Instructional Models for Course-Based Research Experience (CRE) Teaching

The course-based research experience (CRE) with its documented educational benefits is increasingly being implemented in science, technology, engineering, and mathematics education. This article reports on a study that was done over a period of 3 years to explicate the instructional processes involved in teaching an undergraduate CRE. One hundred and two instructors from the established and large multi-institutional SEA-PHAGES program were surveyed for their understanding of the aims and practices of CRE teaching. This was followed by large-scale feedback sessions with the cohort of instructors at the annual SEA Faculty Meeting and subsequently with a small focus group of expert CRE instructors. Using a qualitative content analysis approach, the survey data were analyzed for the aims of inquiry instruction and pedagogical practices used to achieve these goals. The results characterize CRE inquiry teaching as involving three instructional models: 1) being a scientist and generating data; 2) teaching procedural knowledge; and 3) fostering project ownership. Each of these models is explicated and visualized in terms of the specific pedagogical practices and their relationships. The models present a complex picture of the ways in which CRE instruction is conducted on a daily basis and can inform instructors and institutions new to CRE teaching.

A function of yeast mRNA cap methyltransferase, Abd1, in transcription by RNA polymerase II

Capping enzymes bind the phosphorylated pol II CTD permitting cotranscriptional capping of nascent pre-mRNAs. We asked whether these interactions influence pol II function using ChIP in ts mutants of yeast capping enzymes. Pol II occupancy at the 5' ends of PGK1, ENO2, GAL1, and GAL10 was reduced by inactivation of the methyltransferase, Abd1, but not the guanylyltransferase, Ceg1, suggesting that Abd1 contributes to stable promoter binding. At other genes, Abd1 inactivation increased the 5':3' ratio of pol II density in the promoter-proximal region and caused Ser5 hyperphosphorylation of the pol II CTD. These results suggest an additional role for Abd1 in the promoter clearance and/or promoter-proximal elongation steps of transcription. The transcriptional functions of Abd1 are independent of methyltransferase activity. Manipulation of transcription by Abd1 may enhance cotranscriptional capping and also act as a checkpoint to ensure that a nascent transcript has a cap before it can be completed.

Dynamic association of capping enzymes with transcribing RNA polymerase II

The C-terminal heptad repeat domain (CTD) of RNA polymerase II (pol II) is proposed to target pre-mRNA processing enzymes to nascent pol II transcripts, but this idea has not been directly tested in vivo. In vitro, the yeast mRNA capping enzymes Ceg1 and Abd1 bind specifically to the phosphorylated CTD. Here we show that yeast capping enzymes cross-link in vivo to the 5' ends of transcribed genes and that this localization requires the CTD. Both the extent of CTD phosphorylation at Ser 5 of the heptad repeat and the binding of capping enzymes decreased as polymerase moved from the 5' to the 3' ends of the ACT1, ENO2, TEF1, GAL1, and GAL10 genes. Ceg1 is released early in elongation, but Abd1 can travel with transcribing pol II as far as the 3' end of a gene. The CTD kinase, Kin28, is required for binding, and the CTD phosphatase, Fcp1, is required for dissociation of capping enzymes from the elongation complex. CTD phosphorylation and dephosphorylation therefore control the association of capping enzymes with pol II as it transcribes a gene.

Regulation of the Mts1-Mts2-dependent ade6-M26 meiotic recombination hot spot and developmental decisions by the Spc1 mitogen-activated protein kinase of fission yeast

The M26 meiotic recombination hot spot in the ade6 gene of Schizosaccharomyces pombe is activated by the heterodimeric M26 binding protein Mts1-Mts2. The individual Mts1 (Atf1, Gad7) and Mts2 (Pcr1) proteins are also transcription factors involved in developmental decisions. We report that the Mts proteins are key effectors of at least two distinct classes of developmental decisions regulated by the mitogen-activated protein (MAP) kinase cascade. The first class (osmoregulation, spore viability, and spore quiescence) requires the Spc1 MAP kinase and the Mts1 protein but does not require the Mts2 protein. The second class (mating, meiosis, and recombination hot spot activation) requires the Spc1 kinase and the Mts1-Mts2 heterodimer. Northern and Western blotting eliminated any significant role for the Spc1 kinase in regulating the expression levels of the Mts proteins. Gel mobility shift experiments indicated that the Mts1-Mts2 heterodimer does not need to be phosphorylated to bind to ade6-M26 DNA in vitro. However, in vivo dimethyl sulfate footprinting demonstrated that protein-DNA interaction within cells is dependent upon the Spc1 MAP kinase, which phosphorylates the Mts1 protein. Thus, the Spc1 kinase helps regulate the effector activities of the Mts1-Mts2 heterodimer in part by modulating its ability to occupy the M26 DNA site in vivo. Meiotic recombination hot spot function is likely the result of DNA conformational changes imparted by binding of the Mts1-Mts2 meiotic transcription factor.

Biochemical and genetic characterization of the dominant positive element driving transcription ofthe yeast TBP-encoding gene, SPT15

We previously demonstrated that a combination of both positive and negative cis -acting upstream elements control the transcription of the gene encoding TBP ( SPT15 ) in Saccharomyces cerevisiae . One of these elements found in that study, resident between 5' flanking sequences -147 and -128 , and termed PED (for positive element distal), was found to play an essential positive role in driving transcription of the gene encoding TBP. In this report, we map at nucleotide-level resolution, the critical residues which comprise PED, purify and sequence the protein that binds to it and determine that this PED binding factor is Abf1p, an abundant yeast protein previously broadly implicated in both gene regulation and DNA replication. In the case of the TBP-encoding gene, however, Abf1p works through the PED element which is a non-consensus binding site. Based upon the work of others, the PED-variant ABF1 site would be predicted to be a very poor binding site for this factor yet Abf1p binds PED and a consensus ABF1 site with comparable affinity. These results are discussed in light of the broader context of Abf1p-mediated gene regulation.

Genetic tests of the role of Abf1p in driving transcription of the yeast TATA box bindng protein-encoding gene, SPT15

In this report we describe studies which utilized yeast strains bearing gain and loss of function alleles of ABF1 in order to attempt to directly implicate Abf1p in modulating transcription of the TBP-encoding gene, SPT15, in vivo. We found that overexpression of Abf1p in a yeast cell increased transcription of the TBP-encoding gene and that this stimulation depended upon the exact sequence of the Abf1p binding site (ABF1) present in the gene. Further, in a yeast strain expressing a temperature sensitive form of Abf1p, occupancy of the chromosomal ABF1 site in the TBP-encoding gene was immediately lost following a temperature shift. Both results suggest that Abf1p drives transcription of the TBP-encoding gene. Surprisingly though we found that continuous ABF1 cis-element occupancy by Abf1p was not acutely required for normal levels of transcription of either the TBP-encoding gene or other "Abf1p-driven" genes tested. We propose a model to explain these results and suggest mechanisms by which Abf1p could activate gene transcription.

Quantitative imaging of TATA-binding protein in living yeast cells

We describe the quantitative monitoring of TATA-binding protein (TBP) localization and expression in living Saccharomyces cerevisiae cells. We replaced the endogenous TBP with a green fluorescent protein (GFP) x TBP fusion, which was imaged quantitatively by laser scanning confocal microscopy (LSCM). When GFP x TBP expression was altered by using various promoters, the levels measured by LSCM correlated well with the levels determined by immunoblot of whole cell extract protein. These results show that GFP x TBP imaging not only offers a method of measurement equivalent to a more conventional technique but also provides real-time quantitation in living cells and subcellular localization information. Time-lapse confocal imaging of GFP x TBP in mitotic yeast cells revealed that it remains localized to the nucleus and displays an asymmetric distribution (1:0.7) between mother and daughter cells. Based on this and data from a mutant which underexpresses GFP x TBP, we suggest that intracellular levels of TBP are near rate-limiting for growth and viability.

Signal detection and noise suppression using a wavelet transform signal processor: application to ultrasonic flaw detection

The utilization of signal processing techniques in nondestructive testing, especially in ultrasonics, is widespread. Signal averaging, matched filtering, frequency spectrum analysis, neural nets, and autoregressive analysis have all been used to analyze ultrasonic signals. The Wavelet Transform (WT) is the most recent technique for processing signals with time-varying spectra. Interest in wavelets and their potential applications has resulted in an explosion of papers; some have called the wavelets the most significant mathematical event of the past decade. In this work, the Wavelet Transform is utilized to improve ultrasonic flaw detection in noisy signals as an alternative to the Split-Spectrum Processing (SSP) technique. In SSP, the frequency spectrum of the signal is split using overlapping Gaussian passband filters with different central frequencies and fixed absolute bandwidth. A similar approach is utilized in the WT, but in this case the relative bandwidth is constant, resulting in a filter bank with a self-adjusting window structure that can display the temporal variation of the signal's spectral components with varying resolutions. This property of the WT is extremely useful for detecting flaw echoes embedded in background noise. The detection of ultrasonic pulses using the wavelet transform is described and numerical results show good detection even for signal-to-noise ratios (SNR) of -15 dB. The improvement in detection was experimentally verified using steel samples with simulated flaws.

Identification of the cis-acting DNA sequence elements regulating the transcription of the Saccharomyces cerevisiae gene encoding TBP, the TATA box binding protein

TBP, the TATA-box binding protein, plays a key role in eukaryotic gene transcription since it is required for transcription initiation by all three eukaryotic nuclear DNA-dependent RNA polymerases. In order to gain insight into the mechanisms of regulation of this key basal transcription factor, we undertook a mutational analysis of the sequences involved in directing transcription of the gene encoding TBP in Saccharomyces cerevisiae. An extensive family of mutations in the promoter of the gene encoding TBP were fused to the Escherichia coli reporter gene lacZ, transferred back into yeast, and assayed for their ability to direct expression of beta-galactosidase. Levels of beta-galactosidase activity measured from yeast transformed with this family of constructs indicate that both positive- and negative-acting cis-elements located within 400 nucleotides of the transcription start site are involved in regulating transcription of the TBP-encoding gene. Analyses of RNA prepared from these same cells showed that specific transcription initiation is maintained in the mutant reporter constructs and that RNA levels mirror beta-galactosidase levels. In order to corroborate the results of these mutational analyses of the TBP-encoding gene, in vivo cis-element occupancy was examined using several different footprinting reagents. The patterns of protection observed demonstrated that the sequence elements implicated in the control of TBP gene transcription by reporter gene analyses appear to be bound by protein(s) in vivo. Interesting sequence similarities were noted between two TBP-gene regulatory elements and 5'-flanking sequences of genes encoding several other basal transcription factors.

Amino acids bracketing the predicted transmembrane domains of membrane proteins

The cell membrane is a complex mixture of several classes of biomolecules but amino acids and lipids are the main constituents. For this reason we are establishing a data base of transmembrane proteins with the intent of using the data base to identify interfacial peptide sequences useful for studying protein-lipid interactions at membrane interfaces. Our present intention is to characterize transmembrane peptides and amino acids found near the membrane interface. A data base containing only signal peptides is available (G. von Heijne, Prot. Seq. Data Anal. 1:41-42, 1987).