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PubMed2006

Characterization of compensated mutations in terms of structural and physico-chemical properties.

The study of the evolution of compensatory mechanisms among amino acids is paramount to our understanding of intramolecular epistatic interactions. It has been addressed from different points of view, for example much effort has been devoted to establish the number of compensatory mutations required per deleterious mutation. However, we still do not know how the nature of the compensated mutation determines the existence of compensatory mutations. Within this context, recent studies have produced several instances of an interesting phenomenon: human disease-associated residues may sometimes appear as wild-type residues in non-human proteins. This can be explained in terms of compensatory mutations, present in the non-human protein, which would neutralize the damage caused by the disease-associated residue. Therefore, comparison between these compensated mutations and non-compensated pathological mutations provides a simple approach to understand how the nature of the compensated deleterious mutation determines the existence of compensatory mutations. To address this issue, we have obtained a large set of compensated mutations and characterised them with a series of different properties. When comparing the resulting distributions with those from pathological mutations we find that in general compensated mutations are milder than pathological mutations. More precisely, we find that the probability that a compensatory mutation will evolve is directly related (i) to the location in the protein structure and (ii) to changes in physico-chemical properties (e.g. amino acid volume or hydrophobicity) of the compensated mutation.

Animals↗
PubMed1986

The human 18S ribosomal RNA gene: evolution and stability.

We report the 1,870-base-pair primary sequence of a human 18S rRNA gene and propose a secondary structure based on this sequence and the general mammalian structure. A basic secondary structure for the small subunit rRNA has been preserved throughout evolution by compensatory and neutral base changes in double-stranded regions. The molecule contains eight regions that can vary in structure and that comprise 432 bases, while 1,438 bases belong to regions of conserved structure among all species tested. The conserved regions show a remarkably low sequence divergence rate of 0.1% between the human and mouse genes over the approximately 80 million years since the mammalian radiation. This value may make the small subunit rDNA the most highly conserved sequence known. Sequence conservation in higher eukaryotes with multiple copies of the gene is probably achieved by the combination of strong selection and the correction of tandem genes by unequal homologous exchange.

Animals↗
PubMed2004

Knockdown of C-terminal Src kinase by siRNA-mediated RNA interference augments T cell receptor signaling in mature T cells.

C-terminal Src kinase (Csk) controls the Src family kinase Lck, which is essential for T cell antigen receptor (TCR)-mediated signaling. For the first time, we here report the effects of acute elimination of Csk in Jurkat T cells and primary T cells using short interfering (si) RNA. In both cell types, 70-85% knockdown of Csk was achieved within 48 h. No alterations in surface expression of CD3, CD4 or CD8, or in Lck protein level were observed. Phosphorylation of Y505 in Lck was markedly reduced and a concomitant 4-5-fold increase in Lck Y394 phosphorylation was observed both in normal and Jurkat T cells. Kinase assays revealed 2-3-fold higher Lck activity. In Jurkat cells, basal levels of zeta chain phosphorylation were elevated, and spontaneous NFAT-AP-1 activation occurred, indicating aberrant Lck kinase activity. After TCR triggering, Csk knockdown cells revealed faster and stronger, but not sustained, phosphorylation of Lck Y394 and zeta chains compared to control. TCR-induced activation of NFAT-AP-1 and TCR/CD28-stimulated IL-2 secretion occurred at weaker stimuli and with augmented responses in Csk knockdown Jurkat and primary T cells, respectively. Altogether, these data suggest that acute elimination of Csk in T cells without evolution of compensatory mechanisms results in aberrant Lck activity and augmented TCR-stimulated responses.

CSK Tyrosine-Protein Kinase↗
PubMed1993

[From myocardial hypertrophy to heart failure: role of the interstitium].

In the progression from myocardial hypertrophy to heart failure, abnormalities in the interstitial space of the heart seem to play a critical role. The formation of an extracellular oedema and the alterations in coronary subendocardial perfusion are associated with the development of interstitial fibrosis. Cardiac experimental studies documented the presence of augmented interstitial fluid volume and pressure and a subsequent remodelling of the fibrillar network of the extracellular space of the myocardium during the phases of the cardiovascular response to a sudden overload. Variations of the Starling's forces balance caused by enhanced endothelial permeability or due to an impairment of cardiac lymphatic drainage may contribute to the development of an acute heart failure. During stable hyperfunction, the organization of a chronic oedema should account for interstitial changes in the hypertrophic myocardium. Reactive fibrosis seems to be under hormonal control. The activation of the renin-angiotensin-aldosterone system is responsible for interfascicular and intercellular accumulation of fibrillar collagen within the cardiac interstitium. Perivascular fibrosis in the subendocardium may impair intramyocardial distribution of coronary flow. When an inadequate hypertrophy occurs, because of an elevation in ventricular wall stress, myocardial oxygen consumption rises and this may lead to the exhaustion of coronary blood flow reserve in the subendocardial layers. This underperfusion may be responsible for the development of myocardial ischemia. Coronary hemodynamic changes in the microcirculation as those prompted by interstitial alterations may contribute to the onset of myocyte necrosis and to the formation of restorative fibrosis. The progressive mechanical overload of the spared hypertrophied myocytes could explain the initiation of a positive feedback mechanism which perpetuates endomyocardial perfusion impairment, interstitial oedema and remodelling, finally, causing myocyte deaths and fibrous tissue proliferation. These structural alterations and their pathophysiological counterparts appear to be closely related to the evolution from compensatory hypertrophy to chronic myocardial failure in hypertrophic heart disease.

Acute Disease↗
PubMed2000

Scanning the visual world: a study of patients with homonymous hemianopia.

OBJECTIVES: This study examined the scanpaths of patients with homonymous hemianopia while viewing naturalistic pictures in their original and also spatially filtered forms. Features of their scanpaths with respect to various saccade and fixation parameters were examined to determine whether they develop compensatory eye movement strategies. The effects of various lesion parameters including location, size, and age on the evolution of such strategies were considered. METHODS: Eye movements of eight patients with homonymous hemianopia (four left, four right), but lacking neglect, were recorded while they viewed 22 images of real scenes, and they were compared with the eye movements of eight age matched controls. Subjects viewed each image for 3 seconds, initially in a spatially filtered form in which much of the semantic content had been removed, and then in their unfiltered, original form. RESULTS: Patients differed significantly from controls in various fixation and saccade parameters. For fixation parameters patients with hemianopia fixated different spatial positions from controls, made more fixations which were more widely distributed and of shorter duration than controls, and spent a greater proportion of their total fixation time in the area corresponding to their blind hemifield. They did not make significantly more refixations than controls. For saccade parameters patients made more saccades into their blind hemifield, these saccades having shorter latencies and shorter amplitudes than those made into their seeing field, and had longer scanpaths than control subjects. The amplitude of their first saccade was longer than that of controls although its direction did not correlate simply with the side of the field defect. Their mean saccade amplitude was similar to that of controls. Filtering out high spatial frequencies within images seemed to accentuate the described differences between eye movement characteristics of hemianopes and controls. Scanpath differences correlated with increasing age but not location or size of lesions causing the hemianopia. CONCLUSION: Various features of scanpaths produced by hemianopes were different from normal subjects. These differences correlated with lesion age and may reflect the evolution of a compensatory eye movement strategy.

Adult↗
PubMed2003

Evolution of interacting proteins in the mitochondrial electron transport system in a marine copepod.

The extensive interaction between mitochondrial-encoded and nuclear-encoded subunits of electron transport system (ETS) enzymes in mitochondria is expected to lead to intergenomic coadaptation. Whether this coadaptation results from adaptation to the environment or from fixation of deleterious mtDNA mutations followed by compensatory nuclear gene evolution is unknown. The intertidal copepod Tigriopus californicus shows extreme divergence in mtDNA sequence and provides an excellent model system for study of intergenomic coadaptation. Here, we examine genes encoding subunits of complex III of the ETS, including the mtDNA-encoded cytochrome b (CYTB), the nuclear-encoded rieske iron-sulfur protein (RISP), and cytochrome c(1) (CYC1). We compare levels of polymorphism within populations and divergence between populations in these genes to begin to untangle the selective forces that have shaped evolution in these genes. CYTB displays dramatic divergence between populations, but sequence analysis shows no evidence for positive selection driving this divergence. CYC1 and RISP have lower levels of sequence divergence between populations than CYTB, but, again, sequence analysis gives no evidence for positive selection acting on them. However, an examination of variation at cytochrome c (CYC), a nuclear-encoded protein that transfers electrons between complex III and complex IV provides evidence for selective divergence. Hence, it appears that rapid evolution in mitochondrial-encoded subunits is not always associated with rapid divergence in interacting subunits (CYC1 and RISP), but can be in some cases (CYC). Finally, a comparison of nuclear-encoded and mitochondrial-encoded genes from T. californicus suggests that substitution rates in the mitochondrial-encoded genes are dramatically increased relative to nuclear genes.

Adaptation, Biological↗
PubMed2001

Mutation-selection models solved exactly with methods of statistical mechanics.

We reconsider deterministic models of mutation and selection acting on populations of sequences, or, equivalently, multilocus systems with complete linkage. Exact analytical results concerning such systems are few, and we present recent and new ones obtained with the help of methods from quantum statistical mechanics. We consider a continuous-time model for an infinite population of haploids (or diploids without dominance), with N sites each, two states per site, symmetric mutation and arbitrary fitness function. We show that this model is exactly equivalent to a so-called Ising quantum chain. In this picture, fitness corresponds to the interaction energy of spins, and mutation to a temperature-like parameter. The highly elaborate methods of statistical mechanics allow one to find exact solutions for non-trivial examples. These include quadratic fitness functions, as well as 'Onsager's landscape'. The latter is a fitness function which captures some essential features of molecular evolution, such as neutrality, compensatory mutations and flat ridges. We investigate the mean number of mutations, the mutation load, and the variance in fitness under mutation-selection balance. This also yields some insight into the 'error threshold' phenomenon, which occurs in some, but not all, examples.

Evolution, Molecular↗
PubMed2002

Evolution of functionally conserved enhancers can be accelerated in large populations: a population-genetic model.

The evolution of cis-regulatory elements (or enhancers) appears to proceed at dramatically different rates in different taxa. Vertebrate enhancers are often very highly conserved in their sequences, and relative positions, across distantly related taxa. In contrast, functionally equivalent enhancers in closely related Drosophila species can differ greatly in their sequences and spatial organization. We present a population-genetic model to explain this difference. The model examines the dynamics of fixation of pairs of individually deleterious, but compensating, mutations. As expected, small populations are predicted to have a high rate of evolution, and the rate decreases with increasing population size. In contrast to previous models, however, this model predicts that the rate of evolution by pairs of compensatory mutations increases dramatically for population sizes above several thousand individuals, to the point of greatly exceeding the neutral rate. Application of this model predicts that species with moderate population sizes will have relatively conserved enhancers, whereas species with larger populations will be expected to evolve their enhancers at much higher rates. We propose that the different degree of conservation seen in vertebrate and Drosophila enhancers may be explained solely by differences in their population sizes and generation times.

Animals↗
PubMed2004

A Calpha model for the transmembrane alpha helices of gap junction intercellular channels.

Gap junction channels connect the cytoplasms of apposed cells via an intercellular conduit formed by the end-to-end docking of two hexameric hemichannels called connexons. We used electron cryomicroscopy to derive a three-dimensional density map at 5.7 angstroms in-plane and 19.8 angstroms vertical resolution, allowing us to identify the positions and tilt angles for the 24 alpha helices within each hemichannel. The four hydrophobic segments in connexin sequences were assigned to the alpha helices in the map based on biochemical and phylogenetic data. Analyses of evolutionary conservation and compensatory mutations in connexin evolution identified the packing interfaces between the helices. The final model, which specifies the coordinates of Calpha atoms in the transmembrane domain, provides a structural basis for understanding the different physiological effects of almost 30 mutations and polymorphisms in terms of structural deformations at the interfaces between helices, revealing an intimate connection between molecular structure and disease.

Amino Acid Sequence↗
PubMed2001

Calcium needs of the elderly to reduce fracture risk.

Contemporary calcium intakes in the industrialized nations are substantially lower than those to which human physiology is adapted by evolution. As a result, compensatory adjustment is required lifelong. This adjustment consists of high levels of parathyroid activity, leading to parathyroid hyperplasia, high circulating levels of 1,25(OH)2D and high bone turnover. The capacity of these compensatory mechanisms to provide sufficient calcium to offset daily losses from the body declines with age; hence, increasingly the body tears down bone to access its calcium. As a result, the calcium requirement for skeletal maintenance is said to rise with age. Supplemented intakes to a total in the range of 32.5-42.5 mmol (1300-1700 mg)/day have been shown to arrest age-related bone loss and to reduce fracture risk in individuals 65 and older and intakes of 60 mmol (2400 mg), to restore the setting of the parathyroid glands to young adult values. Intakes at such levels also minimize the expression of other disorders such as colon cancer, hypertension and obesity, all of which, while multifactorial, have a calcium deficiency component. Milk, mainly because of constructive interactions among its several key nutrients, is probably the most nutritionally and cost effective way of meeting the calcium requirement in the elderly.

Aged↗
PubMed1995

Volumetric intracoronary ultrasound: a new maximum confidence approach for the quantitative assessment of progression-regression of atherosclerosis?

Quantitative assessment of atherosclerosis during its natural history and following therapeutic interventions is important, as cardiovascular disease remains the most significant cause of morbidity and mortality in industrial societies. While coronary angiography delineates the vessel lumen, permitting only the indirect determination of atherosclerotic wall changes encroaching upon the lumen, intracoronary ultrasound permits direct plaque assessment and quantification. The angiographic percent diameter stenosis, previously suggested as measure of a maximum confidence approach, is still commonly used to quantify stenosis severity, but the reference segments which are required for angiographic interpolation of the normal vessel dimensions are frequently involved in the general process of atherosclerosis, including progression or regression. Considering also the variability of vascular remodeling during the evolution of atherosclerosis, including compensatory enlargement and paradoxical arterial shrinkage, intracoronary ultrasound appears currently to be the only reliable technique to measure plaque burden and progression or regression of atherosclerosis. However, correct matching of the site of measurement at follow-up with the site of the initial ultrasound study is often difficult to achieve, but is significantly facilitated by the use of volumetric intracoronary ultrasound. This approach permits not only area measurement, but also measurement of plaque volume, which appears to be the ideal measure for quantifying the atherosclerotic plaque, as it is highly reproducible and directly reflects the changes of an entire arterial segment.

Animals↗
PubMed2003

Selective constraints on intron evolution in Drosophila.

Intron sizes show an asymmetrical distribution in a number of organisms, with a large number of "short" introns clustered around a minimal intron length and a much broader distribution of longer introns. In Drosophila melanogaster, the short intron class is centered around 61 bp. The narrow length distribution suggests that natural selection may play a role in maintaining intron size. A comparison of 15 orthologous introns among species of the D. melanogaster subgroup indicates that, in general, short introns are not under greater DNA sequence or length constraints than long introns. There is a bias toward deletions in all introns (deletion/insertion ratio is 1.66), and the vast majority of indels are of short length (<10 bp). Indels occurring on the internal branches of the phylogenetic tree are significantly longer than those occurring on the terminal branches. These results are consistent with a compensatory model of intron length evolution in which slightly deleterious short deletions are frequently fixed within species by genetic drift, and relatively rare larger insertions that restore intron length are fixed by positive selection. A comparison of paralogous introns shared among duplicated genes suggests that length constraints differ between introns within the same gene. The janusA, janusB, and ocnus genes share two short introns derived from a common ancestor. The first of these introns shows significantly fewer indels than the second intron, although the two introns show a comparable number of substitutions. This indicates that intron-specific selective constraints have been maintained following gene duplication, which preceded the divergence of the D. melanogaster species subgroup.

Animals↗
PubMed1994

Leeway and constraints in the forced evolution of a regulatory RNA helix.

The start of the coat protein gene of RNA phage MS2 adopts a well-defined hairpin structure of 12 bp (including one mismatch) in which the start codon occupies the loop position. An earlier expression study using partial MS2 cDNA clones had indicated that the stability of this hairpin is important for gene expression. For every -1.4 kcal/mol increase in stability a 10-fold reduction in coat protein was obtained. Destabilizations beyond the wild-type value did not affect expression. These results suggested that the hairpin was tuned in the sense that it has the highest stability still compatible with maximal ribosome loading. Employing an infectious MS2 cDNA clone, we have now tested the prediction that the delta G 0 of the coat protein initiator helix is set at a precise value. We have introduced stabilizing and destabilizing mutations into this hairpin in the intact phage and monitored their evolution to viable species. By compensatory mutations, both types of mutants quickly revert along various pathways to wild-type stability, but not to wild-type sequence. As a rule the second-site mutations do not change the encoded amino acids or the Shine-Dalgarno sequence. The return of too strong hairpins to wild-type stability can be understood from the need to produce adequate supplies of coat protein. The return of unstable hairpins to wild-type stability is not self-evident and is presently not understood. The revertants provide an evolutionary landscape of slightly suboptimal phages, that were stable at least for the duration of the experiment (approximately 20 infection cycles).(ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗
PubMed1994

How frequent are correlated changes in families of protein sequences?

A loss-of-function point mutation in a protein is often rescued by an additional mutation that compensates for the original physical change. According to one hypothesis, such compensation would be most effective in maintaining a structural motif if the two mutated residues were spatial neighbors. If this hypothesis were correct, one would expect that many such compensatory mutations have occurred during evolution and that present-day protein families show some degree of correlation in the occurrence of amino acid residues at positions whose side chains are in contact. Here, a statistical theory is presented which allows evaluation of correlations in a family of aligned protein sequences by assigning a scalar metric (such as charge or side-chain volume) to each type of amino acid and calculating correlation coefficients of these quantities at different positions. For the family of myoglobins it is found that there is a high correlation between fluctuations in neighboring charges. The correlation is close to what would be expected for total conservation of local charge. For the metric side-chain volume, on the other hand, no correlation could be found.

Amino Acid Sequence↗
PubMed2006

[Adult spinal deformities].

Contrary to a commonly held notion, scoliosis, and especially lumbar and thoracolumbar scoliosis, can develop during adulthood. Its evolution is slow and insidious and involves both the anatomic aspect of the curve and the functional aspect (development or worsening of painful spinal or radicular symptoms and/or disequilibrium). This finding underlines the necessity of a regular and extended monitoring of all patients presenting with such a condition. In terms of anatomy, three elements, each of them having a very precise functional impact, may characterize the radiological evolution of those deformities: the development of a rotatory dislocation, stiffness of the primary curve, and especially the lumbo-sacral spine, and the progressive development of a thoracolumbar kyphosis. Three types of treatment are available: rehabilitation, orthopedic treatment and surgery. The first two can act efficiently on painful symptoms and/or disequilibrium but in no case can modify the evolving pattern of the deformity. Surgical treatment is useful in stopping the evolving processes, reequilibrating the trunk on the pelvis and controlling painful lumbar and sometimes radicular phenomenon. Therapeutic and especially surgical indications are complex and by no means can be limited to an angle threshold beyond which surgery is indicated. Those indications depend on the type, the severity and the potential or effective evolution of the primary and compensatory curves, as well as on the age, the functional impact of the deformity and the general medical condition of the patient.

Adult↗