Summary
Volledige samenvatting Biological research techniques
- Course
- Institution
This document contains a complete summary of the course Biological research techniques.
[Show more]
Seller
Follow
MiSaBio
Content preview
Biological research,H1: EXPERIMENTAL DESIGN ................................................................................................................. 1
1.1 SCIENCE?.................................................................................................................................................. 1
1.2 PRINCIPLES OF SCIENCE ............................................................................................................................ 1
1.3 TYPES OF SCIENTIFIC RESEARCH ............................................................................................................... 2
1.4 SAMPLING ................................................................................................................................................. 3
1.5 WHAT IS “GOOD” EXPERIMENTAL DESIGN ?................................................................................................ 4
1.6 STEPS TO DEVELOP EXPERIMENTAL DESIGN .............................................................................................. 4
H2: RULES OF SCIENCE AND CRITICAL THINKING ........................................................................... 7
2.1 THE EMPIRICAL CYCLE ............................................................................................................................... 7
2.2 THE SIX RULES OF SCIENCE ....................................................................................................................... 8
2.3 BAD SCIENCE – EXAMPLE EXERCISE .......................................................................................................... 9
H3: BIOLOGICAL MODELS ..................................................................................................................11
3.1 INTRODUCTION AND HISTORY OF BIOLOGICAL MODELS ........................................................................... 11
3.2 CRITERIA TO BE A GOOD BIOLOGICAL MODEL .......................................................................................... 12
3.3 THE MAIN BIOLOGICAL MODEL ORGANISMS ............................................................................................. 13
H4: LIGHT MICROSCOPY ....................................................................................................................24
4.1 INTRODUCTION ........................................................................................................................................ 24
4.2 BRIGHTFIELD MICROSCOPY ..................................................................................................................... 27
4.3 DARKFIELD MICROSCOPY ........................................................................................................................ 28
4.4 PHASE CONTRAST MICROSCOPY ............................................................................................................. 29
4.5 DIFFERENTIAL INTERFERENCE CONTRAST MICROSCOPY (NOMARSKI) ..................................................... 30
4.6 FLUORESCENCE MICROSCOPY ................................................................................................................ 31
4.7 CONFOCAL MICROSCOPY........................................................................................................................ 32
H5: ELECTRONIC MICROSCOPY ........................................................................................................33
5.2 TRANSMISSION ELECTRON MICROSCOPY (TEM) .................................................................................... 33
5.3 SCANNING ELECTRON MICROSCOPY (SEM)............................................................................................ 36
5.4 SCANNING TUNNELING MICROSCOPY (STM) .......................................................................................... 39
5.5 ATOMIC FORCE MICROSCOPY (AFM) ...................................................................................................... 39
H6: SPECTROSCOPY ...........................................................................................................................43
6.1 ABSORPTION SPECTROSCOPY ................................................................................................................ 43
6.2 FLUORESCENCE SPECTROSCOPY ............................................................................................................ 47
6.3 INFRARED SPECTROSCOPY ...................................................................................................................... 50
6.4 RAMAN SPECTROSCOPY.......................................................................................................................... 52
6.7 NMR SPECTROSCOPY ............................................................................................................................. 55
H7: ELECTROPHORESIS ......................................................................................................................57
7.1 BACKGROUND ......................................................................................................................................... 57
7.2 DENATURING GRADIENT GEL ELECTROPHORESIS (DGGE) ...................................................................... 58
7.3 TEMPERATURE GRADIENT GEL ELECTROPHORESIS (TGGE) .................................................................... 60
7.4 PULSE-FIELD ELECTROPHORESIS (PFGE) ............................................................................................... 61
7.5 CAPILLARY ELECTROPHORESIS (CE) ....................................................................................................... 62
7.6 ELECTROPHORESIS OF PROTEINS ............................................................................................................ 63
7.7 OVERVIEW ELECTROPHORESIS ................................................................................................................ 64
,H8: CHROMATOGRAPHY ....................................................................................................................65
8.1 INTRODUCTION AND GENERAL PRINCIPLES .............................................................................................. 65
8.2 COLUMN CHROMATOGRAPHY .................................................................................................................. 66
8.3 PAPER AND THIN LAYER CHROMATOGRAPHY ........................................................................................... 68
8.4 HIGH-PRESSURE LIQUID CHROMATOGRAPHY (HPLC) ............................................................................. 70
8.5 GAS CHROMATOGRAPHY ......................................................................................................................... 71
8.6 ION EXCHANGE CHROMATOGRAPHY ........................................................................................................ 73
8.7 LIQUID CHROMATOGRAPHY-MASS SPECTROSCOPY (LC/MS) ................................................................. 74
H9: PROTEOMICS .................................................................................................................................75
9.1 INTRODUCTION ........................................................................................................................................ 75
9.2 STRATEGIES FOR PROTEIN SEPARATION .................................................................................................. 77
9.3 GEL-BASED SEPARATION TECHNIQUE: 2DGE .......................................................................................... 77
9.4 LIQUID-CHROMATOGRAPHY BASED SEPARATION TECHNIQUES ................................................................ 79
9.5 STRATEGIES FOR IDENTIFYING PROTEINS ................................................................................................ 81
H10: REMOTE SENSING .......................................................................................................................84
10.1 WHAT IS REMOTE SENSING .................................................................................................................... 84
10.2 REMOTE SENSING: PLATFORMS AND SPATIAL RESOLUTION ................................................................... 84
10.3 DIFFERENT KINDS OF REMOTE SENSING ................................................................................................ 86
10.4 ADVANTAGES AND DISADVANTAGES OF REMOTE SENSING .................................................................... 87
10.5 BIOLOGICAL APPLICATIONS ................................................................................................................... 87
10.6 EXAMPLE EXERCISES............................................................................................................................. 88
H11: NEXT GENERATION SEQUENCING............................................................................................90
11.1 INTRODUCTION...................................................................................................................................... 90
11.2 NGS TECHNIQUES ................................................................................................................................ 92
11.3 ILLUMINA ............................................................................................................................................... 93
11.4 IONTORRENT ......................................................................................................................................... 93
11.5 PACBIO ................................................................................................................................................. 93
11.6 OXFORD NANOPORE ............................................................................................................................. 94
11.7 APPLICATIONS OF NGS ........................................................................................................................ 94
11.8 OVERVIEW NGS .................................................................................................................................... 95
11.9 EXAMPLES OF RESEARCH QUESTIONS AND FITTING NGS ..................................................................... 95
H12: ECOSYSTEM RESEARCH ............................................................................................................97
12.1 INTRODUCTION...................................................................................................................................... 97
12.2 CLIMATE MANIPULATION ........................................................................................................................ 97
12.3 FREE-AIR CO2 ENRICHMENT (FACE)................................................................................................... 100
12.4 FREE-AIR TEMPERATURE INCREASE (FATI) .......................................................................................... 101
12.5 RAIN SIMULATORS, RAIN CURTAINS AND RAINOUT SHELTERS .............................................................. 102
12.6 COMBINATIONS IN THE FIELD ............................................................................................................... 102
12.7 ECOTRONS .......................................................................................................................................... 103
12.8 ENCLOSED AQUATIC SYSTEMS ............................................................................................................ 103
12.9 CONCLUSION ...................................................................................................................................... 103
OVERALL: CHOOSING THE RIGHT TECHNIQUE............................................................................ 104
, H1: Experimental design
1.1 Science?
= a way of knowing things about the natural world, relying on certain principles
= organizes knowledge in the form of testable explanations and predictions about the universe;
relies on empirical evidence obtained through observation, experimentation and logical
reasoning to understand natural phenomena
o Being in a dark room and looking for the black cat using a flashlight
Science is not the only thing to gain information:
• Religion: a set of beliefs, practices and values centred around the worship of a deity or
deities, often involving rituals, moral codes and a worldview that addresses fundamental
questions about existence
o Being in a dark room and believing there is a black cat in the room, without having
ever seen a black cat or seeing a black cat enter the room
• Metaphysics: branch of philosophy that explores fundamental concepts such as
existence, reality, causation, nature of being,.. extending beyond the empirical
observations of the physical world
o Being in a dark room and looking for a black cat that isn’t there
• Philosophy: systematic inquiry into fundamental questions about knowledge, existence,
ethics, reason, mind and language, using critical and logical analysis to seek
understanding and meaning in various aspects of the human experience
o Being in a dark room and looking for a black cat
• Theology: study of the nature of the divine, religious beliefs and the relationship between
humanity and the divine. Often involves interpretation of sacred text and exploration of
religious doctrines and traditions.
o Being in a dark room, looking for a black cat that isn’t there and shouting “I found
it!”
1.2 Principles of science
Science and scientific method rely on fundamental principles:
1. Empiricism: knowledge gained through observation and experimentation
2. Systematic observation: data is collected in an organized and structured manner
3. Reproducibility: experiments and observations should be independently repeatable
4. Falsifiability: scientific theories and hypotheses must be formulated in a way that allows
them to be tested and potentially proven false
5. Objectivity: scientific inquiry should be free from personal bias or preconceived notions
6. Hypothesis testing: formulating clear, testable predictions based on a hypothesis
7. Peer review: evaluation of scientific work by experts in the same field before publication
8. Consistency with existing knowledge: new findings should be consistent with established
scientific principles
9. Openness and transparency: sharing methods, data and findings openly with scientific
community
10. Occam’s razor: when multiple explanations are available is the simplest one often the
most likely
1
The benefits of buying summaries with Stuvia:
Guaranteed quality through customer reviews
Stuvia customers have reviewed more than 700,000 summaries. This how you know that you are buying the best documents.
Quick and easy check-out
You can quickly pay through credit card or Stuvia-credit for the summaries. There is no membership needed.
Focus on what matters
Your fellow students write the study notes themselves, which is why the documents are always reliable and up-to-date. This ensures you quickly get to the core!
Frequently asked questions
What do I get when I buy this document?
You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.
Satisfaction guarantee: how does it work?
Our satisfaction guarantee ensures that you always find a study document that suits you well. You fill out a form, and our customer service team takes care of the rest.
Who am I buying these notes from?
Stuvia is a marketplace, so you are not buying this document from us, but from seller MiSaBio. Stuvia facilitates payment to the seller.
Will I be stuck with a subscription?
No, you only buy these notes for $22.28. You're not tied to anything after your purchase.
Can Stuvia be trusted?
4.6 stars on Google & Trustpilot (+1000 reviews)
62555 documents were sold in the last 30 days
Founded in 2010, the go-to place to buy study notes for 14 years now