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Results for “evolutionary potentiation”

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PubMed1991

Infectivity of cultured Trypanosoma fallisi (Kinetoplastida) to various anuran species and its evolutionary implications.

Trypanosoma fallisi, a hemoflagellate infecting Bufo americanus from Ontario, was grown in vitro, and metatrypanosomes from the primary culture were inoculated into 4 uninfected test groups from 3 anuran families: Bufonidae, Hylidae, and Ranidae. In vitro-cultured T. fallisi was found to infect B. americanus and to induce transient infections in Bufo valliceps and Hyla versicolor. The flagellate was not infective to Rana clamitans. Trypanosoma ranarum was uninfective to the bufonids and hylids tested. These data suggest that the potential for host-switching decreases with increased evolutionary distance of the potential anuran host.

Animals↗
PubMed2006

Using hidden Markov models and observed evolution to annotate viral genomes.

MOTIVATION: ssRNA (single stranded) viral genomes are generally constrained in length and utilize overlapping reading frames to maximally exploit the coding potential within the genome length restrictions. This overlapping coding phenomenon leads to complex evolutionary constraints operating on the genome. In regions which code for more than one protein, silent mutations in one reading frame generally have a protein coding effect in another. To maximize coding flexibility in all reading frames, overlapping regions are often compositionally biased towards amino acids which are 6-fold degenerate with respect to the 64 codon alphabet. Previous methodologies have used this fact in an ad hoc manner to look for overlapping genes by motif matching. In this paper differentiated nucleotide compositional patterns in overlapping regions are incorporated into a probabilistic hidden Markov model (HMM) framework which is used to annotate ssRNA viral genomes. This work focuses on single sequence annotation and applies an HMM framework to ssRNA viral annotation. A description of how the HMM is parameterized, whilst annotating within a missing data framework is given. A Phylogenetic HMM (Phylo-HMM) extension, as applied to 14 aligned HIV2 sequences is also presented. This evolutionary extension serves as an illustration of the potential of the Phylo-HMM framework for ssRNA viral genomic annotation. RESULTS: The single sequence annotation procedure (SSA) is applied to 14 different strains of the HIV2 virus. Further results on alternative ssRNA viral genomes are presented to illustrate more generally the performance of the method. The results of the SSA method are encouraging however there is still room for improvement, and since there is overwhelming evidence to indicate that comparative methods can improve coding sequence (CDS) annotation, the SSA method is extended to a Phylo-HMM to incorporate evolutionary information. The Phylo-HMM extension is applied to the same set of 14 HIV2 sequences which are pre-aligned. The performance improvement that results from including the evolutionary information in the analysis is illustrated.

Algorithms↗
PubMed2002

Heritable variation of sex pheromone composition and the potential for evolution of resistance to pheromone-based control of the Indian meal moth, Plodia interpunctella.

The short-term evolutionary effect of pheromone-based mating disruption on the mating ability of the Indian meal moth, Plodia interpunctella, was investigated. Three independent selection lines were established, and the mating ability of moths in plastic tents treated with high doses of pheromone and in control tents was compared for two consecutive generations. In addition, the heritability of the sex pheromone blend, measured as the ratio of two major pheromone components (Z,E)-9,12-tetradecadienyl acetate and (Z,E)-9,12-tetradecadienol, was estimated. Based on a mother-daughter regression analysis including 21 families, the heritability of the pheromone blend was 0.65 +/- 0.14, indicating a potential for evolutionary change of the character. However, no increase in mating ability of females in pheromone-treated tents or alteration of the pheromone blend was observed in any selection line when compared with control lines, indicating no or weak selection on the pheromone blend as well as other traits influencing mating ability of this species under the created mating disruption conditions. Factors contributing to the lack of selection effects are discussed.

Animals↗
PubMed2001

Acne: a biopsychosocial and evolutionary perspective with a focus on shame.

PURPOSE: Hypotheses regarding the psychological factors implicated in the development and maintenance of acne first emerged in the middle of the eighteenth century. However, the psychodermatological literature from this date relating to acne has variously been described as confusing, overly prone to conjecture and, in particular, atheoretical. The current paper has two key objectives; first, to present a biopsychosocial model of acne development and maintenance and, secondly, to understand the psychosocial strain imposed by acne from an evolutionary perspective with a particular emphasis on body shame reactions. METHODS: The psychodermatological literature relating to acne is reviewed with the data analysed for potential biopsychosocial interactions and shame eliciting responses. RESULTS: The review indicates that acne can be reconceptualized as a biopsychosocial phenomena which, in turn, provides the field with innovative hypotheses for empirical inquiry and the potential for expanding and evaluating treatment options. The evolutionary analysis illustrates that acne provides the potential for distressing body shame reactions due to the skin disease's potential for damaging self-other evaluations of attractiveness. CONCLUSIONS: Acne has tended to be viewed as a minor dermatological complaint which imposes minimal psychological distress upon sufferers. The paper concludes that acne has the ability to elicit in some sufferers significant mental health concerns due to a heightened sense of shame relating to appearance.

Journal Article↗
PubMed2005

Effects of the nematode Gyrinicola batrachiensis on development, gut morphology, and fermentation in bullfrog tadpoles (Rana catesbeiana): a novel mutualism.

We describe a novel mutualism between bullfrog tadpoles (Rana catesbeiana) and a tadpole-specific gastrointestinal nematode (Gyrinicola batrachiensis). Groups of tadpoles were inoculated with viable or nonviable nematode eggs, and development, morphology, and gut fermentation activity were compared between nematode-infected and uninfected tadpoles. Nematode infection accelerated tadpole development; the mean time to metamorphosis was 16 d shorter and the range of times to metamorphosis was narrower in nematode-infected tadpoles than in uninfected tadpoles. At metamorphosis, infected and uninfected bullfrogs did not differ in body size or condition. Colon width, wet mass of colon contents, and concentrations of most fermentation byproducts (short-chain fatty acids: SCFAs) in the hindgut were greater in infected tadpoles. Furthermore, in vitro fermentation yields for all SCFAs combined were over twice as high in infected tadpoles than in uninfected tadpoles. One explanation for accelerated development in infected tadpoles is the altered hindgut fermentation associated with the nematodes. Energetic contributions of fermentation were estimated to be 20% and 9% of the total daily energy requirement for infected and uninfected tadpoles, respectively. Infection by G. batrachiensis nematodes potentially confers major ecological and evolutionary advantages to R. catesbeiana tadpoles. The mutualism between these species broadens our understanding of the taxonomic diversity and physiological contributions of fermentative gut symbionts and suggests that nematodes inhabiting the gut regions of other ectothermic herbivores might have beneficial effects in those hosts.

Animals↗
PubMed1997

Artificial evolution: a new path for artificial intelligence?

Recently there have been a number of proposals for the use of artificial evolution as a radically new approach to the development of control systems for autonomous robots. This paper explains the artificial evolution approach, using work at Sussex to illustrate it. The paper revolves around a case study on the concurrent evolution of control networks and visual sensor morphologies for a mobile robot. Wider intellectual issues surrounding the work are discussed, as is the use of more abstract evolutionary simulations as a new potentially useful tool in theoretical biology.

Artificial Intelligence↗
PubMed1997

Leishmania major: comparison of the cathepsin L- and B-like cysteine protease genes with those of other trypanosomatids.

Cysteine proteases play important roles in the pathogenesis of several parasitic infections and have been proposed as targets for the structure-based strategy of drug design. As a first step toward applying this strategy to design inhibitors as antiparasitic agents for leishmaniasis, we have isolated and sequenced the full-length clones of two cysteine protease genes from Leishmania major. One of the genes is structurally similar to the cathepsin L-like family and the other is similar to the cathepsin B-like family of cysteine proteases. The L. major cathepsin L-like sequence has a proregion that shares high sequence similarity with other cathepsin L sequences but not cathepsin B sequences and has a proline/threonine-rich C-terminal extension. The cathepsin L-like gene occurs in multiple copies, whereas there may be only one copy of the cathepsin B-like gene. Northern blot analyses show that both genes are expressed in the promastigote and amastigote stages, and pulse field gel electrophoresis revealed that the cathepsin L- and B-like genes are each found on two nonhomologous chromosomes. The L. major L-like amino acid sequence is 75% identical to the L. mexicana sequence, 74% identical to the L. pifanoi sequence, 47% identical with the Trypanosoma cruzi sequence, 47% identical with the T. congolense sequence, and 45% identical with the T. brucei sequence. L. major is one of two trypanosomatid species for which a cathepsin B-like gene has been identified and sequenced; its amino acid sequence is 82% identical to the one from L. mexicana. Tree inference based on distance and parsimony methods of kinetoplastid cathepsin L proteins yielded independent support for phylogenetic hypotheses inferred from analyses of ribosomal RNA genes. Because the cathepsin L locus has a high level of phylogenetic signal with respect to trypanosomatid taxa, this locus has great potential utility for investigating the evolutionary history of trypanosomatids and related organisms.

Amino Acid Sequence↗
PubMed2001

Molecular phylogenetics of western North American frogs of the Rana boylii species group.

Phylogenetic relationships among frogs of the genus Rana from western North America are investigated using 2013 aligned bases of mitochondrial DNA sequence from the genes encoding ND1 (subunit one of NADH dehydrogenase), tRNA(Ile), tRNA(Gln), tRNA(Met), ND2, tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr), and COI (subunit I of cytochrome c oxidase), plus the origin for light-strand replication (O(L)) between the tRNA(Asn) and tRNA(Cys) genes. The aligned sequences contain 401 phylogenetically informative characters. A well-resolved phylogenetic hypothesis in which the Rana boylii species group (R. aurora, R. boylii, R. cascadae, R. muscosa, and R. pretiosa) is monophyletic is obtained. Molecular sequence divergence suggests that the R. boylii species group is approximately 8 million years old. The traditional hypothesis showing monophyly of the yellow-legged frogs (R. boylii and R. muscosa) is statistically rejected in favor of a hypothesis in which R. aurora, R. cascadae, and R. muscosa form a clade. Reanalyses of published nuclear ribosomal DNA restriction-site data and allozymic data support a monophyletic R. boylii group, but do not effectively resolve relationships among species within this group. Eight populations of R. muscosa form two major clades separated by a biogeographic break in the Sierra Nevada of California. This biogeographic break is broadly concordant with breaks found in four other amphibian and reptilian taxa. The two major clades within R. muscosa are estimated to have diverged approximately 2.2 million years before present. Each of these major clades contains two subgroups showing approximately 1.5 million years divergence, implicating climatic effects of Pleistocene glaciation in vicariance. The four distinct subgroups of R. muscosa separated by at least 1.4 million years of evolutionary divergence are suggested as potential units for conservation.

Animals↗
PubMed2000

Decrease of phosphoribulokinase activity by antisense RNA in transgenic tobacco: definition of the light environment under which phosphoribulokinase is not in large excess.

To test the hypothesis that the contribution of phosphoribulokinase (PRK) to the control of photosynthesis changes depending on the light environment of the plant, the response of transgenic tobacco (Nicotiana tabacum L.) transformed with antisense PRK constructs to irradiance was determined. In plants grown under low irradiance (330 micromol m(-2) s(-1)) steady-state photosynthesis was limited in plants with decreased PRK activity upon exposure to higher irradiance, with a control coefficient of PRK for CO2 assimilation of 0.25 at and above 800 micromol m(-2) s(-1). The flux control coefficient of PRK for steady-state CO2 assimilation was zero, however, at all irradiances in plant material grown at 800 micromol m(-2) s(-1) and in plants grown in a glasshouse during mid-summer (alternating shade and sun 300-1600 micromol m(-2) s(-1)). To explain these differences between plants grown under low and high irradiances, Calvin cycle enzyme activities and metabolite content were determined. Activities of PRK and other non-equilibrium Calvin cycle enzymes fructose-1,6-bisphosphatase, sedoheptulose-1,7-bisphosphatase and ribulose-1,5-bisphosphate carboxylase-oxygenase were twofold higher in plants grown at 800 micromol m(-2) s(-1) or in the glasshouse than in plants grown at 330 micromol m(-2) s(-1). Activities of equilibrium enzymes transketolase, aldolase, ribulose-5-phosphate epimerase and isomerase were very similar under all growth irradiances. The flux control coefficient of 0.25 in plants grown at 330 micromol m(-2) s(-1) can be explained because low ribulose-5-phosphate content in combination with low PRK activity limits the synthesis of ribulose-1,5-bisphosphate. This limitation is overcome in high-light-grown plants because of the large relative increase in activities of sedoheptulose-1,7-bisphosphatase and fructose-1,6-bisphosphatase under these conditions, which facilitates the synthesis of larger amounts of ribulose-5-phosphate. This potential limitation will have maintained evolutionary selection pressure for high concentrations of PRK within the chloroplast.

Light↗
PubMed1995

The arrestin superfamily: cone arrestins are a fourth family.

Arrestins constitute a superfamily of regulatory proteins that down-regulate phosphorylated G-protein membrane receptors, including rod and cone photoreceptors and adrenergic receptors. The potential role of arrestin in color visual processes led us to identify a cDNA encoding a cone-like arrestin in Xenopus laevis, the principle amphibian biological model system. Alignment of 18 deduced amino acid sequences of all known arrestins from both invertebrate and vertebrate species reveals five arrestin families. Further analysis identifies 7 variable and 4 conservative arrestin structural motifs that may identify potential functional domains. The adaptive evolutionary relationship of Xenopus cone arrestin to the arrestin gene tree suggests high intrafamily homology and early gene duplication events.

Amino Acid Sequence↗
PubMed2004

Mammalian phylogenomics comes of age.

The relatively new field of phylogenomics is beginning to reveal the potential of genomic data for evolutionary studies. As the cost of whole genome sequencing falls, anticipation of complete genome sequences from divergent species, reflecting the major lineages of modern mammals, is no longer a distant dream. In this article, we describe how comparative genomic data from mammals is progressing to resolve long-standing phylogenetic controversies, to refine dogma on how chromosomes evolve and to guide annotation of human and other vertebrate genomes.

Animals↗
PubMed1996

Location of NRAMP1 molecule on the plasma membrane and its association with microtubules.

Natural resistance to infection with intracellular parasites, such as Leishmania, Salmonella, and Mycobacterium, is controlled in mice by the expression of a single dominant gene locus designated Lsh/Ity/Bcg. Natural resistance-associated macrophage protein gene 1 (NRAMP1) was isolated as a candidate gene. NRAMP1 encodes an M(r) 60000 polypeptide with 10-12 potential transmembrane domains and an evolutionary conserved consensus transport motif. The present study shows that the human NRAMP1 molecule is expressed in all cell lineages of macrophage/monocyte and B- and T-lymphocytes. Immunohistochemical analysis using antihuman NRAMP1 antibody provides the direct evidence that the NRAMP1 molecule is located and distributed on the plasma membrane. An NRAMP1-glutathione S-transferase (GST) fusion protein was used to affinity-purify a protein, bound to the NH2-terminal cytoplasmic domain of NRAMP1. It was found that the NRAMP1 molecule was associated with alpha- and beta-tubulin of microtubules. These results suggest that NRAMP1 may function as a molecule, possessing the abilities of membrane-anchoring and microtubule-binding, for the microtubule-mediated transport of vesicles and be a new class of microtubule-associated proteins.

Amino Acid Sequence↗
PubMed1997

Expression of NRAMP1 molecule in human peripheral blood leukocytes.

Natural resistance or susceptibility of host to infection with several intracellular pathogens, such as Mycobacterium, Salmonella and Leishmania, is controlled in mice by the expression of a single dominant gene locus designated Lsh/Ity/Bcg. Natural resistance-associated macrophage protein gene 1 (Nramp1) was isolated as a candidate gene. Nramp1 gene encodes a 60 kDa polypeptide with 10-12 potential transmembrane domains and an evolutionary conserved consensus transport motif. The present study shows that the human NRAMP1 gene is expressed in all established hematopoietic cell lines examined, including monocytes/macrophages and B- and T-lymphocytes. In contrast, cell type-specific expressions are observed in human peripheral blood leukocytes. NRAMP1 expression is very low level in granulocytes. B- and T-lymphocytes are equivalent in the level of NRAMP1 expression. Notable expression of NRAMP1 gene can be detected in the monocyte population. These results have important implications for the host defence mechanisms and the pathogenesis of intracellular pathogens which are recognized and ingested by the mononuclear phagocyte system including monocytes/macrophages.

Animals↗
PubMed1999

Resident aliens: the Tc1/mariner superfamily of transposable elements.

Transgenic technology is currently applied to several animal species of agricultural or medical importance, such as fish, cattle, mosquitos and parasitic worms. However, the repertoire of genetic tools used for molecular analyses of mice and Drosophila is not always applicable to other species. For example, while retroviral enhancer-trap experiments in mice can be based on embryonic stem (ES) cell technology, this is not currently an option with other animals. Similarly, the germline transformation of Drosophila depends on the use of the P-element transposon, which does not jump in other genera. This article analyses the main characteristics of Tc1/mariner transposable elements, examines some of the factors that have contributed to their evolutionary success, and describes their potential, as well as their limitations, for transgenesis and insertional mutagenesis in diverse animals.

Amino Acid Sequence↗
PubMed1991

The extensor medii proprius and anomalous extensor tendons to the long finger.

The extensor medii proprius is a muscle analogous to the extensor indicis proprius in that it has a similar origin, but inserts into the long finger. The extensor indicis et medii communis muscle is an extensor indicis proprius muscle that splits to insert into both the index and long fingers. The extensor tendons to the fingers were dissected in 58 adult hands to determine the incidence and anatomy of the extensor medii proprius and extensor indicis et medii communis. The incidence of the extensor medii proprius was 10.3% and the incidence of the extensor indicis et medii communis was 3.4% in this series. The extensor medii proprius and extensor indicis proprius muscles had a common origin in all cases. The insertion of the extensor medii proprius into the dorsal aponeurosis was palmar and ulnar to the extensor digitorum communis of the long finger, but in one case, the extensor medii proprius inserted into the deep fibrous tissue proximal to the metacarpophalangeal joint. The tendon slip of the extensor indicis et medii communis inserting into the long finger did not insert into the dorsal aponeurosis, but into the deep fibrous tissue near the metacarpophalangeal joint. Both the extensor medii proprius and the extensor indicis et medii communis may represent evolutionary remnants. Awareness of their potential presence and anatomy should be helpful in extensor identification, repair, and transfer.

Fingers↗
PubMed2004

From energy efficiency under stress to rapid development and a long life in natural populations.

Simplistically, high fitness depends upon high energy efficiency in the stressful habitats of organisms in the wild. Rapid development and high survival to adulthood should be followed by long-lived stress-resistant genotypes under this reductionist model. Empirical evidence is very limited because of the common use of benign laboratory environments, which remains a major difficulty in understanding relationships between life-history traits under more natural settings. Heterozygotes tend to show greater energy efficiency than do corresponding homozygotes especially in stressful environments, which leads the above connections among fitness traits. In particular rapid development and increased longevity should be correlated, and underwritten by the availability of metabolic energy. Empirical work is needed based upon severe stresses where a small environmental perturbation cases lethality; drought, heat and nutritional inadequacy are suitable candidate stresses. The importance of viewing fitness in energy terms is emphasized throughout. A byproduct is the potential to fuse functional and evolutionary biology under stressful environments.

Animals↗
PubMed2003

The power and promise of population genomics: from genotyping to genome typing.

Population genomics has the potential to improve studies of evolutionary genetics, molecular ecology and conservation biology, by facilitating the identification of adaptive molecular variation and by improving the estimation of important parameters such as population size, migration rates and phylogenetic relationships. There has been much excitement in the recent literature about the identification of adaptive molecular variation using the population-genomic approach. However, the most useful contribution of the genomics model to population genetics will be improving inferences about population demography and evolutionary history.

Genetics, Population↗
PubMed2006

Developmental instability as an estimator of genetic stress.

To set conservation priorities, scientists should be able to assess the relative threats posed by the effects of loss of genetic variability, inbreeding and outbreeding as these can generate 'genetic stress'. Developmental instability (DI) has been suggested as an indicator of stress, possibly being more sensitive than other measures. However, there is controversy as to whether DI is an accurate and reliable tool for assessing the degree of genetic stress. After 50 years of the presentation of Lerner's conjecture, there are still several unresolved questions about the relationship between DI and genetic stress. Here, we review studies on mechanisms behind DI. The current status on the use of DI as an indicator of genetic stress is discussed, and suggestions are presented on how to obtain more knowledge on the potential of DI in an evolutionary context.

Animals↗