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PubMed1995

Consciousness and the natural method.

'Consciousness' is a superordinate term for a heterogeneous array of mental state types. The types share the property of 'being experienced' or 'being experiences'--'of there being something that it is like for the subject to be in one of these states.' I propose that we can only build a theory of consciousness by deploying 'the natural method' of coordinating all relevant informational resources at once, especially phenomenology, cognitive science, neuroscience and evolutionary biology. I'll provide two examples of the natural method in action in mental domains where an adaptationist evolutionary account seems plausible: (i) visual awareness and (ii) conscious event memory. Then I will discuss a case, (iii), dreaming, where I think no adaptationist evolutionary account exists. Beyond whatever interest the particular cases have, the examination will show why I think that a theory of mind, and the role conscious mentation plays in it, will need to be built domain-by-domain with no a priori expectation that there will be a unified account of the causal role or evolutionary history of different domains and competences.

Animals↗
PubMed1996

Lateral asymmetries in infancy: implications for the development of the hemispheres.

Cerebral asymmetry of cognitive processing of stimulus information is commonly viewed as a neocortical phenomenon. However, a number of lines of evidence give innate asymmetry of brainstem motivating systems, which anticipate experience, a key role. Spontaneous asymmetries of gesture and emotion can be observed in infants, who entirely lack language and visuo-constructive skills. Motives for communication in early life may direct subsequent development of complementary cognitive systems in left and right hemispheres. In split-brain monkeys, lateralized motive sets, intentions for manipulation by one hand, can determine which hemisphere will see and learn. Evolutionary antecedents of cerebral asymmetry appear to affect motivation, social signalling and bimanual coordination, with secondary effect in perceptual processing and learning. The hemispheres of adult humans differ in links with neurochemical system that regulate motor initiatives, exploration and attention, and the approach/withdrawal balance in social encounters. Asymmetries in emotional and communicative behaviour in infancy support evidence that an Intrinsic Motive Formation emerging in the embryo human brain stem regulates asymmetries in development and in functioning of the cerebral cortex.

Cerebral Cortex↗
PubMed2006

Eukaryotic transcription factors in plastids--Bioinformatic assessment and implications for the evolution of gene expression machineries in plants.

The expression of genes in higher plant chloroplasts includes a complex transcriptional regulation which can be explained only in part with the action of the actually known components of the transcriptional machinery. This suggests the existence of still unknown important regulatory factors which influence chloroplast transcription. In order to test if such factors could exist we performed in silico analyses of Arabidopsis genes encoding putative transcription factors looking for putative N-terminal chloroplast transit peptides in the amino acid sequences. Our results suggest that 48 (and maybe up to 100) transcription factors of eukaryotic origin are likely to be imported into plastids. None of them has been described yet. This set of transcription factors highly expands the actually known regulation capacity of the chloroplast transcription machinery and provides a possible explanation for the complex initiation patterns of chloroplast transcripts. As consequence of a massive import of eukaryotic transcription factors a comprehensive reconstruction of the ancient prokaryotic gene expression machinery must be assumed resulting in a novel compatible combination of eukaryotic and prokaryotic protein components. In turn, the opposite process has been induced in the nucleus by the integration of prokaryotic components of the plastid ancestor via its loss of genes during endosymbiosis. Thus, a mutual exchange of regulatory factors, i.e. transcription factors occurred which resulted in the unique signalling network of today's plants. An evolutionary model of how this could have emerged during endosymbiosis in a timely coordinated manner is proposed.

Arabidopsis↗
PubMed1997

Changes in multiple brain regions underlie species differences in a complex, congenital behavior.

The evolutionary brain modifications that produce any complex, congenital behavioral difference between two species have never been identified. Evolutionary processes may (i) alter a single, "higher" brain area that generates and/or coordinates the diverse motor components of a complex act; (ii) separately change independent, "lower" brain areas that modulate the fine motor control of the individual components; or (iii) modify both types of areas. This study explores the brain localization of a species difference in one such behavior, the crowing of chickens (Gallus gallus domesticus) and Japanese quail (Coturnix coturnix japonica). Two major subcomponents of the behavioral difference can be independently transferred with interspecies transplantation of separate brain regions, despite the fact that these components, sound and patterned head movement, occur together in a highly integrated fashion. To our knowledge, this is the first experimental demonstration that species differences in a complex behavior are built up from separate changes to distinct cell groups in different parts of the brain and that these cell groups have independent effects on individual behavioral components.

Animals↗
PubMed2006

How to be early flowering: an evolutionary perspective.

In wild and cultivated annual plant species, flowering time is an important life-history trait that coordinates the life cycle with local environmental conditions. Extensive studies on the genetic basis of flowering time in the model species Arabidopsis thaliana have revealed a complex genetic network that can detect environmental and internal signals. Based on this knowledge and on known pleiotropic effects associated with flowering time genes, we suggest that a natural shift towards an early-flowering life cycle might involve only particular functional regions in a limited number of genes. Our predictions are supported by genetic theories of adaptation and by recent data about genes associated with natural variation. We analyse the extent to which these predictions can also apply to crop species.

Adaptation, Biological↗
PubMed2026

Characterization and functional insights of histone deacetylases in bivalves: implications for temperature and immune response in Chlamys nobilis.

Histone deacetylases serve as pivotal epigenetic regulators that modulate chromatin remodeling and gene transcription, playing critical roles in immune defense and environmental stress responses in aquatic organisms. However, the evolutionary characteristics and functional roles of the HDAC family in bivalves remain poorly understood. In this study, genome-wide identification of the HDAC family across 30 bivalve species yielded 558 HDAC genes. Phylogenetic reconstruction categorized these genes into four conserved groups and revealed a unique, bivalve-specific SIRT8 clade. Using the noble scallop Chlamys nobilis as a representative model, expression profiling revealed distinct expression patterns among CnHDAC members. Class I and most Class III members were predominantly expressed in the gonads, while Class II members were enriched in immune-related tissues, implying their potential involvement in bivalve immunity. Upon temperature stress, CnHDAC1/2, CnHDAC11-1, CnHDAC11-2, CnSIRT2-1, CnSIRT4, CnSIRT6, and CnSIRT8-3 were significantly induced, highlighting their critical roles in temperature adaptation. Upon Vibrio exposure, CnHDAC1/2, CnHDAC8, CnSIRT4, and CnSIRT6 were upregulated, while CnHDAC4/5/7/9, CnHDAC6/10, CnSIRT2-2, CnSIRT5, CnSIRT7, and CnSIRT8-3 were downregulated, suggesting a coordinated epigenetic regulatory mechanism underlying host immune defense. In conclusion, this study systematically elucidates the evolutionary landscape of the HDAC family and underscores its potential involvement in environmental resilience and host immunity, providing a theoretical basis for the breeding of disease-resistant and stress-tolerant aquaculture bivalves.

Animals↗
PubMed1991

Differential distribution of beta-pigment-dispersing hormone (beta-PDH)-like immunoreactivity in the stomatogastric nervous system of five species of decapod crustaceans.

Pigment-dispersing hormone (PDH) acts to disperse pigments within the chromatophores of crustaceans. Using an antibody raised against beta-PDH from the fiddler crab Uca pugilator, we characterized the distribution of beta-PDH-like immunoreactivity in the stomatogastric nervous system of five decapod crustaceans: the crabs, Cancer borealis and Cancer antennarius, the lobsters, Panulirus interruptus and Homarus americanus, and the crayfish, Procambarus clarkii. No somata were stained in the stomatogastric ganglion (STG) or the esophageal ganglion in any of these species. Intense PDH-like staining was seen in the neuropil of the STG in P. interruptus only. In all 5 species, cell bodies, processes, and neuropil within the paired circumesophageal ganglia (CGs) showed PDH-like staining; the pattern of this staining was unique for each species. In each CG, the beta-PDH antibody stained: 1 large cell in C. borealis; 3 small to large cells in C. antennarius; 3-8 medium cells in P. clarkii; 1-4 small cells in H. americanus; and 13-17 small cells in P. interruptus. The smallest cell in each CG in C. antennarius sends its axon, via the inferior esophageal nerves, into the opposite CG; this pair of cells, not labeled in the other species studied, may act as bilateral coordinators of sensory or motor function. These diverse staining patterns imply some degree of evolutionary diversity among these crustaceans. A beta-PDH-like peptide may act as a neuromodulator of the rhythms produced by the stomatogastric nervous system of decapod crustaceans.

Animals↗
PubMedDate not supplied

Timekeeping in genetically programmed aging.

Genetically programmed aging, with its cellular genetic switching implied by the in vitro Hayflick limit, requires additional timing devices to coordinate the switching processes within the different cells of a highly complex life form. Evolutionary arguments have been presented elsewhere to support the need for a centralized timing mechanism as against a localized mean-field alternative. Extensive evidence is now available for the role of the pineal gland and its secreted melatonin in the aging process. The nightly melatonin peak changes with age, thus providing a potential signal to inform all of the cells in the organism of its age. Here it is hypothesized that the decoding of this "durational signal" at the cellular level is carried out with the aid of the sleep induced pCO2 changes in the blood. To test this hypothesis, modifications of the in vitro Hayflick experiment and of the in vivo Pierpaoli longevity experiment involving rhythmic addition of melatonin and pH manipulations are proposed.

Aging↗
PubMed1998

Integrated defense system overlaps as a disease model: with examples for multiple chemical sensitivity.

The central nervous, immune, and endocrine systems communicate through multiple common messengers. Over evolutionary time, what may be termed integrated defense system(s) (IDS) have developed to coordinate these communications for specific contexts; these include the stress response, acute-phase response, nonspecific immune response, immune response to antigen, kindling, tolerance, time-dependent sensitization, neurogenic switching, and traumatic dissociation (TD). These IDSs are described and their overlap is examined. Three models of disease production are generated: damage, in which IDSs function incorrectly; inadequate/inappropriate, in which IDS response is outstripped by a changing context; and evolving/learning, in which the IDS learned response to a context is deemed pathologic. Mechanisms of multiple chemical sensitivity (MCS) are developed from several IDS disease models. Model 1A is pesticide damage to the central nervous system, overlapping with body chemical burdens, TD, and chronic zinc deficiency; model 1B is benzene disruption of interleukin-1, overlapping with childhood developmental windows and hapten-antigenic spreading; and model 1C is autoimmunity to immunoglobulin-G (IgG), overlapping with spreading to other IgG-inducers, sudden spreading of inciters, and food-contaminating chemicals. Model 2A is chemical and stress overload, including comparison with the susceptibility/sensitization/triggering/spreading model; model 2B is genetic mercury allergy, overlapping with: heavy metals/zinc displacement and childhood/gestational mercury exposures; and model 3 is MCS as evolution and learning. Remarks are offered on current MCS research. Problems with clinical measurement are suggested on the basis of IDS models. Large-sample patient self-report epidemiology is described as an alternative or addition to clinical biomarker and animal testing.

Acute-Phase Reaction↗
PubMed1989

Visuomotor coordination in reaching and locomotion.

Locomotion and reaching have traditionally been regarded as separate motor activities. In fact, they may be closely connected both from an evolutionary and a neurophysiological viewpoint. Reaching seems to have evolved from the neural systems responsible for the active and precise positioning of the limb during locomotion; moreover, it seems to be organized in the spinal cord. The motor cortex and its corticospinal outflow are preferentially engaged when precise positioning of the limb is needed during locomotion and are also involved during reaching and active positioning of the hand near objects of interest. All of these motor activities require visuomotor coordination, and it is this coordination that could be achieved by the motor cortex and interconnected parietal and cerebellar areas.

Animals↗
PubMed2000

Phylogeny of the restriction endonuclease-like superfamily inferred from comparison of protein structures.

To date all attempts to derive a phyletic relationship among restriction endonucleases (ENases) from multiple sequence alignments have been limited by extreme divergence of these enzymes. Based on the approach of Johnson et al. (1990), I report for the first time the evolutionary tree of the ENase-like protein superfamily inferred from quantitative comparison of atomic coordinates of structurally characterized enzymes. The results presented are in harmony with previous comparisons obtained by crystallographic analyses. It is shown that lambda-exonuclease initially diverged from the common ancestor and then two "endonucleolytic" families branched out, separating "blunt end cutters" from "5' four-base overhand cutters." These data may contribute to a better understanding of ENases and encourage the use of structure-based methods for inference of phylogenetic relationship among extremely divergent proteins. In addition, the comparison of three-dimensional structures of ENase-like domains provides a platform for further clustering analyses of sequence similarities among different branches of this large protein family, rational choice of homology modeling templates, and targets for protein engineering.

Catalytic Domain↗
PubMed2006

Johannes Reinke (1839-1931) and his "Dominanten" theory--an early concept of gene regulation and morphogenesis.

Johannes Reinke (1839-1931) was one of the most eminent and influential botanists, politician, philosopher and "anti-Haeckelist" of the 19th century. Educated in the mid 19th century he had faced revolutionary changes in the scientific understanding of the origin and evolution of life. Working mainly at the phenotypic level, Reinke was interested in the basic mechanisms and the guiding idea behind all processes which coordinated gene regulation and morphogenesis. What drove Reinke in his search of regulatory mechanisms for evolutionary patterns and processes was his religious belief. For the origin of the very first life, Reinke believed in creation but once life was established, evolution followed natural laws. This led to his early concept of "Dominanten" entities, which regulate gene transcription and morphogenesis, anticipating the ideas of Goldschmidt and v. Uexküll.

Animals↗
PubMed2006

Role of the [2Fe-2S]2+ cluster in biotin synthase: mutagenesis of the atypical metal ligand arginine 260.

Biotin synthase (BS) is an S-adenosylmethionine (AdoMet)-dependent radical enzyme that catalyzes the addition of sulfur to dethiobiotin. Like other AdoMet radical enzymes, BS contains a [4Fe-4S] cluster that is coordinated by a highly conserved CxxxCxxC sequence motif and by the methionyl amine and carboxylate of AdoMet. The close association of the [4Fe-4S]+ cluster with AdoMet facilitates reductive cleavage of the sulfonium and the generation of transient 5'-deoxyadenosyl radicals, which are then proposed to sequentially abstract hydrogen atoms from the substrate to produce carbon radicals at C9 and C6 of dethiobiotin. BS also contains a [2Fe-2S]2+ cluster located approximately 4-5 A from dethiobiotin, and we have proposed that a bridging sulfide of this cluster quenches the substrate radicals, leading to formation of the thiophane ring of biotin. In BS from Escherichia coli, the [2Fe-2S]2+ cluster is coordinated by cysteines 97, 128, and 188, and the atypical metal ligand, arginine 260. The evolutionary conservation of an arginine guanidinium as a metal ligand suggests a novel role for this residue in tuning the reactivity or stability of the [2Fe-2S]2+ cluster. In this work, we explore the effects of mutagenesis of Arg260 to Ala, Cys, His, and Met. Although perturbations in a number of characteristics of the [2Fe-2S]2+ cluster and the proteins are noted, the reconstituted enzymes have in vitro single-turnover activities that are 30-120% of that of the wild type. Further, in vivo expression of each mutant enzyme was sufficient to sustain growth of a bioB- mutant strain on dethiobiotin-supplemented medium, suggesting the enzymes were active and efficiently reconstituted by the in vivo iron-sulfur cluster (ISC) assembly system. Although we cannot exclude an as-yet-unidentified in vivo role in cluster repair or retention, we can conclude that Arg260 is not essential for the catalytic reaction of BS.

Amino Acid Sequence↗
PubMed2004

Hydrophobic interactions drive ligand-receptor recognition for activation and inhibition of staphylococcal quorum sensing.

Two-component systems represent the most widely used signaling paradigm in living organisms. Encoding the prototypical two-component system in Gram-positive bacteria, the staphylococcal agr (accessory gene regulator) operon uses a polytopic receptor, AgrC, activated by an autoinducing peptide (AIP), to coordinate quorum sensing with the global synthesis of virulence factors. The agr locus has undergone evolutionary divergence, resulting in the formation of several distinct inter- and intraspecies specificity groups, such that most cross-group AIP-receptor interactions are mutually inhibitory. We have exploited this natural diversity by constructing and analyzing AgrC chimeras generated by exchange of intradomain segments between receptors of different agr groups. Functional chimeras fell into three general classes: receptors with broadened specificity, receptors with tightened specificity, and receptors that lack activation specificity. Testing of these chimeric receptors against a battery of AIP analogs localized the primary ligand recognition site to the receptor distal subdomain and revealed that the AIPs bind primarily to a putative hydrophobic pocket in the receptor. This binding is mediated by a highly conserved hydrophobic patch on the AIPs and is an absolute requirement for interactions in self-activation and cross-inhibition of the receptors. It is suggested that this recognition scheme provides the fundamental basis for agr activation and interference.

Amino Acid Sequence↗
PubMed1999

Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts.

Prior studies of a broad array of seed plants have reported strong correlations among leaf life span, specific leaf area, nitrogen concentration, and carbon assimilation rates, which have been interpreted as evidence of coordinated leaf physiological strategies. However, it is not known whether these relationships reflect patterns of evolutionary convergence, or whether they are due to contrasting characteristics of major seed plant lineages. We reevaluated a published data set for these seven traits measured in over 100 species, using phylogenetic independent contrasts calculated over a range of alternative seed plant phylogenies derived from recent molecular systematic analyses. In general, pairwise correlations among these seven traits were similar with and without consideration of phylogeny, and results were robust over a range of alternative phylogenies. We also evaluated relationships between these seven traits and lamina area, another important aspect of leaf function, and found moderate correlations with specific leaf area (0.64), mass-based photosynthesis (0.54), area-based nitrogen (-0.56), and leaf life span (-0.42). However, several of these correlations were markedly reduced using independent contrasts; for example, the correlation between leaf life span and lamina area was reduced to close to zero. This change reflects the large differences in both these traits between conifers and angiosperms and the absence of a relationship between the traits within these groups. This analysis illustrates that most interspecific relationships among leaf functional traits, considered across a broad range of seed plant taxa, reflect significant patterns of correlated evolutionary change, lending further support to the adaptive interpretation of these relationships.

Journal Article↗
PubMed2002

Elucidation of primary (alpha(3)N) and vestigial (alpha(5)) heavy metal-binding sites in Staphylococcus aureus pI258 CadC: evolutionary implications for metal ion selectivity of ArsR/SmtB metal sensor proteins.

Despite a common evolutionary origin, individual members of the ArsR/SmtB family of bacterial metal-responsive transcriptional repressors sense a wide range of heavy-metal ions. The molecular basis for this metal ion selectivity is unclear. Here, we establish that Staphylococcus aureus plasmid pI258 CadC, a Cd(II)/Pb(II)/Bi(III)/Zn(II) sensor, contains two distinct metal-binding sites: a thiolate-rich alpha(3)N site comprised exclusively of cysteine ligands that preferentially binds larger, softer metal ions such as Cd(II), Pb(II) and Bi(III); and a second C-terminal alpha(5) site, found at the dimer interface, that is devoid of cysteine ligands and preferentially binds smaller, harder metal ions [Co(II) and Zn(II)] concurrently with metal binding to the alpha(3)N site. Optical absorption and X-ray spectroscopies reveal that the alpha(3)N site can adopt distinct coordination geometries in order to accommodate different metal ions, i.e. Cd(II), Bi(III), Co(II) and Zn(II) form distorted tetrahedral S(4) complexes, while Pb(II) adopts a trigonal S(3) complex. Characterization of mutant CadCs reveals that the alpha(3)N site is composed of Cys58 and Cys60 from the alpha(3) helix of the helix-turn-helix DNA-binding domain and Cys7 and/or Cys11 from the N-terminal "arm" of CadC; Cys11 is excluded from the Pb(II) coordination sphere. Only the thiolate-rich alpha(3)N site is metalloregulatory for repressor binding to a fluorescein-labeled cad O/P oligonucleotide upon coordination to Cd(II), Pb(II), Bi(III), Zn(II), and weakly for Co(II). Substitution of Cys60 and Cys7 with non-ligating residues specifically abrogates metal-dependent negative regulation of cad O/P binding, despite the fact that C60G and C7G CadCs maintain high affinity for metals in altered coordination complexes. These findings reveal that formation of metal coordination bonds to Cys7 and Cys60 play primary roles in transducing the allosteric response in CadC. The evolutionary implications for metal ion selectivity of ArsR/SmtB metal sensor proteins are discussed.

Allosteric Regulation↗
PubMed2006

Metazoan OXPHOS gene families: evolutionary forces at the level of mitochondrial and nuclear genomes.

Mitochondrial and nuclear DNAs contribute to encode the whole mitochondrial protein complement. The two genomes possess highly divergent features and properties, but the forces influencing their evolution, even if different, require strong coordination. The gene content of mitochondrial genome in all Metazoa is in a frozen state with only few exceptions and thus mitochondrial genome plasticity especially concerns some molecular features, i.e. base composition, codon usage, evolutionary rates. In contrast the high plasticity of nuclear genomes is particularly evident at the macroscopic level, since its redundancy represents the main feature able to introduce genetic material for evolutionary innovations. In this context, genes involved in oxidative phosphorylation (OXPHOS) represent a classical example of the different evolutionary behaviour of mitochondrial and nuclear genomes. The simple DNA sequence of Cytochrome c oxidase I (encoded by the mitochondrial genome) seems to be able to distinguish intra- and inter-species relations between organisms (DNA Barcode). Some OXPHOS subunits (cytochrome c, subunit c of ATP synthase and MLRQ) are encoded by several nuclear duplicated genes which still represent the trace of an ancient segmental/genome duplication event at the origin of vertebrates.

Animals↗
PubMed1997

Analysis of the reaction coordinate of photosynthetic water oxidation by kinetic measurements of 355 nm absorption changes at different temperatures in photosystem II preparations suspended in either H2O or D2O.

Flash-induced absorption changes at 355 nm were measured at different temperatures within the range of 2 degrees C </= theta </= 25 degrees C in dark-adapted PS II core complexes from spinach [O2 evolution rate: 1500 +/- 100 micromol of O2 (mg of Chl)-1 h-1] that were dissolved either in H2O- or in D2O-containing buffer. Comparative measurements were performed at 20 degrees C in H2O- or D2O-containing suspensions of PS II membrane fragments [O2 evolution rate: 600 +/- 40 micromol of O2 (mg of Chl)-1 h-1]. The results obtained reveal the following: (a) The activation energies of the individual redox steps in the water oxidizing complex (WOC) are dependent on the redox state Si with EA(S1-->S2) = 14 kJ/mol, EA(S2-->S3) = 35 kJ/mol, and EA(S3-->-->S0 + O2) = 21 kJ/mol for theta > 11 degrees C, 67 kJ/mol for theta < 11 degrees C in PS II core complexes dissolved in H2O; (b) replacement of exchangeable protons by deuterons causes only minor changes (</=15%) of the activation energies; and (c) the rate constants of these reactions in PS II core complexes are characterized by H/D isotope ratios, ki(H)/ki(D), of 1.6, 2.3, and 1.5 for the transitions S1 --> S2, S2 --> S3, and S3 -->--> S0 + O2, respectively. The corresponding values of PS II membrane fragments are 1.3, 1.3, and 1. 4. Based on these results and corresponding EA data reported in the literature for PS II membrane fragments from spinach [Renger, G., & Hanssum, B. (1992) FEBS Lett. 299, 28-32] and PS II particles from the thermophilic cyanobacterium Synechococcus vulcanus Copeland [Koike, H., Hanssum, B., Inoue, Y., & Renger, G. (1987) Biochim. Biophys. Acta 893, 524-533], the reaction coordinate of the redox sequence in the WOC is inferred to be almost invariant to the evolutionary development from cyanobacteria to higher plants. Furthermore, the rather high activation energy of the S2 --> S3 transition provides evidence for a significant structural change coupled with this reaction. Implications for the mechanism of photosynthetic water oxidation are discussed.

Deuterium Oxide↗