Evolution of higher-organism DNA

A great deal of information about evolutionary events and processes has been inferred from careful studies of fossil records. Other forms of evidence have also contributed greatly to the understanding of evolution. Comparative biochemistry (Florkin, 1949), immunology (Boyden, 1942), protein sequencing (Dayoff, 1969; Anfinsen, 1959), and early DNA studies (McCarthy & Bolton, 1963; Schildkraut, Marmur & Doty, 1961) have for the most part corroborated earlier evolutionary findings, and at the same time provided new understanding of molecular processes in evolution. Of these approaches the comparison of DNA seems most promising since a relatively precise quantitative comparison can be made of all of the genetic material of different species.

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AUGmenting the proteome: Novel initiation codons and their role in protein isoform generation

The Biochemist ◽

10.1042/bio03702019 ◽

2015 ◽

Vol 37 (2) ◽

pp. 19-23

Author(s):

Mark J. Coldwell ◽

Joanne L. Cowan

Keyword(s):

Alternative Splicing ◽

Translation Initiation ◽

Messenger Rna ◽

Genetic Material ◽

Protein Sequencing ◽

Protein Isoforms ◽

Alternative Promoters ◽

Alternative Translation ◽

Initial Hypothesis ◽

Protein Isoform

As the field of molecular biology developed, and the understanding of how inherited genetic material results in the expression of proteins was established, the initial hypothesis was that one gene gave rise to one protein1. As researchers delved deeper into the organization of the genetic code and advances in messenger RNA (mRNA) and protein sequencing were subsequently made, it has become abundantly clear that multiple mechanisms exist meaning that many mRNAs encode more than one version of a protein. Although alternative promoters and alternative splicing play a considerable role in the generation of protein isoforms, in this article we discuss how usage of alternative translation initiation codons in eukaryotes can also lead to an expanded proteome.

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Autonomous variability: phenomenon and possible mechanisms

Ecological genetics ◽

10.17816/ecogen223-10 ◽

2004 ◽

Vol 2 (2) ◽

pp. 3-10

Author(s):

Oleg N Tikhodeyev ◽

Tatyana V Zhurina

Keyword(s):

Developmental Stage ◽

Environmental Influences ◽

Genetic Material ◽

Molecular Processes

The present paper is devoted to autonomous variation. It is shown that such type of variation is determined by entirely stochastic molecular processes. Therefore it can't be reduced to other types of variation that depend on some differences in genetic material, developmental stage or environmental influences. Certain examples of autonomous variation in plants and animals are observed. The possible mechanisms of this variation are discussed.

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New uses for new phylogenies

European Review ◽

10.1017/s106279870000034x ◽

1993 ◽

Vol 1 (1) ◽

pp. 11-19 ◽

Cited By ~ 6

Author(s):

Paul H. Harvey ◽

Sean Nee

Keyword(s):

Molecular Structure ◽

Statistical Methods ◽

Common Ancestor ◽

Genetic Material ◽

Evolutionary Relationships ◽

Evolutionary Trees ◽

Living Species ◽

Molecular Phylogenies ◽

Fossil Records ◽

Ancestral Character States

Comparison of the molecular structure of genetic material from living species reveals evolutionary relationships, and estimates of dates when pairs of species last shared a common ancestor. The resulting evolutionary trees, which are accumulating rapidly in the literature to complement those trees produced from fossil records, can be used to reveal hitherto unsuspected patterns in the evolutionary record. In particular, the trees can be analysed to show when rates of speciation and extinction were abnormally high or low. Together with estimates of ancestral character states and environments, these data throw new light on the reasons for speciation and extinction. This article describes how statistical methods are being developed and used to analyse molecular phylogenies.

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Toward an alignment of the actin molecule within the actin filament

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100075981 ◽

1983 ◽

Vol 41 ◽

pp. 450-451

Author(s):

P.R. Smith ◽

W.E. Fowler ◽

U. Aebi

Keyword(s):

Actin Filament ◽

Diffraction Data ◽

Quantitative Estimate ◽

Molecular Model ◽

Quantitative Comparison ◽

Regulatory Proteins ◽

Essential Information ◽

X Ray ◽

Maximum Resolution ◽

Lack Of Information

An understanding of the specific interactions of actin with regulatory proteins has been limited by the lack of information about the structure of the actin filament. Molecular actin has been studied in actin-DNase I complexes by single crystal X-ray analysis, to a resolution of about 0.6nm, and in the electron microscope where two dimensional actin sheets have been reconstructed to a maximum resolution of 1.5nm. While these studies have shown something of the structure of individual actin molecules, essential information about the orientation of actin in the filament is still unavailable.The work of Egelman & DeRosier has, however, suggested a method which could be used to provide an initial quantitative estimate of the orientation of actin within the filament. This method involves the quantitative comparison of computed diffraction data from single actin filaments with diffraction data derived from synthetic filaments constructed using the molecular model of actin as a building block. Their preliminary work was conducted using a model consisting of two juxtaposed spheres of equal size.

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The quantitative comparison of experimental and simulated diffraction contrast images

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010013688x ◽

1995 ◽

Vol 53 ◽

pp. 102-103

Author(s):

Stuart McKernan

Keyword(s):

Image Processing ◽

Personal Computer ◽

Close Agreement ◽

Quantitative Comparison ◽

Image Simulation ◽

Computing Power ◽

Diffraction Contrast ◽

Simulated Images ◽

Made In

For many years the concept of quantitative diffraction contrast experiments might have consisted of the determination of dislocation Burgers vectors using a g.b = 0 criterion from several different 2-beam images. Since the advent of the personal computer revolution, the available computing power for performing image-processing and image-simulation calculations is enormous and ubiquitous. Several programs now exist to perform simulations of diffraction contrast images using various approximations. The most common approximations are the use of only 2-beams or a single systematic row to calculate the image contrast, or calculating the image using a column approximation. The increasing amount of literature showing comparisons of experimental and simulated images shows that it is possible to obtain very close agreement between the two images; although the choice of parameters used, and the assumptions made, in performing the calculation must be properly dealt with. The simulation of the images of defects in materials has, in many cases, therefore become a tractable problem.

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The zoonotic potential of bat-borne coronaviruses

Emerging Topics in Life Sciences ◽

10.1042/etls20200097 ◽

2020 ◽

Vol 4 (4) ◽

pp. 365-381

Author(s):

Ny Anjara Fifi Ravelomanantsoa ◽

Sarah Guth ◽

Angelo Andrianiaina ◽

Santino Andry ◽

Anecia Gentles ◽

...

Keyword(s):

Genetic Material ◽

Field Research ◽

Sympatric Species ◽

Animal Origin ◽

Mammalian Host ◽

Past Century ◽

The Past ◽

Novel Host ◽

Horseshoe Bat ◽

Human Infections

Seven zoonoses — human infections of animal origin — have emerged from the Coronaviridae family in the past century, including three viruses responsible for significant human mortality (SARS-CoV, MERS-CoV, and SARS-CoV-2) in the past twenty years alone. These three viruses, in addition to two older CoV zoonoses (HCoV-229E and HCoV-NL63) are believed to be originally derived from wild bat reservoir species. We review the molecular biology of the bat-derived Alpha- and Betacoronavirus genera, highlighting features that contribute to their potential for cross-species emergence, including the use of well-conserved mammalian host cell machinery for cell entry and a unique capacity for adaptation to novel host environments after host switching. The adaptive capacity of coronaviruses largely results from their large genomes, which reduce the risk of deleterious mutational errors and facilitate range-expanding recombination events by offering heightened redundancy in essential genetic material. Large CoV genomes are made possible by the unique proofreading capacity encoded for their RNA-dependent polymerase. We find that bat-borne SARS-related coronaviruses in the subgenus Sarbecovirus, the source clade for SARS-CoV and SARS-CoV-2, present a particularly poignant pandemic threat, due to the extraordinary viral genetic diversity represented among several sympatric species of their horseshoe bat hosts. To date, Sarbecovirus surveillance has been almost entirely restricted to China. More vigorous field research efforts tracking the circulation of Sarbecoviruses specifically and Betacoronaviruses more generally is needed across a broader global range if we are to avoid future repeats of the COVID-19 pandemic.

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