Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Evolutionary coordination”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11Linked to original sources
PubMed1990

DNA recombination and natural selection pressure sustain genetic sequence diversity of the feline MHC class I genes.

Sequence comparisons of seven distinct MHC class I cDNA clones revealed that feline class I molecules have a remarkable similarity to human HLA genes in their organization of functional domains as well as in the nonrandom partitioning of genetic variability according to the functional constraints ascribed to different regions of the MHC molecule. The distribution of the pattern of sequence polymorphism in the cat as compared with genetic diversity of human and mouse class I genes provides evidence for four coordinate factors that contribute to the origin and sustenance of abundant allele diversity that characterizes the MHC in the species. These include: (a) a gradual accumulation of spontaneous mutational substitution over evolutionary time; (b) selection against mutational divergence in regions of the class I molecule involved in T cell receptor interaction and also in certain regions that interact with common features of antigens; (c) positive selection pressure in favor of persistence of polymorphism and heterozygosity at 57 nucleotide residues that comprise the antigen recognition site; and (d) periodic intragenic (interallelic) and intergenic recombination within the class I genes. We describe a highly conserved 23-bp nucleotide sequence within the coding region of the first alpha-helix that separates two relatively polymorphic segments located in the alpha 1 domain that may act as a template or "hot spot" for homologous recombination between class I alleles.

Amino Acid Sequence↗
PubMed1975

On the evolution of the physiological model.

Most of us who have concerned ourselves with models can perceive outlines like those above to catalog the future evolution of the expository function of models. In the context of a single class of computerized mathematical models of respiratory physiology, we can observe at once the burgeoning interest among scientists, and the similarities between model activity and the general organization of scientific information for use. Although physiological models have become quite advanced in their subject control, there is relatively little coordinated activity in the mechanization of the purposes and philosophical potential of automata. The outlines, however, are visible. An assiduous pursuit of the notion of "explanation" by machine is a major evolutionary step next to occur. It appears to us that various diagrams similar to Figures 5 or 6 can be created and investigated in terms of their relation to the human mind and in terms of formalizing rules for traversing from one plane to the next. The evolution of models will require program-making programs which can decide when and how to aggregate for deductive inference, and how far to penetrate top-down for explanation. The rules for identifying "second order" effects must be established. The decision to ignore or use these rules will be crucial. These are the means whereby the systems are traversed from plane to plane. In a word, models need to synthesize the means to ignore, "forget," and gloss over; only then will we have useful tools for taking informed action in physiology, diagnosis in medicine, or the writing of "scholarly" reviews.

Computers↗
PubMed2002

Evolutionary conserved sequences are required for the insulation of the vertebrate Hoxd complex in neural cells.

Transcriptional regulation of vertebrate Hox genes involves enhancer sequences located either inside or outside the gene clusters. In the mouse Hoxd complex, for example, series of contiguous genes are coordinately controlled by regulatory sequences located at remote distances. However, in different cellular contexts, Hox genes may have to be insulated from undesirable external regulatory influences to prevent ectopic gene activation, a situation that would likely be detrimental to the developing embryo. We show the presence of an insulator activity, at one extremity of the Hoxd complex, that is composed of at least two distinct DNA elements, one of which is conserved throughout vertebrate species. However, deletion of this element on its own did not detectably affect Hoxd gene expression, unless another DNA fragment located nearby was removed in cis. These results suggest that insulation of this important gene cluster relies, at least in part, upon a sequence-specific mechanism that displays some redundancy.

Animals↗
PubMed1984

Analysis of the codon bias in E. coli sequences.

Fifty-three gene sequences from E. coli containing 18,288 reading frame triplets have been characterized according to the nature and level of average codon preference. The distribution of average preferences is bimodal, with approximately half the genes using an average of only 36 codons, and the remainder just 42 codons. There is a high correlation between the level of codon bias, the tRNA population and the abundance of protein product, indicating biased patterns are exploited by the cell for the production of widely different levels of gene product. This relationship is especially striking in genes involved in the production of components for transcription and translation. Overall, the genes for these processes generate some five-fold more protein than the average in the genome, and use about five fewer codons. The very high codon bias found in the RNA polymerase gene thus provides a simple, autogenous mechanism for the coordinate synthesis of these components and RNA polymerase. A surprisingly high level of codon probability is also found in triplets of the complement of coding sequences. This is apparently due to the evolutionary dispersion of coding sequences and/or the requirement for increased levels of secondary structure in messenger RNAs.

Base Sequence↗
PubMed1996

Protochlorophyllide reduction: a key step in the greening of plants.

The reduction of Protochlorophyllide (Pchlide) is a major regulatory step in the biosynthesis of chlorophyll (Chl) in oxygenic phototrophs. Two different enzymes catalyze this reduction: a light-dependent enzyme (LPOR), which is unique as a consequences of its direct utilization of light for catalysis; and a light-independent Pchlide reductase (DPOR). Since the reduction of Pchlide in angiosperms is catalyzed exclusively by LPOR, they become etiolated in the absence of light. LPOR, a major protein in etioplast membranes, consists of a single polypeptide and it exists as a ternary complex with its substrates, Pchlide and NADPH. By contrast to the copious information about LPOR, limited information about DPOR has been reported. Recent molecular genetic analyses in a cyano-bacterium and a green alga have revealed that at least the three genes, namely, chlL, chlN and chlB, encode proteins essential for the activity of DPOR. These genes are widely distributed among phototrophic organisms with exception of angiosperms and Euglenophyta. This distribution seems to be well correlated with light-independent greening ability. These genes might have been lost during the evolution of gymnosperms to angiosperms. The similarities among the deduced amino acid sequences of the three gene products and the subunits of nitrogenase suggest an evolutionary relationship between DPOR and nitrogenase. The identification of genes for the reduction of Pchlide provides the groundwork for investigations of the mechanism that regulates the synthesis of Chl, which is closely coordinated with greening in plants.

Amino Acid Sequence↗
PubMed2001

Why homeodynamics, not homeostasis?

Ideas of homeostasis derive from the concept of the organism as an open system. These ideas can be traced back to Heraclitus. Hopkins, Bernard, Hill, Cannon, Weiner and von Bertalanffy developed further the mechanistic basis of turnover of biological components, and Schoenheimer and Rittenberg were pioneers of experimental approaches to the problems of measuring pool sizes and dynamic fluxes. From the second half of the twentieth century, a biophysical theory mainly founded on self-organisation and Dynamic Systems Theory allowed us to approach the quantitative and qualitative analysis of the organised complexity that characterises living systems. This combination of theoretical framework and more refined experimental techniques revealed that feedback control of steady states is a mode of operation that, although providing stability, is only one of many modes and may be the exception rather than the rule. The concept of homeodynamics that we introduce here offers a radically new and all-embracing concept that departs from the classical homeostatic idea that emphasises the stability of the internal milieu toward perturbation. Indeed, biological systems are homeodynamic because of their ability to dynamically self-organise at bifurcation points of their behaviour where they lose stability. Consequently, they exhibit diverse behaviour; in addition to monotonic stationary states, living systems display complex behaviour with all its emergent characteristics, i.e., bistable switches, thresholds, waves, gradients, mutual entrainment, and periodic as well as chaotic behaviour, as evidenced in cellular phenomena such as dynamic (supra)molecular organisation and flux coordination. These processes may proceed on different spatial scales, as well as across time scales, from the very rapid processes within and between molecules in membranes to the slow time scales of evolutionary change. It is dynamic organisation under homeodynamic conditions that make possible the organised complexity of life.

Hemodynamics↗
PubMed2004

Genes and chromosomes: control of development.

The past decade has witnessed immense progress in research into the molecular basis behind the developmental regulation of genes. Sets of genes functioning under hierarchical control have been identified, evolutionary conserved systems of genes effecting the cell-to-cell transmission of transmembrane signals and assigned a central role in morphogenesis have been intensively studied; the concept of genomic regulatory networks coordinating expression of many genes has been introduced, to mention some of the major breakthroughs. It should be noted that the temporal and tissue-specific parameters of gene expression are correctly regulated in development only in the context of the chromosome and that they are to a great extent dependent on the position of the gene on the chromosome or the interphase nucleus. Moreover epigenetic inheritance of the gene states through successive cell generations has been conducted exclusively at the chromosome level by virtue of cell or chromosome memory. The ontogenetic memory is an inherent property of the chromosome and cis-regulation has a crucial role in its maintenance.

Animals↗
PubMed1997

[Neurophysiology in status epilepticus].

Cases of status epilepticus (SE) require rapid diagnosis and treatment, including simultaneous, coordinated clinical and neurophysiological assessment. The EEG is the essential diagnostic support that confirms the presence of SE and allows for its differentiation from other processes, and the characterization of type and evolutionary phase, while elucidating situations such as covert SE and nonconvulsive SE whose clinical expression is scarce and diagnosis and management difficult. Finally, EEG monitoring serves to guide treatment and recognize when crises have passed, evaluate drug response and monitor the differed evolutionary control of SE.

Diagnosis, Differential↗
PubMed1997

Hydrogenase genes from Rhizobium leguminosarum bv. viciae are controlled by the nitrogen fixation regulatory protein nifA.

Rhizobium leguminosarum bv. viciae expresses an uptake hydrogenase in symbiosis with peas (Pisum sativum) but, unlike all other characterized hydrogen-oxidizing bacteria, cannot express it in free-living conditions. The hydrogenase-specific transcriptional activator gene hoxA described in other species was shown to have been inactivated in R. leguminosarum by accumulation of frameshift and deletion mutations. Symbiotic transcription of hydrogenase structural genes hupSL originates from a -24/-12 type promoter (hupSp). A regulatory region located in the -173 to -88 region was essential for promoter activity in R. leguminosarum. Activation of hupSp was observed in Klebsiella pneumoniae and Escherichia coli cells expressing the K. pneumoniae nitrogen fixation regulator NifA, and in E. coli cells expressing R. meliloti NifA. This activation required direct interaction of NifA with the essential -173 to -88 regulatory region. However, no sequences resembling known NifA-binding sites were found in or around this region. NifA-dependent activation was also observed in R. etli bean bacteroids. NifA-dependent hupSp activity in heterologous hosts was also absolutely dependent on the RpoN sigma-factor and on integration host factor. Proteins immunologically related to integration host factor were identified in R. leguminosarum. The data suggest that hupSp is structurally and functionally similar to nitrogen fixation promoters. The requirement to coordinate nitrogenase-dependent H2 production and H2 oxidation in nodules might be the reason for the loss of HoxA in R. leguminosarum and the concomitant NifA control of hup gene expression. This evolutionary acquired control would ensure regulated synthesis of uptake hydrogenase in the most common H2-rich environment for rhizobia, the legume nodule.

Bacterial Proteins↗
PubMed1999

Molecular evolution of a developmental pathway: phylogenetic analyses of transforming growth factor-beta family ligands, receptors and Smad signal transducers.

Intercellular signaling by transforming growth factor-beta (TGF-beta) proteins coordinates developmental decisions in many organisms. A receptor complex and Smad signal transducers are required for proper responses to TGF-beta signals. We have taken a phylogenetic approach to understanding the developmental evolutionary history of TGF-beta signaling pathways. We were interested in detecting evolutionary influences among the physically interacting multigene families encoding TGF-beta ligands, receptors, and Smads. Our analyses included new ligands and Smads identified from genomic sequence as well as the newest published family members. From an evolutionary perspective we find that (1) TGF-beta pathways do not predate the divergence of animals, plants, and fungi; (2) ligands of the TGF-beta/activin subfamily likely originated after the divergence of nematodes and arthropods; (3) type I receptors from Caenorhabditis elegans are distinct from other receptors and may reflect an ancestral transitional state between type I and type II receptors; and (4) the Smad family appears to be evolving faster than, and independently of, ligands and receptors. From a developmental perspective we find (1) numerous phylogenetic associations not previously detected in each multigene family; (2) that there are unidentified pathway components that discriminate between type I and type II receptors; (3) that there are more Smads to be discovered in Drosophila and mammals; and (4) that the number of C-terminal serines is the best predictor of a Smad's role in TGF-beta signal transduction. We discuss these findings with respect to the coevolution of physically interacting genes.

Amino Acid Sequence↗
PubMed2005

Evolution under tight linkage to mating type.

Recent large-scale sequencing studies of mating type loci in a number of organisms offer insight into the origin and evolution of these genomic regions. Extensive tracts containing genes with a wide diversity of functions typically cosegregate with mating type. Cases in which mating type determination entails complementarity between distinct transcription units may descend from systems in which close physical linkage facilitated the coordinated expression and cosegregation of the interacting genes. In response to the particular selection pressures associated with the maintenance of more than one mating type, this nucleus of low recombination may expand over evolutionary time, engulfing neighboring tracts bearing genes with no direct role in reproduction. This scenario is consistent with the present-day structure of some mating type loci, including regulators of homomorphic self-incompatibility in angiosperms (S-loci). Recombination suppression and enforced S-locus heterozygosity accelerate the accumulation of genetic load and promote genetic associations between S-alleles and degenerating genes in cosegregating tracts. This S-allele-specific load may influence the evolution of self-incompatibility systems.

Animals↗
PubMed1998

Complex movement patterns: modifiability and constraints.

Most behaviours involve complex morphological systems and vice versa morphological systems are used by the organism in many different ways. During evolution and ontogeny changes in kinematics and function of skeletal and muscular systems must be coordinated with changes in their neural control. Neuromotor patterns are sometimes believed to be conserved in evolution, leading to diversification at the level of musculoskeletal design. Vertebrate motor patterns used in feeding are reviewed to examine this hypothesis. Stereotyped behaviour is not necessarily the result of phylogenetic constraints but may also result from the functional demands imposed by the mechanics of the jaw apparatus and the nature of the task performed. Sensory feedback and descending control not only contribute to 'online' control of movement but also shape the development of motor patterns and learning behaviour and indicate a potentially large flexibility. The neural and sensory apparatus that produces this flexibility will be subject to evolutionary modification. In the absence of a demand for flexibility motor patterns may become stereotyped in some species, while they are very flexible in others. To the extent that morphological systems perform independent movements during different behaviours, separate basic motor patterns may be required, which may be coordinated in different ways.

Animals↗
PubMed2026

Evolutionary Reorganization of Transcriptomic Architecture Across a UVB Tolerance Gradient in Fish.

Environmental stressors such as ultraviolet radiation impose strong selective pressures on organisms, yet how adaptation to such stressors shapes transcriptomic responses at the network level remains poorly understood. Although stratospheric ozone is recovering globally, substantial regional variation in UV exposure persists, particularly in high-altitude environments where extreme UV levels can occur. Here, we compared three fish models representing distinct biological responses to UVB exposure: wild-type zebrafish (Danio rerio), a melanin-deficient zebrafish mutant (nacre) lacking a major protective mechanism against UVB damage, and the high-altitude Andean killifish Orestias ascotanensis, a species naturally exposed to extreme UVB radiation. Together, these models define a gradient spanning physiological protection, impaired protection, and evolutionary adaptation to UVB stress. Using RNA-seq and protein-protein interaction networks, we show that transcriptomic responses differ markedly across this gradient. Wild-type and nacre zebrafish exhibited relatively limited transcriptomic changes (∼2%-2.4% of genes changing), whereas O. ascotanensis displayed a large-scale and highly coordinated response (∼21.6% of genes changing) characterized by functionally specialized networks enriched in DNA repair pathways. These differences involved not only transcriptomic magnitude but also marked reorganization of transcriptomic architecture. Integration with positive selection analyses revealed that positively selected genes were concentrated within highly interconnected regions of transcriptomic networks, consistent with adaptation involving network reorganization. Furthermore, ortholog-based analyses suggest that adaptive responses involve differential reorganization of a conserved functional background. Together, our results support a model in which adaptation to environmental stress is associated with the reorganization of conserved transcriptomic networks across physiological and evolutionary contexts, providing a systems-level perspective on the molecular basis of adaptation.

UVB radiation↗
PubMed2026

Seed shattering habit in millets and the secrets of the abscission layer - a comprehensive review.

Though seed shattering continues to be a significant barrier affecting yield stability and harvesting efficiency in millets and other grasses, millets are increasingly acknowledged as climate-resilient, nutrient-rich 2007cereal crops with the potential to strengthen global nutritional and food security under the combined pressures of climate change, population growth, and limited natural resources. Since strong artificial selection favoured non-shattering phenotypes during domestication, seed shattering, an adaptive trait in wild species that promotes seed dispersal through the formation and activation of specialised abscission layers, became a distinguishing feature of cultivated cereals. With a focus on the morphological, physiological, hormonal, and genetic modulation of the abscission zone, this article summarizes the state of the art regarding seed shattering in millets. Abscission layer morphology, location, and lignification vary greatly among grasses, from well-defined lignified zones in rice and sorghum to non-lignified and anatomically subtle zones in Setaria and Panicum species. Cell wall-modifying enzymes like polygalacturonases, cellulases, expansins, and pectin methylesterases that mediate middle lamella degradation are modulated by coordinated hormonal signalling involving auxin, ethylene, and abscisic acid, which controls the timing and progression of cell separation at the physiological level. Domestication-related genes, including SH1, qSH1, SH4, and LES1, demonstrate convergent evolutionary mechanisms controlling abscission layer development in a variety of grass lineages at the molecular level. Understanding these regulatory networks has been greatly enhanced by recent developments in transcriptomics, functional genomics, and genome sequencing in both model species and underused millets. The role of millets as climate-smart cereals for sustainable future agriculture is reinforced by the integration of anatomical, physiological, and genetic insights, which offer a solid basis for targeted breeding and genome-editing strategies intended to improve seed retention, enhance yield stability, and increase harvest efficiency.

Abscission Layer↗
PubMed2005

Influence of structure on binding of chlorophylls to peptide ligands.

Four classes of chlorophyll (Chl), a, b, c, and d, are involved in photosynthesis within cyanobacteria, algae, and plants. These classes have different evolutionary origins, chemical properties, and biological functions. Our results demonstrate that peptide-bound ligands provided by the imidazole group of histidine and the charge-compensated glutamate-arginine ion pair readily form coordination bonds with Chls a and d but do not interact significantly with Chls b and c. These ligands are apparently not sufficiently strong Lewis bases to displace strongly coordinated water from Chls b and c. These differences determine specificity of binding of Chls in light-harvesting complexes and play an important role in assembly of stable Chl-protein complexes, which has had a profound impact on the evolution of photosynthetic organisms.

Amino Acid Sequence↗
PubMed1998

Functional phylogeny: the use of the sensitivity of ribosomes to protein synthesis inhibitors as a tool to study the evolution of organisms.

In order to study the functional phylogeny of organisms, forty different protein synthesis inhibitors with diverse domain and functional specificities have been used to analyze forty archaeal, bacterial and eukaryotic translational systems. The inhibition curves generated with the different ribosome-antibiotic pairs have shown very interesting similarities among organisms belonging to the same phylogenetic group, confirming the feasibility of using such information in the development of evolutionary studies. A new method to extract most of the information contained in the inhibition curves is presented. Using a statistical treatment based on the principal components analysis of the data, we have defined coordinates for the organisms which have allowed us to perform a functional clustering of them. The phenograms obtained are very similar to those generated by 16/18S rRNA sequence comparison. These results prove the phylogenetic value of our functional analysis and suggest an interesting intersection between genotypic and phenotypic (functional) information.

Animals↗
PubMed1990

Minimizing problems between vascular trainees and general surgery residents.

The current problems and conflicts associated with training of vascular and general surgery residents exemplify the larger dilemma of educating subspecialists while preserving the wellspring of general surgery. Previous vascular fellowship programs during the era of evolution of our subspecialty were characterized by clinical preceptorships or research programs with little thought about the impact on training of general surgery residents. The current era of educational safeguards permits approved vascular training programs provided that adequate educational experience, operative caseload, and appropriate supervision are ensured for both the vascular and general surgical trainee. The future portends significant changes in general surgical and subspecialty training to enhance the career goals of all surgical residents. Such evolutionary changes are necessary to not only capitalize on the benefits of subspecialty care but also enhance the professional standing and expertise of the general surgeon. These modifications in training programs will require the coordinated efforts of major societal, governmental, accrediting, and certifying organizations.

Accreditation↗
PubMed2000

The internalist stance. A linguistic practice enclosing dynamics

Natural dynamics, as manifested in evolutionary processes, refer to material bodies in movement in the present progressive mode. Any interacting material body in the present progressive mode must be sentient to others because there can be no global agency coordinating it to others in a globally synchronous manner. The internalist perspective, or the worm's eye view, referring primarily to the present progressive mode, renders local material bodies, large or small, subject to an inevitable inconsistency among local representations of neighborhood events registered in the local present perfect tense. Any sentient material body experiencing this inconsistency subsequently transforms itself into an inconsistency-free representation. The descriptive scheme unique to the internalist stance is internal and dynamic in the sense that it constantly strives to update constituent local representations, attempting to eliminate any inconsistencies residing within antecedent local representations. Compared to external descriptions of invariable universals grounded upon the Cartesian epistemic split, which are complementary to dynamics, internal description serves as a linguistic means of embodying natural dynamics even without recourse to the notion called forces. This makes our language powerful enough to enclose natural dynamics of material bodies in the empirical domain.

Journal Article↗