Chemistry & Biochemistry Research Works
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Item A Matrix Universe as the Origin of Inertia and Momentum and Translocation as a Chemical Reaction(2003-03) Hansen, John NormanIt is proposed that there is a matrix structure of the universe that persists both in the presence and absence of physical objects, and that chemical reactions involve reorganization of electronic orbitals within this matrix structure. The mechanism by which objects translocate within this matrix is similar to the chemical reaction mechanism, and therefore requires moving objects to cross transition-state energy barriers. This involves an input of energy, which is the origin of inertia and momentum. The matrix concept is used to derive equations of motion that conform to Newton’s laws and include terms for inertia and momentum.Item v-RIO1 – an atypical protein kinase from the parasitic nematode Trichostrongylus vitrinus(Springer Nature, 2008-09-22) Hu, Min; LaRonde-LeBlanc, Nicole; Sternberg, Paul W; Gasser, Robin BProtein kinases are key enzymes that regulate a wide range of cellular processes, including cell-cycle progression, transcription, DNA replication and metabolic functions. These enzymes catalyse the transfer of phosphates to serine, threonine and tyrosine residues, thus playing functional roles in reversible protein phosphorylation. There are two main groups, namely eukaryotic protein kinases (ePKs) and atypical protein kinases (aPKs); RIO kinases belong to the latter group. While there is some information about RIO kinases and their roles in animals, nothing is known about them in parasites. This is the first study to characterise a RIO1 kinase from any parasite. A full-length cDNA (Tv-rio-1) encoding a RIO1 protein kinase (Tv-RIO1) was isolated from the economically important parasitic nematode Trichostrongylus vitrinus (Order Strongylida). The uninterrupted open reading frame (ORF) of 1476 nucleotides encoded a protein of 491 amino acids, containing the characteristic RIO1 motif LVHADLSEYNTL. Tv-rio-1 was transcribed at the highest level in the third-stage larva (L3), and a higher level in adult females than in males. Comparison with homologues from other organisms showed that protein Tv-RIO1 had significant homology to related proteins from a range of metazoans and plants. Amino acid sequence identity was most pronounced in the ATP-binding motif, active site and metal binding loop. Phylogenetic analyses of selected amino acid sequence data revealed Tv-RIO1 to be most closely related to the proteins in the species of Caenorhabditis. A structural model of Tv-RIO1 was constructed and compared with the published crystal structure of RIO1 of Archaeoglobus fulgidus (Af-Rio1). This study provides the first insights into the RIO1 protein kinases of nematodes, and a foundation for further investigations into the biochemical and functional roles of this molecule in biological processes in parasitic nematodes.Item Treefall(Vantage Press, 1999-12) Hansen, John; Hansen, J. Norman; Hansen, John NormanThis file is an electronic facsimile of Treefall as published in book form by Vantage Press, 1999. It was authored by John Hansen, who is also J. Norman Hansen and John Norman Hansen at the University of Maryland, College Park. Hansen is a biochemist, and this is written from the perspective of a biochemistry professor. A record of Hansen's scientific publications is available at: https://scholar.google.com/citations?user=GkWED_QAAAAJ&hl=en Treefall originated as a philosophy. It presents philosophical arguments with respect to the nature of Reality. It also presents novel alternatives to conventional Physics, with respect to the mechanism of translocation, along with the basis of inertia and momentum. It is argued that the apparently simple process of translocation is actually a complex chemical reaction. For translocation to occur, an object has to have an input of energy to cross a transition state, in order become the same object in a new location. In the Appendix, this process is treated as a chemical reaction that obeys traditional chemical mechanisms, which always include transition states. The logical outcome of this idea is that, by the treatment of translocation as a chemical reaction, an equation can be derived that describes the process of translocation in terms of chemical kinetics. The gratifying aspect is that this equation includes terms for inertia and momentum. Inertia and momentum have heretofore not been explainable by first principles of physics. That 'translocation as a chemical reaction' provides explanations of inertia and momentum is an argument it favor of the concept.Item Construction and Characterization of a Torsional Pendulum that Detects a Novel Form of Cranial Energy(2009) Hansen, John Norman; Lieberman, Joshua A.A torsional pendulum consisting of a dome-shaped energy collector and a nylon monofilament support fiber was suspended above the cranium of a seated human subject and the effects of the subject on the oscillations of the pendulum were measured. There were dramatic effects, with FFT analysis of the oscillation signal showing many new frequencies in addition to the natural frequency of 0.034 Hz. The lowest new frequencies (0.0-0.002 Hz) were accompanied by a shift in the Center of Oscillation (COO) of the pendulum, and the higher frequencies were associated with changes in the amplitude of oscillation. The Delta COO (7.3 deg) and the amplitude (12 deg) effects were substantial, and would require forces equivalent to 34 and 56 mg, respectively. Residual effects on the Delta COO and amplitudes persisted for at least 30 min after the subject departed, and the rate at which they subsided conformed to the kinetics of a chemical relaxation process with a relaxation time of 600 sec. Shifts in the magnitude of the Delta COO with the subject present also conformed to chemical relaxations processes, with relaxation times of 35 and 200 sec. It is proposed that the energy that drives the anomalous oscillations when the subject is present is the result of enzyme-mediated energy transductions that convert metabolic energy into a form of energy that can affect the pendulum. Although highly speculative, it is suggested that aspects of quantum entanglement are involved in the energy transduction process.Item Large and Stable Transmembrane Pores from Guanosine-Bile Acid Conjugates(Journal of the American Chemical Society, 2008-02-15) Ma, Ling; Melegari, Monica; Colombini, Marco; Davis, JefferyItem Flexibility and Control of Protein-DNA Loops(World Scientific Publishing Company, 2006-10) Kahn, Jason D.; Cheong, Raymond; Edelman, Laurence M.; Mehta, Ruchi A.; Morgan, Michael A.Protein-DNA loops are essential for efficient transcriptional repression and activation. The geometry and stability of the archetypal Lac repressor tetramer (LacI)-DNA loop were investigated using designed hyperstable loops containing lac operators bracketing a sequence-directed bend. Electrophoretic mobility shift assays, DNA cyclization, and bulk and single-molecule fluorescence resonance energy transfer (FRET) demonstrate that the DNA sequence controls whether the LacI-DNA loop forms a compact loop with positive writhe or an open loop with little writhe. Monte Carlo methods for simulation of DNA ring closure were extended to DNA loops, including treatment of variable protein hinge angles. The observed distribution of topoisomer products upon cyclization provides a strong constraint on possible models. The experiments and modeling imply that LacI-DNA can adopt a wide range of geometries but has a strong intrinsic preference for an open form. The flexibility of LacI helps explain in vivo observations that DNA looping is less sensitive to DNA length and shape than would be expected from the physical properties of DNA. While DNA cyclization suggests two pools of precursor loops for the 9C14 construct, single-molecule FRET demonstrates a single population. This discrepancy suggests that the LacI-DNA structure is strongly influenced by flanking DNA.