G.Lab. Book
1
Introduction
1.1
Design principles
1.2
Credits
2
Microbiology
2.1
Microbial growth
2.2
Binary fission
2.3
Biofilm
2.4
Absorbance
2.5
Calibration curve
2.6
Winogradsky Column
2.7
Dilution
2.8
Isolation cultures
3
Microbial Metabolisms
3.1
Phototrophy
3.2
Chemotrophy
3.3
Autotrophy
3.4
Heterotrophy
3.5
Photoautotrophy
3.6
Photoheterotrophy
3.7
Chemoorganotrophy
3.8
Chemolithotrophy
3.9
Fermentation
3.10
Methanogenesis
3.11
Sulphate-reduction
4
Chemistry
4.1
Solution
4.2
Solubility
4.3
Temperature
4.4
pH and pOH - pondus Hydrogenium and pondus OH
4.5
MVpH - MilliVolt pH
4.6
ORP - Oxidation Reduction Potential
4.7
DO - Dissolved Oxygen
4.8
Conductibility (spc)
4.9
TDS - Total Dissolved Solids
4.10
Salinity
4.11
Density
4.12
Alkalinity
4.13
Melting Temperature
4.14
Gas laws
5
Geochemistry
5.1
Sulphide
5.2
Iron
5.3
DOC - Dissolved Organic Carbon
5.4
DIC - Dissolved Inorganic Carbon
5.5
EA - Elemental Analysis
5.6
ICP-ms - Inductively Coupled Plasma - mass spectrometry
5.7
IC - Ion Chromatography
5.8
Isotope
5.9
POM - Particulate Organic Matter
6
Biogeochemical Cycles
6.1
Water cycle
6.2
Carbon cycle
6.3
Nitrogen cycle
6.4
Phosphorus cycle
6.5
Sulphur cycle
6.6
Hydrogen cycle
7
Molecular Biology
7.1
DNA extraction protocol
7.2
Electrophoresis gel DNA
7.3
PCR
7.4
Nanodrop
7.5
Qubit
7.6
Protein extraction
8
Extreme Environments
8.1
Sea ice, permafrost and polar regions
8.2
Cold seeps and mud volcanoes
8.3
Shallow water-hydrothermal vents
8.4
Hot-springs, fumaroles and mud volcanoes
8.5
Hyperacidic lakes and volcanoes
8.6
Deserts and arid environments
8.7
Acid mine drainage
8.8
Deep-sea anoxic lakes and brines
8.9
Deep-sea hydrothermal vents
8.10
Serpentinizing environments
8.11
Deep-sea sediments and trenches
8.12
Soda lakes and hypersaline lakes
8.13
Nuclear contaminated sites
9
Protocols
9.1
Molecular Biology Protocols
9.1.1
Phenol-Chloroform DNA extraction
9.1.2
Proteinase K (100 mg/mL) DNA extraction
9.1.3
Powersoil Kit Qiagen Dna extraction
9.2
Geochemistry Protocols
9.2.1
Sulphide
9.2.2
Ferrous Iron
9.2.3
Alkalinity
9.2.4
Silica
10
Bioinformatic
10.1
16S rRNA analysis
10.2
Shotgun metagenomic analysis
10.3
Pipelines
11
Statistic
11.1
Mean
11.2
Median
11.3
Standard Deviations
11.4
Variance
11.5
P-Value
11.6
T-Test
11.7
Anova test
11.8
GGplot2
11.8.1
geompoint
12
Geology
12.1
Plate Tectonics
12.2
Subduction zones
13
Polygons Plot
13.0.1
Polygon plot features
13.0.2
The inception
13.0.3
Reading the Polygon plot
13.0.4
Using the Polygon plots: the Shiny app
13.0.5
Polygons plot array
13.0.6
List of future features
13.0.7
How to cite the Polygon plot
13.0.8
Questions, support and contribute!
13.0.9
Gallery of Polygons
14
Contacts
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G.Lab. Book
Chapter 9
Protocols
9.1
Molecular Biology Protocols
9.1.1
Phenol-Chloroform DNA extraction
9.1.2
Proteinase K (100 mg/mL) DNA extraction
9.1.3
Powersoil Kit Qiagen Dna extraction
9.2
Geochemistry Protocols
9.2.1
Sulphide
9.2.2
Ferrous Iron
9.2.3
Alkalinity
9.2.4
Silica