Life at High Pressure: In the Deep Sea and Other Environments

Foreword
Preface
Contents
1: High Pressure and High-Pressure Environments
	1.1 High-Pressure Environments
		1.1.1 Measuring Pressure
			Box 1.1 Units Used to Measure Pressure
		1.1.2 Negative Pressure
	1.2 The Deep Ocean
		1.2.1 The Ocean Depths and Their Inhabitants
		1.2.2 Freshwater Lakes and Ice
	1.3 The Deep Biosphere
		1.3.1 Oceanic Crust
		1.3.2 Continental Crust
	1.4 High-Pressure Joints
	1.5 The Modern Classification of Organisms
		Box 1.2
	References
2: High Pressure: Molecules, Chemical Process and Cellular Structures
	2.1 Water, Dissolved Salts and Proteins
		Box 2.1: Viscosity
	2.2 Chemical Reactions in Solution, at High Pressure
		2.2.1 Equilibria
			Box 2.2: Effect of Pressure on Dissociation
		2.2.2 Rates of Reaction
			2.2.2.1 Simple Reactions, Not Involving an Enzyme
			2.2.2.2 Enzyme Catalysed Reactions
				Box 2.3: Measuring an Activation Volume (DeltaV*) and an Equilibrium Volume (DeltaV)
	2.3 The Affinity of an Enzyme for Its Substrate
		Box 2.4: Measuring How High Pressure Affects the Affinity of an Enzyme for Its Substrate
	2.4 Cells Under High Pressure
		2.4.1 Cell Membranes
			Box 2.5: Measuring the Fluidity of Lipid Bilayers at High Pressure
		2.4.2 Cytoplasm
			Box 2.6: Cytoplasm Under High Pressure
		2.4.3 Cell Organelles
	2.5 Prokaryotes
	2.6 Proteins
		2.6.1 Actin
		2.6.2 Tubulin
			Box 2.7: Mitosis
		2.6.3 A Special Enzyme, ATP Synthase
			2.6.3.1 The ATP Synthase Under High Pressure
	References
3: The High Pressure Micro-environment of Vertebrate Load Bearing Joints
	3.1 Introduction
	3.2 Micro-pressures
	3.3 Load Bearing Joints; Cartilage and Bone Cells Exist in Pressurised Environments
		3.3.1 Bone
	3.4 Experiments with Chondrocytes
		3.4.1 The Response of Chondrocytes in Their Matrix to Physiological Pressures
	3.5 Does High Hydrostatic Pressure Cause Pathological Effects?
	3.6 Conclusion
	References
4: Effects of High Pressure on the Activity of Ordinary Animals, Including Humans, and on the Function of Their Excitable Cell...
	4.1 Early and Modern Observations, Mostly on Invertebrates
		Box 4.1: The Problem of Very Small Hydrostatic Pressures
	4.2 Effects of Pressure on the Activity of Fish
	4.3 Effects of Pressure on the Activity of Air-Breathing Vertebrates
		4.3.1 The Pressure Tolerance of Aquatic and Air-Breathing Vertebrates
		4.3.2 HPNS
		4.3.3 Free Escape from Submarines
	4.4 Reflexes
	4.5 Excitable Membranes
		4.5.1 Effects of Pressure on Isolated Neurons
			Box 4.2: The Resting Potential
		4.5.2 Measuring Ionic Currents by Different Methods
		4.5.3 How High Pressure Affects Excitable Membranes
			4.5.3.1 Single Channel Recording at High Pressure
	4.6 Effects of Pressure on Synapses
		Box 4.3: The Working Synapse
		Box 4.4
	4.7 Post Script
	4.8 Conclusion
	References
5: The Effects of Decompression and Subsequent Re-compression on the Activity of Deep-Sea Animals and Eukaryote Cells. The Iso...
	5.1 Deep-Sea Amphipods
		5.1.1 Amphipods Collected with Decompression
		5.1.2 Amphipods from Lake Baikal
	5.2 The Isobaric Collection of Deep-Sea Animals: Retrieval Without Decompression
		5.2.1 The Isobaric Trap
		5.2.2 Other Isobaric Collections
		5.2.3 When to Use Isobaric Collecting Equipment?
		5.2.4 The Isobaric Collection of Deep-Sea Fish
	5.3 Resuscitation of Animals and Their Tissues from the Effects of Hydraulic Decompression
		5.3.1 The Resuscitation of Deep-Sea Fish by High Pressure
			5.3.1.1 Fish from Lake Baikal
		5.3.2 The Resuscitation of Isolated Fish Tissue by High Pressure
			5.3.2.1 Fish Swimming Muscle
			5.3.2.2 Fish Heart Muscle
		5.3.3 Fish Neurons
	5.4 The Tolerance of Other Deep-Sea Animals to Decompression
		5.4.1 Animals from Great and Moderate Depths
		5.4.2 The Antioxidative Defences of Deep-Sea Animals
		5.4.3 Deep-Sea Fish Cells and Tissues In Vitro
	5.5 Other Deep-Sea Animals
	5.6 Microbial Eukaryotes
		5.6.1 Protists
		5.6.2 Fungi
	5.7 Conclusion
	References
6: Molecular Adaptation to High Pressure: Proteins in Deep-Sea Animals
	6.1 Protein Adaptation
		6.1.1 Intrinsic Adaption of Proteins to High Pressure
			6.1.1.1 Structural Proteins
			6.1.1.2 Enzymes
			6.1.1.3 Visual Pigments
				Box 6.1 Opsins
	6.2 Extrinsic Adaptation of Proteins to High Pressure
		6.2.1 Pressure Protection
		6.2.2 Compatible Solutes
		6.2.3 TMAO in Deep-Sea Animals
		6.2.4 Some Implications of the Extrinsic Adaptation of Proteins to High Pressure
	6.3 How Does TMAO Counteract the Effects of High Pressure on Proteins?
	6.4 Conclusions
	References
7: Molecular Adaptation to High Pressure: Membranes
	7.1 Homeoviscous Adaptation
	7.2 Membranes from Deep-sea Fish
		7.2.1 The Fluidity of the Lipid Bilayer in Deep-sea Fish Membranes
		7.2.2 The Lipid Composition of Deep-sea Fish Membranes
	7.3 Homeoviscous Adaptation in the Membranes of Deep-sea Bacteria
		7.3.1 Some Physiological Functions Related to the Membranes of Marine Bacteria
	7.4 Bacteria in the Deep Biosphere
		7.4.1 Sample Collection
		7.4.2 Membrane Lipids in Bacteria From the Deep Biosphere
	7.5 Homeoviscous Adaptation: Other Aspects
	7.6 Do Shallow Water Cells Show Homeoviscous Adaptation When Exposed to High Pressure?
	References
8: Prokaryotes at High Pressure in the Oceans and Deep Biosphere
	8.1 Microorganisms in the Deep Sea and Their Collection
	8.2 Effects of Decompression on Deep-Sea Bacteria
		8.2.1 Bacteria Decompressed During Collection and Recompressed
		8.2.2 Isobaric Samples
		8.2.3 Bacteria from the Hadal Zone
	8.3 Growing Bacteria at High Pressure
		8.3.1 Continuous Culture Methods
	8.4 Pressure Experienced by Sinking Particles
	8.5 Eukaryotic Microorganisms
	8.6 Viruses
	8.7 Microorganisms in the Deep Biosphere
		8.7.1 The Presence and Activity of Microorganisms in the Deep Biosphere
		8.7.2 Growth in High-Pressure Gases
		8.7.3 High Partial Pressures of Helium, Hydrogen and Methane
		8.7.4 Gases Important in the Deep Biosphere
	8.8 Isobaric Samples from the Deep Biosphere
		8.8.1 CORKs and FLOCS
		8.8.2 Pollution in Deep Environments: Hydrocarbons and Other Toxic Compounds
	8.9 Adaptations of the Enzymes of Deep Sea and Deep Biosphere Microorganisms to High Pressure
		8.9.1 Intrinsic Adaptation of Microbial Proteins to High Pressure
		8.9.2 Extrinsic Adaptations of Proteins
	8.10 Conclusion
	References
9: Hydrothermal Vents: The Inhabitants, Their Way of Life and Their Adaptation to High Pressure
	9.1 Hydrothermal Vents: Physical Conditions
	9.2 Geobiochemistry and the Origin of Life
		Box 9.1 Extraterrestrial Life
	9.3 The Inhabitants of the Vent Sites
		9.3.1 Animals
			9.3.1.1 The Tubeworm Riftia
			9.3.1.2 Other Worms
			9.3.1.3 Crabs and Mussels
			9.3.1.4 Shrimps
			9.3.1.5 Fish
		9.3.2 Microorganisms
			9.3.2.1 Eukaryote Microorganisms
			9.3.2.2 Protists
	9.4 Prokaryotes
		9.4.1 Archaea
		9.4.2 Bacteria
			9.4.2.1 Bacteria Growing on Substrates
			9.4.2.2 Bacteria in Water Samples
	9.5 Viruses and Other Mobile Genetic Elements
	9.6 Homeoviscous Adaptation in Hydrothermal Vent Organisms
		9.6.1 Animals
		9.6.2 Bacteria
		9.6.3 Archaea
			9.6.3.1 Archaeal Lipids
			9.6.3.2 Methanococcus janaschii
			9.6.3.3 Thermococcus barophilus
	9.7 The Dispersal from, and the Colonisation of, Hydrothermal Vents
		9.7.1 Dispersal from Hydrothermal Vents
		9.7.2 Abyssal and Benthic Animals Also Produce Planktonic Larva
		9.7.3 Pelagic Adults and Larvae
		9.7.4 Colonisation
	References
10: Buoyancy at Depth
	10.1 Densities of Sea Water and Cell Constituents
	10.2 Small Planktonic Organisms
	10.3 Buoyancy in Larger Animals Living at Significant Pressures
		10.3.1 Ionic Regulation in Bathypelagic Squid
	10.4 Gas Phase Buoyancy
		10.4.1 Cephalopods
			Box 10.1 Solute Coupled Water Transport in Nautilus
		10.4.2 The Gas-Filled Swim Bladder of Bony Fishes
			Box 10.2 Hydrostatic pressure affects gas solubility
		10.4.3 Other Functions of the Swim Bladder
	10.5 Buoyancy Provided by Oil and Lipid
		10.5.1 The Sperm Whale
		10.5.2 Fish Buoyed by Oil and Lipids
			10.5.2.1 Cartilaginous Fish
			10.5.2.2 Bony Fish
	References
11: Divers: Air-Breathing Animals, Including Humans, at High Pressure
	11.1 Breath-Hold Diving
		11.1.1 Humans
		11.1.2 Specialised Deep-Diving Birds and Mammals
	11.2 Deep-Diving Lungs Under Pressure
		11.2.1 Consequences of Gas Dissolved in Tissues Under Pressure
			11.2.1.1 Nitrogen
			11.2.1.2 Oxygen
	11.3 Pressure Effects on Some Cells in Diving Animals
		11.3.1 Muscle Enzymes
		11.3.2 Red Cells
		11.3.3 Platelets
		11.3.4 Excitable Cells
	11.4 Human Diving Supported by a Self-Contained Gas Supply
		11.4.1 Gases Breathed at High Pressure
		11.4.2 Oxygen
		11.4.3 Nitrogen and Other Anaesthetic Inert Gases
			11.4.3.1 Anaesthesia and Inert Gas Narcosis Are Reversed by Pressure
				Box 11.1
	11.5 The High-Pressure Neurological Syndrome, HPNS
	11.6 Decompression
	11.7 Conclusion
	References
12: Adaptation to High Pressure in the Laboratory
	12.1 Microorganisms
		12.1.1 Escherichia coli
		12.1.2 Other Examples of Organisms Surviving Very High Pressures
		12.1.3 Photobacterium profundum
		12.1.4 Other Microorganisms
		12.1.5 Yeast, Saccharomyces sp., a Eukaryote Microorganism
	12.2 Animals
		12.2.1 Shallow Water Animals
			12.2.1.1 The Design of Experiments Eliciting Stress Responses and the Expression of Other Genes
		12.2.2 Animals from Deeper Water: Acclimation to Atmospheric Pressure
		12.2.3 Genetic Adaptation
		12.2.4 The Eel, Anguilla anguilla
	12.3 Conclusion
	References
13: High-Pressure Equipment for Use in the Laboratory, at Sea and at Depth
	13.1 Generating High Pressure
		13.1.1 Pumps
		13.1.2 Generating Pressure by Centrifugation
	13.2 High-Pressure Plumbing
	13.3 Pressure Vessels
	13.4 Safety
	13.5 Examples of High-Pressure Experimental Apparatus
		13.5.1 Experiments with Small Animals
		13.5.2 Electrical Recording at High Pressure (Fig. 13.2)
			13.5.2.1 Patch Clamp Recording at High Pressure
		13.5.3 Other High-Pressure Apparatus
			13.5.3.1 Stopping a Reaction at High Pressure
			13.5.3.2 Starting a Physiological Reaction at High Pressure
			13.5.3.3 Measuring High Hydrostatic Pressure in Load-Bearing Joints
	13.6 High-Pressure Windows
		13.6.1 Small High-Pressure Windows
		13.6.2 Large High-Pressure Windows
	13.7 The Isobaric Collection and Transfer of Organisms from High-Pressure Environments
		Box 13.1 Isobaric Collection of Small Deep-Sea Animals
		13.7.1 Isobaric Collection of Deep-Sea Animals Using Equipment Operated from a Surface Ship
			13.7.1.1 Isobaric Trapping of Benthic Animals
		13.7.2 Isobaric Collection of Fish from a Surface Ship
		13.7.3 The Isobaric Collection of Animals Using a Submersible
	13.8 The Isobaric Collection of Microorganisms
		13.8.1 Meso and Bathy Pelagic Microorganisms
		13.8.2 DEEPBATH
		13.8.3 Microorganisms from Deep-Sea Animals
		13.8.4 Fluid and Dissolved Gas Samplers
	13.9 Isobaric Recovery from the Deep Biosphere
		13.9.1 Isobaric Drill Cores
		13.9.2 CORKS and FLOCS: Drill Hole Sampling
	References
Index