Comparative studies on the suitability of two aphelinids, Aphelinus asychis WALKER and Aphelinus varipes FÖRSTER (Hym., Aphelinidae), for the biological control of Aphis gossypii GLOVER (Hom., Aphididae)

Die Gurkenblattlaus Aphis gossypii GLOVER (Hom., Aphididae) ist ein weltweit verbreiteter, polyphager Schädling, dessen Wirtspflanzenspektrum verschiedene Feld- und Gewächshauskulturen wie z. B. Malvaceen (Baumwolle, Hibiskus) und Curcurbitaceen (Gurken, Melonen, Zucchini) umfasst. In Europa stellt die Gurkenblattlaus einen wichtigen Schädling an Gurkenkulturen im Unterglasanbau dar (VAN SCHELT 1993) und sie tritt vermehrt auch an anderen Gewächshauskulturen auf (VAN STEENIS 1992). Aufgrund der Resistenzentwicklung von A. gossypii gegenüber zahlreichen chemischen Insektiziden gewinnt die biologische Bekämpfung unter Verwendung von Nützlingen zunehmend an Bedeutung. Bisher wurden der Parasitoid Aphelinus colemani VIERECK (Hym., Braconidae) und die räuberische Gallmückenlarve Aphidoletes aphidimyza RONDANI (Dipt., Cecidomyiidae) zur Bekämpfung dieser Blattlausart verwendet, jedoch mit nur mäßigen Erfolgen (VAN STEENIS 1994, VAN STEENIS & EL- KHAWASS 1995). TAKADA (2002) berichtet, dass die zwei Parasitoide Aphelinus asychis WALKER und Aphelinus varipes FÖRSTER (Hym., Aphelinidae) ein Potential zur biologischen Bekämpfung von A. gossypii an verschiedenen Gewächshauskulturen in Japan besitzen. Das Ziel der vorliegenden Studie war daher zu untersuchen, welcher dieser zwei Parasitoide zur biologischen Bekämpfung von A. gossypii an Gurken besser geeignet ist. Dazu wurden in Laborversuchen einige biologische Parameter wie Entwicklung, „host feeding“-Verhalten und Parasitierungsleistung beider Arten ermittelt und verglichen.The cotton aphid is a phytophagous cosmopolitan species and an important pest on cucumber in European greenhouses. Because of increased insecticide resistance and destruction of natural enemies through the use of pesticides current research is directed towards the development of management. systems that use biological control methods. The present laboratory study was designed to compare two aphelinids, Aphelinus asychis WALKER and Aphelinus varipes FÖRSTER, according to some life table characteristics parasitizing the cotton aphid, Aphis gossypii GLOVER. The traits studied were developmental time, adult emergence rate, host feeding and parasitation. The results showed that both species were able to complete their development with exclusively this host. Moreover, they can host feed and parasitize successfully on A. gossypii-nymphs. Developmental duration from egg to mummification and from mummification to emergence of adults were 7,1 days and 6,9 days for A. asychis and 9,1 days and 10,3 days for A. varipes, respectively. Adult emergence rates were higher for A. asychis (75%) than for A. varipes (53%). Comparison of the impact on A. gossypii of both parasitoids indicated that A. asychis was more effective than A. varipes. In total A. asychis killed an average of 17,1 and A. varipes an average of 4,8 A. gossypii-nymphs/day. Consequently, A. asychis seems to be a promising natural enemy which could contribute to a successful biological control program for A. gossypii. However, it´s biology, ecology and control efficiency need further information

Fine-tuning structural RNA alignments in the twilight zone

Bremges A, Schirmer S, Giegerich R. Fine-tuning structural RNA alignments in the twilight zone. BMC Bioinformatics. 2010;11(1): 222

Comparing forests

Schirmer S. Comparing forests. Bielefeld: Bielefeld University; 2011.Various methods have been proposed for RNA secondary structure comparison, and new ones are still being developed. It seems that there is no appropriate distance measure for structure comparison yet. Such a distance measure should appropriately capture the features of the secondary structure to determine the distance. Thus, the measure also depends on the representation of the secondary structure, which may introduce artefacts in the distance computation. Our goal is to find a distance function that avoids artefacts caused by the representation, and is based on a reasonable representation of the secondary structure. After a discussion of common distance functions for RNA secondary structures, we focus on the forest alignment distance, which represents the secondary structures in a natural way with regard to the nesting and adjacency relation of substructures. In the main part of this work, we extend the gap model of the forest alignment distance to make it suitable for affine gap costs. This leads to a new algorithm variant, which is explained in this thesis, and is implemented in the new version of the tool RNAforester 2.0. In addition, we provide a mechanism to speed up the alignment process by anchoring of subalignments. The anchoring information is based on the overall shape of the molecule, and is obtained by the method of abstract shape analysis. Another contribution is the discussion of the well-formed RNA forest alignment concept. I adapt the case distinction in the recurrences that were designed to construct well-formed RNA forest alignment, to ensure that the deletion and insertion of a pairing relation between two bases is handled in an appropriate way. The affine gap scoring scheme brings an additional constant factor of ≈ 7 into the computation. It improves structure alignments in many cases, if combined with the right scoring parameters. The anchoring of subalignments leads to an average speedup of factor ≈ 3 compared to the usual computation, dependent on number and placement of the anchors

Forest Alignment with Affine Gaps and Anchors

Schirmer S, Giegerich R. Forest Alignment with Affine Gaps and Anchors. Combinatorial Pattern Matching. 2011:104-117

Browsing RNA Structures by Interactive Sonification

Grond F, Janssen S, Schirmer S, Hermann T. Browsing RNA Structures by Interactive Sonification. In: Bresin R, Hermann T, Hunt A, eds. Proceedings of the 3rd Interactive Sonification Workshop. KTH, Stockholm, Sweden: KTH School of Computer Science and Communication (CSC); 2010: 11-16.This paper presents a new interactive sonification technique 1 to browse ribonucleic acid (RNA) secondary structures using a combined auditory and visual interface. 2 Despite the existence of several optimization criteria for RNA sequences, it is still necessary to manually inspect a huge number of the resulting structures in detail. Our first sonifications turn RNA structures into auditory timbre gestalts according to the shape classes they belong to, so that transitions amongst shape classes becomes clearly audible, while scanning over a visual display

Supplementary Material for "Browsing RNA Structures by Interactive Sonification"

Grond F, Janssen S, Schirmer S, Hermann T. Supplementary Material for "Browsing RNA Structures by Interactive Sonification". Bielefeld University; 2010.<img src="https://pub.uni-bielefeld.de/download/2698354/2702778" width="200" style="float:right;"> This paper presents a new interactive sonification technique to browse ribonucleic acid secondary structures using a combined auditory and visual interface. Despite the existence of several optimization criteria for searching an optimal structure within the numerous possible structures of an RNA sequence, it is still necessary to manually inspect a huge number of the resulting structures in detail. We describe briefly the background of RNA structure representation and typical search scenarios. Then we discuss the audio-visual browser in detail, with a special focus on the sound design, data-to-sound mapping and interactive aspects. The sonifications we propose turn RNA structures into auditory timbre gestalts according to the shape classes they belong to. Various research-relevant phenomena become clearly audible such as transitions among shape classes and different free energies of selected folds. Both can be simultaneously assessed in an interface that allows for an integrated audio-visual perception

Evolutionary Diversification of Host-Targeted; Bartonella; Effectors Proteins Derived from a Conserved FicTA Toxin-Antitoxin Module

Proteins containing a FIC domain catalyze AMPylation and other post-translational modifications (PTMs). In bacteria, they are typically part of FicTA toxin-antitoxin modules that control conserved biochemical processes such as topoisomerase activity, but they have also repeatedly diversified into host-targeted virulence factors. Among these,; Bartonella; effector proteins (Beps) comprise a particularly diverse ensemble of FIC domains that subvert various host cellular functions. However, no comprehensive comparative analysis has been performed to infer molecular mechanisms underlying the biochemical and functional diversification of FIC domains in the vast Bep family. Here, we used X-ray crystallography, structural modelling, and phylogenetic analyses to unravel the expansion and diversification of Bep repertoires that evolved in parallel in three; Bartonella; lineages from a single ancestral FicTA toxin-antitoxin module. Our analysis is based on 99 non-redundant Bep sequences and nine crystal structures. Inferred from the conservation of the FIC signature motif that comprises the catalytic histidine and residues involved in substrate binding, about half of them represent AMP transferases. A quarter of Beps show a glutamate in a strategic position in the putative substrate binding pocket that would interfere with triphosphate-nucleotide binding but may allow binding of an AMPylated target for deAMPylation or another substrate to catalyze a distinct PTM. The β-hairpin flap that registers the modifiable target segment to the active site exhibits remarkable structural variability. The corresponding sequences form few well-defined groups that may recognize distinct target proteins. The binding of Beps to promiscuous FicA antitoxins is well conserved, indicating a role of the antitoxin to inhibit enzymatic activity or to serve as a chaperone for the FIC domain before translocation of the Bep into host cells. Taken together, our analysis indicates a remarkable functional plasticity of Beps that is mostly brought about by structural changes in the substrate pocket and the target dock. These findings may guide future structure-function analyses of the highly versatile FIC domains