Discovery and Investigation of Misincorporation of Serine at Asparagine Positions in Recombinant Proteins Expressed in Chinese Hamster Ovary Cells

Misincorporation of amino acids in proteins expressed in Escherichia coli has been well documented but not in proteins expressed in mammalian cells under normal recombinant protein production conditions. Here we report for the first time that Ser can be incorporated at Asn positions in proteins expressed in Chinese hamster ovary cells. This misincorporation was discovered as a result of intact mass measurement, peptide mapping analysis, and tandem mass spectroscopy sequencing. Our analyses showed that the substitution was not related to specific protein molecules or DNA codons and was not site-specific. We believe that the incorporation of Ser at sites coded for Asn was due to mischarging of tRNA^Asn rather than to codon misreading. The rationale for substitution of Asn by Ser and not by other amino acids is also discussed. Further investigation indicated that the substitution was due to the starvation for Asn in the cell culture medium and that the substitution could be limited by using the Asn-rich feed. These observations demonstrate that the quality of expressed proteins should be closely monitored when altering cell culture conditions.     

Pollen concentration analysis of Ancestral Pueblo dietary variation

Previous coprolite research on the Colorado Plateau has shown that macrofossils are a useful way of statistically demonstrating prehistoric dietary variation of Ancestral Pueblos (Anasazi). Up until now, pollen concentration from human coprolites has not been used for comparative, statistical study. We present here the statistical analysis of pollen concentration values of coprolites from two Ancestral Pueblo sites, Salmon Ruin and Antelope House. The data show that although most pollen types do not show statistically significant variation, there are some types that show how different Ancestral Pueblo populations adapted to plant resources in different environments. The analysis indicates that future work should focus more on pollen concentration analysis of coprolites.     

A nanocompartment system (Synthosome) designed for biotechnological applications

A nanocompartment system based on two deletion mutants of the large channel protein FhuA (FhuA Delta1-129; FhuA Delta1-160) and an ABA triblock copolymer (PMOXA-PDMS-PMOXA) has been developed for putative biotechnological applications. FhuA is ideally suited for applications in biotechnology due to its monomeric structure, large pore diameter (39-46 A elliptical cross-section) that ensures rapid compound flux, and solved crystallographic structure. Two areas of application were targeted as proof of principle: (A) selective product recovery in nanocompartments and (B) enzymatic conversion in nanocompartments. Selective recovery of negatively charged compounds has been achieved on the example of sulforhodamine B by using positively charged polylysine molecules as trap inside the nanocompartment. Conversion in nanocompartments has been achieved by 3,3',5,5'-tetramethylbenzidine oxidation employing horseradish peroxidase (HRP).     

Increased field resistance to Tilletia caries provided by a specific antifungal virus gene in genetically engineered wheat

The field performance of a viral gene in two Swiss wheat ( Triticum aestivum ) varieties showed 10% increased fungal resistance against Tilletia caries (stinking smut). To the best of our knowledge, this is the first report of improved resistance against any fungus in the field achieved by genetic engineering in wheat. The genetically modified wheat lines previously showed a c . 30% decrease in symptoms of T. caries in the glasshouse (Clausen, M., Kräuter, R., Schachermayr, G., Potrykus, I. and Sautter, C. (2000) Antifungal activity of a virally encoded gene in transgenic wheat. Nat. Biotechnol . 18 , 446–449), depending on the fungal strain inoculated. A glasshouse experiment run in parallel to the field test, and using the same collection of T. caries , gave the same results. In a dose–response experiment with isolated fungal strains, in which the infection pressure was varied via the spore concentration, the transgene behaved as a quantitative resistance gene and shifted the S-shaped dose–response curve towards higher resistance. The transgene was shown to be highly specific for fungi of the order Ustilaginales. Tests of the transgene using cell cultures of eukaryotes, including hamster and human, showed no significant side-effects with respect to biosafety. Endogenous pathogen-related genes were also activated on fungal infection in the presence of the kp4 transgene.     

Systematic in vivo RNAi analysis of putative components of the Drosophila cell death machinery

Despite the identification of numerous key players of the cell death machinery, little is known about their physiological role. Using RNA interference (RNAi) in vivo, we have studied the requirement of all Drosophila caspases and caspase-adaptors in different paradigms of apoptosis. Of the seven caspases, Dronc, drICE, Strica and Decay are rate limiting for apoptosis. Surprisingly, Hid-mediated apoptosis requires a broader range of caspases than apoptosis initiated by loss of the caspase inhibitor DIAP1, suggesting that Hid causes apoptosis not only by antagonizing DIAP1 but also by activating DIAP1-independent caspase cascades. While Hid killing requires Strica, Decay, Dronc/Dark and drICE, apoptosis triggered by DIAP1 depletion merely relied upon Dronc/Dark and drICE. Furthermore, we found that overexpression of DIAP2 can rescue diap1-RNAi-mediated apoptosis, suggesting that DIAP2 regulates caspases directly. Consistently, we show that DIAP2 binds active drICE. Since DIAP2 associates with Hid, we propose a model whereby Hid co-ordinately targets both DIAP1 and DIAP2 to unleash drICE.     

Persistent inhibition of FLIPL expression by lentiviral small hairpin RNA delivery restores death-receptor-induced apoptosis in neuroblastoma cells

Neuroblastoma represents the most common and deadly solid tumour of childhood, which disparate biological and clinical behaviour can be explained by differential regulation of apoptosis. To understand mechanisms underlying death resistance in neuroblastoma cells, we developed small hairpin of RNA produced by lentiviral vectors as tools to selectively interfere with FLIP_L, a major negative regulator of death receptor-induced apoptosis. Such tools revealed highly efficient in interfering with FLIP_L expression and function as they almost completely repressed endogenous and/or exogenously overexpressed FLIP_L protein and fully reversed FLIP_L-mediated TRAIL resistance. Moreover, interference with endogenous FLIP_L and FLIP_S significantly restored FasL sensitivity in SH-EP neuroblastoma cell line. These results reveal the ability of lentivirus-mediated shRNAs to specifically and persistently interfere with FLIP expression and support involvement of FLIP in the regulation of death receptor-mediated apoptosis in neuroblastoma cells. Combining such tools with other therapeutic modalities may improve treatment of resistant tumours such as neuroblastoma.     

Rapid typing of Moraxella catarrhalis subpopulations based on outer membrane proteins using mass spectrometry

Moraxella catarrhalis is a major mucosal pathogen of the human respiratory tract both in children and in adults. Two subpopulations of this organism have been described that differ in 16S rRNA gene sequence and virulence traits. Three 16S rRNA types have been defined. 2-DE followed by protein identification by MS revealed significant differences in the outer membrane protein (OMP) patterns of each M. catarrhalis 16S rRNA type. Approximately 130 features were detected on the 2-DE map of each M. catarrhalis 16S rRNA type. However, only 50 features were expressed by all strains. Furthermore, direct profiling of isolated OMP using MALDI-TOF MS resulted in a characteristic spectral fingerprint for each 16S rRNA type. Fingerprints remained identical when intact cells instead of isolated OMP were analyzed. This finding suggests that the source of desorbed ions is the outer membrane. Based on the fingerprint we were able to assign 18 well-characterized clinical M. catarrhalis isolates to the correct subpopulation. Therefore, MALDI-TOF of intact M. catarrhalis provides a rapid and robust tool for M. catarrhalis strain typing that could be applied in epidemiological studies.     

Unveiling electrotransformation of Moraxella catarrhalis as a process of natural transformation

The human respiratory tract pathogen Moraxella catarrhalis is a naturally competent microorganism. However, electrotransformation has long been used to introduce foreign DNA into this organism. This study demonstrated that electrotransformants obtained with linear or circular nonreplicating plasmid DNA originated exclusively from natural transformation processes taking place during the recovery phase after the application of current. Only replicating plasmid DNA could be introduced into M. catarrhalis by electrotransformation, in a type IV pilus-independent manner. Electrotransformation with homologous genomic DNA indicated that restriction of double-stranded DNA was independent of type III restriction-methylation systems. Nontransformability of M. catarrhalis by electrotransformation was observed using double- as well as single-stranded DNA. In addition, the study showed that natural competence is a very constant feature of M. catarrhalis.     

Gender dependency of circadian blood pressure and heart rate profiles in spontaneously hypertensive rats: effects of beta-blockers

This study investigated (i) blood pressure (BP), heart rate (HR), and their relation to urinary NOx and eNOS protein expression in male and female spontaneously hypertensive rats (SHR), as well as (ii) gender-dependent cardiovascular effects of nebivolol (NEB) in comparison to metoprolol (MET) in SHR. BP and HR were measured telemetrically after a single intraperitoneal application of NEB or MET at 07.00 and 19.00 h in male rats and at 19.00 h in proestrus female rats. The two β-blockers varied in time of decreasing BP and HR and also in duration. In males, MET decreased BP and HR for few hours exclusively when applied at the onset of the activity phase (i.e., at 19.00 h), while after its application at 07.00 h, BP and HR were unchanged. In females, MET also caused a short-lasting BP and HR reduction, with the effect being more pronounced than in males. In males, NEB at either dosing time decreased HR and BP to a greater extent than did MET. This effect was evident both during the activity and rest periods and persisted for at least five days. In females, NEB provoked a similar, but more pronounced, effect on BP and HR in comparison to males. These findings demonstrate that significant gender-dependent differences in the circadian profile of BP and HR exist. BP and urinary NOx as well as eNOS expression are inversely correlated, and the cardiovascular effects of NEB and MET vary, depending on the time of application as well as gender.     

Statistical analysis of intrahelical ionic interactions in alpha-helices and coiled coils

There are many controversies concerning whether ionic interactions in alpha-helices and coiled coils actually contribute to the stabilisation and formation of these structures. Here we used a statistical approach to probe this question. We extracted unique alpha-helical and coiled coil structures from the protein database and analysed the ionic interactions between positively and negatively charged residues. The ionic interactions were categorized according to the type, spacing and order of the residues involved. Separate datasets were produced depending on the number of alpha-helices in the coiled coils and the mutual orientation of the helices. We compared the frequency of residue configurations able to form ionic interactions with their probability to form the interaction. We found a correlation between the two variables in alpha-helices, antiparallel two-stranded coiled coils and parallel two-stranded coiled coils. This indicates that some ionic interactions are indeed important for the formation and stabilisation of alpha-helices and coiled coils. We concluded that the configurations, which have simultaneously a large probability to form the ionic interaction and a frequent occurrence, are those, which have the most stabilising effect. These are the 4RE, 3ER and 4ER interactions.