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PubMed1988

Homology in classical and molecular biology.

Hypotheses of homology are the basis of comparative morphology and comparative molecular biology. The kinds of homologous and nonhomologous relations in classical and molecular biology are explored through the three tests that may be applied to a hypothesis of homology: congruence, conjunction, and similarity. The same three tests apply in molecular comparisons and in morphology, and in each field they differentiate eight kinds of relation. These various relations are discussed and compared. The unit or standard of comparison differs in morphology and in molecular biology; in morphology it is the adult or life cycle, but with molecules it is the haploid genome. In morphology the congruence test is decisive in separating homology and nonhomology, whereas with molecular sequence data similarity is the decisive test. Consequences of this difference are that the boundary between homology and nonhomology is not the same in molecular biology as in morphology, that homology and synapomorphy can be equated in morphology but not in all molecular comparisons, and that there is no detected molecular equivalent of convergence. Since molecular homology may reflect either species phylogeny or gene phylogeny, there are more kinds of homologous relation between molecular sequences than in morphology. The terms paraxenology and plerology are proposed for two of these kinds--respectively, the consequence of multiple xenology and of gene conversion.

Anatomy, Comparative↗
PubMed1988

Soluble, prolonged-acting insulin derivatives. III. Degree of protraction, crystallizability and chemical stability of insulins substituted in positions A21, B13, B23, B27 and B30.

It was previously demonstrated that insulins to which positive charge has been added by substituting B13 glutamic acid with a glutamine residue, B27 threonine with an arginine or lysine residue, and by blocking the C-terminal carboxyl group of the B-chain by amidation, featured a prolonged absorption from the subcutis of rabbits and pigs after injection in solution at acidic pH. The phenomenon is ascribed to a low solubility combined with the readiness by which these analogs crystallize as the injectant is being neutralized in the tissue. However, acid solutions of insulin are chemically unstable as A21 asparagine both deamidates to aspartic acid and takes part in formation of covalent dimers via alpha-amino groups of other molecules. In order to circumvent the instability, substitutions were introduced in position A21, in addition to those in B13, B27 and B30, challenging the fact that A21 asparagine has been conserved in this position throughout the evolution. Biological potency was retained when glycine, serine, threonine, aspartic acid, histidine and arginine were introduced in this position, although to a varying degree. In the crystal structure of insulin a hydrogen bond bridges the alpha-nitrogen of A21 with the backbone carbonyl of B23 glycine. In order to investigate the importance of this hydrogen bond for biological activity a gene for the single-chain precursor B-chain(1-29)-Ala-Ala-Lys-A-chain(1-21) featuring an A21 proline was synthesized. However, this single-chain precursor failed to be properly produced by yeast, pointing to the formation of this hydrogen bond as an essential step in the folding process. The stability of the A21-substituted analogs in acid solutions (pH 3-4) with respect to deamidation and formation of dimers was approximately 5-10 times higher than that of human insulin in neutral solution. The rate of absorption of most insulins is decreased by increasing the Zn2+ concentration of the preparation. However, one analog with A21 glycine showed first-order absorption kinetics in pigs with a half-life of approximately 25 h, independent of the Zn2+ concentration. The day-to-day variation of the absorption of this analog was significantly lower than that of the conventional insulin suspensions, a property that might render such an insulin useful in the attempts to improve glucose control in diabetics by a more predictable delivery of basal insulin.

Absorption↗
PubMed1992

ATP-dependent bacterial transporters and cystic fibrosis: analogy between channels and transporters.

The traffic ATPases superfamily includes known transporters, both prokaryotic and eukaryotic, including the medically important proteins, P-glycoprotein, and the cystic fibrosis gene product (CFTR), which is known to be a Cl- channel. The structure and mechanism of action of the best-studied members of the superfamily, the periplasmic permeases, are described and related to that of CFTR and eukaryotic traffic ATPases in general. The contention is put forward that the distinction between the architecture and mechanisms of action of channels and transporters is blurred.

Adenosine Triphosphate↗
PubMed1995

The treatment of multiple sclerosis: current and future.

During the past year observations have been published that might lead to further improvement in the design of future clinical trials. At the same time, results of clinical trials have become available that suggest that a number of treatments could be of benefit in the care of patients in the various phases of multiple sclerosis. Future multiple sclerosis clinical trials should involve a blinded investigator restricted to assessing the clinical outcome variables, and because current evidence suggests that magnetic resonance imaging gives an objective and sensitive reflection of the biological evolution of the disease, such scanning should also be included. The use of a composite outcome variable in a trial of chronic progressive multiple sclerosis should also be considered in order to increase the percentage of patients reaching the clinical endpoint. In 1994 recommendations were published for the selection of relapsing-remitting patients for treatment with interferon beta-1b; furthermore, large and well performed clinical trials demonstrated that interferon beta-1a and copolymer-1 are also partially effective, though not curative, for these patients. Two smaller studies suggested that low-dose methotrexate and cladribine might have a beneficial effect on the course of the disease in patients with secondary chronic progressive multiple sclerosis, the former drug probably being less toxic. Unfortunately, therapeutic perspectives for patients with primary progressive multiple sclerosis are less promising at present. Several studies suggest that 4-aminopyridine and tizanidine have therapeutic potential for symptomatic treatment; the former by improving neurological deficits, the latter by relieving troublesome spasticity.(ABSTRACT TRUNCATED AT 250 WORDS)

Adjuvants, Immunologic↗
PubMed1992

Limited MHC polymorphism in the southern elephant seal: implications for MHC evolution and marine mammal population biology.

Genes of the major histocompatibility complex (MHC) are highly polymorphic in most terrestrial mammal populations so far studied. Exceptions to this are typically populations that lack genome-wide diversity. Here I show that two populations of the southern elephant seal (Mirounga leonina) have low DNA restriction fragment length polymorphism at MHC loci when compared with terrestrial mammals. Limited studies on MHC polymorphism in two cetacean species suggest this is a feature of marine mammal populations in general. MHC polymorphism is thought to be maintained by balancing selection, and several types of disease-based and reproductive-based mechanisms have been proposed. For the three marine mammal species examined, the low MHC polymorphism cannot be explained by low genome-wide diversity, or by any reproductive-based selection pressure. It can, however, be explained by diminished exposure to pathogenic selection pressure compared with terrestrial mammals. Reduced exposure to pathogens would also mean that marine mammal populations may be susceptible to occasional pathogen-induced mass mortalities.

Animals↗
PubMed2000

The origin of alternation of generations in land plants: a focus on matrotrophy and hexose transport.

A life history involving alternation of two developmentally associated, multicellular generations (sporophyte and gametophyte) is an autapomorphy of embryophytes (bryophytesphytes + vascular plants). Microfossil data indicate that Mid Late Ordovician land plants possessed such a life cycle, and that the origin of alternation of generations preceded this date. Molecular phylogenetic data unambiguously relate charophycean green algae to the ancestry of monophyletic embryophytes, and identify bryophytes as early-divergent land plants. Comparison of reproduction in charophyceans and bryophytes suggests that the following stages occurred during evolutionary origin of embryophytic alternation of generations: (i) origin of oogamy; (ii) retention of eggs and zygotes on the parental thallus; (iii) origin of matrotrophy (regulated transfer of nutritional and morphogenetic solutes from parental cells to the next generation); (iv) origin of a multicellular sporophyte generation; and (v) origin of non-flagellate, walled spores. Oogamy, egg/zygote retention and matrotrophy characterize at least some modern charophvceans, and are postulated to represent pre-adaptative features inherited by embryophytes from ancestral charophyceans. Matrotrophy is hypothesized to have preceded origin of the multicellular sporophytes of' plants, and to represent a critical innovation. Molecular approaches to the study of the origins of matrotrophy include assessment of hexose transporter genes and protein family members and their expression patterns. The occurrence in modern charophyceans and bryophytes of chemically resistant tissues that exhibit distinctive morphology correlated with matrotrophy suggests that Early-Mid Ordovician or older microfossils relevant to the origin of land plant alternation of generations may be found.

Animals↗
PubMed2000

Begging and bleating: the evolution of parent-offspring signalling.

The evolution of biological signalling in the face of evolutionary conflicts of interest is an active area of evolutionary ecology, and one to which Maynard Smith has made important contributions. We explore the major theoretical challenges in the field, concentrating largely on how offspring signal to their parents when there is the potential for parent-offspring conflict. Costly offspring solicitation (begging etc.) has been interpreted in terms of a Zahavi Grafen honest handicap signal, but this has been challenged on the grounds of' the costs of signalling. We review this controversy and also explore the issue of pooling versus separating signalling equilibrium. An alternative explanation for costly begging is that it is due to sibling competition, and we discuss the relationship between these ideas and signalling models in families with more than one offspring. Finally we consider signal uncertainty, how signalling models can be made dynamic, and briefly how they may be tested experimentally.

Animal Communication↗
PubMed2004

Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species.

The human diseases melioidosis and glanders are caused by the bacteria Burkholderia pseudomallei and B. mallei respectively, and both species are regarded as potential biowarfare agents. We used B. pseudomallei DNA microarrays to compare the genomes of several clinical and environmental isolates of B. pseudomallei, B. mallei, and B. thailandensis, a closely related but avirulent species. Open reading frames (ORFs) deleted between the three species were associated with diverse cellular functions, including nitrogen and iron metabolism, quorum sensing, and polysaccharide production. Deleted ORFs in B. mallei exhibited significant genomic clustering, whereas deletions in B. thailandensis were more uniformly dispersed, suggesting that B. mallei and B. thailandensis may have diverged from B. pseudomallei and each other via distinct mechanisms. The genomes of independent B. pseudomallei isolates were highly conserved with a large-scale variance of less than 3% between isolates, and at least three distinct molecular subtypes could be defined. An analysis of subtype-specific genomic regions suggests that DNA loss has played an important role in the evolutionary radiation of B. pseudomallei in the natural environment. Our results raise several hypotheses concerning the possible mechanisms underlying the diverse biological properties exhibited by members of the Burkholderia family.

Bacterial Typing Techniques↗
PubMed2000

Boundary spatiotemporal correlations in a self-organized critical model of punctuated equilibrium

In a semi-infinite geometry, a one-dimensional, M-component model of biological evolution realizes microscopically an inhomogeneous branching process for M-->infinity. This implies a size distribution exponent tau(')=7/4 for avalanches starting at a free, "dissipative" end of the evolutionary chain. A bulklike behavior with tau(')=3/2 is restored by "conservative" boundary conditions. These are such as to strictly fix to its critical, bulk value the average number of species directly involved in an evolutionary avalanche by the mutating species located at the chain end. A two-site correlation function exponent tau(')(R)=4 is also calculated exactly in the "dissipative" case, when one of the points is at the border. Together with accurate numerical determinations of the time recurrence exponent tau(')(first), these results show also that, no matter whether dissipation is present or not, boundary avalanches have the same space and time fractal dimensions as those in the bulk, and their distribution exponents obey the basic scaling laws holding there.

Journal Article↗
PubMed2005

Extremal dynamics on complex networks: analytic solutions.

The Bak-Sneppen model displaying punctuated equilibria in biological evolution is studied on random complex networks. By using the rate equation and the random walk approaches, we obtain the analytic solution of the fitness threshold xc to be 1/((k)f+1), where (k)f=(k2)/(k) (=(k)) in the quenched (annealed) updating case, where kn is the nth moment of the degree distribution. Thus, the threshold is zero (finite) for the degree exponent gamma<3 (gamma>3) for the quenched case in the thermodynamic limit. The theoretical value xc fits well to the numerical simulation data in the annealed case only. Avalanche size, defined as the duration of successive mutations below the threshold, exhibits a critical behavior as its distribution follows a power law, Pa(s) approximately s(-3/2).

Journal Article↗
PubMed1999

Transformation of the collateral vascular bundles into amphivasal vascular bundles in an Arabidopsis mutant.

Arabidopsis inflorescence stems develop a vascular pattern similar to that found in most dicots. The arrangement of vascular tissues within the bundle is collateral, and vascular bundles in the stele are arranged in a ring. Although auxin has been shown to be an inducer of vascular differentiation, little is known about the molecular mechanisms controlling vascular pattern formation. By screening ethyl methanesufonate-mutagenized populations of Arabidopsis, we have isolated an avb1 (amphivasal vascular bundle) mutant with a novel vascular pattern. Unlike the collateral vascular bundles seen in the wild-type stems, the vascular bundles in the avb1 stems were similar to amphivasal bundles, i.e. the xylem completely surrounded the phloem. Furthermore, branching vascular bundles in the avb1 stems abnormally penetrated into the pith, which resulted in a disruption in the ring-like arrangement of vascular bundles in the stele. The avb1 mutation did not affect leaf venation pattern and root vascular organization. Auxin polar transport assay indicated that the avb1 mutation did not disrupt the auxin polar transport activity in inflorescence stems. The avb1 mutation also exhibited pleiotropic phenotypes, including curled stems and extra cauline branches. Genetic analysis indicated that the avb1 mutation was monogenic and partially dominant. The avb1 locus was mapped to a region between markers mi69 and ASB2, which is covered by a yeast artificial chromosome clone, CIC9E2, on chromosome 5. Isolation of the avb1 mutant provides a novel means to study the evolutionary mechanisms controlling the arrangement of vascular tissues within the bundle, as well as the mechanisms controlling the arrangement of vascular bundles in the stele.

Arabidopsis↗
PubMed1990

A yeast mitochondrial leader peptide functions in vivo as a dual targeting signal for both chloroplasts and mitochondria.

A fusion protein was expressed in transgenic tobacco and yeast cells to examine the functional conservation of mechanisms for importing precursor proteins from the cytosol into mitochondria and chloroplasts. The test protein consisted of the mitochondrial leader peptide from the yeast precursor to cytochrome oxidase subunit Va (prC5) fused to the reporter protein chloramphenicol acetyltransferase. This protein, denoted prC5/CAT, was transported into the mitochondrial interior in yeast and tobacco cells. In both organisms, the mitochondrial form of prC5/CAT was smaller than the primary translation product, suggesting that proteolytic processing occurred during the transport process. prC5/CAT also was translocated into chloroplasts in vivo, accumulating to approximately the same levels as in plant mitochondria. However, accumulation of prC5/CAT in chloroplasts relative to mitochondria varied with the conditions under which plants were grown. The chloroplast form of prC5/CAT also appeared to have been proteolytically processed, yielding a mature protein of the same apparent size as that seen in mitochondria of either tobacco or yeast. Chloramphenicol acetyltransferase lacking a mitochondrial targeting peptide did not associate with either chloroplasts or mitochondria. The results demonstrated that in plant cells a single leader peptide can interact functionally with the protein translocation systems of both chloroplasts and mitochondria, and raised the possibility that certain native proteins might be shared between these two organelles.

Amino Acid Sequence↗
PubMed1991

The focus and conduct of clinical trials.

This paper discusses some issues regarding how putative stop-smoking treatments should be evaluated. Preliminary evaluations of treatments have used withdrawal symptoms as a surrogate for abstinence in an attempt to decide those treatments on which to carry out expensive full-scale clinical trials. However, withdrawal symptom severity has not been shown to relate to long-term abstinence in any prospective studies. Until a better understanding of the relationship between withdrawal symptoms and abstinence is obtained withdrawal symptoms cannot be considered an appropriate surrogate for abstinence. Research is needed into what pattern of short-term abstinence provides the best predictor of long-term abstinence. Evidence from carbon monoxide validation of short-term abstinence raises doubts about whether minor lapses back to smoking are likely to lead to full blown relapse. Further research into the use of expired-air CO in validation of claims of abstinence is required. Finally, the traditional clinical trials format is not well suited to evaluation of treatment programmes with a large behavioural component. An alternative based on the principles underlying biological evolution is proposed.

Clinical Trials as Topic↗
PubMed1994

Common ancestry between IncN conjugal transfer genes and macromolecular export systems of plant and animal pathogens.

The DNA sequence of a cluster of pKM101 conjugal transfer genes was determined and aligned with the genetic map of the plasmid. Eighteen genes were identified, at least eight and probably 11 of which are required for efficient conjugation. These tra genes are homologous to and colinear with genes found in the virB operon of Agrobacterium tumefaciens Ti plasmids. Seven pKM101 tra genes are also homologous to ptl genes of Bordetella pertussis, which direct the export of pertussis toxin. We used TnphoA to construct translational fusions between pKM101 genes and the Escherichia coli phoA gene, which encodes alkaline phosphatase, and provide evidence that at least 11 of the 18 genes are either fully or partially exported from the cytoplasm.

Agrobacterium tumefaciens↗
PubMed2005

The unique structure of archaeal 'hami', highly complex cell appendages with nano-grappling hooks.

Proteinaceous, hair-like appendages known as fimbriae or pili commonly extend from the surface of prokaryotic cells and serve important functions such as cell adhesion, biofilm formation, motility and DNA transfer. Here we show that a novel group of archaea from cold, sulphidic springs has developed cell surface appendages of an unexpectedly high complexity with a well-defined base-to-top organization. It represents a new class of filamentous cell appendages, for which the term 'hamus' is proposed. Each archaeal cell is surrounded by a halo of about 100 hami, which mediate strong adhesion of the cells to surfaces of different chemical composition. The hami are mainly composed of 120 kDa subunits and remained stable in a broad temperature and pH range (0-70 degrees C; 0.5-11.5). Electron microscopy and cryo-electron tomography revealed that the hamus filament possesses a helical basic structure. At periodic distances, three prickles emanate from the filament, giving it the character of industrially produced barbwire. At its distal end the hami carry a tripartite, barbed grappling hook (60 nm in diameter). The architecture of this molecular hook is reminiscent of man-made fishhooks, grapples and anchors. It appears that nature has developed a perfect mechanical nano-tool in the course of biological evolution, which also might prove useful in the field of nanobiotechnology.

Archaea↗