Abstract:
Filament bundles (rods) of cofilin and actin (1:1) form in neurites of stressed neurons where they inhibit synaptic function. Live-cell imaging of rod formation is hampered by the fact that overexpression of a chimera of wild type cofilin with a fluorescent protein causes formation of spontaneous and persistent rods, which is exacerbated by the photostress of imaging. The study of rod induction in living cells calls for a rod reporter that does not cause spontaneous rods. From a study in which single cofilin surface residues were mutated, we identified a mutant, cofilinR21Q, which when fused with monomeric Red Fluorescent Protein (mRFP) and expressed several fold above endogenous cofilin, does not induce spontaneous rods even during the photostress of imaging. CofilinR21Q-mRFP only incorporates into rods when they form from endogenous proteins in stressed cells. In neurons, cofilinR21Q-mRFP reports on rods formed from endogenous cofilin and induced by all modes tested thus far. Rods have a half-life of 30–60 min upon removal of the inducer. Vesicle transport in neurites is arrested upon treatments that form rods and recovers as rods disappear. CofilinR21Q-mRFP is a genetically encoded rod reporter that is useful in live cell imaging studies of induced rod formation, including rod dynamics, and kinetics of rod elimination.

Abstract:
Neurites of neurons under acute or chronic stress form bundles of filaments (rods) containing 1:1 cofilin:actin, which impair transport and synaptic function. Rods contain disulfide cross-linked cofilin and are induced by treatments resulting in oxidative stress. Rods form rapidly (5–30 min) in >80% of cultured hippocampal or cortical neurons treated with excitotoxic levels of glutamate or energy depleted (hypoxia/ischemia or mitochondrial inhibitors). In contrast, slow rod formation (50% of maximum response in ~6 h) occurs in a subpopulation (~20%) of hippocampal neurons upon exposure to soluble human amyloid-β dimer/trimer (Aβd/t) at subnanomolar concentrations. Here we show that proinflammatory cytokines (TNFα, IL-1β, IL-6) also induce rods at the same rate and within the same neuronal population as Aβd/t. Neurons from prion (PrPC)-null mice form rods in response to glutamate or antimycin A, but not in response to proinflammatory cytokines or Aβd/t. Two pathways inducing rod formation were confirmed by demonstrating that NADPH-oxidase (NOX) activity is required for prion-dependent rod formation, but not for rods induced by glutamate or energy depletion. Surprisingly, overexpression of PrPC is by itself sufficient to induce rods in over 40% of hippocampal neurons through the NOX-dependent pathway. Persistence of PrPC-dependent rods requires the continuous activity of NOX. Removing inducers or inhibiting NOX activity in cells containing PrPC-dependent rods causes rod disappearance with a half-life of about 36 min. Cofilin-actin rods provide a mechanism for synapse loss bridging the amyloid and cytokine hypotheses for Alzheimer disease, and may explain how functionally diverse Aβ-binding membrane proteins induce synaptic dysfunction.

Abstract:
MUC1 is a glycoprotein that plays an important role in cancer pathogenesis. In order to study the effect of glycosylation on the conformational propensities of the tandem repeat domain of MUC1, we have determined the structure of the MUC1 tandem repeat peptide AHGVTSAPDTRPAPGSTAPP, O-glycosylated with the trisaccharide (α-Glc-1,4-β-Glc-1,4-α-GalNAc-) at Thr5. This glycopeptide was synthesized to model a heavily Oglycosylated threonine residue in the tandem repeat domain. The NMR experiments used in this study included TOCSY, NOESY, ROESY, DQF-COSY, HSQC and 1D NMR. The peak volumes determined using the program SPARKY were converted into distance constraints using the program CALIBA. The programs FiSiNOE and HABAS were used to generate angle constraints. Using conformational restraints obtained from NMR, the program DYANA was used to determine the structures of the peptide. Finally, structural refinement was performed within the SYBYL software package using GLYCAM parameters and Kollman-all atom types. The presence of strong sequential αN connectivities suggested an extended conformation of the peptide backbone. Strong sequential αδ connectivities were indicative of a trans conformation of the Ala-Pro peptide bonds. In addition, presence of sequential NN connectivities in the peptide segments Gly3-Val4-Thr5-Ser6, Asp9-Thr10-Arg11 and Gly-Ser16 were indicative of twist-like conformations of the peptide backbone in these peptide segments.

Abstract:
Woody biomass is a widely-used and favourable material for energy production due to its carbon neutral status. Energy is generally derived either through direct combustion or gasification. The Irish forestry sector is forecasted to expand significantly in coming years, and so the opportunity exists for the bioenergy sector to take advantage of the material for which there will be no demand from current markets. A by-product of wood processing, wood dust is the cheapest form of wood material available to the bioenergy sector. Currently wood dust is primarily processed into wood pellets for energy generation. Research was conducted on post-processing birch wood dust; the calorific value and the Wobbe Index were determined for a number of wood particle sizes and wood dust concentrations. The Wobbe Index determined for the upper explosive concentration (4000 g/m3) falls within range of that of hydrogen gas, and wood dust-air mixtures of this concentration could therefore behave in a similar manner in a gas turbine. Due to its slightly lower HHV and higher particle density, however, alterations to the gas turbine would be necessary to accommodate wood dust to prevent abrasive damage to the turbine. As an unwanted by-product of wood processing the direct use of wood dust in a gas turbine for energy generation could therefore have economic and environmental benefits.

Abstract:
We describe an extensive study of search in GSAT, an approximation procedure for propositional satisfiability. GSAT performs greedy hill-climbing on the number of satisfied clauses in a truth assignment. Our experiments provide a more complete picture of GSAT's search than previous accounts. We describe in detail the two phases of search: rapid hill-climbing followed by a long plateau search. We demonstrate that when applied to randomly generated 3SAT problems, there is a very simple scaling with problem size for both the mean number of satisfied clauses and the mean branching rate. Our results allow us to make detailed numerical conjectures about the length of the hill-climbing phase, the average gradient of this phase, and to conjecture that both the average score and average branching rate decay exponentially during plateau search. We end by showing how these results can be used to direct future theoretical analysis. This work provides a case study of how computer experiments can be used to improve understanding of the theoretical properties of algorithms.

Abstract:
Biological networks are constructed of repeated simplified patterns, or modules, called network motifs. Network motifs can be found in a variety of organisms including bacteria, plants, and animals, as well as intracellular transcription networks for gene expression and signal transduction processes in neuronal circuits. Standard models of signal transduction events for synaptic plasticity and learning often fail to capture the complexity and cooperativity of the molecular interactions underlying these processes. Here, we apply network motifs to a model for signal transduction during an in vitro form of eyeblink classical conditioning that reveals an underlying organization of these molecular pathways. Experimental evidence suggests there are two stages of synaptic AMPA receptor (AMPAR) trafficking during conditioning. Synaptic incorporation of GluR1-containing AMPARs occurs early to activate silent synapses conveying the auditory conditioned stimulus and this initial step is followed by delivery of GluR4 subunits that supports acquisition of learned conditioned responses (CRs). Overall, the network design of the two stages of synaptic AMPAR delivery during conditioning describes a coherent feed-forward loop (C1-FFL) with AND logic. The combined inputs of GluR1 synaptic delivery AND the sustained activation of 3-phosphoinositide-dependent protein-kinase-1 (PDK-1) results in synaptic incorporation of GluR4-containing AMPARs and the gradual acquisition of CRs. The network architecture described here for conditioning is postulated to act generally as a sign-sensitive delay element that is consistent with the non-linearity of the conditioning process. Interestingly, this FFL structure also performs coincidence detection. A motif-based approach to modeling signal transduction can be used as a new tool for understanding molecular mechanisms underlying synaptic plasticity and learning and for comparing findings across forms of learning and model systems.

Abstract:
While greenhouse gases trap heat emanating from the Earth and thereby heat the surface atmosphere, they act as emitters in the high atmosphere and cool the air there. In 1989 Roble and Dickinson (1989) estimated the cooling that would occur in the thermosphere (250–500 km altitude) due to a doubling of greenhouse gas densities. Ever since, long-term data bases have been scoured for evidence of this thermospheric "global cooling." Here we show evidence that the thermosphere did indeed cool over the period 1966–1987, but the data suggest that the cooling accelerated at a "breakpoint year" around 1979 to a rate far larger than may be attributed to greenhouse cooling. This 1979 breakpoint year appears to coincide with a breakpoint year in ozone (O3) column density. Further, the cooling was confined largely to the daytime thermosphere while the nighttime showed only a small trend. These results suggest, first, that the greenhouse cooling of the thermosphere may well not be detectable with current data sets and, second, that the long-term cooling that is clearly seen may be due largely to O3 depletion.

Abstract:
A powerful number is a positive integer n satisfying the property that p2 divides n whenever the prime p divides n; i.e., in the canonical prime decomposition of n, no prime appears with exponent 1. In [1], S.W. Golomb introduced and studied such numbers. In particular, he asked whether (25,27) is the only pair of consecutive odd powerful numbers. This question was settled in [2] by W.A. Sentance who gave necessary and sufficient conditions for the existence of such pairs. The first result of this paper is to provide a generalization of Sentance's result by giving necessary and sufficient conditions for the existence of pairs of powerful numbers spaced evenly apart. This result leads us naturally to consider integers which are representable as a proper difference of two powerful numbers, i.e. n=p1 ￠ ’p2 where p1 and p2 are powerful numbers with g.c.d. (p1,p2)=1. Golomb (op.cit.) conjectured that 6 is not a proper difference of two powerful numbers, and that there are infinitely many numbers which cannot be represented as a proper difference of two powerful numbers. The antithesis of this conjecture was proved by W.L. McDaniel [3] who verified that every non-zero integer is in fact a proper difference of two powerful numbers in infinitely many ways. McDaniel's proof is essentially an existence proof. The second result of this paper is a simpler proof of McDaniel's result as well as an effective algorithm (in the proof) for explicitly determining infinitely many such representations. However, in both our proof and McDaniel's proof one of the powerful numbers is almost always a perfect square (namely one is always a perfect square when n ￠ ‰ ￠2(mod4)). We provide in §2 a proof that all even integers are representable in infinitely many ways as a proper nonsquare difference; i.e., proper difference of two powerful numbers neither of which is a perfect square. This, in conjunction with the odd case in [4], shows that every integer is representable in infinitely many ways as a proper nonsquare difference. Moreover, in §2 we present some miscellaneous results and conclude with a discussion of some open questions.

Abstract:
We study the head-on collision of linearly polarized, high frequency plane gravitational waves and their electromagnetic counterparts in the Einstein-Maxwell theory. The post-collision space-times are obtained by solving the vacuum Einstein-Maxwell field equations in the geometrical optics approximation. The head-on collisions of all possible pairs of these systems of waves is described and the results are then generalised to non-linearly polarized waves which exhibit the maximum two degrees of freedom of polarization.