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PubMedDate not supplied

Biology of the cold adapted archaeon, Methanococcoides burtonii determined by proteomics using liquid chromatography-tandem mass spectrometry.

Genome sequence data of the cold-adapted archaeon, Methanococcoides burtonii, was linked to liquid chromatography-mass spectrometry analysis of the expressed-proteome to define the key biological processes functioning at 4 degrees C. 528 proteins ranging in pI from 3.5 to 13.2, and 3.5-230 kDa, were identified. 133 identities were for hypothetical proteins, and the analysis of these is described separately (Goodchild et al. manuscript in preparation). DNA replication and cell division involves eucaryotic-like histone and MC1-family DNA binding proteins, and 2 bacterial-like FtsZ proteins. Eucaryotic-like, core RNA polymerase machinery, a bacterial-like antiterminator, and numerous bacterial-like regulators enable transcription. Motility involves flagella synthesis regulated by a bacterial-like chemotaxis system. Lsmalpha and Lsmgamma were coexpressed raising the possibility of homo- and hetero-oligomeric complexes functioning in RNA processing. Expression of FKBP-type and cyclophilin-type peptidyl-prolyl cis-trans isomerases highlights the importance of protein folding, and novel characteristics of folding in the cold. Thirteen proteins from a superoperon system encoding proteasome and exosome subunits were expressed, supporting the functional interaction of transcription and translation pathways in archaea. Proteins involved in every step of methylotropic methanogenesis were identified. CO(2) appears to be fixed by a modified Calvin cycle, and by carbon monoxide dehydrogenase. Biosynthesis involves acetyl-CoA conversion to pyruvate by a non-oxidative pentose phosphate pathway, and gluconeogenesis for the conversion of pyruvate to carbohydrates. An incomplete TCA cycle may supply biosynthetic intermediates for amino acid biosynthesis. A novel finding was the expression of Tn11- and Tn12-family transposases, which has implications for genetic diversity and fitness of natural populations. Characteristics of the fundamental cellular processes inferred from the expressed-proteome highlight the evolutionary and functional complexity existing in this domain of life.

Adaptation, Physiological↗
PubMed2025

Resource presentation dictates genetic and phenotypic adaptation in yeast.

BACKGROUND: Environments shape adaptive trajectories of populations, often leading to adaptive parallelism in identical, and divergence in different environments. However, how does the likelihood of these possibilities change with minute changes in the environment remain unclear. RESULTS: In this study, we evolved Saccharomyces cerevisiae in environments which differed only in the manner in which the sugar source is presented to the population. In one set of populations, carbon was presented as a mixture of glucose-galactose, and in the other, as melibiose, a glucose-galactose disaccharide. Since the two environments differed in how the two monosaccharides are packaged, we call these environments 'synonymous'. Our results show that even subtle environmental differences can lead to differing phenotypic responses between the two sets of evolved populations. However, despite different adaptive responses, pleiotropic effects of adaptation are largely predictable. We also show that distinct genomic targets of adaptation between the two sets of evolved populations are functionally convergent. CONCLUSION: This study highlights how subtle environmental differences dictate phenotypic and genetic adaptation of populations. Additionally, these results also suggest the predictive potential of ancestor's fitness in understanding pleiotropic responses. Our work underscores the importance of studying more such environments to understand the generality of adaptive responses in populations.

Saccharomyces cerevisiae↗
PubMed2005

Natural selection and the conditions for existence: representational vs. conditional teleology in biological explanation.

Human intentional action, including the design and use of artifacts, involves the prior mental representation of the goal (end) and the means to achieve that goal. This representation is part of the efficient cause of the action, and thus can be used to explain both the action and the achievement of the end. This is intentional teleological explanation. More generally, teleological explanation that depends on the real existence of a representation of the goal (and the means to achieve it) can be called representational teleological explanation. Such explanations in biology can involve both external representations (e.g., ideas in the mind of God) and internal representations (souls, vital powers, entelechies, developmental programs, etc.). However, another type of explanation of intentional action (or any other process) is possible. Given that an action achieving a result occurs, the action can be explained as fulfilling the necessary conditions (means) for that result (end), and, reciprocally, the result explained by the occurrence of those necessary conditions. This is conditional teleological explanation. For organisms, natural selection is often understood metaphorically as the designer, intentionally constructing them for certain ends. Unfortunately, this metaphor is often taken rather too literally, because it has been difficult to conceive of another way to relate natural selection to the process of evolution. I argue that combining a conditional teleological explanation of organisms and of evolution provides such an alternative. This conditional teleology can be grounded in existence or survival. Given that an organism exists, we can explain its existence by the occurrence of the necessary conditions for that existence. This principle of the 'conditions for existence' was introduced by Georges Cuvier in 1800, and provides a valid, conditional teleological method for explaining organismal structure and behavior. From an evolutionary perspective, the conditions for existence are the range of boundary conditions within which the evolutionary process must occur. Moreover, evolutionary change itself can be subjected to conditional teleological explanation, because natural selection theory is primarily a theory about the relation between the conditions for the existence of organisms and the conditions for the existence of traits in populations. I show that failure to distinguish representational from conditional teleological explanation has confused previous attempts to clarify the relation of teleology to biology.

Adaptation, Biological↗
PubMedDate not supplied

Bleaching adaptation in photoreceptors.

Bleaching adaptation is the reduction in sensitivity of photoreceptors to light, following large photoconversion of rhodopsin molecules. It is accompanied by a prolonged dark excitation, and the two processes may be causally linked. There are remarkable similarities in the prolonged dark excitation of vertebrate rods and invertebrate photoreceptors. There is much evidence to indicate that prolonged dark excitation is tightly linked to processes that occur at the photo-pigment level. A molecular mechanism is suggested to explain the prolonged dark excitation. According to this model, quenching of photoreceptor excitation operates by phosphorylation of metarhodopsin (M) molecules. When unphosphorylated M molecules exist in the dark, they give rise to prolonged dark excitation. This prolonged dark excitation seems to be coupled to photoreceptors' desensitization by an unknown mechanism.

Adaptation, Biological↗
PubMed1978

[Scotopic visual pigments in 3 Percidae: Perca flavescens, Stizostedion vitreum and S. canadense].

The scotopic visual pigments of three percids from Quebec waters, viz. the yellow perch (Perca flavescens), the walleye (Stizostedion vitreum) and the sauger (S. canadense), were studied in situ using a microspectrophotometer-computer complex. The difference spectra show that the three fishes possess a porphyropsin whose lambda max. is at 530 nm in the yellow perch, 533 nm in the walleye and at 536 in the sauger. This variation corresponds to the tendency of the visual pigments to fit the preferred environments. The three species studied also have different modes of life. The yellow perch inhabits mostly shallow, clear waters while the walleye and sauger prefer turbid waters. The retinal structure and responses also differ among them. Since the difference in lambda max. is so small, the differences in habitat and behaviour may be attributed to morphological differences in the retina rather than to its visual pigment content.

Adaptation, Biological↗
PubMed1979

Maintenance of the adequate function is a general principle of survival of organisms.

A general theory which describes the existence of live organisms is introduced; this theory is the Principle of Adequate Function and it describes all the situations in which live organisms may exist, whether healthy or sick at both physiological and pathological conditions. In biology, so far, the existence of living organisms under physiological conditions is described by homeostasis, and under pathological conditions specific immunity is used. As it is shown below, adaptation and non-specific resistance provide a much broader basis of how living organisms exist under both physiological and pathological conditions. This general theory does not interfere with the notions of homeostasis, adaptation, and specific immunity but includes them as particular cases. It is proposed that the principle of adequate function supplements the description of life processes by the evolutionary principle; it describes the laws of existence and function of a particular individual.

Adaptation, Biological↗