Molecular Evolution

Genome architecture is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large.

A gene is the entire nucleic acid sequence that is necessary for the controlled production of its final product (RNA or Protein). The basic unit of genome architecture is gene these correspond to specific regions in chromosomes (genome), these regions are further organized exons/introns, transcripts, promoter regions, Repetitive regions, Telomeres, centromeres, CpG Islands. In Prokaryotic most bacterial genomes are carried in one circular chromosome Stable replication requires one replication origin (ORI) The Genome is packed with polyamines (stabilizing proteins), In Eukaryotic: The genome is distributed over several linear chromosomes Stable replication occurs from several replication origins within each chromosome, and additionally requires centromeres, Telomeres.

Chromosomes are the units of inheritance within the nuclei of all eukaryote cells. The idea of evolution as a principle for the origin of biodiversity fits all phenomena of life, including the carriers of nuclear inheritance, the chromosomes. Insights into the evolutionary mechanisms that contribute to the shape, size, composition, number and redundancy of chromosomes elucidate the high plasticity of nuclear genomes at the chromosomal level, and the potential for genome modification in the course of breeding processes. The many genetic engineering successes indicates that there is little effect of chromosomal location, providing the gene and its cis-acting regulatory machinery are transplanted together.

DNA sequences is presented for use in phylogenetic estimation. A Markov process is used to describe substitutions between codons. Transition/transversion rate bias and codon usage bias are allowed in the model, and selective restraints at the protein level are accommodated using physicochemical distances between the amino acids coded for by the codons. Analyses of two data sets suggest that the new codon-based model can provide a better fit to data than can nucleotide-based models and can produce more reliable estimates of certain biologically important measures such as the transition/transversion rate ratio and the synonymous/nonsynonymous substitution rate ratio.

The transcriptome is the set of all RNA molecules, including mRNA, tRNA, rRNA and other non-coding RNA transcribed in one cell or a population of cells. It differs from the exome in that it includes only those RNA molecules found in a specified cell population, and usually includes the amount or concentration of each RNA molecule in addition to the molecular identities.

Conferences on Phylogenetic Tree are The 2^nd Systematic and Evolutionary Biology Conference (SEBC 2016) Nanjing, China- CP 2016, The 22^nd International Conference on Principles and Practice of Constraint Programming, Toulouse, France- Annual Scientific Retreat, UCLA, CA, USA- VIIIth Southern Connection Congress 2016, Punta Arenas, Chile- 18th International Conference on Veterinary and Biomedical Sciences, London, UK- BAMM-Biology and Mathematics through Medicine, Virginia, USA- ICTP-SAIFR School on Physics Applications in Biology, São Paulo, Brazil- Fourteenth Asia Pacific Bioinformatics Conference, CA, USA- Conference: Synthetic Biology, Paris, France- 7th Swedish Meeting on Mathematics in Biology, Uppsala University, Sweden.

Nucleic acid metabolism is the process by which nucleic acids (DNA and RNA) are synthesized and degraded. Nucleic acids are polymers of nucleotides. Nucleotide synthesis is an anabolic mechanism generally involving the chemical reaction of phosphate, pentose sugar, and a nitrogenous base. The ordered assembly of deoxyribonucleotides into DNA and of ribonucleotides into RNA involves somewhat simpler cellular mechanisms than the correct assembly of the amino acids in a protein chain.

The ribosome is a complex molecular machine found within all living cells that serves as the site of biological protein synthesis (translation). Ribosomes link amino acids together in the order specified by messenger RNA (mRNA) molecules. The ribosomes and associated molecules are also known as the  translational apparatus. The mitochondrion (plural mitochondria) is a double membrane-bound organelle found in most eukaryotic cells. Several characteristics make mitochondria unique. The number of mitochondria in a cell can vary widely by organism, tissue, and cell type.

Genome evolution is the process by which a genome changes in structure over time, through mutation, horizontal gene transfer, and sexual reproduction. The study of genome evolution involves multiple fields including structural analysis of the genome, genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics.

Darwin recognized the processes of speciation and the extinctions of species. We now understand many of the genome-scale processes occurring during evolution involving mutations, amplification, loss or homogenization of sequences; rearrangement, fusion and fission of chromosomes; and horizontal transfer of genes or genomes through polyploidy or other mechanisms. DNA sequence information, combined with appropriate informatic tools and experimental approaches including generation of synthetic hybrids, comparison of genotypes across environments, and modelling of genomic responses, is now letting us link genome behaviour with its consequences. The understanding of genome evolution will be of critical value both for conservation of the biodiversity of the plant kingdom and addressing the challenges of breeding new and more sustainable crops to feed the human population.

Molecular genetics is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. The result of a molecular genetic analysis is expressed in a genetic tree. Molecular genetics are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. Molecular genetics have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist. Here, we review the major methods of molecular genetic analysis, including parsimony, distance, likelihood and Bayesian methods.

The term molecular genetics sometimes refers to a fundamental theory alleging that genes direct all life processes through the production of polypeptides, sometimes to a more modest basic theory about the expression and regulation of genes at the molecular level, and sometimes to an investigative approach applied throughout biomedical science that is based on investigative strategies grounded in the basic theory about genes.

Proteins are the essential building blocks of living cells; indeed, life can be viewed as resulting substantially from the chemical activity of proteins. Because of their importance, it is hardly surprising that ancestors for most proteins observed today were already present at the time of the 'last common ancestor', a primordial organism from which all life on earth is descended. Proteins are strings of amino acids transcribed from genes, and they typically fold into a particular shape to perform some function in a living system. Proteins evolve when one amino acid is substituted for another.

Proteins are strings of amino acids transcribed from genes, and they typically fold into a particular shape to perform some function in a living system. Proteins evolve when one amino acid is substituted for another. Amino acid substitutions occur frequently as species evolve from a common ancestor. In 1965 Emil Zuckerkandl and Linus Pauling observed that the rate of change in the amino acid sequence of hemoglobin was linear in time across species. This led to the idea of a molecular clock, or constant underlying rate of change that characterizes the evolution of a protein.

Molecular oncology is an interdisciplinary medical speciality at the interface of medicinal chemistry and oncology that refers to the investigation of the chemistry of cancer and tumors at the molecular scale along with the development and application of molecularly targeted therapies. Evolving molecular techniques used in the clinical laboratory are becoming increasingly important across nearly all fields of medicine.

In molecular oncology are identified genes that are involved in the development of cancer. The researches combine diverse techniques ranging from genomics, computational biology, tumor imaging, in vitro and in vivo functional models to study biological and clinical phenotypes. The proteins produced by these genes may serve as targets for novel chemotherapy drugs and other cancer treatments, or imaging scans. Scientists use a range of techniques to validate the role of the novel candidate genes in the development of cancer. The ultimate aim is to translate these findings into improved treatment options for cancer patients.

Depending on the relative importance assigned to the various forces of evolution, three perspectives provide evolutionary explanations for molecular evolution. Selectionist hypotheses argue that selection is the driving force of molecular evolution. Neutralist hypotheses emphasize the importance of mutation, purifying selection, and random genetic drift. Mutationists hypotheses emphasize random drift and biases in mutation patterns.

Life on this earth simply did not start out with animals. All the life on earth started from the primordial ooze where inorganic molecules produced organic molecules, organic molecules formed bigger molecules, and, eventually organic molecules hang together inside membranes. This leads to cell-like structures and then cells. Simpler cells lead to more complex cells. Eventually, and it did take a while, we get the cells that make up animals.

All animals and plants are classified as multicellular eukaryotes: their bodies are made up of large numbers of cells, and microscopic inspection of these cells reveals that they contain a nucleus and a number of other organelles. Compared to prokaryotic organisms such as bacteria, plants and animals have a relatively recent evolutionary origin. DNA evidence suggests that the first eukaryotes evolved from prokaryotes, between 2500 and 1000 million years ago. That is, eukaryotes as a taxon date from the Proterozoic Era, the final Era of the Precambrian. Fossils of both simple unicellular and more complex multicellular organisms are found in abundance in rocks from this period of time. In fact, the name "Proterozoic" means "early life".

Genome data have revealed great variation in the numbers of genes in different organisms, which indicates that there is a fundamental process of genome evolution: the origin of new genes. However, there has been little opportunity to explore how genes with new functions originate and evolve. The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes. Current knowledge of the origin of new genes encompasses information regarding both protein-coding genes and RNA genes. All of these genes are transcribed, but only protein-coding genes are translated into proteins. New gene origination is a driving force of evolutionary innovation in all organisms. Recent research has focused on identifying the mechanisms that generate new genes, and scientists have found that these mechanisms involve a variety of molecular events, all of which must occur in the germ line to be inherited by the next generation. After the germ-line mutational event, the new gene (e.g., a new gene duplicate located on human chromosome 2) will be polymorphic in the population; in other words, not all second chromosomes in the population will carry the duplication. Subsequently, the two most likely outcomes for the new gene are fixation.

Conferences on Origin of New Genes are CP 2016, The 22^nd International Conference on Principles and Practice of Constraint Programming, Toulouse, France- The 2^nd Systematic and Evolutionary Biology Conference (SEBC 2016) Nanjing, China- 7th Swedish Meeting on Mathematics in Biology, Uppsala University, Sweden- Annual Scientific Retreat, UCLA, CA, USA- VIIIth Southern Connection Congress 2016, Punta Arenas, Chile- 18th International Conference on Veterinary and Biomedical Sciences, London, UK- BAMM-Biology and Mathematics through Medicine, Virginia, USA- ICTP-SAIFR School on Physics Applications in Biology, São Paulo, Brazil- Fourteenth Asia Pacific Bioinformatics Conference, CA, USA- Conference: Synthetic Biology, Paris, France.

Molecular Phylogentics is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships.   The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and     the demographic changes and migration patterns of species. Phylogenies have permeated nearly every branch of biology, and the plethora of phylogenetic methods and software packages that are now available may seem daunting to an experimental biologist.