Showing 71 - 80 of 733 Items
Probing the mechanism of recognition of ssDNA by the Cdc13-DBD
Date: 2008-03-01
Creator: Aimee M. Eldridge, Deborah S. Wuttke
Access: Open access
- The Saccharomyces cerevisiae protein Cdc13 tightly and specifically binds the conserved G-rich single-stranded overhang at telomeres and plays an essential role in telomere end-protection and length regulation. The 200 residue DNA-binding domain of Cdc13 (Cdc13-DBD) binds an 11mer single-stranded representative of the yeast telomeric sequence [Tel11, d(GTGTGGGTGTG)] with a 3 pM affinity and specificity for three bases (underlined) at the 5′ end. The structure of the Cdc13-DBD bound to Tel11 revealed a large, predominantly aromatic protein interface with several unusual features. The DNA adopts an irregular, extended structure, and the binding interface includes a long (∼30 amino acids) structured loop between strands β2-β3 (L2-3) of an OB-fold. To investigate the mechanism of ssDNA binding, we studied the free and bound states of Cdc13-DBD using NMR spectroscopy. Chemical shift changes indicate that the basic topology of the domain, including L2-3, is essentially intact in the free state. Changes in slow and intermediate time scale dynamics, however, occur in L2-3, while conformational changes distant from the DNA interface suggest an induced fit mechanism for binding in the 'hot spot' for binding affinity and specificity. These data point to an overall binding mechanism well adapted to the heterogeneous nature of yeast telomeres. © 2008 The Author(s).
Thompson's group F is not almost convex
Date: 2003-12-01
Creator: Sean Cleary, Jennifer Taback
Access: Open access
- We show that Thompson's group F does not satisfy Cannon's almost convexity condition AC(n) for any positive integer n with respect to the standard generating set with two elements. To accomplish this, we construct a family of pairs of elements at distance n from the identity and distance 2 from each other, which are not connected by a path lying inside the n-ball of length less than k for increasingly large k. Our techniques rely upon Fordham's method for calculating the length of a word in F and upon an analysis of the generators' geometric actions on the tree pair diagrams representing elements of F. © 2003 Elsevier Inc. All rights reserved.
A genome-wide screen identifies genes that affect somatic homolog pairing in drosophila
Date: 2012-07-01
Creator: Jack R. Bateman, Erica Larschan, Ryan D'Souza, Lauren S. Marshall, Kyle E., Dempsey, Justine E. Johnson, Barbara G. Mellone, Mitzi I. Kuroda
Access: Open access
- In Drosophila and other Dipterans, homologous chromosomes are in close contact in virtually all nuclei, a phenomenon known as somatic homolog pairing. Although homolog pairing has been recognized for over a century, relatively little is known about its regulation. We performed a genome-wide RNAibased screen that monitored the X-specific localization of the male-specific lethal (MSL) complex, and we identified 59 candidate genes whose knockdown via RNAi causes a change in the pattern of MSL staining that is consistent with a disruption of X-chromosomal homolog pairing. Using DNA fluorescent in situ hybridization (FISH), we confirmed that knockdown of 17 of these genes has a dramatic effect on pairing of the 359 bp repeat at the base of the X. Furthermore, dsRNAs targeting Pr-set7, which encodes an H4K20 methyltransferase, cause a modest disruption in somatic homolog pairing. Consistent with our results in cultured cells, a classical mutation in one of the strongest candidate genes, pebble (pbl), causes a decrease in somatic homolog pairing in developing embryos. Interestingly, many of the genes identified by our screen have known roles in diverse cell-cycle events, suggesting an important link between somatic homolog pairing and the choreography of chromosomes during the cell cycle. © 2012 Bowers et al.
Inelastic channels in WW scattering
Date: 1993-01-01
Creator: S. G. Naculich, C. P. Yuan
Access: Open access
- If the electroweak symmetry-breaking sector becomes strongly interacting at high energies, it can be probed through longitudinal W scattering. We present a model with many inelastic channels in the WLWL scattering process, corresponding to the production of heavy fermion pairs. These heavy fermions affect the elastic scattering of WL's by propagating in loops, greatly reducing the amplitudes in some charge channels. We conclude that the symmetry-breaking sector cannot be fully explored by using, for example, the WL±WL± mode alone, even when no resonance is present; all WLWL→WLWL scattering modes must be measured. © 1993 The American Physical Society.
Extinction in competitive lotka-volterra systems
Date: 1995-01-01
Creator: Mary Lou Zeeman
Access: Open access
- It is well known that for the two species autonomous competitive Lotka-Volterra model with no fixed point in the open positive quadrant, one of the species is driven to extinction, whilst the other population stabilises at its own carrying capacity. In this paper we prove a generalisation of this result to arbitrary finite dimension. That is, for the n-species autonomous competitive Lotka-Volterra model, we exhibit simple algebraic criteria on the parameters which guarantee that all but one of the species is driven to extinction, whilst the one remaining population stabilises at its own carrying capacity. © 1995 American Mathematical Society.
Atmospheric variability of methyl chloride during the last 300 years from an Antarctic ice core and firn air
Date: 2004-01-28
Creator: M. Aydin, E. S. Saltzman, W. J. De Bruyn, S. A. Montzka, J. H., Butler, M. Battle
Access: Open access
- Measurements of methyl chloride (CH3Cl) in Antarctic polar ice and firn air are used to describe the variability of atmospheric CH3Cl during the past 300 years. Firn air results from South Pole and Siple Dome suggest that the atmospheric abundance of CH3Cl increased by about 10% in the 50 years prior to 1990. Ice core measurements from Siple Dome provide evidence for a cyclic natural variability on the order of 10%, with a period of about 110 years in phase with the 20th century rise inferred from firn air. Thus, the CH3Cl increase measured in firn air may largely be a result of natural processes, which may continue to affect the atmospheric CH3Cl burden during the 21st century. Copyright 2004 by the American Geophysical Union.
Precision measurement of the Ds*+-Ds+ mass difference
Date: 1994-01-01
Creator: D. N. Brown, J. Fast, R. L. McIlwain, T. Miao, D. H., Miller, M. Modesitt, D. Payne, E. I. Shibata, I. P.J. Shipsey, P. N. Wang, M. Battle, J. Ernst, Y. Kwon, S. Roberts, E. H. Thorndike, C. H. Wang, J. Dominick, M. Lambrecht, S. Sanghera, V. Shelkov, T. Skwarnicki, R. Stroynowski, I. Volobouev, G. Wei, P. Zadorozhny, M. Artuso, M. Goldberg, D. He, N. Horwitz, R. Kennett, R. Mountain
Access: Open access
- We have measured the vector-pseudoscalar mass splitting M(Ds*+)-M(Ds+)=144.220.470.37 MeV significantly more precisely than the previous world average. We minimize the systematic errors by also measuring the vector-pseudoscalar mass difference M(D*0)-M(D0) using the radiative decay D*0D0, obtaining [M(Ds*+)-M(Ds+)]-[M(D*0)-M(D0)] =2.090.470.37 MeV. This is then combined with our previous high-precision measurement of M(D*0)-M(D0), which used the decay D*0D00. We also measure the mass difference M(Ds+)-M(D+)=99.50.60.3 MeV, using the + decay modes of the Ds+ and D+ mesons. © 1994 The American Physical Society.
Incidence, size and spatial structure of clones in second-growth stands of coast redwood, Sequoia sempervirens (Cupressaceae)
Date: 2004-07-01
Creator: Vladimir Douhovnikoff, Adelaide M. Cheng, Richard S. Dodd
Access: Open access
- The ecology and evolutionary potential of coast redwood (Sequoia sempervirens) is significantly influenced by the important role clonal spread plays in its reproduction and site persistence. In nine second-growth stands, amplified fragment length polymorphisms (AFLPs) were used to identify redwood clonal architecture. Clones (multistem genets) dominated sites by representing an average of 70% of stems measured, ranging in size from two to 20 stems. As a result, a relatively small number of genets can monopolize a disproportionate amount of site resources, are more likely to persist over time, and have greater on-site genetic representation. Clones were not limited to fairy-ring structures, but consisted of a wide range of shapes including concentric rings, ring chains, disjunct, and linear structures. Between-ramet distances of up to 40 m were measured, indicating that clonal reproduction is not limited to basal stump resprouting. Clonal structure in second-growth stands was similar to earlier reports from old growth, emphasizing the importance of site persistence and long-term, gradual site development. Smaller ramet numbers per genet in old growth is probably due to local within-genet self thinning. Management and conservation of redwoods will benefit from a better understanding of the dynamics and structure of clonal spread in these forests.
Observation of a new charmed strange meson
Date: 1994-01-01
Creator: Y. Kubota, M. Lattery, J. K. Nelson, S. Patton, D., Perticone, R. Poling, V. Savinov, S. Schrenk, R. Wang, M. S. Alam, I. J. Kim, B. Nemati, J. J. O'Neill, H. Severini, C. R. Sun, M. M. Zoeller, G. Crawford, C. M. Daubenmier, R. Fulton, D. Fujino, K. K. Gan, K. Honscheid, H. Kagan, R. Kass, J. Lee, R. Malchow, F. Morrow, Y. Skovpen, M. Sung, C. White, F. Butler
Access: Open access
- Using the CLEO II detector, we have obtained evidence for a new meson decaying to D0K+. Its mass is 2573.2-1.6+1.7±0.8±0.5 MeV/c2 and its width is 16-4+5±3 MeV/c2. Although we do not establish its spin and parity, the new meson is consistent with predictions for an L=1, S=1, JP=2+ charmed strange state. © 1994 The American Physical Society.
Mass Spectrometry Quantification, Localization, and Discovery of Feeding-Related Neuropeptides in Cancer borealis
Date: 2021-02-17
Creator: Kellen Delaney, Mengzhou Hu, Tessa Hellenbrand, Patsy S. Dickinson, Michael P., Nusbaum, Lingjun Li
Access: Open access
- The crab Cancer borealis nervous system is an important model for understanding neural circuit dynamics and modulation, but the identity of neuromodulatory substances and their influence on circuit dynamics in this system remains incomplete, particularly with respect to behavioral state-dependent modulation. Therefore, we used a multifaceted mass spectrometry (MS) method to identify neuropeptides that differentiate the unfed and fed states. Duplex stable isotope labeling revealed that the abundance of 80 of 278 identified neuropeptides was distinct in ganglia and/or neurohemal tissue from fed vs unfed animals. MS imaging revealed that an additional 7 and 11 neuropeptides exhibited altered spatial distributions in the brain and the neuroendocrine pericardial organs (POs), respectively, during these two feeding states. Furthermore, de novo sequencing yielded 69 newly identified putative neuropeptides that may influence feeding state-related neuromodulation. Two of these latter neuropeptides were determined to be upregulated in PO tissue from fed crabs, and one of these two peptides influenced heartbeat in ex vivo preparations. Overall, the results presented here identify a cohort of neuropeptides that are poised to influence feeding-related behaviors, providing valuable opportunities for future functional studies.