Process performance of parallel bioreactors for batch cultivation of Streptomyces tendae

Batch cultivations of the nikkomycin Z producer Streptomyces tendae were performed in three different parallel bioreactor systems (milliliter-scale stirred-tank reactors, shake flasks and shaken microtiter plate) in comparison to a standard liter-scale stirred-tank reactor as reference. Similar dry cell weight concentrations were measured as function of process time in stirred-tank reactors and shake flasks, whereas only poor growth was observed in the shaken microtiter plate. In contrast, the nikkomycin Z production differed significantly between the stirred and shaken bioreactors. The measured product concentrations and product formation kinetics were almost the same in the stirred-tank bioreactors of different scale. Much less nikkomycin Z was formed in the shake flasks and MTP cultivations, most probably due to oxygen limitations. To investigate the non-Newtonian shear-thinning behavior of the culture broth in small-scale bioreactors, a new and simple method was applied to estimate the rheological behavior. The apparent viscosities were found to be very similar in the stirred-tank bioreactors, whereas the apparent viscosity was up to two times increased in the shake flask cultivations due to a lower average shear rate of this reactor system. These data illustrate that different engineering characteristics of parallel bioreactors applied for process development can have major implications for scale-up of bioprocesses with non-Newtonian viscous culture broths.     

Confidence measures for protein fold recognition

MOTIVATION: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a sensitive searching method to identify possible candidates and, second, to assign a confidence to the putative candidates in order to select the best one. For searching methods where the score distributions are known, p-values are used as confidence measure with great success. For the cases where such theoretical backing is absent, we propose empirical approximations to p-values for searching procedures. RESULTS: As a baseline, we review the performances of different methods for detecting remote protein folds (sequence alignment and threading, with and without sequence profiles, global and local). The analysis is performed on a large representative set of protein structures. For fold recognition, we find that methods using sequence profiles generally perform better than methods using plain sequences, and that threading methods perform better than sequence alignment methods. In order to assess the quality of the predictions made, we establish and compare several confidence measures, including raw scores, z-scores, raw score gaps, z-score gaps, and different methods of p-value estimation. We work our way from the theoretically well backed local scores towards more explorative global and threading scores. The methods for assessing the statistical significance of predictions are compared using specificity--sensitivity plots. For local alignment techniques we find that p-value methods work best, albeit computationally cheaper methods such as those based on score gaps achieve similar performance. For global methods where no theory is available methods based on score gaps work best. By using the score gap functions as the measure of confidence we improve the more powerful fold recognition methods for which p-values are unavailable. AVAILABILITY: The benchmark set is available upon request.     

Low fertility in contemporary humans and the mate value of their children: sex-specific effects on social status indicators

Evolutionary explanations of low fertility in modern affluent societies commonly state that low fertility is the outcome of high parental investments in the quality of their children. Although the empirical evidence that modern parents do face a quantity–quality trade-off is strong, two issues that are relevant from an evolutionary perspective have not received much attention. First, sex differences in the proximate aspects of quality have been largely ignored. Second, the relationship between the quantity of children and their reproductive success in contemporary low-fertility societies remains unclear. In this article, we study the quantity–quality trade-off as a trade-off between the number of children and the mate value and reproductive success of those children. We examine the trade-off in two steps. First, a lower number of children is expected to increase the mate value of these children. Second, greater mate value is expected to lead to greater reproductive success. Using sex-specific indicators of mate value, we test these hypotheses in a representative sample of the Dutch population aged 55–85 in 1992 (n=3229). This sample contains information on three successive generations in which the middle generation has completed fertility. We find support for the first hypothesis, but only partial support for the second hypothesis. A higher number of children is traded off against the mate value of the children, but not against their reproductive success. We conclude that the conditions under which the quantity of children is traded off against their reproductive success depend on the social environment.     

Proteolytic Degradation of Alzheimer's Disease Amyloid β-Peptide by a Metalloproteinase from Microglia Cells

Abstract: The cerebral deposition of amyloid β-peptide (Aβ) is a histopathological characteristic of Alzheimer's disease. Because an impaired clearance of Aβ might be involved in the disease, we investigated the proteolytic degradation of synthetic Aβ (40-residue peptide) in cultures of glial cells and characterized a protease involved. Whereas rat astrocytes had a very low degradation capacity, cultivated rat microglia cells cleaved Aβ. Microglia activity was considerably enhanced by stimulation with lipopolysaccharide and to a lesser extent by phorbol esters. Most of the Aβ-degrading activity was released into the medium. By use of selective inhibitors the protease was characterized as a metalloprotease of ∼200 kDa that was different from neutral endopeptidase (a neuropeptide-degrading enzyme), matrix metalloproteases, or macrophage elastase. Its activity was efficiently reduced by four hydroxamic acid-based zinc-metalloprotease inhibitors that have been shown to inhibit membrane protein secretases (disintegrins). We conclude that activated microglia cells might impair amyloid plaque formation by release of a metalloprotease that degrades soluble Aβ before polymerization.     

PbGP43 Genotyping Using Paraffin-Embedded Biopsies of Human Paracoccidioidomycosis Reveals a Genetically Distinct Lineage in the Paracoccidioides brasiliensis Complex

Mycopathologia - Paracoccidioidomycosis (PCM) is a systemic mycosis caused by a group of cryptic species embedded in the Paracoccidioides brasiliensis complex and Paracoccidioides lutzii. Four...     

Circadian Clock Genes Contribute to the Regulation of Hair Follicle Cycling

Hair follicles undergo recurrent cycling of controlled growth (anagen), regression (catagen), and relative quiescence (telogen) with a defined periodicity. Taking a genomics approach to study gene expression during synchronized mouse hair follicle cycling, we discovered that, in addition to circadian fluctuation, CLOCK–regulated genes are also modulated in phase with the hair growth cycle. During telogen and early anagen, circadian clock genes are prominently expressed in the secondary hair germ, which contains precursor cells for the growing follicle. Analysis of Clock and Bmal1 mutant mice reveals a delay in anagen progression, and the secondary hair germ cells show decreased levels of phosphorylated Rb and lack mitotic cells, suggesting that circadian clock genes regulate anagen progression via their effect on the cell cycle. Consistent with a block at the G1 phase of the cell cycle, we show a significant upregulation of p21 in Bmal1 mutant skin. While circadian clock mechanisms have been implicated in a variety of diurnal biological processes, our findings indicate that circadian clock genes may be utilized to modulate the progression of non-diurnal cyclic processes.