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Search Results: 1 - 10 of 424313 matches for " Paul M. Johnson "
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Structural Properties of the RNA Synthesized by Glutamate Dehydrogenase for the Degradation of Total RNA  [PDF]
Godson O. Osuji, Paul M. Johnson
Advances in Enzyme Research (AER) , 2018, DOI: 10.4236/aer.2018.63004
Abstract: Glutamate dehydrogenase (GDH)-synthesized RNA, a nongenetic code-based RNA is suitable for unraveling the structural constraints imposed on the regulation (transcription, translation, siRNA etc.) of metabolism by genetic code. GDH-synthesized RNAs have been induced in whole plants to knock out target mRNA populations thereby producing plant phenotypes that are allergen-free; enriched in fatty acids, essential amino acids, shikimic acid, resveratrol etc. Methods applied hereunder for investigating the structural properties of GDH-synthesized RNA included purification of GDH isoenzymes, synthesis of RNA by the isoenzymes, reverse transcription of the RNA to cDNA, sequencing of the cDNA, computation of the G+C-contents, profiling the stability through PCR amplification compared with genetic code-based DNA; and biochemical characterization of the RNAs synthesized by individual hexameric isoenzymes of GDH. Single product bands resulted from the PCR amplification of the cDNAs of GDH-synthesized RNA, whereas several bands resulted from the amplification of genetic code-based DNA. The cDNAs have wide G+C-contents (35% to 59%), whereas genetic code-based DNA has narrower G+C-contents (50% to 60%). The GDH β6 homo-hexameric isoenzyme synthesized the A+U-rich RNAs, whereas the a6, and α6 homo-hexameric isoenzymes synthesized the G+C-rich RNAs. Therefore, the RNA synthesized by GDH is different from genetic code-based RNAs. In vitro chemical reactions revealed that GDH-synthesized RNA degraded total RNA to lower molecular weight products. Therefore, GDH-synthesized RNA is RNA enzyme. Dismantling of the structural constraints imposed on RNA by genetic code liberated RNA to become an enzyme with specificity to degrade unwanted transcripts. The RNA enzyme activity of GDH-synthesized RNA is ubiquitous in cells; it is readily induced by treatment of plants with mineral nutrients etc. and may simplify experimental approaches in plant enzymology and molecular biology research projects.
Horticultural Production of Ultra High Resveratrol Peanut  [PDF]
Godson O. Osuji, Paul Johnson, Eustace Duffus, Sela Woldesenbet, Jeneanne M. Kirven
Agricultural Sciences (AS) , 2017, DOI: 10.4236/as.2017.810086
Abstract:
Background: Resveratrol naturally occurring antioxidant in peanut (Legume: Arachis hypogaea) has phytochemical human health dietary effects associated with reduced inflammatory cancer risks. Its levels in peanut are ultra-low and variable (0 to 26 μg·g-1), which has made it difficult to market as a consistent high resveratrol produce. Objective: Understanding the regulation of resveratrol accumulation in peanut might lead to development of new techniques for optimizing and stabilizing its yield. Method: Peanuts were cultivated in horticultural field plots and treated with solutions of mineral salts (sulfate, potassium, phosphate, ammonium ion) that were optimized in stoichiometric (reactive) ratios. Peanut seed’s RNAs were subjected to Northern blot analysis for profiling the RNAs synthesized by glutamate dehydrogenase (GDH), and mRNAs encoding resveratrol synthase. The seed’s extracts were analyzed by GC-MS for determination of the resveratrol and fatty acid compositions. Result: Stoichiometric mixes of mineral ions induced the peanut GDH to synthesize some RNA that silenced the mRNAs encoding resveratrol synthase, phosphoglucomutase, isocitrate lyase, malate synthase, enolase, phosphoenolpyruvate carboxylase, malate dehydrogenase, and phosphoglycerate mutase in the control, KN-, and NPKS-treated but not in the NPPK-treated peanut. These resulted to decreased resveratrol content (6.0 μg·g-1) in the control peanut but maximized it (1.15 mg·g-1) in the NPPK-treated peanut. Therefore, resveratrol accumulation was optimized by coupling of glycolysis and citric-glyoxylic acid cycles to resveratrol biosynthesis. Fatty acid content of control (55.6 g·kg-1) was higher than the NPKS-treated (48.5 g·kg-1) and NPPK-treated peanut (44.9 g·kg-1) meaning that malonyl-CoA intermediate in both fatty acid and stilbenoid pathways was diverted to support maximum resveratrol biosynthesis in the NPPK-treated peanut. Conclusion: The functional coupling of citric-glyoxylic acid cycles and glycolysis to optimize resveratrol biosynthesis may encourage development of horticultural technology specific for production of ultra-high resveratrol peanuts.
Rediscovery of Leptoxis compacta (Anthony, 1854) (Gastropoda: Cerithioidea: Pleuroceridae)
Nathan V. Whelan, Paul D. Johnson, Phil M. Harris
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042499
Abstract: The Mobile River Basin is a hotspot of molluscan endemism, but anthropogenic activities have caused at least 47 molluscan extinctions, 37 of which were gastropods, in the last century. Nine of these suspected extinctions were in the freshwater gastropod genus Leptoxis (Cerithioidea: Pleuroceridae). Leptoxis compacta, a Cahaba River endemic, has not been collected for >70 years and was formally declared extinct in 2000. Such gastropod extinctions underscore the imperilment of freshwater resources and the current biodiversity crisis in the Mobile River Basin. During a May 2011 gastropod survey of the Cahaba River in central Alabama, USA, L. compacta was rediscovered. The identification of snails collected was confirmed through conchological comparisons to the L. compacta lectotype, museum records, and radulae morphology of historically collected L. compacta. Through observations of L. compacta in captivity, we document for the first time that the species lays eggs in short, single lines. Leptoxis compacta is restricted to a single location in the Cahaba River, and is highly susceptible to a single catastrophic extinction event. As such, the species deserves immediate conservation attention. Artificial propagation and reintroduction of L. compacta into its native range may be a viable recovery strategy to prevent extinction from a single perturbation event.
In vitro propagation of Solidago virgaurea L. through nodal culture
John Peter Paul J,Revathy I,Johnson, M
Research in Plant Biology , 2012,
Abstract:
The Impact of Volunteer Corn on Crop Yields and Insect Resistance Management Strategies
Paul T. Marquardt,Ryan M. Terry,William G. Johnson
Agronomy , 2013, DOI: 10.3390/agronomy3020488
Abstract: Volunteer corn (VC) has reemerged as a problematic weed in corn/soybean rotational cropping systems. This reemergence and increasing prevalence of volunteer corn has been correlated to an increased adoption of herbicide-resistant (HR) corn hybrids and the adoption of conservation tillage. Since the introduction of HR crops, control options, weed/crop competition, and other concerns ( i.e., insect resistance management of Bt traits) have increased the amount of attention that volunteer corn is receiving. The objective of this review is to discuss what is known about VC prior to and after the introduction of HR crops, and to discuss new information about this important weed.
Total RNA Degradation in Vitro and in Vivo by Glutamate Dehydrogenase-Synthesized RNA Enzyme: Biotechnological Applications  [PDF]
Godson O. Osuji, Wenceslaus C. Madu, Paul M. Johnson
Advances in Bioscience and Biotechnology (ABB) , 2019, DOI: 10.4236/abb.2019.104005
Abstract: Glutamate dehydrogenase regulates crop development, growth, and biomass yield through its synthesis of non-genetic code-based RNA. Understanding the mechanism of GDH-synthesized RNA enzyme would enhance the agriculture innovation capacity of the more than a billion urban gardeners, smallholder, and limited resources indigenous farmers. Different metabolic variants were prepared by treating peanut growing on healthy soil with stoichiometric mixes of mineral salt solutions. Peanut GDH charge isomers were purified to homogeneity by electrophoresis, and made to synthesize RNA enzyme. Peanut total RNA was 5’-end labeled with [γ-32P]ATP and made to react as substrate in vitro with GDH-synthesized RNA from another metabolic variant of peanut. Agarose, and polyacrylamide gel electrophoresis of the reaction products showed that tRNA, rRNA, and most of the mRNAs were degraded to mononucleotides, but total RNAs that were not mixed with GDH-synthesized RNAs were not degraded. When the non-homologous sequence sections of the GDH-synthesized RNA were clipped out, the homologous sections failed to produce Northern bands with peanut total RNA. Therefore, the non-homologous sequence sections served to identify, position, and align the GDH-synthesized RNA to its target total RNA site independent of genetic code; the degradation of total RNA being via non-canonical base alignments in the enzyme-substrate complex, followed by electromagnetic destruction of the total RNA, the less stable of the two kinds of RNA. This is the science-based corner stone that buttresses the crop production efforts of limited resources farmers because GDH-synthesized RNAs quickly degrade superfluous total RNA of the crop in response to the soil mineral nutrient deficiencies thereby minimizing wastage of metabolic energy in the synthesis of unnecessary protein enzymes while optimizing biomass metabolism, crop growth, and maximum crop yields. In vitro hydrolysis of
Hurwitz numbers, ribbon graphs, and tropicalization
Paul Johnson
Mathematics , 2013,
Abstract: Double Hurwitz numbers have at least four equivalent definitions. Most naturally, they count covers of the Riemann sphere by genus g curves with certain specified ramification data. This is classically equivalent to counting certain collections of permutations. More recently, double Hurwitz numbers have been expressed as a count of certain ribbon graphs, or as a weighted count of certain labeled graphs. This note is an expository account of the equivalences between these definitions, with a few novelties. In particular, we give a simple combinatorial algorithm to pass directly between the permutation and ribbon graph definitions. The two graph theoretic points of view have been used to give proofs that double Hurwitz numbers are piecewise polynomial. We use our algorithm to compare these two proofs.
Lattice points and simultaneous core partitions
Paul Johnson
Mathematics , 2015,
Abstract: We observe that for a and b relatively prime, the "abacus construction" identifies the set of simultaneous (a,b)-core partitions with lattice points in a rational simplex. Furthermore, many statistics on (a,b)-cores are piecewise polynomial functions on this simplex. We apply these results to rational Catalan combinatorics. Using Ehrhart theory, we reprove Anderson's theorem that there are (a+b-1)!/a!b! simultaneous (a,b)-cores, and using Euler-Maclaurin theory we prove Armstrong's conjecture that the average size of an (a,b)-core is (a+b+1)(a-1)(b-1)/24. Our methods also give new derivations of analogous formulas for the number and average size of self-conjugate (a,b)-cores. We conjecture a unimodality result for q rational Catalan numbers, and make preliminary investigations in applying these methods to the (q,t)-symmetry and specialization conjectures. We prove these conjectures for low degree terms and when a=3, connecting them to the Catalan hyperplane arrangement and quadratic permutation statistics.
Double Hurwitz numbers via the infinite wedge
Paul Johnson
Mathematics , 2010,
Abstract: We derive an algorithm to produce explicit formulas for certain generating functions of double Hurwitz numbers. These formulas generalize a formula of Goulden, Jackson and Vakil for one part double Hurwitz numbers. Immediate consequences include a new proof that double Hurwitz numbers are piecewise polynomial, an understanding of the chamber structure and wall crossing for these polynomials, and a proof of the Goulden, Jackson and Vakil's Strong Piecewise Polynomiality conjecture. The method is a straightforward application of Okounkov's expression for double Hurwitz numbers in terms of operators on the infinite wedge. We begin with a introduction to the infinite wedge tailored to our use.
Aging partially restores the efficacy of malaria vector control in insecticide-resistant populations of Anopheles gambiae s.l. from Burkina Faso
Christopher M Jones, Antoine Sanou, Wamdaogo M Guelbeogo, N'Fale Sagnon, Paul CD Johnson, Hilary Ranson
Malaria Journal , 2012, DOI: 10.1186/1475-2875-11-24
Abstract: Blood-fed adult Anopheles gambiae s.l. were collected from south-west Burkina Faso and identified to species/form level. Cohorts of the F1 progeny of An. gambiae s.s. S-forms were exposed to deltamethrin (0.05%) at three to five or 17-19 days post-emergence and tested for the frequency of the resistance allele 1014F. Isofemale lines of the M, S- form of An. gambiae s.s. and Anopheles arabiensis were exposed in WHO cone tests to either a) LLINs deployed in households for two years or (b) bendiocarb sprayed walls.Mortality rates in response to deltamethrin (0.05%) increased from levels indicative of strong resistance in three to five day old F1 mosquitoes, to near full susceptibility in the 17-19 day old cohort. On exposure to LLINs sampled from the field, the mortality rate in isofemale lines was higher in older mosquitoes than young (OR = 5.28, CI 95% = 2.81-9.92), although the mortality estimates were affected by the LLIN tested. In general, the LLINs sampled from the field performed poorly in WHO cone bioassays using either laboratory susceptible or field caught mosquito populations. Finally, there was a clear relationship between mortality and age on exposure to bendiocarb-sprayed walls, with older mosquitoes again proving more susceptible (OR = 3.39, CI 95% = 2.35-4.90).Age is a key factor determining the susceptibility of mosquitoes to insecticides, not only in laboratory studies, but in response to field-based vector control interventions. This has important implications for understanding the epidemiological impact of resistance. If mosquitoes old enough to transmit malaria are still being suppressed with available insecticides, is resistance potentially having less of an impact than often assumed? However, the poor performance of LLINs used in this study in Burkina Faso, is a cause for concern and requires urgent investigation.Long-lasting insecticide nets (LLINs) and indoor residual spraying (IRS) have set a benchmark in malaria prevention. Significant reduc
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