Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules.

The accelerating expansion of online bioinformatics tools has profoundly impacted molecular biology, with such tools becoming integral to the modern life sciences. As a result, molecular biology laboratory education must train students to leverage bioinformatics in meaningful ways to be prepared for a spectrum of careers. Institutions of higher learning can benefit from a flexible and dynamic instructional paradigm that blends up-to-date bioinformatics training with best practices in molecular biology laboratory pedagogy. At North Carolina State University, the campus-wide interdisciplinary Biotechnology (BIT) Program has developed cutting-edge, flexible, inquiry-based Molecular Biology Laboratory Education Modules (MBLEMs). MBLEMs incorporate relevant online bioinformatics tools using evidenced-based pedagogical practices and in alignment with national learning frameworks. Students in MBLEMs engage in the most recent experimental developments in modern biology (e.g., CRISPR, metagenomics) through the strategic use of bioinformatics, in combination with wet-lab experiments, to address research questions. MBLEMs are flexible educational units that provide a menu of inquiry-based laboratory exercises that can be used as complete courses or as parts of existing courses. As such, MBLEMs are designed to serve as resources for institutions ranging from community colleges to research-intensive universities, involving a diverse range of learners. Herein, we describe this new paradigm for biology laboratory education that embraces bioinformatics as a critical component of inquiry-based learning for undergraduate and graduate students representing the life sciences, the physical sciences, and engineering.

Role of cell cycle-regulated expression in the localized incorporation of cell wall proteins in yeast.

The yeast cell wall is an essential organelle that protects the cell from mechanical damage and antimicrobial peptides, participates in cell recognition and adhesion, and is important for the generation and maintenance of normal cell shape. We studied the localization of three covalently bound cell wall proteins in Saccharomyces cerevisiae. Tip1p was found only in mother cells, whereas Cwp2p was incorporated in small-to-medium-sized buds. When the promoter regions of TIP1 and CWP2 (responsible for transcription in early G1 and S/G2 phases, respectively) were exchanged, the localization patterns of Tip1p and Cwp2p were reversed, indicating that the localization of cell wall proteins can be completely determined by the timing of transcription during the cell cycle. The third protein, Cwp1p, was incorporated into the birth scar, where it remained for several generations. However, we could not detect any role of Cwp1p in strengthening the birth scar wall or any functional interaction with the proteins that mark the birth scar pole as a potential future budding site. Promoter-exchange experiments showed that expression in S/G2 phase is necessary but not sufficient for the normal localization of Cwp1p. Studies of mutants in which septum formation is perturbed indicate that the normal asymmetric localization of Cwp1p also depends on the normal timing of septum formation, composition of the septum, or both.

The role of cell cycle-regulated expression in the localization of spatial landmark proteins in yeast.

In Saccharomyces cerevisiae, Bud8p and Bud9p are homologous plasma membrane glycoproteins that appear to mark the distal and proximal cell poles, respectively, as potential sites for budding in the bipolar pattern. Here we provide evidence that Bud8p is delivered to the presumptive bud site (and thence to the distal pole of the bud) just before bud emergence, and that Bud9p is delivered to the bud side of the mother-bud neck (and thence to the proximal pole of the daughter cell) after activation of the mitotic exit network, just before cytokinesis. Like the delivery of Bud8p, that of Bud9p is actin dependent; unlike the delivery of Bud8p, that of Bud9p is also septin dependent. Interestingly, although the transcription of BUD8 and BUD9 appears to be cell cycle regulated, the abundance of BUD8 mRNA peaks in G2/M and that of BUD9 mRNA peaks in late G1, suggesting that the translation and/or delivery to the cell surface of each protein is delayed and presumably also cell cycle regulated. The importance of time of transcription in localization is supported by promoter-swap experiments: expression of Bud8p from the BUD9 promoter leads to its localization predominantly to the sites typical for Bud9p, and vice versa. Moreover, expression of Bud8p from the BUD9 promoter fails to rescue the budding-pattern defect of a bud8 mutant but fully rescues that of a bud9 mutant. However, although expression of Bud9p from the BUD8 promoter fails to rescue a bud9 mutant, it also rescues only partially the budding-pattern defect of a bud8 mutant, suggesting that some feature(s) of the Bud8p protein is also important for Bud8p function. Experiments with chimeric proteins suggest that the critical element(s) is somewhere in the extracytoplasmic domain of Bud8p.