The Architecture And Dynamics Of Gene Regulatory Networks Directing Cell-Fate Choice During Murine Hematopoiesis

Mammals produce hundreds of billions of new blood cells every day througha process known as hematopoiesis. Hematopoiesis starts with stem cells that develop into all the different types of cells found in blood by changing their genome-wide gene expression. The remodeling of genome-wide gene expression can be primarily attributed to a special class of proteins called transcription factors (TFs) that can activate or repress other genes, including genes encoding TFs. TFs and their targets therefore form recurrent networks called gene regulatory networks (GRNs). GRNs are crucial during physiological developmental processes, such as hematopoiesis, while abnormalities in the regulatory interactions of GRNs can be detrimental to the organisms. To this day we do not know all the key compo-nents that comprise hematopoietic GRNs or the complete set of their regulatory interactions. Inference of GRNs directly from genetic experiments is low throughput and labor intensive, while computational inference of comprehensive GRNs is challenging due to high processing times. This dissertation focuses on deriving the architecture and the dynamics of hematopoietic GRNs from genome-wide gene expression data obtained from high-resolution time-series experiments. The dissertation also aims to address the technical challenge of speeding up the process of GRN inference. Here GRNs are inferred and modeled using gene circuits, a data-driven method based on Ordinary Differential Equations (ODEs). In gene circuits, the rate of change of a gene product depends on regulatory influences from other genes encoded as a set of parameters that are inferred from time-series data. A twelve-gene GRN comprising genes encoding key TFs and cytokine receptors involved in erythrocyte-neutrophil differentiation was inferred from a high-resolution time-series dataset of the in vitro differentiation of a multipotential cell line. The inferred GRN architecture agreed with prior empirical evidence and pre- dicted novel regulatory interactions. The inferred GRN model was also able to predict the outcome of perturbation experiments, suggesting an accurate inference of GRN architecture. The dynamics of the inferred GRN suggested an alternative explanation to the currently accepted sequence of regulatory events during neutrophil differentiation. The analysis of the model implied that two TFs, C/EBPα and Gfi1, initiate cell-fate choice in the neutrophil lineage, while PU.1, believed to be a master regulator of all white-blood cells, is activated only later. This inference was confirmed in a single-cell RNA-Seq dataset from mouse bone marrow, in which PU.1 upregulation was preceded by C/EBPα and Gfi1 upregulation. This dissertation also presents an analysis of a high-temporal resolution genome-wide gene expression dataset of in vitro macrophage-neutrophil differentiation. Analysis of these data reveal that genome-wide gene expression during differentiation is highly dynamic and complex. A large-scale transition is observed around 8h and shown to be related to wide-spread physiological remodeling of the cells. The genes associated by myeloid differentiation mainly change during the first 4 hours, implying that the cell-fate decision takes place in the first four hours of differentiation. The dissertation also presents a new classification-based model-training technique that addresses the challenge of the high computational cost of inferring GRNs. This method, called Fast Inference of Gene Regulation (FIGR), is demonstrated to be two orders magnitude faster than global non-linear optimization techniques and its computational complexity scales much better with GRN size. This work has demonstrated the feasibility of simulating relatively large realistic GRNs using a dynamical and mechanistically accurate model coupled to high-resolution time series data and that such models can yield novel biological insight. Taken together with the macrophage-neutrophil dataset and the computationally efficient GRN inference methodology, this work should open up new avenues for modeling more comprehensive GRNs in hematopoiesis and the broader field of developmental biology

Disk emission and atmospheric absorption lines in black hole candidate 4U 1630-472

We re-analyzed SUZAKU data of the black hole candidate 4U 1630-472 being in the high/soft state. We show that the continuum X-ray spectrum of 4U 1630-472 with iron absorption lines can be satisfactorily modeled by the spectrum from an accretion disk atmosphere. Absorption lines of highly ionized iron originating in hot accretion disk atmosphere can be an alternative or complementary explanation to the wind model usually favored for these type of sources. We model continuum and line spectra using a single model. Absorption lines of highly ionized iron can origin in upper parts of the disk atmosphere which is intrinsically hot due to high disk temperature. Iron line profiles computed with natural, thermal and pressure broadenings match very well observations. We showed that the accretion disk atmosphere can effectively produce iron absorption lines observed in 4U 1630-472 spectrum. Absorption line arising in accretion disk atmosphere is the important part of the observed line profile, even if there are also other mechanisms responsible for the absorption features. Nevertheless, the wind theory can be an artifact of the fitting procedure, when the continuum and lines are fitted as separate model components.Comment: 10 pages, 4 figures, accepted by Astronomy and Astrophysic

Cardiac responses to hypoxia: the role of pyruvate dehydrogenase complex in carbohydrate utilisation

Accelerated carbohydrate utilisation and suppressed lipid oxidative metabolism are hallmarks of heart failure (HF). Hypoxia mimics failing heart metabolic reprogramming and has been suggested to play a role in cardiac metabolic switch. One aspect of the regulation of cardiac energy metabolism is the pyruvate dehydrogenase complex (PDC). Hypoxia inducible factor (HIF) signalling is thought regulate hypoxia-induced adaptations. HIF transcriptional activity is controlled by prolyl hydroxylase domain (PHD) protein and factor inhibiting HIF (FIH-1). In chapter 3 revealed that relative to baseline, acute hypoxia increased cardiac lactate efflux and suppressed fatty acid oxidation (FAO) rates in non-treated isolated mouse hearts with final cardiac recovery being 63% of baseline values. Hypoxic and post-hypoxic PDC activation, via dichloroacetate (DCA), decreased cardiac lactate release and FAO during reoxygenation, but failed to improve cardiac recovery relative to control hearts. Chapter 4 sought to establish how chronic hypoxia (11%) upregulates cardiac glycolytic flux, determined via 3H-glucose. Findings of this chapter indicate that of four enzymes considered to set the pace of glycolysis, upregulated pyruvate kinase (PK) flux, appears to explain accelerated hypoxia-induced cardiac glycolytic flux. Western blotting analysis revealed increased PK M2 protein isoform. Sustained hypoxia increased pentose phosphate pathway (PPP) flux, but left lactate accumulation unaltered. Chapter 5 examined the role of sustained in vivo hypoxia in modulating cardiac tolerance to subsequent acute H/R injury and chronic PDC activation in modifying hypoxic heart tolerance to acute injury. Chronic hypoxia reduced cardiac tolerance to H/R injury accompanied by increased glycolytic flux and lactate efflux during reoxygenation injury. Chronic PDC activation improved hypoxic heart tolerance to the acute injury and normalized cardiac metabolic flux and reduced tissue lactate accumulation during reoxygenation, indicative of increased carbohydrate oxidation. Collectively, the data appear to imply that forced carbohydrate oxidation normalizes hypoxic heart recovery from acute injury. In chapter 6 we demonstrated that global FIH-1 deletion increased isolated heart glycolytic flux at baseline and during reoxygenated. FIH-1 KO hearts displayed increased reoxygenated hexokinase (HK) and PK activities, but no changes in PK protein isoforms. Functional analysis revealed that FIH-1 deficiency does not affect isolated heart function at baseline and in response to acute injury. Acute PDC activation does not appear to improve cardiac function during acute hypoxic stress. Conversely, chronic PDC activation normalized, via restored metabolic flux, cardiac tolerance to acute injury following sustained in vivo hypoxia. Furthermore, the present thesis revealed increased PPP flux following sustained in vivo hypoxia, and proposed a pivotal role PKM2 may play in the regulation of hypoxic heart carbohydrate metabolism. In addition, we identified FIH-1 as a novel regulator of cardiac carbohydrate metabolism at baseline and following acute hypoxic injury

How to make a better magnet? Insertion of additional bridging ligands into a magnetic coordination polymer

A three-dimensional cyanide-bridged coordination polymer based on FeII (S = 2) and NbIV (S = 1/2) {[FeII(H2O)2]2[NbIV(CN)8]·4H2O}n (Fe2Nb) was modified at the self-assembly stage by inserting an additional formate HCOO− bridge into its cyanide framework. The resulting mixed-bridged {(NH4)[(H2O)FeII-(μ-HCOO)-FeII(H2O)][NbIV(CN)8]·3H2O}n (Fe2NbHCOO) exhibited additional FeII-HCOO-FeII structural motifs connecting each of the two FeII centers. The insertion of HCOO− was possible due to the substitution of some of the aqua ligands and crystallization water molecules in the parent framework by formate anions and ammonium cations. The formate molecular bridge not only shortened the distance between FeII ions in Fe2NbHCOO from 6.609 Å to 6.141 Å, but also created additional magnetic interaction pathways between the magnetic centers, resulting in an increase in the long range magnetic ordering temperature from 43 K for Fe2Nb to 58 K. The mixed-bridged Fe2NbHCOO also showed a much broader magnetic hysteresis loop of 0.102 T, compared to 0.013 T for Fe2Nb

Upnp-Based Discovery And Management Of Hypervisors And Virtual Machines

The paper introduces a Universal Plug and Play based discovery and management toolkitthat facilitates collaboration between cloud infrastructure providers and users. The presentedtools construct a unified hierarchy of devices and their management-related services, thatrepresents the current deployment of users’ (virtual) infrastructures in the provider’s (physical)infrastructure as well as the management interfaces of respective devices. The hierarchycan be used to enhance the capabilities of the provider’s infrastructure management system.To maintain user independence, the set of management operations exposed by a particulardevice is always defined by the device owner (either the provider or user)

Likely additive ergogenic effects of combined pre-exercise dietary nitrate and caffeine ingestion in trained cyclists.

Aims. To evaluate the possible additive effects of beetroot juice plus caffeine on exercise performance. Methods. In a randomized, double-blinded study design, fourteen healthy well-trained men aged 22 ± 3 years performed four trials on different occasions following preexercise ingestion of placebo (PLA), PLA plus 5mg/kg caffeine (PLA+C), beetroot juice providing 8mmol of nitrate (BR), and beetroot juice plus caffeine (BR+C). Participants cycled at 60% maximal oxygen uptake (VO2max) for 30min followed by a time to exhaustion (TTE) trial at 80% VO2max. Saliva was collected before supplement ingestion, before exercise, and after the TTE trial for salivary nitrate, nitrite, and cortisol analysis. Results. In beetroot trials, saliva nitrate and nitrite increased >10-fold before exercise compared with preingestion ( ≤ 0.002). TTE in BR+C was 46% higher than in PLA ( = 0.096) and 18% and 27% nonsignificant TTE improvements were observed on BR+C compared with BR and PLA+C alone, respectively. Lower ratings of perceived exertion during TTE were found during 80% VO2max on BR+C compared with PLA and PLA+C ( < 0.05 for both). Conclusions. Acute preexercise beetroot juice coingestion with caffeine likely has additive effects on exercise performance compared with either beetroot or caffeine alone

Review of commercially available biomarkers in the diagnosis of prostate cancer

Introduction Diagnosing prostate cancer is a complex process. Although PSA testing remains the basic laboratory study, new biomarkers and test are evolving quickly. Aim The aim of this review was to summarize available tests and markers for diagnosing prostate cancer. Materials and methods Literature search was conducted using PubMed and Cohrane databases. Results and conclusions Detailed description of ExoDx, PCA3, SelectMDx, Mi-prostate Score, SChLAP1, PSA, PHI, 4K Score tests was presented. Available test ease qualification for a prostate biopsy or observation. Patients should be qualified individually in deciding on  a specific test to be performed. Urologists should be aware of each test mechanism and limitations.

Ceramika artystyczna/obiekt, 2019: "Tryptyk śląski"

"Śląsk jest dla mnie klinkierowy. Twardy, piękny i doświadczony. Mocno spieczony i zahartowany. Kolory cegły, połyskujące na starych kominach, mają piękne odcienie bordo, cynobru i fioletowawej czerwieni. Kolejne przepływające przezeń chwile wypłukują owe barwy i ranią twardą, jednolitą powierzchnię rysunkiem spękań. Mimo to trudno mi było go zobrazować, ująć w twórczą formę. Punktem wyjścia był dla mnie pamiątkowy zegar rodzinny męża. Wiszący w naszym salonie, niedziałający, ale piękny artefakt, przypominający nam o śląskim dziedzictwie babci Cecylii i dziadka Franciszka." [...] (fragm.