Hematopoietic differentiation: a coordinated dynamical process towards attractor stable states

<p>Abstract</p> <p>Background</p> <p>The differentiation process, proceeding from stem cells towards the different committed cell types, can be considered as a trajectory towards an attractor of a dynamical process. This view, taking into consideration the transcriptome and miRNome dynamics considered as a whole, instead of looking at few 'master genes' driving the system, offers a novel perspective on this phenomenon. We investigated the 'differentiation trajectories' of the hematopoietic system considering a genome-wide scenario.</p> <p>Results</p> <p>We developed serum-free liquid suspension unilineage cultures of cord blood (CB) CD34⁺hematopoietic progenitor cells through erythroid (E), megakaryocytic (MK), granulocytic (G) and monocytic (Mo) pathways. These cultures recapitulate physiological hematopoiesis, allowing the analysis of almost pure unilineage precursors starting from initial differentiation of HPCs until terminal maturation. By analyzing the expression profile of protein coding genes and microRNAs in unilineage CB E, MK, G and Mo cultures, at sequential stages of differentiation and maturation, we observed a coordinated, fully interconnected and scalable character of cell population behaviour in both transcriptome and miRNome spaces reminiscent of an attractor-like dynamics. MiRNome and transcriptome space differed for a still not terminally committed behaviour of microRNAs.</p> <p>Conclusions</p> <p>Consistent with their roles, the transcriptome system can be considered as the state space of a cell population, while the continuously evolving miRNA space corresponds to the tuning system necessary to reach the attractor. The behaviour of miRNA machinery could be of great relevance not only for the promise of reversing the differentiated state but even for tumor biology.</p

Régulation dynamique des protéines impliquée dans la transduction du signal par l'oxyde nitrique

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

“Esquilino chiama Roma”. Conoscenza integrata, condivisa e applicata per la rigenerazione urbana grazie ad una heritage community

Among the richest and most problematic districts in Rome, the Rione Esquilino is marked by very dense historical and archaeological evidence that highlights the city’s grandeur. Here, the complicated overlapping of monuments and late XIXth century urban fabric intertwines with a multi-ethnic social structure. This combines old and new residents, Italians and Europeans, tourists attracted by cheap accommodation, economic operators, mostly Asian and moreover engaged in non-legal activities, and numerous homeless. Such problematic yet fascinating urban situation has stimulated the citizen’s reactions since years and induces the inhabitants to fight for the redemption of the Rione. Recently, the restoration of Bernini’s statue of Santa Bibiana has focussed on the need for a scientific and operating understanding of the causes that generate such urban and social degradation. The assumption that “one cannot inhabit or govern a place without understanding it”, was the trigger to establish the ‘Gruppo di lavoro via Giolitti’, a free working group without legal status. This team has given birth to an urban forum to involve those who believe in the urgency of a shared and applied knowledge process, intended as a collaboration platform based on the assessment of material and immaterial values of cultural heritage. Heritage, in fact, may become a meaningful field of exchange among people that may not share needs and interests, being threatened by primary needs and imminent discomfort, or by the claim of identity living spaces. Connections and gaps between Esquilino and the rest of historic centre of Rome are so evident that the name given to the forum “Esquilino chiama Roma” becomes self-significant. In 2018 three sessions open to the citizenship allowed the team to reorganize the “research- action” into three operational directions: an urban project aiming at the requalification of the district; a program of sustainable socio-cultural cohesion; an evaluation process of the cultural heritage. Integration and interaction among the three, which still lack in the city’s public policies and, also, in Unesco management plan for Rome’s historic centre - encourages in this intent. Equally encouraging is the positive welcome to contracts among public and private stakeholders aiming at sustaining research, at starting-up fund-raising programs, at supporting studies and projects and at implementing knowledge systems on the web. These are actions to create a learning community, at the basis of a heritage community, as suggested by the 2005 Faro Convention

Photophysics of horse heart cytochrome c: time-resolved resonance Raman and transient absorption studies

International audienceTransient resonant Raman studies with 0.6 ps time resolution demonstrate that the methionine is photodissociated from ferrous, but not from ferric cytochrome c. Heme cooling and ligand recombination occur in 1.8 and 5 ps respectively. © 2004 Optical Society of Americ

Photodissociation of heme distal methionine in ferrous cytochrome c revealed by subpicosecond time-resolved resonance raman spectroscopy

International audienceCytochrome c (cyt c) is anelectron-transfer heme protein that also binds nitric oxide (NO). In resting cyt c, two endogenous ligands of the heme iron are histidine-18 (His) and methionine-80 (Met) side chains, and NO binding requires the cleavage of one of the axial bonds. Previous femtosecond transient absorption studies suggested the photolysis of either Fe-His or Fe-Met bonds. We aimed at unequivocally identifying the internal side chain that is photodissociated in ferrous cyt c and at monitoring heme structural dynamics, by means of time-resolved resonance Raman (TR3) spectroscopy with ~0.6 ps time resolution. The Fe-His stretching mode at 216 cm-1 has been observed in photoproduct TR3 spectra for the first time for a c-type heme. The same transient mode was observed for a model ferrous cyt c N-fragment (residues 1-56) ligated with two His in the resting state. Our TR3 data reveal that upon ferrous cyt c photoexcitation, (i) distal Met side chain is instantly released, producing a five-coordinated domed heme structure, (ii) proximal His side chain, coupled to the heme, exhibits distortion due to strain exerted by the protein, and (iii) alteration in heme-cysteine coupling takes place along with the relaxation of the protein-induced deformations of the heme macrocycle. Copyright 2004 American Chemical Society

Ultrafast heme dynamics in ferrous versus ferric cytochrome c studied by time-resolved resonance Raman and transient absorption spectroscopy.

International audienceCytochrome c (Cyt c) is a heme protein involved in electron transfer and also in apoptosis. Its heme iron is bisaxially ligated to histidine and methionine side chains and both ferric and ferrous redox states are physiologically relevant, as well as a ligand exchange between internal residue and external diatomic molecule. The photodissociation of internal axial ligand was observed for several ferrous heme proteins including Cyt c, but no time-resolved studies have been reported on ferric Cyt c. To investigate how the oxidation state of the heme influences the primary photoprocesses, we performed a comprehensive comparative study on horse heart Cyt c by subpicosecond time-resolved resonance Raman and femtosecond transient absorption spectroscopy. We found that in ferric Cyt c, in contrast to ferrous Cyt c, the photodissociation of an internal ligand does not take place, and relaxation dynamics is dominated by vibrational cooling in the ground electronic state of the heme. The intermolecular vibrational energy transfer was found to proceed in a single phase with a temperature decay of 7 ps in both ferric and ferrous Cyt c. For ferrous Cyt c, the instantaneous photodissociation of the methionine side chain from the heme iron is the dominant event, and its rebinding proceeds in two phases, with time constants of 5 and 16 ps. A mechanism of this process is discussed, and the difference in photoinduced coordination behavior between ferric and ferrous Cyt c is explained by an involvement of the excited electronic state coupled with conformational relaxation of the heme

Molecular basis for nitric oxide dynamics and affinity with Alcaligenes xylosoxidans cytochrome c'

International audienceThe bacterial heme protein cytochrome ć from Alcaligenes xylosoxidans (AXCP) reacts with nitric oxide (NO) to form a 5-coordinate ferrous nitrosyl heme complex. The crystal structure of ferrous nitrosyl AXCP has previously revealed that NO is bound in an unprecedented manner on the proximal side of the heme. To understand how the protein structure of AXCP controls NO dynamics, we performed absorption and Raman time-resolved studies at the heme level as well as a molecular computational dynamics study at the entire protein structure level. We found that after NO dissociation from the heme iron, the structure of the proximal heme pocket of AXCP confines NO close to the iron so that an ultrafast (7 ps) and complete (99 ± 1%) geminate rebinding occurs, whereas the proximal histidine does not rebind to the heme iron on the timescale of NO geminate rebinding. The distal side controls the initial NO binding, whereas the proximal heme pocket controls its release. These dynamic properties allow the trapping of NO within the protein core and represent an extreme behavior observed among heme proteins

An apoA-I mimetic peptide increases LCAT activity in mice through increasing HDL concentration

<p>Lecithin cholesterol acyltransferase (LCAT) plays a key role in the reverse cholesterol transport (RCT) process by converting cholesterol to cholesteryl ester to form mature HDL particles, which in turn deliver cholesterol back to the liver for excretion and catabolism. HDL levels in human plasma are negatively correlated with cardiovascular risk and HDL functions are believed to be more important in atheroprotection. This study investigates whether and how D-4F, an apolipoprotein A-I (apoA-I) mimetic peptide, influences LCAT activity in the completion of the RCT process. We demonstrated that the apparent rate constant value of the LCAT enzyme reaction gives a measure of LCAT activity and determined the effects of free metals and a reducing agent on LCAT activity, showing an inhibition hierarchy of Zn²⁺&#62;Mg²⁺&#62;Ca²⁺ and no inhibition with &#946;-mercaptoethanol up to 10 mM. We reconstituted nano-disc particles using apoA-I or D-4F with phospholipids. These particles elicited good activity <i>in vitro</i> in the stimulation of cholesterol efflux from macrophages through the ATP-binding cassette transporter A1 (ABCA1). With these particles we studied the LCAT activity and demonstrated that D-4F did not activate LCAT <i>in vitro</i>. Furthermore, we have done <i>in vivo</i> experiments with apoE-null mice and demonstrated that D-4F (20 mg/kg body weight, once daily subcutaneously) increased LCAT activity and HDL level as well as apoA-I concentration at 72 hours post initial dosing. Finally, we have established a correlation between HDL concentration and LCAT activity in the D-4F treated mice.</p