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At least 1,225 records · Page 68Linked to original sources
PubMed2001

An error-prone T7 RNA polymerase mutant generated by directed evolution.

Viruses replicate their genomes at exceptionally high mutation rates. Their offspring evolve rapidly and therefore, are able to evade common immunological and chemical antiviral agents. In parallel, virus genomes cannot tolerate a further increase in mutation rate: Experimental evidence exists that even few additional mutations are sufficient for the extinction of a viral population. A future antiviral strategy might therefore aim at increasing the error-producing capacity of viral replication enzymes. We employed the principles of directed evolution and developed a scheme for the stringent positive selection of error-prone polymerase activity. A mutant T7 RNA polymerase with a nucleotide substitution error rate at least 20-fold greater than that of the wild-type was selected. This enzyme synthesized highly heterogeneous RNA products in vitro or in vivo and also decreased the replication efficiency of wild-type bacteriophage T7 during infection.

Bacteriophage T7↗
PubMed2000

Reproductive mode and speciation: the viviparity-driven conflict hypothesis.

In birds and frogs, species pairs retain the capacity to produce viable hybrids for tens of millions of years, an order of magnitude longer than mammals. What accounts for these differences in relative rates of pre- and postzygotic isolation? We propose that reproductive mode is a critically important but previously overlooked factor in the speciation process. Viviparity creates a post-fertilization arena for genomic conflicts absent in egg-laying species. With viviparity, conflict can arise between: mothers and embryos; sibling embryos in the womb, and maternal and paternal genomes within individual embryos. Such intra- and intergenomic conflicts result in perpetual antagonistic coevolution, thereby accelerating interpopulation postzygotic isolation. In addition, by generating intrapopulation genetic incompatibility, viviparity-driven conflict favors polyandry and limits the potential for precopulatory divergence. Mammalian diversification is characterized by rapid evolution of incompatible feto-maternal interactions, asymmetrical postzygotic isolation, disproportionate effects of genomically-imprinted genes, and "F(2) hybrid enhancement. " The viviparity-driven conflict hypothesis provides a parsimonious explanation for these patterns in mammalian evolution.

Animals↗
PubMed1999

Homoplasy, homology and the problem of 'sameness' in biology.

The reality of evolution requires some concept of 'sameness'. That which evolves changes its state to some degree, however minute or grand, although parts remain 'the same'. Yet homology, our word for sameness, while universal in the sense of being necessarily true, can only ever be partial with respect to features that change. Determining what is equivalent to what among taxa, and from what something has evolved, remain real problems, but the word homology is not helpful in these problematic contexts. Henning saw this clearly when he coined new terms with technical meanings for phylogenetic studies. Analysis in phylogenetic systematics remains contentious and relatively subjective, especially as new information accumulates or as one changes one's mind about characters. This pragmatic decision making should not be called homology assessment. Homology as a concept anticipated evolution. Homology dates to pre-evolutionary times and represents late 18th and early 19th century idealism. Our attempts to recycle words in science leads to difficulty, and we should eschew giving precise modern definitions to terms that originally arose in entirely different contexts. Rather than continue to refine our homology concept we should focus on issues that have high relevance to modern evolutionary biology, in particular homoplasy--derived similarity--whose biological bases require elucidation.

Adaptation, Biological↗
PubMed1984

The Taung endocast and the lunate sulcus: a rejection of the hypothesis of its anterior position.

Using an independent method of direct tape-arc measurements on six chimpanzee brain casts, it is shown that Falk's (1980, 1983) claims regarding an anterior pongidlike placement of a lunate sulcus on the Taung specimen remain unconfirmed. Thus Holloway's (1981) stereoplotting method of testing Falk's hypothesis is independently confirmed, using the actual specimens rather than photographs of them. Falk's (1980) placement of a lunate sulcus falls at least 2.5 standard deviations anterior to a position expected on the basis of a Pan location.

Animals↗
PubMed2003

Species as family resemblance concepts: the (dis-)solution of the species problem?

The so-called "species problem" has plagued evolutionary biology since before Darwin's publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don't seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical literatures on the species problem, focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require-but cannot be settled by-empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein's idea of "family resemblance" or cluster concepts, and to consider species as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among biologists and philosophers. The current proposal is conceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupré, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion presented here is Templeton's cohesion idea.

Biological Evolution↗
PubMed2005

Different species problems and their resolution.

At least three different issues are commonly referred to by the term "the species problem": one concerns the necessary properties of species, a second the processes responsible for the existence of species, and a third methods for inferring species limits. Solutions have recently been proposed to the first two problems, which are conceptual in nature (the third is methodological). The first equates species with metapopulation lineages and proposes that existence as a separately evolving metapopulation lineage be considered the only necessary property of species. The second views the species category as a cluster concept and proposes that no single process or set of processes be considered necessary for the existence of species. Although these two solutions have been portrayed as being in conflict, they are, in fact, highly compatible. Moreover, the proposals in question clarify the problem concerning methods for inferring the limits of species, which has for a long time been confused with the problem concerning the necessary properties of species. Together these proposals provide the opportunity for biology to move beyond debates about the definition of the species category and focus on estimating the boundaries and numbers of species as well as studying the diverse processes involved in their origin and persistence.

Animals↗
PubMed2003

Theoretical distribution of truncation lengths in incremental truncation libraries.

Incremental truncation is a method for constructing libraries of every one base pair truncation of a segment of DNA. Incremental truncation libraries can be created using a time-dependent nuclease method or through the incorporation of alpha-phosphothioate dNTPs by PCR or by primer extension (THIO(pcr) truncation and THIO(extension) truncation, respectively). Libraries created by the fusion of two truncation libraries, known as ITCHY libraries, can be created using the above methods or by the incremental truncation-like method SHIPREC. Knowing and being able to tailor the distribution of truncations in incremental truncation, ITCHY and SHIPREC libraries would be beneficial for their use in protein engineering and other applications. However, the experimental determination of the distributions would require extensive, cost-prohibitive, DNA sequencing to obtain statistically relevant data. Instead, a theoretical prediction of the distributions was developed. Time-dependent incremental truncation libraries had the most uniform distribution of truncation lengths, but were biased against longer truncations. Essentially uniform distribution over the desired truncation range (from zero to N(max) base pairs) required that truncations be prepared up to at least 1.2-1.5 N(max). THIO(pcr) and THIO(extension) truncation libraries had a very nonuniform distribution of truncation lengths with a bias against longer truncations. Such nonuniformity could be significantly diminished by decreasing the incorporation rate of alphaS-dNTPs but at the expense of having a large fraction of the DNA truncated beyond the desired range or completely degraded. ITCHY libraries created using time-dependent truncation had the most uniform distribution of possible fusions and had the highest fraction of the library being parental-length fusions. However, the distribution of parental-length fusions was biased against fusions near the beginning/ends of genes unless the truncation libraries are prepared with a uniform distribution up to N(max). In contrast, SHIPREC libraries and THIO(pcr) ITCHY libraries, by the very nature of the nonuniform distributions of the truncated DNA, are ensured of having a uniform distribution of fusion points in parental-length fusions. This comes at the expense of having a smaller fraction of the library being parental-length fusions; however, this limitation can be overcome by performing size selection on the library.

Computer Simulation↗
PubMed2006

Evolution of high-performance swimming in sharks: transformations of the musculotendinous system from subcarangiform to thunniform swimmers.

In contrast to all other sharks, lamnid sharks perform a specialized fast and continuous "thunniform" type of locomotion, more similar to that of tunas than to any other known shark or bony fish. Within sharks, it has evolved from a subcarangiform mode. Experimental data show that the two swimming modes in sharks differ remarkably in kinematic patterns as well as in muscle activation patterns, but the morphology of the underlying musculotendinous system (red muscles and myosepta) that drives continuous locomotion remains largely unknown. The goal of this study was to identify differences in the musculotendinous system of the two swimming types and to evaluate these differences in an evolutionary context. Three subcarangiform sharks (the velvet belly lantern shark, Etmopterus spinax, the smallspotted catshark, Scyliorhinus canicula, and the blackmouth catshark, Galeus melanostomus) from the two major clades (two galeans, one squalean) and one lamnid shark, the shortfin mako, Isurus oxyrhinchus, were compared with respect to 1) the 3D shape of myomeres and myosepta of different body positions; 2) the tendinous architecture (collagenous fiber pathways) of myosepta from different body positions; and 3) the association of red muscles with myoseptal tendons. Results show that the three subcarangiform sharks are morphologically similar but differ remarkably from the lamnid condition. Moreover, the "subcarangiform" morphology is similar to the condition known from teleostomes. Thus, major features of the "subcarangiform" condition in sharks have evolved early in gnathostome history: Myosepta have one main anterior-pointing cone and two posterior-pointing cones that project into the musculature. Within a single myoseptum cones are connected by longitudinally oriented tendons (the hypaxial and epaxial lateral and myorhabdoid tendons). Mediolaterally oriented tendons (epineural and epipleural tendons; mediolateral fibers) connect vertebral axis and skin. An individual lateral tendon spans only a short distance along the body (a fraction between 0.05 and 0.075 of total length, L, of the shark). This span is similar in all tendons along the body. Red muscles insert into the midregion of the lateral tendons. The shortfin mako differs substantially from this condition in several respects: Red muscles are internalized and separated from white muscles by a sheath of lubricative connective tissue. They insert into the anterior part of the hypaxial lateral tendon. Rostrocaudally, this tendon becomes very distinct and its span increases threefold (0.06L anteriorly to 0.19L posteriorly). Mediolateral fibers do not form distinct epineural/epipleural tendons in the mako. Since our morphological findings are in good accordance with experimental data it seems likely that the thunniform swimming mode has evolved along with the described morphological specializations.

Animals↗
PubMed2003

Parsing local signal evolution directly from a single-shot MRI signal: a new approach for fMRI.

In this work a new single-shot MRI method, single-shot parameter assessment by retrieval from signal encoding (SS-PARSE), is introduced. This method abandons a fundamental simplifying assumption that is used in conventional MRI methods. Established MRI methods implicitly assume that the local intrinsic signal does not change its amplitude or phase during signal acquisition, even though these changes may be substantial, especially during the relatively long signals used in single-shot image acquisitions. SS-PARSE, on the other hand, acknowledges local decay and phase evolution, and models each signal datum as a sample from (k,t)-space rather than k-space. Because of this more accurate signal model, SS-PARSE promises improved performance in terms of accuracy and robustness, but requires more intensive reconstruction computations. The theoretical properties of the method are discussed, and simulation results are presented that demonstrate more robust and accurate measurements of relaxation rate changes associated with brain activation in functional MRI (fMRI), freedom from geometric errors due to off-resonance frequencies, and better tolerance of the large susceptibility gradients that occur naturally in parts of the brain. In addition, this technique has the potential to assess nonexponential relaxation behavior during a single-shot signal.

Algorithms↗
PubMed2005

Design of combinatorial protein libraries of optimal size.

In this article we introduce a computational procedure, OPTCOMB (Optimal Pattern of Tiling for COMBinatorial library design), for designing protein hybrid libraries that optimally balance library size with quality. The proposed procedure is directly applicable to oligonucleotide ligation-based protocols such as GeneReassembly, DHR, SISDC, and many more. Given a set of parental sequences and the size ranges of the parental sequence fragments, OPTCOMB determines the optimal junction points (i.e., crossover positions) and the fragment contributing parental sequences at each one of the junction points. By rationally selecting the junction points and the contributing parental sequences, the number of clashes (i.e., unfavorable interactions) in the library is systematically minimized with the aim of improving the overall library quality. Using OPTCOMB, hybrid libraries containing fragments from three different dihydrofolate reductase sequences (Escherichia coli, Bacillus subtilis, and Lactobacillus casei) are computationally designed. Notably, we find that there exists an optimal library size when both the number of clashes between the fragments composing the library and the average number of clashes per hybrid in the library are minimized. Results reveal that the best library designs typically involve complex tiling patterns of parental segments of unequal size hard to infer without relying on computational means.

Amino Acid Sequence↗
PubMed1997

Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences.

Sets of genes improved by directed evolution can be recombined in vitro to produce further improvements in protein function. Recombination is particularly useful when improved sequences are available; costs of generating such sequences, however, must be weighed against the costs of further evolution by sequential random mutagenesis. Four genes encoding para-nitrobenzyl (pNB) esterase variants exhibiting enhanced activity were recombined in two cycles of high-fidelity DNA shuffling and screening. Genes encoding enzymes exhibiting further improvements in activity were analyzed in order to elucidate evolutionary processes at the DNA level and begin to provide an experimental basis for choosing in vitro evolution strategies and setting key parameters for recombination. DNA sequencing of improved variants from the two rounds of DNA shuffling confirmed important features of the recombination process: rapid fixation and accumulation of beneficial mutations from multiple parent sequences as well as removal of silent and deleterious mutations. The five to sixfold further enhancement of total activity towards the para-nitrophenyl (pNP) ester of loracarbef was obtained through recombination of mutations from several parent sequences as well as new point mutations. Computer simulations of recombination and screening illustrate the trade-offs between recombining fewer parent sequences (in order to reduce screening requirements) and lowering the potential for further evolution. Search strategies which may substantially reduce screening requirements in certain situations are described.

Carboxylic Ester Hydrolases↗
PubMed1998

An evolutionary link between sporulation and prophage induction in the structure of a repressor:anti-repressor complex.

Spore formation is an extreme response of some bacteria to adversity. In Bacillus subtilis the proteins of the sin, sporulation inhibition, region form a component of an elaborate molecular circuitry that regulates the commitment to sporulation. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer. The interactions governing this curious quaternary transition are revealed in the crystal structure of the SinI-SinR complex. The most striking, and unexpected, finding is that the tertiary structure of the DNA-binding domain of SinR is identical with that of the corresponding domains of the repressor proteins, CI and Cro, of bacteriophage 434 that regulate lysis/lysogeny. This structural similarity greatly exceeds that between SinR and any bacterial protein or between the 434 repressor proteins and their homologues in the closely related bacteriophage lambda. The close evolutionary relationship implied by the structures of SinR and the 434 repressors provokes both comparison of their functions and a speculative consideration of the intriguing possibility of an evolutionary link between the two adaptive responses, sporulation and prophage induction.

Amino Acid Sequence↗
PubMed1993

Seeking the evolutionary regression coefficient: an analysis of what comparative methods measure.

Two alternative classes of comparative statistical method differ in the way that the comparative data are used to test for an association between two quantitative traits. Directional comparative methods use reconstructions of the ancestral character states to calculate the changes between ancestral and descendant conditions along the branches of the phylogenetic tree. The set of changes in two or more traits is used to test for evidence of correlated evolution. Cross-sectional techniques do not estimate changes along the branches of the tree, but rather make comparisons across the tips of a phylogeny, or between pairs of extant taxa (or between their higher nodes). These methods, then, study the association between pairs of traits representing the contemporary endpoints of evolution. The best known of the cross-sectional techniques, the species regression, simply regresses the species values of one variable onto those of another. However, it is shown here analytically that directional and cross-sectional methods, despite making very different use of the data, estimate precisely the same evolutionary parameter: the association between the changes in two variables along the branches of the phylogenetic tree. Thus, comparative statistical techniques are able to recover the historical trends of evolution, that is, the ways in which evolution has proceeded along the branches of the phylogenetic tree, from analysis of the variation among the contemporary species of a phylogeny. This means that the choice between the two alternative traditions of comparative study cannot be based upon what the different methods purport to measure, but rather must be based upon the statistical properties of particular methods. In the light of this result, it is discussed here whether there are statistical reasons to prefer some methods over others.

Animals↗
PubMed1994

Reverse interpretation: a hypothetical selection mechanism for adaptive mutagenesis based on autoregulated mRNA stability.

The problem of adaptive mutagenesis is examined under the assumption that selection occurs through the interaction of cognate mRNA and protein molecules, a phenomenon that has been considered to lead to differential mRNA decay (Kyrpides & Ouzounis, 1993, J. theor. Biol. 163, 373-392). Based on the stereochemical hypothesis, we speculate that the origin of this process relies on an extended form of molecular interactions. This mechanism, termed reverse interpretation, predicts the selective amplification of successful molecular forms with the capability of their immortalization through reverse transcription, in a manner that resembles, but is not equivalent to, reverse translation. Finally, we argue that the proposed mechanism conforms with the Darwinian view of evolutionary change, if variability is considered to be a property of molecular and not cellular populations.

Animals↗
PubMed1994

Species selection on organismal integration.

Selection processes of entities higher than individuals have recently been suggested to play a potential role in macroevolution. In particular, population level traits such as variability seem likely candidates for higher-level selection processes because they interact with population fitness (survival). In this paper, I expand on that theme and argue that a population level trait, such as organismal integration, measured by the genetic variance-covariance matrix, can be subject to interpopulational selection. This is so because a population consisting of individuals with a high degree of integration will respond faster to selection than a less integrated one, and thus more rapidly reach new optima. This idea generates a number of predictions which are supported by data from natural and laboratory populations of a diverse array of organisms. First, the level of genetic integration in morphological characters is generally quite high. Second, there are a number of cases where the within- and among-population correlation matrices are similarly oriented. Third, the main pattern of morphological variation in birds is that species within genera are most exclusively oriented along a size-axis. These results are consistent with the ideas put forward in this paper, though not providing conclusive evidence.

Animals↗