and risk assessment of marketed products and environmental agents has increased substantially over time, resulting in the use of greater numbers of both animals and humans for testing. Today, industry and regulatory bodies worldwide face increasing pressures to demonstrate responsible utilisation of laboratory animals, to limit their use, and to employ alternative non-animal tests. Institutions have also been established to identify, encourage development of, conduct research on, and validate new, improved, and surrogate test methods that will reduce and replace animal use. Two such organisations are ECVAM and the Interagency Coordinating Committee for the Validation of Alternative Methods (ICCVAM). As the evolutionary changes occurring in the field of toxicology result in an unprecedented increase in the introduction of alternative methodologies, these will strain the capacities of such alternative methods institutions. That realisation is causing a shift in thinking and creating an impetus to seek approaches by which to collaborate and develop more-efficient operational procedures for the validation and regulatory acceptance of alternative methods. Similarities in objectives, functions, scientific standards, and commitment to the principles of validation and animal welfare support the value of a cooperative arrangement between ECVAM and ICCVAM, to minimise duplication of effort, maximise productivity, and influence the international adoption of alternative tests. Opportunities for ECVAM-ICCVAM collaboration are discussed, which illustrate the feasibility and potential benefits of such a partnership.

Animal Testing Alternatives↗
PubMed2004

SNAP: workbench management tool for evolutionary population genetic analysis.

UNLABELLED: The reconstruction of population processes from DNA sequence variation requires the coordinated implementation of several coalescent-based methods, each bound by specific assumptions and limitations. In practice, the application of these coalescent-based methods for parameter estimation is difficult because they make strict assumptions that must be verified a priori and their parameter-rich nature makes the estimation of all model parameters very complex and computationally intensive. A further complication is their distribution as console applications that require the user to navigate through console menus or specify complex command-line arguments. To facilitate the implementation of these coalescent-based tools we developed SNAP Workbench, a Java program that manages and coordinates a series of programs. The workbench enhances population parameter estimation by ensuring that the assumptions and program limitations of each method are met and by providing a step-by-step methodology for examining population processes that integrates both summary-statistic methods and coalescent-based population genetic models. AVAILABILITY: SNAP Workbench is freely available at http://snap.cifr.ncsu.edu. The workbench and tools can be downloaded for Mac, Windows and Unix operating systems. Each package includes installation instructions, program documentation and a sample dataset. SUPPLEMENTARY INFORMATION: A description of system requirements and installation instructions can be found at http://snap.cifr.ncsu.edu.

Computer Simulation↗
PubMed2002

Development and evolution of lateral line placodes in amphibians. - II. Evolutionary diversification.

The amphibian lateral line system develops from a series of lateral line placodes. The different phases of development from early induction, to pattern formation, differentiation, morphogenesis, and metamorphic fate were summarized in the first part of this review (Schlosser, 2002a). Here, a survey of the diversity of lateral line systems in amphibians is presented indicating that most phases of lateral line development have been subject to evolutionary changes. Several trends suggest important roles for both adaptive changes and internal constraints in amphibian lateral line evolution. Many of these trends involved the coordinated modification of different derivatives of lateral line placodes suggesting that these placodes are not only autonomous developmental modules, but also units of evolutionary variation that tend to be modified in a coherent and largely context-independent fashion.

Journal Article↗
PubMed1996

Molecular characterization of the 71E late puff in Drosophila melanogaster reveals a family of novel genes.

Early metamorphic development in Drosophila melanogaster is initiated by pulses of the steroid hormone ecdysone, which are transduced into tissue-specific transcriptional cascades. This process begins with the hormone-dependent activation of a set of transcription factors (early genes) that, in turn, activate set of tissue-specific effector genes (late genes). The 71E cytogenetic region of the salivary gland polytene genome contains several ecdysone-regulated transcription units. Molecular techniques were used to analyze these genes, their transcriptional program and their evolutionary relatedness. We find that this region contains a cluster of ten coordinately regulated late genes (L71 genes) that are organized as five divergently transcribed gene pairs. Maximum parsimony analysis suggests that an ancestral L71 gene duplicated to form the first gene pair which was, in turn, duplicated to form the set of gene pairs. The L71 gene products form a family of small, chemically basic proteins with a conserved backbone of cysteine residues. In addition, the 71E region contains another gene (I71-1) with the regulatory and biochemical characteristics of the salivary gland intermolt glue proteins.

Amino Acid Sequence↗
PubMed2001

Genomic and genetic dissection of an archaeal regulon.

The extremely halophilic archaeon Halobacterium sp. NRC-1 can grow phototrophically by means of light-driven proton pumping by bacteriorhodopsin in the purple membrane. Here, we show by genetic analysis of the wild type, and insertion and double-frame shift mutants of Bat that this transcriptional regulator coordinates synthesis of a structural protein and a chromophore for purple membrane biogenesis in response to both light and oxygen. Analysis of the complete Halobacterium sp. NRC-1 genome sequence showed that the regulatory site, upstream activator sequence (UAS), the putative binding site for Bat upstream of the bacterio-opsin gene (bop), is also present upstream to the other Bat-regulated genes. The transcription regulator Bat contains a photoresponsive cGMP-binding (GAF) domain, and a bacterial AraC type helix-turn-helix DNA binding motif. We also provide evidence for involvement of the PAS/PAC domain of Bat in redox-sensing activity by genetic analysis of a purple membrane overproducer. Five additional Bat-like putative regulatory genes were found, which together are likely to be responsible for orchestrating the complex response of this archaeon to light and oxygen. Similarities of the bop-like UAS and transcription factors in diverse organisms, including a plant and a gamma-proteobacterium, suggest an ancient origin for this regulon capable of coordinating light and oxygen responses in the three major branches of the evolutionary tree of life. Finally, sensitivity of four of five regulon genes to DNA supercoiling is demonstrated and correlated to presence of alternating purine-pyrimidine sequences (RY boxes) near the regulated promoters.

Amino Acid Sequence↗
PubMed1999

Localization in the nucleolus and coiled bodies of protein subunits of the ribonucleoprotein ribonuclease P.

The precise location of the tRNA processing ribonucleoprotein ribonuclease P (RNase P) and the mechanism of its intranuclear distribution have not been completely delineated. We show that three protein subunits of human RNase P (Rpp), Rpp14, Rpp29 and Rpp38, are found in the nucleolus and that each can localize a reporter protein to nucleoli of cells in tissue culture. In contrast to Rpp38, which is uniformly distributed in nucleoli, Rpp14 and Rpp29 are confined to the dense fibrillar component. Rpp29 and Rpp38 possess functional, yet distinct domains required for subnucleolar localization. The subunit Rpp14 lacks such a domain and appears to be dependent on a piggyback process to reach the nucleolus. Biochemical analysis suggests that catalytically active RNase P exists in the nucleolus. We also provide evidence that Rpp29 and Rpp38 reside in coiled bodies, organelles that are implicated in the biogenesis of several other small nuclear ribonucleoproteins required for processing of precursor mRNA. Because some protein subunits of RNase P are shared by the ribosomal RNA processing ribonucleoprotein RNase MRP, these two evolutionary related holoenzymes may share common intranuclear localization and assembly pathways to coordinate the processing of tRNA and rRNA precursors.

Amino Acid Sequence↗
PubMed2003

Rana computatrix to human language: towards a computational neuroethology of language evolution.

Walter's Machina speculatrix inspired the name Rana computatrix for a family of models of visuomotor coordination in the frog, which contributed to the development of computational neuroethology. We offer here an 'evolutionary' perspective on models in the same tradition for rat, monkey and human. For rat, we show how the frog-like taxon affordance model provides a basis for the spatial navigation mechanisms that involve the hippocampus and other brain regions. For monkey, we recall two models of neural mechanisms for visuomotor coordination. The first, for saccades, shows how interactions between the parietal and frontal cortex augment superior colliculus seen as the homologue of frog tectum. The second, for grasping, continues the theme of parieto-frontal interactions, linking parietal affordances to motor schemas in premotor cortex. It further emphasizes the mirror system for grasping, in which neurons are active both when the monkey executes a specific grasp and when it observes a similar grasp executed by others. The model of human-brain mechanisms is based on the mirror-system hypothesis of the evolution of the language-ready brain, which sees the human Broca's area as an evolved extension of the mirror system for grasping.

Adaptation, Physiological↗
PubMed2005

Perspectives on the molecular epidemiology of aerodigestive tract cancers.

Improving laboratory techniques and the greater availability of genetic data have led to a flurry of publications from molecular epidemiologic studies on aerodigestive tract cancers. Inconsistent results have been observed in studies of sequence variants, due to limitations such as small sample size, possible detection of false positives, moderate prior probabilities that each SNP confers a substantial increase in cancer risk, and publication bias. Meta- and pooled-analyses were shown to be effective in elucidating modest increases in aerodigestive tract cancer risk attributable to sequence variants. Phenotypic assays developed to quantify an individual's DNA repair capacity have been applied to epidemiological studies on aerodigestive tract cancers. Epigenetic events have also been studied in tumor progression and as susceptibility factors for aerodigestive tract cancers, in smaller scale studies. It is imperative that limitations of previous studies are addressed for future research in the molecular epidemiology of aerodigestive tract cancers. Some recommendations for future research are to: (i) incorporate multiple markers of different types (ex. genotype and phenotype data), (ii) enhance statistical power by conducting studies with larger sample size, and developing consortia to coordinate research efforts, (iii) improve marker selection via a hybrid strategy of incorporating data on evolutionary biology and physico-chemical properties of amino acids, with haplotype/tag SNP data, (iv) employ novel statistical methods such as hierarchical modeling with Bayesian adjustments, false positive reporting probability and modeling of complex pathways. Consortia have been initiated for head and neck cancer (International Head and Neck Cancer Epidemiology Consortium (INHANCE)) and lung cancer (International Lung Cancer Consortium (ILCCO)) with the aim to share comparable data, to focus on rare subgroups such as nonsmokers and to coordinate laboratory analyses. Such collaborative efforts and integration across disciplines will be essential in contributing to the elucidation of genetic susceptibility to aerodigestive tract cancers.

Carcinogens↗
PubMed1981

Linkage and evolutionary diversification of developmentally regulated multigene families: tandem arrays of the 401/18 chorion gene pair in silkmoths.

The coordinately expressed silkmoth chorion genes, 401 and 18, are closely linked as a pair, in divergent orientation. Analysis of overlapping clones (chromosomal "walk") demonstrated that each of the multiple copies of this gene pair is embedded within a larger deoxyribonucleic acid unit, which is tandemly repeated in a few arrays or possibly a single array. Southern analysis and examination of clones from a single individual moth demonstrated that the repeat units are extensively polymorphic in restriction sites, length, and possibly number, no differential amplification was evident during choriogenesis. Intron and 5'-flanking sequences were shown to be specific for the 401/18 gene pair and not to be present elsewhere in the genome. The spatial distribution of variations in the genes and their flanking sequences were examined.

Animals↗
PubMed1999

The simulated evolution of biochemical guilds: reconciling Gaia theory and natural selection.

Gaia theory, which states that organisms both affect and regulate their environment, poses an interesting problem to Neo-Darwinian evolutionary biologists and provides an exciting set of phenomena for artificial-life investigation. The key challenge is to explain the emergence of biotic communities that are capable, via their implicit coordination, of regulating large-scale biogeochemical factors such as the temperature and chemical composition of the biosphere, but to assume no evolutionary mechanisms beyond contemporary natural selection. Along with providing an introduction to Gaia theory, this article presents simulations of Gaian emergence based on an artificial-life model involving genetic algorithms and guilds of simple metabolizing agents. In these simulations, resource competition leads to guild diversity; the ensemble of guilds then manifests life-sustaining nutrient recycling and exerts distributed control over environmental nutrient ratios. These results illustrate that standard individual-based natural selection is sufficient to explain Gaian self-organization, and they help clarify the relationships between two key metrics of Gaian activity: recycling and regulation.

Algorithms↗
PubMed1998

Voluntary wheel running: a review and novel interpretation.

Voluntary wheel running by animals is an activity that has been observed and recorded in great detail for almost a century. This review shows that it is performed, often with startling intensity and coordination, by a wide variety of wild, laboratory and domestic species with diverse evolutionary histories. However, despite the plethora of published studies on wheel running, there is considerable disagreement between many findings, thus leading to a lack of consensus on explanations of the causality and function. In the initial part of this review, I discuss the internal and external factors that may be involved in the causality of this behaviour, with an emphasis on disparities in both the factual and theoretical development of the subject. I then address the various proposed functions of wheel running, again highlighting evidence to the contrary. This leads to the conclusion that any single theory on the basis of wheel running is likely to be simplistic with little generality. I then present a novel, behaviour-based interpretation in which it is argued that wheel running has no directly analogous naturally occurring behaviour, it is (sometimes) performed for its own sake per se rather than as a redirected or substitute activity, and studies on motivation show that wheel running is self-reinforcing and perceived by animals as 'important'. This review proposes that wheel running may be an artefact of captive environments or of the running-wheel itself, possibly resulting from feedback dysfunction. I also discuss the ubiquity and intensity of its performance, along with its great plasticity and maladaptiveness, all indicating that if it is an artefact, it is nevertheless one of great interest to behavioural science. Copyright 1998 The Association for the Study of Animal Behaviour.

Journal Article↗
PubMed1997

Identification of functional surfaces of the zinc binding domains of intracellular receptors.

Transcriptional regulatory factor complexes assemble on genomic response elements to control gene expression. To gain insights on the surfaces that determine this assembly in the zinc binding domains from intracellular receptors, we systematically analyzed the variations in sequence and function of those domains in the context of their invariant fold. Taking the intracellular receptor superfamily as a whole revealed a hierarchy of amino acid residues along the DNA interface that correlated with response element binding specificity. When only steroid receptors were considered, two additional sites appeared: the known dimer interface, and a novel putative interface suitably located to contact regulatory factors bound to the free face of palindromic response elements commonly used by steroid receptors. Surprisingly, retinoic acid receptors, not known to bind palindromic response elements, contain both of these surfaces, implying that they may dimerize at palindromic elements under some circumstances. This work extends Evolutionary Trace analysis of functional surfaces to protein-DNA interactions, suggests how coordinated exchange of trace residues may predictably switch binding specificity, and demonstrates how to detect functional surfaces that are not apparent from sequence comparison alone.

Amino Acid Sequence↗