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An increase in viral replicative capacity drives the evolution of protease inhibitor-resistant human immunodeficiency virus type 1 in the absence of drugs.

Little is known about the factors which drive the evolution of protease inhibitor-resistant human immunodeficiency virus type-1 in the absence of drugs. To examine if viral replicative capacity (RC) is an important determinant, we performed in vitro evolution experiments in the absence of drugs with a unique panel of 6 drug-resistant human immunodeficiency virus type-1 recombinant protease variants with a range of different RC. The experiments revealed that an increase in viral RC was indeed an important determinant of evolution. Initial protease inhibitor-resistant viruses with only a few protease mutations and a lowered RC evolved into viruses with an increased RC, either by reversion of primary resistance mutations or by the acquisition of compensatory mutations. For these viruses with a lowered RC, higher fitness peaks are most likely available in the sequence space. Evolution of these viruses in the absence of drugs will therefore drive them to new fitness peaks. In contrast, viruses with an RC comparable to wild type or even higher than wild type did not show any evolution. In the case of these viruses, it is not so likely that higher fitness peaks are present within the sequence space, and therefore, these variants will persist in the absence of drug pressure.

Amino Acid Substitution↗

Mirror asomatognosia in right lesions stroke victims.

The objectives of this prospective study were: to search for mirror-induced disorders of the body image in right hemisphere stroke victims using a description task of the contralateral upper limb, to analyze their clinical features, and to discuss possible mechanisms. Sixteen consecutive patients with documented unilateral right hemisphere stroke were examined for asomatognosia at the acute phase of stroke, then at least 2 months after stroke under three test conditions: without a mirror, with a conventional mirror, with an inverted mirror. Video recordings of the tests were analyzed to assess performance. The diagnosis of asomatognosia was retained if the subject reported at least one of three sensations: limb transformation, limb strangeness, and/or limb alienation. During the acute phase, 14/16 patients presented manifestations of asomatognosia. All of these spontaneous manifestations had disappeared 2 months later, but were reactivated in 12 patients when exposed to mirror images. The mirror tests revealed four situations: no disorder (n = 4), asomatognosia with both mirrors (n = 5), asomatognosia with the conventional or inverted mirrors (n = 1 and 5), and asomatognosia with the inverted mirror (n = 1). These manifestations were designated as mirror-asomatognosia, a disorder resulting from adaptations of the procedures leading to reorganization of the internal representations of the body image. These findings suggest there are several such internal representations of the body image and that direct body image and mirror body image would be two specific ones. These clinical manifestations and their evolution over time are an expression of the progressive nature of the underlying compensatory mechanisms made possible by brain plasticity.

Adult↗

[Comparative analysis of blood coagulation and various indicators of microcirculation in patients with coronary arteriosclerosis and hypertension in the age aspect].

In patients with hypertensive disease and coronary atherosclerosis the blood-clotting potential increases on account of a rise in the level of procoagulants and inhibition of fibrinolysis. Age-specific differences in the characteristics of the coagulation and fibrinolytic system of the blood are levelled out parallel with the development of atherosclerosis and progressive evolution of hypertensive disease. In patients of advanced age a tendency toward a compensatory increased activity of erythrocytic anticoagulation factors is noted, finding its expression in a drop of the procoagulants level, and increase of anticoagulants and in a rising fibrinolytic activity. Changes in the state of the conjunctival microcirculation and the retinal hemodynamics correlate with the intensity of the pathological process and shifts in the blood coagulation system.

Adaptation, Physiological↗

Compensatory substitutions restore normal core assembly in simian immunodeficiency virus isolates with Gag epitope cytotoxic T-lymphocyte escape mutations.

The evolution of human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) as they replicate in infected individuals reflects a balance between the pressure on the virus to mutate away from recognition by dominant epitope-specific cytotoxic T lymphocytes (CTL) and the structural constraints on the virus' ability to mutate. To gain a further understanding of the strategies employed by these viruses to maintain replication competency in the face of the intense selection pressure exerted by CTL, we have examined the replication fitness and morphological ramifications of a dominant epitope mutation and associated flanking amino acid substitutions on the capsid protein (CA) of SIV/simian-human immunodeficiency virus (SHIV). We show that a residue 2 mutation in the immunodominant p11C, C-M epitope (T47I) of SIV/SHIV not only decreased CA protein expression and viral replication, but it also blocked CA assembly in vitro and virion core condensation in vivo. However, these defects were restored by the introduction of upstream I26V and/or downstream I71V substitutions in CA. These findings demonstrate how flanking compensatory amino acid substitutions can facilitate viral escape from a dominant epitope-specific CTL response through the effects of these associated mutations on the structural integrity of SIV/SHIV.

Amino Acid Sequence↗

Complete sequences of the rRNA genes of Drosophila melanogaster.

In this, the first of three papers, we present the sequence of the ribosomal RNA (rRNA) genes of Drosophila melanogaster. The gene regions of D. melanogaster rDNA encode four individual rRNAs: 18S (1,995 nt), 5.8S (123 nt), 2S (30 nt), and 28S (3,945 nt). The ribosomal DNA (rDNA) repeat of D. melanogaster is AT rich (65.9% overall), with the spacers being particularly AT rich. Analysis of DNA simplicity reveals that, in contrast to the intergenic spacer (IGS) and the external transcribed spacer (ETS), most of the rRNA gene regions have been refractory to the action of slippage-like events, with the exception of the 28S rRNA gene expansion segments. It would seem that the 28S rRNA can accommodate the products of slippage-like events without loss of activity. In the following two papers we analyze the effects of sequence divergence on the evolution of (1) the 28S gene "expansion segments" and (2) the 28S and 18S rRNA secondary structures among eukaryotic species, respectively. Our detailed analyses reveal, in addition to unequal crossing-over, (1) the involvement of slippage and biased mutation in the evolution of the rDNA multigene family and (2) the molecular coevolution of both expansion segments and the nucleotides involved with compensatory changes required to maintain secondary structures of RNA.

Animals↗

Genome size, secondary simplification, and the evolution of the brain in salamanders.

Compared to other vertebrates, even including lampreys and hagfishes in some respects, salamanders exhibit a relatively simple organization of brain and sense organs which is illustrated here using the visual system as an example. The greatest simplicity is found in the bolitoglossine salamanders, yet all bolitoglossines possess highly projectile tongues and rely on vision for survival; furthermore, some species are agile and acrobatic. The unusual features of the visual system of salamanders include small numbers of large neurons, a low degree of morphological differentiation among neurons, a small proportion of myelinated axons in the optic nerve, and an optic tectum consisting essentially of a periventricular cellular layer and a superficial fiber layer. Similar features are found throughout the central nervous system of salamanders and in the lateral line, auditory and olfactory systems as well. Phylogenetic analysis shows that the most parsimonious interpretation of these data is that the simple organization of the brain and sense organs of salamanders was derived secondarily from a more complex ancestral state. We hypothesize that increased genome size has led to simplification of the nervous system in salamanders. Increased genome size appears to have had profound effects on neural development in salamanders, leading to paedomorphosis, the retention of juvenile or even embryonic characteristics into adulthood. In particular, large genome size is associated with large cell size and reduced rates of cell proliferation, migration and differentiation. Secondary simplification has constrained the function of the salamanders' visual system, primarily by increasing cell size and decreasing cell numbers. However, it also has provided an opportunity for the evolution of compensating mechanisms, which have helped to restore or even enhance visual function. Most apparent among the compensatory mechanisms of bolitoglossine salamanders is the presence of well developed ipsilateral retinotectal projections, which apparently enhance depth perception. It is difficult to explain the unusual history of the nervous system in salamanders solely in terms of natural selection and adaptation. Increasing genome size through selfish replication appears to have played a major role in the evolution of salamander brains by imposing functional constraints as well as creating opportunities for overcoming them.

Animals↗

Compensatory adaptation to the deleterious effect of antibiotic resistance in Salmonella typhimurium.

Most chromosomal mutations that cause antibiotic resistance impose fitness costs on the bacteria. This biological cost can often be reduced by compensatory mutations. In Salmonella typhimurium, the nucleotide substitution AAA42 --> AAC in the rpsL gene confers resistance to streptomycin. The resulting amino acid substitution (K42N) in ribosomal protein S12 causes an increased rate of ribosomal proofreading and, as a result, the rate of protein synthesis, bacterial growth and virulence are decreased. Eighty-one independent lineages of the low-fitness, K42N mutant were evolved in the absence of antibiotic to ameliorate the costs. From the rate of fixation of compensated mutants and their fitness, the rate of compensatory mutations was estimated to be > or = 10-7 per cell per generation. The size of the population bottleneck during evolution affected fitness of the adapted mutants: a larger bottleneck resulted in higher average fitness. Only four of the evolved lineages contained streptomycin-sensitive revertants. The remaining 77 lineages contained mutants that were still fully streptomycin resistant, had retained the original resistance mutation and also acquired compensatory mutations. Most of the compensatory mutations, resulting in at least 35 different amino acid substitutions, were novel single-nucleotide substitutions in the rpsD, rpsE, rpsL or rplS genes encoding the ribosomal proteins S4, S5, S12 and L19 respectively. Our results show that the deleterious effects of a resistance mutation can be compensated by an unexpected variety of mutations.

Adaptation, Physiological↗

The ecological and evolutionary interface of hummingbird flight physiology.

The hovering ability, rapidity of maneuvers and upregulated aerobic capacity of hummingbirds have long attracted the interest of flight biologists. The range of intra- and interspecific variation in flight performance among hummingbirds, however, is equally impressive. A dominant theme in hummingbird evolution is progressive invasion of higher-elevation habitats. Hypobaric challenge is met behaviorally through compensatory changes in wingbeat kinematics, particularly in stroke amplitude. Over evolutionary time scales, montane colonization is associated with increases in body mass and relative wing area. Hovering ability has been well-studied in several North American hummingbird taxa, yet the broad range of interspecific variation in hummingbird axial and appendicular anatomy remains to be assessed mechanistically. Such varied features as tail length, molt condition and substantial weight change due to lipid-loading can dramatically alter various features of the flight envelope. Compared with our present knowledge of hovering performance in hummingbirds, the mechanics of forward flight and maneuvers is not well understood. Relationships among flight-related morphology, competitive ability and foraging behavior have been the focus of numerous studies on tropical and temperate hummingbirds. Ecologists have hypothesized that the primary selective agents on hummingbird flight-related morphology are the behaviors involved in floral nectar consumption. However, flight behaviors involved in foraging for insects may also influence the evolution of wing size and shape. Several comparisons of hummingbird communities across elevational gradients suggest that foraging strategies and competitive interactions within and among species vary systematically across elevations as the costs of flight change with body size and wing shape.

Animals↗

Evolutionary and functional analysis of the tailless enhancer in Musca domestica and Drosophila melanogaster.

To further understand the evolutionary dynamics of the regulatory interactions underlying development, we expand on our previous analysis of hunchback and compare the structure and function of the tailless enhancer between Musca domestica and Drosophila melanogaster. Our analysis shows that although the expression patterns and functional protein domains of tll are conserved between Musca and Drosophila, the enhancer sequences are unalignable. Upon closer investigation, we find that these highly diverged enhancer sequences encode the same regulatory information necessary for Bicoid, Dorsal, and the terminal system to drive tll expression. The binding sites for these transcription factors differ in the sequence, number, spacing, and position between the Drosophila and Musca tll enhancers, and we were unable to establish homology between binding sites from each species. This implies that the Musca and Drosophila Bcd-binding sites have evolved de novo in the 100 million years since these species diverged. However, in transgenic Drosophila embryos the Musca tll enhancer is able to drive the same expression pattern as endogenous Drosophila tll. Therefore, during the rapid evolution of enhancer sequences individual binding sites are continually lost and gained, but the transcriptional output is maintained by compensatory mutations in cis and in trans.

Amino Acid Sequence↗

Population consequences of mutagenesis and antimutagenesis.

Although the progress in basic understanding of mutagenesis and in techniques for precise measurement of mutation rates in test systems has been enormous, there has been very little progress in applying this information to estimates of germline mutation in humans, and even less in translating such estimates into quantitative assessments of the impact on future generations. This doesn't mean that new information about the mutation process, and antimutagens in particular, is not useful. Lowering the human mutation rate would be good, even if we can't say how good. Some simple population kinetics of a change of mutation are discussed, and it is shown that future environmental changes can be ignored if we assume that the impact of a disease on human welfare is changed by the environment in the same proportion as its effect on fitness. Since the human mutation rate appears to be much higher in males than in females, it would be especially important to find ways of reducing the male rate. The role of transposable elements in determining human spontaneous mutation rates is unknown, but unless data from experimental organisms are grossly misleading, this role may be substantial. It is sometimes argued that such responses as error-prone repair systems may be an evolutionary strategy to allow the population to try a larger repertoire of mutations in times of environmental change. They may also be a survival strategy. I suggest that, although such an evolutionary strategy may possibly be adopted in asexual organisms with a very high reproductive rate, it is very unlikely in Mendelian species with limited reproduction such as most higher animals. The amount of existing variability in a large population is so great relative to that which arises in a few generations by mutation that segregation and recombination of existing alleles would appear to be a better way of coping with changing environment. As the human age of reproduction has increased in the recent evolutionary past, it is possible that the compensatory adjustment of mutation rates has not been fast enough to keep up. Perhaps evolution of mutation rates is more determined by selection to reduce somatic mutation than by selection to reduce germinal mutation. Regardless of the answer to the question of the optimum mutation rate for long-time evolution, in my view, the optimum mutation rate from the standpoint of human welfare for the foreseeable future is zero.

Animals↗

The broad spectrum of preclinical radiobiology: British contributions.

British radiobiologists have often been at the forefront in taking clinical questions into the laboratory and in taking the results back into the clinic, i.e., what is nowadays labeled as Translational Research. They have published widely and have been very active in lectures, workshops, and discussions, forming an important component of the international communication web, both within the basic science aspects and in the translation from science to medicine, and back again. Major contributions have been made at the cellular and subcellular level, and at the level of multicellular structures, both normal and malignant. The common features of the response of cells to single doses in well-defined conditions have been used to interpret the much greater complexity of tissue and tumor responses treated with repeated small doses in a fractionated course, both of photons and other radiations, with and without chemical modifiers. The many contributions to the field of cell kinetics have provided the tools with which an understanding has been gained of the latency and evolution of radiation damage in different tissues. The prolonged interest in microenvironmental gradients and compensatory responses to injury have provided a framework for designing better radiotherapy schedules, and considerable spin-off to other branches of cancer therapy.

History, 20th Century↗

[The diagnostic significance of immunogenetic markers in vertebrogenic neurological syndromes].

A total of 116 patients presenting with different neurological syndromes of vertebral osteochondrosis were examined. More common in patients with reflex neurological manifestations of osteochondrosis compared with controls (n = 51) was a complete HLA phenotype (heterozygosity) determining better evolutional and biological resistance to injuring factors and ability to produce adequate adaptive and compensatory reactions. The diagnosing of incomplete phenotype in other groups indicated homozygosity of genes and suggested a high risk for development of the disorder. Criteria have been established for a relative risk of development of the disease for all six vertebrogenic neurological syndromes.

Biomarkers↗

[Morphologic characteristics of the liver in the postcholecystectomy syndrome].

Liver biopsies of 152 patients with post-cholecystectomy syndrome are studied. Liver alterations observed in these patients are subdivided into morphological syndromes (portal and periportal hepatitis, liver fibrosis and cirrhosis) and their evolution is investigated. Changes of intrahepatic bile ducts are studied and their adaptive-compensatory character is shown. Compensatory processes in the liver parenchyma are also investigated. Patho- and morphogenesis of alterations observed is discussed.

Adult↗

RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.

We test models for the evolution of helical regions of RNA sequences, where the base pairing constraint leads to correlated compensatory substitutions occurring on either side of the pair. These models are of three types: 6-state models include only the four Watson-Crick pairs plus GU and UG; 7-state models include a single mismatch state that combines all of the 10 possible mismatches; 16-state models treat all mismatch states separately. We analyzed a set of eubacterial ribosomal RNA sequences with a well-established phylogenetic tree structure. For each model, the maximum-likelihood values of the parameters were obtained. The models were compared using the Akaike information criterion, the likelihood-ratio test, and Cox's test. With a high significance level, models that permit a nonzero rate of double substitutions performed better than those that assume zero double substitution rate. Some models assume symmetry between GC and CG, between AU and UA, and between GU and UG. Models that relaxed this symmetry assumption performed slightly better, but the tests did not all agree on the significance level. The most general time-reversible model significantly outperformed any of the simplifications. We consider the relative merits of all these models for molecular phylogenetics.

Base Pairing↗

Kinetics of elemental content changes of bone tissue of mice during evolution under hypokinetic stress.

Concentration of 13 elements in bone tissue of mice held in tightly spaced cages for 3 wk, which caused an acute stress reaction, was determined by means of neutron activation analysis. Functionally different bone tissues of mice skeletons--the femur, accomplishing both supporting and dynamic functions; the parietal bone, being practically immovable; and the ectopic bone, newly formed under kidney capsule in the place of syngeneic bone marrow implantation--were analyzed. Similar dynamics of the elemental composition of investigated bones was found: the progressive demineralization owing to the loss of Ca, P, Mg, and Fe is accompanied by the compensatory inclusion of Sr in the bone tissues. In the ectopic bone, it was not as high. During evolution under hypokinetic stress, the microelement concentrations (Zn, Cr, Rb, Ru, Br, Co, Sb) change significantly. Results obtained form the evidence for some system character of osteoporosis at limited mobility.

Animals↗

[The adaptive-compensatory reactions in adjusting to space flights].

In this paper an evolutionary approach is used to substantiate the steps of life evolution on Earth towards overcoming the gravitational forces with the formation of metabolic cycles controlling the energetic of anti-G processes. The step of an adaptation to hypogravity was similar to return of surface animals to an aquatic environment. The impossibility of coming back to land was the "price" of adaptation to the aquatic environment. This phenomenon was used by the author as a logical model of human adaptation to a weightless environment. The concept of adaptation is examined from two points of view: adaptation and compensation. The scheme contains 4 steps of adaptation to space mission environments: Step I-preadaptation (phase of primary reactions); Step II-compensation of body structures not being in line with the conditions of a novel environment; Step III-the formation of parameters of an organism corresponding to the norm of adaptation to weightlessness; Step IV-the return of cosmonauts to Earth under hypergravity conditions. In compliance with these steps we consider the tasks of supporting space missions to facilitate body readaptation after return to Earth, i.e., to decrease the "price" of adaptation.

Adaptation, Physiological↗

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution.

Various methods for detecting correlation between sites were evaluated by ascertaining their ability to discriminate positively correlated sites from background correlation at randomly evolved sites. A model for generating pairwise correlations of different degrees is also described. An assortment of physicochemical vectors and similarity and difference matrices were used to discriminate correlated change. There was little difference in effectiveness between the different matrices, but there were significant differences between the matrices and the physicochemical vectors. It is shown that all methods investigated exhibit significant inability to screen out background correlation, particularly in the presence of phylogenetic relatedness between the sequences. Methods using the matrices are unable to distinguish positively correlated from negatively correlated, or compensatory, replacements.

Amino Acid Sequence↗

Contour tracking using a knowledge-based snake algorithm to construct three-dimensional pharyngeal bolus movement.

Videofluorography (VFG) using a barium-mixed bolus is in wide clinical use for assessing patients with swallowing disorders. VFG is usually done with both lateral (LA) and anterior-posterior (AP) views, most commonly in two separate sittings. A real-time, three-dimensional (3-D) representation of the evolution of a pharyngeal bolus and its volumetric information can potentially help clinicians analyze and visualize the kinematics of swallowing, dysphagia, and compensatory therapeutic strategies. Active contour models, also known as "Snakes," have been used to solve various image analysis and computer vision problems. We applied a Snake algorithm to automate in part the contour tracking and reconstruction of VFG images to visualize and quantitatively analyze the 3-D evolution of a pharyngeal bolus. To improve the accuracy of the Snake search, we provided the additional "knowledge" of the pharyngeal image itself, which served as an extra constraint to push the Snake curve toward the desired contour. VFG of pharyngeal bolus transport in a normal subject was recorded by using barium-mixed boluses (viscosity: 185 centipoise, density: 2.84 g/cc) with volumes of 5, 10, and 20 ml. The resulting LA and AP video images were digitally captured and matched frame by frame. The knowledge-based Snake search algorithm was used to generate Snake points to satisfy both internal (i.e., smoothness) and external (i.e., boundary fitting) constraints. Using these Snake points, we traced the 3-D bolus movement at each time instant, assuming elliptic geometry in the cross-section of the pharyngeal bolus. By concentrating the 3-D images for each time instant, we developed a 3-D movie representing pharyngeal bolus movement. The efficiency, reproducibility, and accuracy of this algorithm in tracing pharyngeal bolus boundaries and estimating front/tail velocities were assessed and found satisfactory. We conclude that 3-D pharyngeal bolus movement can be traced both accurately and efficiently by using a knowledge-based Snake search algorithm.

Algorithms↗