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Table Of Contents

1 Introduction
1.1 INTRODUCTION
1.2 GENERAL DEFINITIONS
1.3 SIZE CLASSIFICATION
1.4 MAIN SYSTEMATIC GROUPS
1.5 SPECIES DIVERSITY
1.6 ECOLOGICAL POSITION
1.7 DISTRIBUTION PATTERN
1.8 GROWTH AND METABOLISM
1.9 REPRODUCTION AND DEVELOPMENT
1.10 STANDING STOCK AND PRODUCTION
1.11 CONCLUSION
1.12 REFERENCES
2 Samplingand experimentaldesign
2.1 INTRODUCTION
2.2 CONCEPTUAL ISSUES
2.2.2 Integrationof disciplines: zooplankton, between physics andfish
2.2.4 Integrationof approaches: from theory tofield
2.3 DESIGN OF OCEANOGRAPHIC CRUISES AND SURVEYS
SYSTEMATIC DESIGN
RANDOM DESIGN
STRATIFIED RANDOM DESIGN
PREFERENTIAL DESIGN
OTHER DESIGN TYPES
2.4 REFERENCES
3 Collectingzooplankton
3.1 INTRODUCTION
3.2 A SURVEY OF SAMPLING DEVICES
SIMPLE NET SAMPLERS
MULTIPLE SAMPLE INSTRUMENTS
MULTIPLE NET SAMPLERS
3.3 FACTORS INFLUENCING MESOZOOPLANKTON SAMPLES
EFFECT OF AMBIENT LIGHT
MESH AND FRAME COLOR
3.4 HANDLING TOWED SAMPLERS
3.5 CARE OF TOWING CABLES
3.6 HANDLING SAMPLES AND SAMPLE PRESERVATION
3.7 COLLECTION OF LIVE ZOOPLANKTON FOR EXPERIMENTAL STUDIES
3.8 OTHER ZOOPLANKTON INSTRUMENTS USED IN CONJUNCTION WITH NETS
3.8.1 Optical plankton counter
OTHER ZOOPLANKTON INSTRUMENTS USED IN CONJUNCTION WITH NETS 77
3.9 REFERENCES
4.1 INTRODUCTION
4.2 SHIPBOARD SAMPLE TREATMENT
4.3 BIOVOLUME AND BIOMASS DETERMINATIONS (By W. Hagen)
SETTLING VOLUME
DISPLACEMENT VOLUME
WET MASS, FRESH MASS AND LIVE MASS
DRY MASS
ASH-FREE DRY MASS
4.3.3 Biochemical methods
SAMPLE PREPARATION
ELEMENTAL ANALYSIS
ORGANIC CARBON (AND HYDROGEN)
ORGANIC NITROGEN
ORGANIC PHOSPHORUS
ORGANIC COMPOUNDS
PROTEINS
ENERGY CONTENT
ADENOSINE TRIPHOSPHATE (ATP)
4.3.4 Conversion factors and equations
4.4 ABUNDANCE AND SPECIES IDENTIFICATION
MULTIVARIATE CLASSIFICATION TECHNIQUES
RECURRENT GROUP ANALYSIS
MATCHING SPECIES AND SAMPLES: INDICATOR SPECIES ANALYSIS
4.5.4 Analysis ofspatial andtemporal formations
4.6. ACKNOWLEDGMENT
4.7 REFERENCES
5.1 INTRODUCTION
5.2 COLLECTION METHODS
5.2.1 Nano- and microzooplankton
5.2.2 Planktonic sarcodines
5.3 PRESERVATION AND ENUMERATION
PRESERVATION
NANOZOOPLANKTON ENUMERATION
MICROZOOPLANKTON PRESERVATION
MICROZOOPLANKTON ENUMERATION
5.3.3 Planktonic sarcodines
LARGER PLANKTONIC SARCODINE PRESERVATION
LARGER PLANKTONIC SARCODINE ENUMERATION
5.4 DETERMINATION OF BIOMASS: CONVERSION FACTORS
5.4.3 Planktonic sarcodines
5.5 STANDARD PROTOCOLS
5.5.1 Collectionofnano- and microzooplankton
5.5.2 Preservation ofnanozooplankton
5.5.3 Staining and enumeration of nanozooplankton
5.5.4 Preservation ofmicrozooplankton
5.5.4 Enumeration of microzooplankton
5.6 ACKNOWLEDGMENTS
5.7 REFERENCES
6 Acoustical methods
6.1 INTRODUCTION
BACKGROUND
HISTORY
ACTIVE SONAR EQUATION
TARGET STRENGTH MODELS
MEASUREMENT
MODELING
6.2.4 Generic instruments
ECHO SOUNDER
SONAR
ACOUSTIC DOPPLER CURRENT PROFILER (ADCP)
ECHO INTEGRATOR
POST-PROCESSING SYSTEM
ECHOGRAM
ECHO INTEGRATION
TARGET STRENGTH DETERMINATION
POST-PROCESSING AND DATA ANALYSIS
strati®cation
CHOOSING AN ACOUSTIC INSTRUMENT
SINGLE-ANIMAL METHODS
MULTIPLE-ANIMAL METHODS
PARAMETER RANGES FOR SCIENTIFIC ECHO SOUNDERS
6.5 REFERENCES
7 Optical methods
7.1 INTRODUCTION
LIGHT PHENOMENA
ILLUMINATION
WATER AS AN OPTICAL MEDIUM
LIGHT DETECTION
MAGNIFICATION AND RESOLUTION
WATER MEDIUM
ANIMAL-DEPENDENT EFFECTS
IMAGING
BRIGHT-FIELD MICROSCOPY
CONTRAST TECHNIQUES
FLUORESCENCE MICROSCOPY
SILHOUETTE PHOTOGRAPHY
OPTICAL PLANKTON COUNTING
Optical plankton counter
VIDEO PLANKTON RECORDING
Video plankton recorder
IMAGING VERSUS QUANTIFICATION
VENUE AND DEPLOYMENT
OPERATING RANGES OF TWO SYSTEMS
7.3 MEASUREMENT PROTOCOLS, MODEL COMPUTATIONS, AND EXAMPLES
7.3.1 Silhouette photographyin thelaboratory
PROCEDURES
FURTHER PROCESSING OF THE FILM
7.3.2 Optical plankton counter
CALIBRATION INCLUDING COMPARISONS
LIMITATIONS
OPERATING SCENARIO
APPLICATIONS
7.4 ACKNOWLEDGMENTS
7.5 REFERENCES
8.4.1 Methodological approaches
8.4.2 Indirect methodsto measure assemblagegrazing
CORRELATION OF NATURAL CONSUMER^PREY CYCLES
EXTRAPOLATION OF LABORATORY RATES TO THE FIELD
THE PIGMENT BUDGET
ACID LYSOZYME ASSAY
FOOD TRACERS: INERT PARTICLES
FOOD TRACERS: PREY CELLS
FOOD TRACERS: RADIOISOTOPES
FOOD VACUOLE CONTENTS
PREY REMOVAL
8.4.4 Direct methodstomeasure assemblage grazing rates
SEA WATER DILUTION METHOD
WORKING PROCEDURES FOR THE SEA WATER DILUTION METHOD
SIZE FRACTIONATION METHODS
METABOLIC INHIBITOR METHOD
8.5 MESO- AND MACROZOOPLANKTON
8.5.1 Empirical relationships
SAMPLING
PREPARATION FOR ANALYSIS
GUT CLEARANCE COEFFICIENT
SORTING ANIMALS
EXTRACTION
PIGMENT ANALYSIS
TRANSFORMATION TO CARBON
PIGMENT DESTRUCTION
8.5.3 Working procedures for thegutfluorescence method
SUPPLIES
MEASUREMENT AND CALCULATIONS
COMMENTS AND SPECIAL PRECAUTIONS
GENERAL PROCEDURES
SPECIAL CASE: COPEPOD MANDIBLES IN STOMACH CONTENTS
DIGESTION
NON-HOMOGENEOUS FOOD MATERIAL
FOOD SELECTIVITY
SLOPPY FEEDING
LOSSES FROM FECAL MATERIAL
ABSORBANCE OF IT IN THE DIGESTIVE TRACT
PRODUCTION OF NON-FECAL MATERIAL MIXED WITH FECES
ASH-RATIO METHOD
CHLOROPHYL-RATIO METHOD
SILICA-RATIO METHOD
METHODOLOGICAL COMPARISONS
WORKING PROCEDURES FOR LABORATORY EXPERIMENTS WITH ISOTOPES
WORKING PROCEDURES FOR FIELD EXPERIMENTS
BOTTLE EFFECTS DURING INCUBATIONS
ESTIMATES OF COMMUNITY GRAZING RATE
COLLECTION OF ZOOPLANKTON
THE FOOD SOURCE
EXPERIMENTS
SUB-SAMPLING
MICROSCOPIC EXAMINATION OF SUB-SAMPLES
FEEDING RATE CALCULATIONS
AMYLASE
TRYPSIN
8.6 DIFFICULTIES WITH SPECIFIC ZOOPLANKTON GROUPS
8.6.2 Laboratory experiments
8.7 OMNIVORY
8.7.1 A general method to estimate omnivory
COLLECTION OF CONSUMERS
COLLECTION AND HANDLING OF WATER
SAMPLE COLLECTION, PROCESSING AND ANALYSIS
DATA ANALYSIS
8.8 FACTORS REGULATING FEEDING RATE
FUNCTIONAL RESPONSE. MODEL I
FUNCTIONAL RESPONSE. MODEL II
FUNCTIONAL RESPONSE. MODIFIED MODEL II
FUNCTIONAL RESPONSE. MODEL III
DESIGN OF FUNCTIONAL RESPONSE EXPERIMENTS
CALCULATING CURVE FITS IN FUNCTIONAL RESPONSE EXPERIMENTS
8.8.5 Palatability/toxicity of foodorganisms
8.8.6 Physical environmental factors
TEMPERATURE
LIGHT
SPATIAL CONSTRAINTS
8.9 PREDATION BEHAVIORAL MODELS
8.10 CONCLUDING REMARKS
8.11 ACKNOWLEDGMENTS
8.12 REFERENCES
9.1.4 Evaluation of environmental impacts
9.1.5 Estimation of secondary production
9.2 MODELS OF GROWTH AND FECUNDITY
9.2.1 Physiological or laboratory-derived budgetarymodels
9.2.2 Temperature-dependentempirical model
9.2.3 Global model ofin-situ weight-specific growth
9.3 DETERMINATION OF EGG PRODUCTION RATE: BROADCAST SPAWNING COPEPODS
DETERMINATION OF EGG PRODUCTION RATE: BROADCAST SPAWNING COPEPODS 407
CAPTURE AND HANDLING
DURATION OF INCUBATION
INCUBATION CONTAINERS AND DENSITY OF FEMALES
LIGHT REGIME
FOOD SUPPLY
9.3.3 Statistical considerations
9.3.4 Estimation of spawning frequency from preservedsamples
9.4 EGG PRODUCTION RATES OF EGG CARRYING COPEPODS
9.5 THE DETERMINATION OF GROWTH RATE
ESTIMATION OF DEVELOPMENT TIME
ESTIMATION OF MEAN WEIGHT
LIMITATIONS AND SOURCES OF ERROR
9.5.2 Direct measurement ofgrowth rate
THE BASIC METHOD
9.6 BIOCHEMICAL AND RADIOCHEMICAL METHODS
9.6.1 Ratios of biochemical quantities
9.6.4 Radiochemical methods
IN VITRO INCORPORATION
IN VIVO UPTAKE
IN VIVO INJECTION
IN VIVO INGESTION
CAPTURE
SORTING THE CATCH
INCUBATION
MOLTING RATES
GROWTH RATES
CREATION OF ARTIFICIAL COHORTS: ALTERNATIVE TECHNIQUES
CHANGING THE WATER
9.9 ACKNOWLEDGMENTS
9.10 REFERENCES
10 Metabolism
Review
10.1 OXYGEN CONSUMPTION AS AN INDEX OF METABOLISM
10.2 NITROGEN AND PHOSPHORUS METABOLISM
10.3 MEASURING METABOLIC RATE ON LIVE ZOOPLANKTON
10.4 METABOLIC RATE AND ENZYMATIC INDICES
10.4.2 Enzymes ofintermediary metabolism
10.5 CONCLUDING REMARKS
Practice (T. Ikeda and J.J. Torres)
10.6 COLLECTION AND HANDLING OF ZOOPLANKTON
10.7 RESPIRATION
10.8 EXCRETION (T. Ikeda)
10.8.3 Ammonia andinorganic phosphate analysis
10.9 REFERENCES
11.1 BACKGROUND
11.2 TECHNICAL APPROACHES TO DETERMINING GENETIC DIVERSITY
11.2.4 Oligonucleotide probe hybridization
11.3 STATISTICAL APPROACHES TO ASSESSING GENETIC DIVERSITY AND STRUCTURE
11.3.1. Statistical measuresof genetic diversity
11.3.2 Statistical measuresof genetic structure
PHYLOGENETIC ANALYSIS
11.4.1 Preservationand storage in ethanol
11.4.3 Formalin, glutaraldehyde, and otherbad things
11.5 GENERAL RECOMMENDATIONS
11.6 MEASUREMENT PROTOCOLS
11.6.3 General laboratory rules
SAMPLE PRESERVATION
GEL ELECTROPHORESIS
GEL PURIFICATION OF DNA
BUFFERS AND FREQUENTLY USED SOLUTIONS
SAFETY INFORMATION
11.7 FURTHER READING
11.8 ACKNOWLEDGMENTS
11.9 REFERENCES
12 Modeling zooplankton dynamics
12.1 INTRODUCTION
12.2 MODELING APPROACHES AND TECHNIQUES
12.2.1 Steps of model building
CHOICE OF STATE AND FORCING VARIABLES
CHOICE OF MODEL UNITS
IDENTIFICATION OF PARAMETERS
12.2.2 Themathematical description of the system
SYSTEMS OF EQUATIONS
NUMERICAL METHODS
12.3 MODELS OF INDIVIDUAL BIOENERGETICS AND LIFE-HISTORY TRAITS
12.3.1 Individual bioenergetics
BUDGET OF INDIVIDUAL ZOOPLANKTON
MODELS OF INDIVIDUAL BIOENERGETICS AND LIFE-HISTORY TRAITS 577
INGESTION RATE
ASSIMILATION AND EGESTION
EXCRETION AND RESPIRATION ^ ENERGETIC COSTS
GROWTH AND EGG PRODUCTION MODELS
DEVELOPMENTAL STAGE DURATIONS OF CRUSTACEAN ZOOPLANKTON
MORTALITY RATES
INVERSE METHODS TO ESTIMATE VITAL RATES
12.3.3 Evolutionaryforces on the organism
12.4 POPULATION MODELS
12.4.1 Populations described by onevariable
DISCRETE-TIME DIFFERENCE EQUATION MODELS AND MATRIX MODELS
CONTINUOUS-TIME STRUCTURED POPULATION MODELS
STAGE-STRUCTURED POPULATION MODELS BASED ON ODEs
DELAY DIFFERENTIAL EQUATION MODELS
STRUCTURED POPULATION MODELS TO ESTIMATE DEMOGRAPHIC PARAMETERS
STOCHASTICITY IN STRUCTURED POPULATION MODELS
12.4.3 Individual-based models of a population
BUILDING AN IBM
OBJECT-ORIENTED PROGRAMING (OOP)
CONSTRAINTS IN BEHAVIOR
12.4.4 Models of interactions betweenzooplankton populations
INTERACTION MODEL WITH TWO VARIABLES
POPULATION INTERACTIONS USING STRUCTURED POPULATION MODELS
12.5 MODELS OF ZOOPLANKTON COMMUNITIES
12.5.1 Zooplanktonbulk models in ecosystem models
FROM A SINGLE GRAZER TO SEVERAL GRAZERS
SIZE-STRUCTURED ECOSYSTEM MODELS
SIZE SPECTRUM THEORY
12.6 MODELING SPATIAL DYNAMICS OF ZOOPLANKTON
MODELING ZOOPLANKTON BEHAVIOR AT THE `MICRO-SCALE'
EVOLUTIONARY MODELING APPROACHES FOR OPTIMAL SPATIAL DISTRIBUTIONS
GRID-BASED MODELS
12.6.3 CouplingIBMs and spatially explicit models
MODELING PASSIVE DISPERSION WITH ADREs
MODELING ACTIVE VERTICAL SWIMMING WITH ADREs
12.7 ACKNOWLEDGMENTS
12.8 REFERENCES
INDEX
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Zoo Plankton Methodology Manual Harris Et Al

Zoo Plankton Methodology Manual Harris Et Al

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Published by Laura Sampson

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Published by: Laura Sampson on Sep 11, 2011
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