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S Kauffman

Publications and source records attributed to S Kauffman.

At least 19 recordsLinked to original sources
PubMed2003

A system for studying genetic changes in Candida albicans during infection.

Candida albicans is a diploid yeast with a dimorphic life history. It exists commensally in many healthy humans but becomes a potent pathogen in immunocompromised hosts. The underlying genetic mechanisms by which C. albicans switches from a commensal to a pathogenic form in the host are not well understood. To study the evolution of virulence in mammalian hosts, we used GAL1 as selectable marker system that allows for both positive and negative selection in selective media. We show that the deletion of one or both copies of GAL1 in the C. albicans genome does not change virulence in a systemic mouse model. We obtained estimates for the frequency of mitotic recombination at the GAL1 locus during systemic infection. Our observations suggest that genetic changes such as mitotic recombination and gene conversion occur at a high enough frequency to be important in the transition of C. albicans from a commensal to a pathogenic organism.

Animals↗
PubMed2001

WdChs2p, a class I chitin synthase, together with WdChs3p (class III) contributes to virulence in Wangiella (Exophiala) dermatitidis.

The chitin synthase structural gene WdCHS2 was isolated by screening a subgenomic DNA library of Wangiella dermatitidis by using a 0.6-kb PCR product of the gene as a probe. The nucleotide sequence revealed a 2,784-bp open reading frame, which encoded 928 amino acids, with a 59-bp intron near its 5' end. Derived protein sequences showed highest amino acid identities with those derived from the CiCHS1 gene of Coccidioides immitis and the AnCHSC gene of Aspergillus nidulans. The derived sequence also indicated that WdChs2p is an orthologous enzyme of Chs1p of Saccharomyces cerevisiae, which defines the class I chitin synthases. Disruptions of WdCHS2 produced strains that showed no obvious morphological defects in yeast vegetative growth or in ability to carry out polymorphic transitions from yeast cells to hyphae or to isotropic forms. However, assays showed that membranes of wdchs2Delta mutants were drastically reduced in chitin synthase activity. Other assays of membranes from a wdchs1Deltawdchs3Deltawdchs4Delta triple mutant showed that their residual chitin synthase activity was extremely sensitive to trypsin activation and was responsible for the majority of zymogenic activity. Although no loss of virulence was detected when wdchs2Delta strains were tested in a mouse model of acute infection, wdchs2Deltawdchs3Delta disruptants were considerably less virulent in the same model, even though wdchs3Delta strains also had previously shown no loss of virulence. This virulence attenuation in the wdchs2Deltawdchs3Delta mutants was similarly documented in a limited fashion in more-sensitive cyclophosphamide-induced immunocompromised mice. The importance of WdChs2p and WdChs3p to the virulence of W. dermatitidis was then confirmed by reconstituting virulence in the double mutant by the reintroduction of either WdCHS2 or WdCHS3 into the wdchs2Deltawdchs3Delta mutant background.

Amino Acid Sequence↗
PubMed2001

Does pre-dialysis care management reap rewards for patients, renal staff, and payers.

This article describes one renal disease management organization's experience in implementing a pre-dialysis care management program to improve outcomes in patients who develop end-stage renal disease (ESRD). Optimal Renal Care, a national renal disease management company, has implemented care management programs for 600+ ESRD patients and 600+ pre-ESRD patients in Oregon (1998) and Hawaii (1999). This article describes our Oregon pre-ESRD program's start-up experience.

Disease Management↗
PubMed2000

Rational evolutionary design: the theory of in vitro protein evolution.

Directed evolution uses a combination of powerful search techniques to generate proteins with improved properties. Part of the success is due to the stochastic element of random mutagenesis; improvements can be made without a detailed description of the complex interactions that constitute function or stability. However, optimization is not a conglomeration of random processes. Rather, it requires both knowledge of the system that is being optimized and a logical series of techniques that best explores the pathways of evolution (Eigen et al., 1988). The weighing of parameters associated with mutation, recombination, and screening to achieve the maximum fitness improvement is the beginning of rational evolutionary design. The optimal mutation rate is strongly influenced by the finite number of mutants that can be screened. A smooth fitness landscape implies that many mutations can be accumulated without disrupting the fitness. This has the effect of lowering the required library size to sample a higher mutation rate. As the sequence ascends the fitness landscape, the optimal mutation rate decreases as the probability of discovering improved mutations also decreases. Highly coupled regions require that many mutations be simultaneously made to generate a positive mutant. Therefore, positive mutations are discovered at uncoupled positions as the fitness of the parent increases. The benefit of recombination is twofold: it combines good mutations and searches more sequence space in a meaningful way. Recombination is most beneficial when the number of mutants that can be screened is limited and the landscape is of an intermediate ruggedness. The structure of schema in proteins leads to the conclusion that many cut points are required. The number of parents and their sequence identity are determined by the balance between exploration and exploitation. Many disparate parents can explore more space, but at the risk of losing information. The required screening effort is related to the number of uphill paths, which decreases more rapidly for rugged landscapes. Noise in the fitness measurements causes a dramatic increase in the required mutant library size, thus implying a smaller optimal mutation rate. Because of strict limitations on the number of mutants that can be screened, there is motivation to optimize the content of the mutant library. By restricting mutations to regions of the gene that are expected to show improvement, a greater return can be made with the same number of mutants. Initial studies with subtilisin E have shown that structurally tolerant positions tend to be where positive activity mutants are made during directed evolution. Mutant fitness information is produced by the screening step that has the potential to provide insight into the structure of the fitness landscape, thus aiding the setting of experimental parameters. By analyzing the mutant fitness distribution and targeting specific regions of the sequence, in vitro evolution can be accelerated. However, when expediting the search, there is a trade-off between rapid improvement and the quality of the long-term solution. The benefit of neutrality has yet to be captured with in vitro protein evolution. Neutral theory predicts the punctuated emergence of novel structure and function, however, with current methods, the required time scale is not feasible. Utilizing neutral evolution to accelerate the discovery of new functional and structural solutions requires a theory that predicts the behavior of mutational pathways between networks. Because the transition from neutral to adaptive evolution requires a multi-mutational switch, increasing the mutation rate decreases the time required for a punctuated change to occur. By limiting the search to the less coupled region of the sequence (smooth portion of the fitness landscape), the required larger mutation rate can be tolerated. Advances in directed evolution will be achieved when the driving forces behind such proce

Evolution, Molecular↗
PubMed1999

A proposal regarding the mechanism which underlies lineage choice during hematopoietic differentiation.

We present a simple Boolean Network model of a genetic regulatory network which can account for the differentiation of hemopoietic cells. In this model while decision choice is stochastic, the probability of differentiating along a specific pathway is determined by the gene expression state of the cell when the signal to differentiate appears. This probability can be altered by the acute and chronic needs of the individual. Mutations disrupt normal maturation. The paper also presents a larger Boolean Network model which can be used to study normal and leukemic stem cell attractor states.

Cell Differentiation↗
PubMed1999

Criticality and scaling in evolutionary ecology.

Fluctuations in ecological systems are known to involve a wide range of spatial and temporal scales, often displaying self-similar (fractal) properties. Recent theoretical approaches are trying to shed light on the nature of these complex dynamics. The results suggest that complexity in ecology and evolution comes from the network-like structure of multispecies communities that are close to instability. If true, these ideas might change our understanding of how complexity emerges in the biosphere and how macroevolutionary events could be decoupled from microevolutionary ones.

Journal Article↗
PubMed1999

Thinking combinatorially.

Biopolymers and chemical compounds with novel functions can be selected or screened from randomized libraries. Recently, it has become possible to augment the functions of biopolymers via the conjugation or incorporation of unnatural chemical moieties. In the future, it should prove possible to engineer systems that can self-evolve and thereby reveal unexpected emergent properties.

Biopolymers↗
PubMed1995

Adaptive walks with noisy fitness measurements.

Adaptive walks constitute an optimization technique for searching a space of possible solutions, for example, a space of different molecules. The goal is to find a point in space (a molecule) that is optimal or near-optimal in some property, generally referred to as the 'fitness', such as its ability to bind to a given receptor. Adaptive walking, an analog of natural selection, is a powerful technique for searching landscapes. However, errors in the measurements will cause errors in the adaptive walks. Mutant molecules of higher fitness may be ignored or mutants of lower fitness may be accepted. To examine the effect of measurement error on adaptive walks, we simulate single-agent hill-climbing walks on NK landscapes of varying ruggedness where Gaussian noise is added to the fitness values to model measurement error. We consider both constant measurement noise and noise whose variance decays exponentially with fitness. We show that fitness-independent noise can cause walks to 'melt' off the peaks in a landscape, wandering in larger regions as the noise increases. However, we also show that a small amount of noise actually helps the walk perform better than with no noise. For walks in which noise decreases exponentially with fitness, the most characteristic behavior is that the walk meanders throughout the landscape until it stumbles across a point of relatively high fitness, then it climbs the landscape towards the nearest peak. Finally, we characterize the balance between selection pressure and noise and show that there are several classes of walk dynamic behavior.

Algorithms↗
PubMed1993

Is morphogenesis an intrinsically robust process?

Because morphogenesis is dynamically complex, involving many processes operating over different spatial and temporal scales, it is generally assumed that the stability and repeatability of development depends primarily upon accurate control over parameter values i.e. a precise genetic program. However, it is possible that the dynamic coupling between the different mechanisms involved in development reduces the choices available to the system because of bias in successive symmetry-breaking events. Evidence for such stable cascades in morphogenetic processes is described, and a general argument is presented for morphogenesis as an intrinsically robust process. The evolutionary implications of the hypothesis are considerable.

Acetabularia↗
PubMed1987

Towards a general theory of adaptive walks on rugged landscapes.

Adaptive evolution, to a large extent, is a complex combinatorial optimization process. In this article we take beginning steps towards developing a general theory of adaptive "walks" via fitter variants in such optimization processes. We introduce the basic idea of a space of entities, each a 1-mutant neighbor of many other entities in the space, and the idea of a fitness ascribed to each entity. Adaptive walks proceed from an initial entity, via fitter neighbors, to locally or globally optimal entities that are fitter than their neighbors. We develop a general theory for the number of local optima, lengths of adaptive walks, and the number of alternative local optima accessible from any given initial entity, for the baseline case of an uncorrelated fitness landscape. Most fitness landscapes are correlated, however. Therefore we develop parts of a universal theory of adaptation on correlated landscapes by adaptive processes that have sufficient numbers of mutations per individual to "jump beyond" the correlation lengths in the underlying landscape. In addition, we explore the statistical character of adaptive walks in two independent complex combinatorial optimization problems, that of evolving a specific cell type in model genetic networks, and that of finding good solutions to the traveling salesman problem. Surprisingly, both show similar statistical features, encouraging the hope that a general theory for adaptive walks on correlated and uncorrelated landscapes can be found. In the final section we explore two limits to the efficacy of selection. The first is new, and surprising: for a wide class of systems, as the complexity of the entities under selection increases, the local optima that are attainable fall progressively closer to the mean properties of the underlying space of entities. This may imply that complex biological systems, such as genetic regulatory systems, are "close" to the mean properties of the ensemble of genomic regulatory systems explored by evolution. The second limit shows that with increasing complexity and a fixed mutation rate, selection often becomes unable to pull an adapting population to those local optima to which connected adaptive walks via fitter variants exist. These beginning steps in theory development are applied to maturation of the immune response, and to the problem of radiation and stasis. Despite the limitations of the adaptive landscape metaphor, we believe that further development along the lines begun here will prove useful.

Adaptation, Biological↗
PubMed1987

Polyclonal polymorphic B-cell lymphoproliferative disorder with prominent pulmonary involvement in children with acquired immune deficiency syndrome.

Four cases of pediatric Acquired Immune Deficiency Syndrome (AIDS) with lymphoproliferative disorder are described and other lymphoid lesions in previously reported cases of pediatric AIDS are reviewed. The lymphoproliferative disorder was characterized by polyclonal, polymorphic B-cell content without evidence of cellular atypia, necrosis or prominent mitotic activity but with predominantly extranodal systemic and prominent pulmonary involvement. Since the lesion has overlapping features it is considered to be intermediate between benign and malignant lymphoproliferations and designated as polyclonal, polymorphic B-cell lymphoproliferative disorder (PBLD) of pediatric AIDS. The PBLD is part of a spectrum of lymphoid lesions in pediatric AIDS consisting of follicular lymphoid hyperplasia of nodal and extranodal sites, pulmonary lymphoid hyperplasia/lymphoid interstitial pneumonitis complex (PLH/LIP complex) in cases previously reported by the authors, and also malignant lymphoma reported by others. It is possible that Epstein-Barr virus (EBV) by itself or in synergism with human T-lymphotropic virus-type III (HTLV-III) is related to pathogenesis of PBLD in children with AIDS.

Acquired Immunodeficiency Syndrome↗
PubMed1986

Angiotensin II binding sites in individual segments of the rat nephron.

The sites of action of angiotensin II along the nephron are not well defined and both proximal and distal effects are suggested. Using a microassay that permits measurement of hormone binding in discrete tubule segments, we determined the binding sites of 125I-angiotensin II along the nephron of Sprague-Dawley rats. Specific binding in proximal convoluted tubule (PCT) (at 25 degrees C, pH 7.4) was linearly related to tubule length and saturable, with an apparent maximal binding capacity of approximately 300 amol X cm-1. Binding specificity was verified in competition experiments that revealed significant (P less than 0.001) and comparable competition for radioligand binding by angiotensin II and angiotensin precursor, metabolite, and analogues, whereas unrelated peptides of similar size (bradykinin, ACTH [1-10]) were without effect. The profile of specific angiotensin II binding along the nephron was: PCT, 216 +/- 13; pars recta, 86 +/- 14; medullary thick ascending limb of Henle's loop, 46 +/- 8; cortical thick ascending limb of Henle's loop, 77 +/- 8; distal convoluted tubule, 49 +/- 10; cortical collecting tubule, 15 +/- 1; medullary collecting tubule, 32 +/- 7 amol X cm-1. These results indicate the presence of specific angiotensin II binding sites in all tubule segments studied, but binding capacity was highest in the proximal convoluted tubule, in agreement with transport studies that localize the effects of the hormone in this segment.

Angiotensin II↗
PubMed1982

Natural history of "high-risk" bundle-branch block: final report of a prospective study.

We conducted a prospective study in which 554 patients with chronic bifascicular and trifascicular conduction abnormalities were followed for an average of 42.4 +/- 8.5 months. Heart block occurred in 19 patients, and 17 were successfully treated. The actuarial five-year mortality from an event that could conceivably have been a bradyarrhythmia was 6 per cent (35 per cent from all causes). Of the 160 deaths 67 (42 per cent) were sudden; most of these were not ascribable to bradyarrhythmia but to tachyarrhythmia and myocardial infarction. Mortality was higher in patients with coronary-artery disease (P less than 0.01) and congestive heart failure (P less than 0.05). Patients in whom syncope developed before or after entry into the study had a 17 per cent incidence of heart block (2 per cent in those without syncope)(P less than 0.05); however, no single variable was predictive of which patients were at high risk of death from a bradyarrhythmia. The predictors of death were increasing age, congestive heart failure, and coronary-artery disease; the predictors of sudden death were coronary-artery disease and increasing age. The risks of heart block and of death from a bradyarrhythmia are low; in most patients, heart block can be recognized and successfully treated with a pacemaker.

Aged↗