Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat.

Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.

Computational study of new 1,2,3-triazole derivative of lithocholic acid: Structural aspects, non-linear optical properties and molecular docking studies as potential PTP 1B enzyme inhibitor.

We have reported synthesis of a novel 1,2,3-triazole conjugate of lithocholic acid by 1,3-dipolar cycloaddition reaction. The molecular properties such as geometry, conformations, bond lengths and dihedral angles were investigated theoretically. The bond order analysis was performed using Wiberg bond order (WBO), Fuzzy bond order (FBO) and Laplacian bond order (MBO) method. Electronic properties of molecule such as electrostatic surface potential analysis, frontier molecular orbital analysis, reduced density gradient, total density of states, and global chemical reactivity indices have been investigated. The nonlinear optical properties were also investigated. Total dipole moment, mean polarizability and hyperpolarizability were found to be much higher than standard urea molecule which suggests that it could act as potential NLO material. The molecular docking calculations are also performed to investigate its potential as PTP 1B enzyme inhibitor.

Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.

Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups-rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed ß-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats-freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210). These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism's genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe's respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.

A green, multicomponent, regio- and stereo-selective 1,3-dipolar cycloaddition of azides and azomethine ylides generated in situ with bifunctional dipolarophiles using PEG-400.

A series of novel dispiropyrrolidine-linked 1,2,3-triazole derivatives have been prepared by one-pot, four-component protocol that employed 5-arylidene-3-(prop-2-ynyl)thiazolidine-2,4-dione, isatin, sarcosine and substituted azides using Cu(I) generated in situ as catalyst in PEG-400 as a highly efficient and green media. This is the first report of a four-component reaction involving a classical Huisgen reaction, in which the two dipolar moieties (substituted azides and in situ generated azomethine ylides) react with acetylenic and olefinic dipolarophiles, respectively. The 1,3-dipolar cycloaddition proceeds in a highly regio- and stereo-selective manner. This methodology can be an ideal tool for the preparation of biologically important five-membered heterocyclic compounds in one pot.

Synthesis, biological activities and SAR studies of novel 1-Ethyl-7-methyl-4-oxo-1,4-dihydro-[1,8]naphthyridine-3-carboxylic acid based diacyl and sulfonyl acyl hydrazines.

BACKGROUND: Diacyl hydrazines have attracted significant interest in medicine, pesticide chemistry and material science. It is an important class of insect growth regulators. In this study, acyl hydrazine, the essential active group was incorporated in to nalidixic acid with the aim of combining the active groups to generate more potent agrochemical. RESULTS: Various nalidixic acid based diacyl and sulphonyl acyl hydrazines derivatives were synthesized and characterized by spectral techniques. These compounds were screened for the antifungal activity against five pathogenic fungi, nitrification inhibitory activity and insect growth regulator (IGR) activity against Spodoptera litura. The fungicidal activity was screened against R. bataticola, S. rolfsii, R. solani, F. oxysporum and A. porri. Most of the compounds showed moderate to good antifungal activity against A. porri (ED50 = 29.6-495.9 µg/mL). All the compounds showed significant nitrification inhibitory activity at 5% level. IGR activity was examined by feeding method against S. litura. CONCLUSION: The study revealed that a few compounds possessed good activity against three different pests namely certain fungus, soil bacteria and insect, among which, compound 37 (R' = 4-chlorophenyl) behaved the best.

Draft Genome Sequence of Sphingobium ummariense Strain RL-3, a Hexachlorocyclohexane-Degrading Bacterium.

Here, we report the draft genome sequence of the hexachlorocyclohexane (HCH)-degrading bacterium Sphingobium ummariense strain RL-3, which was isolated from the HCH dumpsite located in Lucknow, India (27°00'N and 81°09'E). The annotated draft genome sequence (4.75 Mb) of strain RL-3 consisted of 139 contigs, 4,645 coding sequences, and 65% G+C content.

Draft Genome Sequence of Sphingobium sp. Strain HDIPO4, an Avid Degrader of Hexachlorocyclohexane.

Sphingobium sp. strain HDIPO4 was isolated from a hexachlorocyclohexane (HCH) dumpsite and degraded HCH isomers rapidly. The draft genome sequence of HDIPO4 (~4.7 Mbp) contains 143 contigs and 4,646 coding sequences with a G+C content of 65%.

Draft Genome Sequence of a Hexachlorocyclohexane-Degrading Bacterium, Sphingobium baderi Strain LL03T.

Sphingobium baderi strain LL03(T) was isolated from hexachlorocyclohexane (HCH)-contaminated soil from Spolana, Czech Republic. Strain LL03(T) is a mutant that is deficient in linB and linC (genes that encode hexachlorocyclohexane haloalkane dehalogenase and dehydrogenase, respectively). The draft genome sequence of LL03(T) (~4.85 Mb) consists of 92 contigs and 4,914 coding sequences, with a G+C content of 63.5%.

Draft Genome Sequence of Sphingobium lactosutens Strain DS20T, Isolated from a Hexachlorocyclohexane Dumpsite.

Sphingobium lactosutens DS20(T) has been isolated from the hexachlorocyclohexane (HCH) dumpsite in Lucknow, India, but does not degrade any of the HCH isomers. Here, we present the ~5.36-Mb draft genome sequence of strain DS20(T), which consists of 110 contigs and 5,288 coding sequences, with a G+C content of 63.1%.

Genome Sequence of Novosphingobium lindaniclasticum LE124T, Isolated from a Hexachlorocyclohexane Dumpsite.

Novosphingobium lindaniclasticum LE124(T) is a hexachlorocyclohexane (HCH)-degrading bacterium isolated from a high-dosage-point HCH dumpsite (450 mg HCH/g soil) located in Lucknow, India (27°00'N and 81°09'E). Here, we present the annotated draft genome sequence of strain LE124(T), which has an estimated size of 4.86 Mb and is comprised of 4,566 coding sequences.

Draft Genome Sequence of Sphingobium quisquiliarum Strain P25T, a Novel Hexachlorocyclohexane (HCH)-Degrading Bacterium Isolated from an HCH Dumpsite.

Here, we report the draft genome sequence (4.2 Mb) of Sphingobium quisquiliarum strain P25(T), a natural lin (genes involved in degradation of hexachlorocyclohexane [HCH] isomers) variant genotype, isolated from a heavily contaminated (450 mg HCH/g of soil) HCH dumpsite.

Draft Genome Sequence of Sphingobium chinhatense Strain IP26T, Isolated from a Hexachlorocyclohexane Dumpsite.

Sphingobium chinhatense strain IP26(T) is a conducive hexachlorocyclohexane (HCH) degrader isolated from a heavily contaminated (450 mg HCH/g soil) HCH dumpsite. IP26(T) degrades α-, ß-, γ-, and δ-HCH, which are highly persistent in the environment. Here we report the draft genome sequence (~5.8 Mbp) of this strain.

Synthesis, antimicrobial evaluation and QSAR analysis of novel nalidixic acid based 1,2,4-triazole derivatives.

Novel nalidixic acid based 1,2,4-triazole derivatives were synthesized and characterized using spectral techniques like (1)H NMR, (13)C NMR, IR and mass spectrometry. All these compounds were screened for antimicrobial activity against five bacteria and two pathogenic fungi. Most of these compounds showed better antimicrobial activity than the parent compound, 4-amino-5-mercapto-1,2,4-triazole. Among all the screened compounds, 3-{6-(2-chlorophenyl)-1,2,4-triazolo [3,4-b] [1,3,4]thiadiazol-3-yl}-1-ethyl-7-methyl-1,8-naphthyridin-4(1H)-one (23) was emerged as promising antimicrobial agent (MIC = 16 µg/mL). Quantitative structure activity relationship (QSAR) analysis was carried out using various distance-based topological indices, steric and hydrophobic parameters. Based on the QSAR analysis it is indicative that lipophilic and steric parameters are the pre-requisites for these molecules to act as potent antimicrobial agents.

Synthesis of nalidixic acid based hydrazones as novel pesticides.

Thirty-one substituted hydrazones of nalidixic acid hydrazide were synthesized and characterized by spectral techniques. These compounds were evaluated for various biological activities, namely, fungicidal, insecticidal, and nitrification inhibitory activities. The antifungal activity was evaluated against five pathogenic fungi, namely, Rhizoctonia bataticola , Sclerotium rolfsii , Rhizoctonia solani , Fusarium oxysporum , and Alternaria porii . They showed maximum inihibition against A. porii with ED(50) = 34.2-151.3 microg/mL. The activity was comparable to that of a commercial fungicide, hexaconazole (ED(50) = 25.4 microg/mL). They were also screened for insecticidal activity against third-instar larvae of Spodoptera litura and adults of Callosobruchus maculatus and Tribollium castaneum . Most of them showed 70-100% mortality against S. litura through feeding method at 0.1% dose. These compounds were not found to be effective nitrification inhibitors.

In-gel detection of urease activity by nitroprusside-thiol reaction.

A new staining method for urease activity in non-denaturing polyacrylamide gels is described. The increase in local pH of the gel, resulting from ureolytic activity of urease, causes a purple red coloured band after incubation of the polyacrylamide gel with urea. Staining of urease activity using this method is very specific for catalytically active urease even in crude preparations. Detection of urease activity by this method is rapid, simple and economical. The described method is also more sensitive than existing methods of urease staining. A minimum of 0.25 mU of urease activity can be detected after 5 min of incubation with the substrate. The method has been used to demonstrate the presence of different charge isoforms of urease in a member of the plant family Cucurbitaceae.

Mapping of a major QTL for pre-harvest sprouting tolerance on chromosome 3A in bread wheat.

Quantitative trait loci (QTL) analysis was conducted for pre-harvest sprouting tolerance (PHST) in bread wheat for a solitary chromosome 3A, which was shown to be important for this trait in earlier studies. An inter-varietal mapping population in the form of recombinant inbred lines (RILs) developed from a cross between SPR8198 (a PHS tolerant genotype) and HD2329 (a PHS susceptible cultivar) was used for this purpose. The parents and the RIL population were grown in six different environments and the data on PHS were collected in each case. A framework linkage map of chromosome 3A with 13 markers was prepared and used for QTL analysis. A major QTL (QPhs.ccsu-3A.1) was detected on 3AL at a genetic distance of approximately 183 cM from centromere, the length of the map being 279.1 cM. The QTL explained 24.68% to 35.21% variation in individual environments and 78.03% of the variation across the environments (pooled data). The results of the present study are significant on two counts. Firstly, the detected QTL is a major QTL, explaining up to 78.03% of the variation and, secondly, the QTL showed up in all the six environments and also with the pooled data, which is rather rare in QTL analysis. The positive additive effects in the present study suggest that a superior allele of the QTL is available in the superior parent (SPR8198), which can be used for marker-aided selection for the transfer of this QTL allele to obtain PHS-tolerant progeny. It has also been shown that the red-coloured grain of PHS tolerant parent is not associated with the QTL for PHST identified during the present study, suggesting that PHS tolerant white-grained cultivars can be developed.

Structural characterization, expression analysis and evolution of the red/far-red sensing photoreceptor gene, phytochrome C (PHYC), localized on the 'B' genome of hexaploid wheat (Triticum aestivum L.).

Phytochromes are a family of red/far-red light perceiving photoreceptors. The monocot phytochrome family is represented by three members, PHYA, PHYB and PHYC. We have isolated and characterized the first PHY gene member (TaPHYC) from common wheat, Triticum aestivum var. CPAN1676. It codes for a species of the photoreceptor, phyC, which is known to be light-stable in all plants analyzed so far. A sequence of 7.2 kb has been determined, which includes 3.42 kb of coding region. This is the second full-length PHYC gene sequenced from a monocot (first was from rice). TaPHYC gene shares structural similarities with the rice PHYC containing four exons and three introns in the coding region. The 5' UTR is 1.0-kb-long and harbors an upstream open reading frame (URF) encoding 28 aa. Southern blot analysis of TaPHYC indicates that it represents single locus in the wheat genome, although the possibility of additional loci cannot be completely ruled out. Chromosomal localization using nullisomic-tetrasomic lines of Triticum aestivum var. Chinese Spring places TaPHYC on chromosome 4B. PHYC represents a constitutively expressed gene in all the organs tested and under light/dark conditions. However, PHYC was found to be developmentally regulated showing maximal expression in 3-day-old dark-grown seedlings, which declined thereafter. In silico analysis has also been done to compare TaPHYC gene with the partial sequences known from other wheat species and cultivars. The presence of a topoisomerase gene immediately downstream of the PHYC gene, both in rice and wheat genomes, presents yet another example of synteny in cereals and its possible significance has been discussed.

Bone morphogenetic protein 9: a potent modulator of cartilage development in vitro.

Few publications describe the activity of bone morphogenetic protein-9 (BMP-9), but the consensus of these largely in vivo studies is that while BMP-9 can induce ectopic bone formation at relatively large concentrations, it is primarily active in non-skeletal locations--including the liver, nervous system and marrow. To study the effects of BMP-9 on chondrogenesis in a well-defined environment, calf articular chondrocytes were seeded onto biodegradable PGA scaffolds. The resulting cell-polymer constructs were cultured in either control medium or medium supplemented with 1, 10, 50 or 100 ng/ml of BMP-9. After 4 weeks of in vitro culture, all concentrations of BMP-9 increased the total mass of the constructs, and the amounts of collagen, glycosaminoglycans (GAG) and cells per construct. On a mass percentage basis, BMP-9 tended to increase GAG, to decrease the relative amount of collagen and had little effect on the relative amount of cells. BMP-9 elicited qualitatively similar responses as BMP-2, -12 and -13. However, in contrast to BMP-12 and -13, BMP-9 (at concentrations > or = 10 ng/ml) induced hypertrophic chondrocyte formation and was the only BMP tested to induce mineralization. Taken together, these data suggest that BMP-9 is a potent modulator of cartilage development in vitro.

Isolation and molecular characterization of the COP1 gene homolog from rice, Oryza sativa L. subsp. Indica var. Pusa Basmati 1.

The COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) gene has been identified earlier from dicot species namely Arabidopsis, tomato and pea. The protein encoded by this gene acts as a molecular switch that negatively regulates the transition from the skotomorphogenic to the photomorphogenic mode of plant development. We have isolated and characterized the COP1 homolog from a monocot species, i.e. rice (var. Pusa Basmati 1). All the functional domains (Zn-binding RING finger motif, coiled-coil region, WD-40 repeats, cytoplasmic/nuclear localization sequences and protein-protein interaction domains) that are known in the COP1 proteins from dicots are conserved in COP1 from rice as well. The transcript levels of COP1 vary in various tissues of the rice plant. These variations were found to be development-dependent and do not solely depend on the light conditions.

OsIAA1, an Aux/IAA cDNA from rice, and changes in its expression as influenced by auxin and light.

The Aux/IAA class of genes are rapidly induced by exogenous auxins and have been characterized extensively from many dicot species like Arabidopsis, Glycine max and Pisum sativum. We report here the isolation and characterization of rice (Oryza sativa L. subsp. Indica) OsIAA1 cDNA as a monocot member of the Aux/IAA gene family. The predicted amino acid sequence of OsIAA1 corresponds to a protein of ca. 26 kDa, which harbors all four characteristic domains known to be conserved in Aux/IAA proteins. The conservation of these Aux/IAA genes indicates that auxins have essentially a similar mode of action in monocots and dicots. Northern blot analysis revealed that the OsIAA1 transcript levels decrease in the excised coleoptile segments on auxin starvation, and the level is restored when auxin is supplemented; the increase in OsIAA1 transcript level was apparent within 15 to 30 min of auxin application. Auxin-induced OsIAA1 expression appears to be correlated with the elongation of excised coleoptile segments. In light-grown rice seedlings, OsIAA1 is preferentially expressed in roots and basal segment of the seedling, whereas in the etiolated rice seedlings, the OsIAA1 transcripts are most abundant in the coleoptile. A comparative analysis in light- and dark-grown seedling tissues indicates that the OsIAA1 transcript levels decrease on illumination.