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PubMed2004

The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens.

The evolution of ecological specialization is expected to carry a cost, due to either antagonistic pleiotropy or mutation accumulation. In general, it has been difficult to distinguish between these two possibilities. Here, we demonstrate that the experimental evolution of niche-specialist genotypes of the bacterium Pseudomonas fluorescens that colonize the air-broth interface of spatially structured microcosms is accompanied by pleiotropic fitness costs in terms of reduced carbon catabolism. Prolonged selection in spatially structured microcosms caused the cost of specialization to decline without loss of the benefits associated with specialization. The decline in the cost of specialization can be explained by either compensatory adaptation within specialist lineages or clonal competition among specialist lineages. These results provide a possible explanation of conflicting accounts for the cost of specialization.

Adaptation, Physiological↗
PubMed1993

High evolutionary divergence of the 5.8S ribosomal DNA in Mimulus glaucescens (Scrophulariaceae).

Ribosomal DNA sequences for the ITS 1, 5.8S, ITS 2 and adjoining regions of the 18S and 25S were obtained from Mimulus glaucescens (Scrophulariaceae) via cloned PCR products. The spacer sequences were completely unrelated to other plant taxa, although spacer lengths were approximately the same. Interestingly, the Mimulus 5.8S sequence was much more divergent than other higher-plant rDNA sequences. Consideration of the secondary structure of the 5.8S rRNA shows that most of the changes in Mimulus are compensatory and preserve the basic secondary structure of the mature RNA molecule.

Base Sequence↗
PubMed1995

Sensation-seeking and emotional disturbances in depression: relationships and evolution.

The French abbreviated form of the sensation-seeking scale was given to 183 hospitalized depressed subjects meeting the DSM-III-R criteria for major depression. Depressed subjects, men and women, scored significantly lower than controls from the general population, paired as to age and sex, on all of the subscales. There was no relationship to the intensity of depression and anxiety. Relationships between emotional disturbances and sensation-seeking were differentiated according to the specificity of each subscale and to age and sex. There was no significant difference between baseline and after-treatment sensation-seeking scores and subjects at discharge still scored significantly lower than controls. Hypotheses on evolution at a later date after the hospitalization are made. The finding of positive relationships for some subjects between sensation-seeking and anhedonia is interpreted in regard to a compensatory process.

Adult↗
PubMed2005

The rate of compensatory mutation in the DNA bacteriophage phiX174.

A compensatory mutation occurs when the fitness loss caused by one mutation is remedied by its epistatic interaction with a second mutation at a different site in the genome. This poorly understood biological phenomenon has important implications, not only for the evolutionary consequences of mutation, but also for the genetic complexity of adaptation. We have carried out the first direct experimental measurement of the average rate of compensatory mutation. An arbitrary selection of 21 missense substitutions with deleterious effects on fitness was introduced by site-directed mutagenesis into the bacteriophage phiX174. For each deleterious mutation, we evolved 8-16 replicate populations to determine the frequency at which a compensatory mutation, instead of the back mutation, was acquired to recover fitness. The overall frequency of compensatory mutation was approximately 70%. Deleterious mutations that were more severe were significantly more likely to be compensated for. Furthermore, experimental reversion of deleterious mutations revealed that compensatory mutations have deleterious effects in a wild-type background. A large diversity of intragenic compensatory mutations was identified from sequencing fitness-recovering genotypes. Subsequent analyses of intragenic mutation diversity revealed a significant degree of clustering around the deleterious mutation in the linear sequence and also within folded protein structures. Moreover, a likelihood analysis of mutation diversity predicts that, on average, a deleterious mutation can be compensated by about nine different intragenic compensatory mutations. We estimate that about half of all compensatory mutations are located extragenically in this organism.

Adaptation, Biological↗
PubMed1997

An analysis of simultaneous variation in protein structures.

The simultaneous substitution of pairs of buried amino acid side chains during divergent evolution has been examined in a set of protein families with known crystal structures. A weak signal is found that shows that amino acid pairs near in space in the folded structure preferentially undergo substitution in a compensatory way. Three different physicochemical types of covariation 'signals' were then examined separately, with consideration given to the evolutionary distance at which different types of compensation occur. Where the compensatory covariation tends towards retaining the combined residue volumes, the signal is significant only at very low evolutionary distances. Where the covariation compensates for changes in the hydrogen bonding, the signal is strongest at intermediate evolutionary distances. Covariations that compensate for charge variations appeared with equal strength at all the evolutionary distances examined. A recipe is suggested for using the weak covariation signal to assemble the predicted secondary structural elements, where the evolutionary distance, covariation type and weighting are considered together with the tertiary structural context (interior or surface) of the residues being examined.

Computer Simulation↗
PubMed2005

Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects.

Many symbioses between bacteria and insects resulted from ancient infections followed by strict vertical transmission within host lineages. The strong bottlenecks under which this transmission occurs promote the neutral fixation of slightly deleterious mutations by genetic drift. As predicted by Muller's ratchet, this fixation will drive endosymbiotic bacteria through an irreversible dynamics of fitness loss. The chaperonin GroEL has been proposed as a compensatory mechanism whereby endosymbiotic bacteria of aphids persist. Here, we show that endosymbiotic bacteria of insects from two phylogenetically very distant bacterial phyla have fixed amino acid substitutions by positive selection in functionally important GroEL regions involved in either GroES/peptide binding or in the en bloc movement of the GroEL apical domain. These results, together with the high levels of constitutive expression of GroEL in these endosymbionts, provide valuable insights into the evolution of a molecular mechanism responsible for the maintenance of the symbiotic lifestyle.

Adaptation, Biological↗
PubMed1999

Involvement of the subthalamic nucleus in glutamatergic compensatory mechanisms.

The purpose of the present study was to investigate whether the subthalamic nucleus (STN) was implicated in the glutamatergic compensatory mechanisms which have been shown to mask the parkinsonian motor abnormalities at the end of the presymptomatic period in experimental parkinsonism. Using multiunit electrophysiological recordings, we follow changes of activity occurring in the STN and in both the pars externalis and the pars internalis of the globus pallidus of monkeys chronically intoxicated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), according to a protocol designed to mimic the gradual evolution of dopaminergic neuronal death. STN activity augmented significantly in the course of treatment, even before the first appearance of clinical signs (P < 0.01). This result would indicate that the STN, which increases its level of activity even before the end of the presymptomatic period, is principally responsible for the instigation of glutamatergic compensatory mechanisms which allow the maintenance of the striatal dopaminergic homeostasis.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗
PubMed2005

Adaptive evolution by optimizing expression levels in different environments.

Organisms adapt to environmental changes through the fixation of mutations that enhance reproductive success. A recent study by Dekel and Alon demonstrated that Escherichia coli adapts to different growth conditions by fine-tuning protein levels, as predicted by a simple cost-benefit model. A study by Fong et al. showed that independent evolutionary trajectories lead to similar adaptive endpoints. Initial mutations on the path to adaptation altered the mRNA levels of numerous genes. Subsequent optimization through compensatory mutations restored the expression of most genes to baseline levels, except for a small set that retained differential levels of expression. These studies clarify how adaptation could occur by the alteration of gene expression.

Bacteria↗
PubMed2001

Obesity cardiomyopathy: pathophysiology and evolution of the clinical syndrome.

Obesity produces an increase in total blood volume and cardiac output because of the high metabolic activity of excessive fat. In moderate to severe cases of obesity, this may lead to left ventricular dilation, increased left ventricular wall stress, compensatory (eccentric) left ventricular hypertrophy, and left ventricular diastolic dysfunction. Left ventricular systolic dysfunction may occur if wall stress remains high because of inadequate hypertrophy. Right ventricular structure and function may be similarly affected by the aforementioned morphologic and hemodynamic alterations and by pulmonary hypertension related to the sleep apnea/ obesity hypoventilation syndrome. The term obesity cardiomyopathy is applied when these cardiac structural and hemodynamic changes result in congestive heart failure. Obesity cardiomyopathy typically occurs in persons with severe and long-standing obesity. The predominant causes of death in those with obesity cardiomyopathy are progressive congestive heart failure and sudden cardiac death.

Cardiomyopathies↗
PubMedDate not supplied

[Hemodynamics of the eyes in diabetes mellitus].

The authors present evidence on the state of hemodynamics of the eye in patients suffering from diabetes mellitus on the basis of rheoophthalmographic and ophthalmoscopic studies with the use of the method of fluorescent angiography of the retina. The volume circulation of the eye proved to be connected with the intraophthalmic pressure and depended on the degree of affection of the eye vessels. Its changes were two-stage in character and depended on the state of the venous outflow. Diabetic retinopathy of the II stage served as the stage during which there was a sharp reduction of compensatory possibilities of hemodynamics, and further progress of vascular disturbances were observed. Rheoophthalmography permits to assess indirectly the degree of compensation of hemodynamic disturbances and can be used to asses clinical evolution of diabetic retinopathy.

Adolescent↗
PubMedDate not supplied

[Doppler ultrasonography of the common carotid artery in persons of different age].

The author carried out ultrasonography of the common carotid arteries by the method based on Doppler's phenomenon in 100 subjects aged 16--86 years. The maximal, minimal and mean flow velocity, vascular resistance, and symmetry and shape of the recorded curve were evaluated. Early and progressing with age changes were found in the curve indicating decreasing vascular wall elasticity. The maximal flow velocity decreased also rapidly. On the other hand, the mean and the minimal flow velocity and the index of vascular resistance remained without substantial changes up to the age of 70 years. In later age the minimal and mean flow velocity decreased rapidly and the index of vascular resistance increased greatly. This suggested accelerated rate of atherosclerosis development and/or exhaustion of compensatory mechanisms. In 3 cases of considerable asymmetry of the curve was observed caused by asymptomatic stenosis of one artery. Doppler ultrasonography could be useful at the time of intensification and evolution of atherosclerotic changes in the carotid arteries, and their effect on the condition of cerebral circulation.

Adolescent↗
PubMed1989

Dinoflagellates in evolution. A molecular phylogenetic analysis of large subunit ribosomal RNA.

The sequence of the large subunit ribosomal RNA (LsuRNA) gene of the dinoflagellate Prorocentrum micans has been determined. The inferred rRNA sequence [3408 nucleotides (nt)] is presented in its most probable secondary structure based on compensatory mutations, energy, and conservation criteria. No introns have been found but a hidden break is present in the second variable domain, 690 nt from the 5' end, as judged by agarose gel electrophoresis and primer extension experiments. Prorocentrum micans LsuRNA length and G+C content are close to those of ciliates and yeast. The conserved portions of the molecule (1900 nt) have been aligned with corresponding sequences from various eukaryotes, including five protista, one metaphyta, and three metazoa. An extensive phylogenetic study was performed, comparing two phenetic methods (neighbor joining on difference matrix, and Fitch and Margoliash on Knuc values matrix) and one cladistic (parsimony). The three methods led to similar tree topologies, except for the emergence of yeast that groups with ciliates and dinoflagellates when phenetic methods are used, but emerges later in the most parsimonious tree. This discrepancy was checked by statistical analyses on reduced trees (limited to four species) inferred using parsimony and evolutionary parsimony methods. The data support the phenetic tree topologies and a close relationship between dinoflagellates, ciliates, and yeast.

Animals↗
PubMed1992

Evolutionary adaptation to different thermal environments via transcriptional regulation.

Populations of the teleost fish Fundulus heteroclitus are subjected to the clinical variation in environmental temperatures that occurs along the eastern seacoast of North America. In concordance with this change in temperature is the clinal variation in the enzyme concentration of the heart-type lactate dehydrogenase (LDH-B; E.C.1.1.1.27). Previously we have shown that the compensating change in the LDH-B enzyme concentration is due to a change in the amount of LDH-B mRNA, but we did not define whether this was due to differences in mRNA stability or to differences in rate of transcription. The results presented here help clarify the molecular mechanism responsible for the variation in Ldh-B gene expression: the rate of transcription from the Ldh-B locus is significantly different between populations, and this difference is responsible for the compensatory change in LDH-B enzyme concentration.

Adaptation, Biological↗
PubMed2001

Noncoding RNA gene detection using comparative sequence analysis.

BACKGROUND: Noncoding RNA genes produce transcripts that exert their function without ever producing proteins. Noncoding RNA gene sequences do not have strong statistical signals, unlike protein coding genes. A reliable general purpose computational genefinder for noncoding RNA genes has been elusive. RESULTS: We describe a comparative sequence analysis algorithm for detecting novel structural RNA genes. The key idea is to test the pattern of substitutions observed in a pairwise alignment of two homologous sequences. A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show a pattern of compensatory mutations consistent with some base-paired secondary structure. We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. Given an input pairwise sequence alignment (e.g. from a BLASTN comparison of two related genomes) we classify the alignment into the coding, RNA, or null class according to the posterior probability of each class. CONCLUSIONS: We have implemented this approach as a program, QRNA, which we consider to be a prototype structural noncoding RNA genefinder. Tests suggest that this approach detects noncoding RNA genes with a fair degree of reliability.

Algorithms↗
PubMed1984

[The ambitio-impulse different from narcissism].

We should not let our dynamic drive bog down in the ambiguous concept of "libido". A concept which disturbed Freud himself as is clearly demonstrated in his latest works and which has been considerably misused afterwards. In order to achieve this aim we have in the light of psychopathology, of the symbolic nature of dreams and of our own personal experience set to describe three fundamental drives-the real roots of Man unseparable from his constitution-namely 1. ambitio: (which prompts Man to assert himself, to develop and dominate); 2. agressio: (the urge to defend our internal territory or to overcome obstacles according to our will); 3. attractio: (the disposition to be moved or attracted by this or that object). The present paper shall deal with ambitio which is not to be mixed up with conscious ambition. This unconscious drive, axial and archaic which nourishes the evolution of all living matter (even a tree trunk) should not be interspersed with guilt but is indispensable to our emergence from the Cosmos. Ambitio can be subject to hypertrophy by a compensatory process in cases of megalomania and on the contrary it can be atrophied in the case of a failure syndrome or inferiority complex for example. The most delicate stage of the process is that of its taming and of its conscious acceptance. All things which if properly dealt with and if we want to avoid the traps of authoritarianism or of the narcissistic delusion will lead us in the interest of others, to the most realistic modesty.

Acute Disease↗
PubMedDate not supplied

Two AGAMOUS-like MADS-box genes from Taihangia rupestris (Rosaceae) reveal independent trajectories in the evolution of class C and class D floral homeotic functions.

Duplicate genes may be retained by sub- and/or neofunctionalization through changes in gene expression and/or coding sequence, and therefore have the potential to contribute to the genetic robustness and diversification of an organism. In this study, two MADS-box genes were isolated from Taihangia rupestris, a core eudicot species belonging to the Rosaceae. Sequence and phylogenetic analyses revealed that they are clade members of the euAG and PLE lineages, respectively, and hence the two genes are named TrAG (Taihangia rupestris AGAMOUS) and TrSHP (Taihangia rupestris SHATTERPROOF). Southern blot analysis shows that TrSHP is a single-copy gene in the T. rupestris genome. In situ hybridization analyses show that both TrAG and TrSHP are mainly expressed in the stamens, carpels, and ovules. When the stamen primordia are firstly observed, TrAG is initially expressed in the floral meristem domain that will initiate stamens and carpels. In contrast, no TrSHP signal is observed at this developmental stage. At late stages of carpel development, TrAG expression is detected in the ovules, ovaries, and developing styles and stigmas, whereas TrSHP expression is tightly restricted to the ovules. The transgenic Arabidopsis plants containing 35S::TrAG and 35S::TrSHP, respectively, showed similar phenotypes, including homeotic conversions of sepals into carpelloid structures bearing ovules and petals into staminoid organs, and the fruits shattering prematurely along the dehiscence zone. In addition, the phenotype of the transgenic 35S::TrSHP Arabidopsis plants revealed that perianth abscission was inhibited. Yeast two-hybrid assays indicated that TrAG can interact with TrSEP3, whereas TrSHP cannot. The data suggest that the euAG and PLE paralogs, TrAG and TrSHP, may have subfunctionalized and/or neofunctionalized through changes in expression patterns and accumulating variations in the coding regions. Taking these findings together with those available expression and functional data from Arabidopsis and other species, we conclude that the compensatory ways vary among the euAG and PLE lineage pairs in eudicot species.

Blotting, Southern↗
PubMed2002

Dobzhansky-Muller incompatibilities in protein evolution.

We study fitness landscape in the space of protein sequences by relating sets of human pathogenic missense mutations in 32 proteins to amino acid substitutions that occurred in the course of evolution of these proteins. On average, approximately 10% of deviations of a nonhuman protein from its human ortholog are compensated pathogenic deviations (CPDs), i.e., are caused by an amino acid substitution that, at this site, would be pathogenic to humans. Normal functioning of a CPD-containing protein must be caused by other, compensatory deviations of the nonhuman species from humans. Together, a CPD and the corresponding compensatory deviation form a Dobzhansky-Muller incompatibility that can be visualized as the corner on a fitness ridge. Thus, proteins evolve along fitness ridges which contain only approximately 10 steps between successive corners. The fraction of CPDs among all deviations of a protein from its human ortholog does not increase with the evolutionary distance between the proteins, indicating that substitutions that carry evolving proteins around these corners occur in rapid succession, driven by positive selection. Data on fitness of interspecies hybrids suggest that the compensatory change that makes a CPD fit usually occurs within the same protein. Data on protein structures and on cooccurrence of amino acids at different sites of multiple orthologous proteins often make it possible to provisionally identify the substitution that compensates a particular CPD.

Amino Acid Sequence↗
PubMed2005

Maintaining a conserved methylation in plant and insect U2 snRNA through compensatory mutation by nucleotide insertion.

The extensive post-transcriptional modification of U2 snRNA is required for spliceosome assembly and pre-mRNA splicing in vertebrates. However, the rare modification of U2 snRNA in yeast implies a different mechanism for regulating spliceosome biogenesis in single-celled eukaryotes. To understand the evolutionary pattern of U2 snRNA methylation, we determined for the first time, the 2'-O-methylations of U2 snRNA in Oryza sativa, Arabidopsis thaliana and Drosophila melanogaster, and revealed two methylations which are conserved in a crucial region of U2 snRNA in plants. Interestingly, one of the methylations, U2-Cm29 is also methylated in D. melanogaster, but not in vertebrates. According to the methylation of U2-C29, computational analysis of databases identified three canonical box C/D snoRNAs, named OsmgU2-29, AtmgU2-29 and DmmgU2-28, as small methylation guides of U2 snRNA from O. sativa, A. thaliana and D. melanogaster, respectively. Although very divergent in their sequence, the three snoRNAs exhibit in common an 11 nucleotide-long sequence complementarity to corresponding U2 snRNA, implying a functional constraint on the modification during evolution. Interestingly, a nucleotide is found to be inserted both in U2 snRNA and DmmgU2-28 and maintains a perfect match of duplex specifying the methylation of C28 in Drosophila U2 snRNA. This is the first time a new model is being provided for compensatory mutations between a small guide RNA and its target by nucleotide insertion, instead of the known nucleotide substitution. In contrast to small Cajal body-specific RNAs (scaRNAs), the snoRNAs are similar to the reported singlet guide RNAs and are known to localize in nucleolus.

Animals↗