BI 559 Lecture 4: How to read and present scientific papers
Part I: Reading papers
(DALL-E)
Scientific papers generally contain 5 sections
Scientific papers generally contain 5 sections
(Forgive me for using a different paper from the one we’re going over today as an example, but I used this one because the sections are clearly labeled)
Scientific papers generally contain 5 sections
Abstract: describe the key finding and results of the paper with minimal background in 1 paragraph
Abstract
Scientific papers generally contain 5 sections
Title: describe the key result in one sentence or less
Abstract
Title
Abstract: describe the key finding and results of the paper with minimal background in 1 paragraph
Scientific papers generally contain 5 sections
Introduction: provide the key background and context for the paper’s results.
What is known?
What is the knowledge gap?
How is this paper filling the gap?
No discussion of results yet.
(Usually 1-2 pages)
Introduction
Scientific papers generally contain 5 sections
Results: What were the experiments and their outcomes? For a computational or mathematical paper, what was the model and what are its predictions?
The meat of the paper; can be very long (3+ pages)
Scientific papers generally contain 5 sections
Discussion: What are the broader implications of the work?
This section lets the authors speculate without necessarily providing thorough evidence
Scientific papers generally contain 5 sections
Methods: What experimental or computational techniques were used?
Key for people seeking to perform similar experiments or reproduce the results.
Sometimes in supplementary.
Scientific papers generally contain 5 sections
Supplementary Material: Contains important data, math, etc that was deemed unnecessary for the main text. For some papers, this is very important; sadly it’s often very long
Also called supplementary information, supporting information, etc
Scientific papers generally contain 5 sections
Important notes:
Read the paper in a different order from how it’s written!
Reading order:
Going through an example provides a guide
Going through an example provides a guide
The “megaplate” paper
1. Abstract
1. Abstract
Let’s read it and identify:
1. Abstract
Let’s read it and identify:
1. Abstract
Let’s read it and identify:
1. Abstract
Let’s read it and identify:
2. Introduction
Which part is the introduction?
2. Introduction
Which part is the introduction?
2. Introduction
This part sets up key background and context and a very general question: “how do populations evolve in spatially varying environments?
2. Introduction
This part introduces how the authors will answer the question, but doesn’t yet get into their results
3. Methods
The methods for this paper are in the supplementary material!
3. Methods
4. Figures/Results
The results are most of this paper.
We’ll go through them while we make a presentation about this paper.
5. Discussion
Pretty short here
6. Supplementary
Part II: Presenting papers
Your goal presenting a paper is to clearly present the main motivation of the study and their results.
During this section, we’ll quickly put together a presentation of Baym, et al. using the following approach
Before we do that, we will go over Joe’s Rules for presentations.
Joe’s Rules
1. Establish the main question or goal
Usually in the abstract and intro:
1. Establish the main question or goal
Usually in the abstract and intro:
1. Establish the main question or goal
Usually in the abstract and intro:
Intro
1. Establish the main question or goal
Usually in the abstract and intro:
Intro
1. Establish the main question or goal
Usually in the abstract and intro:
Intro
How do bacteria evolve in spatially varying environments?
→Find a visual to show this.
In general, it’s excellent to usual visuals to show key background. You can often find them in papers cited in the intro.
1. Establish the main question or goal
They also indirectly state a hypothesis in the intro
Intro
Adaptation dynamics should depend on the geometry of the environment
How do bacteria evolve in spatially varying environments?
Usual laboratory environment:
Usual wild environment:
Well-mixed, i.e. all cells experiencing the same environment
*wiki
Spatially varied, i.e. a cell’s environment change depending on where it is
1. Establish the main question or goal (potential slide)
Needed: a controlled, spatially varying environment to investigate bacterial evolution
1. Establish the main question or goal: transition into results (potential slide)
How can factors that impact bacterial growth be precisely spatially controlled?
2. Describe the method
Many papers display this in Figure 1
The Microbial Evolution and Growth Arena (MEGA)-plate allows the study of bacterial evolution in a spatially varying environment
Diagram:
Top photo:
120 cm (3.9 feet)
60 cm (2 feet)
antibiotic
MIC = minimum inhibitory concentration (don’t need to explain measurement, but be aware); it’s in the SM
Potential slide content:
2. Describe the method
Systematic control of spatial environment
Direct observation of microbial fitness
Potential less crowded slide:
Two antibiotics were tested, trimethoprim (TMP) and ciprofloxacin (CPR)
Ink facilitates colony photography
Swim agar lets cells spread across the plate before antibiotic gradients diffuse away
2. Describe the method (potential slide)
Why is the plate so big??
Top photo:
120 cm (3.9 feet)
60 cm (2 feet)
Standard bacterial plate
3. Describe the results
This almost always involves going through each figure in the paper
But don’t just show the figure!
Try to figure out the key messages of the figure and break them apart into separate slides.
3. Describe the results (potential slide)
Growing bacteria on the MEGAplate leads to the sequential emergence of resistant mutants
For images that are white or colored objects on a black background, I like to make the slides black!
Trimethoprim gradient
3. Describe the results
If you have cool movies, play them all
Ciprofloxacin gradient
3. Describe the results (potential slide)
Resistant lineages block off other by spreading out in space
Spatially varying antibiotic concentration
Time
*Joe’s Rule #2!!! (always explain axes)
This aspect ratio is difficult to see on the screen. Try breaking the graph up.
3. Describe the results (potential slide)
Resistant lineages block off other by spreading out in space
Spatially varying antibiotic concentration
Time
3. Describe the results (potential slide)
Resistant lineages block off other by spreading out in space
Appearance of mutant
Spreading out to block other lineages
3. Describe the results (potential slide)
Mutants become increasingly resistant to antibiotics
3. Describe the results (potential slide)
Mutants become increasingly resistant to antibiotics
Dots are points where they sampled bacteria to measure antibiotic tolerance
3. Describe the results (potential slide)
Mutants become increasingly resistant to antibiotics
Dots are points where they sampled bacteria to measure antibiotic tolerance
Color gives how tolerant the samples were
3. Describe the results (potential slide)
Mutants become increasingly resistant to antibiotics
Dots are points where they sampled bacteria to measure antibiotic tolerance
Color gives how tolerant the samples were
*Inset region from previous slides
3. Describe the results
Cleary describe the transitions between results. Often the transitions arise from questions raised by experimental results.
3. Describe the results
Cleary describe the transitions between results. Often the transitions arise from questions raised by experimental results.
For a lineage to propagate, it not only must be more tolerant of the antibiotic, it has to reach the region of high antibiotic first.
How does the geometry of selection impact bacterial adaptation?
3. Describe the results (potential slide)
The MEGAplate enables systematic study of how spatial antibiotic landscapes impact adaptation
Transition from lo to hi antibiotic
Increasing intermediate concentration
3. Describe the results (potential slide)
Cells straight from 0 to hi antibiotic are not able to adapt
Emerging lineage due to diffusive dilution of antibiotic, not microbial resistance
3. Describe the results (potential slide)
By progressing first through an intermediate concentration, cells can adapt
3. Describe the results (potential slide)
By progressing first through an intermediate concentration, cells can adapt
Trimethoprim [MIC]:
3000
300
0
30
3000
3
0
0
3000
3. Describe the results (potential slide)
Intermediate antibiotic enables adaptation, but high intermediates impede evolution
*Remember to explain axes!
3. Describe the results
Another transition:
Find a visual to illustrate this.
Perhaps highlight the resistant lineages on the plate and pose the question of what the mutations are.
3. Describe the results (potential slide)
The MEGAplate enables sampling and genotyping of resistant lineages
Are there common mutations?
Are there multiple mutations?
3. Describe the results (potential slide)
Resistant lineages separated into minimally and highly mutated groups
Sequencing results from 251 isolate MEGAplate lineages:
Lineages with >60 mutations
Lineages with <12 mutations
All highly mutated lineages have a mutation to dnaQ (proofreading DNA polymerase)
No minimally mutated lineages have dnaQ mutations
3. Describe the results (potential slide)
Highly mutated lineages did not adapt faster and were enriched in synonymous mutations
*Note that you need to make a choice for how to present this data.
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
This plot shows a ton of information at once.
Break it down.
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
First cover this
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
Each bar is a gene where they found a mutation
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
Each bar is a gene where they found a mutation
Y-axis is how many times that gene had a mutation
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
Each bar is a gene where they found a mutation
Y-axis is how many times that gene had a mutation
This bar contains all genes that showed only 1 mutation across all samples
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
Each bar is a gene where they found a mutation
Y-axis is how many times that gene had a mutation
This bar contains all genes that showed only 1 mutation across all samples
Color shows biological process involved
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
Each bar is a gene where they found a mutation
Y-axis is how many times that gene had a mutation
This bar contains all genes that showed only 1 mutation across all samples
Color shows biological process involved
Shading shows the kind of mutation
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
Many lineages had mutations to folA, the specific target of TMP
3. Describe the results (potential slide)
Non-synonymous TMP mutants often had mutations in specific pathways
Many lineages had mutations to folA, the specific target of TMP
But not all!
3. Describe the results
Non-synonymous mutants often had mutations in specific pathways
The inset shows the specific sampled lineages that had soxR mutations. This is actually never mentioned in the main text.
Leave this out of the slides!!! (Joe’s Rule #1)
3. Describe the results
The next section examines fit mutants that are blocked by lineages in front of them. It’s interesting, but difficult to read and therefore present. We’ll do our best.
3. Describe the results (potential slide)
Resistant mutants often showed low growth yield, which was later compensated
The authors track growth through white level in the photo at several points on the plate
3. Describe the results (potential slide)
Resistant mutants often showed low growth yield, which was later compensated
Some lineages show full fitness (cyan)
Other show partial fitness that’s later compensated by another mutation (magenta)
3. Describe the results
The authors find that the compensatory mutants were occasionally more fit than the full fitness mutants, but could not propagate because they were spatially trapped
3. Describe the results (potential slide)
Compensatory mutants become spatially trapped, but can be more fit than cells at the front
3. Describe the results
The supplementary material contains an experiment showing that trapped lineages can outcompete lineages from the front when they’re not trapped.
Let’s add this!
3. Describe the results (potential slide)
Spatially trapped lineages can be as or more fit than lineages at the front
3. Describe the results (potential slide)
Spatially trapped lineages can be as or more fit than lineages at the front
More cells here
(Not the strongest result in the paper)
3. Describe the results (potential slide)
Trapped lineages can outgrow the front when moved to a higher antibiotic concentration
5. Examine whether claims are justified
In Baym, et al., the claims are not very specific, so it’s not as straightforward to critique them. Nonetheless, it’s nice to return to the explicit claims.
5. Examine whether claims are justified (potential slide)
The authors made two explicit conclusions in the abstract
1
2
Are these conclusions justified?
5. Examine whether claims are justified (potential slide)
Claim 1: lineages diversified phenotypically and genotypically
Do lineages diversify phenotypically?
Return to each major claim, show data that supports it, and offer potential alternatives
Yes, they develop different antibiotic tolerance
5. Examine whether claims are justified (potential slide)
Claim 1: lineages diversified phenotypically and genotypically
Do lineages diversify genotypically?
Return to each major claim, show data that supports it, and offer potential alternatives
Yes, they show many mutations
5. Examine whether claims are justified (potential slide)
Claim 1: lineages diversified phenotypically and genotypically
Do lineages diversify genotypically?
Return to each major claim, show data that supports it, and offer potential alternatives
Yes, they show many mutations
One small critique: the authors do not check that all these mutations do confer TMP resistance. For three genes not previously associated with TMP resistance they do, but for all others, they just cite evidence that mutations to those pathways can confer resistance.
5. Examine whether claims are justified (potential slide)
Claim 2: highly resistant mutants can be spatially trapped
Return to each major claim, show data that supports it, and offer potential alternatives
This is a good experiment.
5. Examine whether claims are justified (potential slide)
Claim 2: highly resistant mutants can be spatially trapped
Return to each major claim, show data that supports it, and offer potential alternatives
This data is sketchy.
5. Examine whether claims are justified (potential slide)
No specific predictions were tested.
Offer any general critiques or remarks
They refer vaguely to predictions of spatial models, but don’t offer any themselves. This arguably takes away slightly from their result. If the system is so powerful for investigating spatial evolution models, which one are you investigating?
The paper, however, yields extremely rich data about evolution in spatially varying environments and shows a method to investigate specific models later on.
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