Impact of the cold shock phenomenon on quantification of intracellular metabolites in bacteria

In the present work the effect of quenching on quantification of intracellular metabolites in Corynebacterium glutamicum was investigated. C. glutamicum showed a high sensitivity to cold shock. Quenching of the cells by -50 degrees C buffered methanol prior to cell separation and extraction led to drastically reduced concentrations for free intracellular amino acids compared to those for nonquenched filtration. As demonstrated for glutamate and glutamine, this was clearly due to a more than 90% loss of these compounds from the cell interior into the medium during quenching. With lower methanol concentration in the quenching solution the metabolic losses were significantly lower but still amounted to about 30%. Due to the fact that quenching with ice-cold NaCl (0.9%) also resulted in significantly lower pool sizes for intracellular amino acids, a basic cold shock phenomenon is most likely the reason for the observed effects. The results clearly demonstrate that quenching combined with cell separation for concentration of the cells and removal of the medium is not applicable for intracellular metabolite analysis in C. glutamicum. Sampling by quick filtration without quenching allows complete cell separation and authentic quantification of intracellular metabolite pools exhibiting time constants significantly larger than sampling time.     

Review: Minibioreactors

The performance of currently available minibioreactors with volumes below about 100 ml is reviewed. Bioreactors are characterized by their area of application, by mass transfer and mixing characteristics and by their suitability for on-line monitoring and control. The review comprises shaken bioreactors such as shake-flasks, microtiter plates and test-tubes, stirred bioreactors including spinner-flasks for the cultivation of mammalian cells and various special reactors particularly involving on-line monitoring as e.g. membrane inlet mass spectrometry and NMR.     

On-line oxygen uptake rate and culture viability measurement of animal cell culture using microplates with integrated oxygen sensors

O2 uptake rates of animal cells (Chinese hamster ovary-CHO) were measured in 96-well microtiter plates by integrating with fluorescent sensors thereby measuring fluorescence intensity ratios of an O2-sensitive and an insensitive fluorophor. O2 consumption rate was estimated from measured dissolved O2 and from O2 mass transfer coefficient determined in advance. Specific uptake decreased with time from 3.2 x 10(-13) mol O2 cell(-1) h(-1) at 15 h cultivation to 1.8 x 10(-13) mol O2 cell(-1) h(-1) at 48 h. Specific O2 uptake was also determined by sampling from a spinner-flask culture giving identical values. A cell viability assay for cultures based on O2 measurements is described in which cells are incubated outside the fluorescence reader and then the dissolved O2 is measured only once at a fixed time after the start of incubation. This protocol can be directly applied for high-throughput measurements.     

Photochemical genotoxicity: principles and test methods. Report of a GUM task force

In recent years, assessing the photogenotoxic potential of a compound became an issue for certain drugs and cosmetical products. Therefore, existing methods performed according to international guidelines (e.g. OECD guidelines) were adapted to the use of concurrent UV-visible (UV-Vis) light irradiation for the assessment of photomutagenicity/photogenotoxicity. In this review, photobiological bases of the processes occurring in the cell after irradiation with UV- and/or visible (vis)-light as well as a compilation of testing methods is presented. Methods comprise cell free investigations on naked DNA and in vitro methods, such as the photo-Ames test, the photo-HPRT/photo-mouse lymphoma assay (MLA), the photo-micronucleus test (MNT), the photo-chromosomal aberration test (CA) and the photo-Comet assay. A compilation of the currently available international literature of compounds tested on photogenotoxicity is given for each method. The state of the art of photogenotoxicity testing as well as the rational for testing are outlined in relation to the recommendations reached in expert working groups at different international meetings and to regulatory guidance papers. Finally, photogenotoxicity testing as predictor of photocarcinogenicity and in the light of risk assessment is discussed.     

Identification and molecular modelling of a mutation in the motor head domain of myosin VIIA in a family with autosomal dominant hearing impairment (DFNA11)

Myosin VIIA is an unconventional myosin that has been implicated in Usher syndrome type 1B, atypical Usher syndrome, non-syndromic autosomal recessive hearing impairment (DFNB2) and autosomal dominant hearing impairment (DFNA11). Here, we present a family with non-syndromic autosomal dominant hearing impairment that clinically resembles the previously published DFNA11 family. The affected family members show a flat audiogram at young ages and only modest progression, most clearly at the high frequencies. In addition, they suffer from minor vestibular symptoms. Linkage analysis yielded a maximum two-point lodscore of 3.43 for marker D11S937 located within 1 cM of the myosin VIIA gene. The myosin VIIA gene was sequenced and 11 nucleotide variations were found. Ten nucleotide changes represent benign intronic variants, silent exon mutations or non-pathologic amino acid substitutions. One variant, a c.1373AT transversion that is heterozygously present in all affected family members and absent in 300 healthy individuals, is predicted to result in an Asn458Ile amino acid substitution. Asn458 is located in a region of the myosin VIIA motor domain that is highly conserved in different classes of myosins and in myosins of different species. To evaluate whether the Asn458Ile mutation was indeed responsible for the hearing impairment, a molecular model of myosin VIIA was built based on the known structure of the myosin II heavy chain from Dictyostelium discoideum. In this model, conformational changes in the protein caused by the amino acid substitution Asn458Ile are predicted to disrupt ATP/ADP binding and impair the myosin power-stroke, which would have a severe effect on the function of the myosin VIIA protein.     

Inositol 1,4,5-trisphosphate and its co-players in the concert of Ca2+ signalling--new faces in the line up

Release of Ca2+ from intracellular stores can occur by different intracellular messengers such as InsP3, cADPR and NAADP. Although in some cells messengers may operate on different stores, there are also Ca2+ stores with sensitivities for all three of these messengers. It is well documented, that InsP3- and cADPR-sensitive Ca2+ stores are involved in the activation of "store-operated Ca2+ channels" (SOCC). It has not yet been unequivocally shown, however, if Ca2+ release from stores, which respond to NAADP but not to InsP3 or cADPR, also generate signals which lead to "store-operated Ca2+ entry". Neither localization nor the mechanism of coupling to the plasma membrane of those InsP3- and cADPR-sensitive Ca2+ stores which activate SOCCs is yet clear. In this review localization and properties of InsP3-, cADPR- and NAADP-sensitive Ca2+ pools and their mutual interactions are discussed. Differential sensitivities of Ca2+ release mechanisms to InsP3, cADPR and NAADP have consequences on Ca2+ release, Ca2+ oscillations, propagation of Ca2+ waves and on activation of SOCC. Possible interaction of InsP3R and cADPR with candidates of SOCCs (TRP channels) and mechanisms involved in the regulation of SOCCs (activation-deactivation) will be elaborated.     

A Rhizobium leguminosarum lipopolysaccharide lipid-A mutant induces nitrogen-fixing nodules with delayed and defective bacteroid formation

Lipopolysaccharides from pea-nodulating strain Rhizobium leguminosarum by. viciae 3841, as all other members of the family Rhizobiaceae with the possible exception of Azorhizobium caulinodans, contains a very long chain fatty acid; 27-hydroxyoctacosanoic acid (27OHC28:0) in its lipid A region. The exact function and importance of this residue, however, is not known. In this work, a previously constructed mutant, Rhizobium leguminosarum by. viciae 22, deficient in the fatty acid residue, was analyzed for its symbiotic phenotype. While the mutant was able to form nitrogen-fixing nodules, a detailed study of the timing and efficiency of nodulation using light and electron microscopy showed that there was a delay in the onset of nodulation and nodule tissue invasion. Further, microscopy showed that the mutant was unable to differentiate normally forming numerous irregularly shaped bacteroids, that the resultant mature bacteroids were unusually large, and that several bacteroids were frequently enclosed in a single symbiosome membrane, a feature not observed with parent bacteroids. In addition, the mutant nodules were delayed in the onset of nitrogenase production and showed reduced nitrogenase throughout the testing period. These results imply that the lack of 27OHC28:0 in the lipid A in mutant bacteroids results in altered membrane properties that are essential for the development of normal bacteroids.     

Messenger RNA turnover in eukaryotes: pathways and enzymes

The control of mRNA degradation is an important component of the regulation of gene expression since the steady-state concentration of mRNA is determined both by the rates of synthesis and of decay. Two general pathways of mRNA decay have been described in eukaryotes. Both pathways share the exonucleolytic removal of the poly(A) tail (deadenylation) as the first step. In one pathway, deadenylation is followed by the hydrolysis of the cap and processive degradation of the mRNA body by a 5' exonuclease. In the second pathway, the mRNA body is degraded by a complex of 3' exonucleases before the remaining cap structure is hydrolyzed. This review discusses the proteins involved in the catalysis and control of both decay pathways.     

Metabolic network simulation using logical loop algorithm and Jacobian matrix

A novel method to accomplish efficient numerical simulation of metabolic networks for flux analysis was developed. The only inputs required are the set of stoichiometric balances and the atom mapping matrices of all components of the reaction network. The latter are used to automatically calculate isotopomer mapping matrices. Using the symbolic toolbox of MATLAB the analytical solution of the stoichiometric balance equation system, isotopomer balances and the analytical Jacobian matrix of the total set of stoichiometric and isotopomer balances are created automatically. The number of variables in the isotopomer distribution equation system is significantly reduced applying modified isotopomer mapping matrices. These allow lumping of several consecutive isotopomer reactions into a single one. The solution of the complete system of equations is improved by implementing an iterative logical loop algorithm and using the analytical Jacobian matrix. This new method provided quick and robust convergence to the root of such equation systems in all cases tested. The method was applied to a network of lysine producing Corynebacterium glutamicum. The resulting equation system with the dimension of 546 x 546 was directly derived from 12 isotopomer balance equations. The results obtained yielded identical labeling patterns for metabolites as compared to the relaxation method.