Mating of 2 Laboratory Saccharomyces cerevisiae Strains Resulted in Enhanced Production of 2-Phenylethanol by Biotransformation of L-Phenylalanine

2-Phenylethanol (2-PE) is an aromatic alcohol with a rosy scent which is widely used in the food, fragrance, and cosmetic industries. Promising sources of natural 2-PE are microorganisms, especially yeasts, which can produce 2-PE by biosynthesis and biotransformation. Thus, the first challenging goal in the development of biotechnological production of 2-PE is searching for highly productive yeast strains. In the present work, 5 laboratory Saccharomyces cerevisiae strains were tested for the production of 2-PE. Thereafter, 2 of them were hybridized by a mating procedure and, as a result, a new diploid, S. cerevisiae AM1-d, was selected. Within the 72-h batch culture in a medium containing 5 g/L of L-phenylalanine, AM1-d produced 3.83 g/L of 2-PE in a shaking flask. In this way, we managed to select the diploid S. cerevisiae AM1-d strain, showing a 3- and 5-fold increase in 2-PE production in comparison to parental strains. Remarkably, the enhanced production of 2-PE by the hybrid of 2 yeast laboratory strains is demonstrated here for the first time

Ribosomal DNA status inferred from DNA cloud assays and mass spectrometry identification of agarose-squeezed proteins interacting with chromatin (ASPIC-MS)

Ribosomal RNA-encoding genes (rDNA) are the most abundant genes in eukaryotic genomes. To meet the high demand for rRNA, rDNA genes are present in multiple tandem repeats clustered on a single or several chromosomes and are vastly transcribed. To facilitate intensive transcription and prevent rDNA destabilization, the rDNA-encoding portion of the chromosome is confined in the nucleolus. However, the rDNA region is susceptible to recombination and DNA damage, accumulating mutations, rearrangements and atypical DNA structures. Various sophisticated techniques have been applied to detect these abnormalities. Here, we present a simple method for the evaluation of the activity and integrity of an rDNA region called a “DNA cloud assay”. We verified the efficacy of this method using yeast mutants lacking genes important for nucleolus function and maintenance (RAD52, SGS1, RRM3, PIF1, FOB1 and RPA12). The DNA cloud assay permits the evaluation of nucleolus status and is compatible with downstream analyses, such as the chromosome comet assay to identify DNA structures present in the cloud and mass spectrometry of agarose squeezed proteins (ASPIC-MS) to detect nucleolar DNA-bound proteins, including Las17, the homolog of human Wiskott-Aldrich Syndrome Protein (WASP

The Peroxisomal Targeting Signal 3 (PTS3) of the Budding Yeast Acyl-CoA Oxidase Is a Signal Patch

The specificity of import of peroxisomal matrix proteins is dependent on the targeting signals encoded within their amino acid sequences. Two known import signals, peroxisomal targeting signal 1 (PTS1), positioned at the C-termini and PTS2 located close to N-termini of these proteins are recognized by the Pex5p and Pex7p receptors, respectively. However, in several yeast species, including Saccharomyces cerevisiae, proteins exist that are efficiently imported into peroxisomes despite having neither PTS1 nor PTS2 and for which no other import signal has been determined. An example of such a protein is S. cerevisiae acyl-CoA oxidase (AOx) encoded by the POX1 gene. While it is known that its import is driven by its interaction with the N-terminal segment of Pex5p, which is separate from its C-terminal PTS1-recognizing tetratricopeptide domain, to date, no AOx polypeptide region has been implicated as critical for this interaction, and thus would constitute the long-sought PTS3 signal. Using random mutagenesis combined with a two-hybrid screen, we identified single amino acid residues within the AOx polypeptide that are crucial for this interaction and for the peroxisomal import of this protein. Interestingly, while scattered throughout the primary sequence, these amino acids come close to each other within two domains of the folded AOx. Although the role of one or both of these regions as the PTS3 signal is not finally proven, our data indicate that the signal guiding AOx into peroxisomal matrix is not a linear sequence but a signal patch

Differential regulation of serum microRNA expression by HNF1β and HNF1α transcription factors.

We aimed to identify microRNAs (miRNAs) under transcriptional control of the HNF1β transcription factor, and investigate whether its effect manifests in serum.This article is freely available via Open Access. Click on the 'Additional Link' above to access the full-text via the publisher's site.Published (Open Access

inverted CERN School of Computing 2016

We’re all involved in some software/physics projects. As a rule of thumb projects start really simple - a couple of scripts, classes and a few external dependencies. At this phase delivering a release to our clients is simple. We can compile the project locally and deliver compiled sources, for example by e-mail. Unfortunately, in most cases the growth of projects is inevitable. Our simple approaches to build, test and deliver applications are not sufficient. We start to spend more and more time on these ‘administrative’ procedures than on the real developments. As the project grows, our productivity declines and we are less responsive to requests from our clients. In this lecture I will try to present common delivery patterns and tools which facilitate these processes. After introducing Continuous Delivery, I will switch the topic and try to answer the question how much should we invest in quality and how to do it efficiently. My observations reveal that software quality is often considered as the slowing down force. Following this false belief I would like to convince people that software quality can accelerate development within our projects

1st Developers@CERN Forum

The TE-MPE-MS Software team is a small group of people responsible for developing software for machine protection. Main projects include mostly software for the equipment supervision and testing. The usage of the Scrum methodology involves getting clients’ feedback as soon as possible which pushed the requirement to integrate all the time and deliver software in small chunks. To meet these requirements the team successfully implemented Continuous Integration and Delivery processes using multiple open source and proprietary products including: Gradle, Flyway, JUnit+Mockito, SonarQube and Bamboo. The idea for the presentation is to present our implementation of the CI/CD paradigms and explain on real live examples advantages and drawbacks of the current solution. During the presentation we will try to cover all the required steps which should automatically triggered by a developer’s commit. The presentation should give users a good hands-on experience on basic CI/CD principles and allow them to design and implement simple software delivery platform. ![CI/CD][1] [1]: https://wikis.cern.ch/download/attachments/77562499/continuous%20delivery%20diagram.jpg?version=1&modificationDate=1413356546000&api=v

A Genomic Screen Revealing the Importance of Vesicular Trafficking Pathways in Genome Maintenance and Protection against Genotoxic Stress in Diploid Saccharomyces cerevisiae Cells

The ability to survive stressful conditions is important for every living cell. Certain stresses not only affect the current well-being of cells but may also have far-reaching consequences. Uncurbed oxidative stress can cause DNA damage and decrease cell survival and/or increase mutation rates, and certain substances that generate oxidative damage in the cell mainly act on DNA. Radiomimetic zeocin causes oxidative damage in DNA, predominantly by inducing single- or double-strand breaks. Such lesions can lead to chromosomal rearrangements, especially in diploid cells, in which the two sets of chromosomes facilitate excessive and deleterious recombination. In a global screen for zeocin-oversensitive mutants, we selected 133 genes whose deletion reduces the survival of zeocin-treated diploid Saccharomyces cerevisiae cells. The screen revealed numerous genes associated with stress responses, DNA repair genes, cell cycle progression genes, and chromatin remodeling genes. Notably, the screen also demonstrated the involvement of the vesicular trafficking system in cellular protection against DNA damage. The analyses indicated the importance of vesicular system integrity in various pathways of cellular protection from zeocin-dependent damage, including detoxification and a direct or transitional role in genome maintenance processes that remains unclear. The data showed that deleting genes involved in vesicular trafficking may lead to Rad52 focus accumulation and changes in total DNA content or even cell ploidy alterations, and such deletions may preclude proper DNA repair after zeocin treatment. We postulate that functional vesicular transport is crucial for sustaining an integral genome. We believe that the identification of numerous new genes implicated in genome restoration after genotoxic oxidative stress combined with the detected link between vesicular trafficking and genome integrity will reveal novel molecular processes involved in genome stability in diploid cells

Multicad Support in CERN's PLM

Designing an accelerator complex and its surrounding technical infrastructure requires the participation of multiple disciplines, such as mechanical engineering, civil engineering, or services. Different fields have different needs and may use different tools. At CERN, CATIA is the official CAD tool for 3D mechanical design and integration, but for specific needs alternative tools are being used, such as AutoCAD for 2D, Revit for BIM and Inventor for specific 3D designs such as robotics or external collaborations. Until now, the main focus of the PLM service for CAD data management has been put on supporting CERN's official and main mechanical CAD tool, CATIA. We are currently migrating to a new PLM platform, and one of the requirements is that the new platform should be able to support any CAD tool in use at CERN, both today and in the future. This paper first describes how CAD tools were supported in the past and what the limitations were. It then explains how multiple heterogeneous CAD tools will be managed in the new PLM platform and how this can simplify the support of additional CAD tools in the future. Finally, this paper suggests possible future paths of improvements, in particular in terms of data exchange, visualization and integration between different CAD tools

CERN's New PLM Platform & Consolidation of Legacy Tools: What's New and What's Next?

Long-term CERN projects such as the LHC or the FCC require the ability to store, validate and archive large sets of engineering data (documentation, various reports, 3D models, 2D drawings). The current engineering tools at CERN manage several million documents that go through various lifecycles and workflows. A continu-ous increase in the complexity of projects and exchanges between CERN and external partners requires contin-uous improvement of engineering tools. In the initial part, this paper presents the purpose of the PLM service, legacy tools used for managing engi-neering data at CERN and motivations for their modernisation. The main part of the paper focuses on CERN’s new PLM, its components and current functionality. In this section, we will learn how multiple tools were consolidated into one single platform, how having one platform allowed us to streamline engineering processes and stimulate collaboration between engineers. The last part draws perspectives for next steps in the PLM platform evolution and explains how having one common PLM platform can enable CERN to profit from modern engineering concepts

Tensorics - A Java library for manipulating multi-dimensional data

Accelerator control software often has to handle multi-dimensional data of physical quantities when aggregating readings from multiple devices (e.g. the reading of an orbit in the LHC). When storing such data as nested hashtables or lists, the ability to do structural operations or calculations along an arbitrary dimensions is hampered. Tensorics is a Java library that provides a solution for these problems. A Tensor is a n-dimensional data structure, and both structural (e.g. extraction) and mathematical operations are possible along any dimension. Any Java class or interface can serve as a dimension, with coordinates being instances of a dimension class. This contribution will elaborate on the design and the functionality of the Tensorics library and highlight existing use cases in operational LHC control software, e.g. the LHC luminosity server or the LHC chromaticity correction application