Computational and phylogenetic validation of nematode horizontal gene transfer

Sequencing of expressed genes has shown that nematodes, particularly the plant-parasitic nematodes, have genes purportedly acquired from other kingdoms by horizontal gene transfer. The prevailing orthodoxy is that such transfer has been a driving force in the evolution of niche specificity, and a recent paper in BMC Evolutionary Biology that presents a detailed phylogenetic analysis of cellulase genes in the free-living nematode Pristionchus pacificus at the species, genus and family levels substantiates this hypothesis

Tourism policy and destination marketing in developing countries: the chain of influence

Tourism marketers including destination marketing organisations (DMOs) and international tour operators play a pivotal role in destination marketing, especially in creating destination images. These images, apparent in tourist brochures, are designed to influence tourist decision-making and behaviour. This paper proposes the concept of a “chain of influence” in destination marketing and image-making, suggesting that the content of marketing materials is influenced by the priorities of those who design these materials, e.g. tour operators and DMOs. A content analysis of 2,000 pictures from DMO and tour operator brochures revealed synergies and divergence between these marketers. The brochure content was then compared to the South African tourism policy, concluding that the dominant factor in the chain of influence in the South African context is in fact its organic image

Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01

<p>Abstract</p> <p>Background</p> <p>Many strains of <it>Thermus </it>have been isolated from hot environments around the world. <it>Thermus scotoductus </it>SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different <it>Thermus thermophilus </it>strains have been completed. This paper represents the completed genome from a second <it>Thermus </it>species - <it>T. scotoductus</it>.</p> <p>Results</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the <it>Thermus thermophilus </it>genomes. The <it>T. thermophilus </it>megaplasmid genes are part of the <it>T. scotoductus </it>chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of <it>T. scotoductus and T. thermophilus</it>. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from <it>Meiothermus ruber</it>. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of <it>Thermus scotoductus </it>was confirmed experimentally as expected as most of the proteins of the natural transformation system of <it>Thermus thermophilus </it>are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle.</p> <p>Conclusions</p> <p>The genome of <it>Thermus scotoductus </it>SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to <it>Thermus thermophilus</it>. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of <it>Thermus scotoductus </it>illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome.</p

Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover

<p>Abstract</p> <p>Background</p> <p>Natural acquisition of novel genes from other organisms by horizontal or lateral gene transfer is well established for microorganisms. There is now growing evidence that horizontal gene transfer also plays important roles in the evolution of eukaryotes. Genome-sequencing and EST projects of plant and animal associated nematodes such as <it>Brugia</it>, <it>Meloidogyne</it>, <it>Bursaphelenchus </it>and <it>Pristionchus </it>indicate horizontal gene transfer as a key adaptation towards parasitism and pathogenicity. However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes.</p> <p>Results</p> <p>We examine the transfer of cellulase genes to the free-living and beetle-associated nematode <it>Pristionchus pacificus</it>, for which detailed phylogenetic knowledge is available, to address predictions by evolutionary theory for successful gene transfer. We used transcriptomics in seven <it>Pristionchus </it>species and three other related diplogastrid nematodes with a well-defined phylogenetic framework to study the evolution of ancestral cellulase genes acquired by horizontal gene transfer. We performed intra-species, inter-species and inter-genic analysis by comparing the transcriptomes of these ten species and tested for cellulase activity in each species. Species with cellulase genes in their transcriptome always exhibited cellulase activity indicating functional integration into the host's genome and biology. The phylogenetic profile of cellulase genes was congruent with the species phylogeny demonstrating gene longevity. Cellulase genes show notable turnover with elevated birth and death rates. Comparison by sequencing of three selected cellulase genes in 24 natural isolates of <it>Pristionchus pacificus </it>suggests these high evolutionary dynamics to be associated with copy number variations and positive selection.</p> <p>Conclusion</p> <p>We could demonstrate functional integration of acquired cellulase genes into the nematode's biology as predicted by theory. Thus, functional assimilation, remarkable gene turnover and selection might represent key features of horizontal gene transfer events in nematodes.</p

Professional development and sustainable development goals

Professional development is defined as a consciously designed systematic process that helps professionals to attain, utilize, and retain knowledge, skills, and expertise. It is simply a process of obtaining skills, qualifications, and experience that help in advancement in one’s career. In the field of education, it is defined as the process of improving staff skills and competencies needed to produce outstanding performance of students. It also refers to a process of improving an organization’s staff capabilities through access to education and training opportunities for better output. Professional development can include a variety of approaches such as formal and informal education, vocational, specialized, or skill-based training, or advanced professional learning

The Double-stranded RNA–dependent Protein Kinase Differentially Regulates Insulin Receptor Substrates 1 and 2 in HepG2 Cells

The RNA-dependent protein kinase (PKR), initially known as a virus infection response protein, is found to differentially regulate two major players in the insulin signaling pathway, IRS1 and IRS2. PKR up-regulates the inhibitory phosphorylation of IRS1 and the expression of IRS2 at the transcriptional level

A global agenda for advancing freshwater biodiversity research

This manuscript is a contribution of the Alliance for Freshwater Life (www.allianceforfreshwaterlife.org). We thank Nick Bond, Lisa Bossenbroek, Lekima Copeland, Dean Jacobsen, Maria Cecilia Londo?o, David Lopez, Jaime Ricardo Garcia Marquez, Ketlhatlogile Mosepele, Nunia Thomas-Moko, Qiwei Wei and the authors of Living Waters: A Research Agenda for the Biodiversity of Inland and Coastal Waters for their contributions. We also thank Peter Thrall, Ian Harrison and two anonymous referees for their valuable comments that helped improve the manuscript. Open access funding enabled and organised by Projekt DEAL

Photobiocatalytic chemistry of oxidoreductases using water as the electron donor

[EN] To date, water has been poorly studied as the sacrificial electron donor for biocatalytic redox reactions using isolated enzymes. Here we demonstrate that water can also be turned into a sacrificial electron donor to promote biocatalytic redox reactions. The thermodynamic driving force required for water oxidation is obtained from UV and visible light by means of simple titanium dioxide-based photocatalysts. The electrons liberated in this process are delivered to an oxidoreductase by simple flavin redox mediators. Overall, the feasibility of photobiocatalytic, water-driven bioredox reactions is demonstrated.Financial support from the Spanish Science and Innovation Ministry (Consolider Ingenio 2010-MULTICAT CSD 2009-00050, Subprograma de apoyo a Centros y Universidades de Excelencia Severo Ochoa SEV 2012 0267). M. M. acknowledges the Spanish Science and Innovation Ministry for a 'Juan de la Cierva' postdoctoral contract. S. G. acknowledges the European Union Marie Curie Programme (ITN 'Biotrains', Grant Agreement No. 238531).Mifsud Grau, M.; Gargiulo, S.; Iborra Chornet, S.; Arends, IWCE.; Hollmann, F.; Corma Canós, A. (2014). Photobiocatalytic chemistry of oxidoreductases using water as the electron donor. Nature Communications. 5:1-6. https://doi.org/10.1038/ncomms4145S165Bornscheuer, U. T. et al. Engineering the third wave of biocatalysis. Nature 485, 185–194 (2012).Breuer, M. et al. Industrial methods for the production of optically active intermediates. Angew. Chem. Int. Ed. 43, 788–824 (2004).Pollard, D. J. & Woodley, J. M. Biocatalysis for pharmaceutical intermediates: the future is now. Trends Biotechnol. 25, 66–73 (2007).Ran, N., Zhao, L., Chen, Z. & Tao, J. Recent applications of biocatalysis in developing green chemistry for chemical synthesis at the industrial scale. Green. Chem. 10, 361–372 (2008).Schmid, A. et al. Industrial biocatalysis today and tomorrow. Nature 409, 258–268 (2001).Schmid, A., Hollmann, F., Park, J. B. & Bühler, B. The use of enzymes in the chemical industry in Europe. Curr. Opin. Biotechnol. 13, 359–366 (2002).Schoemaker, H. E., Mink, D. & Wubbolts, M. G. Dispelling the myths-biocatalysis in industrial synthesis. Science 299, 1694–1697 (2003).Turner, N. J. & O’Reilly, E. Biocatalytic retrosynthesis. Nat. Chem. Biol. 9, 285–288 (2013).Drauz K., Gröger H., May O. (eds)Enzyme Catalysis in Organic Synthesis Wiley-VCH: Weinheim, (2012).Weckbecker, A., Gröger, H. & Hummel, W. Regeneration of nicotinamide coenzymes: principles and applications for the synthesis of chiral compounds. inBiosystems Engineering I: Creating Superior Biocatalysts pp195–242Springer: Berlin, (2010).Van der Donk, W. A. & Zhao, H. Recent developments in pyridine nucleotide regeneration. Curr. Opin. Biotechnol. 14, 421–426 (2003).Wu, H. et al. Methods for the regeneration of nicotinamide coenzymes. Green. Chem. 15, 1773–1789 (2013).Rodriguez, C., Lavandera, I. & Gotor, V. Recent advances in cofactor regeneration systems applied to biocatalyzed oxidative processes. Curr. Org. Chem. 16, 2525–2541 (2012).Reipa, V., Mayhew, M. P. & Vilker, V. L. A direct electrode-driven P450 cycle for biocatalysis. Proc. Natl Acad. Sci. USA 94, 13554–13558 (1997).Bernard, J., van Heerden, E., Arends, I. W. C. E., Opperman, D. J. & Hollmann, F. Chemoenzymatic reduction of conjugated C=C double bonds. Chem. Cat. Chem. 4, 196–199 (2012).Hollmann, F., Arends, I. W. C. E. & Bühler, K. Biocatalytic redox reactions for organic synthesis: nonconventional regeneration methods. Chem. Cat. Chem. 2, 762–782 (2010).Hollmann, F., Hofstetter, K., Habicher, T., Hauer, B. & Schmid, A. Direct electrochemical regeneration of monooxygenase subunits for biocatalytic asymmetric epoxidation. J. Am. Chem. Soc. 127, 6540–6541 (2005).Hollmann, F., Lin, P.-C., Witholt, B. & Schmid, A. Stereospecific biocatalytic epoxidation: the first example of direct regeneration of a fad-dependent monooxygenase for catalysis. J. Am. Chem. Soc. 125, 8209–8217 (2003).Hollmann, F. & Schmid, A. Towards [Cp*Rh(bpy)(H2O)]2+-promoted P450 catalysis: direct regeneration of CytC. J. Inorg. Biochem. 103, 313–315 (2009).Hollmann, F., Taglieber, A., Schulz, F. & Reetz, M. T. A light-driven stereoselective biocatalytic oxidation. Angew. Chem. Int. Ed. 46, 2903–2906 (2007).Mifsud Grau, M. et al. Photoenzymatic reduction of C=C double bonds. Adv. Synth. Catal. 351, 3279–3286 (2009).Ruinatscha, R., Dusny, C., Buehler, K. & Schmid, A. Productive asymmetric styrene epoxidation based on a next generation electroenzymatic methodology. Adv. Synth. Catal. 351, 2505–2515 (2009).Schwaneberg, U., Appel, D., Schmitt, J. & Schmid, R. D. P450 in biotechnology: zinc driven ω-hydroxylation of p-nitrophenoxydodecanoic acid using P450 BM-3 F87A as a catalyst. J. Biotechnol. 84, 249–257 (2000).Taglieber, A., Schulz, F., Hollmann, F., Rusek, M. & Reetz, M. T. Light-Driven Biocatalytic Oxidation and Reduction Reactions: Scope and Limitations. Chem. Bio. Chem. 9, 565–572 (2008).Udit, A. K., Arnold, F. H. & Gray, H. B. Cobaltocene-mediated catalytic monooxygenation using holo and heme domain cytochrome P450 BM3. J. Inorg. Biochem. 98, 1547–1550 (2004).Udit, A. K., Hill, M. G., Bittner, V. G., Arnold, F. H. & Gray, H. B. Reduction of dioxygen catalyzed by pyrene-wired heme domain cytochrome p450 bm3 electrodes. J. Am. Chem. Soc. 126, 10218–10219 (2004).Unversucht, S., Hollmann, F., Schmid, A. & van Pée, K.-H. FADH2-Dependence of Tryptophan 7-Halogenase. Adv. Synth. Catal. 347, 1163–1167 (2005).Zilly, F. E., Taglieber, A., Schulz, F., Hollmann, F. & Reetz, M. T. Deazaflavins as mediators in light-driven cytochrome P450 catalyzed hydroxylations. Chem. Commun. 7152–7154 (2009).Yehezkeli, O. et al. Integrated photosystem II-based photo-bioelectrochemical cells. Nat. Commun. 3, 742 (2012).Duan, L. et al. A molecular ruthenium catalyst with water-oxidation activity comparable to that of photosystem II. Nat. Chem. 4, 418–423 (2012).Dau, H., Zaharieva, I. & Haumann, M. Recent developments in research on water oxidation by photosystem II. Curr. Opin. Chem. Biol. 16, 3–10 (2012).Qu, Y. & Duan, X. Progress, challenge and perspective of heterogeneous photocatalysts. Chem. Soc. Rev. 42, 2568–2580 (2013).Takanabe, K. & Domen, K. Preparation of inorganic photocatalytic materials for overall water splitting. Chem. Cat. Chem. 4, 1485–1497 (2012).Wee, T.-L. et al. Photochemical synthesis of a water oxidation catalyst based on cobalt nanostructures. J. Am. Chem. Soc. 133, 16742–16745 (2011).Cargnello, M. & Fornasiero, P. Photocatalysis by nanostructured TiO2 based semiconductors. inHandbook of Green Chemistry, Green Nanoscience (eds Selva M., Perosa A. Wiley-VCH: Weinheim, (2010).Liu, S. Q. & Chen, A. C. Coadsorption of horseradish peroxidase with thionine on TiO2: Nanotubes for biosensing. Langmuir 21, 8409–8413 (2005).Zhang, Y., He, P. L. & Hu, N. F. Horseradish peroxidase immobilized in TiO2 nanoparticle films on pyrolytic graphite electrodes: direct electrochemistry and bioelectrocatalysis. Electrochim. Acta 49, 1981–1988 (2004).Chen, D., Zhang, H., Li, X. & Li, J. H. Biofunctional titania nanotubes for visible-light-activated photoelectrochemical biosensing. Anal. Chem. 82, 2253–2261 (2010).Gomes Silva, C. U., Juárez, R., Marino, T., Molinari, R. & García, H. Influence of excitation wavelength (UV or visible light) on the photocatalytic activity of titania containing gold nanoparticles for the generation of hydrogen or oxygen from water. J. Am. Chem. Soc. 133, 595–602 (2010).Opperman, D. J., Piater, L. A. & van Heerden, E. A novel chromate reductase from Thermus scotoductus SA-01 related to old yellow enzyme. J. Bacteriol. 190, 3076–3082 (2008).Opperman, D. J. et al. Crystal structure of a thermostable old yellow enzyme from Thermus scotoductus SA-01. Biochem. Biophys. Res. Commun. 393, 426–431 (2010).Choi, S. H. et al. The influence of non-stoichiometric species of V/TiO2 catalysts on selective catalytic reduction at low temperature. J. Mol. Catal. A: Chem. 304, 166–173 (2009)

A Link among DNA Replication, Recombination, and Gene Expression Revealed by Genetic and Genomic Analysis of TEBICHI Gene of Arabidopsis thaliana

Spatio-temporal regulation of gene expression during development depends on many factors. Mutations in Arabidopsis thaliana TEBICHI (TEB) gene encoding putative helicase and DNA polymerase domains-containing protein result in defects in meristem maintenance and correct organ formation, as well as constitutive DNA damage response and a defect in cell cycle progression; but the molecular link between these phenotypes of teb mutants is unknown. Here, we show that mutations in the DNA replication checkpoint pathway gene, ATR, but not in ATM gene, enhance developmental phenotypes of teb mutants, although atr suppresses cell cycle defect of teb mutants. Developmental phenotypes of teb mutants are also enhanced by mutations in RAD51D and XRCC2 gene, which are involved in homologous recombination. teb and teb atr double mutants exhibit defects in adaxial-abaxial polarity of leaves, which is caused in part by the upregulation of ETTIN (ETT)/AUXIN RESPONSIVE FACTOR 3 (ARF3) and ARF4 genes. The Helitron transposon in the upstream of ETT/ARF3 gene is likely to be involved in the upregulation of ETT/ARF3 in teb. Microarray analysis indicated that teb and teb atr causes preferential upregulation of genes nearby the Helitron transposons. Furthermore, interestingly, duplicated genes, especially tandemly arrayed homologous genes, are highly upregulated in teb or teb atr. We conclude that TEB is required for normal progression of DNA replication and for correct expression of genes during development. Interplay between these two functions and possible mechanism leading to altered expression of specific genes will be discussed

Tm1: A Mutator/Foldback Transposable Element Family in Root-Knot Nematodes

Three closely related parthenogenetic species of root-knot nematodes, collectively termed the Meloidogyne incognita-group, are economically significant pathogens of diverse crop species. Remarkably, these asexual root-knot nematodes are capable of acquiring heritable changes in virulence even though they lack sexual reproduction and meiotic recombination. Characterization of a near isogenic pair of M. javanica strains differing in response to tomato with the nematode resistance gene Mi-1 showed that the virulent strain carried a deletion spanning a gene called Cg-1. Herein, we present evidence that the Cg-1 gene lies within a member of a novel transposable element family (Tm1; Transposon in Meloidogyne-1). This element family is defined by composite terminal inverted repeats of variable lengths similar to those of Foldback (FB) transposable elements and by 9 bp target site duplications. In M. incognita, Tm1 elements can be classified into three general groups: 1) histone-hairpin motif elements; 2) MITE-like elements; 3) elements encoding a putative transposase. The predicted transposase shows highest similarity to gene products encoded by aphids and mosquitoes and resembles those of the Phantom subclass of the Mutator transposon superfamily. Interestingly, the meiotic, sexually-reproducing root-knot nematode species M. hapla has Tm1 elements with similar inverted repeat termini, but lacks elements with histone hairpin motifs and contains no elements encoding an intact transposase. These Tm1 elements may have impacts on root-knot nematode genomes and contribute to genetic diversity of the asexual species