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PubMed1989

The role of cometary particle coalescence in chemical evolution.

Important prebiotic organic compounds might have been transported to Earth in dust or produced in vapor clouds resulting from atmospheric explosions or impacts of comets. These compounds coalesced in the upper atmosphere with particles ejected from craters formed by impacts of large objects. Coalescence during exposure to UV radiation concentrated organic monomers and enhanced formation of oligomers. Continuing coalescence added material to the growing particles and shielded prebiotic compounds from prolonged UV radiation. These particles settled into the lower atmosphere where they were scavenged by rain. Aqueous chemistry and evaporation of raindrops containing nomomers in high temperature regions near the Earth's surface also promoted continued formation of oligomers. Finally, these oligomers were deposited in the oceans where continued prebiotic evolution led to the most primitive cell. Results of our studies suggest that prebiotic chemical evolution may be an inevitable consequence of impacting comets during the late accretion of planets anywhere in the universe if oceans remained on those planetary surfaces.

Amino Acids↗
PubMed2005

The dynamics of adaptation: an illuminating example and a Hamilton-Jacobi approach.

Our starting point is a selection-mutation equation describing the adaptive dynamics of a quantitative trait under the influence of an ecological feedback loop. Based on the assumption of small (but frequent) mutations we employ asymptotic analysis to derive a Hamilton-Jacobi equation. Well-established and powerful numerical tools for solving the Hamilton-Jacobi equations then allow us to easily compute the evolution of the trait in a monomorphic population when this evolution is continuous but also when the trait exhibits a jump. By adapting the numerical method we can, at the expense of a significantly increased computing time, also capture the branching event in which a monomorphic population turns dimorphic and subsequently follow the evolution of the two traits in the dimorphic population. From the beginning we concentrate on a caricatural yet interesting model for competition for two resources. This provides the perhaps simplest example of branching and has the great advantage that it can be analyzed and understood in detail.

Adaptation, Biological↗
PubMed2003

[Negative selection and computer models of the joint evolution of the patterns of polygenes, transposable elements, and origin identity labels].

Computer simulation of the population dynamics of the genomic patterns of polygenes, transposable elements (TEs), and origin identity labels (OILs) in the course of negative selection for an additive quantitative trait has been performed. It was demonstrated that active polygene alleles disappear very rapidly, whereas the patterns of TEs and OILs continue their evolution determined by strict selective inbreeding and gene drift. Dendrograms of the patterns of polygenes, TEs, and OILs were constructed for all generations. It was demonstrated that the final consensus pattern of OILs consists of the fragments of the original patterns, which contain neither active polygene alleles nor modifier or marker TEs. Neutral TE copies were present in the final pattern, as should be expected in the case of gene drift. Inbreeding coefficient increased steadily but by generation 100 reached values higher than 0.9. All other parameters and initial conditions being the same, the responses to negative and positive selections were asymmetric.

Animals↗
PubMed2006

Fructosyltransferase and invertase genes evolved by gene duplication and rearrangements: rice, perennial ryegrass, and wheat gene families.

The invertase enzyme family is responsible for carbohydrate metabolism in rice, perennial ryegrass, and wheat. Fructan molecules accumulate in cell vacuoles of perennial ryegrass and wheat and are associated with abiotic stress tolerance. High levels of amino acid similarity between the fructosyltransferases responsible for fructan accumulation indicates that they may have evolved from invertase-like ancestral genes. In this study, we have applied comparative genomics to determine the mechanisms that lead to the evolution of fructosytransferase and invertase genes in rice, perennial ryegrass, and wheat. Duplications and rearrangements have been inferred to generate variant forms of the rice invertases since divergence from a common grass progenitor. The occurrence of multiple copies of fructosyltransferase genes indicated that duplication events continued during evolution of the wheat and perennial ryegrass lineages. Further gene rearrangements were evident in perennial ryegrass genes, albeit at a reduced level compared with the rice invertases. Gene orthologs were largely static after duplication during evolution of the wheat lineage. This study details evolutionary events that contribute to fructosyltransferase and invertase gene variation in grasses.

Amino Acid Sequence↗
PubMed2002

Analytical model of nonlinear, single-mode, classical Rayleigh-Taylor instability at arbitrary Atwood numbers.

An analytical model of the nonlinear bubble evolution of single-mode, classical Rayleigh-Taylor instability at arbitrary Atwood numbers (A(T)) is presented. The model is based on an extension of Layzer's theory [Astrophys. J. 122, 1 (1955)] previously applied only to the fluid-vacuum interfaces (A(T) = 1). The model provides a continuous bubble evolution from the earlier exponential growth to the nonlinear regime when the bubble velocity saturates at U(b) = square root of [2A(T)/(1+A(T)) (g/C(g)k)], where k is the perturbation wave number, g is the interface acceleration, and C(g) = 3 and C(g) = 1 for the two-dimensional and three-dimensional geometries, respectively.

Journal Article↗
PubMed1999

How the licensure process will evolve.

BACKGROUND AND OVERVIEW: All aspects of dental licensure are continuing to evolve. This article describes the changes that are occurring in the licensure process and projects the direction and magnitude of future changes. CONCLUSIONS: The author predicts that national board examinations will continue to move away from recall of facts and toward assessment of basic science and clinical principles as they apply to clinical decision making and delivery of care. Clinical examinations will continue their evolution to become even more reliable and valid. Licensure by credentials will be adopted by more states, thus addressing concerns about mobility that are expressed by many practitioners. PRACTICE IMPLICATIONS: Despite all of this projected progress, the dental profession should expect elevated public pressure for greater accountability unless it takes a proactive position to ensure the continued competency of all practitioners.

Clinical Competence↗
PubMed2002

Out of Africa again and again.

The publication of a haplotype tree of human mitochondrial DNA variation in 1987 provoked a controversy about the details of recent human evolution that continues to this day. Now many haplotype trees are available, and new analytical techniques exist for testing hypotheses about recent evolutionary history using haplotype trees. Here I present formal statistical analysis of human haplotype trees for mitochondrial DNA, Y-chromosomal DNA, two X-linked regions and six autosomal regions. A coherent picture of recent human evolution emerges with two major themes. First is the dominant role that Africa has played in shaping the modern human gene pool through at least two--not one--major expansions after the original range extension of Homo erectus out of Africa. Second is the ubiquity of genetic interchange between human populations, both in terms of recurrent gene flow constrained by geographical distance and of major population expansion events resulting in interbreeding, not replacement.

Africa↗
PubMed2005

[Therapeutic behavior of a hydrocolloid dressing. Its evolution in the treatment of acute and chronic dermal ulcers].

OBJECTIVE: Evaluate the behavior of a Sureskin II hydrocolloid dressing in the treatment of acute and chronic dermal ulcers in daily clinical practice. METHODS: By means of an observational, multi-centric, prospective, open study of a series of clinical cases on patients afflicted by acute and chronic ulcers. This study lasted through 20 dressing changes or until the ulcer was cured. During the initial visit, the characteristics of the lesion were evaluated; in continuation, the evolution of a lesion as dressings were changed was evaluated; and during the final visit, the professional team evaluated the final traits of the lesion along with the overall behavior of the dressing applied. RESULTS: This study evaluated 1080 patients whose average age was 72.3 years. At the conclusion of this study the investigators noticed that the size of these ulcers had significantly reduced from the start to the end of treatment. Epithelization increased from 43.2 to 71.9%. 98.3% of patients in this study considered this dressing brand easy to apply Seepage of exudation diminished from 31.77 to 14.6%. The presence of maceration, erythema and eczema also reduced from 29.2 to 12.5%, from 37.6 to 13.1% and from 9.7 to 6.3% respectively. The symptoms of infection or inflammation dropped from 22.6 to 7.6%. Patients' complaints of pain when their dressings were changed dropped 29.4%. 90.7% of these patients stated this treatment alleviated their symptoms and allowed them to carry on their daily activities in a normal fashion. CONCLUSION: The results of this study show that the use of Sureskin II is effective, therefore making it a first choice therapeutic option for treating patients suffering from acute and chronic dermal ulcers.

Acute Disease↗
PubMed1999

Origin of a new Phytophthora pathogen through interspecific hybridization.

Plant disease epidemics resulting from introductions of exotic fungal plant pathogens are a well known phenomenon. An associated risk-that accelerated pathogen evolution may be occurring as a consequence of genetic exchange between introduced, or introduced and resident, fungal pathogens-is largely unrecognized. This is, in part, because examples of natural, interspecific hybridization in fungi are very rare. Potential evolutionary developments range from the acquisition of new host specificities to emergence of entirely new pathogen taxa. We present evidence from cytological behavior, additive nucleotide bases in repetitive internal transcribed spacer regions of the rRNA-encoding DNA (rDNA), and amplified fragment length polymorphisms of total DNA that a new, aggressive Phytophthora pathogen of alder trees in Europe comprises a range of heteroploid-interspecific hybrids involving a Phytophthora cambivora-like species and an unknown taxon similar to Phytophthora fragariae. The hybrids' marked developmental instabilities, unusual morphological variability, and evidence for recombination in their internal transcribed spacer profiles indicates that they are of recent origin and that their evolution is continuing. The likelihood of such evolutionary events may be increasing as world trade in plants intensifies. However, routine diagnostic procedures currently in use are insufficiently sensitive to allow their detection.

Biological Evolution↗
PubMed2004

Ultrafast 2D NMR spectroscopy using a continuous spatial encoding of the spin interactions.

A new protocol for acquiring multidimensional NMR spectra within a single scan is introduced and illustrated. The approach relies on applying a pair of frequency-chirped excitation and storage pulses in combination with echoing magnetic field gradients, in order to impart the kind of linear spatial encoding of the NMR interactions that is required by ultrafast 2D NMR spectroscopy. It is found that when dealing with 2D NMR experiments involving a t1 amplitude-modulation of the spin evolution, such continuous encoding scheme presents a number of advantages over alternatives employing discrete excitation pulses. From an experimental standpoint this is mainly reflected by the use of a single pair of bipolar gradients during the course of the indirect-domain encoding, as opposed to the numerous (and more intense) gradient echoes required so far. In terms of the spectral outcome, main advantages of the continuous spatial encoding scheme are the avoidance of "ghost peaks" and of "enveloping effects" associated to the discrete excitation mode. The principles underlying this new spatial encoding protocol are derived, and its applicability is demonstrated with homo- and heteronuclear 2D ultrafast NMR applications on small molecule and on protein samples.

Carbon Isotopes↗
PubMed2006

Conversion from calcineurin inhibitors to everolimus in kidney transplant recipients with malignant neoplasia.

Cancer has been reported to be more common among kidney transplant recipients than waiting-list patients or the general population. Use of anticalcineurin agents and azathioprine are relevant risk factors. Nine renal allograft recipients (seven men and two women) of mean age 67.6 (55-77) years and mean time after transplantation of 30.7 (58-216) months were switched to everolimus-based immunosuppression because of the presence of biopsy-proven malignancies (eight patients) or neurological tacrolimus toxicity (one patient). One patient with posttransplant lymphoproliferative disease also received chemotherapy with a good evolution at 6 months. He showed an initial increase in the protein to creatinine ratio (peak 3.3 mg/mg at 3 months) that was controlled by increasing the enalapril dose. One patient with skin cancer and severe atheromatosis (baseline SCr 2.5 mg/dL, creatinine clearance 17 mL/min, and protein to creatinine ratio 3.2 mg/mg), had cyclosporine and everolimus overlapped for 25 days, showing a continued poor evolution requiring dialysis initiation at 3 months after switch. The other six patients with recurrent skin cancers had good cancer evolution, with no new skin tumors and regression of skin lesions in three, including not biopsied actinic keratosis. Sudden switching from calcineurin inhibitors to everolimus is safe and may be used in long-term transplant recipients with malignancies. In patients with advanced chronic nephropathy this approach appeared to be less beneficial.

Aged↗
PubMed2004

Quantum random walks and piecewise deterministic evolutions.

In the continuous space and time limit, we show that the probability density to find the quantum random walk (QRW) driven by the Hadamard "coin" solves a hyperbolic evolution equation similar to the one obtained for a random two-velocity evolution with spatially inhomogeneous transition rates between the velocity states. In spite of the presence of a nonlinear drift term, it is remarkable that the QRW position can easily be described in simple analytical terms. This allows us to derive the quadratic time dependence of the variance typical for the QRW.

Journal Article↗
PubMed2003

Ileal pouch-anal anastomosis for ulcerative colitis and familial adenomatous polyposis: historical development and current status.

In summary, the history and development of the proctocolectomy and ileal pouch-anal anastomosis has involved innovative animal and clinical research by several surgical investigators. This evolution followed the classic process of academic surgical progress: a clinical problem is identified; solutions are studied in the laboratory; and these solutions are applied back to the clinical situation with success. Dr. Sabiston's disappointment with clinical results in ulcerative colitis and familial polyposis patients led to laboratory experiments in which a new technique was shown safe in dogs. The further work of his collaborator Dr. Ravitch as well as that of Sir Alan Parks and Dr. Utsunoimya proved small-scale clinical application of the new technique. Finally, large-scale outcomes work by Dr. Fazio at the Cleveland Clinic Foundation and others has allowed further refinements to occur and has highlighted other areas to study. The work of these investigators and other has allowed lack of a permanent ostomy with satisfactory functional results in more than 95% of patients. Continued experience with these procedures has and will lead to further improvements in operative times, morbidity rates, and functional results. Although research in this area will continue, the evolution of this operation has allowed it to become the gold standard for the treatment of ulcerative colitis and familial adenomatous polyposis.

Adenomatous Polyposis Coli↗
PubMed2005

Analysis of the human Alu Ye lineage.

BACKGROUND: Alu elements are short (approximately 300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30-50 million years ago. Alu elements are therefore a rich source of inter- and intra-species primate genomic variation. RESULTS: A total of 153 Alu elements from the Ye subfamily were extracted from the draft sequence of the human genome. Analysis of these elements resulted in the discovery of two new Alu subfamilies, Ye4 and Ye6, complementing the previously described Ye5 subfamily. DNA sequence analysis of each of the Alu Ye subfamilies yielded average age estimates of approximately 14, approximately 13 and approximately 9.5 million years old for the Alu Ye4, Ye5 and Ye6 subfamilies, respectively. In addition, 120 Alu Ye4, Ye5 and Ye6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity. CONCLUSION: The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Detailed sequence analysis of several Alu pre-integration sites indicated that multiple types of events had occurred, including gene conversions, near-parallel independent insertions of different Alu elements and Alu-mediated genomic deletions. A potential hotspot for Alu insertion in the Fer1L3 gene on chromosome 10 was also identified.

Alu Elements↗
PubMed1963

On biochemical variability and innovation.

Examples of variability and apparent innovation presented in this paper are but a portion of the many examples in the literature. Thus, the notion of the "unity of biochemistry" has been advanced in an overly simplified form and reflects a primitive stage in the development of the discipline. Cells contain many more compounds and biosynthetic mechanisms than we had suspected or list in our texts. Accordingly, either early chemical evolution was far more extensive than we have postulated or an evolution of biochemical synthesis and function took place which was more extensive than has been postulated; perhaps both have occurred. The chemical choices available from the environment have been considerable rather than limited and the cells have chosen, adapted, improved upon a limited number of these, and in turn have themselves been selected. In the case of the naturally occurring antibiotic substances, biosynthetic mechanisms for compounds which do not fit within the cells' own nucleic acids and proteins to advantage have nevertheless been preserved since they contribute to survival. On the other hand, some of these compounds such as alpha-ribazole, are fitted to other metabolic uses. The existence of the large number of uncommon relatives of the common components of the nucleic acids and proteins in turn implies an enormous untapped area of potential knowledge concerning their paths of biosyntheses and the genetic and physiological controls for these same paths. That these compounds exist perhaps also indicates an expanded material basis for a continuing biochemical evolution.

Biochemical Phenomena↗
PubMed2006

An unusual mode of concerted evolution of the EGF-TM7 receptor chimera EMR2.

The epidermal growth factor (EGF)-TM7 receptors CD97, EMR1, EMR2, EMR3, and EMR4 form a group of adhesion class heptahelical molecules predominantly expressed by cells of the immune system. These receptors bind cellular ligands through EGF-like domains, localized N-terminal to a large extracellular region. Remarkably, EMR2 possesses a chimeric structure with a seven-span transmembrane (TM7) region most related to EMR3 and an EGF domain region nearly identical to CD97. By comparing EGF-TM7 receptors in primates and dogs, we identified an intriguing pattern of concerted evolution, apparently mediated by gene conversion, among EMR2 and the oppositely orientated and physically adjacent genes CD97 and EMR3. This concerted evolution has continuously maintained the chimeric structure of EMR2 since early mammal radiation. Most highly conserved between EMR2 and CD97 is the fourth EGF domain, which mediates binding to chondroitin sulfate, a ligand specificity shared by both receptors. Another ligand, CD55, is bound effectively only by CD97. We show that different molecular mechanisms (mutations vs. alternative splicing) prevent CD55 binding by EMR2 in hominoids. Our findings illustrate how various and partially opposing evolutionary events have shaped the structure and ligand specificity of a modern mammalian gene family.

Amino Acid Sequence↗
PubMed2003

Alu elements and hominid phylogenetics.

Alu elements have inserted in primate genomes throughout the evolution of the order. One particular Alu lineage (Ye) began amplifying relatively early in hominid evolution and continued propagating at a low level as many of its members are found in a variety of hominid genomes. This study represents the first conclusive application of short interspersed elements, which are considered nearly homoplasy-free, to elucidate the phylogeny of hominids. Phylogenetic analysis of Alu Ye5 elements and elements from several other subfamilies reveals high levels of support for monophyly of Hominidae, tribe Hominini and subtribe Hominina. Here we present the strongest evidence reported to date for a sister relationship between humans and chimpanzees while clearly distinguishing the chimpanzee and human lineages.

Alu Elements↗