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Reconstruction of ancestral proteomes

Toni Gabaldón and Martijn A. Huynen

in Ancestral Sequence Reconstruction

Published in print:
2007
Published Online:
September 2008
ISBN:
9780199299188
eISBN:
9780191714979
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199299188.003.0012
Subject:
Biology, Evolutionary Biology / Genetics

The process of inferring the set of proteins that was likely encoded in the genome of an extinct organism is called Ancestral Proteome Reconstruction. This process usually involves the comparison of ... More


Symbiomics

Jan Sapp

in Genesis: The Evolution of Biology

Published in print:
2003
Published Online:
September 2007
ISBN:
9780195156195
eISBN:
9780199790340
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195156195.003.0019
Subject:
Biology, Evolutionary Biology / Genetics

This chapter discusses the concept of symbiosis. Although the bacteria living in our bodies have recently begun to attract some medical interest, for most of the 20th century symbiosis research had ... More


Organelle Genetics: Yeast and Chlamydomonas

Rowland H. Davis

in The Microbial Models of Molecular Biology: From Genes to Genomes

Published in print:
2003
Published Online:
April 2010
ISBN:
9780195154368
eISBN:
9780199893935
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780195154368.003.0014
Subject:
Biology, Biochemistry / Molecular Biology

This chapter begins with a discussion of the origins of yeast mitochondrial work. It then discusses the development of Chlamydomonas reinhardtii as a model organism. It also shows how early work on ... More


Membranes as sites of energy transduction Membranes as sites of energy transduction

Timothy J. Bradley

in Animal Osmoregulation

Published in print:
2008
Published Online:
April 2010
ISBN:
9780198569961
eISBN:
9780191728273
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198569961.003.0009
Subject:
Biology, Animal Biology

Because membranes are impermeable to most solutes, gradients can be established and maintained between intra- and extracellular compartments. These gradients serve as forms of energy storage that can ... More


Mitonuclear Ecology

Geoffrey E. Hill

Published in print:
2019
Published Online:
June 2019
ISBN:
9780198818250
eISBN:
9780191859465
Item type:
book
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198818250.001.0001
Subject:
Biology, Ecology, Evolutionary Biology / Genetics

Eukaryotes were born of a chimeric union of two prokaryotes. The legacy of this fusion is organisms with both a nuclear and mitochondrial genome that must work in a coordinated fashion to enable ... More


Evolution of the Cell

Franklin M. Harold

in On Life: Cells, Genes, and the Evolution of Complexity

Published in print:
2022
Published Online:
December 2021
ISBN:
9780197604540
eISBN:
9780197604571
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780197604540.003.0006
Subject:
Biology, Microbiology

Cells are life’s basic building blocks, and there is no more profound question than how they came to be. What made this murky subject accessible is the invention of methods to sequence nucleic acids ... More


Emergence of the Eukaryotes: The Second Mystery in Cell Evolution

Franklin M. Harold

in In Search of Cell History: The Evolution of Life's Building Blocks

Published in print:
2014
Published Online:
May 2015
ISBN:
9780226174143
eISBN:
9780226174310
Item type:
chapter
Publisher:
University of Chicago Press
DOI:
10.7208/chicago/9780226174310.003.0007
Subject:
Biology, Biochemistry / Molecular Biology

The origin of eukaryotic cells is a mystery second only to the origin of life itself. The problem is that eukaryotes make up a distinctive clade, conspicuously different from prokaryotes, yet they ... More


Symbionts into Organelles: Mitochondria, Plastids, and Their Kin

Franklin M. Harold

in In Search of Cell History: The Evolution of Life's Building Blocks

Published in print:
2014
Published Online:
May 2015
ISBN:
9780226174143
eISBN:
9780226174310
Item type:
chapter
Publisher:
University of Chicago Press
DOI:
10.7208/chicago/9780226174310.003.0008
Subject:
Biology, Biochemistry / Molecular Biology

Mitochondria and plastids are the workhorses of eukaryotic metabolism. It is outrageous but indisputably true that they evolved from endosymbiotic Bacteria during the genesis of eukaryotic ... More


Genetic Variation in Natural Populations

Fred W. Allendorf, W. Chris Funk, Sally N. Aitken, Margaret Byrne, and Gordon Luikart

in Conservation and the Genomics of Populations

Published in print:
2022
Published Online:
April 2022
ISBN:
9780198856566
eISBN:
9780191889912
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198856566.003.0003
Subject:
Biology, Biodiversity / Conservation Biology, Evolutionary Biology / Genetics

Genetic variation among individuals within populations and among populations can be assessed at the chromosomal, protein, or DNA sequence level. The best tool or approach depends on the question ... More


Physiological responses of marine invertebrates to thermal stress

Nia M. Whiteley and Clara L. Mackenzie

in Stressors in the Marine Environment: Physiological and ecological responses; societal implications

Published in print:
2016
Published Online:
May 2016
ISBN:
9780198718826
eISBN:
9780191788352
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198718826.003.0004
Subject:
Biology, Aquatic Biology, Ecology

Marine invertebrates display a tremendous range of thermal sensitivities and thermal tolerance limits, but they can all experience thermal stress at their upper thermal limits. Such limits are shaped ... More


Mutualisms and ecosystem-level processes

Nancy Collins Johnson

in Mutualism

Published in print:
2015
Published Online:
September 2015
ISBN:
9780199675654
eISBN:
9780191809422
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780199675654.003.0012
Subject:
Biology, Ecology, Evolutionary Biology / Genetics

Mutualism research generally focuses on communities and populations but exciting insights emerge when mutualisms are investigated from an ecosystem perspective. This chapter explores the ways that ... More


The genomic architecture of eukaryotes

Geoffrey E. Hill

in Mitonuclear Ecology

Published in print:
2019
Published Online:
June 2019
ISBN:
9780198818250
eISBN:
9780191859465
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198818250.003.0001
Subject:
Biology, Ecology, Evolutionary Biology / Genetics

Eukaryotes are chimeras—the product of an ancient fusion of a bacterium and an archaeon. Mitochondrial genomes only code for a few dozen products, so more than 1000 nuclear genes create most of the ... More


Oxygen: boon yet bane—introducing oxygen toxicity and reactive species

Barry Halliwell and John M.C. Gutteridge

in Free Radicals in Biology and Medicine

Published in print:
2015
Published Online:
October 2015
ISBN:
9780198717478
eISBN:
9780191802133
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/acprof:oso/9780198717478.003.0001
Subject:
Biology, Biochemistry / Molecular Biology, Disease Ecology / Epidemiology

This chapter explains how oxygen (O2) came to be present in the Earth’s atmosphere (the evolution of photosynthesis), the changes in O2 levels that occurred during the Earth’s history, and how they ... More


Microbiome

Jonathon Keats

in Virtual Words: Language on the Edge of Science and Technology

Published in print:
2010
Published Online:
November 2020
ISBN:
9780195398540
eISBN:
9780197562826
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780195398540.003.0006
Subject:
Computer Science, Programming Languages

Sequencing the 3.2 billion base pairs of the human genome took thirteen years and cost $3 billion. Yet even before the genome was released in 2003, scientists were beginning to question whether an ... More


Markov Random Fields On Undirected Graphs

Ulf Grenander and Michael I. Miller

in Pattern Theory: From representation to inference

Published in print:
2006
Published Online:
November 2020
ISBN:
9780198505709
eISBN:
9780191916564
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198505709.003.0005
Subject:
Computer Science, Programming Languages

This chapter focuses on random fields on lattices and undirected graphs. Discrete finite state spaces are examined in the context of Markov and Gibbs fields. The ... More


Dendritic Spines

Christof Koch

in Biophysics of Computation: Information Processing in Single Neurons

Published in print:
1998
Published Online:
November 2020
ISBN:
9780195104912
eISBN:
9780197562338
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780195139853.003.0018
Subject:
Computer Science, Mathematical Theory of Computation

Dendritic spines, sometimes also called dendritic thorns, are tiny, specialized protoplasmic protuberances that cover the surface of many neurons. First described by Ramón y Cajal (1909; 1991) in ... More


Information Bounds For Automated Object Recognition

Ulf Grenander and Michael I. Miller

in Pattern Theory: From representation to inference

Published in print:
2006
Published Online:
November 2020
ISBN:
9780198505709
eISBN:
9780191916564
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780198505709.003.0016
Subject:
Computer Science, Programming Languages

Examine information bounds for understanding rigid object recognition involving the low-dimensional matrix groups. Minimum-mean-squared error bonds and mutual ... More


Diffusion in Biological Systems

W. Mark Saltzman

in Drug Delivery: Engineering Principles for Drug Therapy

Published in print:
2001
Published Online:
November 2020
ISBN:
9780195085891
eISBN:
9780197560501
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780195085891.003.0009
Subject:
Chemistry, Medicinal Chemistry

Drug diffusion is an essential mechanism for drug dispersion throughout biological systems. Diffusion is fundamental to the migration of agents in the body and, as we will see in Chapter 9, ... More


Roots, Shoots, Leaves, and Grapes

David R. Dalton

in The Chemistry of Wine: From Blossom to Beverage and Beyond

Published in print:
2018
Published Online:
November 2020
ISBN:
9780190687199
eISBN:
9780197559802
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780190687199.003.0015
Subject:
Chemistry, Organic Chemistry

As noted earlier and as anticipated by Charles and Francis Darwin it has been argued that plants sense the direction of gravity (gravitropism) by movement of starch granules found in cells called ... More


One Final Word: Sex

Mary Jane West-Eberhard

in Developmental Plasticity and Evolution

Published in print:
2003
Published Online:
November 2020
ISBN:
9780195122343
eISBN:
9780197561300
Item type:
chapter
Publisher:
Oxford University Press
DOI:
10.1093/oso/9780195122343.003.0039
Subject:
Earth Sciences and Geography, Palaeontology: Earth Sciences

Sex transforms life. It affects morphology and behavior. It diverts enormous amounts of time and energy from the business of survival. It can even distract ... More


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