Imagining, designing, and interpreting experiments: Using quantitative assessment to improve instruction in scientific reasoning.

Effectively teaching scientific reasoning requires an understanding of the challenges students face when learning these skills. We designed an assessment that measures undergraduate student abilities to form hypotheses, design experiments, and interpret data from experiments in cellular and molecular biology. The assessment uses intermediate-constraint free-response questions with a defined rubric to facilitate use with large classes, while identifying common reasoning errors that may prevent students from becoming proficient at designing and interpreting experiments. The assessment measured a statistically significant improvement in a senior-level biochemistry laboratory course, and a larger improvement between the biochemistry lab students and a separate cohort in a first-year introductory biology lab course. Two common errors were identified for forming hypotheses and using experimental controls. Students frequently constructed a hypothesis that was a restatement of the observation it was supposed to explain. They also often made comparisons to control conditions not included in an experiment. Both errors were most frequent among first-year students, and decreased in frequency as students completed the senior-level biochemistry lab. Further investigation of the absent controls error indicated that difficulties with reasoning about experimental controls may be widespread in undergraduate students. The assessment was a useful instrument for measuring improvement in scientific reasoning at different levels of instruction, and identified errors that can be targeted to improve instruction in the process of science.

Battle of the Bacteria: Characterizing the Evolutionary Advantage of Stationary Phase Growth.

Providing students with authentic research opportunities has been shown to enhance learning and increase retention in STEM majors. Accordingly, we have developed a novel microbiology lab module, which focuses on the molecular mechanisms of evolution in E. coli, by examining the growth advantage in stationary phase (GASP) phenotype. The GASP phenotype is demonstrated by growing cells into long-term stationary phase (LTSP) and then competing them against un-aged cells in a fresh culture. This module includes learning goals related to strengthening practical laboratory skills and improving student understanding of evolution. In addition, the students generate novel data regarding the effects of different environmental stresses on GASP and the relationship between evolution, genotypic change, mutation frequency, and cell stress. Pairs of students are provided with the experimental background, select a specific aspect of the growth medium to modify, and generate a hypothesis regarding how this alteration will impact the GASP phenotype. From this module, we have demonstrated that students are able to achieve the established learning goals and have produced data that has furthered our understanding of the GASP phenotype. Journal of Microbiology & Biology Education.

Correlation, necessity, and sufficiency: Common errors in the scientific reasoning of undergraduate students for interpreting experiments.

Gaining an understanding of how science works is central to an undergraduate education in biology and biochemistry. The reasoning required to design or interpret experiments that ask specific questions does not come naturally, and is an essential part of the science process skills that must be learned for an understanding of how scientists conduct research. Gaps in these reasoning skills make it difficult for students to become proficient in reading primary scientific literature. In this study, we assessed the ability of students in an upper-division biochemistry laboratory class to use the concepts of correlation, necessity, and sufficiency in interpreting experiments presented in a format and context that is similar to what they would encounter when reading a journal article. The students were assessed before and after completion of a laboratory module where necessary vs. sufficient reasoning was used to design and interpret experiments. The assessment identified two types of errors that were commonly committed by students when interpreting experimental data. When presented with an experiment that only establishes a correlation between a potential intermediate and a known effect, students frequently interpreted the intermediate as being sufficient (causative) for the effect. Also, when presented with an experiment that tests only necessity for an intermediate, they frequently made unsupported conclusions about sufficiency, and vice versa. Completion of the laboratory module and instruction in necessary vs. sufficient reasoning showed some promise for addressing these common errors.

New ideas for an old enzyme: A short, question-based laboratory project for the purification and identification of an unknown LDH isozyme.

Enzyme purification projects are an excellent way to introduce many aspects of protein biochemistry, but can be difficult to carry out under the constraints of a typical undergraduate laboratory course. We have designed a short laboratory project for the purification and identification of an "unknown" lactate dehydrogenase (LDH) isozyme that can fit into a multiproject course without consuming too many laboratory days. The streamlined purification utilizes ammonium sulfate precipitation, affinity chromatography, and size exclusion chromatography to give good recovery of LDH with minimal equipment requirements, and can be completed in three laboratory periods of 3-4 hours. As part of this, we have designed a novel, qualitative format for an LDH activity assay that allows students to rapidly screen their column chromatography fractions without the need of a spectrophotometer or plate reader. The analysis phase of the project is question-driven, and can be completed in two laboratory periods. The students must determine which purification technique was most effective by quantifying LDH activity and total protein content at each step of the purification, and then identify their unknown isozyme through agarose gel electrophoresis. This module provides an engaging format for teaching protein biochemistry, with the flexibility to allow an instructor to modify it for their particular curriculum.

Positive and negative regulation of cellular sensitivity to anti-cancer drugs by FGF-2.

The development of resistance to chemotherapy by tumor cells remains a constant limitation to the treatment of cancer. Over the last several years, fibroblast growth factor-2 (FGF-2) has emerged as a growth factor that is capable of modifying the sensitivity of normal and tumor cells to anti-cancer drugs. FGF-2 can produce both drug resistance and drug sensitization in different cell types treated with a variety of cytotoxic agents. An understanding of the differential cellular trafficking and biological activities of the multiple FGF-2 isoforms will help in determining the circumstances under which FGF-2 acts to inhibit versus potentiate drug action. Recent advances suggest that expression of FGF-2 in tumor cells is involved with loss of response to chemotherapy in vivo. Thus, the manipulation of FGF-2 activities to increase the effectiveness of chemotherapeutic agents may have important clinical implications.

Chemosensitization by fibroblast growth factor-2 is not dependent upon proliferation, S-phase accumulation, or p53 status.

Fibroblast growth factor-2 (bFGF/FGF-2) is a pleiotropic growth factor that functions as a survival factor and directs apoptosis during embryogenesis and development. As a survival factor, FGF-2 would be expected to protect cells against drug toxicities. Such protection has been reported in some cells treated with some chemotherapeutic drugs. However, we recently demonstrated that FGF-2 can sensitize NIH 3T3 mouse fibroblasts to the cytotoxic and apoptotic effects of cisplatin. Sensitization requires prolonged incubation of cells with FGF-2 before the addition of cisplatin, and it requires an FGF-2 concentration (5-10 ng/mL) that is higher than that needed for its mitogenic effects (0.5 ng/mL). We now report that FGF-2 can also sensitize MCF7 human breast cancer cells and A2780 human ovarian cancer cells, as well as NIH 3T3 cells, to cisplatin. FGF-2 did not affect the cisplatin sensitivity of SKOV3 ovarian cancer cells or a panel of seven pancreatic cancer cell lines. We have demonstrated that the sensitizing effect is not simply a function of the mitogenic activity of FGF-2 on cells, as we did not observe sensitization with other growth-stimulatory factors (FGF-1 and epidermal growth factor); the sensitizing effect of FGF-2 was observed even with cell lines that were not growth-stimulated by FGF-2; and sensitization was not restricted to cells in S-phase of the cell cycle. These results indicate that cell proliferation is neither necessary nor sufficient for sensitization by FGF-2. Moreover, sensitization to cisplatin appears to be p53-independent, as p53-null 3T3 10-1 cells were equally sensitized by FGF-2. Finally, FGF-2 also sensitized NIH 3T3 and MCF7 cells to carboplatin, and had smaller effects on the sensitivity of these cell lines to doxorubicin and docetaxel. FGF-2 had no effect on sensitivity to etoposide in any cell line tested. Therefore, sensitization by FGF-2 was most effective with the platinum compounds, suggesting that this activity may be specific to particular mechanisms of drug action.