The Significance of Wild Plants in the Evolutionary Ecology of Three Major Viruses Infecting Cultivated Sweetpotato in Uganda

The studies presented in this thesis contribute to the understanding of evolutionary ecology of three major viruses threatening cultivated sweetpotato (Ipomoea batatas Lam) in East Africa: Sweet potato feathery mottle virus (SPFMV; genus Potyvirus; Potyviridae), Sweet potato chlorotic stunt virus (SPCSV; genus Crinivirus; Closteroviridae) and Sweet potato mild mottle virus (SPMMV; genus Ipomovirus; Potyviridae). The viruses were serologically detected and the positive results confirmed by RT-PCR and sequencing. SPFMV was detected in 24 wild plant species of family Convolvulacea (genera Ipomoea, Lepistemon and Hewittia), of which 19 species were new natural hosts for SPFMV. SPMMV and SPCSV were detected in wild plants belonging to 21 and 12 species (genera Ipomoea, Lepistemon and Hewittia), respectively, all of which were previously unknown to be natural hosts of these viruses. SPFMV was the most abundant virus being detected in 17% of the plants, while SPMMV and SPCSV were detected in 9.8% and 5.4% of the assessed plants, respectively. Wild plants in Uganda were infected with the East African (EA), common (C), and the ordinary (O) strains, or co-infected with the EA and the C strain of SPFMV. The viruses and virus-like diseases were more frequent in the eastern agro-ecological zone than the western and central zones, which contrasted with known incidences of these viruses in sweetpotato crops, except for northern zone where incidences were lowest in wild plants as in sweetpotato. The NIb/CP junction in SPMMV was determined experimentally which facilitated CP-based phylogenetic and evolutionary analyses of SPMMV. Isolates of all the three viruses from wild plants were genetically similar to those found in cultivated sweetpotatoes in East Africa. There was no evidence of host-driven population genetic structures suggesting frequent transmission of these viruses between their wild and cultivated hosts. The p22 RNA silencing suppressor-encoding sequence was absent in a few SPCSV isolates, but regardless of this, SPCSV isolates incited sweet potato virus disease (SPVD) in sweetpotato plants co-infected with SPFMV, indicating that p22 is redundant for synergism between SCSV and SPFMV. Molecular evolutionary analysis revealed that isolates of strain EA of SPFMV that is largely restricted geographically in East Africa experience frequent recombination in comparison to isolates of strain C that is globally distributed. Moreover, non-homologous recombination events between strains EA and C were rare, despite frequent co-infections of these strains in wild plants, suggesting purifying selection against non-homologous recombinants between these strains or that such recombinants are mostly not infectious. Recombination was detected also in the 5 - and 3 -proximal regions of the SPMMV genome providing the first evidence of recombination in genus Ipomovirus, but no recombination events were detected in the characterized genomic regions of SPCSV. Strong purifying selection was implicated on evolution of majority of amino acids of the proteins encoded by the analyzed genomic regions of SPFMV, SPMMV and SPCSV. However, positive selection was predicted on 17 amino acids distributed over the whole the coat protein (CP) in the globally distributed strain C, as compared to only 4 amino acids in the multifunctional CP N-terminus (CP-NT) of strain EA largely restricted geographically to East Africa. A few amino acid sites in the N-terminus of SPMMV P1, the p7 protein and RNA silencing suppressor proteins p22 and RNase3 of SPCSV were also submitted to positive selection. Positively selected amino acids may constitute ligand-binding domains that determine interactions with plant host and/or insect vector factors. The P1 proteinase of SPMMV (genus Ipomovirus) seems to respond to needs of adaptation, which was not observed with the helper component proteinase (HC-Pro) of SPMMV, although the HC-Pro is responsible for many important molecular interactions in genus Potyvirus. Because the centre of origin of cultivated sweetpotato is in the Americas from where the crop was dispersed to other continents in recent history (except for the Australasia and South Pacific region), it would be expected that identical viruses and their strains occur worldwide, presuming virus dispersal with the host. Apparently, this seems not to be the case with SPMMV, the strain EA of SPFMV and the strain EA of SPCSV that are largely geographically confined in East Africa where they are predominant and occur both in natural and agro-ecosystems. The geographical distribution of plant viruses is constrained more by virus-vector relations than by virus-host interactions, which in accordance of the wide range of natural host species and the geographical confinement to East Africa suggest that these viruses existed in East African wild plants before the introduction of sweetpotato. Subsequently, these studies provide compelling evidence that East Africa constitutes a cradle of SPFMV strain EA, SPCSV strain EA, and SPMMV. Therefore, sweet potato virus disease (SPVD) in East Africa may be one of the examples of damaging virus diseases resulting from exchange of viruses between introduced crops and indigenous wild plant species. Keywords: Convolvulaceae, East Africa, epidemiology, evolution, genetic variability, Ipomoea, recombination, SPCSV, SPFMV, SPMMV, selection pressure, sweetpotato, wild plant species Author s Address: Arthur K. Tugume, Department of Agricultural Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O Box 27, FIN-00014, Helsinki, Finland. Email: tugume.arthur@helsinki.fi Author s Present Address: Arthur K. Tugume, Department of Botany, Faculty of Science, Makerere University, P.O. Box 7062, Kampala, Uganda. Email: aktugume@botany.mak.ac.ug, tugumeka@yahoo.com

X-Ray Studies On Crystalline Complexes Involving Amino-Acids And Peptides .11. Peptide Aggregation And Water-Structure In The Crystals Of A Hydrated 1-1 Complex Between L-Histidyl-L-Serine And Glycyl-L-Glutamic Acid

The hexahydrate of a 1:1 complex between L-histidyl-L-serine and glycyl-L-glutamic acid crystallizes in space group P1 with a = 4.706(1), b= 8.578(2), c= 16.521(3) ÅA; α= 85.9(1), β= 89.7(1)°, = 77.4(1). The crystal structure, solved by direct methods, has been refined to an R value of 0.046 for 2150 observed reflections. The two peptide molecules in the structure have somewhat extended conformations. The unlike molecules aggregate into separate alternating layers. Each layer is stabilized by hydrogen bonded head-to-tail sequences as well as sequences of hydrogen bonds involving peptide groups. The arrangement of molecules in each layer is similar to one of the plausible idealized arrangements of L-alanyl-L-alanine worked out from simple geometrical considerations. Adjacent layers in the structure are held together by interactions involving side chains as well as water molecules. The water structure observed in the complex provides a good model, at atomic resolution, for that in protein crystals. An interesting feature of the crystal structure is the existence of two water channels in the interfaces between adjacent peptide layers.

Studies in metal-ammonia reduction. Part 4. Reduction and reductive methylation of 7-methoxy-3,4-dihydrophenanthren-1(2H)-one and 7-methoxy-1,2-dihydrophenanthren-4(3H)-one

Birch reduction and reductive methylations of the title compounds have been investigated. 7-Methoxy-3,4-dihydrophenanthren-1(2H)-one (2) yields the cis-3,4,9,10,11,12-hexahydro-derivative (15) while the 7-methoxy-1,2-dihydrophenanthren-4(3H)-one (5) is reduced to the corresponding 1,2,9,10-tetrahydro-derivative (7). The factors influencing the mechanism of the reduction process have been discussed. The reductive methylation products of the ketone (2) are useful substrates in the synthesis of 9-methyl steroids.

Structural Studies of Analgesics and Their Interactions. VIII.* Rotational Isomerism and Disorder in the Crystal Structure of Meelofenamie Acid

Meclofenamic acid, C I4HIICI2NO2, probably the most potent among analgesic fenamates, crystallizes in the triclinic space group P1, with a = 8.569 (5), b = 8.954(8), c -- 9.371 (4) A, ct = 103.0 (2), fl -- 103.5 (2), y = 92.4 (2) ° , Z = 2, D m = 1.43 (4), D c = 1.41 Mg m -3. The structure was solved by direct methods and refined to R = 0.135 for 1062 observed reflections. The anthranilic acid moiety in the molecule is nearly planar and is nearly perpendicular to the 2,6-dichloro-3-methylphenyl group. The molecules, which exist as hydrogen-bonded dimers, have an internal hydrogen bond involving the imino and the carboxyl groups. The methyl group is disordered and occupies two positions with unequal occupancies. The disorder can be satisfactorily explained in terms of the rotational isomerism of the 2,6-dichloro-3-methylphenyl group about the bond which connects it to the anthranilic acid moiety and the observed occupancies on the basis of packing considerations.

Amide-catalysed isomerisation of 5,6-dihydroisoquinolines: a novel synthesis of 1,2-dihydroisoquinolines

Knoevenagel condensation of 2-acylcyclohexanones or 2-ethoxycarbonylcyclohexanone with either cyanoacetamide or malononitrile followed by silver salt alkylation gave the 5,6,7,8-tetrahydroisoquinolines (3a–i). Chromic acid oxidation of the 5,6,7,8-tetrahydroisoquinolines (3a–i) to the corresponding tetralones (4a–i) followed by sodium borohydride reduction and p-toluenesulphonic acid-catalysed dehydration of the resulting alcohols (5a–i) gave the 5,6-dihydroisoquinolines (6a–i). Reaction of 5,6-dihydroisoquinolines (6a–g) with potassium amide in liquid ammonia gave a mixture of the 1,3-dihydroisoquinolines (7a–g) and the isoquinolines (8a–g). The C-1 unsubstituted 1,2-dihydroisoquinoline (7c) was found to be very unstable. In the case of the 5,6-dihydroisoquinolines (6h and 6i), reaction of potassium amide in liquid ammonia resulted in a mixture of 1-aminoisoquinoline (9) and the isoquinolines (8h and 8i). All the above compounds have been characterised by spectral data. A probable pathway for the formation of the 1,2-dihydroisoquinolines (7a–g) and the isoquinolines (8a–i) is suggested.

Aromatic amines and their derivatives. Part 3. The synthesis and crystal structure of 4,4-NN-tetramethyl-NN-dinitroso-2,2-methylenedianiline

The synthesis of 4,4,N,N-tetramethyl-NN-dinitroso-2,2-methylenedianiline (1) by the route p-MeC6H4NH2+ HCHO + OH–(p-MeC6H4NMe)2CH2(7b); (7b)+ acid at 70 °C 4,N-dimethyl-6-(N-methyl-p-toluidinomethyl)aniline (4b); (4b)+ acid at 130 °C 4,4,NN-tetramethyl-2,2-methylenedianiline (3b); (3b)+ HNO2(1), is described. Aspects of the 1H n.m.r. spectra of the above and related compounds are discussed. A crystal-structure analysis of compound (1) shows one of the N-nitroso-groups to be disordered with the endo-form being in preponderance (4 : 1) over the exo-form. The other N-nitroso-group is exclusively exo in the solid state. There is little or no resonance between the benzene ring and the nitroso-group attached to the ring, the two groups being almost perpendicular to each other. In one of the N-nitroso-groups, the nitrogen atom deviates significantly from the plane of the benzene ring to which it is attached. Both amide nitrogen atoms show some pyramidal character.

L-Tyrosyl-L-glutarnie Acid Monohydrate, C14H18N206.H20

Mr=328.32, triclinic, P1, a=5.801 (1), b=7.977(1), c=9.110(2)A, ~t=102.33 (1), fl= 97.92 (1), y= 109.82 (1) °, v= 377.2 (1) A 3 at 293 K, Z=I, D x=1.45, D m=1.45 g cm -3, 2(MoKs)= 0.7107 A, ~ = 0.74 cm -1, F(000) = 174.0. R = 0.046 for 990 unique observed [F o > 4O(Fo)] reflections. The crystal structure is stabilized by extensive hydrogen bonding involving all N and O atoms.

The role of triplet states in the emission mechanism of polymer light-emitting diodes

The blue emission of polyfluorene (PF)-based light-emitting diodes (LEDs) is known to degrade due to a low-energy green emission, which hitherto has been attributed to oxidative defects. By studying the electroluminescence (EL) from ethyl-hexyl substituted PF LEDs in the presence of oxygen and in an inert atmosphere, and by using trace quantities of paramagnetic impurities (PM) in the polymer, we show that the triplet states play a major role in the low-energy emission mechanism. Our time-dependent many-body studies show a large cross-section for the triplet formation in the EL process in the presence of PM, primarily due to electron-hole recombination processes.

Structural studies of analgesics and their interactions. III. The crystal and molecular structure of amidopyrine

Amidopyrine (1-phenyl-2,3-dimethyl-4-dimethylaminopyrazolone), C13HzvN30, a dimethylamino derivative of antipyrine and an important analgesic and antipyretic agent, crystallizes in the triclinic space group P1 with four molecules in a unit cell of dimensions a= 7.458 (5), b = 10.744 (5), c= 17.486 (15)/~,, e=98.6 (2),/~= 85.6 (3), y= 108-6 (2) . The structure was solved by direct methods and refined to an R value of 0.055 for 3706 photographically observed reflexions. The dimensions of the two crystallographically independent molecules are very nearly the same. The pyrazolone moiety in the molecule has dimensions comparable to those in antipyrine. Unlike antipyrine, the molecular dimensions of amidopyrine in the free state (the present structure) are close to those found in some of its hydrogenbonded complexes. Thus it appears that the presence of the dimethylamino group makes the molecule more resistant to changes in its dimensions resulting from molecular association. An attempt has also been made to correlate the polar nature of the pyrazolone moiety and the hybridization state of the hetero nitrogen atoms in antipyrine, amidopyrine and their complexes.

Studies in terpenoids. Part XXXI. Synthesis of pyrocurzerenone, a furosesquiterpenoid from Curcuma zedoaria

7-Acetonyloxy-5-methyl--tetralone (Vc) was cyclodehydrated to 7,8-dihydro-1,5-dimethylnaphtho[2,1-b]furan-9(6H)-one (VIa), the structure of which was established by an independent synthesis from methyl 4-(4-acetonyloxy-2-methylphenyl)butyrate (IXd). Similarly, 7-acetonyloxy-2,5-dimethyl--tetralone (Vf), synthesized via 4-(5-isopropyl-4-methoxy-2-methylphenyl)-2-methylbutyric acid (XIIb) and 7-methoxy-2,5-dimethyl--tetralone (Vd), was cyclodehydrated to 7,8-dihydro-1,5,8-trimethylnaphtho[2,1-b]furan-9(6H)-one (VIb), which on reduction and dehydration furnished pyrocurzerenone (6,7-dihydro-1,5,8-trimethylnaphtho[2,1-b]furan)(I). The deisopropylation and cyclodehydration of (XIIb) to (Vd) were effected in one step by treatment with polyphosphoric acid.

Studies in terpenoids. Part XXX. Synthesis of pterosin E, a sesquiter-penoid from bracken

Pterosin E (2,5,7-trimethyl-1-oxoindan-6-ylacetic acid)(Ia), a naturally occurring sesquiterpenoid has been synthesized starting from -bromomesitylene (IIIa). Alkylation of diethyl methylmalonate with (IIIa) gave the diester (IIIb) which was converted into the cyanomethyl diester (IVb). Hydrolysis of (IVb) to the dicarboxylic acid (V) followed by its cyclodehydration gave pterosin E.

Structure of a dimer of ageratochromene

A solid obtained in the dimerisation of ageratochromene (6,7-dimethoxy-2,2-dimethyl-1-benzopyran)(II) in the presence of acid has been shown to be 5,6,6a,6b,7,12b-hexahydro-1,2,10,11-tetramethoxy-5,5,7,7-tetramethylcyclopenta[1,2-c;5,4,3-de]bis[1]benzopyran (IV) by a study of its n.m.r. and mass spectra.

The Crystal and Molecular Structure of l-(Diphenylmethyl)azetidin-3-ol

1-(Diphenylmethyl)azetidin-3-ol is triclinic, space group P1, with a=8.479(2), b=17.294(4),c = 10.606 (3) A, a = 118.59 (2),/~ = 100.30 (2), y = 89.63 (2) °, Z = 4. The structure was solved by multisolution methods and refined to an R of 0.044 for 2755 reflexions. The four-membered rings in the two independent molecules are puckered with dihedral angles of 156 and 153 ° . The two molecules differ in conformation with respect to rotation of the phenyl rings about the C-C bonds. The structure is stabilized by a network of O-H. • • N intermolecular hydrogen bonds.

X-ray studies on crystalline complexes involving amino acids and peptides. XXIII. Variability in ionization state, conformation and molecular aggregation in the complexes of succinic acid with DL- and L-lysine

Crystalline complexes of succinic acid with DL- and L-lysine have been prepared and analysed by X-ray diffraction. DL-Lysine complex: C6HIsN202 + 1 2- 1 ~C4H404 .~C4H604, Mr -- 264"2, PI, a = 5"506 (4), =8.070(2), c=14.089(2) A,, a=92.02(1), /3= 100"69 (3), y = 95"85 (3) ~>, Z = 2, Dx = 1"44 g cm -3, R = 0.059 for 2546 observed reflections. Form I of the e-lysine complex: C6HIsN20-, ~ .C4H504, Mr = 264.2, P1, a = 5" 125 (2), b = 8"087 (1), c = 8"689 (1) A,, a = 112.06 (1), /3 = 99.08 (2), y = 93"77(2) °, Z--l, D,,,=1"34(3), Dx=l"34gcm 3 R = 0.033 for 1475 observed reflections. Form II of + I 2- the e-lysine complex: C6H15N202 .,iC4H404 .- 1 I ") 4C4H604.4(C4HsO4""H'"CaH404)" , Mr = 264"2, P1, a = 10.143 (4), b = 10.256 (2), c = 12"916 (3) A,, a = 105.00 (2),/3 = 99-09 (3), y = 92"78 (3)::, Z = 4, Dm= 1"37(4), D,.= 1.38gcm 3, R=0.067 for 2809 observed reflections. The succinic acid molecules in the structures exhibit a variety of ionization states. Two of the lysine conformations found in the complexes have been observed for the first time in crystals containing lysine. Form II of the L-lysine complex is highly pseudosymmetric. In all the complexes, unlike molecules aggregate into separate alternating layers. The basic element of aggregation in the lysine layer in the complexes is an S2-type head-to-tail sequence. This element combines in different ways in the three structures. The basic element of aggre gation in the succinic acid layer in the complexes is a hydrogen-bonded ribbon. The ribbons are interconnected indirectly through amino groups in the lysine layer.

Observation of a mixed antiparallel and parallel beta-sheet motif in the crystal structure of Boc-Ala-Ile-Aib-OMe

A diastereomeric mixture of the tripeptide Boc-Ala-Ile-Aib-OMe crystallized in the space group P1 from CH3OH/H2O. The unit cell parameters are a = 10.593(2) A, b = 14.377(3) A, c = 17.872(4) A, alpha = 104.41(2) degrees, beta = 90.55(2) degrees, gamma = 106.91(2) degrees, V = 2512.4 A3, Z = 4. X-Ray crystallographic studies show the presence of four molecules in the asymmetric unit consisting of two pairs of diastereomeric peptides, Boc-L-Ala-L-Ile-Aib-OMe and Boc-L-Ala-D-Ile-Aib-OMe. The four molecules in the asymmetric unit form a rarely found mixed antiparallel and parallel beta-sheet hydrogen bond motif. The Ala and (L,D)-Ile residues in all the four molecules adopt the extended conformations, while the phi, psi values of the Aib residues are in the right-handed helical region. In one of the molecules the Ile sidechain adopts the unusual gauche conformation about the C beta-C gamma bond.