Scientific Writing Work Samples
This page shows various samples of Kimberly Decker's scientific writing. Examples include published articles in peer-reviewed journals, figure design and composition, abstracts for academic grant applications, as well as research and reporting related to experiment design and optimization.
Following is an excerpt from a published paper in Developmental Biology, which includes the article abstract.
Following is a figure composed for the same published Developmental Biology paper.
Click here to download a copy of the Developmental Biology article.
Scientific Abstracts and Grant Proposals
Following is an abstract written for a scientific meeting.
Acute lymphoblastic leukemia is a childhood blood disease characterized by uncontrolled growth of immature blood cells. Normally, stem cells mature within the bone marrow to become a wide range of cell types including antibody-producing B-cells that protect the body from infection and cancer. Leukemia is characterized by changes to genes that control normal B-cell development. Early in their development, B-cells must respond appropriately to competing signals that trigger cell growth and differentiation. For example, the protein Early B-cell Factor 1 (EBF1) is an essential protein that regulates B-cell development and inhibits cell growth, driving early B-cells to become mature B-cells. On the other hand, zinc finger protein 521 (Zfp521) is also present in early B-cells and likely determines whether cells should multiply or differentiate. Studies show that Zfp521 prevents EBF1 from turning on genes, probably through physical interaction. We suggest that Zfp521 promotes growth of immature cells by repressing EBF1 and inhibiting maturation of B-cells, and as cells mature, EBF1 prevents cell growth by inhibiting Zfp521. In humans and mice, EBF1 and Zfp521 are implicated in numerous types of leukemia. The goal of this project is to understand how interaction between EBF1 and Zfp521 contributes to normal B-cell development. First, the physical and functional interactions between EBF1 and Zfp521 will be characterized and second, a three-dimensional picture of how EBF1 binds to Zfp521 will be generated. Being able to visualize the interaction between EBF1 and Zfp521 will help us understand the functional roles of these proteins during normal B-cell development and shed light on how changes to EBF1 or Zfp521 leads to leukemia. EBF1 and Zfp521 are prospective biomarkers for diagnosis of pediatric leukemia and will likely be useful prognostic markers as well. This work will increase understanding of the causes of leukemia, and potentially provide new targets for the development of treatments for leukemia.
Following is an excerpt from an NIH grant proposal.
Experiment Design: Troubleshooting and problem analysis
The following writing sample was produced from research into a recurring problem related to the production of insect cells that would express a specific potein of interest. This document was submitted to a number of investgiators, and the report was used to inform my design of new experimental protocols to solve the identified problem.
INSTABILITY PROBLEMS RELATED TO RECOMBINANT BACULOVIRUS
Multiple rounds of plaque purification
Homologous recombination between a foreign DNA sequence in a transfer plasmid and the polyhedron gene in wild-type baculoviral DNA is necessary to produce recombinant viral DNA molecules that will express the protein of interest in insect cells. A double recombination event is required; however, single recombination events are far more frequent events. Recombinants produced by single recombination events are genetically unstable and will be lost within a round or two of viral replication. This is likely the problem we are experiencing.
Baculoviral plaque assays are used to distinguish between the small population of recombinant virus progeny and the large population of parental viral progeny. Visual screening (using marker genes, such as beta-galactosidase) is often used, but this screening technique will mark progeny resulting from both single and double recombination events. This pitfall is avoided by using the marker for prescreening, following by additional screening to confirm the double crossover event and produce a clonal stock of recombinant virus. Many references have been found in which researchers address this problem by performing multiple rounds (commonly 3) of plaque purification.
It is generally important to purify recombinant virus away from non-recombinant, parental, or improperly recombined viral DNA by plaque purification. Contamination with wildtype species, in particular, will lead to dilution of your recombinant virus over time because they generally infect and replicate at higher efficiency than recombinant virus.
Numerous commercial systems are marketed as follows: “can be used to clone and express genes from the baculovirus without plaque purification or selection in bacteria.” However, skipping plaque purification is ill advised because insect cells transfected using the in vitro recombination reaction can produce both recombinant and parental viral progeny, despite the application of negative selection pressure against the parental virus by TK and ganciclovir. One or more rounds of plaque purification are recommended.
Recombination via transposition less stable
Some commercial systems (e.g., Bac-to-Bac from Invitrogen) use an in vivo transposition approach to produce recombinant baculoviruses at 100% efficiency. Unfortunately, a disadvantage of this system is that recombinant baculoviruses retain the bacterial replicon, which appears to be associated with high levels of genetic instability upon serial passage of these viruses in insect cells. This instability problem has been addressed in a commercial product called FlashBac (Oxford Expression Technologies) that retains high recombinant yield. Baculovirus vectors produced using the Bac-toBac or FlashBac systems should be subjected to at least one round of plaque purification.
Spontaneous excision of BAC vector sequences
“Repeated baculovirus infections in cultured insect cells lead to the generation of defective interfering viruses (DIs) which accumulate at the expense of the intact helper virus and compromise heterologous protein expression ... resulting in the spontaneous deletion of the BAC vector including the expression cassette from the viral genome upon passage in insect cells … and a more stable virus is generated…. This phenomenon is known as passage effect and causes a sharp drop in protein production upon serial passage of baculoviruses in cultured insect cells.” (Pijlman 2003) Pijlman and colleagues isolated the production of DIs to the non-essential p94 viral gene. Unfortunately, there does not yet appear to be a commercial bacmid product available that addresses this problem.