A New System for the Evaluation of the Fermentation Quality of Silages

Depending on the content of nitrate in green forage, the pattern of fermentation products in silages differ significantly (Weiß & Kaiser, 2001). The systems, which are now common in practice for evaluating the quality of silage fermentation, characterise fermentation quality incorrectly because the evaluation is influenced by the chemical composition of green forage. The aim of this work was to derive an evaluation system for fermentation quality, which is independent from the chemical composition of green forage

Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints.

The mapping between biological genotypes and phenotypes plays an important role in evolution, and understanding the properties of this mapping is crucial to determine the outcome of evolutionary processes. One of the most striking properties observed in several genotype-phenotype (GP) maps is the positive correlation between the robustness and evolvability of phenotypes. This implies that a phenotype can be strongly robust against mutations and at the same time evolvable to a diverse range of alternative phenotypes. Here, we examine the causes for this positive correlation by introducing two analytically tractable GP map models that follow the principles of real biological GP maps. The first model is based on gene-like GP maps, reflecting the way in which genetic sequences are organized into protein-coding genes, and the second one is based on the GP map of RNA secondary structure. For both models, we find that a positive correlation between phenotype robustness and evolvability only emerges if mutations at one sequence position can have non-local effects on the sequence constraints at another position. This highlights that non-local effects of mutations are closely related to the coexistence of robustness and evolvability in phenotypes, and are likely to be an important feature of many biological GP maps

Using small samples to estimate neutral component size and robustness in the genotype-phenotype map of RNA secondary structure.

In genotype-phenotype (GP) maps, the genotypes that map to the same phenotype are usually not randomly distributed across the space of genotypes, but instead are predominantly connected through one-point mutations, forming network components that are commonly referred to as neutral components (NCs). Because of their impact on evolutionary processes, the characteristics of these NCs, like their size or robustness, have been studied extensively. Here, we introduce a framework that allows the estimation of NC size and robustness in the GP map of RNA secondary structure. The advantage of this framework is that it only requires small samples of genotypes and their local environment, which also allows experimental realizations. We verify our framework by applying it to the exhaustively analysable GP map of RNA sequence length L = 15, and benchmark it against an existing method by applying it to longer, naturally occurring functional non-coding RNA sequences. Although it is specific to the RNA secondary structure GP map in the first place, our framework can probably be transferred and adapted to other sequence-to-structure GP maps.MW was supported by the EPSRC and the Gatsby Charitable Foundation. SEA was supported by the Gatsby Charitable Foundation

Neutral components show a hierarchical community structure in the genotype-phenotype map of RNA secondary structure.

Genotype-phenotype (GP) maps describe the relationship between biological sequences and structural or functional outcomes. They can be represented as networks in which genotypes are the nodes, and one-point mutations between them are the edges. The genotypes that map to the same phenotype form subnetworks consisting of one or multiple disjoint connected components-so-called neutral components (NCs). For the GP map of RNA secondary structure, the NCs have been found to exhibit distinctive network features that can affect the dynamical processes taking place on them. Here, we focus on the community structure of RNA secondary structure NCs. Building on previous findings, we introduce a method to reveal the hierarchical community structure solely from the sequence constraints and composition of the genotypes that form a given NC. Thereby, we obtain modularity values similar to common community detection algorithms, which are much more complex. From this knowledge, we endorse a sampling method that allows a fast exploration of the different communities of a given NC. Furthermore, we introduce a way to estimate the community structure from genotype samples, which is useful when an exhaustive analysis of the NC is not feasible, as is the case for longer sequence lengths.MW was supported by the EPSRC and the Gatsby Charitable Foundation. SEA was supported by the Gatsby Charitable Foundation and the Alan Turing Institute

Sialic Acid in Human Serum and Cerebrospinal Fluid. Comparison of methods and reference values

Peer Reviewe

New Results on Inhibition of Clostridia Development in Silages

The prevention of clostridial activity in silages is one of the most important aims in silage making. Clostridial activity in silages is especially expressed as the occurrence of butyric acid and as increased content of clostridial spores. A rapid reduction in the pH value at the beginning of fermentation process is considered as the most important factor for inhibition of clostridial development. It is assumed, that, if the “critical pH value” will be quickly achieved, clostridial activity in silages can be stopped. In experiments concerning the fermentation process it was found that the effect of acidification and dry matter content on the clostridial activity is different in ensiling material, containing nitrate, and in nitrate-free material. The object of the present paper was to clarify the conditions for clostridial development during the fermentation process, including examination of factors such as dry matter content, acidification and nitrate content

Effects of Diversity on Multi-agent Systems: Minority Games

We consider a version of large population games whose agents compete for resources using strategies with adaptable preferences. The games can be used to model economic markets, ecosystems or distributed control. Diversity of initial preferences of strategies is introduced by randomly assigning biases to the strategies of different agents. We find that diversity among the agents reduces their maladaptive behavior. We find interesting scaling relations with diversity for the variance and other parameters such as the convergence time, the fraction of fickle agents, and the variance of wealth, illustrating their dynamical origin. When diversity increases, the scaling dynamics is modified by kinetic sampling and waiting effects. Analyses yield excellent agreement with simulations.Comment: 41 pages, 16 figures; minor improvements in content, added references; to be published in Physical Review

Molecular gas heating in Arp 299

Understanding the heating and cooling mechanisms in nearby (Ultra) luminous infrared galaxies can give us insight into the driving mechanisms in their more distant counterparts. Molecular emission lines play a crucial role in cooling excited gas, and recently, with Herschel Space Observatory we have been able to observe the rich molecular spectrum. CO is the most abundant and one of the brightest molecules in the Herschel wavelength range. CO transitions are observed with Herschel, and together, these lines trace the excitation of CO. We study Arp 299, a colliding galaxy group, with one component harboring an AGN and two more undergoing intense star formation. For Arp 299 A, we present PACS spectrometer observations of high-J CO lines up to J=20-19 and JCMT observations of $^{13}$CO and HCN to discern between UV heating and alternative heating mechanisms. There is an immediately noticeable difference in the spectra of Arp 299 A and Arp 299 B+C, with source A having brighter high-J CO transitions. This is reflected in their respective spectral energy line distributions. We find that photon-dominated regions (PDRs) are unlikely to heat all the gas since a very extreme PDR is necessary to fit the high-J CO lines. In addition, this extreme PDR does not fit the HCN observations, and the dust spectral energy distribution shows that there is not enough hot dust to match the amount expected from such an extreme PDR. Therefore, we determine that the high-J CO and HCN transitions are heated by an additional mechanism, namely cosmic ray heating, mechanical heating, or X-ray heating. We find that mechanical heating, in combination with UV heating, is the only mechanism that fits all molecular transitions. We also constrain the molecular gas mass of Arp 299 A to 3e9 Msun and find that we need 4% of the total heating to be mechanical heating, with the rest UV heating