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Results for “balancing selection”

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PubMed2005

The application of statistical physics to evolutionary biology.

A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.

Adaptation, Biological↗

PubMed2006

Microtubule bundling and nested buckling drive stripe formation in polymerizing tubulin solutions.

Various mechanisms govern pattern formation in chemical and biological reaction systems, giving rise to structures with distinct morphologies and physical properties. The self-organization of polymerizing microtubules (MTs) is of particular interest because of its implications for biological function. We report a study of the microscopic structure and properties of the striped patterns that spontaneously form in polymerizing tubulin solutions and propose a mechanism driving this assembly. Microscopic observations reveal that the pattern comprises wave-like MT bundles. The retardance of the solution and the fluorescence intensity of labeled MTs vary periodically in space, suggesting a coincident periodic variation in MT alignment and density. This wave-like structure forms through the development and coordinated buckling of initially aligned MT bundles. Both static magnetic fields and convective flow can induce the initial alignment. The nesting of the buckled MT bundles gives rise to density variations that are in quantitative accord with the data. We further propose that the buckling wavelength is selected by a balance between the bending energy of the bundles and the elastic energy of the MT network surrounding them. These studies reveal a unique physical chemical mechanism by which mechanical buckling couples with protein polymerization to produce macroscopic patterns. Self-organization of this type may be important to the formation of certain biological structures.

Animals↗

PubMed2002

Long-term microclimatic stress causes rapid adaptive radiation of kaiABC clock gene family in a cyanobacterium, Nostoc linckia, from "Evolution Canyons" I and II, Israel.

Cyanobacteria are the only prokaryotes known thus far possessing regulation of physiological functions with approximate daily periodicity, or circadian rhythms, that are controlled by a cluster of three genes, kaiA, kaiB, and kaiC. Here we demonstrate considerably higher genetic polymorphism and extremely rapid evolution of the kaiABC gene family in a filamentous cyanobacterium, Nostoc linckia, permanently exposed to the acute natural environmental stress in the two microsite evolutionary models known as "Evolution Canyons," I (Mount Carmel) and II (Upper Galilee) in Israel. The family consists of five distinct subfamilies (kaiI-kaiV) comprising at least 20 functional genes and pseudogenes. The obtained data suggest that the duplications of kai genes have adaptive significance, and some of them are evolutionarily quite recent (approximately 80,000 years ago). The observed patterns of within- and between-subfamily polymorphisms indicate that positive diversifying, balancing, and purifying selections are the principal driving forces of the kai gene family's evolution.

Bacterial Proteins↗

PubMed2002

Gene expression data analysis with a dynamically extended self-organized map that exploits class information.

MOTIVATION: Currently the most popular approach to analyze genome-wide expression data is clustering. One of the major drawbacks of most of the existing clustering methods is that the number of clusters has to be specified a priori. Furthermore, by using pure unsupervised algorithms prior biological knowledge is totally ignored Moreover, most current tools lack an effective framework for tight integration of unsupervised and supervised learning for the analysis of high-dimensional expression data and only very few multi-class supervised approaches are designed with the provision for effectively utilizing multiple functional class labeling. RESULTS: The paper adapts a novel Self-Organizing map called supervised Network Self-Organized Map (sNet-SOM) to the peculiarities of multi-labeled gene expression data. The sNet-SOM determines adaptively the number of clusters with a dynamic extension process. This process is driven by an inhomogeneous measure that tries to balance unsupervised, supervised and model complexity criteria. Nodes within a rectangular grid are grown at the boundary nodes, weights rippled from the internal nodes towards the outer nodes of the grid, and whole columns inserted within the map The appropriate level of expansion is determined automatically. Multiple sNet-SOM models are constructed dynamically each for a different unsupervised/supervised balance and model selection criteria are used to select the one optimum one. The results indicate that sNet-SOM yields competitive performance to other recently proposed approaches for supervised classification at a significantly reduced computational cost and it provides extensive exploratory analysis potentiality within the analysis framework. Furthermore, it explores simple design decisions that are easier to comprehend and computationally efficient.

Algorithms↗

PubMed1991

The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations.

When two samples of DNA sequences are compared, one way in which they may differ is in the presence of fixed differences, which are defined as sites at which all of the sequences in one sample are different from all of the sequences in a second sample. The probability distribution of the number of fixed differences is developed. The theory employs Wright-Fisher genealogies and the infinite sites mutation model. For the case when both samples are drawn randomly from the same population it is found that genealogies permitting fixed differences are very unlikely. Thus the mere presence of fixed differences between samples is statistically significant, even for small samples. The theory is extended to samples from populations that have been separated for some time. The relationship between a simple Poisson distribution of mutations and the distribution of fixed differences is described as a function of the time since populations have been isolated. It is shown how these results may contribute to improved tests of recent balancing or directional selection.

Base Sequence↗

PubMedDate not supplied

Understanding human DNA sequence variation.

Over the past century researchers have identified normal genetic variation and studied that variation in diverse human populations to determine the amounts and distributions of that variation. That information is being used to develop an understanding of the demographic histories of the different populations and the species as a whole, among other studies. With the advent of DNA-based markers in the last quarter century, these studies have accelerated. One of the challenges for the next century is to understand that variation. One component of that understanding will be population genetics. We present here examples of many of the ways these new data can be analyzed from a population perspective using results from our laboratory on multiple individual DNA-based polymorphisms, many clustered in haplotypes, studied in multiple populations representing all major geographic regions of the world. These data support an "out of Africa" hypothesis for human dispersal around the world and begin to refine the understanding of population structures and genetic relationships. We are also developing baseline information against which we can compare findings at different loci to aid in the identification of loci subject, now and in the past, to selection (directional or balancing). We do not yet have a comprehensive understanding of the extensive variation in the human genome, but some of that understanding is coming from population genetics.

Base Sequence↗

PubMed2001

Short-term orlistat treatment does not affect mineral balance and bone turnover in obese men.

Orlistat is a gastrointestinal lipase inhibitor that is used to reduce dietary fat absorption and to enhance weight loss in subjects consuming a hypocaloric diet. To assess whether orlistat has an effect on the metabolism of six minerals, a 21-d, double-blind, randomized, parallel-group, placebo-controlled mineral balance study was conducted in obese (body mass index > 30 kg/m(2)) men. Subjects consumed a hypocaloric diet with a constant daily mineral content and received daily oral treatment with orlistat (120 mg three times daily) (n = 14) or placebo (three times daily) (n = 14) for 21 d. After a 14-d equilibration period, calcium, phosphorus, magnesium, iron, copper and zinc balances were assessed for d 15-21. In addition, the effect of diet and orlistat treatment on bone metabolism was estimated from measurement of biomarkers of bone formation and bone resorption. Serum and urine electrolytes were also measured at baseline and at the end of treatment. Orlistat inhibited fat absorption by approximately 33% (P < 0.05). There were no significant differences in mineral apparent absorption, urinary mineral loss or mineral balance between the orlistat and placebo groups. Markers of bone turnover and serum and urine electrolytes did not differ between the orlistat and placebo groups. Orlistat was well tolerated; adverse events were of mild or moderate intensity, and the majority of these events were unrelated or remotely related to study treatment. In obese men consuming a hypocaloric diet, the administration of orlistat had no significant effect on the balance of six selected minerals. In addition, biomarkers of bone turnover, as well as serum and urine electrolytes, were not affected by orlistat treatment.

Adult↗

PubMed2005

Genome plasticity and ori-ter rebalancing in Salmonella typhi.

Genome plasticity resulting from frequent rearrangement of the bacterial genome is a fascinating but poorly understood phenomenon. First reported in Salmonella typhi, it has been observed only in a small number of Salmonella serovars, although the over 2,500 known Salmonella serovars are all very closely related. To gain insights into this phenomenon and elucidate its roles in bacterial evolution, especially those involved in the formation of particular pathogens, we systematically analyzed the genomes of 127 wild-type S. typhi strains isolated from many places of the world and compared them with the two sequenced strains, Ty2 and CT18, attempting to find possible associations between genome rearrangement and other significant genomic features. Like other host-adapted Salmonella serovars, S. typhi contained large genome insertions, including the 134 kb Salmonella pathogenicity island, SPI7. Our analyses showed that SPI7 disrupted the physical balance of the bacterial genome between the replication origin (ori) and terminus (ter) when this DNA segment was inserted into the genome, and rearrangement in individual strains further changed the genome balance status, with a general tendency toward a better balanced genome structure. In a given S. typhi strain, genome diversification occurred and resulted in different structures among cells in the culture. Under a stressed condition, bacterial cells with better balanced genome structures were selected to greatly increase in proportion; in such cases, bacteria with better balanced genomes formed larger colonies and grew with shorter generation times. Our results support the hypothesis that genome plasticity as a result of frequent rearrangement provides the opportunity for the bacterial genome to adopt a better balanced structure and thus eventually stabilizes the genome during evolution.

Evolution, Molecular↗

PubMedDate not supplied

Platinum coat color locus in the deer mouse.

Platinum coat color in the deer mouse, Peromyscus maniculatus, is an autosomal recessive trait marking a locus, pt, distinct from silver (si), albino (c), blonde (bl), brown (b), and agouti (a). Platinum deer mice are conspicuously pale, with light ears and tail stripe. The pewter trait is allelic with and phenotypically identical to platinum, and represents an independent recurrence of this mutant. The rate of recoveries of coat color mutations from wild deer mice is consistent with available data for recurring mutation rates balanced by strong selection against the recessive phenotype.

Alleles↗

PubMed1993

Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex.

Two regions of the genome, a 1-kbp portion of the zeste locus and a 1.1-kbp portion of the yolk protein 2 locus, were sequenced in six individuals from each of four species: Drosophila melanogaster, D. simulans, D. mauritiana, and D. sechellia. The species and strains were the same as those of a previous study of a 1.9-kbp region of the period locus. No evidence was found for recent balancing or directional selection or for the accumulation of selected differences between species. Yolk protein 2 has a high level of amino acid replacement variation and a low level of synonymous variation, while zeste has the opposite pattern. This contrast is consistent with information on gene function and patterns of codon bias. Polymorphism levels are consistent with a ranking of effective population sizes, from low to high, in the following order: D. sechellia, D. melanogaster, D.mauritiana, and D. simulans. The apparent species relationships are very similar to those suggested by the period locus study. In particular, D. simulans appears to be a large population that is still segregating variation that arose before the separation of D. mauritiana and D. sechellia. It is estimated that the separation of ancestral D. melanogaster from the other species occurred 2.5-3.4 Mya. The separations of D. sechellia and D. mauritiana from ancestral D. simulans appear to have occurred 0.58-0.86 Mya, with D. mauritiana having diverged from ancestral D. simulans 0.1 Myr more recently than D. sechellia.

Animals↗

PubMed2004

Strong genetic clines and geographical variation in gene flow in the rocky intertidal barnacle Balanus glandula.

A long-standing issue in marine biology is identifying spatial scales at which populations of sessile adults are connected by planktonic offspring. We examined the genetic continuity of the acorn barnacle Balanus glandula, an abundant member of rocky intertidal communities of the northeastern Pacific Ocean, and compared these genetic patterns to the nearshore oceanography described by trajectories of surface drifters. Consistent with its broad dispersal potential, barnacle populations are genetically similar at both mitochondrial (cytochrome oxidase I) and nuclear (elongation factor 1-alpha) loci across broad swaths of the species' range. In central California, however, there is a striking genetic cline across 475 km of coastline between northern and southern populations. These patterns indicate that gene flow within central California is far more restricted spatially than among other populations. Possible reasons for the steep cline include the slow secondary introgression of historically separated populations, a balance between diversifying selection and dispersal, or some mix of both. Geographic trajectories of oceanic drifters closely parallel geographical patterns of gene flow. Drifters placed to the north (Oregon; approximately 44 degrees N) and south (Santa Barbara, California; approximately 34 degrees N) of the cline disperse hundreds of kilometers within 40 days, yet over the long-term their trajectories never overlapped. The lack of communication between waters originating in Oregon and southern California probably helps to maintain strong genetic differentiation between these regions. More broadly, the geographical variation in gene flow implies that focusing on species-level averages of gene flow can mask biologically important variance within species which reflects local environmental conditions and historical events.

Animals↗

PubMed1993

The defibrillation threshold: a comparison of anesthetics and measurement methods.

In 18 open-chested mongrel dogs (18.0 +/- 1.7 kg) we compared three anesthetics and three methods for measuring the defibrillation threshold. Six animals were anesthetized with pentobarbital (30 mg/kg) and maintained with a pentobarbital infusion (4 mg/kg per hour). All other animals were anesthetized with sodium brevital (10 mg/kg) and maintained with either halothane gas (1.5%, N = 6) or isoflurane gas (1.8%, N = 6). In each dog, we measured the energy required for 50% successful defibrillation (E50) with: (A) a 3 reversal--up/down method; (B) a 15 shock--up/down method; and (C) a percent success method. Anesthetics and methods were selected in a balanced random order. Ventricular fibrillation was induced with 50 Hz electrical pacing. After 15 seconds, monophasic truncated exponential shocks were delivered by way of a spring-patch electrode configuration. The animal was rescued (if needed) and fibrillation/defibrillation episodes were repeated at 3 minute intervals. After each determination of the E50, the E50 was delivered in ten successive defibrillation trials to determine its actual success rate. We found no significant difference in E50 among anesthetics; a significant difference (P < 0.05) in E50 between method C (9.7 +/- 2.6 joules) and method B (8.2 +/- 1.6 joules); no significant difference among anesthetics or methods for the actual success rate of the E50 (45 +/- 21% successful); and method A required significantly fewer fibrillation episodes and number of shocks and less cumulative energy than the other methods. We concluded that the anesthetics tested had little effect on E50 but that the method used to determine E50 could have an effect.(ABSTRACT TRUNCATED AT 250 WORDS)

Anesthetics↗

PubMed2005

Coagulation profile and liver function in 102 patients after total cavopulmonary connection at mid term follow up.

OBJECTIVE: To examine coagulation factors and liver function test abnormalities in patients after total cavopulmonary connection (TCPC). DESIGN: Cross sectional study comprising clinical and echocardiographic evaluation, and biochemical and coagulation profile screening. SETTING: Tertiary referral centre. METHODS: 102 patients aged 4-24 years (median 10 years) at one to eight years (median five years) after TCPC were examined. All patients were maintained on a low dose of aspirin. 96% of patients were in a good clinical condition (New York Heart Association class I or II). No intracardiac thrombi were detected on echocardiography and ventricular function was good in 91% of patients. RESULTS: Total bilirubin was increased in 27% and gamma glutamyltransferase in 54% of patients. Serum total protein, albumin, and prealbumin were normal in almost in all patients. Compared with the control group, patients after TCPC had significantly lower fibrinogen, factor V, factor VII, and protein C concentrations, prolonged international normalised ratio, and increased antithrombin III concentration. Factor V concentration was abnormally decreased in 35%, factor VII in 16%, and protein C in 28% of patients. Antithrombin III was increased in 23% of patients. Factor VII, factor V, protein C, and antithrombin III correlated significantly with serum prealbumin. There was also a significant correlation between procoagulant factor VII and both anticoagulant protein C and antithrombin III. CONCLUSIONS: Almost half of patients after TCPC had laboratory signs of mild cholestasis. Decreased liver synthesis of procoagulant and anticoagulant factors was observed but overall coagulation homeostasis appeared to be in balance in this selected group of patients with a good clinical outcome.

Adolescent↗

PubMed2001

Advances in neuroprotection trials.

With technological assistance, approaches to acute stroke trials may be improved. Dose selection, eligibility criteria, control of confounding factors and endpoints can each be optimised. Adaptive randomisation techniques and Bayesian approaches can assist not only dose selection, but also balance of prognostic factors between treatment groups. Magnetic resonance imaging can facilitate enrichment of the trial population with potential responders. Utilisation of existing trial databases can enhance statistical approaches to outcome assessment. Confounding imbalance may also be limited by controlling or adjusting for concomitant conditions and their management. Recent trials have not yet identified a neuroprotectant, but have greatly assisted the prospects of success.

Brain Ischemia↗

PubMed2004

The use of a cell-cycle phase-marker may decrease the percentage of errors when using FISH in PGD.

Fluorescent DNA probes are used to characterise the chromosome constitution of preimplantation embryos. FISH is used to select normal or balanced embryos in carriers of balanced chromosomal rearrangements, for embryo sexing or for aneuploidy screening in women of advanced age, who have had recurrent abortions or IVF failures. In most cases, FISH is performed on interphase blastomeres which are asynchronously dividing cells, that can be in G1, S or G2. However, a correct interpretation of a double FISH signal, which may correspond to a split signal, to a replicated chromosome region or to the presence of an extra chromosome is essential to establish an accurate diagnosis. To determine if the cell stage could influence the interpretation of FISH results, we compared the signal characteristics of one locus-specific probe, two different subtelomere region probes, and a centromere region probe in non-dividing Sertoli cells and in proliferating lymphocytes. Most cells had two signals per chromosome pair (i.e., a situation corresponding to G0 in Sertoli cells and to G1 or to a prereplication stage in lymphocytes). Nevertheless, in proliferating cells the percentage of nuclei with a number of signals different from the expected (two unreplicated chromosomes per pair) was different from that found in non-dividing cells (P < 0.05). It was estimated that 10.8% of double dots in dividing cells resulted from DNA replication. The sequence of replication was first the locus-specific region, second a telomere region, and third the centromere. In conclusion, the DNA replication process could result in errors of interpretation (misdiagnosis) in 7% of proliferating cells. Thus, the use of a cell cycle phase-specific marker could avoid errors by indicating the cell stage in which the nucleus analysed is found.

Adult↗

PubMed1994

Increased hypothalamic glutamate receptors induced by water deprivation.

To examine the role of receptor changes in the adaptive response to physiological stimulation, the density and distribution of excitatory amino acid receptors within the hypothalamus and other brain regions were examined in rats deprived of water for 2 days. Membrane binding assay revealed an increase in glutamate receptor density and a small shift in the affinity of glutamate for the receptor. Regional analysis of these changes by receptor autoradiography specific for NMDA, non-NMDA or metabotropic glutamate receptor binding indicated that NMDA and metabotropic receptor densities are increased in the brain. Regional increases were found principally for the NMDA receptor binding within the supraoptic nucleus, anterior hypothalamus, caudate-putamen and globus pallidus with no significant changes in 24 other brain regions. No significant changes were found in any brain regions for AMPA receptors. Metabotropic and kainate receptors tended to parallel the NMDA receptor changes, although few regions reached statistical significance. These changes indicate that brain regions associated with water balance regulation show selective adaptive increases in NMDA receptors during water deprivation which may facilitate prolonged activation of these cells.

Animals↗

PubMed1995

Target organ status and serum lipids in patients with white coat hypertension.

Target organ status and serum lipids were investigated in white coat hypertension in comparison with sustained hypertension and normotension. We selected three groups balanced for sex, age, body mass index, and smoking habit: 50 sustained hypertensives (clinical hypertension and 24-hour ambulatory blood pressure > 135/85 mm Hg, a cutoff limit obtained from a normotensive population), 25 white coat hypertensives (clinical hypertension and 24-hour ambulatory blood pressure < 135/85 mm Hg), and normotensives. Subjects underwent echocardiographic examinations to assess left ventricular mass index, carotid ultrasonography to evaluate intima-media thickness and atherosclerotic plaques, venous occlusion plethysmography to record minimum forearm vascular resistance, and determinations of serum lipid profile and 24-hour urinary albumin excretion. Compared with sustained hypertensives, the white coat hypertensives had significantly lower values of left ventricular mass index (125.9 +/- 20 versus 97.6 +/- 11.5 g/m2, P < .05, intima-media thickness (0.85 +/- 0.18 versus 0.71 +/- 0.15 mm, P < .05), minimum forearm vascular resistance (2.33 +/- 0.11 versus 2.04 +/- 0.08 resistance units, P < .05), urinary albumin excretion values (15.1 +/- 13.8 versus 4.45 +/- 1.48 mg per 24 hours, P < .0001), prevalence of left ventricular hypertrophy (versus 4%, P < .002), intima-media thickening 28% versus 4%, P < .015), and microalbuminuria (22% versus 0%, P < .015). No significant difference, however, was observed between the white coat hypertensives and the normotensives. Serum lipid profile was similar in the white coat hypertensives and in the normotensives.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2026

The molecular similarity landscape of preclinical cancer models to patient tumors.

Selecting appropriate preclinical models is fundamental for translational oncology, yet a large-scale, multi-omic quantitative comparison of their similarity to primary human tumors is lacking. To address this, we integrated transcriptomic, proteomic, and genomic profiles from over 10,000 primary tumors from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC), alongside 4,000 preclinical models. Using a robust computational framework, we revealed a clear hierarchy of transcriptomic and proteomic similarity to patient tumors: with patient-dervied xenografts (PDXs) having greater transcriptomic and proteomic similarity to patient tumors (>) compared with patient-derived organoids (PDOs), which are equal in hierarchy to that of PDX-dervied organoids (PDXOs) > cell lines. We also quantified high molecular conservation (Pearson correlation coefficient = 0.96) across paired in vitro to in vivo platform (organoids to PDX) transitions. Furthermore, genomic analysis demonstrated that whole-exome sequencing (WES) outperforms RNA-seq in detecting DNA variants, and it identified a clonal complexity hierarchy (cell lines > PDXOs > PDXs > PDOs) reflecting the effect of passaging history on intratumor heterogeneity. Ultimately, this study delivers a comprehensive quantitative benchmark, establishing a population-level hierarchy of molecular similarity between preclinical models and primary tumors and providing a data-driven reference for model selection. These findings offer a data-driven framework for selecting models that balance biological representativeness with experimental practicality.

Humans↗