Chemistry & Biochemistry Research Works

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    A Matrix Universe as the Origin of Inertia and Momentum and Translocation as a Chemical Reaction
    (2003-03) Hansen, John Norman
    It 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.
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    A Reply to van den Berg and van der Sluys: Effects Resembling a Bio-Field on a Torsion Pendulum Cannot Be Caused by Heated Air Currents Generated by the Subject
    (Society of Scientific Exploration, 2015) Hansen, J. Norman; Lieberman, Joshua A
    A Reply to van den Berg and van der Sluys: Effects Resembling a Bio-Field on a Torsion Pendulum Cannot Be Caused by Heated Air Currents Generated by the Subject
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    HUMAN SUBJECT EFFECTS ON TORSION PENDULUM OSCILLATIONS: IMPORTANCE OF ESTABLISHING THE CONTRIBUTION OF THERMAL CONVECTION AIR CURRENTS
    (Elsevier, 2017-02) Hansen, John Norman
    Studies of thermal effects on torsion pendulum oscillations.
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    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 B
    Protein 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.
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    Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability
    (Springer Nature, 2012-12-12) Joardar, Vinita; Abrams, Natalie F; Hostetler, Jessica; Paukstelis, Paul J; Pakala, Suchitra; Pakala, Suman B; Zafar, Nikhat; Abolude, Olukemi O; Payne, Gary; Andrianopoulos, Alex; Denning, David W; Nierman, William C
    The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25–36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies. Despite the conservation of the core genes, the mitochondrial genomes of Aspergillus and Penicillium species examined here exhibit significant amount of interspecies variation. Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing.