TY  - JOUR
AB  - Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis. Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.
AU  - Bolger, M.E.*
AU  - Schwacke, R.*
AU  - Gundlach, H.
AU  - Schmutzer, T.*
AU  - Chen, J.*
AU  - Arend, D.*
AU  - Oppermann, M.*
AU  - Weise, S.M.*
AU  - Lange, M.*
AU  - Fiorani, F.*
AU  - Spannagl, M.
AU  - Scholz, U.*
AU  - Mayer, K.F.X.
AU  - Usadel, B.*
C1  - 51296
C2  - 43153
CY  - Amsterdam
SP  - 46-52
TI  - From plant genomes to phenotypes.
JO  - J. Biotechnol.
VL  - 17
PB  - Elsevier Science Bv
PY  - 2017
SN  - 0168-1656
ER  - 

TY  - JOUR
AB  - Plant genetic resources are a substantial opportunity for plant breeding, preservation and maintenance of biological diversity. As part of the German Network for Bioinformatics Infrastructure (de.NBI) the German Crop BioGreenformatics Network (GCBN) focuses mainly on crop plants and provides both data and software infrastructure which are tailored to the needs of the plant research community. Our mission and key objectives include: (1) provision of transparent access to germplasm seeds, (2) the delivery of improved workflows for plant gene annotation, and (3) implementation of bioinformatics services that link genotypes and phenotypes. This review introduces the GCBN's spectrum of web-services and integrated data resources that address common research problems in the plant genomics community.
AU  - Schmutzer, T.*
AU  - Bolger, M.E.*
AU  - Rudd, S.*
AU  - Chen, J.*
AU  - Gundlach, H.
AU  - Arend, D.*
AU  - Oppermann, M.*
AU  - Weise, S.M.*
AU  - Lange, M.*
AU  - Spannagl, M.
AU  - Usadel, B.*
AU  - Mayer, K.F.X.
AU  - Scholz, U.*
C1  - 51521
C2  - 43286
CY  - Amsterdam
SP  - 37-45
TI  - Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives.
JO  - J. Biotechnol.
VL  - 261
PB  - Elsevier Science Bv
PY  - 2017
SN  - 0168-1656
ER  - 

TY  - JOUR
AB  - As Chinese Hamster Ovary (CHO) cells are the cell line of choice for the production of human-like recombinant proteins, there is interest in genetic optimization of host cell lines to overcome certain limitations in their growth rate and protein secretion. At the same time, a detailed understanding of these processes could be used to advantage by identification of marker transcripts that characterize states of performance.In this context, microRNAs (miRNAs) that exhibit a robust correlation to the growth rate of CHO cells were determined by analyzing miRNA expression profiles in a comprehensive collection of 46 samples including CHO-K1, CHO-S and CHO-DUKXB11, which were adapted to various culture conditions, and analyzed in different growth stages using microarrays. By applying Spearman or Pearson correlation coefficient criteria of. >. |0.6|, miRNAs with high correlation to the overall growth, or growth rates observed in exponential, serum-free, and serum-free exponential phase were identified. An overlap of twelve miRNAs common for all sample sets was revealed, with nine positively and three negatively correlating miRNAs.The here identified panel of miRNAs can help to understand growth regulation in CHO cells and contains putative engineering targets as well as biomarkers for cell lines with advantageous growth characteristics.
AU  - Klanert, G.*
AU  - Jadhav, V.*
AU  - Shanmukam, V.*
AU  - Diendorfer, A.*
AU  - Karbiener, M.*
AU  - Scheideler, M.
AU  - Bort, J.H.*
AU  - Grillari, J.*
AU  - Hackl, M.*
AU  - Borth, N.*
C1  - 48972
C2  - 41517
CY  - Amsterdam
SP  - 150-161
TI  - A signature of 12 microRNAs is robustly associated with growth rate in a variety of CHO cell lines.
JO  - J. Biotechnol.
VL  - 235
PB  - Elsevier Science Bv
PY  - 2016
SN  - 0168-1656
ER  - 

TY  - JOUR
AB  - Anastomosis group AG1-IB isolates of the anamorphic basidiomycetous fungus Rhizoctonia solani Kühn affect various agricultural and horticultural important crops including bean, rice, soybean, figs, hortensia, cabbage and lettuce. To gain insights into the genome structure and content, the first draft genome sequence of R. solani AG1-IB isolate 7/3/14 was established. Four complete runs on the Genome Sequencer (GS) FLX platform (Roche Applied Science) yielding approx. a 25-fold coverage of the R. solani genome were accomplished. Assembly of the sequence reads by means of the gsAssembler software version 2.6 applying the heterozygotic mode resulted in numerous contigs and scaffolds and a predicted size of 87.1Mb for the diploid status of the genome. 'Contig-length vs. read-count' analysis revealed that the assembled contigs can be classified into five different groups. Detailed BLAST-analysis revealed that most contigs of group II feature high-scoring matches to other contigs of the same group suggesting that distinguishable allelic variants exist for many genes. Due to the supposed diploid and heterokaryotic nature of R. solani AG1-IB 7/3/14, this result has been anticipated. However, the heterokaryotic character of the isolate is not really supported by sequencing data obtained for the isolate R. solani AG1-IB 7/3/14. Coverage of group III contigs is twice as high as for group II contigs which can also be explained by the diploid status of the genome and indistinguishable alleles on homologous chromosomes. Assembly of sequence data led to the identification of the rRNA unit (group V contigs) and the mitochondrial (mt) genome (group IV contigs) which is a circular molecule of 162,751bp in size featuring a GC-content of 36.4%. The R. solani 7/3/14 mt-genome is one of the largest fungal mitochondrial genomes known to date. Its large size essentially is due to the presence of numerous non-conserved hypothetical ORFs and introns. Gene prediction for the R. solani AG1-IB 7/3/14 genome was conducted by the Augustus Gene Prediction Software for Eukaryotes (version 2.6.) applying the parameter set for the fungus Coprinopsis cinerea okayama 7#130. Gene prediction and annotation provided first insights into the R. solani AG1-IB 7/3/14 gene structure and content. In total, 12,422 genes were predicted. The average number of exons per gene is five. Exons have a mean length of 214bp, whereas introns on average are 66bp in length. Annotation of the genome revealed that 4169 of 12,422 genes could be assigned to KOG functional categories.
AU  - Wibberg, D.*
AU  - Jelonek, L.*
AU  - Rupp, O.*
AU  - Hennig, M.*
AU  - Eikmeyer, F.*
AU  - Goesmann, A.*
AU  - Hartmann, A.
AU  - Borriss, R.*
AU  - Grosch, R.*
AU  - Pühler, A.*
AU  - Schlüter, A.*
C1  - 26266
C2  - 32152
SP  - 142-155
TI  - Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14.
JO  - J. Biotechnol.
VL  - 167
IS  - 2
PB  - Elsevier Science
PY  - 2013
SN  - 0168-1656
ER  - 

TY  - JOUR
AU  - Olbrich, M.*
AU  - Betz, G.*
AU  - Bahnweg, G.*
AU  - Welzl,  G.*
AU  - Ernst, D.
C1  - 45408
C2  - 37318
SP  - S120
TI  - Effects of abiotic and biotic stress on gene transcription in European beech (Fagus sylvatica L.): From saplings to mature beech trees.
JO  - J. Biotechnol.
VL  - 150S
PY  - 2010
SN  - 0168-1656
ER  - 

TY  - JOUR
AB  - Reduction of 17-ketosteroids is a biocatalytic process of economic significance for the production of steroid drugs. This reaction can be catalyzed by different microbial 17ß-hydroxysteroid dehydrogenases (17ß-HSD), like the 17ß-HSD activity of Saccharomyces cerevisiae, Pichia faranosa and Mycobacterium sp., and by purified 3ß,17ß-HSD from Pseudomonas testosteroni. In addition to the bacterial 3ß,17ß-HSD the 17ß-HSD of the filamentous fungus Cochliobolus lunatus is the only microbial 17ß-HSD that has been expressed as a recombinant protein and fully characterized. On the basis of its modeled 3D structure, we selected several positions for the replacement of amino acids by site-directed mutagenesis to change substrate specificity, alter coenzyme requirements, and improve overall catalytic activity. Replacement of Val161 and Tyr212 in the substrate-binding region by Gly and Ala, respectively, increased the initial rates for the conversion of androstenedione to testosterone. Replacement of Tyr49 within the coenzyme binding site by Asp changed the coenzyme specificity of the enzyme. This latter mutant can convert the steroids not only in the presence of NADP+ and NADPH, but also in the presence of NADH and NAD+. The replacement of His164, located in the non-flexible part of the ‘lid’ covering the active center resulted in a conformation of the enzyme that possessed a higher catalytic activity.
AU  - Kristan, K.*
AU  - Stojan, J.*
AU  - Adamski, J.
AU  - Lanisnik Rizner, T.*
C1  - 3717
C2  - 24516
SP  - 123-130
TI  - Rational design of novel mutants of fungal 17β-hydroxysteroid dehydrogenase.
JO  - J. Biotechnol.
VL  - 129
IS  - 1
PB  - Elsevier
PY  - 2007
SN  - 0168-1656
ER  - 

TY  - JOUR
AU  - Schulte, U.*
AU  - Becker, B.
AU  - Mewes, H.-W.
AU  - Mannhaupt, G.
C1  - 22358
C2  - 21236
SP  - 3-13
TI  - Large scale analysis of sequences from Neurospora crassa.
JO  - J. Biotechnol.
VL  - 94
PY  - 2002
SN  - 0168-1656
ER  -