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PubMed2025

Evolutionary and Functional Analysis of Caspase-8 and ASC Interactions to Drive Lytic Cell Death, PANoptosis.

Caspases are evolutionarily conserved proteins essential for driving cell death in development and host defense. Caspase-8, a key member of the caspase family, is implicated in nonlytic apoptosis, as well as lytic forms of cell death. Recently, caspase-8 has been identified as an integral component of PANoptosomes, multiprotein complexes formed in response to innate immune sensor activation. Several innate immune sensors can nucleate caspase-8-containing PANoptosome complexes to drive inflammatory lytic cell death, PANoptosis. However, how the evolutionarily conserved and diverse functions of caspase-8 drive PANoptosis remains unclear. To address this, we performed evolutionary, sequence, structural, and functional analyses to decode caspase-8's complex-forming abilities and its interaction with the PANoptosome adaptor ASC. Our study distinguished distinct subgroups within the death domain superfamily based on their evolutionary and functional relationships, identified homotypic traits among subfamily members, and captured key events in caspase evolution. We also identified critical residues defining the heterotypic interaction between caspase-8's death effector domain and ASC's pyrin domain, validated through cross-species analyses, dynamic simulations, and in vitro experiments. Overall, our study elucidated recent evolutionary adaptations of caspase-8 that allowed it to interact with ASC, improving our understanding of critical molecular associations in PANoptosome complex formation and the underlying PANoptotic responses in host defense and inflammation. These findings have implications for understanding mammalian immune responses and developing new therapeutic strategies for inflammatory diseases.

Caspase 8↗
PubMed2007

The dynamic changes in roles of learning through the Baldwin effect.

The interaction between evolution and learning called the Baldwin effect is a two-step evolutionary scenario caused by the balances between benefit and cost of learning in general. However, little is known about the dynamic evolution of these balances in complex environments. Our purpose is to give a new insight into the benefit and cost of learning by focusing on the quantitative evolution of phenotypic plasticity under the assumption of epistatic interactions. For this purpose, we have constructed an evolutionary model of quantitative traits by using an extended version of Kauffman's NK fitness landscape. Phenotypic plasticity is introduced into our model; whether each phenotype is plastic or not is genetically defined, and plastic phenotypes can be adjusted by learning. The simulation results clearly show that drastic changes in roles of learning cause three-step evolution through the Baldwin effect and also cause the evolution of genetic robustness against mutations. We also conceptualize four different roles of learning by using a hill-climbing image of a population on a fitness landscape.

Biological Evolution↗
PubMed1989

Towards an artificial brain.

Three components of a brain model operating on neuromolecular computing principles are described. The first component comprises neurons whose input-output behavior is controlled by significant internal dynamics. Models of discrete enzymatic neurons, reaction-diffusion neurons operating on the basis of the cyclic nucleotide cascade, and neurons controlled by cytoskeletal dynamics are described. The second component of the model is an evolutionary learning algorithm which is used to mold the behavior of enzyme-driven neurons or small networks of these neurons for specific function, usually pattern recognition or target seeking tasks. The evolutionary learning algorithm may be interpreted either as representing the mechanism of variation and natural selection acting on a phylogenetic time scale, or as a conceivable ontogenetic adaptation mechanism. The third component of the model is a memory manipulation scheme, called the reference neuron scheme. In principle it is capable of orchestrating a repertoire of enzyme-driven neurons for coherent function. The existing implementations, however, utilize simple neurons without internal dynamics. Spatial navigation and simple game playing (using tic-tac-toe) provide the task environments that have been used to study the properties of the reference neuron model. A memory-based evolutionary learning algorithm has been developed that can assign credit to the individual neurons in a network. It has been run on standard benchmark tasks, and appears to be quite effective both for conventional neural nets and for networks of discrete enzymatic neurons. The models have the character of artificial worlds in that they map the hierarchy of processes in the brain (at the molecular, neuronal, and network levels), provide a task environment, and use this relatively self-contained setup to develop and evaluate learning and adaptation algorithms.

Artificial Intelligence↗
PubMed2006

Virus fitness: concept, quantification, and application to HIV population dynamics.

Viral fitness has been broadly studied during the past three decades, mainly to test evolutionary models and population theories difficult to analyze and interpret with more complex organisms. More recent studies, however, are focused in the role of fitness on viral transmission, pathogenesis, and drug resistance. Here, we used human immunodeficiency virus (HIV) as one of the most relevant models to evaluate the importance of viral quasispecies and fitness in HIV evolution, population dynamics, disease progression, and potential clinical implications.

Anti-HIV Agents↗
PubMedDate not supplied

Non equilibrium thermodynamics and the city: a new approach to urban studies.

A city can be conceived as a complex self-adaptive system. The multiple interactions among its structural elements and dynamic agents, its organization on multiple time-space scales, its exchanges with the external context, its irreversible dynamics, are signs of complexity. Some concepts from the evolutionary thermodynamics, such us the theory of dissipative structures, could be extended to the city in order to investigate its behaviour. This theoretical framework suggests to analyze the city in terms of entropy and negentropy production. An emergy analysis (spelled with an "m") of an urban region is presented in order to investigate how cities maintain their organization (and decrease their entropy) by virtue of constant energy inflows from the external environment. As a result, a non-homogeneous spatial pattern of emergy density is shown as an attempt to investigate the multiple relations and energy exchanges that take place in an urban region. This approach to urban studies introduces a new energy-based vision to understand cities.

Cities↗
PubMed2005

Taxonomic affinities and evolutionary history of the Early Pleistocene hominids of Java: dentognathic evidence.

Temporal changes, within-group variation, and phylogenetic positions of the Early Pleistocene Javanese hominids remain unclear. Recent debate focused on the age of the oldest Javanese hominids, but the argument so far includes little morphological basis for the fossils. To approach these questions, we analyzed a comprehensive dentognathic sample from Sangiran, which includes most of the existing hominid mandibles and teeth from the Early Pleistocene of Java. The sample was divided into chronologically younger and older groups. We examined morphological differences between these chronological groups, and investigated their affinities with other hominid groups from Africa and Eurasia. The results indicated that 1) there are remarkable morphological differences between the chronologically younger and older groups of Java, 2) the chronologically younger group is morphologically advanced, showing a similar degree of dentognathic reduction to that of Middle Pleistocene Chinese H. erectus, and 3) the chronologically older group exhibits some features that are equally primitive as or more primitive than early H. erectus of Africa. These findings suggest that the evolutionary history of early Javanese H. erectus was more dynamic than previously thought. Coupled with recent discoveries of the earliest form of H. erectus from Dmanisi, Georgia, the primitive aspects of the oldest Javanese hominid remains suggest that hominid groups prior to the grade of ca. 1.8-1.5 Ma African early H. erectus dispersed into eastern Eurasia during the earlier Early Pleistocene, although the age of the Javanese hominids themselves is yet to be resolved. Subsequent periods of the Early Pleistocene witnessed remarkable changes in the Javanese hominid record, which are ascribed either to significant in situ evolution or replacement of populations.

Adult↗
PubMed2006

Get the balance right: mitofusins roles in health and disease.

Mitochondria are highly dynamic organelles exhibiting an elaborate morphology and fine structure. Fusion and fission processes contribute to the maintenance and dynamics of mitochondrial morphology. The Mitofusins, a class of evolutionary conserved GTPases of the mitochondrial outer membrane, are essential for the controlled fusion of mitochondrial membranes. Genetic and biochemical data propose a model in which functional domains, such as the GTPase domain and the C-terminally located coiled coil structure, act in an orchestrated manner to coordinate the tethering and mitochondrial outer membrane fusion. In addition, recent reports shed new light on the physiological importance of Mitofusin function suggesting a role in mitochondrial metabolism, apoptosis as well as cellular signalling. Mutations identified in the human Mfn2 gene from patients with the peripheral neuropathy Charcot-Marie-Tooth Type 2A invoke a direct correlation between mitochondrial morphology and function.

Adaptor Proteins, Signal Transducing↗
PubMed2000

The first object oriented monitor for intravenous anesthesia.

OBJECTIVE: To describe the design and implementation of "INFUSION TOOLBOX," a software tool to control and monitor multiple intravenous drug infusions simultaneously using pharmacokinetic and pharmacodynamic principles. METHODS: INFUSION TOOLBOX has been designed to present a graphical interface. Object Oriented design was used and the software was implemented using Smalltalk, to run on a PC. Basic tools are available to manage patient, drugs, pumps and reports. These tools are the PatientPanel, the DrugPanel, the PumpPanel and the HistoryPanel. The screen is built dynamically. The panels may be collapsed or closed to avoid a crowded display. We also built control panels such as the Target ControlPanel which calculates the best infusion sequence to bring the drug concentration in the plasma compartment to a preset value. Before drug delivery, the user enters the patient's data, selects a drug, enters its dilution factor and chooses a pharmacokinetic model. The calculated plasma concentration is continually displayed and updated. The anesthetist may ask for the history of the delivery to obtain a graphic report or to add events to the logbook. A panel targeting the effect is used when a pharmacodynamic model is known. Data files for drugs, pumps and surgery are upgradable. DISCUSSION: By creating a resizeable ControlPanel we enable the anesthetist to display the information he wishes, when he wishes it. The available panels are diverse enough to meet the anesthetist needs; they may be adapted to the drug used, pumps used and surgery. It is the anesthetist who builds dynamically its different control screens. CONCLUSION: By adopting an evolutionary solution model we have achieved considerable success in building our drug delivery monitor. In addition we have gained valuable insight into the anesthesia information domain that will allow us to further enhance and expand the system.

Anesthesia, Intravenous↗
PubMed2000

The ecological cost of sex.

Why sex prevails in nature remains one of the great puzzles of evolution. Sexual reproduction has an immediate cost relative to asexual reproduction, as males only express their contribution to population growth through females. With no males to sustain, an asexual mutant can double its relative representation in the population in successive generations. This is the widely accepted 'twofold cost of males'. Many studies have attempted to explain how sex can recoup this cost from fitness benefits associated with the recombination of parental genotypes, but these require complex biological environments that cycle over evolutionary timescales. In contrast, we have considered the ecological dynamics that govern asexual invasion. Here we show the existence of a threshold growth rate for the sexual population, above which the invasion is halted by intraspecific competition. The asexual population then exerts a weaker inhibitory effect on the carrying capacity of the sexual population than on its own carrying capacity. The stable outcome of this is coexistence on a depleted resource base. Under these ecological circumstances, longer-term benefits of sex may eventually drive out the asexual competitor.

Animals↗
PubMed1999

Coalescent estimates of HIV-1 generation time in vivo.

The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model of viral dynamics and was found to be on the order of one to two days per generation. Here, we describe a new method based on coalescence theory that allows the estimate of generation times to be derived by using nucleotide sequence data and a reconstructed genealogy of sequences obtained over time. The method is applied to sequences obtained from a long-term nonprogressing individual at five sampling occasions. The estimate of viral generation time using the coalescent method is 1.2 days per generation and is close to that obtained by mathematical modeling (1.8 days per generation), thus strengthening confidence in estimates of a short viral generation time. Apart from the estimation of relevant parameters relating to viral dynamics, coalescent modeling also allows us to simulate the evolutionary behavior of samples of sequences obtained over time.

DNA, Viral↗
PubMed1997

The variety of explanations of living forms and structures.

Over the last decades the image of vertebrate morphology has become at some places chaotic and even opportunistic, which seems to be due to the lack of appraisal or recognition of the leading concepts of the field. This paper analyses the changes in morphology, and shows that these changes have enriched research aims and that the discipline has a clear methodological and philosophical coherence. The situation in morphology is analysed from a semi-historical and review-like point of view to see what aspect is aimed at for explanation, and what types of explanation are used. A preliminary conclusion is reached that the animal form still has to be explained, and that the types of explanation for living form and structure can be divided into three main categories: (1) a category of typological explanation: (2) a category of functional explanation, including a specific constructional explanation; and (3) a category of causal explanation. Each of these categories has a static and a dynamic aspect. The dynamic aspect includes an explanation connected to life time (the system dynamic and morphogenetic explanation) and an explanation connected to evolutionary time (the historical explanation). These categories are used for structure at the molecular up to and including the organismic level of organization. The main challenge for the future is to integrate these different categories of form-explanation and determine their relative dominance when a theory of biology, that is of biological form and activity, is developed.

Animals↗
PubMed1991

Germline selection: population genetic aspects of the sexual/asexual life cycle.

Population geneticists make a distinction between sexual and asexual organisms depending on whether individuals inherit genes from one or two parents. When individual genes are considered, this distinction becomes less satisfactory for multicellular sexual organisms. Individual genes pass through numerous asexual mitotic cell divisions in the germline prior to meiosis and sexual recombination. The processes of mitotic mutation, mitotic crossing over, and mitotic gene conversion create genotypic diversity between diploid cells in the germline. Genes expressed in the germline whose products affect cell viability (such as many "housekeeping" enzymes) may be subjected to natural selection acting on this variability resulting in a non-Mendelian output of gametes. Such genes will be governed by the population genetics of the sexual/asexual life cycle rather than the conventional sexual/Mendelian life cycle. A model is developed to investigate some properties of the sexual/asexual life cycle. When appropriate parameter values were included in the model, it was found that mutation rates per locus per gamete may vary by a factor of up to 100 if selection acts in the germline. Sexual/asexual populations appear able to evolve to a genotype of higher fitness despite intervening genotypes of lower fitness, reducing the problems of underdominance and Wright's adaptive landscape encountered by purely sexual populations. As might be expected this ability is chiefly determined by the number of asexual mitotic cell divisions within the germline. The evolutionary consequences of "housekeeping" loci being governed by the dynamics of the sexual/asexual life cycle are considered.

Animals↗
PubMed2000

Sexually transmitted diseases in polygynous mating systems: prevalence and impact on reproductive success.

Studies of disease in relation to animal mating systems have focused on sexual selection and the evolution of sexual reproduction. Relatively little work has examined other aspects of ecological and evolutionary relationships between host social and sexual behaviour, and dynamics and prevalence of infectious diseases; this is particularly evident with respect to sexually transmitted diseases (STDs). Here, we use a simulation approach to investigate rates of STD spread in host mating systems ranging from permanent monogamy to serial polygyny or polyandry and complete promiscuity. The model assumes that one sex (female) is differentially attracted to the other, such that groups of varying size are formed within which mating and disease transmission occur. The results show that equilibrium disease levels are generally higher in females than males and are a function of variance in male mating success and the likelihood of a female switching groups between mating seasons. Moreover, initial rates of disease spread (determining whether an STD establishes in a population) depend on patterns of host movement between groups, variance in male mating success and host life history (e.g. mortality rates). Male reproductive success can be reduced substantially by a sterilizing STD and this reduction is greater in males that are more 'attractive' to females. In contrast, females that associate with more attractive males have lower absolute fitness than females associating with less attractive males. Thus, the potential for STDs to act as a constraint on directional selection processes leading to polygyny (or polyandry) is likely to depend on the details of mate choice and group dynamics.

Animals↗
PubMed2025

Chromosomal resistance mutations facilitate acquisition of multidrug-resistant plasmids in Escherichia coli.

Bacteria can gain multiple resistance mechanisms in a single step by the acquisition of multidrug-resistant (MDR) plasmids, but it is unclear how antibiotic selection during the acquisition of MDR plasmids affects the evolution of additional resistance mechanisms. Through conjugating separate extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing MDR plasmids into plasmid-naive Escherichia coli hosts, we examine the effects of acquisition of a single plasmid or co-acquisition of multiple plasmids upon fitness costs, resistance and subsequent genomic adaptation. We show that acquisition of pOXA-48, encoding OXA-48 carbapenemase, is associated with highly variable fitness costs and levels of resistance to ertapenem in transconjugants independent of the presence of pLL35. This phenomenon was not observed during the acquisition of ESBL CTX-M-15-encoding pLL35 alone. Within a single growth cycle, transconjugants receiving pOXA-48 rapidly gained parallel mutations affecting the membrane porin OmpF, or its regulators OmpR or EnvZ. These chromosomal mutations were not compensatory for the fitness costs imposed by the plasmid, nor did they provide significant increases in resistance to carbapenems in the absence of the pOXA-48. Rather, they acted synergistically with the plasmid-encoded carbapenemase, which alone only provided marginal resistance, together providing high-level resistance to ertapenem. Such rapid evolutionary processes may play an important role in plasmid dynamics within environments with strong antibiotic selection for plasmid-encoded antimicrobial resistance genes (ARGs), particularly when these ARGs provide only marginal resistance.

Escherichia coli↗
PubMed2005

Phase transitions in multiplicative competitive processes.

We introduce a discrete multiplicative process as a generic model of competition. Players with different abilities successively join the game and compete for finite resources. Emergence of dominant players and evolutionary development occur as a phase transition. The competitive dynamics underlying this transition is understood from a formal analogy to statistical mechanics. The theory is applicable to bacterial competition, predicting novel population dynamics near criticality.

Animals↗
PubMed1996

Parent participation: a concept analysis.

Parent participation has become a central tenet of paediatric nursing in the United Kingdom. The purpose of this paper is to explore the meaning of parent participation, to clarify the concept to benefit children and their families, and to increase understanding among practitioners. The concept analysis utilized was directed by Rodgers' "evolutionary approach' that views concept development as an ongoing dynamic process. A review of British literature and research studies indicated that parent participation is a complex and multi-dimensional concept. In the evolution of parent participation, the terminology changed from "parental involvement' to "partnership in care', to "care-by-parent' and finally to "family-centred care'. The analysis reveals a lack of coherence in the descriptions, with the terminology changing but the underlying theme remaining parent participation. Parent participation can be conceptualized as a composite of attributes that relate to the family, the nurse and their relationships. Those attributes include: negotiation, control, willingness, competence and autonomy. The concept of family-centred care is gradually assuming importance in the literature. This acknowledgement of the family is long overdue. However the concept remains poorly defined and urgent clarification is needed in this area. To adopt a family-centred care approach, a radical paradigm shift is required.

Clinical Competence↗
PubMed2002

Mapping epigenetic quantitative trait loci (QTL) altering a developmental trajectory.

Genetic variation in a quantitative trait that changes with age is important to both evolutionary biologists and breeders. A traditional analysis of the dynamics of genetic variation is based on the genetic variance-covariance matrix among different ages estimated from a quantitative genetic model. Such an analysis, however, cannot reveal the mechanistic basis of the genetic variation for a growth trait during ontogeny. Age-specific genetic variance at time t conditional on the causal genetic effect at time t - 1 implies the generation of episodes of new genetic variation arising during the interval t - 1 to t. In the present paper, the conditional genetic variance estimated from Zhu's (1995) conditional model was partitioned into its underlying individual quantitative trait loci (QTL) using molecular markers in an F2 progeny of poplars (Populus trichocarpa and Populus deltoides). These QTL, defined as epigenetic QTL, govern the alterations of growth trajectory in a population. Three epigenetic QTL were detected to contribute significantly to variation in growth trajectory during the period from the establishment year to the subsequent year in the field. It is suggested that the activation and expression of epigenetic QTL are influenced by the developmental status of trees and the environment in which they are grown.

Analysis of Variance↗
PubMed2006

Neural processing of counting in evolved spiking and McCulloch-Pitts agents.

This article investigates the evolution of autonomous agents that perform a memory-dependent counting task. Two types of neurocontrollers are evolved: networks of McCulloch-Pitts neurons, and spiking integrate-and-fire networks. The results demonstrate the superiority of the spiky model in evolutionary success and network simplicity. The combination of spiking dynamics with incremental evolution leads to the successful evolution of agents counting over very long periods. Analysis of the evolved networks unravels the counting mechanism and demonstrates how the spiking dynamics are utilized. Using new measures of spikiness we find that even in agents with spiking dynamics, these are usually truly utilized only when they are really needed, that is, in the evolved subnetwork responsible for counting.

Animals↗