Solvent effect on librational dynamics of spin-labelled haemoglobin by ED- and CW-EPR

Two-pulse, echo-detected electron paramagnetic resonance (ED-EPR) spectra and continuous-wave EPR (CW-EPR) spectra were used to investigate the solvent effect on the librational motion of human haemoglobin spin-labelled on cysteine β93 with the nitroxide derivative of maleimide, 6-MSL. Protein samples fully hydrated in phosphate buffer solution (PBS), in a 60% v/v glycerol/water mixture and in the lyophilized form were measured at cryogenic temperature in the frozen state. The protein librational motion was characterized by the amplitude–correlation time product, 〈α ²〉τ _c, deduced from the ED-EPR spectra. The librational amplitude, 〈α ²〉, was determined independently, from the motionally averaged hyperfine splitting in the CW-EPR spectra, and the librational correlation time, τ _c, was derived from the combination of the pulsed and conventional EPR data. Rapid librational motion of small amplitude was detected in all samples. In each case, the librational dynamics was restricted up to 180 K, beyond which it increased steeply for the hydrated protein in PBS and in the presence of glycerol. In contrast, in the dehydrated protein, the librational dynamics was hindered and less dependent on temperature up to ~240 K. In all samples, 〈α ²〉 deviated from small values only for T > 200 K, where a rapid increase of 〈α ²〉 was evident for the hydrated samples, whereas limited temperature variation was shown in the lyophilized samples. The librational correlation time was in the sub-nanosecond regime and weakly dependent on temperature. The results evidence that solvent favours protein dynamics.     

Cancer physics: diagnostics based on damped cellular elastoelectrical vibrations in microtubules

This paper describes a proposed biophysical mechanism of a novel diagnostic method for cancer detection developed recently by Vedruccio. The diagnostic method is based on frequency selective absorption of electromagnetic waves by malignant tumors. Cancer is connected with mitochondrial malfunction (the Warburg effect) suggesting disrupted physical mechanisms. In addition to decreased energy conversion and nonutilized energy efflux, mitochondrial malfunction is accompanied by other negative effects in the cell. Diminished proton space charge layer and the static electric field around the outer membrane result in a lowered ordering level of cellular water and increased damping of microtubule-based cellular elastoelectrical vibration states. These changes manifest themselves in a dip in the amplitude of the signal with the fundamental frequency of the nonlinear microwave oscillator—the core of the diagnostic device—when coupled to the investigated cancerous tissue via the near-field. The dip is not present in the case of healthy tissue.     

Chronic stress in pregnant guinea pigs (<Emphasis Type="Italic">Cavia aperea f. porcellus</Emphasis>) attenuates long-term stress hormone levels and body weight gain,but not reproductive output

Stress, when extreme or chronic, can have a negative impact on health and survival of mammals. This is especially true for females during reproduction when self-maintenance and investment in offspring simultaneously challenge energy turnover. Therefore, we investigated the effects of repeated stress during early- and mid-gestation on the maternal stress axis, body weight gain and reproductive output. Female guinea pigs (Cavia aperea f. porcellus, n = 14) were either stressed (treatment: exposure to strobe light in an unfamiliar environment on gestational day -7, 0, 7, 14, 21, 28, 35, 42) or left completely undisturbed (control) throughout pregnancy. Females of both groups received the same respective diets, and reproductive parameters were evaluated upon parturition. Additionally, hormonal data were obtained from blood and feces. The stress exposure induced a significant increase in plasma cortisol concentrations during the afternoon. In contrast to this short-term response in plasma cortisol concentrations, we found no significant differences in the levels of cortisol metabolites in feces collected after stress exposure between groups and even significantly decreased levels of fecal cortisol metabolites on non-stress days over time in treatment females. Among treatment females, gain in body weight was attenuated over gestation and body weight was lower compared to control females during lactation, especially in cases of large litter sizes. No differences could be seen in the reproductive parameters. We conclude that repeated stress exposure with strobe light during early- and mid-gestation results in a down-regulation of the hypothalamic–pituitary–adrenal axis and lower weight gain in treatment females, but has no effect on reproductive output.     

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

New parameter sets of the GROMOS biomolecular force field, 54A7 and 54B7, are introduced. These parameter sets summarise some previously published force field modifications: The 53A6 helical propensities are corrected through new φ/ψ torsional angle terms and a modification of the N–H, C=O repulsion, a new atom type for a charged −CH₃ in the choline moiety is added, the Na⁺ and Cl⁻ ions are modified to reproduce the free energy of hydration, and additional improper torsional angle types for free energy calculations involving a chirality change are introduced. The new helical propensity modification is tested using the benchmark proteins hen egg-white lysozyme, fox1 RNA binding domain, chorismate mutase and the GCN4-p1 peptide. The stability of the proteins is improved in comparison with the 53A6 force field, and good agreement with a range of primary experimental data is obtained.     

Glucoamylases: structural and biotechnological aspects

Glucoamylases, one of the main types of enzymes involved in starch hydrolysis, are exo-acting enzymes that release consecutive glucose units from the non-reducing ends of starch molecules. Glucoamylases are microbial enzymes, present in bacteria, archaea, and fungi but not in plants and animals. Structurally, they are classified in family 15 of glycoside hydrolases and characterised by the invariable presence of a catalytic domain with (α/α)₆-fold, often bound to a non-catalytic domain of diverse origin and function. Fungal glucoamylases are biotechnologically very important as they are used industrially in large amounts and have been extensively studied during the past 30 years. Prokaryotic glucoamylases are of biotechnological relevance for being generally thermophilic enzymes, active at elevated temperatures.     

A model for dynamics of primer extension by eukaryotic DNA primase

A mathematical model is proposed for processive primer extension by eukaryotic DNA primase. The model uses available experimental data to predict rate constants for the dynamic behavior of primase activity as a function of NTP concentration. The model also predicts some data such as the binding affinities of the primase for the DNA template and for the RNA primer.     

The improvement of riboflavin production in <Emphasis Type="Italic">Ashbya gossypii</Emphasis> via disparity mutagenesis and DNA microarray analysis

We generated a high riboflavin-producing mutant strain of Ashbya gossypii by disparity mutagenesis using mutation of DNA polymerase δ in the lagging strand, resulting in loss of DNA repair function by the polymerase. Among 1,353 colonies generated in the first screen, 26 mutants produced more than 3 g/L of riboflavin. By the second screen and single-colony isolation, nine strains that produced more than 5.2 g/L of riboflavin were selected as high riboflavin-producing strains. These mutants were resistant to oxalic acid and hydrogen peroxide as antimetabolites. One strain (W122032) produced 13.7 g/L of riboflavin in a 3-L fermentor using an optimized medium. This represents a ninefold improvement on the production of the wild-type strain. Proteomic analysis revealed that ADE1, RIB1, and RIB5 proteins were expressed at twofold higher levels in this strain than in the wild type. DNA microarray analysis showed that purine and riboflavin biosynthetic pathways were upregulated, while pathways related to carbon source assimilation, energy generation, and glycolysis were downregulated. Genes in the riboflavin biosynthetic pathway were significantly overexpressed during both riboflavin production and stationary phases, for example, RIB1 and RIB3 were expressed at greater than sixfold higher levels in this strain compared to the wild type. These results indicate that the improved riboflavin production in this strain is related to a shift in carbon flux from β-oxidation to the riboflavin biosynthetic pathway.     

Overcoming substrate inhibition during biological treatment of monoaromatics: recent advances in bioprocess design

The biological removal of monoaromatic compounds from contaminated environments, usually arising from industrial activity, is challenging because of the inherent toxicity of these compounds to microorganisms, particularly at the concentrations that can be encountered in industrial waste streams. A wide range of bioprocess designs have been proposed and tested with the aim of achieving high removal efficiencies, with varying degrees of technical success, and potential for practical implementation. This review reports on the progress on variations of well-known themes made in the last 3–4 years, as well as new bioprocess technologies that address the cytotoxicity of monoaromatics directly. Areas for further research are also proposed.     

Effects of a defective ERAD pathway on growth and heterologous protein production in <Emphasis Type="Italic">Aspergillus niger</Emphasis>

Endoplasmic reticulum associated degradation (ERAD) is a conserved mechanism to remove misfolded proteins from the ER by targeting them to the proteasome for degradation. To assess the role of ERAD in filamentous fungi, we have examined the consequences of disrupting putative ERAD components in the filamentous fungus Aspergillus niger. Deletion of derA, doaA, hrdC, mifA, or mnsA in A. niger yields viable strains, and with the exception of doaA, no significant growth phenotype is observed when compared to the parental strain. The gene deletion mutants were also made in A. niger strains containing single- or multicopies of a glucoamylase–glucuronidase (GlaGus) gene fusion. The induction of the unfolded protein response (UPR) target genes (bipA and pdiA) was dependent on the copy number of the heterologous gene and the ERAD gene deleted. The highest induction of UPR target genes was observed in ERAD mutants containing multiple copies of the GlaGus gene. Western blot analysis revealed that deletion of the derA gene in the multicopy GlaGus overexpressing strain resulted in a 6-fold increase in the intracellular amount of GlaGus protein detected. Our results suggest that impairing some components of the ERAD pathway in combination with high expression levels of the heterologous protein results in higher intracellular protein levels, indicating a delay in protein degradation.