Strategies to increase tolerance and robustness of industrial microorganisms

The development of a cost-competitive bioprocess requires that the cell factory converts the feedstock into the product of interest at high rates and yields. However, microbial cell factories are exposed to a variety of different stresses during the fermentation process. These stresses can be derived from feedstocks, metabolism, or industrial production processes, limiting production capacity and diminishing competitiveness. Improving stress tolerance and robustness allows for more efficient production and ultimately makes a process more economically viable. This review summarises general trends and updates the most recent developments in technologies to improve the stress tolerance of microorganisms. We first look at evolutionary, systems biology and computational methods as examples of non-rational approaches. Then we review the (semi-)rational approaches of membrane and transcription factor engineering for improving tolerance phenotypes. We further discuss challenges and perspectives associated with these different approaches

Laser Control of Dissipative Two-Exciton Dynamics in Molecular Aggregates

There are two types of two-photon transitions in molecular aggregates, that is, non-local excitations of two monomers and local double excitations to some higher excited intra-monomer electronic state. As a consequence of the inter-monomer Coulomb interaction these different excitation states are coupled to each other. Higher excited intra-monomer states are rather short-lived due to efficient internal conversion of electronic into vibrational energy. Combining both processes leads to the annihilation of an electronic excitation state, which is a major loss channel for establishing high excitation densities in molecular aggregates. Applying theoretical pulse optimization techniques to a Frenkel exciton model it is shown that the dynamics of two-exciton states in linear aggregates (dimer to tetramer) can be influenced by ultrafast shaped laser pulses. In particular, it is studied to what extent the decay of the two-exciton population by inter-band transitions can be transiently suppressed. Intra-band dynamics is described by a dissipative hierarchy equation approach, which takes into account strong exciton-vibrational coupling in the non-Markovian regime.Comment: revised version, fig. 8 ne

Adverse Reaction Reports Analysis Tool

The goal of this project is to create a working alternative to the FDA Drug Safety Evaluator\u27s current medical error analysis workflow. By prioritizing a visualization-focused application, investigators are able to easily identify trends and important reports. Using treemap visualizations, bar charts, and area charts, an investigator is able to sift through medical error reports by patient demographic, report statistics, and date, allowing specific reports to be found easily. Specific reports have all of their metadata displayed in a tabular view and can be interacted with to show the report\u27s narrative. The application allows for the evaluators to mark and store significant reports in cases that provide further statistical analysis on the annotated reports stored inside them

An Entry/Gateway® cloning system for general expression of genes with molecular tags in Drosophila melanogaster

<p>Abstract</p> <p>Background</p> <p>Tagged fusion proteins are priceless tools for monitoring the activities of biomolecules in living cells. However, over-expression of fusion proteins sometimes leads to the unwanted lethality or developmental defects. Therefore, vectors that can express tagged proteins at physiological levels are desirable tools for studying dosage-sensitive proteins. We developed a set of Entry/Gateway^®vectors for expressing fluorescent fusion proteins in <it>Drosophila melanogaster</it>. The vectors were used to generate fluorescent CP190 which is a component of the <it>gypsy </it>chromatin insulator. We used the fluorescent CP190 to study the dynamic movement of related chromatin insulators in living cells.</p> <p>Results</p> <p>The Entry/Gateway^®system is a timesaving technique for quickly generating expression constructs of tagged fusion proteins. We described in this study an Entry/Gateway^®based system, which includes six P-element destination vectors (P-DEST) for expressing tagged proteins (eGFP, mRFP, or myc) in <it>Drosophila melanogaster </it>and a TA-based cloning vector for generating entry clones from unstable DNA sequences. We used the P-DEST vectors to express fluorecent <it>CP190 </it>at tolerable levels. Expression of <it>CP190 </it>using the UAS/Gal4 system, instead, led to either lethality or underdeveloped tissues. The expressed eGFP- or mRFP-tagged CP190 proteins are fully functional and rescued the lethality of the homozygous <it>CP190 </it>mutation. We visualized a wide range of CP190 distribution patterns in living cell nuclei, from thousands of tiny particles to less than ten giant ones, which likely reflects diverse organization of higher-order chromatin structures. We also visualized the fusion of multiple smaller insulator bodies into larger aggregates in living cells, which is likely reflective of the dynamic activities of reorganization of chromatin in living nuclei.</p> <p>Conclusion</p> <p>We have developed an efficient cloning system for expressing dosage-sensitive proteins in <it>Drosophila melanogaster</it>. This system successfully expresses functional fluorescent CP190 fusion proteins. The fluorescent CP190 proteins exist in insulator bodies of various numbers and sizes among cells from multiple living tissues. Furthermore, live imaging of the movements of these fluorescent-tagged proteins suggests that the assembly and disassembly of insulator bodies are normal activities in living cells and may be directed for regulating transcription.</p

Cinnamic acid and p-coumaric acid are metabolized to 4-hydroxybenzoic acid by Yarrowia lipolytica

Yarrowia lipolytica has been explored as a potential production host for flavonoid synthesis due to its high tolerance to aromatic acids and ability to supply malonyl-CoA. However, little is known about its ability to consume the precursors cinnamic and p-coumaric acid. In this study, we demonstrate that Y. lipolytica can consume these precursors through multiple pathways that are partially dependent on the cultivation medium. By monitoring the aromatic acid concentrations over time, we found that cinnamic acid is converted to p-coumaric acid. We identified potential proteins with a trans-cinnamate 4-monooxygenase activity in Y. lipolytica and constructed a collection of 15 knock-out strains to identify the genes responsible for the reaction. We identified YALI1_B28430g as the gene encoding for a protein that converts cinnamic acid to p-coumaric acid (designated as TCM1). By comparing different media compositions we found that complex media components (casamino acids and yeast extract) induce this pathway. Additionally, we discover the conversion of p-coumaric acid to 4-hydroxybenzoic acid. Our findings provide new insight into the metabolic capabilities of Y. lipolytica and hold great potential for the future development of improved strains for flavonoid production

The chromosomal association/dissociation of the chromatin insulator protein Cp190 of Drosophila melanogaster is mediated by the BTB/POZ domain and two acidic regions

<p>Abstract</p> <p>Background</p> <p>Chromatin insulators or boundary elements are a class of functional elements in the eukaryotic genome. They regulate gene transcription by interfering with promoter-enhancer communication. The Cp190 protein of <it>Drosophila </it><it>melanogaster </it>is essential to the function of at least three-types of chromatin insulator complexes organized by Su(Hw), CTCF and BEAF32.</p> <p>Results</p> <p>We mapped functional regions of Cp190 in vivo and identified three domains that are essential for the insulator function and for the viability of flies: the BTB/POZ domain, an aspartic acid-rich (D-rich) region and a C-terminal glutamic acid-rich (E-rich) region. Other domains including the centrosomal targeting domain and the zinc fingers are dispensable. The N-terminal CP190BTB-D fragment containing the BTB/POZ domain and the D-rich region is sufficient to mediate association with all three types of insulator complexes. The fragment however is not sufficient for insulator activity or viability. The Cp190 and CP190BTB-D are regulated differently in cells treated with heat-shock. The Cp190 dissociated from chromosomes during heat-shock, indicating that dissociation of Cp190 with chromosomes can be regulated. In contrast, the CP190BTB-D fragment didn't dissociate from chromosomes in the same heat-shocked condition, suggesting that the deleted C-terminal regions have a role in regulating the dissociation of Cp190 with chromosomes.</p> <p>Conclusions</p> <p>The N-terminal fragment of Cp190 containing the BTB/POZ domain and the D-rich region mediates association of Cp190 with all three types of insulator complexes and that the E-rich region of Cp190 is required for dissociation of Cp190 from chromosomes during heat-shock. The heat-shock-induced dissociation is strong evidence indicating that dissociation of the essential insulator protein Cp190 from chromosomes is regulated. Our results provide a mechanism through which activities of an insulator can be modulated by internal and external cues.</p

Stress granules as crucibles of ALS pathogenesis

Amyotrophic lateral sclerosis (ALS) is a fatal human neurodegenerative disease affecting primarily motor neurons. Two RNA-binding proteins, TDP-43 and FUS, aggregate in the degenerating motor neurons of ALS patients, and mutations in the genes encoding these proteins cause some forms of ALS. TDP-43 and FUS and several related RNA-binding proteins harbor aggregation-promoting prion-like domains that allow them to rapidly self-associate. This property is critical for the formation and dynamics of cellular ribonucleoprotein granules, the crucibles of RNA metabolism and homeostasis. Recent work connecting TDP-43 and FUS to stress granules has suggested how this cellular pathway, which involves protein aggregation as part of its normal function, might be coopted during disease pathogenesis

Determination of elemental compositions by gas chromatography - time of flight mass spectrometry using chemical and electron ionization.

n/