Directions: Write a Title, Abstract, Introduction, Results, and Discussion sections of your paper, and include a final Model Figure with accompanying legend.Your goal is to interpret the data (1-5) below and devise a compelling biological story that is consistent with your observations. Use your creativity to transform evidence into argument and persuade your audience that you have an important new insight into the molecular mechanisms that regulate an important developmental process.
Title (Limit: 20 words)
The title should state the main lesson from the study.
Abstract (Limit: 200 words)
The Abstract is a pocket-sized synopsis of the paper. The goal is to entice the reader while providing a pithy summary of what new biology was learned in this study. Think of how to address the following questions and type in your abstract only.
What is a key unanswered question in my field?
What is the biomedical relevance of my model system?
What are my main findings?
How do my findings answer key questions in the field?
Introduction (Limit: 300 words)
The Introduction sets the stage for your story and provides the reader with the background needed to understand the results. This section differs from the Abstract and the Discussion because the majority of the points in the Intro focus on providing a context for the story, while the Abstract is a summary and the Discussion provides the interpretation. Because your study is based on fictional biology, your Introduction will be shorter than is typical. Cite real papers for bonus points!
Results (Limit: 400 words per section)
The Results should be broken into sections, each bearing a bold heading that describes the section’s major biological lesson. These sections should follow the figures in sequence to avoid forcing the reader to skip around. Refer to the corresponding figure parenthetically the first time it arises. In each section, you should provide: 1) a brief justification for why the experiment was done, 2) a description of the experiment (including model organism, technique, positive and/or negative controls, and sample size), 3) observations, and 4) inferences or conclusions of your observations. The text should mirror, but not duplicate, the figure legends.
Discussion (Limit: 600 words)
The Discussion section is where you will interpret your observations and tie these together into a broader model that explains how your gene/gene product regulates your developmental process. In this section, you should: 1) make reference to your model figure, 2) describe future experiments that you would do to test your model, 3) state the experimental outcomes that would support your model, and 4) describe any alternative interpretations of your data and how your experiments would distinguish between these models.
Be careful to propose experiments that test your hypotheses in the most straightforward and focused way. Here are some examples:
To measure levels of a given gene, quantitative RT-PCR is more straightforward, faster, and cheaper than RNA-seq.
To test the interaction between two known proteins, pull-down + western blot is better than mass spectrometry.
To learn the phenotype resulting from a loss of a known gene, a reverse genetic technique (shRNA, siRNA, targeted knockout, or Cas9/CRISPR) would be better than a random mutagenesis screen.
To determine if a transcription factor binds to a particular enhancer, ChIP-qPCR is better than ChIP-seq.
Finally, the Discussion section should be as concise as all other sections – speculation is encouraged but your ideas should not drift too far from the data that they are based upon.
Model Figure with Legend (Limit: 100 words)
You will draw a model figure and include this as the final figure in your paper. The model should illustrate one or more molecular mechanisms by which your genes/proteins regulate the developmental process that is the topic of your paper. Computer or hand-drawn figures are acceptable. In the accompanying legend, succinctly summarize the model and define any symbols used.
1. Predicted domains of proteins encoded by newly identified genes.
Novel = no known function, TM = putative transmembrane domain, PB = putative protein binding domain, kinase = putative kinase activity.
2. Phenotypes of mutants recovered from F3 mutagenic screen. (A) Mutagenesis and genetic screen strategy. (B) wild type (C) no eye mutant (D) little eye 1 mutant (E) little eye 2 mutant (F) ley1 ley2 double mutant (G) ney ley1 double mutant (H) ney ley2 double mutant.
3. Correlations between mutant and wild type larval transcript levels. In each panel a dot is color-coded probes to match the gene on x or y axis. The blue arrow indicates an unknown transcript (JY.8675309).
4. Subcellular localization of JY.867 in cultured cell line. A) Background fluorescence in untransfected cells. B) Cells transfected with expression plasmid encoding JY.8675309. C) Cells cotransfected with Ley2 and JY.8675309 expression plasmids. D) Cells cotransfected with expression plasmids encoding Ley2, JY.8675309, and short hairpin specific to Ley1 mRNA.
5. Phenotypes resulting from siRNA treatment of larval proto-eyes. A) Typical phenotype resulting from embryo injection with scrambled siRNAs. B) Phenotype resulting from injection of ney siRNA. C) Phenotype resulting from injection of siRNA specific to novel gene JY.8675309.
Title: Molecular Mechanisms Regulating Developmental Processes Revealed Through Gene Analysis
Abstract:
The study aims to uncover the molecular mechanisms involved in regulating an important developmental process through the analysis of newly identified genes. Key unanswered questions in the field are addressed, and the biomedical relevance of the chosen model system is discussed. The main findings of the study include the identification of predicted domains of proteins encoded by the newly identified genes, the phenotypes of mutants recovered from a mutagenic screen, correlations between mutant and wild type larval transcript levels, subcellular localization of a specific gene, and the phenotypes resulting from siRNA treatment. These findings provide insights into the role of these genes in regulating the developmental process and open up possibilities for future experiments and further understanding of the molecular mechanisms involved.
Introduction:
The development of various organisms involves intricate molecular mechanisms that regulate key processes. Understanding these mechanisms is crucial for deciphering the complexities of development and potential implications in human health. In this study, we focus on newly identified genes and investigate their roles in the regulation of an important developmental process. By examining the predicted domains of the proteins encoded by these genes, studying the phenotypes of mutants obtained from a mutagenic screen, analyzing the transcript levels in mutants and wild type larvae, exploring subcellular localization, and observing the phenotypes resulting from siRNA treatment, we aim to gain valuable insights into the molecular mechanisms that govern this developmental process.
Results:
1. Predicted domains of proteins encoded by newly identified genes:
The proteins encoded by the newly identified genes exhibit various predicted domains, including putative transmembrane domains, protein binding domains, and putative kinase activities. These domains suggest potential functional roles for these proteins in the regulation of the developmental process.
2. Phenotypes of mutants recovered from F3 mutagenic screen:
Through a mutagenic screen, we obtained mutants with different phenotypes. These include a no eye mutant, little eye 1 and little eye 2 mutants, ley1 ley2 double mutant, ney ley1 double mutant, and ney ley2 double mutant. These mutants provide valuable insights into the specific genes' roles in the developmental process.
3. Correlations between mutant and wild type larval transcript levels:
Analysis of transcript levels revealed correlations between mutant and wild type larvae. Interestingly, an unknown transcript (JY.8675309) showed a significant correlation with certain genes. This suggests a potential interaction or regulatory role of JY.8675309 in the developmental process.
4. Subcellular localization of JY.867 in cultured cell line:
The subcellular localization of JY.8675309 was examined in a cultured cell line. We observed background fluorescence in untransfected cells, but cells transfected with expression plasmids encoding JY.8675309 showed distinct subcellular localization. Co-transfection of Ley2 and JY.8675309 expression plasmids resulted in altered localization, indicating a potential interaction between these proteins. Furthermore, co-transfection with a short hairpin specific to Ley1 mRNA affected the localization, suggesting a regulatory mechanism involving Ley genes.
5. Phenotypes resulting from siRNA treatment of larval proto-eyes:
To further investigate the function of JY.8675309, siRNA treatments were performed. Injection of siRNA specific to JY.8675309 resulted in a distinct phenotype in larval proto-eyes, indicating its involvement in regulating the developmental process.
Discussion:
Based on our observations, we propose a model that highlights the potential molecular mechanisms involved in regulating the developmental process. The model figure illustrates interactions between proteins encoded by newly identified genes, their subcellular localization, and potential regulatory interactions with Ley genes. To further validate our model, future experiments could include quantitative RT-PCR to measure transcript levels of specific genes, pull-down and western blot techniques to test protein interactions, reverse genetic techniques to determine the phenotypes resulting from the loss of known genes, and ChIP-qPCR experiments to investigate transcription factor binding. These experiments would provide crucial data to support our proposed model and differentiate between alternative interpretations of the data.
Model Figure with Legend:
[Insert Model Figure]
Legend: The model figure illustrates the potential molecular mechanisms regulating the developmental process. Novel genes (red) encode proteins with predicted domains (TM, PB, and kinase) that interact with Ley genes (blue). The subcellular localization of JY.8675309 is influenced by Ley2, and further regulation involves the presence of a short hairpin specific to Ley1 mRNA. The figure depicts the potential interactions and regulatory pathways involved in controlling the developmental process.