Steven Wormsley

A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis

Although the U3 small nucleolar RNA (snoRNA), a member of the box C/D class of snoRNAs, was identified with the spliceosomal small nuclear RNAs (snRNAs) over 30 years ago, its function and its associated protein components have remained more elusive. The U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA in all organisms where it has been tested. Biochemical and genetic analyses suggest that U3–pre-rRNA base-pairing interactions mediate endonucleolytic pre-rRNA cleavages. Here we have purified a large ribonucleoprotein (RNP) complex from Saccharomyces cerevisiae that contains the U3 snoRNA and 28 proteins. Seventeen new proteins (Utp1–17) and Rrp5 were present, as were ten known components. The Utp proteins are nucleolar and specifically associated with the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. On the basis of its large size (80S; calculated relative molecular mass of at least 2,200,000) and function, this complex may correspond to the terminal knobs present at the 5′ ends of nascent pre-rRNAs. We have termed this large RNP the small subunit (SSU) processome.

Mpp10p, a U3 small nucleolar ribonucleoprotein component required for pre-18S rRNA processing in yeast.

We have isolated and characterized Mpp10p, a novel protein component of the U3 small nucleolar ribonucleoprotein (snoRNP) from the yeast Saccharomyces cerevisiae. The MPP10 protein was first identified in human cells by its reactivity with an antibody that recognizes specific sites of mitotic phosphorylation. To study the functional role of MPP10 in pre-rRNA processing, we identified the yeast protein by performing a GenBank search. The yeast Mpp10p homolog is 30% identical to the human protein over its length. Antibodies to the purified yeast protein recognize a 110-kDa polypeptide in yeast extracts and immunoprecipitate the U3 snoRNA, indicating that Mpp10p is a specific protein component of the U3 snoRNP in yeast. As a first step in the genetic analysis of Mpp10p function, diploid S. cerevisiae cells were transformed with a null allele. Sporulation and tetrad analysis indicate that MPP10 is an essential gene. A strain was constructed where Mpp10p is expressed from a galactose-inducible, glucose- repressible promoter. After depletion of Mpp10p by growth in glucose, cell growth is arrested and levels of 18S and its 20S precursor are reduced or absent while the 23S and 35S precursors accumulate. This pattern of accumulation of rRNA precursors suggests that Mpp10p is required for cleavage at sites A0, A1, and A2. Pulse-chase analysis of newly synthesized pre-rRNAs in Mpp10p-depleted yeast confirms that little mature 18S rRNA formed. These results reveal a novel protein essential for ribosome biogenesis and further elucidate the composition of the U3 snoRNP.

An analysis of the Candida albicans genome database for soluble secreted proteins using computer-based prediction algorithms.

We sought to identify all genes in the Candida albicans genome database whose deduced proteins would likely be soluble secreted proteins (the secretome). While certain C. albicans secretory proteins have been studied in detail, more data on the entire secretome is needed. One approach to rapidly predict the functions of an entire proteome is to utilize genomic database information and prediction algorithms. Thus, we used a set of prediction algorithms to computationally define a potential C. albicans secretome. We first assembled a validation set of 47 C. albicans proteins that are known to be secreted and 47 that are known not to be secreted. The presence or absence of an N‐terminal signal peptide was correctly predicted by SignalP version 2.0 in 47 of 47 known secreted proteins and in 47 of 47 known non‐secreted proteins. When all 6165 C. albicans ORFs from CandidaDB were analysed with SignalP, 495 ORFs were predicted to encode proteins with N‐terminal signal peptides. In the set of 495 deduced proteins with N‐terminal signal peptides, 350 were predicted to have no transmembrane domains (or a single transmembrane domain at the extreme N‐terminus) and 300 of these were predicted not to be GPI‐anchored. TargetP was used to eliminate proteins with mitochondrial targeting signals, and the final computationally‐predicted C. albicans secretome was estimated to consist of up to 283 ORFs. The C. albicans secretome database is available at http://info.med.yale.edu/intmed/infdis/candida/ Copyright

Timing of revenue streams from newly recruited faculty: implications for faculty retention.

Purpose To determine the timing and magnitude of revenues generated by newly recruited faculty, to facilitate configuration of recruitment packages appropriately matched to expected financial returns. Method The aggregate of all positive cash flows to central college of medicine administration—from research, clinical care, tuition, philanthropy, and royalties and patents, from all faculty newly recruited to the University of Arizona College of Medicine between 1998 and 2004—was quantified using the net present value (npv) methodology, which incorporates the time value of money. Results Tenure-track faculty and, in particular, those with laboratory research programs, generated the highest positive central cash flows. The npv for positive cash flows (npv[+]) during 6 and 10 years for newly recruited assistant professors with laboratory research programs were

Strategies for defining financial benchmarks for the research mission in academic health centers.

118,600 and

A comprehensive space management model for facilitating programmatic research

255,400, respectively, and, for professors with laboratory research programs,

Polypyrimidine tract binding protein interacts with sequences involved in alternative splicing of beta-tropomyosin pre-mRNA.

172,600 and

Alternative splicing of beta-tropomyosin pre-mRNA: cis-acting elements and cellular factors that block the use of a skeletal muscle exon in nonmuscle cells.

298,000, respectively (associate professors were not analyzed because of limited numbers). Faculty whose appointments at the University of Arizona College of Medicine exceeded 15 years in duration were the most productive in central revenue generation, far in excess of their numbers proportionate to the total. Conclusions The results emphasize the critical importance of faculty retention, because even those newly recruited faculty who are most successful in central revenue generation (tenure track with laboratory research programs) must be retained for periods well in excess of 10 years to recoup the initial central investment required for their recruitment.

M Phase Phosphoprotein 10 Is a Human U3 Small Nucleolar Ribonucleoprotein Component

Valid financial benchmarks are needed for the research mission in academic health centers (AHCs). Databases listing institutional success in obtaining sponsored research funding are publicly available. However, these databases are generally not adjusted for AHC size, confounding useful comparisons between institutions. The authors suggest simple strategies, which depend on a form of ratio analysis, to circumvent this limitation. Annual rates of growth (rates of return, Rf) are determined for total National Institutes of Health research grant dollars, number of research grants, and average dollars per research grant for 15 U.S. AHCs. Selected institutions are compared to one another and to the total pool of medical school funding. Performance is evaluated over a ten-year period (1992–2001) to illustrate the advantages, limitations, and applications of the ratio analysis approach. Alternative strategies are suggested for individual AHCs to evaluate their departmental and organizational performance, again without regard to institution size, and also dependent on ratios. Application of these strategies, especially when individualized to the particular AHC, permits more accurate assessment of past performance and more accurate and effective planning for future growth.

Fibrillarin-associated box C/D small nucleolar RNAs in Trypanosoma brucei. Sequence conservation and implications for 2'-O-ribose methylation of rRNA.

In FY04, the authors developed and implemented models to manage existing and incremental research space, and to facilitate programmatic research, at the University of Arizona College of Medicine. Benchmarks were set for recovery of total sponsored research dollars and for facilities and administrative (F&A) dollars/net square foot (nsf) of space, based on college-wide metrics. Benchmarks were applied to units (departments, centers), rather than to individual faculty. Performance relative to the benchmark was assessed using three-year moving averages, and applied to existing blocks of space. Space was recaptured or allocated, in all cases to programmatic themes, using uniform policies. F&A revenues were returned on the basis of performance relative to a benchmark. During the first two years after implementation of the model (FY05 and FY06), and for the 24 units occupying research space, median total sponsored research revenue/nsf increased from