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Chapter 1
Cells, Genomes, and Evolution

What are Cells?
Cells are the smallest and basic units of life, whether it is a single cell that forms the entire organism, e.g., in a bacterium, or trillions of…
The Tree of Life - Bacteria, Archaea, Eukaryotes
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the…
Prokaryotic Cells
Prokaryotes are small unicellular organisms that include the domains — Archaea and Bacteria. Bacteria include many common microorganisms, such…
Eukaryotic Compartmentalization
One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles, such as the nucleus and mitochondria, that…
Eukaryotic Evolution
The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to…
Animal and Plant Cell Structure
Animal and plant cells not only differ in their structure, function, and mode of nutrition but also in how they reproduce, specialize, and organize…
Cytoplasm
The cytoplasm consists of organelles and a framework of protein scaffolds called the cytoskeleton suspended in an aqueous solution, the cytosol. The…
The Nucleus
The nucleus is a membrane-bound organelle that acts as a control center in a eukaryotic cell. It contains chromosomal DNA, which controls gene…
The DNA Helix
Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most…
The Central Dogma
The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins. RNA is the Missing Link…
Mutations
Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors.…
Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One…
Gene Families
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or…
Gene Evolution - Fast or Slow?
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do…
Types of Genetic Transfer Between Organisms
Genetic transfer occurs when genetic information is passed from one organism to another. It occurs via two mechanisms: vertical gene transfer and…
Quantitative Approaches for Studying Cellular Structures and Organelle Morphology in <em>Caenorhabditis elegans</em>
Defining the cellular mechanisms underlying disease is essential for the development of novel therapeutics. A strategy frequently used to unravel…
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Distilling and reporting large datasets, such as whole genome or transcriptome data, is often a daunting task. One way to break down results is to…
Genetic Modification of Cyanobacteria by Conjugation Using the CyanoGate Modular Cloning Toolkit
Cyanobacteria are a diverse group of prokaryotic photosynthetic organisms that can be genetically modified for the renewable production of useful…

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