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At least 145 records · Page 8Linked to original sources
PubMed2005

Evolution of sexual dimorphism and male dimorphism in the expression of beetle horns: phylogenetic evidence for modularity, evolutionary lability, and constraint.

Beetle horns are enlarged outgrowths of the head or thorax that are used as weapons in contests over access to mates. Horn development is typically confined to males (sexual dimorphism) and often only to the largest males (male dimorphism). Both types of dimorphism result from endocrine threshold mechanisms that coordinate cell proliferation near the end of the larval period. Here, we map the presence/absence of each type of dimorphism onto a recent phylogeny for the genus Onthophagus (Coleoptera: Scarabaeidae) to explore how horn development has changed over time. Our results provide empirical support for several recent predictions regarding the evolutionary lability of developmental thresholds, including uncoupled evolution of alternative phenotypes and repeated fixation of phenotypes. We also report striking evidence of a possible developmental constraint. We show that male dimorphism and sexual dimorphism map together on the phylogeny; whenever small males have horns, females also have horns (and vice versa). We raise the possibility that correlated evolution of these two phenomena results from a shared element in their endocrine regulatory mechanisms rather than a history of common selection pressures. These results illustrate the type of insight that can be gained only from the integration of developmental and evolutionary perspectives.

Animals↗
PubMed1989

Stereophotogrammetric analysis of occlusal morphology of extant hominoid molars: phenetics and function.

Because teeth are commonly preserved in the fossil record, dental remains have often been employed in estimating evolutionary relationships among fossil hominoids. This is appropriate, however, only to the extent that dental morphology is phylogenetically informative. I have used phenetic analytic techniques to assess whether hominoid molars are likely to be useful for phylogenetic inference. Thirty-four occlusal landmarks for first and second molars were chosen; seven on each maxillary and ten on each mandibular tooth. Three-dimensional locations of these points were determined from stereophotographs of dental arcades of more than 260 specimens from six taxa (gorilla, chimpanzee, human, orangutan, siamang, and gibbon). Analytic emphasis was on canonical variates analyses of landmark coordinates for mandibular and maxillary second molars, adjusted for intergroup size differences. There is little correspondence between the systematic implications of hominoid molar morphometrics and reliable estimates of evolutionary propinquity based on interhominoid biomolecular similarities. The former seem to have been determined largely by dietary constraints. Although this suggests the possibility of using the protocol employed here to infer diets of fossil hominoids, molar crown measurements seem unlikely to serve well as phylogenetic indicators in the Hominoidea.

Animals↗
PubMed2005

YB-1 coordinates vascular smooth muscle alpha-actin gene activation by transforming growth factor beta1 and thrombin during differentiation of human pulmonary myofibroblasts.

Profibrotic regulatory mechanisms for tissue repair after traumatic injury have developed under strong evolutionary pressure to rapidly stanch blood loss and close open wounds. We have examined the roles played by two profibrotic mediators, transforming growth factor beta1 (TGFbeta1) and thrombin, in directing expression of the vascular smooth muscle alpha-actin (SMalphaA) gene, an important determinant of myofibroblast differentiation and early protein marker for stromal cell response to tissue injury. TGFbeta1 is a well known transcriptional activator of the SMalphaA gene in myofibroblasts. In contrast, thrombin independently elevates SMalphaA expression in human pulmonary myofibroblasts at the posttranscriptional level. A common feature of SMalphaA up-regulation mediated by thrombin and TGFbeta1 is the involvement of the cold shock domain protein YB-1, a potent repressor of SMalphaA gene transcription in human fibroblasts that also binds mRNA and regulates translational efficiency. YB-1 dissociates from SMalphaA enhancer DNA in the presence of TGFbeta1 or its Smad 2, 3, and 4 coregulatory mediators. Thrombin does not effect SMalphaA gene transcription but rather displaces YB-1 from SMalphaA exon 3 coding sequences previously shown to be required for mRNA translational silencing. The release of YB-1 from promoter DNA coupled with its ability to bind RNA and shuttle between the nucleus and cytoplasm is suggestive of a regulatory loop for coordinating SMalphaA gene output in human pulmonary myofibroblasts at both the transcriptional and translational levels. This loop may help restrict organ-destructive remodeling due to excessive myofibroblast differentiation.

Actins↗
PubMed1990

Chromatin studies reveal that an ERE is located far upstream of a vitellogenin gene and that a distal tissue-specific hypersensitive site is conserved for two coordinately regulated vitellogenin genes.

Estrogen induces the expression of three vitellogenin genes in chicken hepatocytes. To survey the vitellogenin III (VTGIII) gene region for possible distal regulatory sequences, we identified tissue-specific hypersensitive (HS) sites within a 45 kb chromatin region spanning this gene. Five constitutive HS sites were found to mark the VTGIII gene region in hormone-naive hepatocytes. Strikingly, the constitutive HS site located 5.5 kb upstream of the VTGIII gene and a previously identified HS site located within the coordinately regulated VTGII gene mapped to nearly identical copies of a 72 bp sequence. Moreover, it would appear that there has been evolutionary pressure to retain specifically this 72 bp of VTGII-like sequence near the VTGIII gene subsequent to the VTGIII and VTGII genes becoming unlinked approximately 16 Myr ago. Two additional sets of HS sites were induced in the VTGIII gene region in response to estrogen. One set mapped immediately upstream of the gene in the vicinity of what we show to be a functional estrogen response element (ERE). The other induced HS site mapped 7.5 kb upstream of the gene. This far-upstream region was sequenced and was found to contain two imperfect ERE consensus sequences spaced 88 bp apart. In transient expression assays neither of these individual imperfect ERE sequences was functional, but a fragment spanning both sequences behaved as a strong ERE. In contrast to this synergism between imperfect ERE sequences, the presence of an NF-1 binding site 23 bp away from the more distal imperfect ERE sequence was not sufficient to render the latter a functional ERE in our assays.

Animals↗
PubMed2001

Do lung remodeling, repair, and regeneration recapitulate respiratory ontogeny?

Herein we posit that modeling of the lungs during morphogenesis, repair, and regeneration is tightly coordinated by conserved stimulatory and inhibitory signaling mechanisms, including specific transcriptional factors, cytokines, peptide growth factors, proteases, and matrix elements. This evolutionary-developmental (evo-devo) functional conservation has been extended to morphogenesis of the respiratory tracheae in Drosophila. Fifty or more genes direct fruit fly tracheal organogenesis. Among them, hedgehog, patched, smoothened, cubitus interruptus, branchless, breathless, sprouty, decapentaplegic, and mad are functionally conserved between flies, mice, and humans. For example, fibroblast growth factor (FGF) signaling is essential, not only for fly trachea and mouse bronchial branching morphogenesis, but also for postnatal modeling and repair of alveoli. Likewise, sprouty family genes act as inducible negative regulators of FGF signaling, which in part may determine interbranch length during bronchial development. Alveolar epithelial survival, migration, and proliferation during remodeling after hyperoxic injury also require FGF signaling. In addition, FGF signaling appears to regulate a small (< 5%) population of putative alveolar stem/ progenitor cells that express telomerase and are relatively resistant to hyperoxic apoptosis. We speculate that genes in evo-devo functionally conserved signaling pathways such as FGF-FGF receptor-Sprouty may provide novel therapeutic targets to augment lung repair and induce lung regeneration.

Adult↗
PubMed1986

Molecular, serologic, and functional evidence for an apparent HLA-DR triplet.

During routine typing procedures the individual GER was demonstrated to possess an unusual class II phenotype exhibiting three DR serotypes (DR1, DR2, DRw6). Closer serologic examination on this person's family showed that the DR1 and DR2 antigens segregated together on one haplotype. Biochemical evidence will be presented that the B cell line derived from the individual GER expresses five distinct types of DR molecules. Antigen presentation studies proved that the DR molecules carrying either DR1, DR2, or DRw6 (DRw13) allodeterminants are not only coordinately expressed but also are functional. No evidence could be found for altered DQ expression. The implications of these findings for the evolutionary aspects of the MHC class II region will be discussed.

Antigen-Presenting Cells↗
PubMed2004

Why cooperate? An economic perspective is not enough.

Cooperation is usually explained from an economic perspective focused mainly on the tangible outcomes received by individuals that are also dependent on the behavior of others, with little reference to the actual behaviors used when cooperating. The potential consequences of social dimensions associated with cooperative behaviors are minimized in Skinnerian and game-theory models by means of anonymous subjects that behave individually while physically isolated in separate chambers. When cooperation and non-cooperation occur in the real world, however, they are often associated not only with different outcomes but also with different behaviors. Unlike non-cooperation, cooperative behaviors are usually intrinsically social, influenced by the presence and behaviors of familiar partners. Research is described that addresses whether the social dimensions of cooperative actions go beyond mere description of behaviors to also explain why cooperation occurs. One way to resolve the relative importance of economic and social factors for explanations of cooperation is to measure choice between the options of cooperation and non-cooperation. The economic perspective, linked to models derived from game theory, frames the question as a choice determined by differences in tangible outcomes such as food or money that, in evolutionary terms, are surrogates for gains in fitness. From a behavioral perspective, the choice between cooperation and non-cooperation is also determined by social dimensions associated only with cooperation. The influence of social cooperation on preference was examined by means of two rectangular chambers interconnected by a T-maze. In one chamber, pairs of laboratory rats were reinforced with saccharin solution for coordinating back-and-forth shuttling; in the second chamber, a single animal was reinforced for back-and-forth shuttling performed in isolation. With outcomes equalized between the two options, cooperation was preferred by the majority of subjects. Moreover, variation in the relative rate of reinforcement during cooperation was not a strong predictor of choice whereas the level of intra-pair coordination was positively related to preference. Implications of this result are discussed for both method and theory, including the hypothesis that the preference is influenced by intrinsic reinforcements evoked by cooperating. The consequences for evolutionary fitness would then arise not only from tangible outcomes but from the relationships that develop when cooperating even when immediate and tangible pay-offs are absent, insufficient or sub-optimal. The impact of cooperative relationships on fitness may therefore not occur immediately but in the future, and perhaps in another context, when they influence outcomes that have a significant impact on survival and reproduction.

Animals↗
PubMed2005

The making of gametes in higher plants.

Higher plants have evolved to be one of the predominant life forms on this planet. A great deal of this evolutionary success relies in a very short gametophytic phase which underlies the sexual reproduction cycle. Sexual plant reproduction takes place in special organs of the flower. In most species the processes of gametogenesis, pollination, syngamy and embryogenesis are sequentially coordinated to give rise to a functional seed in a matter of few weeks. Any of these processes is so intricately complex and precisely regulated that it becomes no wonder that each involves more specific genes and cellular processes than any other function in the plant life cycle. While variability generation - the evolutionary output of the sexual cycle - is the same as in any other Kingdom, plants do it using a completely original set of mechanisms, many of which are not yet comprehended. In this paper, we cover the fundamental features of male and female gametogenesis. While the physiological and cellular bases of these processes have been continuously described since the early nineteen century, recent usage of Arabidopsis and other species as central models has brought about a great deal of specific information regarding their genetic regulation. Transcriptomics has recently enlarged the repertoire and pollen became the first gametophyte to have a fully described transcriptome in plants. We thus place special emphasis on the way this newly accumulated genetic and transcriptional information impacts our current understanding of the mechanisms of gametogenesis.

Flowers↗
PubMed1983

Human behavioral development and genetics.

Behavioral development during childhood is examined in relation to recent concepts and data from evolutionary theory and developmental genetics. The epigenetic framework of Waddington is proposed as a powerful tool for analyzing the progressions in behavior, particularly for recognizing that development involves coordinated pathways of change over time. Many of these pathways appear to depend upon the activity of timed gene-action systems that switch off and on according to a predetermined plan. Behavioral development thus gives expression to the dynamics of preprogrammed change; and in this perspective, behavioral discontinuities may be as strongly rooted in the epigenetic ground plan as the continuities are. The present paper aims to pull together some common themes from different areas that bear on the central issues of behavioral development--the neural foundations, the time course followed, the interplay of maturation and experience, the extent of preorganization furnished by the genetic program, and the adaptive significance of such behaviors in an evolutionary perspective. The final section touches on some hypotheses drawn from developmental neurobiology and developmental genetics that may enrich the analyses of human behavioral development.

Biological Evolution↗
PubMedDate not supplied

Reversible hexa- to penta-coordination of the heme Fe atom modulates ligand binding properties of neuroglobin and cytoglobin.

Neuroglobin (Ngb) and cytoglobin (Cygb) are two recently discovered intracellular members of the vertebrate hemoglobin (Hb) family. Ngb, predominantly expressed in nerve cells, is of ancient evolutionary origin and is homologous to nerve-globins of invertebrates. Cygb, present in many different tissues, shares common ancestry with myoglobin (Mb) and can be traced to early vertebrate evolution. Ngb is held to facilitate O2 diffusion to the mitochondria and to protect neuronal cells from hypoxic-ischemic insults, may be an oxidative stress-responsive sensor protein for signal transduction, and may carry out enzymatic activities, such as NO/O2 scavenging. Cygb is linked to collagen synthesis, may provide O2 for enzymatic reactions, and may be involved in a ROS(NO)-signaling pathway(s). Ngb and Cgb display the classical three-over-three alpha-helical fold of Hb and Mb, and are endowed with a hexa-coordinate heme-Fe atom, in their ferrous and ferric forms, having the heme distal HisE7 residue as the endogenous ligand. Reversible hexa- to penta-coordination of the heme Fe atom modulates ligand binding properties of Ngb and Cygb. Moreover, Ngb and Cygb display a tunnel/cavity system within the protein matrix held to facilitate ligand channeling to/from the heme, multiple ligand copies storage, multi-ligand reactions, and conformational transitions supporting ligand binding.

Animals↗
PubMed2002

Prediction of coordination number and relative solvent accessibility in proteins.

Knowing the coordination number and relative solvent accessibility of all the residues in a protein is crucial for deriving constraints useful in modeling protein folding and protein structure and in scoring remote homology searches. We develop ensembles of bidirectional recurrent neural network architectures to improve the state of the art in both contact and accessibility prediction, leveraging a large corpus of curated data together with evolutionary information. The ensembles are used to discriminate between two different states of residue contacts or relative solvent accessibility, higher or lower than a threshold determined by the average value of the residue distribution or the accessibility cutoff. For coordination numbers, the ensemble achieves performances ranging within 70.6-73.9% depending on the radius adopted to discriminate contacts (6A-12A). These performances represent gains of 16-20% over the baseline statistical predictor, always assigning an amino acid to the largest class, and are 4-7% better than any previous method. A combination of different radius predictors further improves performance. For accessibility thresholds in the relevant 15-30% range, the ensemble consistently achieves a performance above 77%, which is 10-16% above the baseline prediction and better than other existing predictors, by up to several percentage points. For both problems, we quantify the improvement due to evolutionary information in the form of PSI-BLAST-generated profiles over BLAST profiles. The prediction programs are implemented in the form of two web servers, CONpro and ACCpro, available at http://promoter.ics.uci.edu/BRNN-PRED/.

Amino Acids↗
PubMed1996

A structural model for the membrane-integral domain of succinate: quinone oxidoreductases.

Many succinate:quinone oxidoreductases in bacteria and mitochondria, i.e. succinate:quinone reductases and fumarate reductases, contain in the membrane anchor a cytochrome b whose structure and function is poorly understood. Based on biochemical data and polypeptide sequence information, we show that the anchors in different organisms are related despite an apparent diversity in polypeptide and heme composition. A general structural model for the membrane-integral domain of the anchors is proposed. It is an antiparallel four-helix bundle with a novel arrangement of hexa-coordinated protoheme IX. The structure can be applied to a larger group of membrane-integral cytochromes of b-type and has evolutionary and functional implications.

Amino Acid Sequence↗
PubMed1997

On the theory of folding kinetics for short proteins.

BACKGROUND: Recent data have suggested two principles that are central to the work we describe here. First, proteins are the result of evolutionary 'sequence selection' to optimize the energy of the native state. Second, the overlap with the native state is a qualitatively suitable reaction coordinate for modeling folding kinetics. The former principle is bolder and better established. RESULTS: Employing only these two principles, we have constructed a non-phenomenological, correlated energy landscape theory that predicts single barrier protein folding kinetics. Moreover, we are able to analytically describe the nature of the free energetic barrier between the denatured and native states of a protein and to detail the nature of folding kinetics for short proteins. Our model predicts Hammond behavior and also describes how mutations can lead to drastic differences in folding times. CONCLUSIONS: We find that folding and unfolding kinetics can be characterized by a single thermodynamic parameter and, moreover, that Monte Carlo simulation data on folding and unfolding rates with different temperatures and mutations collapse with this characterization. Our results also delineate a regime in which kinetics may proceed via a single unique nucleus.

Computer Simulation↗
PubMed2005

The social nature of primate cognition.

The hypothesis that the enlarged brain size of the primates was selected for by social, rather than purely ecological, factors has been strongly influential in studies of primate cognition and behaviour over the past two decades. However, the Machiavellian intelligence hypothesis, also known as the social brain hypothesis, tends to emphasize certain traits and behaviours, like exploitation and deception, at the expense of others, such as tolerance and behavioural coordination, and therefore presents only one view of how social life may shape cognition. This review outlines work from other relevant disciplines, including evolutionary economics, cognitive science and neurophysiology, to illustrate how these can be used to build a more general theoretical framework, incorporating notions of embodied and distributed cognition, in which to situate questions concerning the evolution of primate social cognition.

Animals↗
PubMed2005

Phenotypic and genotypic expression of self-incompatibility haplotypes in Arabidopsis lyrata suggests unique origin of alleles in different dominance classes.

The highly divergent alleles of the SRK gene in outcrossing Arabidopsis lyrata have provided important insights into the evolutionary history of self-incompatibility (SI) alleles and serve as an ideal model for studies of the evolutionary and molecular interactions between alleles in cell-cell recognition systems in general. One tantalizing question is how new specificities arise in systems that require coordination between male and female components. Allelic recruitment via gene conversion has been proposed as one possibility, based on the division of DNA sequences at the SRK locus into two distinctive groups: (1) sequences whose relationships are not well resolved and display the long branch lengths expected for a gene under balancing selection (Class A); and (2) sequences falling into a well-supported group with shorter branch lengths (Class B) that are closely related to an unlinked paralogous locus. The purpose of this study was to determine if differences in phenotype (site of expression assayed using allele-specific reverse transcription-polymerase chain reaction) or function (dominance relationships assayed through controlled pollinations) accompany the sequence-based classification. Expression of Class A alleles was restricted to floral tissues, as predicted for genes involved in the SI response. In contrast, Class B alleles, despite being tightly linked to the SI phenotype, were unexpectedly expressed in both leaves and floral tissues; the same pattern found for a related unlinked paralogous sequence. Whereas Class A included haplotypes in three different dominance classes, all Class B haplotypes were found to be recessive to all except one Class A haplotype. In addition, mapping of expression and dominance patterns onto an S-domain-based genealogy suggested that allelic dominance may be determined more by evolutionary history than by frequency-dependent selection for lowered dominance as some theories suggest. The possibility that interlocus gene conversion might have contributed to allelic diversity is discussed.

Alleles↗
PubMedDate not supplied

[Evolutionary aspects of affective disorders, critical review and proposal of a new model].

Evolutionary psychopathology incorporates psychiatry into biology via theory of evolution, generating new etiological hypothesis for mental disorders. For evolutionary psychopathology emotions are a response system or a genetically programmed, specialized state of functioning, formed by natural selection, that allows us to adapt to the environment, increasing the ability to cope with threats and opportunities. Emotions exert their function by coordinated physiological, psychological and behavioral changes. Many functions have been suggested for low mood or depression, including communicating a need for help, signaling yielding in a hierarchy conflict, fostering disengagement for commitments to unreachable goals, regulating patterns of investment, parallelism with despair phase of separation from mother situation in monkeys, hibernation, etc. Despite other evolutionary models, our model not only tries to explain depression but mania, hypomania and other affective disorders as well. For us, most affective disorders are pathological states (and not adaptive ones), due to dysfunction of an innate precipitating mechanism (IPM). IPM function is to regulate energy and activity levels according to intensity and duration of light (namely IPM-A). This IPM-A is responsible for vegetative, endocrine and behavioral responses that are present in humans and more ancient phylogenetic animals. More recently in the phylogeny, other mechanisms (IPM-AA) have coupled to this IPM-A. In the human being, the precipitating factors of IPM-AA are predominately social. IPM-AA add new responses (such as mood) to the older responses of IPM-A.

Biological Evolution↗
PubMed1998

Complete calibration of a stereo photogrammetric system through control points of unknown coordinates.

This paper presents a new method for calibrating a video 3D stereo-photogrammetric system. The external parameters and the focal lengths of the cameras are determined from the epipolar constraint and the principal points are computed through the minimisation of a cost function carried out through an evolutionary optimisation. The method has been made more robust with a deterministic annealing procedure of the search region amplitude. Calibration is carried out by moving a rigid bar, carrying two markers on its extremities, inside the working volume. The distance between the two markers is the only measure required. Tests on real data are reported which show that the obtained accuracy is comparable to the one achieved calibrating with control points of known 3D coordinates.

Calibration↗
PubMed2005

Biochemistry of V(D)J recombination.

The genes that encode immunoglobulin and T cell receptor proteins are assembled from component gene segments in a reaction known as V(D)J recombination. The reaction, and its crucial mediators RAG1 and RAG2, are essential for lymphocyte development and hence for adaptive immunity. Here we consider the biochemistry of this reaction, focusing on the DNA transactions and the proteins involved. We discuss how the RAG proteins interact with DNA and how coordinate cleavage of the DNA at two sites might be achieved. Finally, we consider the RAG proteins and V(D)J recombination from an evolutionary point of view.

Animals↗