Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “compensatory evolution”

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 397 records · Page 22Linked to original sources
PubMed2005

The cost of living large: comparative gliding performance in flying lizards (Agamidae: Draco).

Despite exhibiting considerable interspecific variation in body mass, flying lizards of the genus Draco are isometric in their area-mass scaling relationships and exhibit no significant compensatory variation in wing aspect ratio. Thus, larger species are expected to be relatively poor gliders, in lieu of behavioral or physiological compensation, when compared with smaller congeners. Here we tested this hypothesis by conducting gliding performance trials for 11 Draco species spanning virtually the entire size range of the genus. We considered three primary performance variables: maximum velocity adjusted for wind conditions, height lost over a standard horizontal glide distance, and glide angle. Comparative analysis confirmed that larger species are relatively poor gliders and do not compensate substantially for their higher wing loadings via either behavioral or physiological mechanisms. Flying lizards were found to exhibit substantial context-dependent variation in glide performance, with smaller species often exhibiting extensive variation in height lost and glide angle between trials. Variation also was observed in empirically derived velocity profiles, with only a subset of individuals appearing to perform equilibrium glides. Such size-dependent variation in performance has important consequences for the ecology and evolution of flying lizards and other glissant taxa.

Animals↗
PubMed2003

A diversity of U1 small nuclear RNAs in the silk moth Bombyx mori.

Variants of U1 small nuclear RNAs (snRNAs) have been previously detected in a permanent cell line (BmN) of the silk moth Bombyx mori. In this study, the existence of U1 snRNA isoforms in the silk gland (SG) of the organism is investigated. The polyploidy (approximately 200,000X the 2N somatic value) state of the B. mori silk gland cells represents a unique system to explore the potential presence and differential expression of multiple U1 variants in a normal tissue. B. mori U1-specific RT-PCR libraries from the silk gland were generated and five U1 isoforms were isolated and characterized. Nucleotide differences, structural alterations, as well as protein and RNA interaction sites were examined in these variants and compared to the previously reported isoforms from the transformed BmN cell line. In all these SG U1 variants, variant sites and inter-species differences are located in moderately conserved regions. Substitutional or compensatory changes were found in the double stranded areas and clustered in moderately conserved regions. Some of the changes generate stronger base pairing. Calculated free energy (DeltaG) values for the entire U1 snRNA secondary structures and for the individual stem/loops (I, II, III and IV) domains of the isoforms were generated and compared to determine their structural stability. Using phylogenetic analysis, an evolutionary parallelism is observed between the polymorphic sites in B. mori and variant locations found among animal and plant species.

Animals↗
PubMed2006

Pseudo-messenger RNA: phantoms of the transcriptome.

The mammalian transcriptome harbours shadowy entities that resist classification and analysis. In analogy with pseudogenes, we define pseudo-messenger RNA to be RNA molecules that resemble protein-coding mRNA, but cannot encode full-length proteins owing to disruptions of the reading frame. Using a rigorous computational pipeline, which rules out sequencing errors, we identify 10,679 pseudo-messenger RNAs (approximately half of which are transposon-associated) among the 102,801 FANTOM3 mouse cDNAs: just over 10% of the FANTOM3 transcriptome. These comprise not only transcribed pseudogenes, but also disrupted splice variants of otherwise protein-coding genes. Some may encode truncated proteins, only a minority of which appear subject to nonsense-mediated decay. The presence of an excess of transcripts whose only disruptions are opal stop codons suggests that there are more selenoproteins than currently estimated. We also describe compensatory frameshifts, where a segment of the gene has changed frame but remains translatable. In summary, we survey a large class of non-standard but potentially functional transcripts that are likely to encode genetic information and effect biological processes in novel ways. Many of these transcripts do not correspond cleanly to any identifiable object in the genome, implying fundamental limits to the goal of annotating all functional elements at the genome sequence level.

Animals↗
PubMed2004

Gender differences in height: an evolutionary perspective.

Homo sapiens (H. sapiens) exhibits growth characteristics not observed in other mammals, including other primates. Both male and female H. sapiens experience pubertal growth spurts and are not sexually dimorphic in adult stature. These unique growth characteristics must have evolved to benefit the reproductive success and survival of the species. The H. sapiens childhood is relatively protracted, and the pubertal growth spurt may be a compensatory measure to attain adult size in a relatively short time. Because reproductive patterns of H. sapiens have evolved away from a male-dominated social structure, large male size no longer confers a reproductive advantage. The relatively large female size of H. sapiens might have evolved to support the birth of offspring with ever-increasing cranial characteristics. Growth in H. sapiens depends largely on GH-dependent STAT5b regulation of IGF-I expression. STAT5b in other mammals contributes to growth in males only. Although speculative, the loss of sexual dimorphism in H. sapiens may reflect a progressive dependence on STAT5b to control growth.

Biological Evolution↗
PubMed1995

Healing of the patellar tendon after harvesting of its mid-third for anterior cruciate ligament reconstruction and evolution of the unclosed donor site defect.

The purpose of this study was (a) to evaluate by ultrasonography the healing of the patellar tendon after its mid-third was removed for anterior cruciate ligament (ACL) reconstruction in two randomized groups of patients in whom the tendon donor site was either left open or closed; (b) to compare clinical, radiographic, and isokinetic studies of these two groups to evaluate the incidence of patellofemoral disorders. We performed 61 ACL reconstructions (22 males, 39 females) using the arthroscopically assisted in-out technique. All operations were performed by the same surgeon, and the patients were all subjected to the same postoperative protocol. The tendon defect was left open in 25 subjects (group A) and was closed in 36 subjects (group B). Postoperative patellar tendon behavior was evaluated in these two groups by ultrasonography at 3, 6, 9, and 12 months. The vertical position of the patella was measured in the follow-up lateral view at 45 degrees of flexion and compared to that of the untreated knee. A clinical evaluation was performed throughout the follow-up period, and patellofemoral problems (pain, stiffness, patello-femoral crepitus) were evaluated and recorded using a modified Larsen and Lauridsen rating scale. Isokinetic evaluation was carried out at 6 months, and a quadriceps index of the two groups was recorded. Ultrasonography showed that healing of the patellar tendon initially progressed with a compensatory hypertrophy in width and thickness. The width was greater in group B (P < 0.01). In group A we observed in the cross-sections a characteristic image of two cords separated by a low signal bridge which we defined as a "binocular pattern." Areas of high ultrasound signal intensities persisted after 1 year in the open group; such areas were filled with scar tissue. In the closed group the ultrasound tendon signal returned to normal at 1 year. At 6 months the clinical, radiographic and isokinetic findings did not significantly differ between the open and closed groups. We conclude that defect closure after patellar tendon harvesting does not significantly influence the extensor apparatus.

Adolescent↗
PubMed1999

After portal branch ligation in rat, nuclear factor kappaB, interleukin-6, signal transducers and activators of transcription 3, c-fos, c-myc, and c-jun are similarly induced in the ligated and nonligated lobes.

Several studies have emphasized the involvement of transcription factors, cytokines, and proto-oncogenes in initiating the regenerative process after partial hepatectomy. To assess whether these events do specifically occur in a cellular system undergoing regeneration, we studied the induction of nuclear factor kappaB (NFkappaB), interleukin-6 (IL-6), signal transducers and activators of transcription 3 (Stat3), c-fos, c-myc, c-jun, after portal branch ligation (PBL), which produces atrophy of the deprived lobes (70% of the liver parenchyma), whereas the perfused lobes undergo compensatory regeneration. Nuclear extracts and total RNA were prepared from control livers as well as from atrophying and regenerating lobes at 0.5, 1, 2, 5, and 8 after PBL. NFkappaB and Stat3 induction were studied by electrophoretic mobility shift assays and Western blotting. IL-6 and proto-oncogenes expressions were assessed by reverse transcription polymerase chain reaction and Northern blotting, respectively. Assays were also performed after a sham operation. NFkappaB and Stat3 protein expression and DNA binding were rapidly and similarly induced in nuclear extracts from the atrophying and regenerating lobes. IL-6 was elevated in both lobes from 1 to 8 hours after PBL as well as c-fos, c-myc, and c-jun during the first 2 hours. IL-6 and Stat3 but not NFkappaB were also elevated after a sham operation. These findings suggest that the cellular and molecular changes occurring early in a regenerating liver are nonspecific, possibly stress-induced, cellular responses. They do not indicate the future evolution towards atrophy or regeneration.

Animals↗
PubMed2000

Double-hairpin elements in the mitochondrial DNA of allomyces: evidence for mobility.

The mitochondrial DNA (mtDNA) of the chytridiomycete fungus Allomyces macrogynus contains 81 G+C-rich sequence elements that are 26-79 bases long and can be folded into a unique secondary structure consisting of two stem-loops. At the primary sequence level, the conservation of these double-hairpin elements (DHEs) is variable, ranging from marginal to complete identity. Forty of these DHEs are inserted in intergenic regions, 35 in introns, and 6 in variable regions of rRNA genes. Ten DHEs are inserted into other DHE elements (twins); two even form triplets. A comparison of DHE sequences shows that loop regions contain more sequence variation than helical regions and that the latter often contain compensatory base changes. This suggests a functional importance of the DHE secondary structure. We further identified nine DHEs in a 4-kb region of Allomyces arbusculus, a close relative of A. macrogynus. Eight of these DHEs are highly similar in sequence (90%-100%) to those in A. macrogynus, but only five are inserted at the same positions as in A. macrogynus. Interestingly, DHEs are also found in the mtDNAs of other chytridiomycetes, as well as certain zygomycete and ascomycete fungi. The overall distribution pattern of DHEs in fungal mtDNAs suggests that they are mobile elements.

Base Sequence↗
PubMed1998

Modelling the secondary structures of slippage-prone hypervariable RNA regions: the example of the tiger beetle 18S rRNA variable region V4.

Variable regions within ribosomal RNAs frequently vary in length as a result of incorporating products of slippage. This makes constructing secondary structure models problematic because base homology is difficult or impossible to establish between species. Here, we model such a region by comparing the results of the MFOLD suboptimal folding algorithm for different species to identify conserved structures. Based on the reconstruction of base change on a phylogenetic tree of the species and comparison against null models of character change, we devise a statistical analysis to assess support of these structures from compensatory and semi-compensatory (i.e. G.C to G.U or A.U to G.U) mutations. As a model system we have used variable region V4 from cicindelid (tiger beetle) small subunit ribosomal RNAs (SSU rRNAs). This consists of a mixture of conserved and highly variable subregions and has been subject to extensive comparative analysis in the past. The model that results is similar to a previously described model of this variable region derived from a different set of species and contains a novel structure in the central, highly variable part. The method we describe may be useful in modelling other RNA regions that are subject to slippage.

Animals↗
PubMed2005

Detection of hepatitis B virus genotypes and mutants: current status.

Characterization results of the hepatitis B virus (HBV) genome before, during and after antiviral treatment have changed in the last year for a number of reasons. First of all, with the introduction of more nucleoside and nucleotide antiviral therapies, it has become clear that variants or mutants do emerge in time. Viral genomic changes in the HBV polymerase gene can result in a direct antiviral effect, but compensatory mutations can also be identified during prolonged treatment periods. Furthermore, there is an increasing number of reports suggesting that HBV genotypes can be related to, for example, disease progression or the effect of antiviral treatment itself (alpha-interferon or lamivudine). Combined with HBV DNA viral load monitoring, an increase in viral load or a limited reduction during treatment is indicative of genomic changes related to resistance. However, these genomic changes can also be present in the absence of an increase in HBV DNA. Methodologies for the detection of these variants, as well as the determination of genotypes, are rather straightforward. Sequence analysis is time-consuming and expensive, but provides the most information, particularly if not all information on mutations related to antiviral resistance is known. However, the sensitivity of direct sequencing for the presence of minor variant populations is poor, and no mixtures of variant populations are, in general, detected. The ability to detect minor populations and, if possible, even quantify them, gives more insightful information on the dynamic evolution of the virus itself. Antiviral treatment can result in the appearance of more than one population of variants, which can be present for a prolonged period of time, and even remain undetected with current technologies. However, screening specifically for these variant populations before starting treatment for so-called untreated patients (who have received no antiviral treatment for, e.g., 6 months) has already shown that the effects of treatment can be biased. Furthermore, the detection of more dynamic viral populations - including both wild-type and resistant variants - during, but also after therapy, does provide helpful information in the analysis of virological data. Technologies enabling the detection and quantification of these variant populations are presented and discussed.

Antiviral Agents↗
PubMed1999

[Spinal deformity in the adult].

PROGRESSIVE DEFORMATION DURING ADULTHOOD: Though not commonly recognized, lumbar and thoracoscoliosis can progress during adulthood. This slow, insidious evolution concerns not only the anatomic configuration of the spinal curatures (three dimensional angular deformation) but also spinal function (development or aggravation of spinal or radicular pain and/or impaired equilibrium). This fact emphasizes the importance of regular prolonged surveillance of all patients with spinal deformations. RADIOLOGICAL CHANGES: Three anatomic elements affecting function are evidenced on serial x-rays: development of rotational dislocation, stiffening of the main curvature, especially in the lumbosacral spine, and progressive instaliation, thoracolumbar kyphosis. TREATMENT: Three types of treatment can be proposed: physical therapy, orthopedic treatment, surgery. Physical therapy and orthopedic treatment can relieve pain and improve equilibrium but cannot change the progressive pattern of the spinal deviation. Surgery also provides effective symptom relief and has the advantage of definitively stopping the progression of the deformation. INDICATIONS: Indications are much more complex than simply determining an angle of deformation beyond which surgery is needed. For each case, indications are established on knowledge of the type of deformation, its extent, potential or ongoing modifications in the main curvature and compensatory curvatures, the patient's age, as well as the functional impairment and the patient's general status.

Adult↗
PubMed2003

Genomic organization of the rDNA cistron of the teleost fish Cyprinus carpio.

The seasonal adaptation of the teleost Cyprinus carpio to the cyclical changes of its habitat demands physiological compensatory responses. The process involves profound nucleolar adjustments and remarkable changes in rRNA synthesis, which affects ribosomal biosynthesis. In this context, we have demonstrated that the synthesis of several proteins involved in ribosomal biogenesis as protein kinase CK2, ribosomal protein L41 and nucleolin, as well as U3 snoRNP, are differentially regulated in summer-acclimatized carp compared to the cold-season adapted fish. To understand the mechanisms involved in the seasonal regulation of rRNA gene transcription, we have been studying the carp rDNA cistron structure. Because the cis-elements that regulate the expression of the tandem organized ribosomal genes are located in the non-transcribed intergenic spacer (IGS), we analyzed the primary structure of the carp rDNA gene IGS. The gene organization is similar to that described from other vertebrate species, including numerous repetitive sequences, the transcription start site, and some potential cis-elements such as ribosomal enhancers, proximal terminator and transcriptional terminators. Ribosomal DNA is a remarkable case of gene duplication and has been used as a model to test the concerted evolution theory. We performed sequence comparison analyses of 18S rRNA coding sequences from carp with different species, data with which an unrooted phylogram was constructed.

Animals↗
PubMed2000

TSG101 protein steady-state level is regulated posttranslationally by an evolutionarily conserved COOH-terminal sequence.

Antisense inactivation of the tsg101 tumor susceptibility gene in murine NIH3T3 fibroblasts leads to neoplastic transformation and tumorigenesis, which are reversed by restoration of tsg101 activity. tsg101 deficiency is associated with a series of mitosis-related abnormalities, whereas overexpression of TSG101 can also result in neoplastic transformation and the perturbation of cell cycling. Together, these observations imply that TSG101 production outside of a narrow range can lead to abnormal cell growth. We report here that the TSG101 protein is maintained at an almost constant steady-state level in cultured murine and human cells and that this occurs through a posttranslational process involving TSG101 protein degradation. Sustained overproduction of TSG101 from chromosomally inserted adventitious constructs resulted in compensatory down-regulation of endogenous TSG101 and replacement of the native protein by the adventitious one. Using deletion mutants of TSG101, we mapped the region responsible for autoregulation of the TSG101 steady-state level to an evolutionarily conserved sequence, here termed the "steadiness box," located near TSG101's COOH-terminal end. Our results suggest a model in which the biological effects of TSG101 are modulated either by self-promoted proteolysis or participation with other cellular protein(s) in a proteolytic feedback-control loop.

Amino Acid Sequence↗
PubMed1989

Genetic segregation and the maintenance of sexual reproduction.

Sexual reproduction confronts evolutionary biology with a paradox: other things being equal, an asexual (all-female) population will have twice the reproductive potential of a competing sexual population and therefore should rapidly drive the sexual population to extinction. Thus, the persistence of sexual reproduction in most life forms implies a compensatory advantage to sexual reproduction. Work on this problem has emphasized the evolutionary advantages produced by the genetic recombination that accompanies sexual reproduction. Here we show that genetic segregation produces an advantage to sexual reproduction even in the absence of an advantage from recombination. Segregation in a diploid sexual population allows selection to carry a single advantageous mutation to a homozygous state, whereas two separate mutations are required in a parthenogenetic population. The complete fixation of advantageous mutations is thus delayed in a heterozygous state in asexual populations. Calculation of the selective load incurred suggests that it may offset the intrinsic twofold reproductive advantage of asexual reproduction and maintain sexual reproduction in diploid populations.

Animals↗
PubMed1996

Phylogeny of the Mycoplasma mycoides cluster as determined by sequence analysis of the 16S rRNA genes from the two rRNA operons.

The so-called Mycoplasma mycoides cluster consists of six species or subspecies of mycoplasmas (Mollicutes). These species are pathogenic for ruminants and some of them are of great concern in veterinary medicine. The members of the M. mycoides cluster have two rRNA operons (rrnA and rrnB). The nucleotide sequences of the 16S rRNA genes of 10 strains, representing all of the known species and subspecies of the M. mycoides cluster, were determined by direct automated solid-phase DNA sequencing. The sequences of both rRNA operons were determined by a novel strategy involving in vitro amplification by PCR with one operon-specific primer pair and one general primer pair. Interestingly, sequence differences (polymorphisms) between the two operons were observed for all strains. Two strains of M. capricolum subsp. capripneumoniae were sequenced, and 15 polymorphisms were found in the type strain (F38) and 17 polymorphisms were found in the other strain (4/2LC). Eight polymorphisms were found in the 16S rRNA genes of the M. mycoides subsp. mycoides small-colony type, and sequence length variations in a poly(A) region were observed in the 16S rRNA genes of the two operons of this species. Secondary-structure analysis showed that polymorphisms were present in both stem and loop regions. The nucleotide substitutions in the polymorphic sites of the stem regions often resulted in a change from a canonical to a noncanonical base pairing or vice versa. A compensatory mutation was never observed in the other nucleotide of the base pair. Phylogenetic analysis based on the 16S rRNA sequences indicated that Mycoplasma sp. strain PG50 should be included in the M. capricolum species group. Furthermore, the 16S rRNA sequences of M. mycoides subsp. capri and the M. mycoides subsp. mycoides large-colony type were 99.9% identical. We therefore suggest that these species be reclassified in a common species group (for instance, "Mycoplasma capri") distinct from the M. mycoides subsp. mycoides small-colony type, which formed an intermediate branch between the M. capricolum species group and the M. capri species group.

Base Sequence↗
PubMed1998

Long-term evolution of cardiomyopathy in dialysis patients.

BACKGROUND: Left ventricular enlargement is very common at the inception of dialysis therapy, and highly predictive of future cardiac morbidity and mortality. It is not known whether cardiac size increases further while on dialysis therapy and whether potentially reversible risk factors for later progression can be identified. METHODS; Baseline and yearly echocardiograms were performed in a prospective inception cohort of 433 dialysis patients. The mean patient follow-up was 41 months; 29 patients had four consecutive echocardiograms at yearly intervals. RESULTS: The patient subset with four echocardiograms was older (58 vs. 51 years, P = 0.02) and had a lower mass ventricular mass index (128 vs. 149 g/m2, P = 0.02) than the parent group. Using repeated measures analysis of variance, applied to those with four echocardiograms, there were progressive increases over time in posterior wall thickness (P = 0.015), left ventricular end-diastolic diameter, left ventricular mass index (P = 0.001), and cavity volume index (P = 0. 001). Mass-to-volume ratios did not change. The biggest changes in mass (18 g/m2 - 14%)and volume index (13 ml/m2 - 18%) occurred between baseline and year 1, although increases in both were seen after year 1. Hemodialysis versus peritoneal dialysis (41 g/m2, P = 0.008) and anemia (10 g/m2 per 1 g/dl drop in hemoglobin, P = 0.02) were associated with progressive left ventricular enlargement, but only within the first year of dialysis therapy. The left ventricular enlargement seen after year 1 was independent of anemia, blood pressure, serum albumin and mode of dialysis. CONCLUSIONS: Progressive cardiac enlargement, particularly left ventricular dilation with compensatory hypertrophy, continues after starting dialysis therapy. Most of the additional cardiac enlargement seems to occur in the first year of dialysis therapy, suggesting that intervention beyond one year may be relatively ineffective.

Blood Pressure↗
PubMed2000

Hunger, eating, and ill health.

Humans and other warm-blooded animals living with continuous access to a variety of good-tasting foods tend to eat too much and suffer ill health as a result--a finding that is incompatible with the widely held view that hunger and eating are compensatory processes that function to maintain the body's energy resources at a set point. The authors argue that because of the scarcity and unpredictability of food in nature, humans and other animals have evolved to eat to their physiological limits when food is readily available, so that excess energy can be stored in the body as a buffer against future food shortages. The discrepancy between the environment in which the hunger and eating system evolved and the food-replete environments in which many people now live has led to the current problem of overconsumption existing in many countries. This evolutionary perspective has implications for understanding the etiology of anorexia nervosa.

Animals↗
PubMed2000

The survival of slow reproducers.

Multicellularity, and the attendant segregation of the germ line, entails the loss of reproductive capacity by the soma: in Volvox carteri, less than 1 cell in 100 contributes to the next generation. However, compensatory advantages are unlikely to be very large (Koufopanou & Bell, 1993. Proc. R. Soc. Lond. (B) 254,107-113). Somewhat similarly, sex implies the generation of males, hence a dramatic reproductive slowdown (Barton & Charlesworth, 1998. Science281, 1986-1990); yet, a compensating (two-fold) advantage of sex has not been found. Here, I try to evaluate the actual cost of maintaining slow reproductive cycles, namely cycles that necessitate the production of "dead end" units such as somatic cells or males. In a quantitative model for the competition of individuals with different, heritable reproductive rates, this cost turns out to be unexpectedly small, and may even sometimes become irrelevant. The bases for this are made fairly clear: thus, when all enjoy high fecundity (e.g. a long reproductive life) the handicap of a slower reproduction vanishes; alternatively, a slight separation of ecological niches may be sufficient for survival of slower but otherwise unchanged reproducers; and finally, inherent to slow reproduction is a low rate of destabilizing genetic change. These facts are largely independent of the formal model details, and are supported by direct computer simulations. They give a quantitative basis for analysing the evolution and prevalence of slow life cycles. The implications of these findings for the evolution of multicellularity are briefly discussed.

Animals↗
PubMed2000

Does a retrograde response in human aging and longevity exist?

The retrograde response (RR) is a compensatory mechanism by which mutant strains of yeast are able to cope with mitochondrial DNA (mtDNA) impairments by up-regulating the expression of the stress-responder nuclear genes and significantly increasing lifespan. Starting from the observation that both mtDNA variability and Tyrosine hydroxylase (THO, stress-responder gene) variability are correlated with human longevity, we asked ourselves whether mechanisms similar to RR may exist in humans. As a first investigative step we have analyzed the distribution of the mtDNA inherited variants (haplogroups) according to THO genotypes in three sample groups of increasing ages (20-49 years; 50-80 years; centenarians). We found that the mtDNA haplogroups and the THO genotypes are associated randomly in the first group, while in the second group, and particularly in the centenarians, a non-random association is observed between the mtDNA and nuclear DNA variability. Moreover, in centenarians the U haplogroup is over-represented (p=0.012) in subjects carrying the THO genotype unfavorable to longevity. On the whole these findings are in line with the hypothesis that longevity requires particular interactions between mtDNA and nuclear DNA and do not exclude the possibility that an RR has been maintained throughout evolution and it is present in higher organisms.

Adult↗