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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 31 May 2016, Vol.113(22), pp.E3054-6
    Description: Author contributions: F.B., J.S., and F.F. designed research; F.B., C.L.W., and F.F. performed research; F.B., C.L.W., and F.F. analyzed data; and F.B., C.L.W., J.S., and F.F. wrote the paper.
    Keywords: Gene Transfer, Horizontal ; Genome
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: 2012, Vol.7(8), p.e43036
    Description: The production of antimicrobial peptides (AMPs) is a major defense mechanism against pathogen infestation and of particular importance for insects relying exclusively on an innate immune system. Here, we report on the characterization of three AMPs from the carpenter ant Camponotus floridanus . Due to sequence similarities and amino acid composition these peptides can be classified into the cysteine-rich (e.g. defensin) and glycine-rich (e.g. hymenoptaecin) AMP groups, respectively. The gene and cDNA sequences of these AMPs were established and their expression was shown to be induced by microbial challenge. We characterized two different defensin genes. The defensin-2 gene has a single intron, whereas the defensin-1 gene has two introns. The deduced amino acid sequence of the C. floridanus defensins is very similar to other known ant defensins with the exception of a short C-terminal extension of defensin-1. The hymenoptaecin gene has a single intron and a very peculiar domain structure. The corresponding precursor protein consists of a signal- and a pro-sequence followed by a hymenoptaecin-like domain and six directly repeated hymenoptaecin domains. Each of the hymenoptaecin domains is flanked by an EAEP-spacer sequence and a RR-site known to be a proteolytic processing site. Thus, proteolytic processing of the multipeptide precursor may generate several mature AMPs leading to an amplification of the immune response. Bioinformatical analyses revealed the presence of hymenoptaecin genes with similar multipeptide precursor structure in genomes of other ant species suggesting an evolutionary conserved important role of this gene in ant immunity.
    Keywords: Research Article ; Biology ; Genetics And Genomics ; Immunology ; Evolutionary Biology ; Biochemistry
    E-ISSN: 1932-6203
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  • 3
    Language: English
    In: The Conradian, 1 April 2011, Vol.36(1), pp.94-97
    Description: Lindau's background as a long-time teacher, diplomat, and journalist in Japan, China, India, and the United States in the 1860s and in France in the 1870s, then as chief press officer of the Chancellor of the Republic in the German Empire in the 1880s...
    Keywords: Social sciences -- Communications -- Narratives ; Physical sciences -- Earth sciences -- Geography ; Behavioral sciences -- Anthropology -- Ethnology ; Behavioral sciences -- Anthropology -- Ethnology ; Arts -- Literature -- Literary elements
    ISSN: 09512314
    Source: Archival Journals (JSTOR)
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  • 4
    Language: English
    In: 2012, Vol.7(9), p.e45682
    Description: Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.
    Keywords: Research Article ; Biology ; Biochemistry
    E-ISSN: 1932-6203
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  • 5
    Language: English
    In: PLoS ONE, 01 February 2011, Vol.6(2), p.e16931
    Description: 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...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: Molecular Phylogenetics and Evolution, June 2012, Vol.63(3), pp.585-588
    Description: ► New ITS2 Workbench integrates taxon sampling, structure prediction, alignment and tree reconstruction into one workflow. ► ITS2 database manages 280,000 ITS2 sequences and their individual secondary structures. ► Simultaneous rRNA sequence–structure analysis. ► Interactive taxon sampling. ► Quality checks and adaptive taxon sampling lead to more accurate phylogenies. The first step of any molecular phylogenetic analysis is the selection of the species and sequences to be included, the taxon sampling. Already here different pitfalls exist. Sequences can contain errors, annotations in databases can be inaccurate and even the taxonomic classification of a species can be wrong. Usually, these artefacts become evident only after calculation of the phylogenetic tree. Following, the taxon sampling has to be corrected iteratively. This can become tedious and time consuming, as in most cases the taxon sampling is de-coupled from the further steps of the phylogenetic analysis. Here, we present the ITS2 Workbench ( ), which eliminates this problem by a tight integration of taxon sampling, secondary structure prediction, multiple alignment and phylogenetic tree calculation. The ITS2 Workbench has access to more than 280,000 ITS2 sequences and their structures provided by the ITS2 database enabling sequence–structure based alignment and tree reconstruction. This allows the interactive improvement of the taxon sampling throughout the whole phylogenetic tree reconstruction process. Thus, the ITS2 Workbench enables a fast, interactive and iterative taxon sampling leading to more accurate ITS2 based phylogenies.
    Keywords: Taxon Sampling ; Sequence–Structure Blast ; Tree Reconstruction ; Internal Transcribed Spacer 2 ; Quality Control ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
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  • 7
    Language: English
    In: PLoS ONE, 2010, Vol.5(3), p.e9502
    Description: Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. ; Here we present to the best of our knowledge the first comprehensive study of on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. ; The proteome reference map of provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades.
    Keywords: Research Article ; Biochemistry -- Protein Chemistry ; Biotechnology -- Protein Chemistry And Proteomics ; Chemical Biology -- Protein Chemistry And Proteomics
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: Nucleic acids research, January 2010, Vol.38(Database issue), pp.D275-9
    Description: 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 length 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.
    Keywords: Databases, Genetic ; Databases, Nucleic Acid ; Computational Biology -- Methods ; DNA, Ribosomal Spacer -- Genetics ; Plants -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 9
    Language: English
    In: PLoS ONE, 01 December 2010, Vol.5(12), p.e15788
    Description: Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 10
    Language: English
    In: BMC Cancer, August 4, 2011, Vol.11, p.335
    Description: Background Male breast cancer (MBC) is a rare disease accounting for approximately 1% of all breast carcinomas. Presently treatment recommendations are derived from the standards for female breast cancer. However, those approaches might be inadequate because of distinct gender specific differences in tumor biology of breast cancer. This study was planned in order to contrast potential differences between female and male breast cancer in both tumor biological behavior and clinical management. Methods MBC diagnosed between 1995-2007 (region Chemnitz/Zwickau, Saxony, Germany) was retrospectively analyzed. Tumor characteristics, treatment and follow-up of the patients were documented. In order to highlight potential differences each MBC was matched with a female counterpart (FBC) that showed accordance in at least eight tumor characteristics (year of diagnosis, age, tumor stage, nodal status, grade, estrogen- and progesterone receptors, HER2 status). Results 108 male/female matched-pairs were available for survival analyses. In our study men and women with breast cancer had similar disease-free (DFS) and overall (OS) survival. The 5-years DFS was 53.4% (95% CI, range 54.1-66.3) in men respectively 62.6% (95% CI, 63.5-75.3) in women (p 〉 0.05). The 5-years OS was 71.4% (95% CI, 62.1-72.7%) and 70.3% (95% CI, 32.6-49.6) in women (p 〉 0.05). In males DFS analyses revealed progesterone receptor expression as the only prognostic relevant factor (p = 0.006). In multivariate analyses for OS both advanced tumor size (p = 0.01) and a lack of progesterone receptor expression were correlated (p = 0.01) with poor patients outcome in MBC. Conclusion Our comparative study revealed no survival differences between male and female breast cancer patients and gives evidence that gender is no predictor for survival in breast cancer. This was shown despite of significant gender specific differences in terms of frequency and intensity of systemic therapy in favor to female breast cancer.
    Keywords: Women's Health -- Research ; Progesterone Receptors -- Health Aspects ; Progesterone Receptors -- Research ; Male Breast Cancer -- Care And Treatment ; Male Breast Cancer -- Patient Outcomes ; Male Breast Cancer -- Research ; Male Breast Cancer -- Diagnosis
    ISSN: 1471-2407
    Source: Cengage Learning, Inc.
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