Altered expression response upon repeated gene repression in single yeast cells.

Cells must continuously adjust to changing environments and, thus, have evolved mechanisms allowing them to respond to repeated stimuli. While faster gene induction upon a repeated stimulus is known as reinduction memory, responses to repeated repression have been less studied so far. Here, we studied gene repression across repeated carbon source shifts in over 1,500 single Saccharomyces cerevisiae cells. By monitoring the expression of a carbon source-responsive gene, galactokinase 1 (Gal1), and fitting a mathematical model to the single-cell data, we observed a faster response upon repeated repressions at the population level. Exploiting our single-cell data and quantitative modeling approach, we discovered that the faster response is mediated by a shortened repression response delay, the estimated time between carbon source shift and Gal1 protein production termination. Interestingly, we can exclude two alternative hypotheses, i) stronger dilution because of e.g., increased proliferation, and ii) a larger fraction of repressing cells upon repeated repressions. Collectively, our study provides a quantitative description of repression kinetics in single cells and allows us to pinpoint potential mechanisms underlying a faster response upon repeated repression. The computational results of our study can serve as the starting point for experimental follow-up studies.

Phase I/IIa clinical trial of a novel hTERT peptide vaccine in men with metastatic hormone-naive prostate cancer.

In newly diagnosed metastatic hormone-naive prostate cancer (mPC), telomerase-based immunotherapy with the novel hTERT peptide vaccine UV1 can induce immune responses with potential clinical benefit. This phase I dose escalation study of UV1 evaluated safety, immune response, effects on prostate-specific antigen (PSA) levels, and preliminary clinical outcome. Twenty-two patients with newly diagnosed metastatic hormone-naïve PC (mPC) were enrolled; all had started androgen deprivation therapy and had no visceral metastases. Bone metastases were present in 17 (77%) patients and 16 (73%) patients had affected lymph nodes. Three dose levels of UV1 were given as intradermal injections combined with GM-CSF (Leukine®). Twenty-one patients in the intention-to-treat population (95%) received conformal radiotherapy. Adverse events reported were predominantly grade 1, most frequently injection site pruritus (86.4%). Serious adverse events considered possibly related to UV1 and/or GM-CSF included anaphylactic reaction in two patients and thrombocytopenia in one patient. Immune responses against UV1 peptides were confirmed in 18/21 evaluable patients (85.7%), PSA declined to <0.5 ng/mL in 14 (64%) patients and in ten patients (45%) no evidence of persisting tumour was seen on MRI in the prostatic gland. At the end of the nine-month reporting period for the study, 17 patients had clinically stable disease. Treatment with UV1 and GM-CSF gave few adverse events and induced specific immune responses in a large proportion of patients unselected for HLA type. The intermediate dose of 0.3 mg UV1 resulted in the highest proportion of, and most rapid UV1-specific immune responses with an acceptable safety profile. These results warrant further clinical studies in mPC.

Comprehensive quantitative comparison of the membrane proteome, phosphoproteome, and sialiome of human embryonic and neural stem cells.

Human embryonic stem cells (hESCs) can differentiate into neural stem cells (NSCs), which can further be differentiated into neurons and glia cells. Therefore, these cells have huge potential as source for treatment of neurological diseases. Membrane-associated proteins are very important in cellular signaling and recognition, and their function and activity are frequently regulated by post-translational modifications such as phosphorylation and glycosylation. To obtain information about membrane-associated proteins and their modified amino acids potentially involved in changes of hESCs and NSCs as well as to investigate potential new markers for these two cell stages, we performed large-scale quantitative membrane-proteomic of hESCs and NSCs. This approach employed membrane purification followed by peptide dimethyl labeling and peptide enrichment to study the membrane subproteome as well as changes in phosphorylation and sialylation between hESCs and NSCs. Combining proteomics and modification specific proteomics we identified a total of 5105 proteins whereof 57% contained transmembrane domains or signal peptides. The enrichment strategy yielded a total of 10,087 phosphorylated peptides in which 78% of phosphopeptides were identified with ≥99% confidence in site assignment and 1810 unique formerly sialylated N-linked glycopeptides. Several proteins were identified as significantly regulated in hESCs and NSC, including proteins involved in the early embryonic and neural development. In the latter group of proteins, we could identify potential NSC markers as Crumbs 2 and several novel proteins. A motif analysis of the altered phosphosites showed a sequence consensus motif (R-X-XpS/T) significantly up-regulated in NSC. This motif is among other kinases recognized by the calmodulin-dependent protein kinase-2, emphasizing a possible importance of this kinase for this cell stage. Collectively, this data represent the most diverse set of post-translational modifications reported for hESCs and NSCs. This study revealed potential markers to distinguish NSCs from hESCs and will contribute to improve our understanding on the differentiation process.

A novel method for the simultaneous enrichment, identification, and quantification of phosphopeptides and sialylated glycopeptides applied to a temporal profile of mouse brain development.

We describe a method that combines an optimized titanium dioxide protocol and hydrophilic interaction liquid chromatography to simultaneously enrich, identify and quantify phosphopeptides and formerly N-linked sialylated glycopeptides to monitor changes associated with cell signaling during mouse brain development. We initially applied the method to enriched membrane fractions from HeLa cells, which allowed the identification of 4468 unique phosphopeptides and 1809 formerly N-linked sialylated glycopeptides. We subsequently combined the method with isobaric tagging for relative quantification to compare changes in phosphopeptide and formerly N-linked sialylated glycopeptide abundance in the developing mouse brain. A total of 7682 unique phosphopeptide sequences and 3246 unique formerly sialylated glycopeptides were identified. Moreover 669 phosphopeptides and 300 formerly N-sialylated glycopeptides differentially regulated during mouse brain development were detected. This strategy allowed us to reveal extensive changes in post-translational modifications from postnatal mice from day 0 until maturity at day 80. The results of this study confirm the role of sialylation in organ development and provide the first extensive global view of dynamic changes between N-linked sialylation and phosphorylation.

Quantitative phosphoproteomic analysis of early alterations in protein phosphorylation by 2,3,7,8-tetrachlorodibenzo-p-dioxin.

A comprehensive quantitative analysis of changes in protein phosphorylation preceding or accompanying transcriptional activation by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in 5L rat hepatoma cells was performed using the SILAC approach. Following exposure of the cells to DMSO or 1 nM TCDD for 0.5 to 2 h, 5648 phosphorylated peptides corresponding to 2156 phosphoproteins were identified. Eight peptides exhibited a statistically significantly altered phosphorylation because of TCDD exposure and 22 showed a regulation factor of ≥ 1.5 in one of the experiments per time point. The vast majority of the TCCD-induced phosphorylation changes had not been reported before. The transcription factor ARNT, the obligate partner for gene activation by the TCDD-bound Ah receptor, exhibited an up-regulation of its Ser77 phosphorylation, a modification known to control the differential binding of ARNT homodimers and heterodimers to different enhancers suggesting that this phosphorylation represents a novel mechanism contributing to the alteration of gene expression by TCDD. Other proteins with altered phosphorylation included, among others, various transcriptional coregulators previously unknown to participate in TCDD-induced gene activation, regulators of small GTPases of the Ras superfamily, UBX domain-containing proteins and the oncogenic protein LYRIC. The results open up new directions for research on the molecular mechanisms of dioxin action and toxicity.

Modeling early treatment response in AML from cell-free tumor DNA.

Monitoring disease response after intensive chemotherapy for acute myeloid leukemia (AML) currently requires invasive bone marrow biopsies, imposing a significant burden on patients. In contrast, cell-free tumor DNA (ctDNA) in peripheral blood, carrying tumor-specific mutations, offers a less-invasive assessment of residual disease. However, the relationship between ctDNA levels and bone marrow blast kinetics remains unclear. We explored this in 10 AML patients with NPM1 and IDH2 mutations undergoing initial chemotherapy. Comparison of mathematical mixed-effect models showed that (1) inclusion of blast cell death in the bone marrow, (2) transition of ctDNA to peripheral blood, and (3) ctDNA decay in peripheral blood describes kinetics of blast cells and ctDNA best. The fitted model allows prediction of residual bone marrow blast content from ctDNA, and its scaling factor, representing clonal heterogeneity, correlates with relapse risk. Our study provides precise insights into blast and ctDNA kinetics, offering novel avenues for AML disease monitoring.

Effect of Using Different Chemical Dispersing Agents in Grain Size Analyses of Fluvial Sediments via Laser Diffraction Spectrometry.

Laser diffraction spectrometry allows for efficiently obtaining high-resolution grain size data. However, pretreatment and dispersion of aggregates in sediment samples are essential pre-requisites for acquiring accurate results using this method. This study evaluates the effectiveness of five dispersing agents in deflocculating the investigated fluvial sediments and the resulting grain size distribution obtained by laser diffraction spectrometry. We also examine the ability of the different dispersing agents to deflocculate sediment samples treated by thermal combustion. Distilled water presented a low efficiency in deflocculating the samples and yielded a near-zero clay content for samples with an expected clay content. The other chemical dispersants were effective in dispersing aggregates and yielding clay, albeit with different efficiencies. Calgon had the highest dispersing ability, followed closely by sodium tripolyphosphate. The performance of chemical treatment with sodium oxalate approaches that of sodium tripolyphosphate. However, it leads to the formation of precipitates in the samples, obscuring the actual grain size data. Sodium pyrophosphate derived the least amount of deflocculation among the four chemical dispersants. Furthermore, all the chemical dispersants were found to be ineffective in dispersing aggregates in samples treated by thermal combustion.

Leisure walks modulate the cognitive and affective representation of the corona pandemic: Employing Cognitive-Affective Maps within a randomized experimental design.

In response to the corona pandemic, many leisure activities have been restricted while walking has been explicitly endorsed by health authorities. We investigated how leisure walking affects individuals' attitudes to the pandemic. We used Cognitive-Affective Maps (CAMs) to measure individual's cognitive and affective attitudes toward the corona pandemic and related issues. In a controlled randomized experiment, we asked (N = 66) participants to draw a CAM before and after a walk. Participants in a control group drew CAMs before and after any self-chosen activity at home. We found that walking led to a more negative evaluation of the pandemic itself, likely due to a more intense reflection, while in everyday routines one has already adapted to it. In further qualitative post hoc assessments of the CAMs, we observed that negative concepts other than corona disappeared after walking. We conclude that leisure walks have complex effects on individuals' cognitive and affective conceptualization of the corona pandemic. Hence, the exact mechanisms of these effects need to be examined in future research. Our study has also shown that CAMs are a promising tool for measuring experimental interventions in health psychology.

First demonstration of leukemia imaging with the proliferation marker 18F-fluorodeoxythymidine.

UNLABELLED: Acute myeloid leukemia (AML) is a neoplasm of hematopoietic stem cells with partial or complete loss of the ability to differentiate but with preserved proliferation capacity. The aim of our study was to evaluate if the in vivo proliferation marker 3'-deoxy-3'-18F-fluorothymidine (FLT) is suitable for visualizing leukemia manifestation sites and if 18F-FLT is a surrogate marker for disease activity. METHODS: In this pilot study, 10 patients with AML underwent pretherapeutic imaging with 18F-FLT PET or 18F-FLT PET/CT. The biodistribution of 18F-FLT was assessed 60 min after intravenous injection of the radiotracer. Standardized uptake values were calculated for reference segments of bone marrow, spleen, and normal organs. 18F-FLT PET in 10 patients with benign pulmonary nodules and the absence of malignant or inflammatory disease served as controls. RESULTS: Retention of 18F-FLT was observed predominantly in bone marrow and spleen and was significantly higher in AML patients than in controls (mean 18F-FLT SUV in bone marrow, 11.5 and 6.6, P < 0.05; mean 18F-FLT SUV in spleen, 6.1 and 1.8, P < 0.05). Outside bone marrow, focal 18F-FLT uptake showed extramedullary manifestation sites of leukemia in 4 patients (meningeal disease, pericardial, abdominal, testicular, and lymph node), proven by other diagnostic procedures. CONCLUSION: This pilot study indicated that PET using 18F-FLT is able to visualize extramedullary manifestation sites of AML and reflects disease activity. Because 18F-FLT uptake in bone marrow is caused by a combination of both neoplastic and normal hematopoietic cells, the correlation of 18F-FLT uptake in bone marrow and leukemic blast infiltration did not reach statistical significance.

Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism.

Bedaquiline (BDQ), an ATP synthase inhibitor, is the first drug to be approved for treatment of multidrug-resistant tuberculosis in decades. Though BDQ has shown excellent efficacy in clinical trials, its early bactericidal activity during the first week of chemotherapy is minimal. Here, using microfluidic devices and time-lapse microscopy of Mycobacterium tuberculosis, we confirm the absence of significant bacteriolytic activity during the first 3-4 days of exposure to BDQ. BDQ-induced inhibition of ATP synthesis leads to bacteriostasis within hours after drug addition. Transcriptional and proteomic analyses reveal that M. tuberculosis responds to BDQ by induction of the dormancy regulon and activation of ATP-generating pathways, thereby maintaining bacterial viability during initial drug exposure. BDQ-induced bacterial killing is significantly enhanced when the mycobacteria are grown on non-fermentable energy sources such as lipids (impeding ATP synthesis via glycolysis). Our results show that BDQ exposure triggers a metabolic remodelling in mycobacteria, thereby enabling transient bacterial survival.

The auricle's cavum conchae composite graft in nasal reconstruction.

BACKGROUND: Autologous transplants consisting of skin and cartilage, so-called composite grafts (CGs), are useful in nasal reconstruction of multilayered defects. A CG from the auricle's cavum conchae serves both functional and esthetic demands. This article outlines the indications and the requirements of the CG, making special considerations to improve wound healing, and discusses our results in consideration with recent publications. METHODS: A retrospective case-control study assessing the functional and esthetic long-term results in the donor and recipient site is presented. RESULTS: Between 2005 and 2011, 91 patients received differently sized CGs of the auricle for nasal reconstruction. In 85/91 cases the donor site defect was closed using a retroauricular pedicled island flap. Six of 91 defects were closed primarily. Indications were multilayered defects of the nasal vestibule, the nasal floor, the inner nasal valve, and the lateral sidewall. The main indication for surgery was skin malignancies. One of 91 major and 14/91 minor complications were observed. Seventy-seven of 91 patients received a custom-made prosthesis to prevent stenotic scarring. The 2.5-year follow-up showed excellent results of stability and shape at the donor and recipient site. CONCLUSION: The auricular inner lining CG is a versatile and reliable autologous transplant, which is ideal for multilayered nasal reconstruction because of easy harvesting, little donor site morbidity, and its convex shape. Septal splints and custom-made prosthesis secure healing and prevent stenotic scarring.