MEXPRESS : visualizing expression, DNA methylation and clinical TCGA data

Background: In recent years, increasing amounts of genomic and clinical cancer data have become publically available through large-scale collaborative projects such as The Cancer Genome Atlas (TCGA). However, as long as these datasets are difficult to access and interpret, they are essentially useless for a major part of the research community and their scientific potential will not be fully realized. To address these issues we developed MEXPRESS, a straightforward and easy-to-use web tool for the integration and visualization of the expression, DNA methylation and clinical TCGA data on a single-gene level (http://mexpress.be). Results: In comparison to existing tools, MEXPRESS allows researchers to quickly visualize and interpret the different TCGA datasets and their relationships for a single gene, as demonstrated for GSTP1 in prostate adenocarcinoma. We also used MEXPRESS to reveal the differences in the DNA methylation status of the PAM50 marker gene MLPH between the breast cancer subtypes and how these differences were linked to the expression of MPLH. Conclusions: We have created a user-friendly tool for the visualization and interpretation of TCGA data, offering clinical researchers a simple way to evaluate the TCGA data for their genes or candidate biomarkers of interest

Childhood IQ and risk of bipolar disorder in adulthood: prospective birth cohort study

Background: Intellectual ability may be an endophenotypic marker for bipolar disorder. Aims: Within a large birth cohort, we aimed to assess whether childhood IQ (including both verbal IQ (VIQ) and performance IQ (PIQ) subscales) was predictive of lifetime features of bipolar disorder assessed in young adulthood. Method: We used data from the Avon Longitudinal Study of Parents and Children (ALSPAC), a large UK birth cohort, to test for an association between measures of childhood IQ at age 8 years and lifetime manic features assessed at age 22–23 years using the Hypomania Checklist-32 (HCL-32; n=1881 individuals). An ordinary least squares linear regression model was used, with normal childhood IQ (range 90–109) as the referent group. We adjusted analyses for confounding factors, including gender, ethnicity, handedness, maternal social class at recruitment, maternal age, maternal history of depression and maternal education. Results: There was a positive association between IQ at age 8 years and lifetime manic features at age 22–23 years (Pearson's correlation coefficient 0.159 (95% CI 0.120–0.198), P>0.001). Individuals in the lowest decile of manic features had a mean full-scale IQ (FSIQ) which was almost 10 points lower than those in the highest decile of manic features: mean FSIQ 100.71 (95% CI 98.74–102.6) v. 110.14 (95% CI 107.79–112.50), P>0.001. The association between IQ and manic features was present for FSIQ, VIQ and for PIQ but was strongest for VIQ. Conclusions: A higher childhood IQ score, and high VIQ in particular, may represent a marker of risk for the later development of bipolar disorder. This finding has implications for understanding of how liability to bipolar disorder may have been selected through generations. It will also inform future genetic studies at the interface of intelligence, creativity and bipolar disorder and is relevant to the developmental trajectory of bipolar disorder. It may also improve approaches to earlier detection and treatment of bipolar disorder in adolescents and young adults

An endoplasmic reticulum (ER)-directed fusion protein comprising a bacterial subtilisin domain and the human cytokine interleukin 6 is efficiently cleaved in planta

A major limitation of plant bioreactors is the lack of suitable and cost-effective purification methods for the extraction of pharmaceutical-grade proteins. In contrast to that, there are numerous established purification systems for heterologous proteins, expressed in Escherichia coli, which are used for the commercial production of therapeutic proteins. Therefore, we wanted to adapt the BioRad Profinity eXact<sup>TM</sup> one-step protein purification system (originally designed for microbial expression platforms) to purify recombinant proteins in crude plant extracts. This system based on the prodomain of microbial subtilase as fusion partner and a column-bound subtilisin protease. The engineered protease captures and cleaves the fusion protein, retaining the tag and releasing the native protein into the eluate. The subtilase tag was fused to human interleukin 6 (IL6) and transiently expressed in Nicotiana benthamiana leaves using the MagnICON system. The fusion protein was expressed at lower levels than native IL6, suggesting it is expressed less efficiently and/or has a lower stability. However, free IL6 was also detected in the extract and was unaffected by the addition of protease inhibitors during extraction, suggesting that the fusion protein is cleaved in planta by endogenous proteases. Purification of the recombinant protein using the Profinity eXact<sup>TM</sup> system reduced the yield still further. The inefficient production of tagged IL6, coupled with the extensive losses during purification, indicate that the Profinity eXact<sup>TM</sup> system is not suitable for the extraction of IL6 from crude plant extracts.Keywords: Tobacco, transient expression, endoplasmic reticulum, Profinity protein purification, partial cleavageAfrican Journal of Biotechnology Vol. 12(3), pp. 311-31

Recombinant production of the human complement factor 5a in Escherichia coli

Up to now, the human complement factor 5a (C5a) has only been produced in small quantities in Escherichia coli in a soluble, bioactive conformation, which is not suitable for commercial production systems. This stems from the extremely high instability of C5a, as well as its aggregation-prone nature. Therefore, we analyzed several different methods for optimizing the solubility and biological activity of C5a produced by E. coli. The solubility of C5a was efficiently improved by expressing it as a glutathione-S-transferase (GST) fusion protein and, to a lesser extent, by lowering the cultivation temperature. Neither reducing the inductor concentration (isopropylthio-β-galactoside, IPTG) of the T7lac promotor nor the concomitant overexpression of endogenous chaperones was effective. However, the biological activity of the protein was improved by the overexpression of chaperones together with cultivation at 22°C, while fusion to GST slightly reduced its activity. Consequently, low cultivation temperature and the overexpression of chaperones seem to be the optimal strategy for expression of appropriate amounts of soluble and functional C5a. These findings should be the basis for the transfer to large-scale fermentation. Using C5a as an example, we showed that strain engineering in combination with specific cultivation conditions improve the production of difficult-to-express proteins in appropriate amounts and in a functional conformation facilitating the commercial manufacturing under good manufacturing practices (GMP) conditions.Keywords: Complement factor 5a (C5a), Origami 2, BL21, periplasm, cytoplasm, chaperones, Glutathione-S-Transferase (GST), temperatur

E- und Blended-Learnung in der Lehre an der HTW Dresden, umgesetzt mit der Lernplattform OPAL

Die HTW Dresden bietet ihren Studienanfänger_innen einen auf OPAL basierenden Blended Learning-Kurs Einführung in das wissenschaftliche Arbeiten an, der mit den Bereichen Selbstmanagement, wissenschaftliches Schreiben, Präsentieren und Poster die Studierenden auf ihr Studium, ihre Abschlussarbeit und deren Verteidigung vorbereitet. Durch engagierte Betreuung bleibt der enge Kontakt zum/zur Lehrenden bestehen und der/die Studierende wird in Problemsituationen aufgefangen und motiviert

MEXPRESS update 2019

The recent growth in the number of publicly available cancer omics databases has been accompanied by the development of various tools that allow researchers to visually explore these data. In 2015, we built MEXPRESS, an online tool for the integration and visualization of gene expression, DNA methylation and clinical data from The Cancer Genome Atlas (TCGA), a large collection of publicly available multi-omics cancer data. MEXPRESS addresses the need for an easy-to-use, interactive application that allows researchers to identify dysregulated genes and their clinical relevance in cancer. Furthermore, while other tools typically do not support integrated visualization of expression and DNA methylation data in combination with the precise genomic location of the methylation, MEXPRESS is unique in how it depicts these diverse data types together. Motivated by the large number of users MEXPRESS has managed to attract over the past 3 years and the recent migration of all TCGA data to a new data portal, we developed a new version of MEXPRESS (https://mexpress.be). It contains the latest TCGA data, additional types of omics and clinical data and extra functionality, allowing users to explore mechanisms of gene dysregulation beyond expression and DNA methylation

The Evolution of Complex Muscle Cell In Vitro Models to Study Pathomechanisms and Drug Development of Neuromuscular Disease

Many neuromuscular disease entities possess a significant disease burden and therapeutic options remain limited. Innovative human preclinical models may help to uncover relevant disease mechanisms and enhance the translation of therapeutic findings to strengthen neuromuscular disease precision medicine. By concentrating on idiopathic inflammatory muscle disorders, we summarize the recent evolution of the novel in vitro models to study disease mechanisms and therapeutic strategies. A particular focus is laid on the integration and simulation of multicellular interactions of muscle tissue in disease phenotypes in vitro. Finally, the requirements of a neuromuscular disease drug development workflow are discussed with a particular emphasis on cell sources, co-culture systems (including organoids), functionality, and throughput.Peer Reviewe

Municipal investment in off-road trails and changes in bicycle commuting in Minneapolis, Minnesota over 10 years: a longitudinal repeated cross-sectional study

Abstract Background We studied the effect of key development and expansion of an off-road multipurpose trail system in Minneapolis, Minnesota between 2000 and 2007 to understand whether infrastructure investments are associated with increases in commuting by bicycle. Methods We used repeated measures regression on tract-level (N = 116 tracts) data to examine changes in bicycle commuting between 2000 and 2008–2012. We investigated: 1) trail proximity measured as distance from the trail system and 2) trail potential use measured as the proportion of commuting trips to destinations that might traverse the trail system. All analyses (performed 2015–2016) adjusted for tract-level sociodemographic covariates and contemporaneous cycling infrastructure changes (e.g., bicycle lanes). Results Tracts that were both closer to the new trail system and had a higher proportion of trips to destinations across the trail system experienced greater 10-year increases in commuting by bicycle. Conclusions Proximity to off-road infrastructure and travel patterns are relevant to increased bicycle commuting, an important contributor to overall physical activity. Municipal investment in bicycle facilities, especially off-road trails that connect a city’s population and its employment centers, is likely to lead to increases in commuting by bicycle