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PubMed2006

Inference in ecology and evolution.

Most ecologists and evolutionary biologists continue to rely heavily on null hypothesis significance testing, rather than on recently advocated alternatives, for inference. Here, we briefly review null hypothesis significance testing and its major alternatives. We identify major objectives of statistical analysis and suggest which analytical approaches are appropriate for each. Any well designed study can improve our understanding of biological systems, regardless of the inferential approach used. Nevertheless, an awareness of available techniques and their pitfalls could guide better approaches to data collection and broaden the range of questions that can be addressed. Although we should reduce our reliance on significance testing, it retains an important role in statistical education and is likely to remain fundamental to the falsification of scientific hypotheses.

Bayes Theorem↗

PubMed2006

Plastid division: evolution, mechanism and complexity.

BACKGROUND: The continuity of chloroplasts is maintained by division of pre-existing chloroplasts. Chloroplasts originated as bacterial endosymbionts; however, the majority of bacterial division factors are absent from chloroplasts and the eukaryotic host has added several new components. For example, the ftsZ gene has been duplicated and modified, and the Min system has retained MinE and MinD but lost MinC, acquiring at least one new component ARC3. Further, the mechanism has evolved to include two members of the dynamin protein family, ARC5 and FZL, and plastid-dividing (PD) rings were most probably added by the eukaryotic host. SCOPE: Deciphering how the division of plastids is coordinated and controlled by nuclear-encoded factors is key to our understanding of this important biological process. Through a number of molecular-genetic and biochemical approaches, it is evident that FtsZ initiates plastid division where the coordinated action of MinD and MinE ensures correct FtsZ (Z)-ring placement. Although the classical FtsZ antagonist MinC does not exist in plants, ARC3 may fulfil this role. Together with other prokaryotic-derived proteins such as ARC6 and GC1 and key eukaryotic-derived proteins such as ARC5 and FZL, these proteins make up a sophisticated division machinery. The regulation of plastid division in a cellular context is largely unknown; however, recent microarray data shed light on this. Here the current understanding of the mechanism of chloroplast division in higher plants is reviewed with an emphasis on how recent findings are beginning to shape our understanding of the function and evolution of the components. CONCLUSIONS: Extrapolation from the mechanism of bacterial cell division provides valuable clues as to how the chloroplast division process is achieved in plant cells. However, it is becoming increasingly clear that the highly regulated mechanism of plastid division within the host cell has led to the evolution of features unique to the plastid division process.

Arabidopsis Proteins↗

PubMed1996

Human evolution and the mitochondrial genome.

The use of mitochondrial DNA (mtDNA) continues to dominate studies of human genetic variation and evolution. Recent work has re-affirmed the strict maternal inheritance of mtDNA, yielded new insights into the extent and nature of intra-individual variation, supported a recent African origin of human mtDNA, and amply demonstrated the utility of mtDNA in tracing population history and in analyses of ancient remains.

Animals↗

PubMed2005

Quantum state reconstruction via continuous measurement.

We present a new procedure for quantum state reconstruction based on weak continuous measurement of an ensemble average. By applying controlled evolution to the initial state, new information is continually mapped onto the measured observable. A Bayesian filter is then used to update the state estimate in accordance with the measurement record. This generalizes the standard paradigm for quantum tomography based on strong, destructive measurements on separate ensembles. This approach to state estimation induces minimal perturbation of the measured system, giving information about observables whose evolution cannot be described classically in real time and opening the door to new types of quantum feedback control.

Journal Article↗

PubMed2005

Adaptive molecular evolution for 13,000 phage generations: a possible arms race.

Bacteriophage phiX174 was evolved on a continuous supply of sensitive hosts for 180 days ( approximately 13,000 phage generations). The average rate of nucleotide substitution was nearly 0.2% (11 substitutions)/20 days, and, surprisingly, substitutions accumulated in a clock-like manner throughout the study, except for a low rate during the first 20 days. Rates of silent and missense substitutions varied over time and among genes. Approximately 40% of the 71 missense changes and 25% of the 58 silent changes have been observed in previous adaptations; the rate of parallel substitution was highest in the early phase of the evolution, but 7% of the later changes had evolved in previous studies of much shorter duration. Several lines of evidence suggest that most of the changes were adaptive, even many of the silent substitutions. The sustained, high rate of adaptive evolution for 180 days defies a model of adaptation to a constant environment. We instead suggest that continuing molecular evolution reflects a potentially indefinite arms race, stemming from high levels of co-infection and the resulting conflict among genomes competing within the same cell.

Adaptation, Biological↗

PubMed2005

Emerging pathogens: the epidemiology and evolution of species jumps.

Novel pathogens continue to emerge in human, domestic animal, wildlife and plant populations, yet the population dynamics of this kind of biological invasion remain poorly understood. Here, we consider the epidemiological and evolutionary processes underlying the initial introduction and subsequent spread of a pathogen in a new host population, with special reference to pathogens that originate by jumping from one host species to another. We conclude that, although pathogen emergence is inherently unpredictable, emerging pathogens tend to share some common traits, and that directly transmitted RNA viruses might be the pathogens that are most likely to jump between host species.

Journal Article↗

PubMed1992

Nurse administrators in job transition: evolution of the issue.

Nurse Executives continually experience legal and ethical dilemmas that affect their personal and professional lives. An issue facing increasing numbers of nurse executives is turnover, whether voluntary or involuntary. The next several columns will explore the nurse administrator in job transition, with the goal of increasing their understanding of their legal rights and responsibilities when dealing with this aspect of their professional practice.

Career Mobility↗

PubMed2003

Cooperation and conflict in the evolution of individuality. IV. Conflict mediation and evolvability in Volvox carteri.

The continued well being of evolutionary individuals (units of selection and evolution) depends upon their evolvability, that is their capacity to generate and evolve adaptations at their level of organization, as well as their longer term capacity for diversifying into more complex evolutionary forms. During a transition from a lower- to higher-level individual, such as the transition between unicellular and multicellular organisms, the evolvability of the lower-level (cells) must be restricted, while the evolvability of the new higher-level unit (multicellular organism) must be enhanced. For these reasons, understanding the factors leading to an evolutionary transition should help us to understand the factors underlying the emergence of evolvability of a new evolutionary unit. Cooperation among lower-level units is fundamental to the origin of new functions in the higher-level unit. Cooperation can produce a new more complex evolutionary unit, with the requisite properties of heritable fitness variations, because cooperation trades fitness from a lower-level (the costs of cooperation) to the higher-level (the benefits for the group). For this reason, the evolution of cooperative interactions helps us to understand the origin of new and higher-levels of fitness and organization. As cooperation creates a new level of fitness, it also creates the opportunity for conflict between levels of selection, as deleterious mutants with differing effects at the two levels arise and spread. This conflict can interfere with the evolvability of the higher-level unit, since the lower and higher-levels of selection will often "disagree" on what adaptations are most beneficial to their respective interests. Mediation of this conflict is essential to the emergence of the new evolutionary unit and to its continued evolvability. As an example, we consider the transition from unicellular to multicellular organisms and study the evolution of an early-sequestered germ-line in terms of its role in mediating conflict between the two levels of selection, the cell and the cell group. We apply our theoretical framework to the evolution of germ/soma differentiation in the green algal group Volvocales. In the most complex member of the group, Volvox carteri, the potential conflicts among lower-level cells as to the "right" to reproduce the higher-level individual (i.e. the colony) have been mediated by restricting immortality and totipotency to the germ-line. However, this mediation, and the evolution of an early segregated germ-line, was achieved by suppressing mitotic and differentiation capabilities in all post-embryonic cells. By handicapping the soma in this way, individuality is ensured, but the solution has affected the long-term evolvability of this lineage. We think that although conflict mediation is pivotal to the emergence of individuality at the higher-level, the way in which the mediation is achieved can greatly affect the longer-term evolvability of the lineage.

Adaptation, Physiological↗

PubMed1997

[Intracranial pressure monitoring as a complementary tests for diagnosing brain death. Preliminary observation through the report of 2 cases].

The clinical evolution of two patients with continuous intracranial pressure (ICP) monitoring, admitted to the Intensive Care Unit of Neurology, University Hospital of Botucatu, and followed until irreversible cardiac failure (ICF) was studied retrospectively. The evolution of ICP showed that it reached a maximum 5 to 12 hours before a decrease in wave amplitude occurred (this was observed approximately 47 to 60 hours before ICF). The tracing became linear approximately 30 hours before ICF in both cases. The clinical diagnosis of brain death (BD) was obtained 3 to 28 hours after the tracing had become linear. The authors suggest that, in absence of sedation, the diagnosis of BD may be made early with the use of ICP monitoring even before the clinical diagnosis, and emphasize the need for more observations in a larger number of patients.

Adult↗

PubMed2005

Stability of the replicator equation for a single species with a multi-dimensional continuous trait space.

The replicator equation model for the evolution of individual behaviors in a single species with a multi-dimensional continuous trait space is developed as a dynamics on the set of probability measures. Stability of monomorphisms in this model using the weak topology is compared to more traditional methods of adaptive dynamics. For quadratic fitness functions and initial normal trait distributions, it is shown that the multi-dimensional continuously stable strategy (CSS) of adaptive dynamics is often relevant for predicting stability of the measure-theoretic model but may be too strong in general. For general fitness functions and trait distributions, the CSS is related to dominance solvability which can be used to characterize local stability for a large class of trait distributions that have no gaps in their supports whereas the stronger neighborhood invader strategy (NIS) concept is needed if the supports are arbitrary.

Adaptation, Physiological↗

PubMed2000

Peripubertal prolactinomas: clinical presentation and long-term outcome with different therapeutic approaches.

UNLABELLED: The evolution of prolactinomas in children and adolescents continues to be controversial. We report on the long-term evolution (2-20 yr) of prolactinomas in 40 patients (29 F, 11 M). In females, the age for the onset of symptoms ranged between 8 and 16 yr and the age at which diagnosis was made ranged from 15 to 19 yr; in males, ages ranged from 8 to 17 yr and from 13.8 to 19 yr, respectively. In females, there was predominance of microprolactinomas (22/ 29) and the symptomatology resulted from functional disorders, whereas in males there was predominance of macroprolactinomas (8/11) and symptoms were caused by tumor mass disorders. Surgery was used as primary therapy in nine patients and as supplemental therapy in six patients. Twenty-four patients were treated primarily with bromocriptine and seven with cabergoline. Of the nine patients treated primarily with surgery, only one achieved gonadotropic axis restoration; in 25/31 patients receiving drug therapy gonadotropic function was restored to normal. Fifteen patients showed complete resolution or substantial shrinkage of tumor. CONCLUSION: In pediatric and adolescent age, there seem to be age- and sex-dependent differences in the clinical presentation of prolactinomas that cannot be accounted for only in terms of time of evolution. Drug therapy can control the disease, normalize prolactin levels and achieve gonadotropic axis restoration in most patients.

Adolescent↗

PubMed1994

Evolutionary optimization of the catalytic properties of a DNA-cleaving ribozyme.

In a previous study [Beaudry, A. A., & Joyce, G. F. (1992) Science 257, 635-641], an in vitro evolution procedure was used to obtain variants of the Tetrahymena ribozyme with 100-fold improved ability to cleave a target single-stranded DNA under physiologic conditions. Here we report continuation of the in vitro evolution process to achieve 10(5)-fold overall improvement in DNA-cleavage activity. In addition, we demonstrate that, by appropriate manipulation of the selection constraints, one can optimize specific catalytic properties of the evolved ribozymes. We first reduced the concentration of the DNA substrate 50-fold to favor ribozymes with improved substrate binding affinity. We then reduced the reaction time 12-fold to favor ribozymes with improved catalytic rate. In both cases, the evolving population responded as expected, first improving substrate binding 25-fold, and then improving catalytic rate about 50-fold. The population of ribozymes has undergone 27 successive generations of in vitro evolution, resulting in, on average, 17 mutations relative to the wild type that are responsible for the improved DNA-cleavage activity.

Animals↗

PubMed2000

Downregulation of 14-3-3sigma prevents clonal evolution and leads to immortalization of primary human keratinocytes.

In human epidermal keratinocytes, replicative senescence, is determined by a progressive decline of clonogenic and dividing cells. Its timing is controlled by clonal evolution, that is, by the continuous transition from stem cells to transient amplifying cells. We now report that downregulation of 14-3-3sigma, which is specifically expressed in human stratified epithelia, prevents keratinocyte clonal evolution, thereby forcing keratinocytes into the stem cell compartment. This allows primary human keratinocytes to readily escape replicative senescence. 14-3-3sigma-dependent bypass of senescence is accompanied by maintenance of telomerase activity and by downregulation of the p16(INK4a) tumor suppressor gene, hallmarks of keratinocyte immortalization. Taken together, these data therefore suggest that inhibition of a single endogenous gene product fosters immortalization of primary human epithelial cells without the need of exogenous oncogenes and/or oncoviruses.

14-3-3 Proteins↗

PubMed1986

Continuous pyruvate carbon flux to newly synthesized cholesterol and the suppressed evolution of pyruvate-generated CO2 in tumors: further evidence for a persistent truncated Krebs cycle in hepatomas.

Viable tissue slices from rat liver and Morris hepatoma 3924A were compared as to their ability to incorporate carbons from [U-14 C]pyruvate into newly synthesized cholesterol versus CO2. By 4 h, the tumor slice incubation had incorporated over 6-fold more pyruvate carbons into the sterol than into CO2, relative to the normal liver slice incubation, per g tissue protein. However, the presence of the mitochondrial citrate exchange carrier inhibitor 1,2,3-benzenetricarboxylate in the incubation inhibited the formation of [14C]cholesterol, while simultaneously leading to an increase in the rate of 14CO2 production in the tumor. In the normal liver system by contrast, benzenetricarboxylate also inhibited [14C]cholesterol formation, but had hardly any effect on the already high rate of 14CO2 production. The ability of benzenetricarboxylate to inhibit the rapid carbon flux from pyruvate to cholesterol, and to steer the metabolic flow of carbons toward oxidative decarboxylation via the Krebs cycle in whole, viable tumor tissue, indirectly emphasizes the importance of the mitochondrial citrate exchange carrier in supporting the decontrol of cholesterogenesis de novo in tumors by accelerating the supply of lipogenic precursor carbons to the tumor cytosol. These studies may be therefore interpreted as extensions, to the level of whole-cell metabolism, of the concept of a persistent 'truncated' Krebs cycle in the mitochondria of metastatic cancer tissue. This concept states, in part, that a rapid efflux of mitochondrially generated citrate would operate preferentially in tumors, and thus provide carbons continuously to the cytoplasmic compartment where the well-established deregulated pathway of cholesterogenesis occurs (Parlo, R.A. and Coleman, P.S. (1984) J. Biol. Chem. 259, 9997-10003; Coleman, P.S. and Lavietes, B.B. (1981) CRC Crit. Rev. Biochem. 11, 341-393).

Animals↗

PubMed1991

Prebiotic chemistry in clouds.

In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical evolution may not have occurred continuously because planetesimals and asteroids impacted the Earth many times during the first billion years, may have sterilized the Earth, and required the process to start over. A rapid process of chemical evolution may have been required in order that life appeared at or before 3.5 billion years ago. Thus, a setting favoring rapid chemical evolution may be required. A chemical evolution hypothesis set forth by Woese in 1979 accomplished prebiotic reactions rapidly in droplets in giant atmospheric reflux columns. However, in 1985 Scherer raised a number of objections to Woese's hypothesis and concluded that it was not valid. We propose a mechanism for prebiotic chemistry in clouds that satisfies Scherer's concerns regarding the Woese hypothesis and includes advantageous droplet chemistry. Prebiotic reactants were supplied to the atmosphere by comets, meteorites, and interplanetary dust or synthesized in the atmosphere from simple compounds using energy sources such as ultraviolet light, corona discharge, or lightning. These prebiotic monomers would have first encountered moisture in cloud drops and precipitation. We propose that rapid prebiotic chemical evolution was facilitated on the primordial Earth by cycles of condensation and evaporation of cloud drops containing clay condensation nuclei and nonvolatile monomers. For example, amino acids supplied by , or synthesized during entry of, meteorites, comets, and interplanetary dust would have been scavenged by cloud drops containing clay condensation nuclei. Polymerization would have occurred within cloud systems during cycles of condensation, freezing, melting, and evaporation of cloud drops. We suggest that polymerization reactions occurred in the atmosphere as in the Woese hypothesis, but life originated in the ocean as in the Oparin-Haldane hypothesis. The rapidity with which chemical evolution could have occurred within clouds accommodates the time constraints suggested by recent astrophysical theories.

Aluminum Silicates↗

PubMed2002

Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD.

Cryptococcus neoformans is a major pathogen of humans throughout the world. Using commercial mAbs to capsular epitopes, strains of C. neoformans manifest five distinct serotypes--A, B, C, D and AD. Previous studies demonstrated significant divergence among serotypes A, B, C and D, which are thought to be haploid. In this study the origins and evolution of strains of serotype AD were investigated. A portion (537 bp) of the laccase gene was cloned and sequenced from 14 strains of serotype AD. Each strain contained two different alleles and sequences for both alleles were obtained. These sequences were compared to those from serotypes A, B, C and D. This analysis indicated that each of the 14 serotype AD strains contained two phylogenetically distinct haplotypes: one haplotype was highly similar to the serotype A group and the other to the serotype D group. To explain the origins of these serotype AD strains, genealogical analysis is consistent with at least three recent and independent hybridization events. The results demonstrate that the evolution of C. neoformans is continuing and dynamic.

Base Sequence↗

PubMedDate not supplied

Evolution and current status of the total artificial heart: the search continues.

Artificial hearts have been used for temporary and permanent replacement of failing human hearts. Attempts at permanent implantation during the 1980s were complicated by a high incidence of infection and thromboembolism, combined with a low quality of life for recipients. Given the success of cardiac transplantation, the artificial heart was relegated to temporary use in critically ill patients who were waiting for a donor heart. Continued difficulties with complications, combined with the success of ventricular assist devices for this purpose, dramatically reduced the use of the artificial heart. However, the recent development of compact electromechanical artificial hearts powered by transcutaneous energy systems has led to renewed hope for the possibility of permanent implantation. Some of these devices have been successful in animal studies and are approaching human trials. After years of hope and disappointment, artificial heart technology may be on the verge of efficacy. The history, status, and future of the artificial heart are discussed.

Animals↗

PubMed1983

Evolution of residual renal function in patients undergoing maintenance haemodialysis or continuous ambulatory peritoneal dialysis.

A study has been carried out to compare over an 18 month period the residual glomerular filtration rate (GFR) measured by the creatinine clearance in two matched groups of 25 patients with end-stage renal disease. One group was treated by continuous ambulatory peritoneal dialysis, the other one by maintenance haemodialysis. GFR was similar in both groups immediately before starting dialysis therapy, respectively 4.3 +/- 2.3 and 4.4 +/- 2.4 ml/min. From the beginning of the dialysis treatment to the eighteenth month there was a significant and progressive decrease of GFR in the group of patients treated by haemodialysis, while in the peritoneal dialysis group GFR and peritoneal clearances remained stable.

Adult↗