Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays

Background DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR) in this yeast species, as compared to S. cerevisiae. Results By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer). To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT) or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal medium as untreated control. DTT treatment was compared with literature data for S. cerevisiae, and revealed similarities, but also important differences between the two yeast species. Overexpression of HAC1, the most direct control for UPR genes, resulted in significant new understanding of this important regulatory pathway in P. pastoris, and generally in yeasts. Conclusion The differences observed between P. pastoris and S. cerevisiae underline the importance of DNA microarrays for industrial production strains. P. pastoris reacts to DTT treatment mainly by the regulation of genes related to chemical stimulus, electron transport and respiration, while the overexpression of HAC1 induced many genes involved in translation, ribosome biogenesis, and organelle biosynthesis, indicating that the regulatory events triggered by DTT treatment only partially overlap with the reactions to overexpression of HAC1. The high reproducibility of the results achieved with two different oligo sets is a good indication for their robustness, and underlines the importance of less stringent selection of regulated features, in order to avoid a large number of false negative results

Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays

Background DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR) in this yeast species, as compared to S. cerevisiae. Results By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer). To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT) or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal medium as untreated control. DTT treatment was compared with literature data for S. cerevisiae, and revealed similarities, but also important differences between the two yeast species. Overexpression of HAC1, the most direct control for UPR genes, resulted in significant new understanding of this important regulatory pathway in P. pastoris, and generally in yeasts. Conclusion The differences observed between P. pastoris and S. cerevisiae underline the importance of DNA microarrays for industrial production strains. P. pastoris reacts to DTT treatment mainly by the regulation of genes related to chemical stimulus, electron transport and respiration, while the overexpression of HAC1 induced many genes involved in translation, ribosome biogenesis, and organelle biosynthesis, indicating that the regulatory events triggered by DTT treatment only partially overlap with the reactions to overexpression of HAC1. The high reproducibility of the results achieved with two different oligo sets is a good indication for their robustness, and underlines the importance of less stringent selection of regulated features, in order to avoid a large number of false negative results

Kaonic atoms measurements at the DAΦNE collider : the SIDDHARTA-2 experiment

The X-ray spectroscopy measurements of light kaonic atoms’ deexcitation towards the fundamental level provide unique information on the low-energy Quantum ChromoDynamics (QCD) in the strangeness sector, being a direct probe of the kaon/nucleon interaction at threshold, unobtainable through the scattering experiments. In this framework, the SIDDHARTA-2 collaboration is going to perform the first kaonic deuterium 2p $\to$ 1s transition measurement at the DAΦNE collider of Istituto Nazionale di Fisica Nucleare – Laboratori Nazionali di Frascati. Combining this measurement with the kaonic hydrogen one performed by SIDDHARTA in 2009 it will be possible to obtain, in a model-independent way, the isospin-dependent antikaon-nucleon scattering lengths. The paper introduces the SIDDHARTA-2 setup, an upgraded version with respect to the one used for the kaonic hydrogen measurement, dedicated to the ambitious kaonic deuterium measurement, together with the preliminary results obtained during the kaonic helium run, preparatory for the SIDDHARTA-2 data taking campaign

TP53 mutation status divides myelodysplastic syndromes with complex karyotypes into distinct prognostic subgroups

Risk stratification is critical in the care of patients with myelodysplastic syndromes (MDS). Approximately 10% have a complex karyotype (CK), defined as more than two cytogenetic abnormalities, which is a highly adverse prognostic marker. However, CK-MDS can carry a wide range of chromosomal abnormalities and somatic mutations. To refine risk stratification of CK-MDS patients, we examined data from 359 CK-MDS patients shared by the International Working Group for MDS. Mutations were underrepresented with the exception of TP53 mutations, identified in 55% of patients. TP53 mutated patients had even fewer co-mutated genes but were enriched for the del(5q) chromosomal abnormality (p 10%), abnormal 3q, abnormal 9, and monosomy 7 as having the greatest survival risk. The poor risk associated with CK-MDS is driven by its association with prognostically adverse TP53 mutations and can be refined by considering clinical and karyotype features

probing strong interaction with siddharta 2

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Enhanced Data Return from Lunar Farside using RF-Optical TT and C

Science return and high bandwidth communications are key issues to support the foreseen endeavours on spaceflights to the Moon and beyond. For a given mass, power consumption and volume, laser communications can offer an increase in TM bandwidth over classical RF technology allowing for a variety of new options, specifically to missions that require very large distances, such as to the Moon and even beyond. This increase in TM data rate allows for more raw scientific data to be sent back to Earth where data processing can be performed on ground. Enhanced sensing techniques could be used that generate more science data and access during flight could be faster. This paper presents an overview of proof of concept test results obtained for optical telemetry return in a field test campaign together with ESA in October 2007. Based on the results obtained, a sample mission is outlined that shows an optical relay on a HALO trajectory at lunar farside, using an integrated RF-optical TT&C transponder concept

Estimation with Non-Ideal Training Information

We consider the problem of channel estimation when non-ideal training information (pilots) is available such as in Turbo equalization, where this information are probabilities about the transmitted symbols of varying reliability. We study how these probabilities can be incorporated into common estimation algorithms by observing the estimation error statistics. We consider the two cases that the probabilities are mapped to a hard- or soft-estimate of the transmitted symbol. It turns out that neither of the two estimates yields always better estimation error variances. However, the channel estimator becomes biased with hard-estimates and we conclude that for the two estimations algorithms analyzed in this paper, soft-estimates are the better choice