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PubMed2002

Secretory compartments as instances of dynamic self-evolving structures.

Biological objects are often "constructive dynamic systems" whose structures evolve as a consequence of their internal dynamics, which in turn is affected by the overall structure. As very few tools are presently adapted to tackle constructive dynamic systems, they constitute fascinating challenges for modeling/simulation. In cell biology, the secretory process in eukaryotic cells corresponds to this type of system, as it appears to autonomously generate new structures as a result of its molecular dynamics. Here I briefly review the only documented case of a membrane-bounded intracellular compartment whose very existence strictly depends on its continued functioning. Indeed, the Golgi apparatus of the yeast Saccharomyces cerevisiae appears at steady-state as a continuously renewed set of transitory membrane-bounded structures that self-mature, rather than as a permanent entity. On the basis of this case and of recent advances in related molecular studies, a detailed model is proposed, that encompasses the birth of a yeast Golgi element and bridges its molecular and morphogenetic aspects. This model is extended to briefly outline three evolutionary "inventions", from S. cerevisiae to another yeast, Pichia pastoris, on to plant, and on to animal cells: stacking, stabilizing and aggregating the primary Golgi elements.

Animals↗
PubMed2002

2.1 Evolving methods of assessment.

This Working Section is concerned with evolving methods of assessment in dental education. It focuses on newer methods of assessment that might have relevance for broader application. Although it cannot provide answers to all the questions it raises, it is hoped that the contribution it makes is of value in the process of the development of a global network in dental education.

Attitude of Health Personnel↗
PubMed2001

Fears, phobias, and preparedness: toward an evolved module of fear and fear learning.

An evolved module for fear elicitation and fear learning with 4 characteristics is proposed. (a) The fear module is preferentially activated in aversive contexts by stimuli that are fear relevant in an evolutionary perspective. (b) Its activation to such stimuli is automatic. (c) It is relatively impenetrable to cognitive control. (d) It originates in a dedicated neural circuitry, centered on the amygdala. Evidence supporting these propositions is reviewed from conditioning studies, both in humans and in monkeys; illusory correlation studies; studies using unreportable stimuli; and studies from animal neuroscience. The fear module is assumed to mediate an emotional level of fear learning that is relatively independent and dissociable from cognitive learning of stimulus relationships.

Animals↗
PubMedDate not supplied

Relative fitness can decrease in evolving asexual populations of S. cerevisiae.

It is generally accepted from the darwinian theory of evolution that a progressive increase in population adaptation will occur in populations containing genetic variation in fitness, until a stable equilibrium is reached and/or the additive genetic variation is exhausted. However, the theoretical literature of population genetics documents exceptions where mean population fitness may decrease in response to evolutionary changes in gene frequency, due to varying selective coefficients, sexual selection or to epistatic interactions between loci. Until now, no examples of such exceptions have been documented from fitness estimates in either natural or experimental populations. We present here direct evidence that, as a result of epistatic interactions between adaptive mutations, mean population fitness can decrease in asexual evolving populations of the yeast Saccharomyces cerevisiae.

Biological Evolution↗
PubMed2000

Evidence that humans evolved from a knuckle-walking ancestor.

Bipedalism has traditionally been regarded as the fundamental adaptation that sets hominids apart from other primates. Fossil evidence demonstrates that by 4.1 million years ago, and perhaps earlier, hominids exhibited adaptations to bipedal walking. At present, however, the fossil record offers little information about the origin of bipedalism, and despite nearly a century of research on existing fossils and comparative anatomy, there is still no consensus concerning the mode of locomotion that preceded bipedalism. Here we present evidence that fossils attributed to Australopithecus anamensis (KNM-ER 20419) and A. afarensis (AL 288-1) retain specialized wrist morphology associated with knuckle-walking. This distal radial morphology differs from that of later hominids and non-knuckle-walking anthropoid primates, suggesting that knuckle-walking is a derived feature of the African ape and human clade. This removes key morphological evidence for a Pan-Gorilla clade, and suggests that bipedal hominids evolved from a knuckle-walking ancestor that was already partly terrestrial.

Animals↗
PubMed2000

The population genetics of ecological specialization in evolving Escherichia coli populations.

When organisms adapt genetically to one environment, they may lose fitness in other environments. Two distinct population genetic processes can produce ecological specialization-mutation accumulation and antagonistic pleiotropy. In mutation accumulation, mutations become fixed by genetic drift in genes that are not maintained by selection; adaptation to one environment and loss of adaptation to another are caused by different mutations. Antagonistic pleiotropy arises from trade-offs, such that the same mutations that are beneficial in one environment are detrimental in another. In general, it is difficult to distinguish between these processes. We analysed the decay of unused catabolic functions in 12 lines of Escherichia coli propagated on glucose for 20,000 generations. During that time, several lines evolved high mutation rates. If mutation accumulation is important, their unused functions should decay more than the other lines, but no significant difference was observed. Moreover, most catabolic losses occurred early in the experiment when beneficial mutations were being rapidly fixed, a pattern predicted by antagonistic pleiotropy. Thus, antagonistic pleiotropy appears more important than mutation accumulation for the decay of unused catabolic functions in these populations.

Adaptation, Physiological↗
PubMed2001

Rewiring the keyboard: evolvability of the genetic code.

The genetic code evolved in two distinct phases. First, the 'canonical' code emerged before the last universal ancestor; subsequently, this code diverged in numerous nuclear and organelle lineages. Here, we examine the distribution and causes of these secondary deviations from the canonical genetic code. The majority of non-standard codes arise from alterations in the tRNA, with most occurring by post-transcriptional modifications, such as base modification or RNA editing, rather than by substitutions within tRNA anticodons.

Animals↗
PubMed2002

Detection of carbonates in dust shells around evolved stars.

Carbonates on large Solar System bodies like Earth and Mars (the latter represented by the meteorite ALH84001) form through the weathering of silicates in a watery (CO3)2- solution. The presence of carbonates in interplanetary dust particles and asteroids (again, represented by meteorites) is not completely understood, but has been attributed to aqueous alteration on a large parent body, which was subsequently shattered into smaller pieces. Despite efforts, the presence of carbonates outside the Solar System has hitherto not been established. Here we report the discovery of the carbonates calcite and dolomite in the dust shells of evolved stars, where the conditions are too primitive for the formation of large parent bodies with liquid water. These carbonates, therefore, are not formed by aqueous alteration, but perhaps through processes on the surfaces of dust or ice grains or gas phase condensation. The presence of carbonates which did not form by aqueous alteration suggests that some of the carbonates found in Solar System bodies no longer provide direct evidence that liquid water was present on large parent bodies early in the history of the Solar System.

Astronomical Phenomena↗
PubMed1999

The pathogenesis of familial hypertrophic cardiomyopathy: early and evolving effects from an alpha-cardiac myosin heavy chain missense mutation.

Familial hypertrophic cardiomyopathy (FHC) is a genetic disorder resulting from mutations in genes encoding sarcomeric proteins. This typically induces hyperdynamic ejection, impaired relaxation, delayed early filling, myocyte disarray and fibrosis, and increased chamber end-systolic stiffness. To better understand the disease pathogenesis, early (primary) abnormalities must be distinguished from evolving responses to the genetic defect. We did in vivo analysis using a mouse model of FHC with an Arg403Gln alpha-cardiac myosin heavy chain missense mutation, and used newly developed methods for assessing in situ pressure-volume relations. Hearts of young mutant mice (6 weeks old), which show no chamber morphologic or gross histologic abnormalities, had altered contraction kinetics, with considerably delayed pressure relaxation and chamber filling, yet accelerated systolic pressure rise. Older mutant mice (20 weeks old), which develop fiber disarray and fibrosis, had diastolic and systolic kinetic changes similar to if not slightly less than those of younger mice. However, the hearts of older mutant mice also showed hyperdynamic contraction, with increased end-systolic chamber stiffness, outflow tract pressure gradients and a lower cardiac index due to reduced chamber filling; all 'hallmarks' of human disease. These data provide new insights into the temporal evolution of FHC. Such data may help direct new therapeutic strategies to diminish disease progression.

Aging↗
PubMed2001

DNA shuffling method for generating highly recombined genes and evolved enzymes.

We introduce a method of in vitro recombination or "DNA shuffling" to generate libraries of evolved enzymes. The approach relies on the ordering, trimming, and joining of randomly cleaved parental DNA fragments annealed to a transient polynucleotide scaffold. We generated chimeric libraries averaging 14.0 crossovers per gene, a several-fold higher level of recombination than observed for other methods. We also observed an unprecedented four crossovers per gene in regions of 10 or fewer bases of sequence identity. These properties allow generation of chimeras unavailable by other methods. We detected no unshuffled parental clones or duplicated "sibling" chimeras, and relatively few inactive clones. We demonstrated the method by molecular breeding of a monooxygenase for increased rate and extent of biodesulfurization on complex substrates, as well as for 20-fold faster conversion of a nonnatural substrate. This method represents a conceptually distinct and improved alternative to sexual PCR for gene family shuffling.

Alleles↗
PubMed1999

Revealing the structure of the oxygen-evolving core dimer of photosystem II by cryoelectron crystallography.

Here we present cryoelectron crystallographic analysis of an isolated dimeric oxygen-evolving complex of photosystem II (at a resolution of approximately 0.9 nm), revealing that the D1-D2 reaction center (RC) proteins are centrally located between the chlorophyll-binding proteins, CP43 and CP47. This conclusion supports the hypothesis that photosystems I and II have similar structural features and share a common evolutionary origin. Additional density connecting the two halves of the dimer, which was not observed in a recently described CP47-RC complex that did not include CP43, may be attributed to the small subunits that are involved in regulating secondary electron transfer, such as PsbH. These subunits are possibly also required for stabilization of the dimeric photosystem II complex. This complex, containing at least 29 transmembrane helices in its asymmetric unit, represents one of the largest membrane protein complexes studied at this resolution.

Cryoelectron Microscopy↗
PubMed1983

Evolving methodologies in computerized European Registries.

The histories and present roles of four European Registries are described. Three are transplant sharing organizations, Eurotransplant (ET), Scandiatransplant (ST), and the United Kingdom Transplant Service (UKTS). The Registry of the European Dialysis and Transplant Association is a patient Registry that tracks patients on dialysis as well as after transplantation and follows them from center to center. The transplant organizations collaborate by linking patient records on the EDTA Register. These large central Registries have evolved specialized computer methodologies for recording the follow-up of patients, researching the patient file, and improving the service to centers. The log-rank test is useful for the evaluation of pooled results. Reliability of donor typings can be verified by testing results for the Hardy-Weinberg equilibrium. A method for the prediction of pool size required to find matched recipients is described. Collaborative studies have been carried out in an attempt to discover the factor(s) responsible for the "center effect." New trends in analysis of transplant results will include detailed documentation of rejection episodes. Compliance by centers contributing to the transplant organizations is ensured by the need for organ interchange, whereas the EDTA Registry depends on the directors of centers being motivated by the publication of pooled statistics and results and by the provision of feedback information to the individual units.

Computers↗
PubMed2004

The synthesis of organic and inorganic compounds in evolved stars.

Recent isotopic analysis of meteorites and interplanetary dust has identified solid-state materials of pre-solar origin. We can now trace the origin of these inorganic grains to the circumstellar envelopes of evolved stars. Moreover, organic (aromatic and aliphatic) compounds have been detected in proto-planetary nebulae and planetary nebulae, which are the descendants of carbon stars. This implies that molecular synthesis is actively happening in the circumstellar environment on timescales as short as several hundred years. The detection of stellar grains in the Solar System suggests that they can survive their journey through the interstellar medium and that they are a major contributor of interstellar grains.

Journal Article↗
PubMed2005

Evidence that sensory traps can evolve into honest signals.

Conventional models explaining extreme sexual ornaments propose that these reflect male genetic quality or are arbitrary results of genetic linkage between female preference and the ornament. The chase-away model emphasizes sexual conflict: male signals attract females because they exploit receiver biases. As males gain control of mating decisions, females may experience fitness costs through suboptimal mating rates or post-copulatory exploitation. Elaboration of male signals is expected if females increase their response threshold to resist such exploitation. If ornaments target otherwise adaptive biases such as feeding responses, selection on females might eventually separate sexual and non-sexual responses to the signal. Here we show that the terminal yellow band (TYB) of several Goodeinae species evokes both feeding and sexual responses; sexual responsiveness phylogenetically pre-dates the expression of the TYB in males and is comparable across taxa, yet feeding responsiveness decreases in species with more elaborated TYBs. Displaying a TYB is costly, and thus provides an example where a trait arose as a sensory trap but has evolved into an honest signal.

Animals↗
PubMed1998

Evolving catalytic antibodies in a phage-displayed combinatorial library.

In vitro affinity maturation for evolving catalytic antibodies has been demonstrated by generating a diverse repertoire of the appropriate complementarity-determining regions on a phage surface. Phage display is followed by a selection based on binding to an altered antigen that was not used at the time of immunization, and provides variants with new catalytic activity and substrate specificity. This library format reduces the time needed to isolate the desired catalytic antibody fragments to under 2 weeks.

Antibodies, Catalytic↗
PubMed2005

Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains.

We have developed a class of binding proteins, called avimers, to overcome the limitations of antibodies and other immunoglobulin-based therapeutic proteins. Avimers are evolved from a large family of human extracellular receptor domains by in vitro exon shuffling and phage display, generating multidomain proteins with binding and inhibitory properties. Linking multiple independent binding domains creates avidity and results in improved affinity and specificity compared with conventional single-epitope binding proteins. Other potential advantages over immunoglobulin domains include simple and efficient production of multitarget-specific molecules in Escherichia coli, improved thermostability and resistance to proteases. Avimers with sub-nM affinities were obtained against five targets. An avimer that inhibits interleukin 6 with 0.8 pM IC50 in cell-based assays is biologically active in two animal models.

Animals↗
PubMed2007

Is HIV-1 evolving to a less virulent form in humans?

During the rapid spread of HIV-1 in humans, the main (M) group of HIV-1 has evolved into ten distinct subtypes, undergone countless recombination events and diversified extensively. The impact of this extreme genetic diversity on the phenotype of HIV-1 has only recently become a research focus, but early findings indicate that the dominance of HIV-1 subtype C in the current epidemic might be related to the lower virulence of this subtype compared with other subtypes. Here, we explore whether HIV-1 has reached peak virulence or has already started the slow path to attenuation.

Animals↗
PubMed2005

Evolving treatment strategies for myeloma.

In this article, we will discuss how treatment strategies for myeloma have evolved and outline the challenges now faced following the introduction of a number of novel active agents. In particular, we will focus on how achieving a maximum response and maintaining such responses is becoming a key therapeutic strategy and how novel agents can be used to achieve this in the context of current strategies such as autologous transplantation.

Angiogenesis Inhibitors↗