Bioscience LabSims - Skills & Competencies

Bioscience LabSims - Skills & Competencies

LabSims for Biosciences - Skills & Competencies

Our interactive, online lab simulations form part of a blended learning experience, designed to enhance your existing workbooks, teaching labs, and assignments. LabSims can be used to enhance all types of academic or experiential programmes, and are designed to develop skills and strengthen competencies.

Below you will find a complete list of our LabSims for Biosciences, with the relevant skills and competencies that their content maps to, accompanied by a link to where you can find out more information about each
one.



Buffers and pH


Calibrating a pH meter

Using instrument and equipment

  • What buttons are commonly found on a pH meter

  • What buffers are regularly used to calibrate pH meters

  • How to calibrate a pH meter with a buffer of known pH 

  • How to check the calibration of the pH meter

Obtaining & Recording Data

  • Why it is important to wash the pH probe between solutions

  • Why it is helpful to calibrate a pH meter against 2 buffers of different pH


Find out more about Calibrating a pH meter
 

Parts of pH probe

Using instruments and equipments

  • What principle components make up a pH probe

Working in a safe manner

  • How to safely lower the pH probe into solution

Concepts, principles and theories

  • How the sample and reference half-cells generate a pH measurement



Find out more about Parts of pH probe
 

Cell Analysis


Flow Cytometry: Fundamentals

Designing & planning experiments 

  • How to configure the optics to split out light of the desired wavelength 

Using instruments & equipment 

  • How the laser, fluidics, optics, detectors and electronics of a flow cytometer together measure light signals  

  • What types of light signal are measured by a flow cytometer and what information they provide

Concepts, principles & theories 

  • How scattered and fluorescent light signals are generated and recorded 

  • What is meant by forward scatter, side scatter and granularity 

  • How the size and granularity of a cell affect the scattered light signals 

Interpreting & analysing data 

  • How to interpret dot plots to distinguish between cell populations 

  • How gating can be used to compare many different parameters and isolate populations of interest



Find out more about Flow Cytometry: Fundamentals
 

Cell Biology


Diffusion and Osmosis

Concepts, principles & theories

  • How concentration, molecule size and temperature affect the rate of diffusion 

  • What is meant by diffusion, osmosis, solute, solvent and water potential

  • How solute concentration relates to water potential and the movement of water molecules

  • How the relative solute concentration can be described in terms of tonicity

  • What similarities and differences define diffusion and osmosis 

  • Where examples of diffusion and osmosis occur in real life



Find out more about Diffusion and Osmosis
 

Cell Culture


Cell Counting Haemocytometer 

Using instruments & equipment 

  • How a haemocytometer can be used to count cells

  • How to affix the coverslip 

  • How to load the sample 

  • How to count cells 

Obtaining and recording data

  • Why it is important to clean the equipment prior to counting

  • Why care must be taken when loading the sample into the chamber

  • Why it is important to mix the sample prior to counting

  • How trypan blue can be used to differentiate between viable and non-viable cells

Manipulating and presenting data 

  • How to calculate the viable cell density of the original sample

  • How to calculate the percentage viability of the original sample



Find out more about Cell Counting Haemocytometer
 

Centrifuges


Purpose and products of centrifugation

Concept, principle and theory

  • What centrifugation is used to achieve 

  • How varying the speed and time affects the separation of particles

Designing & Planning Experiments

  • How to select the appropriate speed and time to separate different sized particles



 

Cloning


Blue-White screening theory

Obtaining & recording data 

  • Why the agar must be supplemented with the appropriate antibiotic, IPTG and X-gal 

Interpreting & analysing results

  • How to identify colonies that have taken up the plasmid with the desired insert

Concepts, principles and theories

  • What is the purpose of blue-white screening 

  • What components make up the lac operon in E. coli 

  • How β-galatosidase activity in E. coli produces blue colonies in the presence of X-gal

  • Why IPTG is seen as an activator of the lac operon 

  • How E. coli are modified genetically to make them suitable for blue-white screening 

  • What is meant by α-complementation

  • Why bacteria that have not taken up the plasmid die before forming colonies 

  • Why bacteria that have taken up the plasmid with no insert will form blue colonies 

  • Why bacteria that have taken up the plasmid with insert will form white colonies



Find out more about Blue-White screening theory
 

Cloning: Overview

Concept, principles and theories

  • What processes are utilised to insert a desired DNA segment into a recipient plasmid

  • How restriction enzyme digests are used to cut out the desired insert and linearize the recipient plasmid 

  • How DNA ligase is used to ligate the insert into the recipient plasmid 

  • How transformation of bacterial cells produces more copies of plasmid DNA 

  • What is meant by a competent bacterial cells 

  • How selection is used to remove cells that have not taken up plasmid 

  • How agarose gel electrophoresis can be used to analyse the success of the cloning



Find out more about Cloning: Overview
 

Cloning: Selection

Designing and planning experiments

  • Why the selectable marker in the plasmid determines the choice of antibiotic used in the agar 

  • Why an L-spreader is the most appropriate instrument to spread culture on agar 

  • How use of a positive control can validate the transformation procedure 

  • How use of a negative control can validate the selection procedure 

Interpreting and analysing data

  • How to use the results of sample and control plates to identify sources of error in the procedure

Concepts, principles and theories

  • How bacterial transformation can produce bacteria with/without the plasmid and with/without the desired insert

  • What is happening on a molecular level when transformed cultures are incubated on agar containing antibiotic



Find out more about Cloning: Selection
 

Cloning and Expression plasmids

Designing and planning experiments

  • What experimental factors must be considered when designing an appropriate plasmid

Concepts, principles and theories

  • How different elements found in cloning plasmids facilitate the insertion, replication and selection of DNA

  • How components within an expression plasmid facilitate the transcription and translation of a protein of interest



 

Miniprep 1: Isolate Plasmid DNA

Obtaining & recording data

  • Which reagents and processes are required to isolate plasmid DNA 

  • When to discard the supernatant and when to discard the pellet 

  • Why it is important to thoroughly mix the contents following resuspension, lysis and neutralisation steps

  • When it is appropriate to vortex samples and when they should be gently inverted

Concepts, principles and theories

  • What is happening on a molecular level during centrifugation, resuspension, lysis and neutralisation steps 



 

Miniprep 2: Purify Plasmid DNA

Using instruments & equipment

  • How the features of a miniprep column facilitate the purification of plasmid DNA 

Obtaining & recording data 

  • Which buffers are required to wash the membrane and elute the plasmid DNA 

  • Why it is important to wash the membrane

Concepts, principles & theories

  • What is happening on a molecular level during each step of the purification process



Find out more about Miniprep 2: Purify Plasmid DNA
 

Plasmid ligation

Designing and planning experiments

  • What reagents and cofactors are required for the ligation reaction 

  • How to select the most suitable restriction enzymes for a double digest 

Concept, principle and theory

  • What is happening on a molecular level during the digestion and ligation reaction 

  • How the use of phosphatase or multiple restriction enzymes can prevent religation of the plasmid DNA 



Find out more about Plasmid ligation
 

Column Chromatography


Gel filtration: separating proteins by size

Concepts, principles & theories 

  • What is the composition of the gel used in the column

  • How protein size affects migration through the gel 

  • How to predict the order of elution of different sized proteins



 

Ion exchange Chromatography

Concept, principle and theory

  • What is the relationship between pH and overall charge on a protein 
  • What is meant by the isoelectric point 
  • How differences in the isoelectric point of proteins can be used to aid protein purification
  • How to predict whether a protein will bind to the column equilibrated at a particular pH when given its isoelectric point 
  • How changing the buffer added to the column affects the pH environment and elution of proteins

Designing & planning experiments 

  • What is the difference between a cation and anion exchange column

Interpreting & analysis data 

  • How to identify the order proteins will reach their isoelectric point when given a graph of charge vs pH



Find out more about Ion exchange Chromatography
 

Running a protein purification column

Using instruments & equipment 

  • What are the main features of a purification column 

  • How to operate the column tap to start and stop the flow of elution 

  • What is used to equilibrate the column prior to adding the protein mixture 

Obtaining & recording data 

  • Why the gel bed must not be allowed to dry 

  • Why care must be taken when pipetting the sample into the top of the column 

  • Why it is important to keep the gel bed flat 

  • When to start and stop collecting each protein as they elute

Dissection


Fish Dissection

Using instruments & equipment 

  • How to make the initial incisions to open up the peritoneal cavity 

  • How to remove the spleen, gonads, digestive tract, liver and gallbladder 

  • How to remove the heart, swim bladder, part of the kidney and gills

  • How to separate the head, remove the top of the skull and dissect out the brain 

Obtaining and recording data

  • How to use a macroscopic key to examine and record the condition of the fins 

  • How to determine the hepatosomatic index

Concepts, Principles & Theories

  • What external features and fins can be identified on a fish

  • What is the role of the swim bladder and gills

  • How to use the terms dorsal, caudal, ventral and cranial to describe the relative positions of organs



Find out more about Fish Dissection
 

Ecology


Fieldwork: Methods and Approaches

Designing and planning experiments

  • How to identify the most appropriate method and approach for sampling rural and urban environments

Concepts, Principles & Theories

  • What is meant by point sampling, line or belt transect, mark-release-recapture and quadrat sampling 

  • What species are suitable for each of the 4 sampling methods 

  • What information can be provided by each of the 4 sampling methods 

  • What is meant by random, stratified and systematic sampling



 

Floral Diagrams and Floral Formulae

Obtaining & Recording Data

  • How to identify and represent diagrammatically the number, size regularity, spacing and arrangement of sepals

  • How to identify and represent diagrammatically the number, size regularity and arrangement of petals 

  • How to identify and represent diagrammatically the number and arrangement of anthers

  • How to identify and represent diagrammatically the number and arrangement of the gynoecium carpels

  • What information can be represented by a floral formula

Interpreting and analysing data

  • How to interpret a floral diagram to construct a floral formula 

Concepts, Principles & Theories

  • What is meant by a whorl and how do the key parts of a flower arrange into whorls

Electrophoresis: Agarose Gel


Agarose Gel: Separating DNA by size

Concepts, principles & theories

  • How the application of an electrical current affects the movement of DNA through the gel  

  • Why the movement of DNA molecules through the gel is affected by their size

  • How DNA molecules of differing sizes move in relation to each other 



 

Agarose Gel Analysis

Interpreting & analysing data 

  • How a transilluminator helps visualise the results of an agarose gel 

  • How to identify the number of different sized DNA fragments in a sample 

  • Why a DNA ladder is loaded alongside the samples 

  • How the different sized DNA ladder bands migrate in relation to each other

  • How to use the DNA ladder bands to estimate the size of sample DNA fragments 



Find out more about Agarose Gel Analysis
 

Loading and Running an Agarose Gel

Using instruments & equipments

  • What equipment is required to run an agarose gel

  • What components of the buffer facilitate the loading, tracking and visualisation of samples 

  • How to position the pipette to load the samples into the wells

  • Why it is important to correctly wire the electrodes to the tank

  • Why it is best to remove the comb after pouring the buffer

Obtaining & recording data 

  • How the amount of buffer added affects the running of the gel 

  • How the voltage selected can affect the running of the gel and the quality of the results

  • Why a DNA ladder is loaded alongside the samples



 

Pouring an Agarose Gel

Using instruments & equipments

  • What equipment is required to create a gel mould

  • Why the length and number of teeth need to be considered when selecting an appropriate comb

  • How to seal the ends of the gel tray to contain the molten agarose

  • Why it is important to wait for the gel to fully set before removing the tape

  • Why the agarose must be poured gently into the tray



Find out more about Pouring an Agarose Gel
 

Electrophoresis: PAGE


Loading and Running an SDS-PAGE Gel

Using instruments & equipment

  • What are the main features of the set-up once the gel is placed in an electrophoresis tank 

  • How to position the pipette tip to carefully deposit the sample in the well of the gel 

  • What are the typical components of the sample loading buffer 

  • Why it is important to correctly wire the electrodes to the tank

  • Where the gel should be trimmed after it has finished running 

Obtaining & recording data 

  • Why a protein ladder is loading alongside the samples 

  • How the voltage selected can affect the running of the gel and the quality of the results



 

Pouring an SDS-PAGE gel

Concepts, Principles and Theories

  • Why a SDS-PAGE gel has both a stacking layer and a separating layer 

Using instruments & equipment 

  • How to insert the plates into the casting frame and stand and test for leaks 

  • How to prepare the separating layer 

  • Why an overlay is required 

  • How to prepare the stacking layer 

  • Why APS and TEMED must be added just before the layer is poured 

  • How the wells of the gel are created



Find out more about Pouring an SDS-PAGE gel
 

SDS-PAGE Analysis

Obtaining & recording data 

  • How to measure the distance the dye front and molecular weight standards have migrated 

Manipulating & presenting data 

  • How to calculate the Rf value for the molecular weight standards 

  • What should be plotted on the axes of a molecular weight standard curve 

Interpreting & analysing data 

  • How to use a standard curve to estimate the molecular weight of an unknown protein 

  • How to identify an unknown protein in the sample based on the molecular weight 



Find out more about SDS-PAGE Analysis
 

SDS-PAGE Staining

Obtaining & recording data 

  • Why an SDS-PAGE gel is stained 

  • Why the gel is washed with destaining solution

  • What is meant by molecular weight standards 

Interpreting & analysing data 

  • How the protein ladder bands of different molecular weights migrate in relation to each other
  • How to identify the number of different protein species in a sample 
  • How to use the molecular weight standards to estimate the size of proteins in a sample


Find out more about SDS-PAGE Staining
 

SDS-PAGE Theory: Separating Proteins by Size

Concepts, principles & theories

  • What SDS-PAGE stands for 

  • How SDS affects a proteins charge and folding 

  • What is the optimal combination of SDS-PAGE gel reagents 

  • How the size of a protein affects the distance travelled through the gel mesh

Enzyme Kinetics


Enzyme-Catalysed Reactions

Concepts, principles & theories

  • How substrate and product concentrations change over time in an enzyme-catalysed reaction 

Interpreting & analysing data 

  • How to calculate the initial rate of reaction from a graph

Manipulating & presenting data 

  • What data is required to generate a Michaelis-Menten plot 



Find out more about Enzyme-Catalysed Reactions
 

Lineweaver-Burk Plot

Manipulating & presenting data 

  • How to transform Michaelis-Menten data into a form suitable for Lineweaver-Burk plotting

Interpreting & analysing data

  • How do the gradient, intercepts and axes of a Lineweaver-Burk plot relate to the components in the equation 

  • How to estimate the Vmax and Km from a Lineweaver-Burk plot

  • What effect competitive and non-competitive inhibitors have on the Vmax and Km values



Find out more about Lineweaver-Burk Plot
 

Michaelis-Menten Plot

Concepts, principles & theories

  • What does the Michaelis-Menten equation and corresponding plot describe 

  • What are the components of the Michaelis-Menten equation and what do they describe

Designing & planning experiment 

  • How to choose a sensible range of substrate concentrations to test 

Interpreting & analysing data 

  • How to estimate the Vmax and Km from a Michaelis-Menten plot



Find out more about Michaelis-Menten Plot
 

Genetics


Crossing Over and Recombination

Concepts, principles & theories

  • What is meant by crossing over, genetic recombination, homologous chromosomes and sister chromatids 

  • What is happening on a molecular level during Meiosis I and II 

  • How does genetic recombination affect the variation through inheritance 

  • How the distance between genetic loci impacts the recombination and co-inheritance frequency 



 

DNA Quantification

Designing and planning experiments

  • How the NanoDrop and Qubit differ in terms of sample preparation, type of measurement and accuracy 

Interpreting and analysing results

  • How to interpret a typical absorbance spectra and results from a NanoDrop

  • What 260/280 and 230/260 ratios are indicative of significant contamination

Concepts, principles and theories

  • Why the absorbance at 260 nm is used to measure DNA concentration 

  • Why the 260/280 and 260/230 ratios indicate the level of protein and salt contamination



Find out more about DNA Quantification
 

Next Generation Sequencing

Concepts, principles & theories 

  • What are the main stages of next generation sequencing 

  • What is happening on a molecular level during sample preparation steps

  • Why it is important to determine the quantity and quality of DNA before starting 

  • What is the purpose of the clustering, multiplexing and sequencing regions of the adapters 

  • What is happening on a molecular level during cluster generation steps

  • Why DNA fragments must be amplified into clusters 

  • What is happening on a molecular level during the sequencing by synthesis steps 

  • How base calls are generated 

Using instruments & equipment 

  • What are the main parts of an Illumina MiSeq



Find out more about Next Generation Sequencing
 

SNP detection with CAPS

Concepts, principles & theories

  • What is meant by a Single Nucleotide Polymorphism (SNP)
  • Why the CAPS method relies on the SNP falling within a restriction enzyme site 
  • How SNPs in restriction enzyme sites affects enzymatic activity 
  • How an SNP in a restriction enzyme site does not affect the length of the expected PCR products
  • How an SNP in a restriction enzyme site does affect the length of the expected digest products

Interpreting & analysing data 

  • How to identify the alleles present in different DNA samples using PCR and agarose gel electrophoresis 



Find out more about SNP detection with CAPS
 

SSLP detection

Concepts, principles & theories 

  • What is meant by simple sequence length polymorphisms (SSLP’s)

  • How an SSLP affects the length of the expected PCR products

Interpreting & analysing data

  • How to identify the alleles present in different DNA samples using PCR and agarose gel electrophoresis
 

Find out more about SSLP detection
 

Glassware


Basic labware

Using instrument and equipment

  • What are the names and features of some common items of labware 

Designing & Planning Experiments

  • What items of labware are suitable for measuring volumes 

  • What items of labware are suitable for storing and mixing solutions 

  • What items of labware are suitable for use in a centrifuge 

  • What items of labware are suitable for use in a spectrophotometer



Find out more about Basic labware
 

Haematology


Blood Smear Preparation

Using instruments & equipment 

  • What equipment is required to prepare a blood smear 

  • Why a blood sample is mixed with EDTA when it is collected 

  • How to spread the blood on a slide to achieve an optimal smear 

  • How to dry the blood smear

Obtaining & recording data 

  • How the quality of the blood smear is affected when the incorrect volume of blood or pressure is applied 

  • How to select an appropriate area of the smear to examine cell morphology and number 

Working in a safe manner 

  • Why gloves must be worn when preparing a blood smear 



Find out more about Blood Smear Preparation
 

Staining Blood Smear: Leishman’s Stain

Designing & planning experiments 

  • What are the advantages of using a Coplin jar as opposed to a Pasteur pipette to apply staining solutions

Concepts, principles & theories 

  • What is the purpose of preparing and staining a blood smear 

Using instruments & equipment 

  • What are the steps and reagents involved in performing a Leishman’s stain

Obtaining & recording data 

  • What is the effect of over or under exposing the blood smear to stain

Histology


Haematoxylin and Eosin (H&E) Stain

Concepts, principles & theories 

  • What is the purpose of a H&E stain 

  • Which cellular structures are stained by Haematoxylin and Eosin 

  • What is the role of the different reagents used in a H&E stain 

Using instruments & equipment 

  • How to prepare the tissue for staining 

  • How to stain the tissue with H&E 

  • How to prepare the tissue for coverslipping 

  • Why the solutions for each phase of the staining process must be applied in a specific order 

Obtaining & recording data 

  • What effect altering the time in the staining solutions has on the quality of the final result

  • How best to adjust the protocol to correct for some common issues with the H&E stain



 

Immunodetection


Sandwich ELISA

Concepts, principles & theories 

  • How antibodies can be used to detect the presence of an analyte within a sample

  • What is happening on a molecular level during each step of the ELISA 

  • What it means to immobilise the antigen and why this is necessary 

  • What is meant by a colorimetric reaction 

  • How the results of an ELISA can be used to estimate the concentration of an analyte in a sample 

Using instruments & equipment 

  • What are the core steps and components of an ELISA 

  • How to immobilise the antigen 

  • How to probe for the presence of antigen 

  • How to detect bound antigen 

Obtaining & recording data 

  • Why including blocking and wash steps increases the sensitivity of the assay 

  • Why samples, standards and controls should be assayed in duplicate or triplicate 

Designing & planning experiment 

  • What controls should be assayed alongside samples in an ELISA 



Find out more about Sandwich ELISA
 

Western Blot

Concepts, principles & theories

  • How antibodies can be used to detect the presence of target protein within a sample

  • What is happening on a molecular level during each step of the immunoblotting process

Using instruments & equipment

  • How to set up the blotting sandwich 

  • How to set up the transfer apparatus 

  • How to label the membrane with primary and secondary antibodies 

  • How to detect the presence of bound antibodies 

  • Why the order of the blotting sandwich components is important

  • Why the orientation of the blotting sandwich in relation to the electrodes is important 

  • Why buffer, a stir bar and an ice pack should be included in the transfer apparatus 

Obtaining and recording data

  • Why including blocking and wash steps improves the sensitivity of the technique 

  • Why a loading control is required 

Designing and planning experiments

  • How to choose the right secondary antibody to pair with the primary antibody 

Interpreting and analysing data

  • How the results of a western blot can be used to confirm the presence of a protein in a mixture of proteins 

  • How a western blot can be used to compare the level of protein between samples



Find out more about Western Blot
 

Lab Equipment


Water Bath

Using instrument and equipment

  • How a thermometer should be used to monitor the temperature of the water bath

  • How the tube should be positioned to prevent leakage and contamination 

  • What level of water and heat should be used to effectively heat the sample



Find out more about Water Bath


Weighing with Taring using a Top Pan Balance

Using instruments and equipments

  • What makes a suitable container for weighing sample in

  • How to tare the balance and transfer and weigh the desired amount of sample  

  • How to reduce spillages when transferring the sample to be weighed

Obtaining & recording data

  • Why it is important to clean and tare the balance prior to use





Mass Spectrometry


Mass Spectrometry: Fundamentals

Concepts, principles & theories 

  • What are the main stages of mass spectrometry analysis 

  • What is meant by the mass-to-charge ratio

  • How particles are separated according to their mass-to-charge ratio

  • Why it is vital the mass spectrometer is kept under high vacuum conditions

  • How the mass of an ion affects its velocity through the drift zone 

Interpreting & analysis data 

  • How to interpret the relative abundance of particles from a mass spectrum



 


Microbiology


Gram stain

Concepts, principles & theories 

  • What is the purpose of a Gram stain

  • How the cell wall of Gram positive and Gram negative bacteria differs

  • What four solutions are used to perform a Gram stain

  • What effect each solution has on the cell wall of Gram positive and negative bacteria 

  • What colour Gram positive and negative bacteria appear after the application of each solution

  • How the Gram stain relies on the differences in the cell walls of Gram positive and negative bacteria

Using instruments & equipment 

  • What order the four solutions are applied

  • How to apply each solution 

  • How to perform a wash step 

Obtaining & recording data 

  • What effect adding too much or too little of each solution has on the final result 



Find out more about Gram Stain
 

Pouring an agar plate

Using instruments & equipment 

  • What equipment is required to pour an agar plate

  • How to flame the neck of the bottle 

  • Why working under a bunsen burner and flaming the neck of the agar bottle helps reduce contamination

  • How to handle the lids of containers to reduce the risk of contamination 

  • How to dry and store the agar plate 

Working in a safe manner 

  • Why care must be taken when flaming the neck of the bottle  

  • Why care must be taken when pouring the agar into the Petri dish



Find out more about Pouring an agar plate
 

Pour plate technique

Using instruments & equipment 

  • What equipment is required to perform the pour plate technique
  • Why plates should be labelled on their base and what it should detail
  • How to flame the neck of the culture and agar bottle 

  • How to transfer the inoculum and molten agar into a Petri dish

  • Why working under a bunsen burner and flaming the neck of the bottles helps reduce contamination

  • How to handle the equipment to reduce the risk of contamination 

Obtaining & recording data 

  • Why plates should be placed upside down in the incubator 
  • Why the plate should be gently swirled to mix the agar and the inoculum 

Working in a safe manner 

  • Why care must be taken when flaming the neck of the bottles

  • Why care must be taken when pipetting the inoculum and pouring the agar into the Petri dish 

Concepts, principle & theories 

  • How the appearance of colonies differs between those growing within the agar and those growing on the surface



Find out more about Pour plate technique
 

Prepare a smear slide

Using instruments & equipment

  • What equipment is required to prepare a smear slide 

  • What should be included in the slide label 

  • How and when to sterilise the inoculation loop 

  • Why the sterile loop should not be used to create a smear while it is hot 

  • How to handle the equipment to reduce the risk of contamination

  • How to dry and heat fix a smear slide 

Obtaining & recording data 

  • What factors affect the distribution of bacteria and quality of the smear 

Working in a safe manner

  • How to reduce the risk of burning yourself when flame sterilising the inoculation loop



Find out more about Prepare a Smear Slide
 

Streak plate technique

Using instruments & equipment 

  • What equipment is required to streak bacteria on an agar plate
  • Why plates should be labelled on their base and what it should detail
  • How to flame the neck of the culture bottle and inoculation loop
  • How to streak a bacterial culture on an agar plate
  • Why working under a bunsen burner and flaming the neck of the culture bottle helps reduce contamination
  • How to handle the equipment to reduce the risk of contamination 
  • Why the sterile loop should not be used to spread bacteria while it is hot 

Obtaining & recording data 

  • What streak pattern is used to achieve discrete colonies

  • Why plates should be placed upside down in the incubator 

  • How the density of bacterial colonies differs in different parts of the streak plate

Working in a safe manner 

  • Why care must be taken when flaming the neck of the bottle

  • How to reduce the risk of burning yourself when sterilising the inoculation loop 



Find out more about Streak plate technique
 

Microscopy


Estimating Size

Using instruments & equipment 

  • Why the eyepiece graticule requires calibration at different magnifications 

  • How to calibrate the eyepiece graticule with a stage micrometer 

Obtaining and recording data 

  • How to line up an object with the scale of the eyepiece graticule 

  • How to use an eyepiece graticule to measure the size of a object viewed down the microscope 

Concepts, principles & theories

  • What lenses contribute to the magnification of an image in a compound light microscope 

  • How to calculate the total magnification of an image when different objective lenses are in use



Find out more about Estimating Size
 

Focusing and Navigating

Using instruments & equipment 

  • How to adjust the coarse and fine focus controls to bring an image into sharp focus

  • Why the magnification should be increased incrementally 

  • Why some objective lens’ require the use of immersion oil 

  • How to apply immersion oil 

  • How to adjust the brightness to increase image clarity 

  • How to use the stage controls to bring an area of interest into the centre of the field of view 

Working in a safe manner 

  • Why care must be taken when raising the stage 

  • Why the coarse focus control should only be used on low power objectives 

Concepts, principles & theories 

  • How the level of magnification affects the depth of focus 

  • How the orientation of the image seen down the microscope compares to the orientation of the sample on the slide



Find out more about Focusing and Navigating
 

Köhler Illumination

Using instruments & equipment 

  • What are the steps involved in setting up a microscope for Köhler illumination

  • What is happening mechanically when the field diaphragm is adjusted 

  • How does adjusting the field diaphragm affect the image seen down the microscope

  • What is happening mechanically when the condenser height is adjusted 

  • How does adjusting the height of the condenser affect the image seen down the microscope

  • What is happening mechanically when the condenser centering screws are adjusted 

  • How does adjusting the centering screws on the condenser affect the image seen down the microscope 

  • What is happening mechanically when the iris diaphragm is adjusted 

  • How does adjusting the iris diaphragm affect the image seen down the microscope 

Concepts, principles & theories 

  • What it means to set a microscope up for Köhler illumination



Find out more about Köhler Illumination
 

Scientific Drawing: High Power Micrograph

Obtaining and recording data

  • Why every structure seen down the microscope does not need to be drawn

  • How to identify areas that should be stippled 

  • How to identify features that should be labelled 

  • What should be included in the labels of a drawing 

  • What should be included in the title 

  • How to calculate the magnification factor to record on the drawing

Scientific Drawing: Low Power Micrograph

Obtaining and recording data

  • Why every structure seen down the microscope does not need to be drawn

  • How to identify areas that should be stippled 

  • How to identify features that should be labelled 

  • What should be included in the labels of a drawing 

  • What should be included in the title 

  • Where the place the scale bar or magnification factor in relation to the drawing



 

Scientific Drawing: Principles

Obtaining & recording data 

  • What should be used to draw the outline and the lines to the labels of the image

  • What should be used to write the labels 

  • What format should the magnification factor be written in 

  • What technique is used to indicate darker areas 

  • What should be included in the title 

  • Why every structure seen does not need to be drawn



Find out more about Scientific Drawing: Principles
 

Setting up a Microscope

Using instruments & equipment 

  • What are the main components of a compound light microscope 

  • How to set the brightness to a suitable level 

  • How to adjust the eyepiece to match the interpupillary distance

  • Why it is best to use the lowest power objective when first examining a slide 

  • How best to position the stage to begin focussing on the sample 

Working in a safe manner 

  • Why care must be taken when raising the stage 



Find out more about Setting up a Microscope
 

Nucleic Acid Extraction


RNA extracts from Animal cells

Using instrument & equipment 

  • How to resuspend the cell pellet in lysis buffer 

  • How the features of a miniprep column facilitate the extraction of RNA 

Obtaining & recording data

  • Why it is important to use a low salt solution to wash residual proteins off the membrane

  • Why it is important to use ethanol to wash salt off the membrane

Concepts, principles and theories

  • What is happening on a molecular level during the lysis, homogenisation and purification steps 

  • How do the components of the lysis and binding buffer facilitate their roles in RNA extraction



Find out more about RNA extracts from Animal cells
 

PCR


Key Stages in Polymerase Chain Reaction 

Concepts, principles & theories

  • What happens during one cycle of amplification

  • What reagents are required to carry out PCR

  • How changes in temperature initiate the different phases of PCR

  • How multiple cycles of PCR can be used to amplify a region of DNA 



 

Running a polymerase chain reaction (PCR)

Designing and planning experiment

  • Why dNTPs, DNA, primers and polymerase enzyme are required in each sample tube 

  • Where primers should be targeted in relation to the region of interest

  • What makes an appropriate positive and negative control in a PCR experiment

Using instruments & equipment

  • How to set the desired cycle settings on the thermocycler 

Obtaining and recording data

  • Why it is important to prepare PCR samples on ice 

  • Why it is best to add the DNA polymerase to the reaction mix last 

Interpreting and analysing results

  • How to use an agarose gel to identify whether samples and controls contain the region of interest 



 

Understanding qPCR

Designing and planning experiments

  • How SYBR green and TaqMan probes differ in their specificity for DNA, interaction with DNA and cost

  • What are some of the key differences between endpoint PCR and qPCR

Interpreting and analysing results

  • What axes are used for an amplification plot 

  • How does the curve on an amplification plot reflect what is happening on a molecular level in the sample

  • How to use an amplification plot to compare the starting quantities of target DNA

Concepts, principles and theories

  • What are the 3 main stages of a PCR cycle and the temperatures at which they occur

  • What is meant by the term fluorophore

  • Why an increase in target DNA proportionally increases the fluorescence by SYBR green

  • Why an increase in target DNA proportionally increases the fluorescence by TaqMan probes 

  • Why the process is called qPCR or RT-PCR



Find out more about Understanding qPCR
 

Pharmacology


Organ bath: Aorta

Using instruments & equipment 

  • What are the different parts of the organ bath equipment

  • How to run a single wash cycle 

Obtaining & recording data 

  • Why the tissue must be washed in between drug applications

  • How to annotate the force-time trace generated by the chart recorder 

Interpreting & analysing 

  • How to describe changes in force recorded on a force-time trace 

  • How to determine the effect of different drugs on the aorta by analysing a force-time trace



Find out more about Organ bath: Aorta
 

Organ Bath: Ileum

Using instruments & equipment 

  • What are the different parts of the organ bath equipment

  • How to run a single wash cycle 

Obtaining & recording data 

  • Why the tissue must be washed in between drug applications

  • How to annotate the force-time trace generated by the chart recorder 

Interpreting & analysing 

  • What receptors are bound by acetylcholine, pilocarpine, mepyramine and histamine

  • How to determine whether a drug causing smooth muscle contraction by analysing a force-time trace



Find out more about Organ Bath: Illeum
 

Physiology


Action Potential

Concepts, principles & theories 

  • What is an action potential 

  • How the distribution of charge is altered from resting state during depolarisation and hyperpolarisation 

  • What channels are involved in generation of an action potential and how they are triggered 

  • Why the resting potential of neurons is negative 

  • What is happening on a molecular level during an action potential and how this relates to a trace of an action potential 

  • How does varying the signal strength and the presence of myelin have on an action potential  



Find out more about Action Potential
 

Electrocardiography (ECG)

Concepts, principles & theories 

  • What are the main parts of the electrical conduction system in the heart 

  • What is meant by a positive deflection and negative deflection 

  • What is happening during the P wave, QRS complex and T wave 

  • What the ST segment and QT interval represent 

  • What is meant by a lead 

Using instruments & equipment 

  • How to position the four limb electrodes for an optimal ECG trace

  • How to configure the positive and negative electrode for limb leads 

Interpreting & analysing data 

  • How ECG traces relate to the underlying cardiac activity

  • How the characteristic waveforms of traces differ between leads 



Find out more about Electrocardiography (ECG)
 

Pipetting


Operating an automated pipette

Using instrument and equipment

  • What are the key controls on a micropipette

  • How to correctly position the pipette to aspirate and dispense liquid 

  • How to depress and release the plunger to the correct stops to withdraw and dispense liquid

  • Why the pipette should not be turned on its side when there is liquid in the tip 



Find out more about Operating an automated pipette
 

Parts of a pipette

Designing & Planning Experiments

  • How to select the most appropriate micropipette for a particular volume

Using instruments & equipments

  • How to identify the key parts of a micropipette

  • What range of volumes can be measured using the standard micropipettes, P20, P200 and P1000



Find out more about Parts of a pipette
 

Prepare an automated pipette

Using instrument and equipment

  • How to inspect a micropipette to ensure it is in good working order prior to use 

  • How to set the volume on the display of a P20, P200 and P1000 to transfer the correct amount of solution

  • How to identify the correct tips to use for a particular micropipette

  • Why it is important to inspect the condition and plunge action of a micropipette prior to use



Find out more about prepare an automated pipette
 

Protein Assays


Bradford Assay 

Concepts, principles & theories

  • How a change in the charge, absorbance max and colour of the CBB dye upon protein binding forms the principle of the assay

  • How protein concentration affects the colour of the solution and the absorbance reading

Designing and planning experiments

  • How the components of the blank, standards and samples differ and why it is important to prepare all three 

Obtaining and recording data

  • Why it is important to mix the solutions prior to measuring the absorbance

  • Why it is important to leave the solutions for 5 minutes prior to measuring the absorbance 

  • Why it is important to blank the spectrophotometer prior to measuring the absorbance 

Interpreting & analysing data 

  • How the accuracy of the interpolation is affected by where the sample concentration falls within the assay range



Find out more about Bradford Assay
 

Safety


Dressing for the clinic

Working in a safe manner

  • What top, legwear and shoes are considered appropriate for the clinic 
  • How hair should be tied up and clothing should not be visible underneath the scrub top 
  • What personal effects are permitted while in the clinic 

Find out more about Dressing for the clinic


Dressing for the Lab

Working in a safe manner

  • When and why it is important to wear goggles, gloves and a lab coat

  • Why it is good practice to wear clothing that covers the knees in the lab

  • Why open-toed shoes should not be worn in the lab

  • Why it is important to tie hair back and remove all loose jewellery in the lab 


Find out more about Dressing for the Lab
 

Safety features and hazards

Working in a safe manner

  • What steps should be taken in an accident or safety emergency in the lab 

  • What the symbols for a first aid kit, fire extinguisher and eye wash station look like

  • Why it is important to not run or use mobile phones in the lab 

  • Why fire doors and corridors should be kept clear of bags and bulky items 

  • What is considered good practice when leaving the work station in the lab


Find out more about Safety features and Hazards
 

Solutions and Dilutions

Performing one step dilutions (over 5mL)

Designing and planning experiment

  • How to select the appropriate equipment to transfer and mix the stock and diluent

Using instruments and equipments

  • What is meant by the terms stock and diluent 

  • How to use a graduated cylinder to measure out the correct volume of solution 

  • How to mix the solution thoroughly after combining



 

Performing one step dilutions (under 5mL)

Designing and planning experiment

  • How to select the appropriate equipment to transfer and mix the stock and diluent

Using instruments and equipments

  • What is meant by the terms stock and diluent 

  • How to set the volume on the pipette display to transfer the correct amount of solution

  • How to mix the solution thoroughly after combining

Preparing serial dilutions

Designing and planning experiment

  • How to select the appropriately sized pipette for transferring the stock and diluent

Using instruments and equipments

  • How to set the volume on the pipette display to transfer the correct amount of solution

  • How to mix the solution thoroughly after combining 

Concepts, principles & theories 

  • What is meant by the terms stock, diluent and serial dilution

  • How to identify the concentration and volumes required for each step in a 10-fold dilution



Find out more about Preparing serial dilutions
 

Spectroscopy and Spectrophotometry


Spectrophotometer: Calibration and Use

Using instruments & equipment 

  • How much solution should be poured into the cuvette 

  • Why the cuvette must be positioned with the light beams passing through the transparent sides

  • Why the lid of the spectrophotometer should be closed when taking readings 

Obtaining & recording data 

  • Why diluent should be used as a reference solution to calibrate the spectrophotometer

Spectrophotometer: Parts and Theory

Designing & planning experiments 

  • How to select an appropriate wavelength to measure the absorbance of a particular substance

Using instruments & equipment 

  • What are the main components of a spectrophotometer 

  • What is the function of the three key internal components, the light source, the filter and the detector 

Interpreting & analysing data 

  • What is described by an absorbance spectra

Concepts, principles & theories 

  • How absorbance is calculated 



 

Calibration curve in Spectrometry

Designing & planning experiments 

  • When is it appropriate to use a calibration curve vs the Beer-Lambert Law

  • What is required to generate a calibration curve 

  • How to choose a sensible range of protein concentrations to generate a calibration curve for a Bradford assay 

Interpreting & analysing data  

  • How to use a calibration curve to estimate the protein concentrations of samples

Concepts, principles & theories

  • How a Bradford assay can be used to assess total protein concentration in a sample



 

Spectroscopy


NMR: fundamentals

Using instruments & equipment 

  • What are the main components of a NMR spectrometer 

Concepts, principles & theories 

  • What is meant by nuclear spin 

  • How nuclei behave in the presence of an externally applied magnetic field

  • How changes in magnetic field lead to signal generation and an NMR spectrum



Find out more about NMR: fundamentals
 



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