Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC-MS/MS data

The study of changes in protein levels between samples derived from cells representing different biological conditions is a key to the understanding of cellular function. There are two main methods available that allow both for global scanning for significantly varying proteins and targeted profiling of proteins of interest. One method is based on 2-D gel electrophoresis and image analysis of labelled proteins. The other method is based on LC-MS/MS analysis of either unlabelled peptides or peptides derived from isotopically labelled proteins or peptides. In this study, the non-labelling approach was used involving a new software, DeCyder MS Differential Analysis Software (DeCyder MS) intended for automated detection and relative quantitation of unlabelled peptides in LC-MS/MS data.Total protein extracts of E. coli strains expressing varying levels of dihydrofolate reductase and integron integrase were digested with trypsin and analyzed using a nanoscale liquid chromatography system, Ettan MDLC, online connected to an LTQTM linear ion-trap mass spectrometer fitted with a nanospray interface. Acquired MS data were subjected to DeCyder MS analysis where 2-D representations of the peptide patterns from individual LC-MS/MS analyses were matched and compared.This approach to unlabelled quantitative analysis of the E. coli proteome resulted in relative protein abundances that were in good agreement with results obtained from traditional methods for measuring protein levels.     

Nature and prevalence of combinations of mental disorders and their association with excess mortality in a population‐based cohort study

The nature and prevalence of combinations of mental disorders and their associations with premature mortality have never been reported in a comprehensive way. We describe the most common combinations of mental disorders and estimate excess mortality associated with these combinations. We designed a population‐based cohort study including all 7,505,576 persons living in Denmark at some point between January 1, 1995 and December 31, 2016. Information on mental disorders and mortality was obtained from national registers. A total of 546,090 individuals (10.5%) living in Denmark on January 1, 1995 were diagnosed with at least one mental disorder during the 22‐year follow‐up period. The overall crude rate of diagnosis of mental disorders was 9.28 (95% CI: 9.26‐9.30) per 1,000 person‐years. The rate of diagnosis of additional mental disorders was 70.01 (95% CI: 69.80‐70.26) per 1,000 person‐years for individuals with one disorder already diagnosed. At the end of follow‐up, two out of five individuals with mental disorders were diagnosed with two or more disorder types. The most prevalent were neurotic/stress‐related/somatoform disorders (ICD‐10 F40‐F48) and mood disorders (ICD‐10 F30‐F39), which – alone or in combination with other disorders – were present in 64.8% of individuals diagnosed with any mental disorder. Mortality rates were higher for people with mental disorders compared to those without mental disorders. The highest mortality rate ratio was 5.97 (95% CI: 5.52‐6.45) for the combination of schizophrenia (ICD‐10 F20‐F29), neurotic/stress‐related/somatoform disorders and substance use disorders (ICD‐10 F10‐F19). Any combination of mental disorders was associated with a shorter life expectancy compared to the general Danish population, with differences in remaining life expectancy ranging from 5.06 years (95% CI: 5.01‐5.11) to 17.46 years (95% CI: 16.86‐18.03). The largest excess mortality was observed for combinations that included substance use disorders. This study reports novel estimates related to the “force of comorbidity” and provides new insights into the contribution of substance use disorders to premature mortality in those with comorbid mental disorders.     

In vitro self-assembly of the light harvesting pigment-protein LH2 revealed by ultrafast spectroscopy and electron microscopy

Controlled ensemble formation of protein-surfactant systems provides a fundamental concept for the realization of nanoscale devices with self-organizing capability. In this context, spectroscopic monitoring of pigment-containing proteins yields detailed structural information. Here we have studied the association behavior of the bacterial light-harvesting protein LH2 from Rhodobacter spheroides in an n,n-dimethyldodecylamine-n-oxide/water environment. Time-resolved studies of the excitation annihilation yielded information about aggregate sizes and packing of the protein complexes therein. The results are compared to transmission electron microscopy images of instantaneously frozen samples. Our data indicate the manifestation of different phases, which are discussed with respect to the thermodynamic equilibrium in ternary protein-surfactant-water systems. Accordingly, by varying the concentration the formation of different types of aggregates can be controlled. Conditions for the appearance of isolated LH2 complexes are defined.     

Inbreeding and sex-biased gene flow in the ant Formica exsecta

Abstract.— The objective of this study was to assess breeding and dispersal patterns of both males and females in a monogyne (a single queen per colony) population of ants. Monogyny is commonly associated with extensive nuptial flights, presumably leading to considerable gene flow over large areas. Opposite to these expectations we found evidence of both inbreeding and sex-biased gene flow in a monogyne population of Formica exsecta . We found a significant degree of population subdivision at a local scale (within islands) for queens (females heading established colonies) and workers, but not for colony fathers (the males mated to the colony queens). However, we found little evidence of population subdivision at a larger scale (among islands). More conclusive support for sex-biased gene flow comes from the analysis of isolation by distance on the largest island, and from assignment tests revealing differences in female and male philopatry. The genetic similarity between pairs of queens decreased significantly when geographical distance increased, demonstrating limited dispersal and isolation by distance in queens. By contrast, we found no such pattern for colony fathers. Furthermore, a significantly greater fraction of colony queens were assigned as having originated from the population of residence, as compared to colony fathers. Inbreeding coefficients were significantly positive for workers, but not for mother queens. The queen-male relatedness coefficient of 0.23 (regression relatedness) indicates that mating occurs between fairly close relatives. These results suggest that some monogyne species of ants have complex dispersal and mating systems that can result in genetic isolation by distance over small geographical scales. More generally, this study also highlights the importance of identifying the relevant scale in analyses of population structure and dispersal.     

Studies of the interactions between the anticytokeratin 8 monoclonal antibody TS1, its antigen and its anti-idiotypic antibody alphaTS1

The monoclonal antibody TS1 against cytokeratin 8 and its antiidiotype alphaTS1 have been used for immunotargeting and therapy of carcinomas in experimental tumor model systems. The interaction surfaces between mab TS1, the cytokeratin 8 epitope, and its anti-idiotypic antibody, alphaTS1, were studied in detail in order to make future veneering of the interactions possible. The V-genes of TS1 and alphaTS1 were cloned and sequenced and the CDRs and the framework residues were identified. Amino acids participating in the interactions were identified following chemical modifications of residues in non-protected and protected molecules of cytokeratin 8, alphaTS1 and TS1. From the sequences, the three-dimensional structures were generated using computer modelling of the antibody variable regions. Several charged amino acid, histidine and tyrosine residues were displayed in the antibody surfaces implicated in the interactions and chemical modification confirmed the importance of these amino acids. The cytokeratin 8 epitope has previously been identified by Johansson et al. and it displays negatively charged amino acid residues which could be identified in the chemical modification. It was also revealed that the TS1 binding to cytokeratin 8 and alphaTS1 respectively are partly overlapping; a histidine identified in TS1 is probably involved only in the interaction with alphaTS1. Furthermore, the chemical modification demonstrated that exchanging aspartic-glutamic acids to asparagine-glutamine residues in TS1 increased the binding of TS1 to cytokeratin 8, indicating that there is at least one acidic amino acid that is an obstacle in the TS1-CK8 binding. The detailed assembly of the interaction surfaces will facilitate the future use of site directed mutagenesis to improve the TS1-CK8 association rate and the clearing of TS1 with alphaTS1 in vivo.     

Segregation to non-dividing cells in recombinant Escherichia coli fed-batch fermentation processes

In Escherichia coli fermentation processes, a drastic drop in viable cell count as measured by the number of colony forming units per ml (c.f.u. ml(-1)) is often observed. This phenomenon was investigated in a process for the production of the recombinant fusion protein, promegapoietin (PMP). After induction, the number of c.f.u. ml(-1) dropped to approximately 10% of its maximum though the biomass concentration continued to increase. Flow cytometric analysis of viability and intracellular concentration of PMP showed that almost all cells were alive and contributed to the production. Thus, the drop in the number of c.f.u. ml(-1) probably reflects a loss of cell division capability rather than cell death.     

Structural proteomics: developments in structure-to-function predictions

The major challenge for post-genomic research is to functionally assign and validate a large number of novel target genes and their corresponding proteins. Functional genomics approaches have, therefore, gained considerable attention in the quest to convert this massive data set into useful information. One of the crucial components for the functional understanding of unassigned proteins is the analysis of their experimental or modeled 3D structures. Structural proteomics initiatives are generating protein structures at an unprecedented rate but our current knowledge of 3D-structural space is still limited. Estimates on the completeness of the 3D-structural coverage of proteins vary but it is generally accepted that only a minority of the structural proteome has a template structure from which reliable conclusions can be drawn. Thus, structural proteomics has set out to build a map of protein structures that will represent all protein folds included in the 'global proteome'.     

Quantification of isoflavones in red clover by high-performance liquid chromatography

An RP-HPLC method for the determination of daidzein, genistein, formononetin and biochanin A in red clover (Trifolium pratense L.) was developed and validated. The compounds are quantified after hydrolytic extraction using an internal standard. On a base-deactivated C(18) column good separation of the analytes, also from accompanying substances, and excellent peak shape are achieved by gradient elution with aqueous sulfuric acid and acetonitrile. The method was applied to the analysis of different red clover cultivars.