Development of a probe-based blotting technique for the detection of Tobacco streak virus

Digoxigenin (DIG)-labeled DNA probe was developed for a sensitive and rapid detection of the Tobacco streak virus (TSV) isolates in India by dot-blot and tissue print hybridization techniques. DIG-labeled DNA probe complementary to the coat protein (CP) region of TSV sunflower isolate was designed and used to detect the TSV presence at field levels. Dot-blot hybridization was used to check a large number of TSV isolates with a single probe. In addition, a sensitivity of the technique was examined with the different sample extraction methods. Another technique, the tissue blot hybridization offered a simple, reliable procedure and did not require a sample processing. Thus, both non-radioactively labeled probe techniques could facilitate the sample screening during TSV outbreaks and offer an advantage in quarantine services.

Nucleotide sequence of the 3terminal region of belladonna mottle virus (renamed Physalis mottle virus) RNA and analysis of the evolutionary relationships among tymoviral coat proteins

The 3' terminal 1255 nt sequence of Physalis mottle virus (PhMV) genomic RNA has been determined from a set of overlapping cDNA clones. The open reading frame (ORF) at the 3' terminus corresponds to the amino acid sequence of the coat protein (CP) determined earlier except for the absence of the dipeptide, Lys-Leu, at position 110-111. In addiition, the sequence upstream of the CP gene contains the message coding for 178 amino acid residues of the C-terminus of the putative replicase protein (RP). The sequence downstream of the CP gene contains an untranslated region whose terminal 80 nucleotides can be folded into a characteristic tRNA-like structure. A phylogenetic tree constructed after aligning separately the sequence of the CP, the replicase protein (RP) and the tRNA-like structure determined in this study with the corresponding sequences of other tymoviruses shows that PhMV wrongly named belladonna mottle virus [BDMV(I)] is a separate tymovirus and not another strain of BDMV(E) as originally envisaged. The phylogenetic tree in all the three cases is identical showing that any subset of genomic sequence of sufficient length can be used for establishing evolutionary relationships among tymoviruses.

Syntheses, X-ray structure and properties of (5-cyclopentadienyl)ruthenium(II) complexes of pyridyl-2-hydrazone ligands

Complexes of the formulae [(-Cp)Ru(PPh3)(2-PPH)]Cl and [(Cp)Ru(PPh3) (py)(1-PPH)]Cl were prepared by reacting pyridyl-2-phenylhydrazone [PPH, C5H4N-2-CH=NNHPh] with (-Cp)Ru(PPh3)2Cl and (-Cp)Ru(PPh3)(py)Cl, respectively. In these complexes the PPH ligand displays bidentate chelating and unidentate modes of bonding. The molecular structure of [(-Cp)Ru(PPh3)(2-PPH)](ClO4)·CH2Cl2 was determined by X-ray crystallography. In this complex the metal is bonded to the N-pyridyl and N-imine atoms of the chelating ligand. 1H NMR spectral data suggests that PPH is bonded to ruthenium through the pyridine moiety of the PPH ligand in [(η-Cp)Ru(PPh3)(py)(η1-PPH)]Cl.

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

Singlet quenching of tetraphenylporphyrin and its metal derivatives by iron(III) coordination compounds

The quenching of fluorescence of the free-base tetraphenylporphyrin, H2TPP, and its metal derivatives, MgTPP and ZnTPP by diverse iron(III) complexes, [Fe(CN)6]3−, Fe(acac)3, [Fe(mnt)2]−, Fe(Salen)Cl, [Fe4S4(SPh)4]2−·, FeTPPCl and [Fe(Cp)2]+ has been studied both in homogeneous medium (CH3CN) and micellar media, SDS., CTAB and Triton X-100. The quenching efficiencies are analysed in terms of diffusional encounters and it has been possible to separate static quenching components. The quenching constants are dependent on the nature of the ligating atoms around iron(III) and also on the extent of π-conjugation of the ligands. The quenching mechanism has been investigated using steady-state irradiation experiments. Evidence for oxidative quenching by iron(III) complexes was obtained, though the spin multiplicities of the excited electronic states of iron(III) complexes permit both energy and electron transfer mechanisms for quenching of the singlet excited state of the porphyrins.

Diruthenium(III) compounds, Ru2O(O2CAr)2(MeCN)4(PPh3)2(ClO4)2.cntdot.H2O and Ru2O(O2CAr)4(PPh3)2, with an (Ru2(.mu.-O)(.mu.-O2CAr)22+) core as model systems for the diiron centers in hemerythrin

Diruthenium(II1) compounds, Ru20(02CAr)2(MeCN)4(PPh3)2(C104)(z1~) Hazn0d R U ~ O ( O ~ C A ~ ) ~(2() P(PA~r ~= )P~h,C6H4-p-OMe), were prepared by reacting R U ~ C I ( O ~ CaAnd~ P)P~h 3 in MeCN and characterized by analytical and spectral data. The molecular structures of 1 with Ar = Ph and of 2 with Ar = C&p-OMe were determined by X-ray crystallography. Crystal data for Ru~~(~~CP~)~(M~CN),(PP~(~la)):~ m(oCnIoc~lin,ic), n~/~cH, ~a O= 27.722 (3) A, b = 10.793 (2) A, c = 23.445 ( 2 )A , fi = 124.18 (l)', V = 5803 A3, and 2 = 4. Cr stal data for Ru~O(O~CC~H~-~-O(M2b~): )o~rth(orPhoPm~bi~c, )Pn~n a, a = 22.767 (5) A, b = 22.084 (7) A, c = 12.904 (3) 1, V = 6488 AS; and 2 = 4. Both 1 and 2 have an (Ruz0(02CAr)z2t1 core that is analogous to the diiron core present in the oxidized form of the nonheme respiratory protein hemerythrin. The Ru-Ru distances of 3.237 (1) and 3.199 ( I ) A observed in 1 and 2, respectively, are similar to the M-M distances known in other model systems. The essentially diamagnetic nature of 1 and 2 is due to the presence of two strongly interacting t22 Ru"' centers. The intense colors of 1 (blue) and 2 (purple) are due to the charge-transfer transition involving an ( R ~ ~ ( f i - 0m)o~ie~ty.) The presence of labile MeCN and carboxylato ancillary ligands in I and 2, respectively, makes these systems reactive toward amine and heterocyclic bases.

Noble metal ionic sites for catalytic hydrogen combustion: spectroscopic insights

A catalytic hydrogen combustion reaction was carried out over noble metal catalysts substituted in ZrO2 and TiO2 in ionic form. The catalysts were synthesized by the solution combustion technique. The compounds showed high activity and CO tolerance for the reaction. The activity of Pd and Pt ion substituted TiO2 was comparable and was higher than Pd and Pt ion substituted ZrO2. The mechanisms of the reaction over the two supports were proposed by making use of the X-ray photoelectron spectroscopy and FT infrared spectroscopic observations. The reaction over ZrO2 supported catalysts was proposed to take place by the utilization of the surface hydroxyl groups while the reaction over TiO2 supported catalysts was hypothesized to be a hybrid mechanism utilizing surface hydroxyl groups and the lattice oxygen.

Heat capacity measurements on Ge20Se80−xBix glasses

The specific heat Cp of glassy Ge20Se80−xBix (0 ≤ × ≤ 12) samples is investigated. The Cp at 323K and the ΔCp at glass transition temperature Tg1 show anomalous features around x = 8 at.%, where p−n conduction type inversion also take place. These features are discussed in the light of Phillips model of phase separation in these glasses at the microscopic level.

Is tetramethyleneethane a ground state triplet?

We have examined a number of possible ways by which tetramethyleneethane (TME) can be a ground state triplet, as claimed by experimental studies, in violation of Ovchinnikov’s theorem for alternant hydrocarbons of equal bond lengths. Model exact π calculations of the low-lying states of TME, 3,4-dimethylenefuran and 3,4-dimethylenepyrrole were carried out using a diagrammatic valence bond approach. The calculations failed to yield a triplet ground state even after (a) tuning of electron correlation, (b) breaking alternancy symmetry, and (c) allowing for geometric distortions. In contrast to earlier studies of fine structure constants in other conjugated systems, the computedD andE values of all the low-lying triplet states of TME for various geometries are at least an order of magnitude different from the experimentally reported values. Incorporation of σ-π mixing by means of UHF MNDO calculations is found to favour a singlet ground state even further. A reinterpretation of the experimental results of TME is therefore suggested to resolve the conflict.

Interaction of Sesbania Mosaic Virus Movement Protein with VPg and P10: Implication to Specificity of Genome Recognition

Sesbania mosaic virus (SeMV) is a single strand positive-sense RNA plant virus that belongs to the genus Sobemovirus. The mechanism of cell-to-cell movement in sobemoviruses has not been well studied. With a view to identify the viral encoded ancillary proteins of SeMV that may assist in cell-to-cell movement of the virus, all the proteins encoded by SeMV genome were cloned into yeast Matchmaker system 3 and interaction studies were performed. Two proteins namely, viral protein genome linked (VPg) and a 10-kDa protein (P10) c v gft encoded by OFR 2a, were identified as possible interacting partners in addition to the viral coat protein (CP). Further characterization of these interactions revealed that the movement protein (MP) recognizes cognate RNA through interaction with VPg, which is covalently linked to the 59 end of the RNA. Analysis of the deletion mutants delineated the domains of MP involved in the interaction with VPg and P10. This study implicates for the first time that VPg might play an important role in specific recognition of viral genome by MP in SeMV and shed light on the possible role of P10 in the viral movement.

Synthesis, characterization, and thermal degradation studies on group VIA derived weak-link polymers

Polymers containing group VIA derived weak links, viz. poly(styrene disulfide) (PSD), poly- (styrene tetrasulfide) (PST), and poly(styrene diselenide) (PSDSE), have been synthesized. The polymers PSD and PST were characterized by NMR, IR, UV, TGA, and fast atom bombardment m w spectrometric (FABMS) techniques. The presence of different configurational sequences in PSD and PST were identified by *3C NMR spectroscopy. PSDSE, being insoluble in common organic solvents, was characterized using solid-state lac NMR (CP-MAS) spectroscopy. Thermal degradation of polymers under direct pyrolysis-mass spectrometric (DP-MS) conditions revealed that all the polymers undergo degradation through the weaklink scission. A comparative study of the pyrolysis products of these polymers with that of poly(styrene peroxide) (PSP) revealed a smooth transformation down the group with no monomer (styrene or oxygen) formation in PSP to only styrene and selenium metal in PSDSE. This trend of group VIA is explained from the energetics of the C-X bond (X = 0, S, and Se) which also seems to be important in addition to the weak X-X bond cleavage. In PSP and PSD, the behavior is also explained from the energetics of the alkoxy and thiyl radicals. The unique exothermic degradation in PSP compared to endothermic degradation in PSD and PSDSE is explained from the nature of the producta of degradation.

Challenges in Earth sciences: the 21st century

The 21st century poses many challenges for global sustainability. Among them, most importantly, the human race will encounter scarcity of raw materials and conventional energy resources. And, India may have to take the brunt of these problems as it is going to be the most populated region of the world with concomitant increase in energy demand and requirement of other resources. India will be the testing ground for introducing newer ways of green technology and innovative principles of resource management and utilization. With the vagaries of potential climate change gathering clouds in the background, Earth sciences will have a special and predominant role in guiding the society in prioritizing our resource discovery, utilization and their consumption and the upkeep of environment. On the fundamental level, Earth sciences are going through a most exciting phase of development as a born-again science. Technological breakthroughs including the satellite-based observations augur well for gaining new insights into Earth processes. A set of exciting fundamental problems that are globally identified will set the stage for an exhilarating period of new discoveries. Improvements in numerical and computer-based techniques will assist in modelling of Earth processes to unprecedented levels. India will have to take special effort in improving the existing experimentation facilities in the Earth science departments of the country, and also the general level of Earth science education to meet the global standards. This article presents an Earth science vision for the 21st century in an Indian context.

Dye sensitized visible light degradation of phenolic compounds

The present research work reports the eosin Y (EY) and fluorescein (FL) sensitized visible light degradation of phenol, 4-chlorophenol (CP), 2,4-dichlorophenol (DCP) and 2,4,6-trichlorophenol (TCP) using combustion synthesized nano-TiO2 (CS TiO2). The rate of degradation of the phenolic compounds was higher in the presence of EY/CS TiO2 compared to FL/CS TiO2 system. A detailed mechanism of sensitized degradation was proposed and a mechanistic model for the rate of degradation of the phenolic compound was derived using the pyramidal network reduction technique. It was found that at low initial dye concentrations, the rate of degradation of the phenolic compound is first order in the concentration of the dye, while at high initial dye concentrations, the rate is first order in the concentration of the phenolic compound. The order of degradation of the different phenolic compounds follows: CP > TCP > DCP > phenol. The different phenolic and dye intermediates that were formed during the degradation were identified by liquid chromatography-mass spectrometry (LC-MS) and the most probable pathway of degradation is proposed. (C) 2010 Elsevier B.V. All rights reserved.