A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices

Proteins evolve under a myriad of biophysical selection pressures that collectively control the patterns of amino acid substitutions. These evolutionary pressures are sufficiently consistent over time and across protein families to produce substitution patterns, summarized in global amino acid substitution matrices such as BLOSUM, JTT, WAG, and LG, which can be used to successfully detect homologs, infer phylogenies, and reconstruct ancestral sequences. Although the factors that govern the variation of amino acid substitution rates have received much attention, the influence of thermodynamic stability constraints remains unresolved. Here we develop a simple model to calculate amino acid substitution matrices from evolutionary dynamics controlled by a fitness function that reports on the thermodynamic effects of amino acid mutations in protein structures. This hybrid biophysical and evolutionary model accounts for nucleotide transition/transversion rate bias, multi‐nucleotide codon changes, the number of codons per amino acid, and thermodynamic protein stability. We find that our theoretical model accurately recapitulates the complex yet universal pattern observed in common global amino acid substitution matrices used in phylogenetics. These results suggest that selection for thermodynamically stable proteins, coupled with nucleotide mutation bias filtered by the structure of the genetic code, is the primary driver behind the global amino acid substitution patterns observed in proteins throughout the tree of life.     

Production of the antibiotic gallidermin by Staphylococcus gallinarum – development of a scale-up procedure

A scale-up strategy into 200 l pilot-scale for the production of the antibiotic gallidermin by Staphylococcus gallinarum Tü 3928 was developed. Large-scale fermentations were simulated by consecutive liquid cultures of smaller scale. Afterwards, optimised cultivation conditions were transferred to pilot-scale. Best results were achieved by addition of Maltose during the late production phase leading to a final concentration of 330 mg gallidermin per litre. Compared to the concentrations found in a non-pulsed pilot-scale fermentations this is an increase of 20–30%.     

Analysis of the effects of maturation treatments on the probabilities of somatic embryo germination and plantlet regeneration in pistachio using a linear logistic method

Embryogenic masses (EMSes) of pistachio (Pistacia vera L.) were proliferated in liquid Murashige and Skoog (MS) medium without growth regulators. To determine the effects of benzylaminopurine (BAP), racemic (±) abscisic acid (ABA) and sucrose treatments during maturation on the subsequent germination and plantlet regeneration, clusters of mature somatic embryos were transferred from maturation medium onto the surface of 0.7% agar-solidified Murashige and Skoog medium. Neither germination nor plantlet development medium contained BAP or ABA. Germination studies were carried out using 80 somatic embryos at every combination of four sucrose concentrations, three maturation periods and either five concentrations of BAP or four of ABA, and the numbers germinating were recorded after four durations of culture. A similar experimental plan was used to study plantlet regeneration. The number of germinated somatic embryos increased markedly with duration of the culture on germination medium, and was influenced by the concentrations of BAP or ABA in the maturation medium; the concentration of sucrose in this medium had little influence. Plantlet regeneration also increased with culture duration and was reduced at the highest levels of BAP or ABA; with ABA, the probability of plantlet regeneration was lower for longer maturation periods. ABA and BAP have similar effects on somatic embryo germination (except at the highest levels used), but BAP is superior to ABA for promoting subsequent plantlet regeneration. Linear logistic models were used to investigate the significance of the treatments, and to estimate the optimum conditions for germination and plantlet regeneration. This revised version was published online in June 2006 with corrections to the Cover Date.     

Development and Applications of a Comprehensive Land Use Classification and Map for the US

Land cover maps reasonably depict areas that are strongly converted by human activities, but typically are unable to resolve low-density but widespread development patterns. Data products specifically designed to resolve land uses complement land cover datasets and likely improve our ability to understand the extent and complexity of human modification. Methods for developing a comprehensive land use classification system are described, and a map of land use for the conterminous United States is presented to reveal what we are doing on the land. The comprehensive, detailed and high-resolution dataset was developed through spatial analysis of nearly two-dozen publicly-available, national spatial datasets – predominately based on census housing, employment, and infrastructure, as well as land cover from satellite imagery. This effort resulted in 79 land use classes that fit within five main land use groups: built-up, production, recreation, conservation, and water. Key findings from this study are that built-up areas occupy 13.6% of mainland US, but that the majority of this occurs as low-density exurban/rural residential (9.1% of the US), while more intensive built-up land uses occupy 4.5%. For every acre of urban and suburban residential land, there are 0.13 commercial, 0.07 industrial, 0.48 institutional, and 0.29 acres of interstates/highways. This database can be used to address a variety of natural resource applications, and I provide three examples here: an entropy index of the diversity of land uses for smart-growth planning, a power-law scaling of metropolitan area population to developed footprint, and identifying potential conflict areas by delineating the urban interface.     

The effect of arylazido aminopropionyl ATP on atropine resistant contractions of the cat urinary bladder

This work was designed to study neurogenic, atropine resistant contractions of the cat urinary bladder. Urinary bladder contractions were induced by pelvic nerve stimulation (PNS) and the administration of acetylcholine (Ach) and purine compounds. The results show that atropine (2 mg/kg) depresses the maintained portion (phase 2) of PNS-induced contractions and Ach-induced contractions while having no effect on the initial portion (phase 1) of the PNS-induced contractions or those contractions induced by the purines. Arylazido aminopropionyl ATP (ANAPP3), an ATP antagonist, depressed phase 1 of the PNS contraction and the purine induced contractions. These results suggest that ATP is responsible for at least part of the atropine-resistant contractions of the cat urinary bladder.     

Nitric oxide promotes resistance to tumor suppression by CTLs

Many human tumors express inducible NO synthetase (NOS2), but the roles of NO in tumor development are not fully elucidated. An important step during tumor development is the acquisition of apoptosis resistance. We investigated the dose-dependent effects of endogenously produced NO on apoptosis using ecdysone-inducible NOS2 cell lines. Our results show that short-term NOS2 expression enhances CD95-mediated apoptosis and T cell cytotoxicity dose dependently. Furthermore, we could show that during chronic exposure to NO, besides the primary cytotoxic NO effect, there is selection of cell clones resistant to NO that show cross-resistance to CD95-induced apoptosis and the killing by CTLs. We propose that NO production could initially act as an autocrine suicide or paracrine killing mechanism in cells undergoing malignant transformation. However, once failed, the outcome is fatal. NO promotes tumor formation by enhancing the selection of cells that can evade immune attack by acquiring apoptosis resistance.     

Dynamics of orthophosphate in yeast cytoplasm

Summary Orthophosphate concentration of baker's yeast Saccharomyces cerevisiae was investigated during dynamic conditions. As an example for those dynamics in cell metabolism the transition from glucose limitation to glucose excess (Crabtree-effect) was choosen. As a result of the metabolic switch from complete to partial oxidative metabolism, the cytoplasmic phosphate concentration increased suddenly from 8.4 mM to a maximum of 17.5 mM and transiently decreased to a minimum of 7.0 mM.