Faculty Scholarship
Showing 451 - 460 of 733 Items
Mutations in a signal sequence for the thylakoid membrane identify multiple protein transport pathways and nuclear suppressors
Date: 1994-07-01
Creator: Tracy A. Smith, Bruce D. Kohorn
Access: Open access
- The apparatus that permits protein translocation across the internal thylakoid membranes of chloroplasts is completely unknown, even though these membranes have been the subject of extensive biochemical analysis. We have used a genetic approach to characterize the translocation of Chlamydomonas cytochrome f, a chloroplast-encoded protein that spans the thylakoid once. Mutations in the hydrophobic core of the cytochrome f signal sequence inhibit the accumulation of cytochrome f, lead to an accumulation of precursor, and impair the ability of Chlamydomonas cells to grow photosynthetically. One hydrophobic core mutant also reduces the accumulation of other thylakoid membrane proteins, but not those that translocate completely across the membrane. These results suggest that the signal sequence of cytochrome f is required and is involved in one of multiple insertion pathways. Suppressors of two signal peptide mutations describe at least two nuclear genes whose products likely describe the translocation apparatus, and selected second- site chloroplast suppressors further define regions of the cytochrome f signal peptide.
A cascading N = 1 Sp(2N + 2M) × Sp(2N) gauge theory
Date: 2002-08-26
Creator: Stephen G. Naculich, Howard J. Schnitzer, Niclas Wyllard
Access: Open access
- We study the N=1 Sp(2N + 2M) × Sp(2N) cascading gauge theory on a stack of N physical and M fractional (half) D3-branes at the singularity of an orientifolded conifold. In addition to the D3-branes and an O7-plane, the background contains eight D7-branes, which give rise to matter in the fundamental representation of the gauge group. The moduli space of the gauge theory is analyzed and its structure is related to the brane configurations in the dual type IIB theory and in type IIA/M-theory. © 2002 Elsevier Science B.V. All rights reserved.
Using 'big data' to explain visits to lakes in 17 US states
Date: 2020-07-01
Creator: Erik Nelson, Maggie Rogers, Spencer Wood, Jesse Chung, Bonnie, Keeler
Access: Open access
- We use large dataset on US lakes from 17 states to estimate the relationship between summertime visits to lakes as proxied by social media use and the lakes' water quality, amenities, and surrounding landscape features and socioeconomic conditions. Prior to estimating these relationships we worked on 1) selecting a parsimonious set of explanatory variables from a roster of more than 100 lake attributes and 2) accounting for the non-random pattern of missing water quality data. These steps 1) improved the interpretability of the estimated visit models and 2) widened our estimated models' scope of statistical inference. We used Machine Learning techniques to select parsimonious sets of explanatory variables and multiple imputation to estimate water quality at lakes missing this data. We found the following relationships between summertime visits to lake and their attributes across the 17-state region. First, we estimated that every additional meter of average summer-time Secchi depth between 1995 and 2014 was associated with at least 7.0% more summer-time visits to a lake between 2005 to 2014, all else equal. Second, we consistently found that lake amenities, such as beaches, boat launches, and public toilets, were more powerful predictors of visits than water quality. Third, we also found that visits to a lake were strongly influenced by the lake's accessibility and its distance to nearby lakes and the amenities the nearby lakes offered. Finally, our results highlight the biased results that "big data"-based research on recreation can generate if non-random missing observation patterns in the data are not corrected.
A critical, analytical framework for the digital machine
Date: 2021-01-01
Creator: Crystal Hall, Eric Chown, Fernando Nascimento
Access: Open access
- The Faculty of Digital and Computational Studies (DCS) at Bowdoin College proposes a critical, analytical framework, referred to as the ‘4As,’ as an interdisciplinary means to interpret, evaluate, and create the data, operations, and devices of computing across all domains of knowledge production. Following other disciplines that have developed in symbiotic relationships to one another, DCS puts computation in conversation with fields from across the arts, humanities, physical, and social sciences. Our foundational premise is the bidirectional influence between these disciplines and digital artifacts and computation. The 4As (artifact, architecture, abstraction, and agency) benefit from both the scepticism of the liberal arts in the face of ubiquitous digital processes and the analytical opening for examining questions pertaining to creative and imaginative alternatives to the digital and computational status quo. We provide an ultra-contemporary case study to demonstrate the framework in use.
Xanthophyll cycle activity in two prominent arctic shrub species
Date: 2017-01-01
Creator: T.S. Magney, B.A. Logan, J.S. Reblin, N.T. Boelman, J.U.H., Eitel, H.E. Greaves, K.L. Griffin, C.M. Prager, L.A. Vierling
Access: Open access
The “New” Prosumer: Collaboration on the Digital and Material “New Means of Prosumption”
Date: 2013-04-13
Creator: George Ritzer
Access: Open access
- Many of “cyber-utopians” have lauded the Internet, especially social networking sites, for a variety of reasons, including making possible a dramatic and revolutionary increase in social collaboration (Benkler, 2007; Tapscott and Williams, 2006). The goal of this essay is to examine- and, at least in part, debunk- this claim from a new and unique sociological perspective- the relationship between collaboration and the “new means of prosumption”. Such an examination is suggested by the fact that collaboration is, by definition, a form of prosumption. That is, it involves one or more parties “producing” and other(s) “consuming” something of mutual interest and importance. However, the collaborative process, like prosumption more generally, is not as separable as all that. In fact, collaboration is a dialectical process in which those involved are continually changing their positions on the prosumption continuum (see below), sometimes they are more
Human protein Sam68 relocalization and interaction with poliovirus RNA polymerase in infected cells
Date: 1996-03-19
Creator: A. E. Mcbride, A. Schlegel, K. Kirkegaard
Access: Open access
- A HeLa cDNA expression library was screened for human polypeptides that interacted with the poliovirus RNA-dependent RNA polymerase, 3D, using the two-hybrid system in the yeast Saccharomyces cerevisiae. Sam68 (Src- associated in mitosis, 68 kDa) emerged as the human cDNA that, when fused to a transcriptional activation domain, gave the strongest 3D interaction signal with a LexA-3D hybrid protein. 3D polymerase and Sam68 coimmunoprecipitated from infected human cell lysates with antibodies that recognized either protein. Upon poliovirus infection. Sam68 relocalized from the nucleus to the cytoplasm, where poliovirus replication occurs. Sam68 was isolated from infected cell lysates with an antibody that recognizes poliovirus protein 2C, suggesting that it is found on poliovirus-induced membranes upon which viral RNA synthesis occurs. These data, in combination with the known RNA- and protein-binding properties of Sam68, make Sam68 a strong candidate for a host protein with a functional role in poliovirus replication.
Contingent planning under uncertainty via stochastic satisfiability
Date: 2003-07-01
Creator: Stephen M. Majercik, Michael L. Littman
Access: Open access
- We describe a new planning technique that efficiently solves probabilistic propositional contingent planning problems by converting them into instances of stochastic satisfiability (SSAT) and solving these problems instead. We make fundamental contributions in two areas: the solution of SSAT problems and the solution of stochastic planning problems. This is the first work extending the planning-as-satisfiability paradigm to stochastic domains. Our planner, ZANDER, can solve arbitrary, goal-oriented, finite-horizon partially observable Markov decision processes (POMDPs). An empirical study comparing ZANDER to seven other leading planners shows that its performance is competitive on a range of problems. © 2003 Elsevier Science B.V. All rights reserved.
Identification of methylated proteins in the yeast small ribosomal subunit: A role for SPOUT methyltransferases in protein arginine methylation
Date: 2012-06-26
Creator: Brian D. Young, David I. Weiss, Cecilia I. Zurita-Lopez, Kristofor J. Webb, Steven G., Clarke, Anne E. McBride
Access: Open access
- We have characterized the posttranslational methylation of Rps2, Rps3, and Rps27a, three small ribosomal subunit proteins in the yeast Saccharomyces cerevisiae, using mass spectrometry and amino acid analysis. We found that Rps2 is substoichiometrically modified at arginine-10 by the Rmt1 methyltransferase. We demonstrated that Rps3 is stoichiometrically modified by ω- monomethylation at arginine-146 by mass spectrometric and site-directed mutagenic analyses. Substitution of alanine for arginine at position 146 is associated with slow cell growth, suggesting that the amino acid identity at this site may influence ribosomal function and/or biogenesis. Analysis of the three-dimensional structure of Rps3 in S. cerevisiae shows that arginine-146 makes contacts with the small subunit rRNA. Screening of deletion mutants encoding potential yeast methyltransferases revealed that the loss of the YOR021C gene results in the absence of methylation of Rps3. We demonstrated that recombinant Yor021c catalyzes ω-monomethylarginine formation when incubated with S-adenosylmethionine and hypomethylated ribosomes prepared from a YOR021C deletion strain. Interestingly, Yor021c belongs to the family of SPOUT methyltransferases that, to date, have only been shown to modify RNA substrates. Our findings suggest a wider role for SPOUT methyltransferases in nature. Finally, we have demonstrated the presence of a stoichiometrically methylated cysteine residue at position 39 of Rps27a in a zinc-cysteine cluster. The discovery of these three novel sites of protein modification within the small ribosomal subunit will now allow for an analysis of their functional roles in translation and possibly other cellular processes. © 2012 American Chemical Society.
Protein arginine methylation in Candida albicans: Role in nuclear transport
Date: 2007-07-01
Creator: Anne E. McBride, Cecilia Zurita-Lopez, Anthony Regis, Emily Blum, Ana, Conboy, Shannon Elf, Steven Clarke
Access: Open access
- Protein arginine methylation plays a key role in numerous eukaryotic processes, such as protein transport and signal transduction. In Candida albicans, two candidate protein arginine methyltransferases (PRMTs) have been identified from the genome sequencing project. Based on sequence comparison, C. albicans candidate PRMTs display similarity to Saccharomyces cerevisiae Hmt1 and Rmt2. Here we demonstrate functional homology of Hmt1 between C. albicans and S. cerevisiae: CaHmt1 supports growth of S. cerevisiae strains that require Hmt1, and CaHmt1 methylates Npl3, a major Hmt1 substrate, in S. cerevisiae. In C. albicans strains lacking CaHmt1, asymmetric dimethylarginine and ω-monomethylarginine levels are significantly decreased, indicating that Hmt1 is the major C. albicans type I PRMT1. Given the known effects of type I PRMTs on nuclear transport of RNA-binding proteins, we tested whether Hmt1 affects nuclear transport of a putative Npl3 ortholog in C. albicans. CaNpl3 allows partial growth of S. cerevisiae npl3Δ strains, but its arginine-glycine-rich C terminus can fully substitute for that of ScNpl3 and also directs methylation-sensitive association with ScNpl3. Expression of green fluorescent protein-tagged CaNpl3 proteins in C. albicans strains with and without CaHmt1 provides evidence for CaHmt1 facilitating export of CaNpl3 in this fungus. We have also identified the C. albicans Rmt2, a type IV fungus- and plant-specific PRMT, by amino acid analysis of an rmt2Δ/rmt2Δ strain, as well as biochemical evidence for additional cryptic PRMTs. Copyright © 2007, American Society for Microbiology. All Rights Reserved.