PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells

The ability to analyze and understand the mechanisms by which cells process information is a key question of systems biology research. Such mechanisms critically depend on reversible phosphorylation of cellular proteins, a process that is catalyzed by protein kinases and phosphatases. Here, we present PhosphoPep, a database containing more than 10 000 unique high-confidence phosphorylation sites mapping to nearly 3500 gene models and 4600 distinct phosphoproteins of the Drosophila melanogaster Kc167 cell line. This constitutes the most comprehensive phosphorylation map of any single source to date. To enhance the utility of PhosphoPep, we also provide an array of software tools that allow users to browse through phosphorylation sites on single proteins or pathways, to easily integrate the data with other, external data types such as protein–protein interactions and to search the database via spectral matching. Finally, all data can be readily exported, for example, for targeted proteomics approaches and the data thus generated can be again validated using PhosphoPep, supporting iterative cycles of experimentation and analysis that are typical for systems biology research

Characterisation of conus venom using polypeptide separation methods and mass spectrometric analysis

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

A new plastic for morphometric investigation of blood vessels, especially in large organs such as the human liver

In this paper a technique is described, using Araldite CY 223 and hardener HY 2967 as injection material, for preparing corrosion casts or histological sections. The plastic has a viscosity (at 39–40°C) similar to that of blood, a gelling time of approximately 17min (at 40°C), and an exothermic transition energy of ΔH = 80.28 ± 3.20 cal/gm. The influence of the plastic on the tissue is discussed. The histological sectioning of fixed tissue containing Araldite‐filled blood vessels after embedding in 2‐hydroxyethyl‐methacrylate (GMA) is described. When using GMA in a modification of the mixtures of Ruddell (1967) and Sims (1974), methylbenzoate is recommended as an intermedium in order to obtain a more uniform infiltration and reproducible section thickness. At the same time methylbenzoate is recommended as a storing fluid. Sections of 2–3 μm afford satisfying morphologic and morphometric results. This method allows various arterial wall dimensions to be measured easily, and provides a suitable means to compare histometric values with SEM data derived from corrosion casts

Balancing protein and energy in Nile tilapia feeds : A meta-analysis

Farmed fish are increasingly grown in intensive and semi-intensive systems where most nutrients are provided by formulated feeds. These are formulated to minimise costs and optimise growth, notably the rate of muscle protein synthesis (i.e., fillet). Protein synthesis depends on the availability of amino acids (i.e., protein) and energy. Thus, fish feeds are often formulated to provide a balanced ratio of protein to energy (P:E). Above and below the optimal dietary P:E, absorbed protein and energy are expected to be under-utilised for body protein synthesis, respectively. Estimates of the optimal dietary P:E vary largely for Nile tilapia (Oreochromis niloticus (L., 1758)). Published values range from 13 to 26 g of dietary protein per MJ of energy. Here, we challenge the idea that growth, protein utilisation efficiency and body composition can all be simultaneously optimised, when Nile tilapia are fed an optimal dietary P:E. Through linear and non-linear regression meta-analyses, we quantitatively describe the effects of protein and energy intake on nutrient partitioning, feed efficiency and growth. We find linear relationships between the dietary P:E and protein retention efficiency. The lack of an inflection contradicts the existence of an optimal P:E. Our regressions of protein and energy intake versus protein gain, indicate that protein gain is often simultaneously limited by both protein and energy intake, and may be limited by other factors than protein and energy intake, such as a maximal protein deposition capacity (PDmax). We conclude that there is no physiological basis for an optimal P:E in Nile tilapia feeds

Reviewing the low efficiency of protein utilization in heavy preruminant calves – a reductionist approach

The efficiency of protein utilization for growth in preruminant calves is decreasing with increasing body weight. In contrast to calves weighing less than 100 kg of body weight, heavy preruminant calves do not respond in protein retention to an increased intake of indispensable amino acids in dose-response studies. The marginal efficiency of protein utilization is low compared with pigs and milk-fed lambs at a similar stage of maturity. A reductionist approach was taken to perceive the potential mechanisms for the low protein utilization in preruminant calves. Neither an imbalance in the dietary protein to energy ratio nor a single limiting indispensable amino acid was responsible for the low efficiency. Also, amino acids were not specifically used to detoxify ammonia. Alternative hypotheses to explain the low efficiency are discussed and result in (i) a reduced post-absorptive supply of amino acids: e.g. by fermentation of milk in the (premature) rumen or preferential amino acid utilization by specific tissues; or (ii) a reduced post-absorptive amino acid utilization: e.g. by decreased insulin sensitivity, utilization of amino acids for gluconeogenesis or an asynchronous nutrient supply. In conclusion, several mechanisms for the low efficiency of protein utilization in heavy preruminant calves were excluded. Other physiological processes which are potentially involved remain to be studied, because the large potential for improving protein utilization in heavy preruminant calves asks for further exploration of their amino acid metabolism