Making Scholarly Activity Available to the Masses: The Scaffolding of Scholarship Throughout the Undergraduate Curriculum

Florida Gulf Coast University’s Quality Enhancement Plan (QEP) focuses on improving student critical thinking, information literacy, and written communication. Rather than developing these skills through traditional methods (e.g., through senior-level, independent research), these learning outcomes are practiced through scholarly experiences. Traditional undergraduate scholarship manifests itself through terminal, senior capstone or research experiences. These, because of the economy of scale, typically reach a minority of students, often just honors students or those approached by faculty mentors. At FGCU, however, scholarly experiences are a part of the curriculum throughout the program of study, and scaffolded to build greater depth and sophistication. Presented here are examples from both a program in STEM (Marine Science) and the humanities (Music Performance). Students in Marine Science receive their first exposure to the vetting of literature and expository scientific writing within their general education science courses. Students are presented with an exercise to evaluate the credibility of web-based literature using the CRAAP test. A semester-long writing assignment has them investigate an earth-process-related problem that has societal consequences. They review and evaluate the secondary literature, prepare a first draft that is critiqued, and then submit a final version while meeting a number of milestones along the way. Students enter the major’s curriculum through a course entitled “Scientific Process”, which introduces them to all aspects of scientific research and culminates with them writing and defending a research proposal they may eventually work to completion. Numerous courses at the upper-class level are designed as scholarly focused or enriched, a branding requiring that certain criteria are met. In these courses, students often participate in genuine collaborative research projects that can lead to student publication and enhance faculty productivity. Finally, as a senior, the capstone course requires that they produce a scholarly poster or oral presentation that is either given in the class or within a university forum. Music Performance students’ experiences track towards demonstration of content mastery in the artifact of a senior recital. In this public display of scholarly achievement a student presents repertoire from major historical eras on his or her instrument or voice for an hour or more. Additionally the students complete a comprehensive document analyzing music in terms of performance practice (how and why certain music should be performed to meet historically appropriate creations and recreations). Students enter this major their freshman year after an audition process and immediately begin developing the skills required to demonstrate proficiency as professional musicians. Experiences performing in ensembles and in private lessons cultivate listening skills to make informed musical judgments. Theory courses develop students’ abilities to hear music with their eyes. Upper level courses require students to clearly articulate in writing their thoughts about music’s formal properties, why certain music requires particular performance considerations, and how to execute those performance requirements in their technique. The conundrum for collection of data is how to assess university-wide learning outcomes in the context of a performance. Without a tangible artifact, FGCU relies on artist teams to develop assessment procedures that accurately capture if students meet targets as demonstrated in performance. Though too early for us to have extensive assessment data, anecdotal evidence suggests students enjoy this approach and are honing their skills within these learning outcomes. We anticipate these improvements will increase graduates’ life-long learning potential, as well as their competitiveness for employment and further education

Cyclin-Dependent Kinase-Like Function Is Shared by the Beta- and Gamma- Subset of the Conserved Herpesvirus Protein Kinases

The UL97 protein of human cytomegalovirus (HCMV, or HHV-5 (human herpesvirus 5)), is a kinase that phosphorylates the cellular retinoblastoma (Rb) tumor suppressor and lamin A/C proteins that are also substrates of cellular cyclin-dependent kinases (Cdks). A functional complementation assay has further shown that UL97 has authentic Cdk-like activity. The other seven human herpesviruses each encode a kinase with sequence and positional homology to UL97. These UL97-homologous proteins have been termed the conserved herpesvirus protein kinases (CHPKs) to distinguish them from other human herpesvirus-encoded kinases. To determine if the Cdk-like activities of UL97 were shared by all of the CHPKs, we individually expressed epitope-tagged alleles of each protein in human Saos-2 cells to test for Rb phosphorylation, human U-2 OS cells to monitor nuclear lamina disruption and lamin A phosphorylation, or S. cerevisiae cdc28-13 mutant cells to directly assay for Cdk function. We found that the ability to phosphorylate Rb and lamin A, and to disrupt the nuclear lamina, was shared by all CHPKs from the beta- and gamma-herpesvirus families, but not by their alpha-herpesvirus homologs. Similarly, all but one of the beta and gamma CHPKs displayed bona fide Cdk activity in S. cerevisiae, while the alpha proteins did not. Thus, we have identified novel virally-encoded Cdk-like kinases, a nomenclature we abbreviate as v-Cdks. Interestingly, we found that other, non-Cdk-related activities reported for UL97 (dispersion of promyelocytic leukemia protein nuclear bodies (PML-NBs) and disruption of cytoplasmic or nuclear aggresomes) showed weak conservation among the CHPKs that, in general, did not segregate to specific viral families. Therefore, the genomic and evolutionary conservation of these kinases has not been fully maintained at the functional level. Our data indicate that these related kinases, some of which are targets of approved or developmental antiviral drugs, are likely to serve both overlapping and non-overlapping functions during viral infections

Relationship between Yeast Polyribosomes and Upf Proteins Required for Nonsense mRNA Decay

In yeast, the accelerated rate of decay of nonsense mutant mRNAs, called nonsense-mediated mRNA decay, requires three proteins, Upf1p, Upf2p, and Upf3p. Single, double, and triple disruptions of the UPF genes had nearly identical effects on nonsense mRNA accumulation, suggesting that the encoded proteins function in a common pathway. We examined the distribution of epitope-tagged versions of Upf proteins by sucrose density gradient fractionation of soluble lysates and found that all three proteins co-distributed with 80 S ribosomal particles and polyribosomes. Treatment of ly-sates with RNase A caused a coincident collapse of polyribosomes and each Upf protein into frac-tions containing 80 S ribosomal particles, as expected for proteins that are associated with polyribosomes. Mutations in the cysteine-rich (zinc finger) and RNA helicase domains of Upf1p caused loss of function, but the mutant proteins remained polyribosome-associated. Density gradi-ent profiles for Upf1p were unchanged in the absence of Upf3p, and although similar, were modestly shifted to fractions lighter than those containing polyribosomes in the absence of Upf2p. Upf2p shifted toward heavier polyribosome fractions in the absence of Upf1p and into fractions containing 80 S particles and lighter fractions in the absence of Upf3p. Our results suggest that the association of Upf2p with polyribosomes typically found in a wild-type strain depends on the presence and opposing effects of Upf1p and Upf3p

Relationship between Yeast Polyribosomes and Upf Proteins Required for Nonsense mRNA Decay

In yeast, the accelerated rate of decay of nonsense mutant mRNAs, called nonsense-mediated mRNA decay, requires three proteins, Upf1p, Upf2p, and Upf3p. Single, double, and triple disruptions of the UPF genes had nearly identical effects on nonsense mRNA accumulation, suggesting that the encoded proteins function in a common pathway. We examined the distribution of epitope-tagged versions of Upf proteins by sucrose density gradient fractionation of soluble lysates and found that all three proteins co-distributed with 80 S ribosomal particles and polyribosomes. Treatment of ly-sates with RNase A caused a coincident collapse of polyribosomes and each Upf protein into frac-tions containing 80 S ribosomal particles, as expected for proteins that are associated with polyribosomes. Mutations in the cysteine-rich (zinc finger) and RNA helicase domains of Upf1p caused loss of function, but the mutant proteins remained polyribosome-associated. Density gradi-ent profiles for Upf1p were unchanged in the absence of Upf3p, and although similar, were modestly shifted to fractions lighter than those containing polyribosomes in the absence of Upf2p. Upf2p shifted toward heavier polyribosome fractions in the absence of Upf1p and into fractions containing 80 S particles and lighter fractions in the absence of Upf3p. Our results suggest that the association of Upf2p with polyribosomes typically found in a wild-type strain depends on the presence and opposing effects of Upf1p and Upf3p

The Majority of Yeast UPF1 Co-localizes with Polyribosomes in the Cytoplasm

In Saccharomyces cerevisiae the UPF1 protein is required for nonsense-mediated mRNA decay, the accelerated turnover of mRNAs containing a nonsense mutation. Several lines of evidence suggest that translation plays an important role in the mechanism of nonsense mRNA decay, including a previous report that nonsense mRNAs assemble in polyribosomes. In this study we show that UPF1 and ribosomal protein Li co-localize in the cytoplasm and that UPF1 co-sediments with polyribosomes. To detect UPF1, three copies of the influenza hemagglutinin epitope were placed at the C-terminus. The tagged protein, UPF1-3EP, retains 86% (± 5%) of function. Using immunological detection, we found that UPF1-3EP is primarily cytoplasmic and was not detected either in the nucleus or in the mitochondrion. UPF1-3EP and Li co-distributed with polyribosomes fractionated in a 7-47% sucrose gradient. The sucrose sedimentation profiles for UPF1-3EP and Li exhibited similar changes using three different sets of conditions that altered the polyribosome profile. When polyribosomes were disaggregated, UPF1-3EP and Li accumulated in fractions coincident with 80S ribosomal particles. These results suggest that UPF1-3EP associates with polyribosomes. L3 and S3 mRNAs, which code for ribosomal proteins of the 60S and 40S ribosomal subunits, respectively, were on average about 100-fold more abundant than UPF1 mRNA. Assuming that translation rates for L3, S3, and UPF1 mRNA are similar, this result suggests that there are far fewer UPF1 molecules than ribosomes per cell. Constraints imposed by the low UPF1 abundance on the functional relationships between UPF1, polyribosomes, and nonsense mRNA turnover are discussed

Impact of Nonsense-Mediated mRNA Decay on the Global Expression Profile of Budding Yeast

Nonsense-mediated mRNA decay (NMD) is a eukaryotic mechanism of RNA surveillance that selectively eliminates aberrant transcripts coding for potentially deleterious proteins. NMD also functions in the normal repertoire of gene expression. In Saccharomyces cerevisiae, hundreds of endogenous RNA Polymerase II transcripts achieve steady-state levels that depend on NMD. For some, the decay rate is directly influenced by NMD (direct targets). For others, abundance is NMD-sensitive but without any effect on the decay rate (indirect targets). To distinguish between direct and indirect targets, total RNA from wild-type (Nmd(+)) and mutant (Nmd(−)) strains was probed with high-density arrays across a 1-h time window following transcription inhibition. Statistical models were developed to describe the kinetics of RNA decay. 45% ± 5% of RNAs targeted by NMD were predicted to be direct targets with altered decay rates in Nmd(−) strains. Parallel experiments using conventional methods were conducted to empirically test predictions from the global experiment. The results show that the global assay reliably distinguished direct versus indirect targets. Different types of targets were investigated, including transcripts containing adjacent, disabled open reading frames, upstream open reading frames, and those prone to out-of-frame initiation of translation. Known targeting mechanisms fail to account for all of the direct targets of NMD, suggesting that additional targeting mechanisms remain to be elucidated. 30% of the protein-coding targets of NMD fell into two broadly defined functional themes: those affecting chromosome structure and behavior and those affecting cell surface dynamics. Overall, the results provide a preview for how expression profiles in multi-cellular eukaryotes might be impacted by NMD. Furthermore, the methods for analyzing decay rates on a global scale offer a blueprint for new ways to study mRNA decay pathways in any organism where cultured cell lines are available

Search for New Particles Decaying to b bbar in p pbar Collisions at sqrt{s}=1.8 TeV

We have used 87 pb^-1 of data collected with the Collider Detector at Fermilab to search for new particles decaying to b bbar. We present model-independent upper limits on the cross section for narrow resonances which excludes the color-octet technirho in the mass interval 350 < M < 440 GeV/c^2. In addition, we exclude topgluons, predicted in models of topcolor-assisted technicolor, of width Gamma = 0.3 M in the mass range 280 < M < 670 GeV/c^2, of width Gamma = 0.5 M in the mass range 340 < M < 640 GeV/c^2, and of width Gamma = 0.7 M in the mass range 375 < M < 560 GeV/c^2.Comment: 17 pages in a LaTex generated postscript file, with one table and four figures. Resubmitted to Physical Review Letters. Minor clarifications were added to the text. The displayed normalization of the resonance models in Figure 2 was modified to correspond to our 95% CL upper limit on the cross section (instead of arbitrary normalization which was used previously). All results are identical to those in the previous submissio

Combined Forward-Backward Asymmetry Measurements in Top-Antitop Quark Production at the Tevatron

The CDF and D0 experiments at the Fermilab Tevatron have measured the asymmetry between yields of forward- and backward-produced top and antitop quarks based on their rapidity difference and the asymmetry between their decay leptons. These measurements use the full data sets collected in proton-antiproton collisions at a center-of-mass energy of $\sqrt s =1.96$ TeV. We report the results of combinations of the inclusive asymmetries and their differential dependencies on relevant kinematic quantities. The combined inclusive asymmetry is $A_{\mathrm{FB}}^{t\bar{t}} = 0.128 \pm 0.025$. The combined inclusive and differential asymmetries are consistent with recent standard model predictions