Synthesis of [6″-H]-, (6″-H)- and (2-H)-maltotriose

To prepare labeled precursors for biosynthetic studies, methods for the specific introduction of tritium and deuterium into the reducing and the terminal glucose unit of maltotriose were developed. Thus [6″-³H]- and (6″-²H)-maltotriose (17) and (18) were prepared via selective methoxytritylation, deprotection and subsequent modified Pfitzner-Moffatt oxidation, followed by reduction with sodium borotritiide or sodium borodeuteride, respectively. A simple two step procedure utilizing the Lobry de Bruyn/van Ekenstein transformation gave (2-²H)maltotriose (20).     

Involvement of T6 pili in biofilm formation by serotype M6 Streptococcus pyogenes

The group A streptococcus (GAS) Streptococcus pyogenes is known to cause self-limiting purulent infections in humans. The role of GAS pili in host cell adhesion and biofilm formation is likely fundamental in early colonization. Pilus genes are found in the FCT (fibronectin-binding protein, collagen-binding protein, and trypsin-resistant antigen) genomic region, which has been classified into nine subtypes based on the diversity of gene content and nucleotide sequence. Several epidemiological studies have indicated that FCT type 1 strains, including serotype M6, produce large amounts of monospecies biofilm in vitro. We examined the direct involvement of pili in biofilm formation by serotype M6 clinical isolates. In the majority of tested strains, deletion of the tee6 gene encoding pilus shaft protein T6 compromised the ability to form biofilm on an abiotic surface. Deletion of the fctX and srtB genes, which encode pilus ancillary protein and class C pilus-associated sortase, respectively, also decreased biofilm formation by a representative strain. Unexpectedly, these mutant strains showed increased bacterial aggregation compared with that of the wild-type strain. When the entire FCT type 1 pilus region was ectopically expressed in serotype M1 strain SF370, biofilm formation was promoted and autoaggregation was inhibited. These findings indicate that assembled FCT type 1 pili contribute to biofilm formation and also function as attenuators of bacterial aggregation. Taken together, our results show the potential role of FCT type 1 pili in the pathogenesis of GAS infections.     

ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway

The N-end rule degradation pathway states that the half-life of a protein is determined by the nature of its N-terminal residue. In Escherichia coli the adaptor protein ClpS directly interacts with destabilizing N-terminal residues and transfers them to the ClpA/ClpP proteolytic complex for degradation. The crucial role of ClpS in N-end rule degradation is currently under debate, since ClpA/ClpP was shown to process selected N-terminal degrons harbouring destabilizing residues in the absence of ClpS. Here, we investigated the contribution of ClpS to N-end rule degradation by two approaches. First, we performed a systematic mutagenesis of selected N-degron model substrates, demonstrating that ClpS but not ClpA specifically senses the nature of N-terminal residues. Second, we identified two natural N-end rule substrates of E. coli : Dps and PATase (YgjG). The in vivo degradation of both proteins strictly relied on ClpS, thereby establishing the function of ClpS as the essential discriminator of the E. coli N-end rule pathway.     

Antimicrobial Efficacy of Surface-Coated External Fixation Pins

In clinical applications, colonization of metal implants by adhesive and biofilm-forming bacteria not only prolong healing but create additional healthcare costs for implant revision and antimicrobial treatment. An in vitro assay was established investigating the antimicrobial surface activity of external fixation pins intended for use in bone fractures and deformities. Test articles made out of stainless steel and coated with a polymer-containing nanoparticulate silver were compared to non-coated reference controls out of stainless steel, copper and titanium. Staphylococcus epidermidis, known as a predominant cause for implant-related infections was used as test organism. Test pins and bacteria were incubated for a period of 20 h found to be sufficient for initiating biofilm formation. After removing non- and low-adherent bacteria by rinsing, two methods were used to isolate high-adherent (sessile) bacteria from the implant surfaces. Besides shaking the implants in a solution containing small glass beads, a cytobrush technique was used to mechanically harvest viable bacteria. Finally, the amount of detached bacteria was determined by plate counts. Several parameters identified to be critical within the different removal procedures such as the inoculum concentration and the shaking time in the presence of glass beads as well as time of the cytobrush treatment were analysed. The final test scheme resulted in the use of an inoculum of 10⁵ colony forming units (CFU) per millilitre, ten rinsing steps for the removal of low adherent bacteria and 5 min of shaking in the presence of glass beads, detaching the high-adherent bacteria. Due to subjective variations impacting the outcome of the procedure, the cytobrush technique was not favoured and finally rejected. Using the in vitro assay developed, it could be demonstrated that fixation pins coated with silver show a 3 log step reduction in the number of biofilm-forming bacteria compared to a non-coated stainless steel or titanium implant. Pins made out of copper showed the highest antimicrobial efficacy, as the number of detached bacteria was found to be below the detection limit, they served as a positive control within this test.     

The transient receptor potential family of ion channels

The transient receptor potential (TRP) multigene superfamily encodes integral membrane proteins that function as ion channels. Members of this family are conserved in yeast, invertebrates and vertebrates. The TRP family is subdivided into seven subfamilies: TRPC (canonical), TRPV (vanilloid), TRPM (melastatin), TRPP (polycystin), TRPML (mucolipin), TRPA (ankyrin) and TRPN (NOMPC-like); the latter is found only in invertebrates and fish. TRP ion channels are widely expressed in many different tissues and cell types, where they are involved in diverse physiological processes, such as sensation of different stimuli or ion homeostasis. Most TRPs are non-selective cation channels, only few are highly Ca²⁺ selective, some are even permeable for highly hydrated Mg²⁺ ions. This channel family shows a variety of gating mechanisms, with modes of activation ranging from ligand binding, voltage and changes in temperature to covalent modifications of nucleophilic residues. Activated TRP channels cause depolarization of the cellular membrane, which in turn activates voltage-dependent ion channels, resulting in a change of intracellular Ca²⁺ concentration; they serve as gatekeeper for transcellular transport of several cations (such as Ca²⁺ and Mg²⁺), and are required for the function of intracellular organelles (such as endosomes and lysosomes). Because of their function as intracellular Ca²⁺ release channels, they have an important regulatory role in cellular organelles. Mutations in several TRP genes have been implicated in diverse pathological states, including neurodegenerative disorders, skeletal dysplasia, kidney disorders and pain, and ongoing research may help find new therapies for treatments of related diseases.     

MGMT: key node in the battle against genotoxicity, carcinogenicity and apoptosis induced by alkylating agents

O(6)-methylguanine-DNA methyltransferase (MGMT) plays a crucial role in the defense against alkylating agents that generate, among other lesions, O(6)-alkylguanine in DNA (collectively termed O(6)-alkylating agents [O(6)AA]). The defense is highly important, since O(6)AA are common environmental carcinogens, are formed endogenously during normal cellular metabolism and possibly inflammation, and are being used in cancer therapy. O(6)AA induced DNA damage is subject to repair, which is executed by MGMT, AlkB homologous proteins (ABH) and base excision repair (BER). Although this review focuses on MGMT, the mechanism of repair by ABH and BER will also be discussed. Experimental systems, in which MGMT has been modulated, revealed that O(6)-methylguanine (O(6)MeG) and O(6)-chloroethylguanine are major mutagenic, carcinogenic, recombinogenic, clastogenic and killing lesions. O(6)MeG-induced clastogenicity and cell death require MutS alpha-dependent mismatch repair (MMR), whereas O(6)-chloroethylguanine-induced killing occurs independently of MMR. Extensive DNA replication is required for O(6)MeG to provoke cytotoxicity. In MGMT depleted cells, O(6)MeG induces apoptosis almost exclusively, barely any necrosis, which is presumably due to the remarkable ability of secondarily formed DNA double-strand breaks (DSBs) to trigger apoptosis via ATM/ATR, Chk1, Chk2, p53 and p73. Depending on the cellular background, O(6)MeG activates both the death receptor and the mitochondrial apoptotic pathway. The inter-individual expression of MGMT in human lymphocytes is highly variable. Given the key role of MGMT in cellular defense, determination of MGMT activity could be useful for assessing a patient's drug sensitivity. MGMT is expressed at highly variable amounts in human tumors. In gliomas, a correlation was found between MGMT activity, MGMT promoter methylation and response to O(6)AA. Although the human MGMT gene is inducible by glucocorticoids and genotoxins such as radiation and alkylating agents, the role of this induction in the protection against carcinogens and the development of chemotherapeutic alkylating drug resistance are still unclear. Modulation of MGMT expression in tumors and normal tissue is currently being investigated as a possible strategy for improving cancer therapy.     

The extent and significance of petroleum hydrocarbon contamination in Crater Lake,Oregon

In order to evaluate hydrocarbon inputs to Crater Lake from anthropogenic and natural sources, samples of water, aerosol, surface slick and sediment were collected and analyzed by gas chromatography-mass spectrometry (GC-MS) for determination of their aliphatic and aromatic hydrocarbon concentrations and compositions. Results show that hydrocarbons originate from both natural (terrestrial plant waxes and algae) and anthropogenic (petroleum use) sources and are entering the lake through direct input and atmospheric transport. The concentrations of petroleum hydrocarbons range from low to undetectable. The distributions and abundances of n-alkanes, polycyclic aromatic hydrocarbons (PAH) and unresolved complex mixture (UCM) from petroleum are similar for all surface slick sampling sites. The estimated levels of PAH in surface slicks range from 7–9 ng/m² which are low. Transport of petroleum-derived hydrocarbons from the lake surface has resulted in their presence in some sediments, particularly near the boat operations mooring (total petroleum HC = 1440 μg/kg, dry wt. compared to naturally derived n-alkanes, 240 μg/kg, dry wt.). The presence of biomarkers such as the tricyclic terpanes, hopanes and steranes in shallow sediments further confirms petroleum input from boat traffic. In the deep lake sediments, petroleum hydrocarbon concentrations were very low (16 μg/kg, dry wt.). Very low concentrations of PAH were detected in shallow sediments (17–40 μg/kg at 5 m depth near the boat operations) and deep sediments (3–15 μg/kg at 580 m depth). The individual PAH concentrations in sediments (μg/kg or ppb range) are at least three orders of magnitude less than reported threshold effects levels (mg/kg or ppm range, test amphipod Hyalella azteca). Therefore, no adverse effects are expected to occur in benthic biota exposed to these sediments. Boating activities are leaving a detectable level of petroleum in surface waters and lake sediments but these concentrations are very low.     

Proteome analysis of rat liver mitochondria reveals a possible compensatory response to endotoxic shock

Organ failure induced by endotoxic shock has recently been associated with affected mitochondrial function. In this study, effects of in vivo lipopolysaccharide-challenge on protein patterns of rat liver mitochondria in treated animals versus controls were studied by two-dimensional electrophoresis (differential image gel electrophoresis). Significant upregulation was found for ATP-synthase alpha chain and superoxide dismutase [Mn]. Our data suggest that endotoxic shock mediated changes in the mitochondrial proteome contribute to a compensatory reaction (adaptation to endotoxic shock) rather than to a mechanism of cell damage.     

Decimal Place Slope,A Fast and Precise Method for Quantifying 13C Incorporation Levels for Detecting the Metabolic Activity of Microbial Species

The metabolic incorporation of stable isotopes such as ¹³C or ¹⁵N into proteins has become a powerful tool for qualitative and quantitative proteome studies. We recently introduced a method that monitors heavy isotope incorporation into proteins and presented data revealing the metabolic activity of various species in a microbial consortium using this technique. To further develop our method using an liquid chromatography (LC)-mass spectrometry (MS)-based approach, we present here a novel approach for calculating the incorporation level of ¹³C into peptides by using the information given in the decimal places of peptide masses obtained by modern high-resolution MS. In the present study, the applicability of this approach is demonstrated using Pseudomonas putida ML2 proteins uniformly labeled via the consumption of [¹³C₆]benzene present in the medium at concentrations of 0, 10, 25, 50, and 100 atom %. The incorporation of ¹³C was calculated on the basis of several labeled peptides derived from one band on an SDS-PAGE gel. The accuracy of the calculated incorporation level depended upon the number of peptide masses included in the analysis, and it was observed that at least 100 peptide masses were required to reduce the deviation below 4 atom %. This accuracy was comparable with calculations of incorporation based on the isotope envelope. Furthermore, this method can be extended to the calculation of the labeling efficiency for a wide range of biomolecules, including RNA and DNA. The technique will therefore allow a highly accurate determination of the carbon flux in microbial consortia with a direct approach based solely on LC-MS.The metabolic incorporation of stable isotopes such as ¹³C or ¹⁵N into proteins has become a powerful component of qualitative and quantitative proteome studies (1). Incorporation of heavy isotopes can be used to analyze microbial processes such as turnover rates and also to help to establish structure-function relationships within microbial communities. Stable isotope probing (SIP¹) techniques based on DNA-SIP (2) and RNA-SIP (3) have been used for this purpose previously. With the introduction of protein-SIP (4), the need for an accurate alternative method for calculating label incorporation into biomolecules arose. Protein-SIP has several advantages compared with DNA/RNA-SIP, the most important being its capacity to detect dynamic levels of incorporation, whereas only labeled or unlabeled states can be categorized by means of DNA/RNA-SIP because of the need to separate ¹³C-DNA/RNA by density gradient centrifugation. Quantitative analysis of ¹³C incorporation levels is of the utmost importance, especially when unraveling carbon fluxes through either microbial communities or food webs with different trophic levels.In contrast to the incorporation of isotopically labeled amino acids, which is often used in quantitative proteomics (5), metabolic labeling by growth substrates and nutrients (e.g. salts) is often imperfect and makes the processing of mass spectrometry (MS) data difficult. For example, when the incorporation of ¹³C exceeds ∼2 atom %, common database search algorithms fail to identify peptides and proteins. The problem can only be managed successfully if a stable, known degree of ¹³C incorporation can be achieved during the experiment (6). Using a low labeling efficiency of roughly 5 atom %, Huttlin et al. (6) chose the altered envelope chain for calculating the incorporation and simultaneously used the signal intensity for a quantitative comparison with the sample that had a natural abundance of ¹³C. Database approaches for peptide identification can cope only with the natural abundance of carbon isotopes; they fail if the incorporation of ¹³C significantly exceeds the natural isotope abundance or if incorporation patterns occur in unpredictable ways (7).The simplest method for determining the incorporation level is to compare the unlabeled average mass of the monoisotopic peptide with the mass of the labeled protein, as estimated by matrix-assisted laser desorption/ionization or electrospray ionization MS (8, 9). A more advanced approach for determining the isotopic mass distribution of peptides is based on the isotopic distribution of the peaks of a peptide envelope (10, 11). Here, for a given isotopomer, the incorporation efficiency is defined as the percentage of incorporated ¹³C atoms with relation to the total number of carbon atoms with the natural isotope abundance (approximately 1.01 atom % ¹³C). As a reference, the theoretical isotopic distribution of a peptide is calculated based upon an algorithm described elsewhere (12). The isotope distribution of both unlabeled and labeled peptides can subsequently be used to calculate the incorporation level. For this method, an Excel spreadsheet (ProSIPQuant.xls) was developed (4). A similar approach, also based on the calculation of isotopic distributions, has been used in other studies (7). In these studies, however, the identification of the peptides is limited to those that have unlabeled counterparts; in addition, an exact calculation can be hampered by overlapping signals coming from additional peaks with similar masses.In the present study, we describe a new way of determining the isotope incorporation level. Our method makes use of characteristic patterns in the digits after the decimal point of the peptide masses generated by high-accuracy instruments such as the linear ion trap LTQ-Orbitrap (Thermo Fisher Scientific, Bremen, Germany). For tryptic peptides, typical regularities in the decimal places of the monoisotopic masses have been observed (13, 14). These observations have been explored in detail for theoretical and experimental data of proteins originating from Helicobacter pylori (15). As a result, a rule called the “half decimal place rule” (HDPR) was defined; it states that the decimal place is nearly half of the first digit for tryptic peptides with masses in the range of 500–1,000 Da. In other words, the exact mass of a peptide is equal to its nominal mass times ∼1.005. Because the difference between ¹²C and ¹³C is slightly greater than 1 Da, exactly 1.0033548378, the decimal places of a tryptic peptide''s mass are shifted in a regular manner by the incorporation level and lead to a significantly increased slope for the digits in the third and fourth place after the decimal point. This shift can be used to estimate the incorporation level of heavy isotopes into the protein. Detecting such shifts requires the highly accurate measurement possible with modern mass spectrometers such as the LTQ-Orbitrap, the Fourier transform ion cyclotron resonance, or the quadrupole time of flight. In this communication, we demonstrate the applicability of this approach using Pseudomonas putida ML2 proteins labeled uniformly via the consumption of [¹³C₆]benzene with five different substrate concentrations (0, 10, 25, 50, and 100 atom % of ¹³C). The ¹³C incorporation was calculated based on several labeled peptides derived from different proteins in one SDS-PAGE band. By these means, we have established a method that allows the determination of ¹³C incorporation into proteins and can be used to assess the metabolic activity of a given species within a mixed community.     

Exploration of environmental changes relates to lifestyle

Decision making in informed animals is often described by optimalitymodels. However, how information about an environment is acquiredis rarely investigated. Cost/benefit considerations suggestthat species differ in this respect according to their lifestyle.We tested the hypothesis that resident species react to changesin their familiar environment earlier and explore it more intensivelythan do nomadic species by observing the response to environmentalchanges (presentation of novel objects) in 10 parrot species.Phylogenetic relationships were taken into account. Residentstouched the novel objects significantly earlier and exploredmore objects than did nomads. In addition, species with a highproportion of fruits in their food spectrum explored more thandid species with other food preferences. The results are inaccordance with different costs and benefits of informationgathering for species that differ in their lifestyle and ecologicaldemands.