The Benefits of Saccharomyces boulardii

ASaccharomyces boulardii strain, which does not carry any auxotrophic markers, was transformed with knockout constructs for the genes HIS3 and ADE2 using the dominant antibiotic marker genes encoding for kanamycin/G418- and nourseothricin/NATR resistance. Thereby, homozygous derivatives that were histidine or adenine deficient were obtained. Histidine prototrophy was easily reconstituted by transforming his-defective diploid derivatives with yeast plasmids carrying the HIS3 gene. Despite different attempts, for example, by creating a rme1::KANX rme1::NATR double-deleted S. boulardii yeast strain (RME1 encodes for Regulator of Meiosis), no visible sporulation to obtain haploid derivatives could be obtained. Besides, no filamentation properties of S. boulardii were observed. As previously mentioned, this yeast strain was confirmed to thrive at 37°C, a temperature disliked by some but not all S. cerevisiae strains used in the laboratory. S. boulardii is a diploid derivative of S. cerevisiae that does not sporulates and survives at temperatures as those found in the human gut. It can be easily manipulated by using conventional yeast methods to introduce auxotrophic markers and obtain heterozygous diploid knockout derivatives that can be transformed with yeast plasmids following conventional yeast protocols, thereby it could be even suited for biochemical and genetic research purposes

Eukaryotic translation elongation factor 1A (eEF1A) domain I from S. cerevisiae is required but not sufficient for inter-species complementation

Ethanolamine phosphoglycerol (EPG) is a protein modification attached exclusively to eukaryotic elongation factor 1A (eEF1A). In mammals and plants, EPG is linked to conserved glutamate residues located in eEF1A domains II and III, whereas in the unicellular eukaryote Trypanosoma brucei, only domain III is modified by a single EPG. A biosynthetic precursor of EPG and structural requirements for EPG attachment to T. brucei eEF1A have been reported, but nothing is known about the EPG modifying enzyme(s). By expressing human eEF1A in T. brucei, we now show that EPG attachment to eEF1A is evolutionarily conserved between T. brucei and Homo sapiens. In contrast, S. cerevisiae eEF1A, which has been shown to lack EPG is not modified in T. brucei. Furthermore, we show that eEF1A cannot functionally complement across species when using T. brucei and S. cerevisiae as model organisms. However, functional complementation in yeast can be obtained using eEF1A chimera containing domains II or III from other species. In contrast, yeast domain I is strictly required for functional complementation in S. cerevisia

XenDB: Full length cDNA prediction and cross species mapping in Xenopus laevis

BACKGROUND: Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have analyzed 350,468 Xenopus laevis Expressed Sequence Tags (ESTs) both to identify full length protein encoding sequences and to develop a unique database system to support comparative approaches between X. laevis and other model systems. DESCRIPTION: Using a suffix array based clustering approach, we have identified 25,971 clusters and 40,877 singleton sequences. Generation of a consensus sequence for each cluster resulted in 31,353 tentative contig and 4,801 singleton sequences. Using both BLASTX and FASTY comparison to five model organisms and the NR protein database, more than 15,000 sequences are predicted to encode full length proteins and these have been matched to publicly available IMAGE clones when available. Each sequence has been compared to the KOG database and ~67% of the sequences have been assigned a putative functional category. Based on sequence homology to mouse and human, putative GO annotations have been determined. CONCLUSION: The results of the analysis have been stored in a publicly available database XenDB . A unique capability of the database is the ability to batch upload cross species queries to identify potential Xenopus homologues and their associated full length clones. Examples are provided including mapping of microarray results and application of 'in silico' analysis. The ability to quickly translate the results of various species into 'Xenopus-centric' information should greatly enhance comparative embryological approaches. Supplementary material can be found at

Fast online 3D reconstruction of dynamic scenes from individual single-photon detection events

In this paper, we present an algorithm for online 3D reconstruction of dynamic scenes using individual times of arrival (ToA) of photons recorded by single-photon detector arrays. One of the main challenges in 3D imaging using single-photon Lidar is the integration time required to build ToA histograms and reconstruct reliable 3D profiles in the presence of non-negligible ambient illumination. This long integration time also prevents the analysis of rapid dynamic scenes using existing techniques. We propose a new method which does not rely on the construction of ToA histograms but allows, for the first time, individual detection events to be processed online, in a parallel manner in different pixels, while accounting for the intrinsic spatiotemporal structure of dynamic scenes. Adopting a Bayesian approach, a Bayesian model is constructed to capture the dynamics of the 3D profile and an approximate inference scheme based on assumed density filtering is proposed, yielding a fast and robust reconstruction algorithm able to process efficiently thousands to millions of frames, as usually recorded using single-photon detectors. The performance of the proposed method, able to process hundreds of frames per second, is assessed using a series of experiments conducted with static and dynamic 3D scenes and the results obtained pave the way to a new family of real-time 3D reconstruction solutions

Protein disulfide isomerase acts as an injury response signal that enhances fibrin generation via tissue factor activation

The activation of initiator protein tissue factor (TF) is likely to be a crucial step in the blood coagulation process, which leads to fibrin formation. The stimuli responsible for inducing TF activation are largely undefined. Here we show that the oxidoreductase protein disulfide isomerase (PDI) directly promotes TF-dependent fibrin production during thrombus formation in vivo. After endothelial denudation of mouse carotid arteries, PDI was released at the injury site from adherent platelets and disrupted vessel wall cells. Inhibition of PDI decreased TF-triggered fibrin formation in different in vivo murine models of thrombus formation, as determined by intravital fluorescence microscopy. PDI infusion increased — and, under conditions of decreased platelet adhesion, PDI inhibition reduced — fibrin generation at the injury site, indicating that PDI can directly initiate blood coagulation. In vitro, human platelet–secreted PDI contributed to the activation of cryptic TF on microvesicles (microparticles). Mass spectrometry analyses indicated that part of the extracellular cysteine 209 of TF was constitutively glutathionylated. Mixed disulfide formation contributed to maintaining TF in a state of low functionality. We propose that reduced PDI activates TF by isomerization of a mixed disulfide and a free thiol to an intramolecular disulfide. Our findings suggest that disulfide isomerases can act as injury response signals that trigger the activation of fibrin formation following vessel injury

Fully-automated root image analysis (faRIA)

High-throughput root phenotyping in the soil became an indispensable quantitative tool for the assessment of effects of climatic factors and molecular perturbation on plant root morphology, development and function. To efficiently analyse a large amount of structurally complex soil-root images advanced methods for automated image segmentation are required. Due to often unavoidable overlap between the intensity of fore- and background regions simple thresholding methods are, generally, not suitable for the segmentation of root regions. Higher-level cognitive models such as convolutional neural networks (CNN) provide capabilities for segmenting roots from heterogeneous and noisy background structures, however, they require a representative set of manually segmented (ground truth) images. Here, we present a GUI-based tool for fully automated quantitative analysis of root images using a pre-trained CNN model, which relies on an extension of the U-Net architecture. The developed CNN framework was designed to efficiently segment root structures of different size, shape and optical contrast using low budget hardware systems. The CNN model was trained on a set of 6465 masks derived from 182 manually segmented near-infrared (NIR) maize root images. Our experimental results show that the proposed approach achieves a Dice coefficient of 0.87 and outperforms existing tools (e.g., SegRoot) with Dice coefficient of 0.67 by application not only to NIR but also to other imaging modalities and plant species such as barley and arabidopsis soil-root images from LED-rhizotron and UV imaging systems, respectively. In summary, the developed software framework enables users to efficiently analyse soil-root images in an automated manner (i.e. without manual interaction with data and/or parameter tuning) providing quantitative plant scientists with a powerful analytical tool. © 2021, The Author(s)

The response to unfolded protein is involved in osmotolerance of Pichia pastoris

Background The effect of osmolarity on cellular physiology has been subject of investigation in many different species. High osmolarity is of importance for biotechnological production processes, where high cell densities and product titers are aspired. Several studies indicated that increased osmolarity of the growth medium can have a beneficial effect on recombinant protein production in different host organisms. Thus, the effect of osmolarity on the cellular physiology of Pichia pastoris, a prominent host for recombinant protein production, was studied in carbon limited chemostat cultures at different osmolarities. Transcriptome and proteome analyses were applied to assess differences upon growth at different osmolarities in both, a wild type strain and an antibody fragment expressing strain. While our main intention was to analyze the effect of different osmolarities on P. pastoris in general, this was complemented by studying it in context with recombinant protein production. Results In contrast to the model yeast Saccharomyces cerevisiae, the main osmolyte in P. pastoris was arabitol rather than glycerol, demonstrating differences in osmotic stress response as well as energy metabolism. 2D Fluorescence Difference Gel electrophoresis and microarray analysis were applied and demonstrated that processes such as protein folding, ribosome biogenesis and cell wall organization were affected by increased osmolarity. These data indicated that upon increased osmolarity less adaptations on both the transcript and protein level occurred in a P. pastoris strain, secreting the Fab fragment, compared with the wild type strain. No transcriptional activation of the high osmolarity glycerol (HOG) pathway was observed at steady state conditions. Furthermore, no change of the specific productivity of recombinant Fab was observed at increased osmolarity. Conclusion These data point out that the physiological response to increased osmolarity is different to S. cerevisiae. Increased osmolarity resulted in an unfolded protein response (UPR) like response in P. pastoris and lead to pre-conditioning of the recombinant Fab producing strain of P. pastoris to growth at high osmolarity. The current data demonstrate a strong similarity of environmental stress response mechanisms and recombinant protein related stresses. Therefore, these results might be used in future strain and bioprocess engineering of this biotechnologically relevant yeast

Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris

<p>Abstract</p> <p>Background</p> <p><it>Pichia pastoris </it>is widely used as a production platform for heterologous proteins and model organism for organelle proliferation. Without a published genome sequence available, strain and process development relied mainly on analogies to other, well studied yeasts like <it>Saccharomyces cerevisiae</it>.</p> <p>Results</p> <p>To investigate specific features of growth and protein secretion, we have sequenced the 9.4 Mb genome of the type strain DSMZ 70382 and analyzed the secretome and the sugar transporters. The computationally predicted secretome consists of 88 ORFs. When grown on glucose, only 20 proteins were actually secreted at detectable levels. These data highlight one major feature of <it>P. pastoris</it>, namely the low contamination of heterologous proteins with host cell protein, when applying glucose based expression systems. Putative sugar transporters were identified and compared to those of related yeast species. The genome comprises 2 homologs to <it>S. cerevisiae </it>low affinity transporters and 2 to high affinity transporters of other Crabtree negative yeasts. Contrary to other yeasts, <it>P. pastoris </it>possesses 4 H⁺/glycerol transporters.</p> <p>Conclusion</p> <p>This work highlights significant advantages of using the <it>P. pastoris </it>system with glucose based expression and fermentation strategies. As only few proteins and no proteases are actually secreted on glucose, it becomes evident that cell lysis is the relevant cause of proteolytic degradation of secreted proteins. The endowment with hexose transporters, dominantly of the high affinity type, limits glucose uptake rates and thus overflow metabolism as observed in <it>S. cerevisiae</it>. The presence of 4 genes for glycerol transporters explains the high specific growth rates on this substrate and underlines the suitability of a glycerol/glucose based fermentation strategy. Furthermore, we present an open access web based genome browser <url>http://www.pichiagenome.org</url>.</p

Phrenic nerve palsy during ablation of atrial fibrillation using a 28-mm cryoballoon catheter: predictors and prevention

Purpose: The purposes of this study were to determine whether predictors of phrenic nerve palsy (PNP) exist and to test whether a standardized ablation protocol may prevent PNP during cryoballoon (CB) ablation using the 28mm CB. Methods: Three-dimensional (3D) geometry of the pulmonary veins (PV) and their relationship to the superior vena cava (SVC) was analyzed. Phrenic nerve (PN) stimulation was performed during ablation of the right-sided PVs with a 28-mm CB. The freezing cycle was immediately terminated in case of loss of PN capture. Results: Sixty-five patients (age, 58 ± 11years; ejection fraction, 0.59 ± 0.06; left atrial size, 40 ± 5mm) with paroxysmal atrial fibrillation were included. No persistent PNP was observed. Transient PNP occurred in 4 of 65 patients (6%). PN function normalized within 24h in all four patients. A short distance between the right superior PV and the SVC was significantly associated with PNP, but left atrial and 3D PV anatomy were not. Low temperature early during the freezing cycle (<−41°C at 30s) predicted PNP with a sensitivity and a specificity of 100 and 98%, respectively. Conclusion: The anatomical relationship between the right superior PV and the SVC is a preprocedural predictor for the development of transient PNP, and low temperature early during ablation at the right superior PV is a sensitive warning sign of impending PNP. Despite the use of the 28mm CB, transient PNP occurred in 6% of patients undergoing CB ablatio