Direct imaging of surface cusp evolution during strained-layer epitaxy and implications for strain relaxation.
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Journal Article↗
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Results for “directed evolution”
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Centrality dependence of charged-hadron transverse-momentum spectra in d+Au collisions at sqrt[s(NN)]=200 GeV.
We have measured transverse momentum distributions of charged hadrons produced in d+Au collisions at sqrt[s(NN)]=200 GeV. The spectra were obtained for transverse momenta 0.25<p(T)<6.0 GeV/c, in a pseudorapidity range of 0.2<eta<1.4 in the deuteron direction. The evolution of the spectra with collision centrality is presented in comparison to p+pmacr; collisions at the same collision energy. With increasing centrality, the yield at high transverse momenta increases more rapidly than the overall particle density, leading to a strong modification of the spectral shape. This change in spectral shape is qualitatively different from observations in Au+Au collisions at the same energy. The results provide important information for discriminating between different models for the suppression of high-p(T) hadrons observed in Au+Au collisions.
Journal Article↗
Seasonal endocrine changes and breeding activity in mediterranean wild ruminants.
The methods of assisted reproduction commonly used in domestic animals are currently being applied to non-domestic species. This is because of the limitation of maintaining the genetic variability in the wild, as it occurs in wild ruminants of the Mediterranean Basin. Despite the apparent progress of the technology, success of the offspring to grow and become healthy adult individuals has remained low in wild species. Difficulties usually arise from insufficient information about basic reproductive biology, such as the seasonal changes in ovarian and testicular activity. Directional adaptive evolution involves development of speciespecific physiological reproductive patterns to cope with various environmental factors. Thus, species originating and living at the same latitude display different reproductive strategies to entrain the breeding activity at an optimal time of the year. The aim of this paper was to present current knowledge on reproductive physiology of Mediterranean wild ruminants as a basic prerequisite for the successful use of assisted reproduction methods. Special emphasis is given to seasonal endocrine changes, ovarian cycles and testicular activity of Iberian wild ruminants, together with the role of social interactions on the regulation of these events.
Animals↗
Developmental selection of mutations.
The direction of evolution may at times be determined by the internal selection of genotypes during development, rather than by the external selection of phenotypes. Biological theory and experiment have reached the point where those concerned with evolutionary problems or with nuclear and cellular organization should consider this possibility.
Biological Evolution↗
Darwinism and the expansion of evolutionary theory.
The essence of Darwinism lies in the claim that natural selection is a creative force, and in the reductionist assertion that selection upon individual organisms is the locus of evolutionary change. Critiques of adaptationism and gradualism call into doubt the traditional consequences of the argument for creativity, while a concept of hierarchy, with selection acting upon such higher-level "individuals" as demes and species, challenges the reductionist claim. An expanded hierarchical theory would not be Darwinism, has strictly defined, but it would capture, in abstract form, the fundamental feature of Darwin's vision--direction of evolution by selection at each level.
Biological Evolution↗
Growth and metabolism of live vaccine strain of Pasteurella tularensis.
The growth and metabolism of the live vaccine strain of Pasteurella tularensis in different media were investigated. Maximal growth was observed in a medium containing a sulfuric acid digest of casein as amino acid source. Amino acid metabolism produced considerable ammonia, and the rate of ammonia evolution was directly proportional to the growth rate. The most likely route for amino acid breakdown is nonspecific oxidative deamination.
Amino Acids↗
Heterogeneity of genome rearrangements in rotaviruses isolated from a chronically infected immunodeficient child.
Rotaviruses with genome rearrangements, isolated from a chronically infected immunodeficient child, were adapted to growth in BSC-1 cells. Preparations of viral RNA from fecal extracts showed a mixed atypical rotavirus RNA profile, which was due to the presence of at least 12 subpopulations of viruses grossly differing in genotype. Besides various forms of genome rearrangements involving segment 8-, 10-, and 11-specific sequences, reassortment in vivo was likely to have occurred during the emergence of these viruses. The protein products of viral genomes with various forms of segmental rearrangements seemed to be largely unaltered. Genome rearrangement is proposed to be a third mechanism directing the evolution of rotaviruses.
Animals↗
Differential NF-kappaB activation after intratracheal endotoxin.
We examined the relationship between nuclear factor (NF)-kappaB DNA binding activity, cytokine gene expression, and neutrophilic alveolitis in rats after intratracheal (IT) instillation of endotoxin [lipopolysaccharide (LPS)]. NF-kappaB activation in lung tissue mirrored neutrophilic alveolitis after IT LPS instillation, with NF-kappaB activation and neutrophilic influx beginning 2 h after IT LPS doses of 0.01 mg/kg or greater. In lung lavage fluid cells, however, transient NF-kappaB activation was present in alveolar macrophages by 15 min after IT LPS instillation, followed by a second peak of NF-kappaB activation corresponding to the onset on neutrophilic alveolitis. For cytokines thought to be NF-kappaB dependent, two different patterns of mRNA expression were found. Interleukin (IL)-1alpha, IL-1beta, and tumor necrosis factor-alpha showed increased mRNA by 30 min after IT LPS instillation, but IL-6- and cytokine-induced neutrophil chemoattractant mRNAs were not substantially increased until 2 h after IT LPS instillation. Therefore, IT LPS causes differential NF-kappaB activation in air space cells and lung tissue, which likely determines production of key cytokines and directs the evolution of neutrophilic alveolitis.
Animals↗
No directionality of short tandem repeat evolution at the HPRT locus in catarrhine primates.
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Animals↗
Tracking micrometastasis to multiple organs with lacZ-tagged CWR22R prostate carcinoma cells.
Metastasis to organs other than lung is rarely observed in animal model systems of human prostate carcinoma (PCA), with the exception of already metastatic isolates of human PCA cultured for long periods of time. To analyze more directly the evolution of metastatic variants from primary PCA tumor isolates, the lacZ histochemical marker gene was transfected into the CWR22Rv1 cell line isolated from the CWR22R xenograft (primary tumor). Three clones of varying lacZ-expression stability were analyzed for tumorigenicity and progression in athymic nude mice. Clones B and D were highly tumorigenic in the subcutis; however, lacZ expression was highly unstable. In contrast, clone H demonstrated highly stable lacZ expression for >25 passages in culture or in animals. Clone H, injected sc in a PBS vehicle, gave a 15-40% tumorigenic take. All primary tumor-bearing animals exhibited micrometastases in lung and other organs. Clone H injected in a Matrigel vehicle gave 100% tumorigenicity, with all animals displaying micrometastases in lung, liver, and/or bone (lower frequency in brain and kidney). Overall, the relative frequency of micrometastasis to multiple organs was lung>liver=bone>>brain>kidney. Overt metastases were never observed in the lung or bone but were occasionally found in liver. lacZ-transfected clone H CWR22Rv1 cells represent a much more accurate model of metastasis of PCA to the organs normally involved in progression of the human disease. Use of marker gene-tagged cells and other high-resolution molecular techniques will now permit analyses of the earliest events in PCA progression and micrometastasis.
Animals↗
Denitrification at a long-term forested land treatment system in the Piedmont of Georgia.
Spray irrigation of forested land can provide an effective system for nutrient removal and treatment of municipal wastewater. Evolution of N2 + N2O from denitrifying activity is an important renovation pathway for N applied to forested land treatment systems. Federal and state guidance documents for design of forested land treatment systems indicate the expected range for denitrification to be up to 25% of applied N, and most forest land treatment systems are designed using values from 15 to 20% of applied N. However, few measurements of denitrification following long-term wastewater applications at forested land treatment sites exist. In this study, soil N2 + N2O-N evolution was directly measured at four different landscape positions (hilltop, midslope, toe-slope, and riparian zone) in a forested land treatment facility in the Georgia Piedmont that has been operating for more than 13 yr. Denitrification rates within effluent-irrigated areas were significantly greater than rates in adjacent nonirrigated buffer zones. Rates of N2 + N2O-N evolved from soil in irrigated forests ranged from 5 to 10 kg ha(-1) yr(-1) N on the three upland landscape positions and averaged 38 kg ha(-1) yr(-1) N within the riparian zone. The relationship between measured riparian zone denitrification rates and soil physical and chemical properties was poor. The best relationship was with soil temperature, with an r2 of 0.18. Overall, on a landscape position weighted basis, only 2.4% of the wastewater-applied N was lost through denitrification.
Ecosystem↗
Adeno-Associated Virus Engineering and Load Strategy for Tropism Modification, Immune Evasion and Enhanced Transgene Expression.
Gene therapy aims to add, replace or turn off genes to help treat disease. To date, the US Food and Drug Administration (FDA) has approved 14 gene therapy products. With the increasing interest in gene therapy, feasible gene delivery vectors are necessary for inserting new genes into cells. There are different kinds of gene delivery vectors including viral vectors like lentivirus, adenovirus, retrovirus, adeno-associated virus et al, and non-viral vectors like naked DNA, lipid vectors, polymer nanoparticles, exosomes et al, with viruses being the most commonly used. Among them, the most concerned vector is adeno-associated virus (AAV) because of its safety, natural ability to efficiently deliver gene into cells and sustained transgene expression in multiple tissues. In addition, the AAV genome can be engineered to generate recombinant AAV (rAAV) containing transgene sequences of interest and has been proven to be a safe gene vector. Recently, rAAV vectors have been approved for the treatment of various rare diseases. Despite these approvals, some major limitations of rAAV remain, namely nonspecific tissue targeting and host immune response. Additional problems include neutralizing antibodies that block transgene delivery, a finite transgene packaging capacity, high viral titer used for per dose and high cost. To deal with these challenges, several techniques have been developed. Based on differences in engineering methods, this review proposes three strategies: gene engineering-based capsid modification (capsid modification), capsid surface tethering through chemical conjugation (surface tethering), and other formulations loaded with AAV (virus load). In addition, the major advantages and limitations encountered in rAAV engineering strategies are summarized.
Dependovirus↗
HIV protease-activated molecular switches based on beta-glucuronidase and alkaline phosphatase.
Our long-term goal is to direct the evolution of novel protease variants. To this end we have engineered a new type of protease-activated reporter enzyme. Many protease-activated enzymes evolved in nature, but the introduction of novel regulatory mechanisms into normally unregulated enzymes poses a difficult design challenge. Random Elongation Mutagenesis [1] was used to fuse the p6 peptide, which is recognized and cleaved by HIV protease, and twelve random sequence amino acids to the C-termini of beta-glucuronidase (GUS) and alkaline phosphatase (AP). The resulting GUS-p6-(NNN)12 and AP-p6-(NNN)12 libraries were expressed in E. coli and screened for clones that were inactivated by the C-terminal extension (tail). The inactivated clones were co-expressed with HIV protease, and those that were re-activated were isolated. The AP and GUS activities of the most responsive clones were each >3.5-fold higher when co-expressed with HIV protease, and this activation is correlated with in vivo proteolysis. It should be possible to generalize this strategy to different reporter enzymes, different target proteases, and perhaps to other types of protein-modifying enzymes.
Alkaline Phosphatase↗
Combinatorial saturation mutagenesis by in vivo overlap extension for the engineering of fungal laccases.
Combinatorial saturation mutagenesis -CSM- is a valuable tool for improving enzymatic properties from hot-spot residues discovered by directed enzyme evolution or performing semi-rational studies. CSM coupled to a reliable high-throughput screening assay -coefficient of variance below 10%- has been used to enhance turnover rates in the fungal laccase variant T2 from Myceliophthora thermophila. The influence of the highly conserved pentapeptide 509-513 on the redox potential of blue-copper containing enzymes is well described. We focused combinatorial saturation mutagenesis in residues Ser510 and Leu513. Libraries were constructed in Saccharomyces cerevisiae by in vivo overlap extension -IVOE- of the PCR products. This methodology provides a simple manner to build CSM libraries avoiding extra PCR reactions, by-products formation and in vitro ligation steps. After exploring more than 1,700 clones, mutant (7E1) with approximately 3-fold higher kinetics than parent type was found. 7E1 showed one synonymous mutation (L513L, CGT/TTG) and one beneficial mutation S510G (TCG/GGG) that can not be achieved by conventional error-prone PCR techniques. Mutation S510G seems to affect the C-terminal plug, which modulates the transit of water and oxygen to the trinuclear copper cluster.
Ascomycota↗
[Acquisition of masticatory structures in mammalian reptiles (preliminary study].
Possession of the masticatory function and apparatus appears as essential for the passage from Reptiles to Mammals. The present study, based on material of the Museum of d'Histoire Naturelle of Paris and on the literature, tries to distinguish the different stages of modification and specialization of feeding device in the cynodont theriodonts, leading to the mammalian stomatognathic system. The relationship between bone components (lateral skull and lower jaw), teeth and muscles are discussed. Induction of these changes comes from the external adductor muscular system in which the transformation from a primitive mass to mammalianlike masticatory muscles, directs this evolution. The conditions of feeding specialization of the Gomphodonts are discussed, as well as their evolutionary failure. Lastly, without taking up the quarrel about the double jaw-joint, it seems for the authors that the jaw-joint transformation appears as the most determinative element for assigning mammalian origins to the Cynodonts.
Animals↗
High frequency of clonally related tumors in cases of multiple synchronous lung cancers as revealed by molecular diagnosis.
In patients with multiple synchronous lung tumors, discrimination of multicentric lung cancers from intrapulmonary metastasis is important for treatment decision, but this is sometimes difficult. The aim of this study was to retrospectively distinguish multicentric lung cancers from intrapulmonary metastases in 14 such cases by loss of heterozygosity (LOH) and p53 mutational status. DNA was extracted from microdissected tumor cells in paraffin-embedded archival tissue, and 3p14.2, 3p21, 3p25, 9p21, and 18q21.1 were investigated for LOH. Exons 5-8 of the p53 gene were examined for mutations by the PCR, followed by single-strand conformation polymorphism analysis and DNA sequencing. For cases with the same LOH pattern, we calculated a clonality index, the probability of the given LOH pattern when these tumors were hypothesized to be independent in origin. Eleven of 14 cases (79%) were thus diagnosed as having pulmonary metastasis and only one case as having genuinely multicentric lung cancers. Two cases presented difficulty in diagnosis. In several cases, the LOH patterns conflicted with p53 mutation patterns, suggesting that clonal evolution is directly affected by certain genetic changes. The combination of p53 with LOH helped increase both the sensitivity and specificity of the assay.
Adult↗
[Biological problems of origin and development of various physiological functions (theory and application)].
The author presents some idea about origin and development of some physiological functions: outer breathing, breath function of blood, blood circulation, thermoregulation, energy supply. The conclusions about main directions of evolution of these functions and duration of their development in phylogeny were drawn. The author gave some examples of abrupt changes of development of these functions in different groups of animals and discussed possible reasons of such changes. General quantitative estimation of the results of evolution of these functions from the position of their summArized efficiency was done. Quantitative characteristics of optimization and efficiency limits of physiological functions were suggested on the base of new data in general biology and comparative physiology. The author put toward the hypothesis about conventional "mistakes" of evolution and showed deep biological reasons of some seriOus illness. The examples of some applied problems in biology, physiology and medicine that can be solved with the data on evolution of physiological functions are presented.
Animals↗
[Fundamental modern possibilities and directions for the prevention of evolution diseases and malformations].
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Biological Evolution↗