Genomes and Genes
Experts and Doctors on phylogeny in Jena, Thuringia, Germany
Locale: Jena, Thuringia, Germany
- Asghar A, Groth M, Siol O, Gaube F, Enzensperger C, Glockner G, et al. Developmental gene regulation by an ancient intercellular communication system in social amoebae. Protist. 2012;163:25-37 pubmed publisher..Glorin communication has parallels with quorum sensing in that the molecule diffuses into the field, stimulates gene expression in receptive cells and coordinates a population-wide response. ..
- Schmidt D, Voelckel C, Hartl M, Schmidt S, Baldwin I. Specificity in ecological interactions: attack from the same lepidopteran herbivore results in species-specific transcriptional responses in two solanaceous host plants. Plant Physiol. 2005;138:1763-73 pubmed..Given that attack from the same herbivore elicits profoundly different responses in two Solanaceaous taxa, we conclude that blueprints for commonly regulated responses to plant-herbivore interactions appear unlikely. ..
- El Adawy H, Hotzel H, Tomaso H, Neubauer H, Taboada E, Ehricht R, et al. Detection of genetic diversity in Campylobacter jejuni isolated from a commercial turkey flock using flaA typing, MLST analysis and microarray assay. PLoS ONE. 2013;8:e51582 pubmed publisher..DNA microarray-based assays had the highest discriminatory power when compared with other genotyping tools. ..
- Kleinteich T, Haas A. Cranial musculature in the larva of the caecilian, Ichthyophis kohtaoensis (Lissamphibia: Gymnophiona). J Morphol. 2007;268:74-88 pubmed..However, the m. pterygoideus and the m. levator quadrati are unique to the Gymnophiona. ..
- Shelomi M, Heckel D, Pauchet Y. Ancestral gene duplication enabled the evolution of multifunctional cellulases in stick insects (Phasmatodea). Insect Biochem Mol Biol. 2016;71:1-11 pubmed publisher..The structural changes enabling these unprecedented activities in the cellulases require further study. ..
- Spröte P, Hynes M, Hortschansky P, Shelest E, Scharf D, Wolke S, et al. Identification of the novel penicillin biosynthesis gene aatB of Aspergillus nidulans and its putative evolutionary relationship to this fungal secondary metabolism gene cluster. Mol Microbiol. 2008;70:445-61 pubmed..Our findings suggest that aatB is a paralogue of aatA. They extend the model of evolution of the penicillin biosynthesis gene cluster by recruitment of a biosynthesis gene and its cis-regulatory sites upon gene duplication. ..
- Krumbholz A, Bininda Emonds O, Wutzler P, Zell R. Phylogenetics, evolution, and medical importance of polyomaviruses. Infect Genet Evol. 2009;9:784-99 pubmed publisher..Finally, we reveal that the hypothesis of a strict codivergence of polyomaviruses with their respective hosts does not represent a realistic assumption in light of phylogenetic findings presented here. ..
- Allan E, Jenkins T, Fergus A, Roscher C, Fischer M, Petermann J, et al. Experimental plant communities develop phylogenetically overdispersed abundance distributions during assembly. Ecology. 2013;94:465-77 pubmed..Our results show that phylogenetic relations between species provide a good guide to understanding community structure and add a new perspective to the evidence that niche complementarity is critical in driving community assembly. ..
- Citiulo F, Jacobsen I, Miramón P, Schild L, Brunke S, Zipfel P, et al. Candida albicans scavenges host zinc via Pra1 during endothelial invasion. PLoS Pathog. 2012;8:e1002777 pubmed publisher..Furthermore, functional similarities with phylogenetically unrelated prokaryotic systems indicate that syntenic zinc acquisition loci have been independently selected during evolution. ..
- Bog M, Baumbach H, Schween U, Hellwig F, Landolt E, Appenroth K. Genetic structure of the genus Lemna L. (Lemnaceae) as revealed by amplified fragment length polymorphism. Planta. 2010;232:609-19 pubmed publisher..In conclusion, AFLP analysis offers a solid base for the identification of Lemna clones, which is particularly important in view of Lemnaceae application in biomonitoring. ..
- Partida Martinez L, de Looss C, Ishida K, Ishida M, Roth M, Buder K, et al. Rhizonin, the first mycotoxin isolated from the zygomycota, is not a fungal metabolite but is produced by bacterial endosymbionts. Appl Environ Microbiol. 2007;73:793-7 pubmed..This finding is of particular interest since Rhizopus microsporus and related Rhizopus species are frequently used in food preparations such as tempeh and sufu. ..
- Ritz M, Millar C, Miller G, Phillips R, Ryan P, Sternkopf V, et al. Phylogeography of the southern skua complex-rapid colonization of the southern hemisphere during a glacial period and reticulate evolution. Mol Phylogenet Evol. 2008;49:292-303 pubmed publisher..Despite significant differences between taxa most populations still exchange genes with neighboring populations of other taxa and speciation is incomplete. ..
- Griebel T, Brinkmeyer M, Böcker S. EPoS: a modular software framework for phylogenetic analysis. Bioinformatics. 2008;24:2399-400 pubmed publisher..Implemented algorithms cover distance-based tree construction, consensus trees and various graph-based supertree methods. The rendering system can be customized for, say, different edge and node styles. ..
- Lin J, Redies C, Luo J. Regionalized expression of ADAM13 during chicken embryonic development. Dev Dyn. 2007;236:862-70 pubmed..Furthermore, ADAM13 mRNA was also detected in several tissues and organs, such as the somites and their derived muscles, the meninges surrounding the spinal cord, the dorsal aorta, the developing kidney, and several digestive organs. ..
- Sauerbrei A, Zell R, Philipps A, Wutzler P. Genotypes of varicella-zoster virus wild-type strains in Germany. J Med Virol. 2008;80:1123-30 pubmed publisher..The possible recombinant could not be classified definitely by the scattered SNP method used and, therefore, has to be confirmed by full-genome sequencing studies...
- Gossner M, Chao A, Bailey R, Prinzing A. Native fauna on exotic trees: phylogenetic conservatism and geographic contingency in two lineages of phytophages on two lineages of trees. Am Nat. 2009;173:599-614 pubmed publisher..Whether it outweighs geographic contingency and mass effects depends on the interplay of phylogenetic scale, local abundance of native tree species, and the biology and evolutionary history of the phytophage taxon. ..
- Docimo T, Reichelt M, Schneider B, Kai M, Kunert G, Gershenzon J, et al. The first step in the biosynthesis of cocaine in Erythroxylum coca: the characterization of arginine and ornithine decarboxylases. Plant Mol Biol. 2012;78:599-615 pubmed publisher..The levels of both ornithine and arginine themselves showed a similar pattern, so it was not possible to assign a preferential role in cocaine biosynthesis to one of these proteins...
- Schwartze V, Hoffmann K, Nyilasi I, Papp T, Vagvolgyi C, de Hoog S, et al. Lichtheimia species exhibit differences in virulence potential. PLoS ONE. 2012;7:e40908 pubmed publisher..Thus, additional factors or a complex interplay of factors determines the virulence of strains. Our data suggest that the clinical situation in fact reflects different virulence potentials in the Lichtheimiaceae. ..
- Hammerbacher A, Ralph S, Bohlmann J, Fenning T, Gershenzon J, Schmidt A. Biosynthesis of the major tetrahydroxystilbenes in spruce, astringin and isorhapontin, proceeds via resveratrol and is enhanced by fungal infection. Plant Physiol. 2011;157:876-90 pubmed publisher..Extracts from STS-overexpressing lines significantly inhibited fungal growth in vitro compared with extracts from control lines, suggesting that spruce stilbenes have a role in antifungal defense. ..
- Otzen C, Müller S, Jacobsen I, Brock M. Phylogenetic and phenotypic characterisation of the 3-ketoacyl-CoA thiolase gene family from the opportunistic human pathogenic fungus Candida albicans. FEMS Yeast Res. 2013;13:553-64 pubmed publisher..albicans virulence. ..
- Mori J, Lu S, Händel M, Totsche K, Neu T, Iancu V, et al. Schwertmannite formation at cell junctions by a new filament-forming Fe(II)-oxidizing isolate affiliated with the novel genus Acidithrix. Microbiology. 2016;162:62-71 pubmed publisher..Thus, strain C25 appeared to have ecological relevance for both the formation and transformation of the pelagic iron-rich aggregates at oxic/anoxic transition zones in the acidic lignite mine lake...
- Kaltenpoth M, Showers Corneli P, Dunn D, Weiss R, Strohm E, Seger J. Accelerated evolution of mitochondrial but not nuclear genomes of Hymenoptera: new evidence from crabronid wasps. PLoS ONE. 2012;7:e32826 pubmed publisher..Thus, our results suggest that the ancestral parasitic lifestyle of Apocrita is unlikely to be the major cause for the elevated substitution rates observed in hymenopteran mitochondrial genomes. ..
- Pandey S, Baldwin I. RNA-directed RNA polymerase 1 (RdR1) mediates the resistance of Nicotiana attenuata to herbivore attack in nature. Plant J. 2007;50:40-53 pubmed..The experiment highlights the value of carrying out 'real-world' tests of gene function early in the discovery process...
- Barazani O, Benderoth M, Groten K, Kuhlemeier C, Baldwin I. Piriformospora indica and Sebacina vermifera increase growth performance at the expense of herbivore resistance in Nicotiana attenuata. Oecologia. 2005;146:234-43 pubmed..These results suggest that Sebacina spp. may interfere with defense signaling and allow plants to increase growth rates at the expense of herbivore resistance mediated by TPIs. ..
- Garcia S, McMahon K, Martinez Garcia M, Srivastava A, Sczyrba A, Stepanauskas R, et al. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton. ISME J. 2013;7:137-47 pubmed publisher..We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria...
- Sudakaran S, Salem H, Kost C, Kaltenpoth M. Geographical and ecological stability of the symbiotic mid-gut microbiota in European firebugs, Pyrrhocoris apterus (Hemiptera, Pyrrhocoridae). Mol Ecol. 2012;21:6134-51 pubmed publisher..Our findings suggest that the firebug mid-gut microbiota constitutes a functionally important and possibly coevolved symbiotic community. ..
- Zell R, Dauber M, Krumbholz A, Henke A, Birch Hirschfeld E, Stelzner A, et al. Porcine teschoviruses comprise at least eleven distinct serotypes: molecular and evolutionary aspects. J Virol. 2001;75:1620-31 pubmed..Sequencing of field isolates collected from animals presenting with neurological disorders prove that other serotypes than PTV-1 may also cause polioencephalomyelitis of swine...
- Glockner G, Scherer S, Schattevoy R, Boright A, Weber J, Tsui L, et al. Large-scale sequencing of two regions in human chromosome 7q22: analysis of 650 kb of genomic sequence around the EPO and CUTL1 loci reveals 17 genes. Genome Res. 1998;8:1060-73 pubmed..The CUTL1 locus, consisting of two splice variants (CDP and CASP), occupies >300 kb. Based on the G, C profile an isochore switch can be defined between the CUTL1 gene and the APS and PMSL12 genes. ..
- Kaur H, Shaker K, Heinzel N, Ralph J, Galis I, Baldwin I. Environmental stresses of field growth allow cinnamyl alcohol dehydrogenase-deficient Nicotiana attenuata plants to compensate for their structural deficiencies. Plant Physiol. 2012;159:1545-70 pubmed publisher..Environmental stresses play an essential role in regulating lignin biosynthesis in lignin-deficient plants. ..
- Hilgenfeld R, Bock A, Wilting R. Structural model for the selenocysteine-specific elongation factor SelB. Biochimie. 1996;78:971-8 pubmed..A phylogenetic comparison of the SelB domains homologous to EF-Tu with those from EF-Tu and initiation factor 2 indicated that SelB forms a separate class of translation factors. ..
- Lackner G, Möbius N, Scherlach K, Partida Martinez L, Winkler R, Schmitt I, et al. Global distribution and evolution of a toxinogenic Burkholderia-Rhizopus symbiosis. Appl Environ Microbiol. 2009;75:2982-6 pubmed publisher..Comparison of host and symbiont phylogenies provides insights into possible cospeciation and horizontal-transmission events. ..
- Lenser T, Theissen G, Dittrich P. Developmental robustness by obligate interaction of class B floral homeotic genes and proteins. PLoS Comput Biol. 2009;5:e1000264 pubmed publisher..This finding strongly corroborates the view that the appearance of this regulatory mechanism during angiosperm phylogeny led to a canalization of flower development and evolution. ..
- Pauchet Y, Freitak D, Heidel Fischer H, Heckel D, Vogel H. Immunity or digestion: glucanase activity in a glucan-binding protein family from Lepidoptera. J Biol Chem. 2009;284:2214-24 pubmed publisher..The noncatalytic betaGRPs may be evolutionarily derived from this newly described enzyme family that continues to function catalytically in digestion and/or pathogen defense. ..
- Bollig F, Mehringer R, Perner B, Hartung C, Schafer M, Schartl M, et al. Identification and comparative expression analysis of a second wt1 gene in zebrafish. Dev Dyn. 2006;235:554-61 pubmed..In adult fish, high expression levels for both genes can be found in gonads, kidney, heart, spleen, and muscle. ..
- Qu N, Schittko U, Baldwin I. Consistency of Nicotiana attenuata's herbivore- and jasmonate-induced transcriptional responses in the allotetraploid species Nicotiana quadrivalvis and Nicotiana clevelandii. Plant Physiol. 2004;135:539-48 pubmed..Elicitation decreases the expression of growth-related genes in all three species. We propose that this is a valuable system to examine the modification of complex, polygenic, adaptive responses during allopolyploid speciation. ..
- Goremykin V, Hirsch Ernst K, Wolfl S, Hellwig F. The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol Biol Evol. 2004;21:1445-54 pubmed..Our findings have general implications for studies of substitution model specification and analyses of concatenated genome data...
- Fu Q, Posth C, Hajdinjak M, Petr M, Mallick S, Fernandes D, et al. The genetic history of Ice Age Europe. Nature. 2016;534:200-5 pubmed publisher..These results document how population turnover and migration have been recurring themes of European prehistory. ..
- Kaltenpoth M, Roeser Mueller K, Koehler S, Peterson A, Nechitaylo T, Stubblefield J, et al. Partner choice and fidelity stabilize coevolution in a Cretaceous-age defensive symbiosis. Proc Natl Acad Sci U S A. 2014;111:6359-64 pubmed publisher..Thus, partner choice can play an important role even in predominantly vertically transmitted symbioses by stabilizing the cooperative association over evolutionary timescales. ..
- Schilling S, Gramzow L, Lobbes D, Kirbis A, Weilandt L, Hoffmeier A, et al. Non-canonical structure, function and phylogeny of the Bsister MADS-box gene OsMADS30 of rice (Oryza sativa). Plant J. 2015;84:1059-72 pubmed publisher..sativa. ..
- Linz J, Baschwitz A, Strutz A, Dweck H, Sachse S, Hansson B, et al. Host plant-driven sensory specialization in Drosophila erecta. Proc Biol Sci. 2013;280:20130626 pubmed publisher..melanogaster. The presumed adaptations observed here follow to a remarkable degree those found in Drosophila sechellia, a specialist upon noni fruit, and suggest a general principle for how specialization affects the sense of smell...
- Dorn A, Ng oma E, Janko K, Reichwald K, Pola ik M, Platzer M, et al. Phylogeny, genetic variability and colour polymorphism of an emerging animal model: the short-lived annual Nothobranchius fishes from southern Mozambique. Mol Phylogenet Evol. 2011;61:739-49 pubmed publisher..furzeri) is unrelated to colour phenotypes of the study species. Our results raise significant implications for future comparative studies of the species and populations analysed in the present work...
- Leitherer S, Clos J, Liebler Tenorio E, Schleicher U, Bogdan C, Soulat D. Characterization of the Protein Tyrosine Phosphatase LmPRL-1 Secreted by Leishmania major via the Exosome Pathway. Infect Immun. 2017;85: pubmed publisher..major led to an increased number of parasites in macrophages. From these data, we conclude that the L. major phosphatase LmPRL-1 contributes to the intracellular survival of the parasites in macrophages. ..
- Schmith A, Groth M, Ratka J, Gatz S, Spaller T, Siol O, et al. Conserved gene regulatory function of the carboxy-terminal domain of dictyostelid C-module-binding factor. Eukaryot Cell. 2013;12:460-8 pubmed publisher..Our data suggest that two functional regions of the CbfA-like proteins evolved at different rates to allow the occurrence of species-specific adaptation processes during genome evolution. ..
- Krumbholz A, Dauber M, Henke A, Birch Hirschfeld E, Knowles N, Stelzner A, et al. Sequencing of porcine enterovirus groups II and III reveals unique features of both virus groups. J Virol. 2002;76:5813-21 pubmed..A reclassification of this group into a new picornavirus genus is suggested. PEV group III viruses are typical enteroviruses. They differ from other enteroviruses by a prolonged stem-loop D of the 5'-cloverleaf structure...
- Kaufmann K, Anfang N, Saedler H, Theissen G. Mutant analysis, protein-protein interactions and subcellular localization of the Arabidopsis B sister (ABS) protein. Mol Genet Genomics. 2005;274:103-18 pubmed..Thus the evolutionary developmental genetics of B(sister) genes can probably only be understood as part of a complex and redundant gene network that may govern ovule formation in a conserved manner, which has yet to be fully explored. ..
- Sauerbrei A, Bohn K, Zell R, Wutzler P. Variability of immediate-early gene 62 in german varicella-zoster virus wild-type strains. J Clin Microbiol. 2009;47:3717-20 pubmed publisher..M1 strains in Germany display a uniform ORF 62 pattern, suggesting that these strains were introduced from Africa and/or Asia via few sources during the last years. ..
- Hettenhausen C, Baldwin I, Wu J. Silencing MPK4 in Nicotiana attenuata enhances photosynthesis and seed production but compromises abscisic acid-induced stomatal closure and guard cell-mediated resistance to Pseudomonas syringae pv tomato DC3000. Plant Physiol. 2012;158:759-76 pubmed publisher..This work highlights the multifaceted functions of NaMPK4 in guard cells and underscores its role in mediating various ecologically important traits. ..
- Kaltenpoth M, Yildirim E, Gürbüz M, Herzner G, Strohm E. Refining the roots of the beewolf-Streptomyces symbiosis: antennal symbionts in the rare genus Philanthinus (Hymenoptera, Crabronidae). Appl Environ Microbiol. 2012;78:822-7 pubmed publisher..It probably evolved along the branch leading to the monophyletic tribe Philanthini, as it seems to be confined to the genera Philanthus, Trachypus, and Philanthinus, which together comprise 172 described species of solitary wasps...
- Pan X, Kage H, Martin K, Nett M. Herpetosiphon gulosus sp. nov., a filamentous predatory bacterium isolated from sandy soil and Herpetosiphon giganteus sp. nov., nom. rev. Int J Syst Evol Microbiol. 2017;67:2476-2481 pubmed publisher..nov., nom. rev. We propose the previously deposited reference strain DSM 589T=NBRC 112828T as the type strain. ..
- Steinchen W, Lackner G, Yasmin S, Schrettl M, Dahse H, Haas H, et al. Bimodular peptide synthetase SidE produces fumarylalanine in the human pathogen Aspergillus fumigatus. Appl Environ Microbiol. 2013;79:6670-6 pubmed publisher..As FA is structurally related to established pharmaceutical products exerting immunomodulatory activity, this work may contribute to our understanding of the virulence of A. fumigatus. ..
- Lange J, Groth M, Schlegel M, Krumbholz A, Wieczorek K, Ulrich R, et al. Reassortants of the pandemic (H1N1) 2009 virus and establishment of a novel porcine H1N2 influenza virus, lineage in Germany. Vet Microbiol. 2013;167:345-56 pubmed publisher..The most frequent genotype emerged at least three times independently, one of which (Papenburg lineage) established a stable infection chain and became more prevalent in pigs than pdmH1N1 in Germany. ..
- Voigt A, Schöfl G, Saluz H. The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens. PLoS ONE. 2012;7:e35097 pubmed publisher..It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions. ..
- Rahman M, Fromm B, Neupert S, Kreusch S, Predel R. Extended FMRFamides in dipteran insects: conservative expression in the neuroendocrine system is accompanied by rapid sequence evolution. Gen Comp Endocrinol. 2009;162:52-8 pubmed publisher..In insects, no other neuropeptide family is known that shows such sequence variability between related species. ..
- Lackner G, Moebius N, Hertweck C. Endofungal bacterium controls its host by an hrp type III secretion system. ISME J. 2011;5:252-61 pubmed publisher..In a control experiment, we demonstrate that under laboratory conditions, rhizoxin production was not required for establishment of the symbiotic interaction. ..
- Pauchet Y, Heckel D. The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer. Proc Biol Sci. 2013;280:20131021 pubmed publisher..We also provide evidence that these genes were originally acquired by P. cochleariae from a species of gammaproteobacteria through HGT. This represents the first example of the presence of genes from the GH11 family in animals. ..
- Behnken S, Hertweck C. Cryptic polyketide synthase genes in non-pathogenic Clostridium SPP. PLoS ONE. 2012;7:e29609 pubmed publisher..This study presents clostridia as a putative source for novel bioactive polyketides...
- Nyakatura K, Bininda Emonds O. Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates. BMC Biol. 2012;10:12 pubmed publisher..We therefore sought to provide an updated estimate of the phylogenetic relationships within all extant Carnivora, again using supertree analysis to be able to analyze as much of the global phylogenetic database for the group as possible...
- Stoessel A, Kilbourne B, Fischer M. Morphological integration versus ecological plasticity in the avian pelvic limb skeleton. J Morphol. 2013;274:483-95 pubmed publisher..Finally, when looking at relative lengths segmented limbs meet the requirements of many-to-one-mapping of phenotype to functional property, in line with a common concept of evolvability of function and morphology. ..
- Steppuhn A, Gaquerel E, Baldwin I. The two alpha-dox genes of Nicotiana attenuata: overlapping but distinct functions in development and stress responses. BMC Plant Biol. 2010;10:171 pubmed publisher..attenuata. In leaf maturation, the two alpha-dox genes have overlapping functions, but only alpha-dox2 is involved in root and flower development and only alpha-dox1 functions in anti-herbivore defense...
- Crocoll C, Asbach J, Novak J, Gershenzon J, Degenhardt J. Terpene synthases of oregano (Origanum vulgare L.) and their roles in the pathway and regulation of terpene biosynthesis. Plant Mol Biol. 2010;73:587-603 pubmed publisher..These results will facilitate metabolic engineering and directed breeding of O. vulgare cultivars with higher quantity of essential oil and improved oil composition...
- Kliebenstein D, Lambrix V, Reichelt M, Gershenzon J, Mitchell Olds T. Gene duplication in the diversification of secondary metabolism: tandem 2-oxoglutarate-dependent dioxygenases control glucosinolate biosynthesis in Arabidopsis. Plant Cell. 2001;13:681-93 pubmed..A third member of this gene family, AOP1, is present in at least two forms and found in all ecotypes examined. However, its catalytic role is still uncertain. ..