Assembling proteomics data as a prerequisite for the analysis of large scale experiments

<p>Abstract</p> <p>Background</p> <p>Despite the complete determination of the genome sequence of a huge number of bacteria, their proteomes remain relatively poorly defined. Beside new methods to increase the number of identified proteins new database applications are necessary to store and present results of large- scale proteomics experiments.</p> <p>Results</p> <p>In the present study, a database concept has been developed to address these issues and to offer complete information via a web interface. In our concept, the Oracle based data repository system SQL-LIMS plays the central role in the proteomics workflow and was applied to the proteomes of <it>Mycobacterium tuberculosis</it>, <it>Helicobacter pylori</it>, <it>Salmonella typhimurium </it>and protein complexes such as 20S proteasome. Technical operations of our proteomics labs were used as the standard for SQL-LIMS template creation. By means of a Java based data parser, post-processed data of different approaches, such as LC/ESI-MS, MALDI-MS and 2-D gel electrophoresis (2-DE), were stored in SQL-LIMS. A minimum set of the proteomics data were transferred in our public 2D-PAGE database using a Java based interface (Data Transfer Tool) with the requirements of the PEDRo standardization. Furthermore, the stored proteomics data were extractable out of SQL-LIMS via XML.</p> <p>Conclusion</p> <p>The Oracle based data repository system SQL-LIMS played the central role in the proteomics workflow concept. Technical operations of our proteomics labs were used as standards for SQL-LIMS templates. Using a Java based parser, post-processed data of different approaches such as LC/ESI-MS, MALDI-MS and 1-DE and 2-DE were stored in SQL-LIMS. Thus, unique data formats of different instruments were unified and stored in SQL-LIMS tables. Moreover, a unique submission identifier allowed fast access to all experimental data. This was the main advantage compared to multi software solutions, especially if personnel fluctuations are high. Moreover, large scale and high-throughput experiments must be managed in a comprehensive repository system such as SQL-LIMS, to query results in a systematic manner. On the other hand, these database systems are expensive and require at least one full time administrator and specialized lab manager. Moreover, the high technical dynamics in proteomics may cause problems to adjust new data formats. To summarize, SQL-LIMS met the requirements of proteomics data handling especially in skilled processes such as gel-electrophoresis or mass spectrometry and fulfilled the PSI standardization criteria. The data transfer into a public domain via DTT facilitated validation of proteomics data. Additionally, evaluation of mass spectra by post-processing using MS-Screener improved the reliability of mass analysis and prevented storage of data junk.</p

IL4I1 Is a Metabolic Immune Checkpoint that Activates the AHR and Promotes Tumor Progression

Immune checkpoint blockade therapy induces the AHR-activating enzyme IL4I1, which promotes tumor progression, through its effects on tumor cell motility and adaptive immunity

The first transcriptome of Italian wall lizard, a new tool to infer about the Island Syndrome

Some insular lizards show a high degree of differentiation from their conspecific mainland populations, like Licosa island lizards, which are described as affected by Reversed Island Syndrome (RIS). In previous works, we demonstrated that some traits of RIS, as melanization, depend on a differential expression of gene encoding melanocortin receptors. To better understand the basis of syndrome, and providing raw data for future investigations, we generate the first de novo transcriptome of the Italian wall lizard. Comparing mainland and island transcriptomes, we link differences in life-traits to differential gene expression. Our results, taking together testis and brain sequences, generated 275,310 and 269,885 transcripts, 18,434 and 21,606 proteins in Gene Ontology annotation, for mainland and island respectively. Variant calling analysis identified about the same number of SNPs in island and mainland population. Instead, through a differential gene expression analysis we found some putative genes involved in syndrome more expressed in insular samples like Major Histocompatibility Complex class I, Immunoglobulins, Melanocortin 4 receptor, Neuropeptide Y and Proliferating Cell Nuclear Antigen

Spatial and temporal variability of rock slope instability in western Norway: : Implications for susceptibility and hazard assessment

Rock slope failures form a frequent hazard to many populated mountain regions. Especially in western Norway, the topographical and meteorological characteristics increase the vulnerability for rock slope failures. A major focus for studies in Norway is to eciently nd and investigate possible future rock slope failures in order to prevent extensive humanitarian disasters. The determination of the critical parameters involved in the development of rock slope failures is crucial in order to optimize hazard recognition. In addition, a better understanding of the spatial and temporal variability of prehistoric and historic rock slope failures as well as present day rock slope instabilities will optimize monitoring and further research on the susceptibility for future rock slope failures. The primary aim of this study is to investigate the spatial and temporal distribution of rock slope instabilities within western Norway. It is further aimed to determine the controlling parameters on the development of rock slope instabilities within the study region. The implemented approaches range from regional scale statistical analyses towards site specic numerical modelling, while a focus is set on quantitative analyses. Within this thesis the main controlling parameters are dened for rockfalls and rock slope instabilities on a regional scale for the entire county of Sogn &amp; Fjordane, western Norway. It is demonstrated that always a combination of several parameters is necessary to destabilize a mountain side. Rockfalls have the strongest spatial relation to the presence of bare rock as well as landslide deposits, the degree of tectonic deformation and the geological lineament density. Large rock slope instabilities develop preferentially within relatively weak rock units, such as phyllites or weathered mac gneisses, and at convex slope breaks. Looking more into detail, a strong structural control is conrmed by numerical modelling for the unstable rock slope at Stampa. Susceptibility and hazard are assessed at dierent scales and with dierent measures. Quantitative rockfall susceptibility is mapped on a regional scale for the entire county of Sogn &amp; Fjordane based on the statistical analysis of a set of controlling factors. In addition, this statistical susceptibility model is combined with a physically based model, restricting the susceptibility map to areas that are steep enough to represent a potential rockfall source. This combination allows using road inventories, with registered impact points instead of release areas, for susceptibility modelling. In contrast, relative susceptibility and also hazard are assessed locally for single parts of the unstable rock slope at Stampa based on morphology and past activity. Present day annual expectable frequencies for rock slope failures of certain volume classes are determined for the Storfjord region in western Norway based on magnitude-frequency analyses. Furthermore, a semi quantitative hazard estimation is obtained for each potential instability based on a qualitative susceptibility assessment of each instability in this region. This PhD thesis presents results of the rst attempts of quantitative statistical analyses of dierent inventories covering rock slope instabilities in Norway. It is shown that susceptibility and hazard can be assessed with dierent measures, forming the basis for further decisions regarding risk assessment and mitigation

Changes in intervertebral disc morphology persist 5 mo after 21-day bed rest

As part of the nutrition- countermeasures (NUC) study in Cologne, Germany in 2010, seven healthy male subjects underwent 21 days of head-down tilt bed rest and returned 153 days later to undergo a second bout of 21-day bed rest. As part of this model, we aimed to examine the recovery of the lumbar intervertebral discs and muscle cross-sectional area (CSA) after bed rest using magnetic resonance imaging and conduct a pilot study on the effects of bed rest in lumbar muscle activation, as measured by signal intensity changes in T2-weighted images after a standardized isometric spinal extension loading task. The changes in intervertebral disc volume, anterior and posterior disc height, and intervertebral length seen after bed rest did not return to prebed-rest values 153 days later. While recovery of muscle CSA occurred after bed rest, increases (P 0.016) in multifidus, psoas, and quadratus lumborum muscle CSA were seen 153 days after bed rest. A trend was seen for greater activation of the erector spinae and multifidus muscles in the standardized loading task after bed rest. Greater reductions of multifidus and psoas CSA muscle and greater increases in multifidus signal intensity with loading were associated with incidence of low back pain in the first 28 days after bed rest (P 0.044). The current study contributes to our understanding of the recovery of the lumbar spine after 21-day bed rest, and the main finding was that a decrease in spinal extensor muscle CSA recovers within 5 mo after bed rest but that changes in the intervertebral discs persist

Dataset of Measured Binaural Room Transfer Functions of Individuals

A dataset of BRIRs from 25 individuals is presented. The BRIRs are recorded in a listening lab (ITU-BS.1116-1) and an empty seminar (V = 182 m³, T60 = 2.0 s). Additionally, for some persons the BRIRs from an acoustic enhanced seminar room and a small lecture hall are included. The recorded source directions with a distance of 2.2 m are 0°, 30°, 60°, 180°, 240°, 300° or all 12 hours positions for the persons with the two additional rooms. The used dataset is stored in the SOFA (Spatially Oriented Format for Acoustics) file format

Taxodioxylon-like charcoal from the Late Miocene of western Bulgaria

We present the first anatomical description and taxonomic interpretation of macroscopic charcoal from the Late Miocene of the Staniantsi Coal Basin in western Bulgaria. The charcoal closely resembles the wood genus Taxodioxylon and thus can most likely be assigned to taxodioid Cupressaceae. This group of plants was part of the peat-forming swamp vegetation during generally drier periods, as shown by previous studies on palynomorphs from the basin. Our report presents the first solid evidence indicating which group of plants and probably which type of vegetation were affected by wildfires during deposition of the peat, although taxodioid Cupressaceae certainly were not the only group of plants affected by these fires; it also represents the first record of taxonomically identifiable palaeobotanical macroremains from the Staniantsi Basin