In vivo crystal formation in Escherichia coli of an over-expressed soluble form of penicillin-binding protein 5

Accumulation of either native membrane-bound or soluble variants of PBP5 over-expressed in the cytoplasm was investigated by electron microscopy of ultra-thin sections. One of the soluble forms of PBP5 (PBP5s353) formed well-ordered crystals inside the cells. Cells sectioned perpendicular to their long axis showed a diamond-shaped crystal whereas cells cut parallel to their long axis contained a long, narrow crystal. In both sectioning directions an ordered ultrastructure was visible as shown by optical diffraction. Computer processing was used to enhance the crystal images. From this the unit cell parameters were calculated as a = 7.6 nm, b = 4 nm, c = 4.2 nm, gamma = 75 degrees. The calculated unit-cell volume of 120 nm3 is large enough to contain one protein molecule.     

Base dynamics of nitroxide-labeled thymidine analogues incorporated into (dA-dT)n by DNA polymerase I from Escherichia coli

Nitroxide-labeled thymidine substrates (dL) for Escherichia coli DNA polymerase I (pol I) were used to synthesize spin-labeled alternating double-stranded copolymers with (dA-dT)n as a template. All dL substrates use an alkane or alkene tether substituted into the 5-position of the pyrimidine ring to link a five- or six-membered ring nitroxide to the pyrimidine base. The kinetics of dL incorporation show some tether dependence with respect to tether length and tether geometry. The electron spin resonance (ESR) spectra of (dA-dT,dL)n duplexes directly formed by polymerization with pol I are compared with the ESR spectra of (dA)n(dT,dL)n duplexes, which are obtained after annealing of nitroxide-labeled single strands with complementary unlabeled single strands. The ESR spectra indicate that nitroxide-labeled analogues with tethers short enough to let the nitroxide ring reside in the major groove are excellent reporter groups for monitoring hybridization. A small difference between the ESR line shapes of the alternating duplexes (dA-dT,dL)n and the homopolymer duplexes (dA)n(dT,dL)n containing the same dL is detectable, suggesting the presence of subtle differences in the base dynamics between both systems. Computer simulation of the ESR spectra of the (dA-dT,dL)n duplexes was successful with the same motional model reported earlier [Kao, S.-C., & Bobst, A.M. (1985) Biochemistry 24, 5465-5469]. The thymidine motion arising from tilting and torsion of base pairs and base twisting in (dA-dT)n is similar to that in (dA)n(dT)n and is of the order of 4 ns.     

Evaluation of growth rate in adhering cell cultures using a simple colorimetric method

In this paper we present a simple colorimetric method for evaluating cell growth in adhering cell cultures. This technique is based on the staining of basophilic cellular compounds (mainly nucleic acids) with methylene blue. To check its reliability, we have compared the quantity of dye fixed by the cells with the number of cells released from the culture substratum by trypsinization, and with the total cellular protein content determined by the Lowry's method. In these experiments we have used human skin fibroblasts and human epithelial cells derived from the epithelium of the full-term umbilical cord. Like other alternative methods, the methylene blue colorimetric technique can be used in 96-well microplates and allows the rapid collection of large amounts of data. As an illustration, we report on the selection of optimal composition of culture medium for human skin fibroblasts.     

Mining oomycete proteomes for metalloproteases leads to identification of candidate virulence factors in Phytophthora infestans

Pathogens deploy a wide range of pathogenicity factors, including a plethora of proteases, to modify host tissue or manipulate host defences. Metalloproteases (MPs) have been implicated in virulence in several animal and plant pathogens. Here we investigated the repertoire of MPs in 46 stramenopile species including 37 oomycetes, 5 diatoms, and 4 brown algae. Screening their complete proteomes using hidden Markov models (HMMs) trained for MP detection resulted in over 4,000 MPs, with most species having between 65 and 100 putative MPs. Classification in clans and families according to the MEROPS database showed a highly diverse MP repertoire in each species. Analyses of domain composition, orthologous groups, distribution, and abundance within the stramenopile lineage revealed a few oomycete-specific MPs and MPs potentially related to lifestyle. In-depth analyses of MPs in the plant pathogen Phytophthora infestans revealed 91 MPs, divided over 21 protein families, including 25 MPs with a predicted signal peptide or signal anchor. Expression profiling showed different patterns of MP gene expression during pre-infection and infection stages. When expressed in leaves of Nicotiana benthamiana, 12 MPs changed the sizes of lesions caused by inoculation with P. infestans; with 9 MPs the lesions were larger, suggesting a positive effect on the virulence of P. infestans, while 3 MPs had a negative effect, resulting in smaller lesions. To the best of our knowledge, this is the first systematic inventory of MPs in oomycetes and the first study pinpointing MPs as potential pathogenicity factors in Phytophthora.     

A Neurocomputational Model of the Mismatch Negativity

The mismatch negativity (MMN) is an event related potential evoked by violations of regularity. Here, we present a model of the underlying neuronal dynamics based upon the idea that auditory cortex continuously updates a generative model to predict its sensory inputs. The MMN is then modelled as the superposition of the electric fields evoked by neuronal activity reporting prediction errors. The process by which auditory cortex generates predictions and resolves prediction errors was simulated using generalised (Bayesian) filtering – a biologically plausible scheme for probabilistic inference on the hidden states of hierarchical dynamical models. The resulting scheme generates realistic MMN waveforms, explains the qualitative effects of deviant probability and magnitude on the MMN – in terms of latency and amplitude – and makes quantitative predictions about the interactions between deviant probability and magnitude. This work advances a formal understanding of the MMN and – more generally – illustrates the potential for developing computationally informed dynamic causal models of empirical electromagnetic responses.     

Über die direkte und indirekte Strahlenwirkung auf Enzyme in der Zelle

Zusammenfassung Es wurde die Röntgenstrahleninaktivierung von Laktatdehydrogenase in Rattenleber und Invertase in Hefe untersucht. Die Inaktivierung war in den feuchten lebenden Zellen und in den getrockneten Zellen praktisch gleich, obwohl ein Beitrag der indirekten Strahlenwirkung in den feuchten Zellen zu erwarten war.Auszugsweise vorgetragen auf dem XI. Internationalen Kongreß für Radiologie, Rom, September 1965     

Population dose from natural radionuclides in phosphate fertilizers

Summary The natural radionuclide content of mineral phosphate fertilizers has been determined gammaspectrometrically. The investigations comprised ca. 70% of the mineral phosphate fertilizers authorized and used in the Federal Republic of Germany (FRG). At maximum, we found specific activities of 62 nCi U_nat/kg, 23 nCi²²⁶Ra/kg, 1.6 nCi Th_nat/kg and 262 nCi⁴⁰K/kg. The mean values, weighted by the percentual agricultural consumption of the main phosphate fertilizer groups in 1973/74 and related to the phosphate content, amounted to 58, 40, 2, and 584 nCi/kg P₂O₅ for U_nat,²²⁶Ra, Th_nat, and⁴⁰K respectively. This resulted in an annual distribution due to phosphate fertilizing of about 3.9 µCi U_nat, 2.7 µCi²²⁶Ra, 0.1 µCi Th_nat, and 39.9 µCi⁴⁰K per ha of arable or pasture land in 1973/74 on the average. From these values the air dose rates over agricultural areas have been estimated under extreme conservative assumptions resulting in an additional external exposure of members of the population of 0.02 mrd/a on the average and 0.4 mrd/a in the region of highest phosphate fertilizing intensity. If it is assumed that radium contained in phosphate fertilizers were completely accumulated in the soils during the last 80 years, this value would be raised to 0.3 mrd/a on the average. The occupational external radiation exposure due to natural radionuclides contained in phosphate fertilizers was estimated to be 0.1 mrd/a on the average and 2.3 mrd/a at maximum for persons working in agriculture. These estimates show that natural radionuclides in phosphate fertilizers contribute but very little to the mean terrestrial radiation exposure of the population which is 50 to 55 mrd/a in Germany. Only for the small group of persons working in fertilizer production plants or storehouses a significant increase of the external radiation exposure has to be expected which could reach a doubling of the mean natural exposure value.Dedicated to Prof. Dr. H. Muth on the occasion on his 60th birthday     

Tracking niche variation over millennial timescales in sympatric killer whale lineages

Niche variation owing to individual differences in ecology has been hypothesized to be an early stage of sympatric speciation. Yet to date, no study has tracked niche width over more than a few generations. In this study, we show the presence of isotopic niche variation over millennial timescales and investigate the evolutionary outcomes. Isotopic ratios were measured from tissue samples of sympatric killer whale Orcinus orca lineages from the North Sea, spanning over 10 000 years. Isotopic ratios spanned a range similar to the difference in isotopic values of two known prey items, herring Clupea harengus and harbour seal Phoca vitulina. Two proxies of the stage of speciation, lineage sorting of mitogenomes and genotypic clustering, were both weak to intermediate indicating that speciation has made little progress. Thus, our study confirms that even with the necessary ecological conditions, i.e. among-individual variation in ecology, it is difficult for sympatric speciation to progress in the face of gene flow. In contrast to some theoretical models, our empirical results suggest that sympatric speciation driven by among-individual differences in ecological niche is a slow process and may not reach completion. We argue that sympatric speciation is constrained in this system owing to the plastic nature of the behavioural traits under selection when hunting either mammals or fish.