Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris

Zakrzewski F, Wenke T, Holtgräwe D, Weisshaar B, Schmidt T. Analysis of a c0t-1 library enables the targeted identification of minisatellite and satellite families in Beta vulgaris. BMC Plant Biology. 2010;10(1): 8.BACKGROUND: Repetitive DNA is a major fraction of eukaryotic genomes and occurs particularly often in plants. Currently, the sequencing of the sugar beet (Beta vulgaris) genome is under way and knowledge of repetitive DNA sequences is critical for the genome annotation. We generated a c0t-1 library, representing highly to moderately repetitive sequences, for the characterization of the major B. vulgaris repeat families. While highly abundant satellites are well-described, minisatellites are only poorly investigated in plants. Therefore, we focused on the identification and characterization of these tandemly repeated sequences. RESULTS: Analysis of 1763 c0t-1 DNA fragments, providing 442 kb sequence data, shows that the satellites pBV and pEV are the most abundant repeat families in the B. vulgaris genome while other previously described repeats show lower copy numbers. We isolated 517 novel repetitive sequences and used this fraction for the identification of minisatellite and novel satellite families. Bioinformatic analysis and Southern hybridization revealed that minisatellites are moderately to highly amplified in B. vulgaris. FISH showed a dispersed localization along most chromosomes clustering in arrays of variable size and number with exclusion and depletion in distinct regions. CONCLUSION: The c0t-1 library represents major repeat families of the B. vulgaris genome, and analysis of the c0t-1 DNA was proven to be an efficient method for identification of minisatellites. We established, so far, the broadest analysis of minisatellites in plants and observed their chromosomal localization providing a background for the annotation of the sugar beet genome and for the understanding of the evolution of minisatellites in plant genomes

Differences in treatment and monitoring of chronic myeloid leukemia with regard to age, but not sex: Results from a population-based study

There are established guidelines for treatment and monitoring of chronic myeloid leukemia (CML) but little is known about routine care. Data on ICD-10 codes as well as prescribed medications were available for 10.5~million patients in the statutory health insurance system in Bavaria for the years 2010 to 2016. Also, data on the molecular and cytogenetic monitoring were integrated. A total of 1714 adult patients with CML were observed. Only 50.8% received more than 67.5 daily doses per quarter year (target: 91.5) while 18.2% did not receive any tyrosine kinase inhibitor (TKI). The median number of daily doses was at least 80 doses per quarter year for all age groups in men, but decreased to 62 doses in elderly women. With this exception, no differences between men and women were observed. The percentage of patients without any TKI increased with age. The median number of molecular examinations was 3.54 independent of age and sex. Even in a highly developed country, still a considerable number of patients with CML seem to not receive adequate treatment, whereas molecular monitoring can be considered satisfactory

Flowers of Deceptive Aristolochia microstoma Are Pollinated by Phorid Flies and Emit Volatiles Known From Invertebrate Carrion

Deceptive flowers decoy pollinators by advertising a reward, which finally is not provided. Numerous deceptive plants are pollinated by Diptera, but the attractive cues and deceptive strategies are only identified in a few cases. A typical fly-deceptive plant genus is Aristolochia, which evolved sophisticated trap flowers to temporarily capture pollinators. Though rarely demonstrated by experimental approaches, Aristolochia species are believed to chemically mimic brood sites, food sources for adult flies, or utilize sexual deception. Indeed, for most species, studies on scent composition and attractive signals are lacking. In this study, we focused on Aristolochia microstoma, a peculiar Greek endemic with flowers that are presented at ground level in the leaf litter or between rocks and are characterized by a unique morphology. We analyzed flower visitor and pollinator spectra and identified the floral scent composition using dynamic headspace and gas chromatography coupled to mass spectrometry (GC/MS). Female and male phorid flies (Phoridae) are the exclusive pollinators, although the flowers are also frequently visited by Sciaridae, as well as typical ground-dwelling arthropods, such as Collembola and arachnids. The carrion-like floral scent mainly consists of the oligosulphide dimethyldisulfide and the nitrogen-bearing compound 2,5-dimethylpyrazine. These compounds together are known to be released from decomposing insects, and thus, we conclude that pollinators are likely deceived by chemical imitation of invertebrate carrion, a deceptive strategy not described from another plant species so far.</jats:p

Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes

Wenke T, Dobel T, Rosleff Sörensen T, Junghans H, Weisshaar B, Schmidt T. Targeted identification of short interspersed nuclear element families shows their widespread existence and extreme heterogeneity in plant genomes. The Plant Cell. 2011;23(9):3117-3128.Short interspersed nuclear elements (SINEs) are non-long terminal repeat retrotransposons that are highly abundant, heterogeneous, and mostly not annotated in eukaryotic genomes. We developed a tool designated SINE-Finder for the targeted discovery of tRNA-derived SINEs. We analyzed sequence data of 16 plant genomes, including 13 angiosperms and three gymnosperms and identified 17,829 full-length and truncated SINEs falling into 31 families showing the widespread occurrence of SINEs in higher plants. The investigation focused on potato (Solanum tuberosum), resulting in the detection of seven different SolS SINE families consisting of 1489 full-length and 870 5' truncated copies. Consensus sequences of full-length members range in size from 106 to 244 bp depending on the SINE family. SolS SINEs populated related species and evolved separately, which led to some distinct subfamilies. Solanaceae SINEs are dispersed along chromosomes and distributed without clustering but with preferred integration into short A-rich motifs. They emerged more than 23 million years ago and were species specifically amplified during the radiation of potato, tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum). We show that tobacco TS retrotransposons are composite SINEs consisting of the 3' end of a long interspersed nuclear element integrated downstream of a nonhomologous SINE family followed by successfully colonization of the genome. We propose an evolutionary scenario for the formation of TS as a spontaneous event, which could be typical for the emergence of SINE families

Secondary use of health care data and left-over biosamples within the ‘Medical Informatics Initiative’ (MII): a quasi-randomized controlled evaluation of patient perceptions and preferences regarding the consent process

Background Data collected during routine health care and ensuing analytical results bear the potential to provide valuable information to improve the overall health care of patients. However, little is known about how patients prefer to be informed about the possible usage of their routine data and/or biosamples for research purposes before reaching a consent decision. Specifically, we investigated the setting, the timing and the responsible staff for the information and consent process. Methods We performed a quasi-randomized controlled trial and compared the method by which patients were informed either in the patient admission area following patient admission by the same staff member (Group A) or in a separate room by another staff member (Group B). The consent decision was hypothetical in nature. Additionally, we evaluated if there was the need for additional time after the information session and before taking the consent decision. Data were collected during a structured interview based on questionnaires where participants reflected on the information and consent process they went through. Results Questionnaire data were obtained from 157 participants in Group A and 106 participants in Group B. Overall, participants in both groups were satisfied with their experienced process and with the way information was provided. They reported that their (hypothetical) consent decision was freely made. Approximately half of the interested participants in Group B did not show up in the separate room, while all interested participants in Group A could be informed about the secondary use of their routine data and left-over samples. No participants, except for one in Group B, wanted to take extra time for their consent decision. The hypothetical consent rate for both routine data and left-over samples was very high in both groups. Conclusions The willingness to support medical research by allowing the use of routine data and left-over samples seems to be widespread among patients. Information concerning this secondary data use may be given by trained administrative staff immediately following patient admission. Patients mainly prefer making a consent decision directly after information is provided and discussed. Furthermore, less patients are informed when the process is organized in a separate room

PTK7 is a positive allosteric modulator of GPR133 signaling in glioblastoma

Summary: The adhesion G-protein-coupled receptor GPR133 (ADGRD1) supports growth of the brain malignancy glioblastoma. How the extracellular interactome of GPR133 in glioblastoma modulates signaling remains unknown. Here, we use affinity proteomics to identify the transmembrane protein PTK7 as an extracellular binding partner of GPR133 in glioblastoma. PTK7 binds the autoproteolytically generated N-terminal fragment of GPR133 and its expression in trans increases GPR133 signaling. This effect requires the intramolecular cleavage of GPR133 and PTK7’s anchoring in the plasma membrane. PTK7’s allosteric action on GPR133 signaling is additive with but topographically distinct from orthosteric activation by soluble peptide mimicking the endogenous tethered Stachel agonist. GPR133 and PTK7 are expressed in adjacent cells in glioblastoma, where their knockdown phenocopies each other. We propose that this ligand-receptor interaction is relevant to the pathogenesis of glioblastoma and possibly other physiological processes in healthy tissues

Diversity of a Complex Centromeric Satellite and Molecular Characterization of Dispersed Sequence Families in Sugar Beet (Beta vulgaris)

Menzel G, Dechyeva D, Wenke T, Holtgräwe D, Weisshaar B, Schmidt T. Diversity of a complex centromeric satellite and molecular characterization of dispersed sequence families in sugar beet (Beta vulgaris). Annals of Botany. 2008;102(4):521-530