Selected codon usage bias in members of the class Mollicutes

Mollicutes are parasitic microorganisms mainly characterized by small cell sizes, reduced genomes and great A and T mutational bias. We analyzed the codon usage patterns of the completely sequenced genomes of bacteria that belong to this class. We found that for many organisms not only mutational bias but also selection has a major effect on codon usage. Through a comparative perspective and based on three widely used criteria we were able to classify Mollicutes according to the effect of selection on codon usage. We found conserved optimal codons in many species and study the tRNA gene pool in each genome. Previous results are reinforced by the fact that, when selection is operative, the putative optimal codons found match the respective cognate tRNA. Finally, we trace selection effect backwards to the common ancestor of the class and estimate the phylogenetic inertia associated with this character. We discuss the possible scenarios that explain the observed evolutionary patterns.     

Importance of stability study of continuous systems for ethanol production

Fuel ethanol industry presents different problems during bioreactors operation. One of them is the unexpected variation in the output ethanol concentration from the bioreactor or a drastic fall in the productivity. In this paper, a compilation of concepts and relevant results of several experimental and theoretical studies about dynamic behavior of fermentation systems for bioethanol production with Saccharomyces cerevisiae and Zymomonas mobilis is done with the purpose of understanding the stability phenomena that could affect the productivity of industries producing fuel ethanol. It is shown that the design of high scale biochemical processes for fuel ethanol production must be done based on stability studies.     

Design and synthesis of biologically active peptides: a 'tail' of amino acids can modulate activity of synthetic cyclic peptides

In earlier work, we synthesized a cyclic 9-amino acid peptide (AFPep, cyclo[EKTOVNOGN]) and showed it to be useful for prevention and therapy of breast cancer. In an effort to explore the structure–function relationships of AFPep, we have designed analogs that bear a short ‘tail’ (one or two amino acids) attached to the cyclic peptide distal to its pharmacophore. Analogs that bore a tail of either one or two amino acids, either of which had a hydrophilic moiety in the side chain (e.g., cyclo[EKTOVNOGN]FS) exhibited greatly diminished biological activity (inhibition of estrogen-stimulated uterine growth) relative to AFPep. Analogs that bore a tail of either one or two amino acids which had hydrophobic (aliphatic or aromatic) side chains (e.g., cyclo[EKTOVNOGN]FI) retained (or had enhanced) growth inhibition activity. Combining in the same biological assay a hydrophilic-tailed analog with either AFPep or a hydrophobic-tailed analog resulted in decreased activity relative to that for AFPep or for the hydrophobic-tailed analog alone, suggesting that hydrophilic-tailed analogs are binding to a biologically active receptor. An analog with a disrupted pharmacophore (cyclo[EKTOVGOGN]) exhibited little or no growth inhibition activity. An analog with a hydrophilic tail and a disrupted pharmacophore (cyclo[EKTOVGOGN]FS) exhibited no growth inhibition activity of its own and did not affect the activity of a hydrophobic-tailed analog, but enhanced the growth inhibition activity of AFPep. These results are discussed in the context of a two-receptor model for binding of AFPep and ring-and-tail analogs. We suggest that tails on cyclic peptides may comprise a useful method to enhance diversity of peptide design and specificity of ligand–receptor interactions.     

Development of a PCR-based assay for rapid detection of class IIa bacteriocin genes

Aims: We have developed a PCR‐based assay using custom designed panel of primers which allows rapid detection of class IIa bacteriocin‐coding genes. To demonstrate the applicability of the developed assay, the method was applied on 40 metagenomic DNA preparations isolated from native microbiota of Polish artisanal cheeses produced in the Tatra Mountains. Methods and Results: The developed assay was designed on the basis of a large scale alignment of class IIa bacteriocin‐coding genes. A panel of seven primer pairs with confirmed ability to detect class IIa bacteriocin‐coding sequences was obtained. The following study has revealed a superb bacteriocinogenic potential of all forty analysed cheese samples. Conclusions: The majority of obtained sequences were lactic acid bacteria (LAB) related, although some sequences showed significant similarity to bacteriocin‐coding sequences present in non‐LAB bacteriocin producers. The results suggest that several potentially new bacteriocin‐coding sequences were found. Significance and Impact of the Study: The developed assay can be extremely helpful in establishing whether isolates from the environment of interest have a potential of synthesizing antilisterial class IIa bacteriocins. Application of the approach may represent a useful tool contributing to ecological studies looking for valuable probiotic, bacteriocinogenic microbiota developing in foods.     

Comparison of culture methods on exopolysaccharide production in the submerged culture of Cordyceps militaris and process optimization

Aims: To improve exopolysaccharides (EPS) production of Cordyceps militaris (C. militaris), effects of different culture method on mycelial biomass and EPS production in the submerged culture of C. militaris were investigated. Methods and Results: A new two‐stage fermentation process for EPS production of C. militaris was designed in this work. Central composite design (CCD) was utilized to optimize the two‐stage fermentation process. The results showed that the two‐stage fermentation process for EPS production was superior to other culture method (conventional static culture and shake culture). CCD revealed that the optimum values of the test variables for EPS production were shaken for 140 h followed by 130‐h static culture. The maximum EPS production reached 3·2 g l^?1 under optimized two‐stage culture and was about 2·3‐fold and 1·6‐fold in comparison with those of original static culture and shake culture. Conclusions: It was indicated that a new two‐stage culture method obtained in this work possessed a high potential for the industrial production for EPS of C. militaris. Significance and Impact of the Study: The fundamental information obtained in this work is complementary to those of previous investigations on the submerged culture of C. militaris for the production of bioactive metabolites.     

Foraging, bioenergetic and predation constraints on diel vertical migration: field observations and modelling of reverse migration by young-of-the-year herring Clupea harengus

This study is the first to characterize temporal changes in blood chemistry of individuals from one population of male sockeye salmon Oncorhynchus nerka during the final 6 weeks of sexual maturation and senescence in the freshwater stage of their spawning migration. Fish that died before the start of their historic mean spawning period (c. 5 November) were characterized by a 20-40% decrease in plasma osmolality, chloride and sodium, probably representing a complete loss of osmoregulatory ability. As fish became moribund, they were further characterized by elevated levels of plasma cortisol, lactate and potassium. Regressions between time to death and plasma chloride (8 October: P < 0·001; 15 October: P < 0·001) indicate that plasma chloride was a strong predictor of longevity in O. nerka. That major plasma ion levels started to decline 2-10 days (mean of 6 days) before fish became moribund, and before other stress, metabolic or reproductive hormone variables started to change, suggests that a dysfunctional osmoregulatory system may initiate rapid senescence and influence other physiological changes (i.e. elevated stress and collapsed reproductive hormones) which occur as O. nerka die on spawning grounds.     

Bayesian adaptive survey protocols for resource management

Transparency in resource management decisions requires a proper accounting of uncertainty at multiple stages of the decision-making process. As information becomes available, periodic review and updating of resource management protocols reduces uncertainty and improves management decisions. One of the most basic steps to mitigating anthropogenic effects on populations is determining if a population of a species occurs in an area that will be affected by human activity. Species are rarely detected with certainty, however, and falsely declaring a species absent can cause improper conservation decisions or even extirpation of populations. We propose a method to design survey protocols for imperfectly detected species that accounts for multiple sources of uncertainty in the detection process, is capable of quantitatively incorporating expert opinion into the decision-making process, allows periodic updates to the protocol, and permits resource managers to weigh the severity of consequences if the species is falsely declared absent. We developed our method using the giant gartersnake (Thamnophis gigas), a threatened species precinctive to the Central Valley of California, as a case study. Survey date was negatively related to the probability of detecting the giant gartersnake, and water temperature was positively related to the probability of detecting the giant gartersnake at a sampled location. Reporting sampling effort, timing and duration of surveys, and water temperatures would allow resource managers to evaluate the probability that the giant gartersnake occurs at sampled sites where it is not detected. This information would also allow periodic updates and quantitative evaluation of changes to the giant gartersnake survey protocol. Because it naturally allows multiple sources of information and is predicated upon the idea of updating information, Bayesian analysis is well-suited to solving the problem of developing efficient sampling protocols for species of conservation concern. © 2011 The Wildlife Society.     

Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution

Although de novo computational enzyme design has been shown to be feasible, the field is still in its infancy: the kinetic parameters of designed enzymes are still orders of magnitude lower than those of naturally occurring ones. Nonetheless, designed enzymes can be improved by directed evolution, as recently exemplified for the designed Kemp eliminase KE07. Random mutagenesis and screening resulted in variants with > 200-fold higher catalytic efficiency and provided insights about features missing in the designed enzyme. Here we describe the optimization of KE70, another designed Kemp eliminase. Amino acid substitutions predicted to improve catalysis in design calculations involving extensive backbone sampling were individually tested. Those proven beneficial were combinatorially incorporated into the originally designed KE70 along with random mutations, and the resulting libraries were screened for improved eliminase activity. Nine rounds of mutation and selection resulted in > 400-fold improvement in the catalytic efficiency of the original KE70 design, reflected in both higher k_cat values and lower K_m values, with the best variants exhibiting k_cat/K_m values of > 5 × 10⁴ s^− 1 M^− 1. The optimized KE70 variants were characterized structurally and biochemically, providing insights into the origins of the improvements in catalysis. Three primary contributions were identified: first, the reshaping of the active-site cavity to achieve tighter substrate binding; second, the fine-tuning of electrostatics around the catalytic His-Asp dyad; and, third, the stabilization of the active-site dyad in a conformation optimal for catalysis.     

Partial edentulism and removable partial denture design in a dental school population: a survey in Greece

Gerodontology 2011; doi: 10.1111/j.1741‐2358.2010.00382.x Partial edentulism and removable partial denture design in a dental school population: a survey in Greece Objectives: To investigate the pattern of partial edentulism and the most frequent designs of cobalt‐chromium removable partial dentures (RPDs), constructed at the Dental School of Athens, Greece. Methods and materials: Five hundred and fifty‐three patients, between 42 and 81 years old, mostly males, treated by undergraduate dental students, were included. The survey was based on visual evaluation of master casts and work authorisation to dental technicians. Aspects examined were: Kennedy Classification, modification areas, major connectors, clasping, placement of rest seats and indirect retention. Results: Kennedy Class I was the most common encountered in the maxilla (50.5%) and in the mandible (70%). The most frequent major connectors were the lingual bar (92.6%) and the U‐shaped palatal strap (54%). The most common clasp was the Roach (69.2%) in Class I and Class II. In Class III and IV, the most common was the occlusally approaching clasp (55% and 70%). The most frequent location of the rest was mesial of abutment teeth. On the average, 39.5% of Class I RPDs and 58.6% of Class II RPDs had indirect retainers. Conclusion: A combination of the two major philosophies of RPD design (biomechanical and hygienic) was evident in the RPDs examined in our study.