6244
2010
eng
article
1
2012-11-10
--
--
The ITS2 Database III-sequences and structures for phylogeny
The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker. In the past, it has mainly been used for species level classifications. Nowadays, a wider applicability becomes apparent. Here, the conserved structure of the RNA molecule plays a vital role. We have developed the ITS2 Database (http://its2.bioapps .biozentrum.uni-wuerzburg.de) which holds information about sequence, structure and taxonomic classification of all ITS2 in GenBank. In the new version, we use Hidden Markov models (HMMs) for the identification and delineation of the ITS2 resulting in a major redesign of the annotation pipeline. This allowed the identification of more than 160 000 correct full ength and more than 50 000 partial structures. In the web interface, these can now be searched with a modified BLAST considering both sequence and structure, enabling rapid taxon sampling. Novel sequences can be annotated using the HMM based approach and modelled according to multiple template structures. Sequences can be searched for known and newly identified motifs. Together, the database and the web server build an exhaustive resource for ITS2 based phylogenetic analyses.
urn:nbn:de:bvb:20-opus-68390
6839
In: Nucleic Acids Research (2010) 38, D275-D279, DOI: 10.1093/nar/gkp966
Christian Koetschan
Frank Foerster
Alexander Keller
Tina Schleicher
Benjamin Ruderisch
Roland Schwarz
Tobias Mueller
Matthias Wolf
Joerg Schultz
deu
swd
Biologie
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/6244/Foerster064_D275.full.pdf
5988
2010
eng
article
1
2012-07-04
--
--
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees
Background: In several studies, secondary structures of ribosomal genes have been used to improve the quality of phylogenetic reconstructions. An extensive evaluation of the benefits of secondary structure, however, is lacking. Results: This is the first study to counter this deficiency. We inspected the accuracy and robustness of phylogenetics with individual secondary structures by simulation experiments for artificial tree topologies with up to 18 taxa and for divergency levels in the range of typical phylogenetic studies. We chose the internal transcribed spacer 2 of the ribosomal cistron as an exemplary marker region. Simulation integrated the coevolution process of sequences with secondary structures. Additionally, the phylogenetic power of marker size duplication was investigated and compared with sequence and sequence-structure reconstruction methods. The results clearly show that accuracy and robustness of Neighbor Joining trees are largely improved by structural information in contrast to sequence only data, whereas a doubled marker size only accounts for robustness. Conclusions: Individual secondary structures of ribosomal RNA sequences provide a valuable gain of information content that is useful for phylogenetics. Thus, the usage of ITS2 sequence together with secondary structure for taxonomic inferences is recommended. Other reconstruction methods as maximum likelihood, bayesian inference or maximum parsimony may equally profit from secondary structure inclusion. Reviewers: This article was reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. Open peer review: Reviewed by Shamil Sunyaev, Andrea Tanzer (nominated by Frank Eisenhaber) and Eugene V. Koonin. For the full reviews, please go to the Reviewers’ comments section.
urn:nbn:de:bvb:20-opus-67832
6783
BIOLOGY DIRECT (2010) 5, DOI: 10.1186/1745-6150-5-4
Alexander Keller
Frank Foerster
Tobias Mueller
Thomas Dandekar
Joerg Schultz
Matthias Wolf
deu
swd
Phylogenie
eng
uncontrolled
phylogenetics
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/5988/schultz_1745_6150_5_4.pdf
4783
2010
eng
doctoralthesis
1
2011-04-28
--
2011-04-07
Secondary (and tertiary) structure of the ITS2 and its application for phylogenetic tree reconstructions and species identification
Sekundär- und Tertiärstruktur der ITS2 und Anwendung für phylogenetische Baumberechnungen und Arteerkennung
Biodiversity may be investigated and explored by the means of genetic sequence information and molecular phylogenetics. Yet, with ribosomal genes, information for phylogenetic studies may not only be retained from the primary sequence, but also from the secondary structure. Software that is able to cope with two dimensional data and designed to answer taxonomic questions has been recently developed and published as a new scientific pipeline. This thesis is concerned with expanding this pipeline by a tool that facialiates the annotation of a ribosomal region, namely the ITS2. We were also able to show that this states a crucial step for secondary structure phylogenetics and for data allocation of the ITS2-database. This resulting freely available tool determines high quality annotations. In a further study, the complete phylogenetic pipeline has been evaluated on a theoretical basis in a comprehensive simulation study. We were able to show that both, the accuracy and the robustness of phylogenetic trees are largely improved by the approach. The second major part of this thesis concentrates on case studies that applied this pipeline to resolve questions in taxonomy and ecology. We were able to determine several independent phylogenies within the green algae that further corroborate the idea that secondary structures improve the obtainable phylogenetic signal, but now from a biological perspective. This approach was applicable in studies on the species and genus level, but due to the conservation of the secondary structure also for investigations on the deeper level of taxonomy. An additional case study with blue butterflies indicates that this approach is not restricted to plants, but may also be used for metazoan phylogenies. The importance of high quality phylogenetic trees is indicated by two ecological studies that have been conducted. By integrating secondary structure phylogenetics, we were able to answer questions about the evolution of ant-plant interactions and of communities of bacteria residing on different plant tissues. Finally, we speculate how phylogenetic methods with RNA may be further enhanced by integration of the third dimension. This has been a speculative idea that was supplemented with a small phylogenetic example, however it shows that the great potential of structural phylogenetics has not been fully exploited yet. Altogether, this thesis comprises aspects of several different biological disciplines, which are evolutionary biology and biodiversity research, community and invasion ecology as well as molecular and structural biology. Further, it is complemented by statistical approaches and development of informatical software. All these different research areas are combined by the means of bioinformatics as the central connective link into one comprehensive thesis.
Biologische Diversität kann mit Hilfe molekularer Sequenzinformation und phylogenetischen Methoden erforscht und erfasst werden. Bei ribosomalen Genen kann man jedoch wertvolle Information nicht nur aus der Primärsequenz beziehen, sondern auch aus der Sekundärstruktur. In den letzen Jahren wurde Software entwickelt, die solche Daten für taxonomische Fragestellung verwerten kann. Diese Arbeit beschäftigt sich mit einer Erweiterung dieser Methodik durch eine Software-Anwendung, die die Annotation des ribosomalen Genes ITS2 deutlich vereinfacht. Mit dieser Studie konnten wir zeigen, dass dies einen entscheidenden Schritt der Sequenz-Struktur-Phylogenie und der Datenerfassung der ITS2-Datenbank darstellt. Die daraus resultierende und frei verfügbare Anwendung ermöglicht Annotationen von hoher Güte. In einer weiteren Studie wurde mittels Simulationen der gesamte Arbeitsfluß der Sequenz-Struktur Phylogenie auf theoretischer Ebene evaluiert. Dabei zeigte sich, dass sich sowohl die Genauigkeit, als auch die Robustheit von phylogenetischen Stammbäumen durch diesen Ansatz deutlich verbessern. Der zweite große Teil der Arbeit befasst sich mit Fallbeispielen, in denen dieser Arbeitsfluß zur Aufklärung von taxomonischen and ökologischen Fragestellungen Anwendung fand. In diesem Rahmen konnten wir mehrere und voneinander unabhängige Phylogenien ermitteln, welche die theoretischen Ergebnisse einer Verbesserung phylogenetischer Bäume auch von biologischer Seite aus bekräftigen. Der Ansatz war anwendbar in sehr feinskaligen Studien auf Art bzw. Gattungsniveau, aber durch die starke Konservierung der Sekundärstruktur auch an sehr weit von einander entfernten taxonomischen Gruppen. Eine weitere Studie, die sich mit der Phylogenie von Bläulingen befasst, zeigt deutlich, dass dieser Ansatz nicht nur für Fragestellungen bei Pflanzen, sondern auch im Tierreich angewandt werden kann. Die Bedeutung von qualitativ hochwertigen Stammbäumen auch für andere Fachbereiche wird an zwei unserer ökologischen Studien deutlich: Mit Hinzunahme von Sekundärstruktur war es uns möglich Fragestellungen über die Evolution von Ameisen-Pflanzen Interaktionen sowie über ökologische Gemeinschaften von Bakterien auf verschiedenen Pflanzenteilen zu beantworten. Zuletzt gehen wir spekulativ auf die Frage ein, wie Strukturphylogenie um die dritte Dimension erweitert werden kann. Dies bleibt zwar spekulativ und wurde nur um ein kleines Fallbeispiel ergänzt, jedoch zeigt sich deutlich, dass das Potential von Strukturphylogenie noch nicht erschöpft ist. Insgesamt befasst sich diese Arbeit mit Aspekten aus verschiedenen biologischen Disziplinen: Evolutionsbiologie und Biodiversitätsforschung, sowie Gemeinschafts- und Invasionsökologie, aber auch Molekular- und Strukturbiologie. Dies wurde ergänzt durch statistische Ansätze und Entwicklung von informatischer Software. Diese verschiedenen Forschungsrichtungen wurden mit Hilfe der Bioinformatik als zentrales Bindeglied vereint.
urn:nbn:de:bvb:20-opus-56151
5615
X123493
Deutsches Urheberrecht
Alexander Keller
deu
swd
Phylogenie
deu
swd
Evolution
deu
swd
Sekundärstruktur
deu
swd
DNS-Sequenz
deu
swd
Algen
deu
swd
Ribosomale RNS
eng
uncontrolled
rRNA
eng
uncontrolled
secondary structure
eng
uncontrolled
phylogeny evolution
eng
uncontrolled
sequence
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/4783/Dissertation_Online.pdf
14086
2011
eng
e16931
2
6
article
1
2016-11-25
--
--
Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life
Background:
Chloroplast-encoded genes (matK and rbcL) have been formally proposed for use in DNA barcoding efforts targeting embryophytes. Extending such a protocol to chlorophytan green algae, though, is fraught with problems including non homology (matK) and heterogeneity that prevents the creation of a universal PCR toolkit (rbcL). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.
Methodology/Principal Findings:
Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.
Conclusions/Significance:
Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages.
PLoS ONE
10.1371/journal.pone.0016931
urn:nbn:de:bvb:20-opus-140866
PLoS ONE 6(2): e16931. doi:10.1371/journal.pone.0016931
Mark A. Buchheim
Alexander Keller
Christian Koetschan
Frank Förster
Benjamin Merget
Matthias Wolf
eng
uncontrolled
RBCL Gene-sequences
eng
uncontrolled
Colonial volvocales chlorophyta
eng
uncontrolled
26S RDNA Data
eng
uncontrolled
Land plants
eng
uncontrolled
Molecular systematics
eng
uncontrolled
Secondary structure
eng
uncontrolled
Nuclear RDNA
eng
uncontrolled
DNA
eng
uncontrolled
Barcodes
eng
uncontrolled
Dasycladales chlorophyta
eng
uncontrolled
Profile distances
Datenverarbeitung; Informatik
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14086/079_Buchheim_PLOS-ONE.PDF
12261
2013
eng
29
10
article
1
2015-12-02
--
--
Only distance matters - non-choosy females in a poison frog population
Background: Females have often been shown to exhibit preferences for certain male traits. However, little is known about behavioural rules females use when searching for mates in their natural habitat. We investigated mate sampling tactics and related costs in the territorial strawberry poison frog (Oophaga pumilio) possessing a lek-like mating system, where both sequential and simultaneous sampling might occur. We continuously monitored the sampling pattern and behaviour of females during the complete period between two successive matings.
Results: We found no evidence that females compared males by visiting them. Instead females mated with the closest calling male irrespective of his acoustic and physical traits, and territory size. Playback experiments in the natural home ranges of receptive females revealed that tested females preferred the nearest speaker and did not discriminate between low and high call rates or dominant frequencies.
Conclusions: Our results suggest that females of O. pumilio prefer the closest calling male in the studied population. We hypothesize that the sampling tactic in this population is affected by 1) a strongly female biased sex ratio and 2) a low variance in traits of available males due to strong male-male competition, preventing low quality males from defending a territory and mating.
Frontiers in Zoology
10.1186/1742-9994-10-29
1742-9994
urn:nbn:de:bvb:20-opus-122617
Frontiers in Zoology 2013, 10:29. doi:10.1186/1742-9994-10-29
Ivonne Meuche
Oscar Brusa
K. Eduard Linsenmair
Alexander Keller
Heike Pröhl
eng
uncontrolled
operational sex ratio
eng
uncontrolled
sequential mate choice
eng
uncontrolled
gray tree frogs
eng
uncontrolled
treefrogs hyla-gratiosa
eng
uncontrolled
male mating success
deu
uncontrolled
Bocas-del-Toro
deu
uncontrolled
dendrobates pumilio
deu
uncontrolled
oophaga pumilio
deu
uncontrolled
pied flycatchers
deu
uncontrolled
sampling behavior
Wechselwarme Wirbeltiere; Pisces (Fische)
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12261/036_Meuche_Frontiers_in_Zoology.pdf
9730
2013
eng
article
1
--
--
--
Diverse Microbiota Identified in Whole Intact Nest Chambers of the Red Mason Bee Osmia bicornis (Linnaeus 1758)
Microbial activity is known to have profound impact on bee ecology and physiology, both by beneficial and pathogenic effects. Most information about such associations is available for colony-building organisms, and especially the honey bee. There, active manipulations through worker bees result in a restricted diversity of microbes present within the colony environment. Microbial diversity in solitary bee nests remains unstudied, although their larvae face a very different situation compared with social bees by growing up in isolated compartments. Here, we assessed the microbiota present in nests and pre-adults of Osmia bicornis, the red mason bee, by culture-independent pyrosequencing. We found high bacterial diversity not comparable with honey bee colonies. We identified a variety of bacteria potentially with positive or negative interactions for bee larvae. However, most of the other diverse bacteria present in the nests seem to originate from environmental sources through incorporated nest building material and stored pollen. This diversity of microorganisms may cause severe larval mortality and require specific physiological or symbiotic adaptations against microbial threats. They may however also profit from such a diverse environment through gain of mutualistic partners. We conclude that further studies of microbiota interaction in solitary bees will improve the understanding of fitness components and populations dynamics.
PLoS One
10.1371/journal.pone.0078296
urn:nbn:de:bvb:20-opus-97305
DNA Analytics Core Facility, Biocenter, University of Wuerzburg, Wuerzburg, Germany
In: PLoS One (2013) 8: 10, doi:10.1371/journal.pone.0078296
Alexander Keller
Gudrun Grimmer
Ingolf Steffan-Dewenter
eng
uncontrolled
bacteria
eng
uncontrolled
bacterial pathogens
eng
uncontrolled
bees
eng
uncontrolled
gut bacteria
eng
uncontrolled
honey bees
eng
uncontrolled
larvae
eng
uncontrolled
Pollen
eng
uncontrolled
Polymerase chain reaction
Tiere (Zoologie)
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2013
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/9730/Keller_journal.pone.0078296.pdf
11009
2014
eng
article
1
2015-02-25
--
--
Confirmation of warfarin resistance of naturally occurring VKORC1 variants by coexpression with coagulation factor IX and in silico protein modelling
Background
VKORC1 has been identified some years ago as the gene encoding vitamin K epoxide reductase (VKOR) – the target protein for coumarin derivates like warfarin or phenprocoumon. Resistance against warfarin and other coumarin-type anticoagulants has been frequently reported over the last 50 years in rodents due to problems in pest control as well as in thrombophilic patients showing variable response to anticoagulant treatment. Many different mutations have already been detected in the VKORC1 gene leading to warfarin resistance in rats, mice and in humans. Since the conventional in vitro dithiothreitol (DTT)-driven VKOR enzymatic assay often did not reflect the in vivo status concerning warfarin resistance, we recently developed a cell culture-based method for coexpression of VKORC1 with coagulation factor IX and subsequent measurement of secreted FIX in order to test warfarin inhibition in wild-type and mutated VKORC1.
Results
In the present study, we coexpressed wild-type factor IX with 12 different VKORC1 variants which were previously detected in warfarin resistant rats and mice. The results show that amino acid substitutions in VKORC1 maintain VKOR activity and are associated with warfarin resistance. When we projected in silico the amino acid substitutions onto the published three-dimensional model of the bacterial VKOR enzyme, the predicted effects matched well the catalytic mechanism proposed for the bacterial enzyme.
Conclusions
The established cell-based system for coexpression of VKORC1 and factor IX uses FIX activity as an indicator of carboxylation efficiency. This system reflects the warfarin resistance status of VKORC1 mutations from anticoagulant resistant rodents more closely than the traditional DTT-driven enzyme assay. All mutations studied were also predicted to be involved in the reaction mechanism.
10.1186/1471-2156-15-17
urn:nbn:de:bvb:20-opus-110095
In: BMC Genetics (2014) 15:17. doi:10.1186/1471-2156-15-17
DNA Analytics Core Facility, Biocenter, University of Würzburg, Würzburg, Germany
Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
Simone Rost
Elisabeth Müller
Alexander Keller
Andreas Fregin
Clemens R. Müller
eng
uncontrolled
VKORC1
eng
uncontrolled
Vitamin K epoxide reductase
eng
uncontrolled
Anticoagulants
eng
uncontrolled
Warfarin
eng
uncontrolled
Coumarin
eng
uncontrolled
Coexpression
eng
uncontrolled
Coagulation factor IX
Medizin und Gesundheit
open_access
Institut für Humangenetik
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2014
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/11009/012_Rost_BMCGenetics.pdf
12573
2015
eng
20
15
article
1
2016-01-27
--
--
Increased efficiency in identifying mixed pollen samples by meta-barcoding with a dual-indexing approach
Background
Meta-barcoding of mixed pollen samples constitutes a suitable alternative to conventional pollen identification via light microscopy. Current approaches however have limitations in practicability due to low sample throughput and/or inefficient processing methods, e.g. separate steps for amplification and sample indexing.
Results
We thus developed a new primer-adapter design for high throughput sequencing with the Illumina technology that remedies these issues. It uses a dual-indexing strategy, where sample-specific combinations of forward and reverse identifiers attached to the barcode marker allow high sample throughput with a single sequencing run. It does not require further adapter ligation steps after amplification. We applied this protocol to 384 pollen samples collected by solitary bees and sequenced all samples together on a single Illumina MiSeq v2 flow cell. According to rarefaction curves, 2,000–3,000 high quality reads per sample were sufficient to assess the complete diversity of 95% of the samples. We were able to detect 650 different plant taxa in total, of which 95% were classified at the species level. Together with the laboratory protocol, we also present an update of the reference database used by the classifier software, which increases the total number of covered global plant species included in the database from 37,403 to 72,325 (93% increase).
Conclusions
This study thus offers improvements for the laboratory and bioinformatical workflow to existing approaches regarding data quantity and quality as well as processing effort and cost-effectiveness. Although only tested for pollen samples, it is furthermore applicable to other research questions requiring plant identification in mixed and challenging samples.
BMC Ecology
10.1186/s12898-015-0051-y
urn:nbn:de:bvb:20-opus-125730
D-1221-2009
BMC Ecology (2015) 15:20 DOI 10.1186/s12898-015-0051-y
Wiebke Sickel
Markus J. Ankenbrand
Gudrun Grimmer
Andrea Holzschuh
Stephan Härtel
Jonathan Lanzen
Ingolf Steffan-Dewenter
Alexander Keller
eng
uncontrolled
pollination ecology
eng
uncontrolled
next generation sequencing
eng
uncontrolled
ITS2
eng
uncontrolled
illumina MiSeq platform
eng
uncontrolled
high throughput sequencing
eng
uncontrolled
DNA barcoding
eng
uncontrolled
NGS
eng
uncontrolled
osmia
eng
uncontrolled
palynolog
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2015
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12573/Keller_s12898-015-0051-y.pdf
18668
2016
eng
155-166
93
article
1
2019-09-02
--
--
Contact of myeloma cells induces a characteristic transcriptome signature in skeletal precursor cells-implications for myeloma bone disease
Physical interaction of skeletal precursors with multiple myeloma cells has been shown to suppress their osteogenic potential while favoring their tumor-promoting features. Although several transcriptome analyses of myeloma patient-derived mesenchymal stem cells have displayed differences compared to their healthy counterparts, these analyses insufficiently reflect the signatures mediated by tumor cell contact, vary due to different methodologies, and lack results in lineage-committed precursors. To determine tumor cell contact-mediated changes on skeletal precursors, we performed transcriptome analyses of mesenchymal stem cells and osteogenic precursor cells cultured in contact with the myeloma cell line INA-6. Comparative analyses confirmed dysregulation of genes which code for known disease-relevant factors and additionally revealed upregulation of genes that are associated with plasma cell homing, adhesion, osteoclastogenesis, and angiogenesis. Osteoclast-derived coupling factors, a dysregulated adipogenic potential, and an imbalance in favor of anti-anabolic factors may play a role in the hampered osteoblast differentiation potential of mesenchymal stem cells. Angiopoietin-Like 4 (ANGPTL4) was selected from a list of differentially expressed genes as a myeloma cell contact-dependent target in skeletal precursor cells which warranted further functional analyses. Adhesion assays with full-length ANGPTL4-coated plates revealed a potential role of this protein in INA6 cell attachment. This study expands knowledge of the myeloma cell contact-induced signature in the stromal compartment of myelomatous bones and thus offers potential targets that may allow detection and treatment of myeloma bone disease at an early stage.
Bone
10.1016/j.bone.2016.08.006
urn:nbn:de:bvb:20-opus-186688
Bone (2016) 93, 155-166. https://doi.org/10.1016/j.bone.2016.08.006
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Julia Dotterweich
Katrin Schlegelmilch
Alexander Keller
Beate Geyer
Doris Schneider
Sabine Zeck
Robert J. J. Tower
Regina Ebert
Franz Jakob
Norbert Schütze
eng
uncontrolled
marrow stromal cells
eng
uncontrolled
Endothelial growth-factor
eng
uncontrolled
precedes multiple-myeloma
eng
uncontrolled
monoclonial gammopathy
eng
uncontrolled
in-vitro
eng
uncontrolled
mesenchymal stem-cells
eng
uncontrolled
undetermined significance
eng
uncontrolled
angiogenic cytokines
eng
uncontrolled
peripheral-blood
eng
uncontrolled
gene-expression
eng
uncontrolled
Multiple myeloma
eng
uncontrolled
Bone disease
eng
uncontrolled
Angiopoietin-like 4
eng
uncontrolled
Gene expression profiling
eng
uncontrolled
Mesenchymal stem cells
eng
uncontrolled
Osteogenic precursor cells
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Lehrstuhl für Orthopädie
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/18668/Dotterweich_Bone_2016.pdf
14600
2016
eng
8
11
article
1
2017-03-22
--
--
Draft genome of the \(Arabidopsis\) \(thaliana\) phyllosphere bacterium, \(Williamsia\) sp. ARP1
The Gram-positive actinomycete \(Williamsia\) sp. ARP1 was originally isolated from the \(Arabidopsis\) \(thaliana\) phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus \(Williamsia\) and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.
Standards in Genomic Sciences
10.1186/s40793-015-0122-x
urn:nbn:de:bvb:20-opus-146008
Standards in Genomic Sciences (2016) 11:8 DOI 10.1186/s40793-015-0122-x
Hannes Horn
Alexander Keller
Ulrich Hildebrandt
Peter Kämpfer
Markus Riederer
Ute Hentschel
eng
uncontrolled
arabidopsis thaliana
eng
uncontrolled
whole genome sequencing
eng
uncontrolled
adaption
eng
uncontrolled
Williamsia sp. ARP1
eng
uncontrolled
phyllosphere
eng
uncontrolled
draft genome
eng
uncontrolled
next generation sequencing
eng
uncontrolled
assembly
eng
uncontrolled
annotation
Genetik und Evolution
open_access
Julius-von-Sachs-Institut für Biowissenschaften
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2016
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14600/Horn_10.1186_s40793-015-0122-x.pdf