Mixed cropping systems for control of weeds and pests in organic oilseed crops

Agricultural advantages of mixed cropping are gained from biological effects like light competition offering weed-suppressing capacities, or by diversification of plant covers to break development cycles of pests. These effects were measured in a two-year project on mixed cropping with organic oilseed crops. It was found that weeds can be efficiently suppressed in organic linseed (Linum usitatissivum) grown in combination with wheat (Triticum aestivum) or false flax (Camelina sativa). Linseed growth was, however, impaired. In organic pea production (Pisum sativum) also, growing the crop as a mixture with false flax led to a significant decrease of weed population. Either culture showed a balanced plant development. In winter rape (Brassica napus) there were suggestions that infestation by insect pests can be directly reduced in mixtures with cereals or legumes and that parasitoids of insect pests are supported

Contribution of organic farming to conserving and improving biodiversity in Germany avi-fauna as an example

Although it is the aim of organic farming to increase biodiversity, there is little information about the impact of organic farming on birds. From 2001 to 2003, the number of breeding birds was recorded annually on the organic experimental farm of the Institute of Organic Farming (600 ha), and on adjacent conventional and organic farms (60 ha and 40 ha) in Northern Germany. The number of skylark (Alauda arvensis) territories increased considerably after the conversion from conventional to organic farming on the premises of the Institute. Their number remained unvaried on the conventional farm. The highest density of skylark territories was found on the farm which has been under organic management for many years. The number of yellowhammer (Emberiza citronella) territories fluctuated largely in relation to the availability of field margin strips, both on conventional and organic land. During the breeding season aerial hunters (swallows and swifts) and raptors significantly preferred organic fields. Outside the breeding season, densities of raptors (in autumn and in winter), seed-eating birds (in autumn) and insect-eating birds (in autumn) were significantly higher on organic than on conventional fields

Development of Collembolans after coversion towards organic farming

In Northern Germany, a diverse and complex experimental farm of the Federal Agricultural Research Centre (FAL) was set-up in 2001 covering all main aspects of organic farming. Previously, the 600 ha farm had been managed conventionally. Adjacent conventional farms were used as reference. The aim of this project was to study collembolans, microbial biomass and soil organic carbon in six organically farmed fields managed as a crop rotation of six different crops compared with an adjacent conventionally managed field. We hypothesised that the specific management in organic farming promotes soil biota. Soil samples were taken during the growing season in 2004. Collembolan abundances and microbial biomass were lower under organic management, but, generally, collembolan diversity was higher in organically farmed fields combined with a shifting in the dominance structure of the species. This result reveals that, even after three years, the soil biota is still changing with management conversion

Natural similarity measures between position frequency matrices with an application to clustering

Motivation: Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding of a TF to a binding site is a well-studied problem in computational biology. The binding sites for one TF are represented by a position frequency matrix (PFM). The discovery of new PFMs requires the comparison to known PFMs to avoid redundancies. In general, two PFMs are similar if they occur at overlapping positions under a null model. Still, most existing methods compute similarity according to probabilistic distances of the PFMs. Here we propose a natural similarity measure based on the asymptotic covariance between the number of PFM hits incorporating both strands. Furthermore, we introduce a second measure based on the same idea to cluster a set of the Jaspar PFMs. Results: We show that the asymptotic covariance can be efficiently computed by a two dimensional convolution of the score distributions. The asymptotic covariance approach shows strong correlation with simulated data. It outperforms three alternative methods. The Jaspar clustering yields distinct groups of TFs of the same class. Furthermore, a representative PFM is given for each class. In contrast to most other clustering methods, PFMs with low similarity automatically remain singletons. Availability: A website to compute the similarity and to perform clustering, the source code and Supplementary Material are available at http://mosta.molgen.mpg.d

An Algorithm to Compute the Character Access Count Distribution for Pattern Matching Algorithms

We propose a framework for the exact probabilistic analysis of window-based pattern matching algorithms, such as Boyer--Moore, Horspool, Backward DAWG Matching, Backward Oracle Matching, and more. In particular, we develop an algorithm that efficiently computes the distribution of a pattern matching algorithm's running time cost (such as the number of text character accesses) for any given pattern in a random text model. Text models range from simple uniform models to higher-order Markov models or hidden Markov models (HMMs). Furthermore, we provide an algorithm to compute the exact distribution of \emph{differences} in running time cost of two pattern matching algorithms. Methodologically, we use extensions of finite automata which we call \emph{deterministic arithmetic automata} (DAAs) and \emph{probabilistic arithmetic automata} (PAAs)~\cite{Marschall2008}. Given an algorithm, a pattern, and a text model, a PAA is constructed from which the sought distributions can be derived using dynamic programming. To our knowledge, this is the first time that substring- or suffix-based pattern matching algorithms are analyzed exactly by computing the whole distribution of running time cost. Experimentally, we compare Horspool's algorithm, Backward DAWG Matching, and Backward Oracle Matching on prototypical patterns of short length and provide statistics on the size of minimal DAAs for these computations

Comparative monolayer investigations of surface properties of negatively charged glycosphingolipids from vertebrates (gangliosides) and invertebrates (SGL-II, lipid IV).

The surface properties of four negatively charged glycosphingolipids from vertebrates, the sialo-glycosphingolipids (=gangliosides) GM1, GD1a, GT1b and a sulfo-glycosphingolipid (=sulfatide), and of the two negatively charged glycosphingolipids from lower invertebrates, the glucurono-glycosphingolipid Lipid IV and the aminophosphono-glycosphingo-lipid SGL-II were investigated in monolayers at the air/water interface. The molecular peculiarities under investigation were surface pressure (π) and surface potential (ΔV) which are described for Lipid IV and SGL-II for the first time. The surface pressure/area isotherms of all glycosphingolipids were typical of a liquid-expanded monolayer and, with the exception of SGL-II, exhibited a phase transition to a liquid-condensed state at surface pressures above 20 mN/m. The surface potential/molecular area data found for gangliosides in the closely packed state at π=30 mN/m (GM1: ΔV = −17 mV; GD1a: ΔV = −35 mV; GT1b: ΔV = −39 mV) showed only a slight influence of the additional number of negatively charged residues. For Lipid IV, the surface behavior was very similar to GM1 both possessing one negative group per molecule, whereas in SGL-II also the surface potential data (ΔV = −173 mV) were different compared with GD1a both possessing two negative groups per molecule. The addition of Ca2+ condensed the monolayers of all glycolipids and increased the potential in the direction to more positive values, but these findings were less effective in SGL-II films. On the basis of monolayer results presented here, in biological membranes of invertebrates especially Lipid IV might play a similar role as the ganglioside GM1 in vertebrate cells

Efficient exact motif discovery

Motivation: The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been satisfactorily solved in an exact and efficient manner. This is partly due to the large number of possibilities of defining the motif search space and the notion of over-representation. Even for well-defined formalizations, the problem is frequently solved in an ad hoc manner with heuristics that do not guarantee to find the best motif

Akzeptanz von Tiergesundheitsplänen bei Landwirten – Ergebnisse einer Befragung bei 60 Betrieben

In organic farming the ambitious claims in enhancing and keeping animal health are often not realised. The implementation of animal health plans should clear this deficit effectively. Experiences with British and Danish herd health plans showed that the acceptance of plans is an essential part for its successful transfer into practice. But anyhow, this aspect has not been regarded sufficiently. To avoid similar mistakes like done in former institution tests a social study is integrated into German projects that deal with the implementation of animal health plans in poultry, dairy, and pig hus-bandry. To get more information about the acceptance, the study requires farmers’ attitudes to herd health plans, the motivation to animal health and financial and work capabilities as well