Experts and Doctors on phylogeny in Freiburg, Baden Württemberg, Germany

Summary

Locale: Freiburg, Baden Württemberg, Germany
Topic: phylogeny

Top Publications

  1. Afonso C, Amarasinghe G, Bányai K, Bào Y, Basler C, Bavari S, et al. Taxonomy of the order Mononegavirales: update 2016. Arch Virol. 2016;161:2351-60 pubmed publisher
    ..This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). ..
  2. Scharf W, Schauer S, Freyburger F, Petrovec M, Schaarschmidt Kiener D, Liebisch G, et al. Distinct host species correlate with Anaplasma phagocytophilum ankA gene clusters. J Clin Microbiol. 2011;49:790-6 pubmed publisher
    ..Whereas the phylogenetic analysis using 16S rRNA gene sequences was not meaningful, we showed that distinct host species correlate with A. phagocytophilum ankA gene clusters. ..
  3. Wüppenhorst N, von Loewenich F, Hobmaier B, Vetter Knoll M, Mohadjer S, Kist M. Culture of a gastric non-Helicobacter pylori Helicobacter from the stomach of a 14-year-old girl. Helicobacter. 2013;18:1-5 pubmed publisher
    ..The strain was cultured using our routine protocol for H. pylori and identified by phylogenetic analyses of partial urease AB and gyrB gene sequences. ..
  4. Pogoda H, Meyer D. Zebrafish Smad7 is regulated by Smad3 and BMP signals. Dev Dyn. 2002;224:334-49 pubmed
    ..In summary, our analyses point out differences of Smad3b and Smad2 functions in zebrafish and provide the first link of smad3 and smad7 function in context of vertebrate development. ..
  5. Jonas D, Spitzmüller B, Daschner F, Verhoef J, Brisse S. Discrimination of Klebsiella pneumoniae and Klebsiella oxytoca phylogenetic groups and other Klebsiella species by use of amplified fragment length polymorphism. Res Microbiol. 2004;155:17-23 pubmed
  6. Anderson A, Hellwig E, Vespermann R, Wittmer A, Schmid M, Karygianni L, et al. Comprehensive analysis of secondary dental root canal infections: a combination of culture and culture-independent approaches reveals new insights. PLoS ONE. 2012;7:e49576 pubmed publisher
    ..Both methods yielded differing results, emphasizing the benefit of combined methods for the detection of the actual microbial diversity in apical periodontitis. ..
  7. Boehm T, Iwanami N, Hess I. Evolution of the immune system in the lower vertebrates. Annu Rev Genomics Hum Genet. 2012;13:127-49 pubmed publisher
    ..The discovery of conserved features of adaptive immunity will guide attempts to generate synthetic immunological functionalities and thus provide new avenues for intervening with faulty immune functions in humans. ..
  8. Gierga G, Voss B, Hess W. The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria. RNA Biol. 2009;6:222-7 pubmed
    ..The genes for ncRNAs of this family are suggested to exist in highly variable copy numbers in the individual genomes, with up to nine copies in some marine Synechococcus. ..
  9. Schmidt J, Kirsch S, Rappold G, Schempp W. Complex evolution of a Y-chromosomal double homeobox 4 (DUX4)-related gene family in hominoids. PLoS ONE. 2009;4:e5288 pubmed publisher

More Information

Publications60

  1. Martin A, Lang D, Hanke S, Mueller S, Sarnighausen E, Vervliet Scheebaum M, et al. Targeted gene knockouts reveal overlapping functions of the five Physcomitrella patens FtsZ isoforms in chloroplast division, chloroplast shaping, cell patterning, plant development, and gravity sensing. Mol Plant. 2009;2:1359-72 pubmed publisher
    ..These results support the concept of a plastoskeleton and its functional integration into the cytoskeleton, at least in the moss P. patens. ..
  2. Moser M, Yu Q, Bode C, Xiong J, Patterson C. BMPER is a conserved regulator of hematopoietic and vascular development in zebrafish. J Mol Cell Cardiol. 2007;43:243-53 pubmed
    ..The generation of the caudal vein is compromised and the pattern guiding of the intersomitic vessels is disturbed, indicating that zbmper is required for early steps in vascular pattern formation and hematopoiesis in zebrafish. ..
  3. Beetz N, Hein L. The physiological roles of phosducin: from retinal function to stress-dependent hypertension. Cell Mol Life Sci. 2011;68:599-612 pubmed publisher
    ..In the second part of this article, findings concerning cardiovascular regulation and their clinical relevance will be discussed on the basis of recently published data from gene-targeted mouse models and human genetic studies. ..
  4. Schröder G, Wehinger E, Schröder J. Predicting the substrates of cloned plant O-methyltransferases. Phytochemistry. 2002;59:1-8 pubmed
    ..The results, confirmed by functional analysis of the recombinant protein, indicated that a careful analysis of the deduced protein sequence can provide clues for predicting the substrates of cloned OMTs. ..
  5. Rentzsch F, Kramer C, Hammerschmidt M. Specific and conserved roles of TAp73 during zebrafish development. Gene. 2003;323:19-30 pubmed
    ..Together, our data point to both conserved and class-specific roles of p73 during vertebrate development. ..
  6. Lang D, Weiche B, Timmerhaus G, Richardt S, Riaño Pachón D, Corrêa L, et al. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2010;2:488-503 pubmed publisher
    ..Our work lays the ground for further interrogation of the shaping of gene regulatory networks underlying the evolution of organism complexity. ..
  7. Buellesbach J, Gadau J, Beukeboom L, Echinger F, Raychoudhury R, Werren J, et al. Cuticular hydrocarbon divergence in the jewel wasp Nasonia: evolutionary shifts in chemical communication channels?. J Evol Biol. 2013;26:2467-78 pubmed publisher
    ..giraulti CHC profiles, which are no longer used as conspecific recognition cues. Our study constitutes the first report of an apparent abandonment of a sexual recognition cue that the receiver did not adapt to. ..
  8. Al Ahmad A, Pelz K, Schirrmeister J, Hellwig E, Pukall R. Characterization of the first oral vagococcus isolate from a root-filled tooth with periradicular lesions. Curr Microbiol. 2008;57:235-8 pubmed publisher
    ..This taxon is a new entry to the list of more than 200 microbial species detected in infected root canal systems. ..
  9. Paponov I, Paponov M, Teale W, Menges M, Chakrabortee S, Murray J, et al. Comprehensive transcriptome analysis of auxin responses in Arabidopsis. Mol Plant. 2008;1:321-37 pubmed publisher
    ..Our analysis provides a roadmap for auxin-dependent processes that underpins the concept of an 'auxin code'--a tissue-specific fingerprint of gene expression that initiates specific developmental processes. ..
  10. Martin A, Lang D, Heckmann J, Zimmer A, Vervliet Scheebaum M, Reski R. A uniquely high number of ftsZ genes in the moss Physcomitrella patens. Plant Biol (Stuttg). 2009;11:744-50 pubmed publisher
    ..Based on all these results, we have renamed the PpFtsZ proteins of family 1 and suggest the existence of a third FtsZ family. No species is known to encode more FtsZ proteins per haploid genome than P. patens...
  11. Richter A, Backofen R. Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?. RNA Biol. 2012;9:954-65 pubmed publisher
    ..bioinf.uni-freiburg.de/Supplements/srna-interact-feat. ..
  12. Parsons J, Altmann F, Arrenberg C, Koprivova A, Beike A, Stemmer C, et al. Moss-based production of asialo-erythropoietin devoid of Lewis A and other plant-typical carbohydrate determinants. Plant Biotechnol J. 2012;10:851-61 pubmed publisher
  13. Ziegler S, Dolch K, Geiger K, Krause S, Asskamp M, Eusterhues K, et al. Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria. ISME J. 2013;7:1725-37 pubmed publisher
    ..This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea. ..
  14. von Loewenich F, Geissdörfer W, Disqué C, Matten J, Schett G, Sakka S, et al. Detection of "Candidatus Neoehrlichia mikurensis" in two patients with severe febrile illnesses: evidence for a European sequence variant. J Clin Microbiol. 2010;48:2630-5 pubmed publisher
    ..16S rRNA and groEL gene sequencing provided evidence of three groups of sequence variants...
  15. Dürr J, Bücking H, Mult S, Wildhagen H, Palme K, Rennenberg H, et al. Seasonal and cell type specific expression of sulfate transporters in the phloem of Populus reveals tree specific characteristics for SO(4)(2-) storage and mobilization. Plant Mol Biol. 2010;72:499-517 pubmed publisher
    ..Taken together, these findings indicate a transcriptional regulation of sulfate distribution in poplar trees. ..
  16. Graeber K, Linkies A, Muller K, Wunchova A, Rott A, Leubner Metzger G. Cross-species approaches to seed dormancy and germination: conservation and biodiversity of ABA-regulated mechanisms and the Brassicaceae DOG1 genes. Plant Mol Biol. 2010;73:67-87 pubmed publisher
    ..Other species of the monophyletic genus Lepidium showed coat or embryo dormancy and are therefore highly suited for comparative seed biology...
  17. Okosun J, Bodor C, Wang J, Araf S, Yang C, Pan C, et al. Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nat Genet. 2014;46:176-181 pubmed publisher
  18. Venkatesh B, Lee A, Ravi V, Maurya A, Lian M, Swann J, et al. Elephant shark genome provides unique insights into gnathostome evolution. Nature. 2014;505:174-9 pubmed publisher
    ..It thus presents a new model for understanding the origin of adaptive immunity. ..
  19. Amarasinghe G, Bao Y, Basler C, Bavari S, Beer M, Bejerman N, et al. Taxonomy of the order Mononegavirales: update 2017. Arch Virol. 2017;162:2493-2504 pubmed publisher
    ..This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV). ..
  20. Kraus F, Haenig B, Kispert A. Cloning and expression analysis of the mouse T-box gene Tbx18. Mech Dev. 2001;100:83-6 pubmed
    ..Other sites of expression include the cranial paraxial mesoderm, the presomitic mesoderm, the anterior somite half, the genital ridge, and the developing limb buds. ..
  21. Peters F, Shinoda Y, McInerney M, Boll M. Cyclohexa-1,5-diene-1-carbonyl-coenzyme A (CoA) hydratases of Geobacter metallireducens and Syntrophus aciditrophicus: Evidence for a common benzoyl-CoA degradation pathway in facultative and strict anaerobes. J Bacteriol. 2007;189:1055-60 pubmed
    ..The steps involved in dienoyl-CoA metabolism appear identical in all nonphotosynthetic anaerobic bacteria, although totally different benzene ring-dearomatizing enzymes are present in facultative and obligate anaerobes...
  22. Bierfreund N, Tintelnot S, Reski R, Decker E. Loss of GH3 function does not affect phytochrome-mediated development in a moss, Physcomitrella patens. J Plant Physiol. 2004;161:823-35 pubmed publisher
    ..No obvious differences between wild type and knockout plants could be detected under the examined conditions, indicating functional redundancy of the two genes...
  23. Wildhagen H, Dürr J, Ehlting B, Rennenberg H. Seasonal nitrogen cycling in the bark of field-grown Grey poplar is correlated with meteorological factors and gene expression of bark storage proteins. Tree Physiol. 2010;30:1096-110 pubmed publisher
    ..We conclude that GABA and arginine potentially contribute to adjust storage processes in the bark of poplar trees to seasonal changes in environmental conditions. ..
  24. Belting H, Wendik B, Lunde K, Leichsenring M, Mössner R, Driever W, et al. Pou5f1 contributes to dorsoventral patterning by positive regulation of vox and modulation of fgf8a expression. Dev Biol. 2011;356:323-36 pubmed publisher
    ..Our data reveals a set of direct and indirect interactions of Pou5f1 with the BMP dorsoventral patterning network that serve to fine-tune dorsoventral patterning mechanisms and coordinate patterning with developmental timing. ..
  25. Welsch R, W st F, B r C, Al Babili S, Beyer P. A third phytoene synthase is devoted to abiotic stress-induced abscisic acid formation in rice and defines functional diversification of phytoene synthase genes. Plant Physiol. 2008;147:367-80 pubmed publisher
    ..Since the genomic structures of OsPSY2 and OsPSY3 are comparable, we conclude that they originated from the most recent common ancestor, OsPSY1...
  26. Tucker M, Roodbarkelari F, Truernit E, Adamski N, Hinze A, Lohmüller B, et al. Accession-specific modifiers act with ZWILLE/ARGONAUTE10 to maintain shoot meristem stem cells during embryogenesis in Arabidopsis. BMC Genomics. 2013;14:809 pubmed publisher
    ..Reduced SQN expression levels in Col-0 correlate with transposon insertions adjoining the transcriptional start site, which may contribute to stem cell maintenance in other ZLL-independent accessions. ..
  27. Dear T, Meier N, Hunn M, Boehm T. Gene structure, chromosomal localization, and expression pattern of Capn12, a new member of the calpain large subunit gene family. Genomics. 2000;68:152-60 pubmed
    ..4 cM. Refined mapping of Capn5, also previously localized to chromosome 7, indicated that it was not closely linked to Capn12, mapping tightly linked to a marker positioned at 48.5 cM. ..
  28. Koch M, Schulze J, Hansen U, Ashwodt T, Keene D, Brunken W, et al. A novel marker of tissue junctions, collagen XXII. J Biol Chem. 2004;279:22514-21 pubmed
    ..This novel gene product, collagen XXII, is the first specific extracellular matrix protein present only at tissue junctions. ..
  29. Rensing S, Maier U. Phylogenetic analysis of the stress-70 protein family. J Mol Evol. 1994;39:80-6 pubmed
    ..We present a phylogenetic tree containing all known stress-70 subfamilies and demonstrate the usefulness of stress-70 protein sequences for the estimation of intertaxonic phylogeny...
  30. Sander A, Ruess M, Bereswill S, Schuppler M, Steinbrueckner B. Comparison of different DNA fingerprinting techniques for molecular typing of Bartonella henselae isolates. J Clin Microbiol. 1998;36:2973-81 pubmed
    ..Our results suggest that the genetic heterogeneity of B. henselae strains is high. The methods applied were found useful for typing B. henselae isolates, providing tools for epidemiological and clinical follow-up studies...
  31. Hallast P, Maisano Delser P, Batini C, Zadik D, Rocchi M, Schempp W, et al. Great ape Y Chromosome and mitochondrial DNA phylogenies reflect subspecies structure and patterns of mating and dispersal. Genome Res. 2016;26:427-39 pubmed publisher
    ..Cross-species comparison within a single MSY phylogeny emphasizes the low human diversity, and reveals species-specific branch length variation that may reflect differences in long-term generation times. ..
  32. Schweizer M, Schleer H, Pietrek M, Liegibel J, Falcone V, Neumann Haefelin D. Genetic stability of foamy viruses: long-term study in an African green monkey population. J Virol. 1999;73:9256-65 pubmed
    ..5 to 100%), and only a minimal genetic drift was recognized within the series of isolates. In conclusion, the low in vivo divergency of FV SU suggests that genetic variability is not important for the maintenance of FV persistence...
  33. Mechichi T, Stackebrandt E, Gad on N, Fuchs G. Phylogenetic and metabolic diversity of bacteria degrading aromatic compounds under denitrifying conditions, and description of Thauera phenylacetica sp. nov., Thauera aminoaromaticasp. nov., and Azoarcus buckelii sp. nov. Arch Microbiol. 2002;178:26-35 pubmed
  34. Helmstädter M, Lüthy K, Gödel M, Simons M, Ashish -, Nihalani D, et al. Functional study of mammalian Neph proteins in Drosophila melanogaster. PLoS ONE. 2012;7:e40300 pubmed publisher
    ..Hereby, we establish D. melanogaster as a genetic system to specifically model molecular Neph1 functions in vivo and identify a conserved amino acid motif linking Neph1 to Drosophila Kirre function. ..
  35. Haecker A, Gross Hardt R, Geiges B, Sarkar A, Breuninger H, Herrmann M, et al. Expression dynamics of WOX genes mark cell fate decisions during early embryonic patterning in Arabidopsis thaliana. Development. 2004;131:657-68 pubmed
    ..Together, our data suggest that during plant embryogenesis region-specific transcription programs are initiated very early in single precursor cells and that WOX genes play an important role in this process. ..
  36. Paponov I, Teale W, Lang D, Paponov M, Reski R, Rensing S, et al. The evolution of nuclear auxin signalling. BMC Evol Biol. 2009;9:126 pubmed publisher
  37. Schaaf A, Reski R, Decker E. A novel aspartic proteinase is targeted to the secretory pathway and to the vacuole in the moss Physcomitrella patens. Eur J Cell Biol. 2004;83:145-52 pubmed publisher
    ..Above all the functionality of the secretory and the vacuolar targeting signals make them become useful tools for biotechnological approaches...
  38. Pfreundt U, Stal L, Voß B, Hess W. Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium. ISME J. 2012;6:1367-77 pubmed publisher
  39. Chacinska A, Guiard B, Müller J, Schulze Specking A, Gabriel K, Kutik S, et al. Mitochondrial biogenesis, switching the sorting pathway of the intermembrane space receptor Mia40. J Biol Chem. 2008;283:29723-9 pubmed publisher
  40. Viktorin G, Chiuchitu C, Rissler M, Varga Z, Westerfield M. Emx3 is required for the differentiation of dorsal telencephalic neurons. Dev Dyn. 2009;238:1984-98 pubmed publisher
    ..Previously, emx3 was thought to be fish-specific. However, we found all three emx orthologs in Xenopus tropicalis and opossum (Monodelphis domestica) genomes, indicating that emx3 was present in an ancestral tetrapod genome. ..
  41. Hagemann S, Gunther T, Dennemärker J, Lohmüller T, Bromme D, Schüle R, et al. The human cysteine protease cathepsin V can compensate for murine cathepsin L in mouse epidermis and hair follicles. Eur J Cell Biol. 2004;83:775-80 pubmed
  42. Epting D, Vorwerk S, Hageman A, Meyer D. Expression of rasgef1b in zebrafish. Gene Expr Patterns. 2007;7:389-95 pubmed
    ..Finally, we show that early zygotic expression is regulated by Nodal and FGF signals and that these signals have different activities in regulating the level and distribution of early zygotic rasgef1b mRNA expression. ..
  43. Hein S, Scholz I, Voß B, Hess W. Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. RNA Biol. 2013;10:852-64 pubmed publisher
    ..Indeed, we identified one of these genes, sll7009, as encoding a negative regulator specific for the CRISPR1 subtype I-D system in Synechocystis sp PCC6803. ..
  44. Sturm G, Jacobs J, Sproer C, Schumann P, Gescher J. Leucobacter chromiiresistens sp. nov., a chromate-resistant strain. Int J Syst Evol Microbiol. 2011;61:956-60 pubmed publisher
    ..nov. is proposed. The type strain is strain JG 31(T) (?=?DSM 22788(T) ?=?CCOS 200(T))...
  45. Youssar L, Grüning B, Günther S, Hüttel W. Characterization and phylogenetic analysis of the mitochondrial genome of Glarea lozoyensis indicates high diversity within the order Helotiales. PLoS ONE. 2013;8:e74792 pubmed publisher
    ..Further mitochondrial genomes are required in order to determine whether there is a continuous transition between the different forms of mitochondrial genomes or G. lozoyensis belongs to a distinct subgroup within Helotiales. ..
  46. Dick A, Meier A, Hammerschmidt M. Smad1 and Smad5 have distinct roles during dorsoventral patterning of the zebrafish embryo. Dev Dyn. 1999;216:285-98 pubmed
  47. Mahler J, Driever W. Expression of the zebrafish intermediate neurofilament Nestin in the developing nervous system and in neural proliferation zones at postembryonic stages. BMC Dev Biol. 2007;7:89 pubmed
  48. Rensing S, Ick J, Fawcett J, Lang D, Zimmer A, Van de Peer Y, et al. An ancient genome duplication contributed to the abundance of metabolic genes in the moss Physcomitrella patens. BMC Evol Biol. 2007;7:130 pubmed
    ..patens. This might, at least partly, explain the versatility of metabolism, as described for P. patens and other mosses, in comparison to other land plants. ..
  49. Dear T, Moller A, Boehm T. CAPN11: A calpain with high mRNA levels in testis and located on chromosome 6. Genomics. 1999;59:243-7 pubmed
    ..The discovery of this new calpain emphasizes the complexity of the calpain family, with members being distinguished on the basis of protease activity, calcium dependence, and tissue expression. ..
  50. Reuter S, Torok M, Holden M, Reynolds R, Raven K, Blane B, et al. Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland. Genome Res. 2016;26:263-70 pubmed publisher
    ..We have generated a resource for the future surveillance and outbreak investigation of MRSA in the United Kingdom and Ireland and have shown the value of this during outbreak investigation and tracking of antimicrobial resistance. ..
  51. Kaiser S, Biehler K, Jonas D. A Stenotrophomonas maltophilia multilocus sequence typing scheme for inferring population structure. J Bacteriol. 2009;191:2934-43 pubmed publisher