Simultaneous detection of aneuploidies for chromosomes 4, 6, 10 and 17 by automated four colour I-FISH in high hyperdiploid acute lymphoblastic leukemia : diagnostic assessment, clonal heterogeneity and chromosomal instability in adults

SummarySimultaneous detection of aneuploidies for chromosomes 4, 6,10 and 17 by automated four color l-FISH in high hyperdiploid acute lymphoblastic leukemia: diagnostic assessment, clonal heterogeneity and chromosomal instability in adultsAnna Talamo BlandinService de Génétique Médicale, Unité de Cytogénétique du Cancer, CHUVAcute lymphoblastic leukemia (ALL) is a malignant hemopathy characterized by the accumulation of the immature lymphoid cells in the bone marrow and, most often, in the peripheral blood. ALL is a heterogeneous disease with distinct biological and prognostic entities. At diagnosis, cytogenetic and molecular findings constitute important and independent prognostic factors. High hyperdiploidy with 51-67 chromosomes (HeH), one of the largest cytogenetic subsets of ALL, in childhood particularly, is generally associated with a relatively favorable outcome. Chromosome gain is nonrandom, extracopies of some chromosome occurring more frequently than those of others. Concurrent presence of trisomy for chromosomes 4, 10 and 17 confers an especially good prognosis. The first aim of our work was to develop an automated four color interphase fluorescence in situ hybridization (l-FISH) methodology and to assess its ability to detect concurrent aneuploidies 4, 6, 10 and 17 in 10 ALL patients. Various combinations of aneuploidies were identified. All clones detected by conventional cytogenetics were also observed by l-FISH. However, in all patients, l-FISH revealed numerous additional abnormal clones, leading to a high level of clonal heterogeneity. Our second aim has been to investigate the nature and origin of this clonal heterogeneity and to test for the presence of chromosome instability (CIN) in HeH ALL at initial presentation. Ten HeH ALL and 10 non-HeH ALL patients were analysed by four colour l-FISH and numerical CIN values were determined for all four chromosomes together and for each chromosome and patient group, an original approach in ALL. CIN values in HeH ALL proved to be much higher than#iose in non-HeH ALL, suggesting that numerical CIN may be at the origin of the high level of clonal heterogeneity revealed by l-FISH. Our third aim has been to study the evolution of these cytogenetic features during the course of the disease in 10 HeH ALL patients. Clonal heterogeneity was also observed again during disease progression, particularly at relapse. Clones detected at initial presentation generally reappeared in relapse, in most cases with newly generated ones. A significant correlation between the number of abnormal clones and CIN suggested that the higher the instability, the larger the number of abnormal clones. Whereas clonal heterogeneity and its evolution most probably result from underlying chromosome instability, operating processes remain conjectural.RésuméLa leucémie lymphoblastique aiguë (LLA) est une hémopathie maligne qui résulte de l'accumulationde cellules lymphoïdes immatures dans la moelle osseuse, et, le plus souvent, dans le sangpériphérique également. La LLA est une affection hétérogène au sein de laquelle se distinguentplusieurs entités biologiques et pronostiques. Les données cytogénétiques et moléculaires font partieintégrante du diagnostic et jouent un rôle essentiel dans l'évaluation du pronostic. L'hyperdiploïdieélevée à 51-­67 chromosomes (HeH), relativement fréquente, en particulier chez l'enfant, s'associe àun pronostic favorable. Le gain de chromosomes ne relève pas du hasard, certains chromosomesétant plus fréquemment impliqués que d'autres. La présence simultanée des trisomies 4, 6, et 17s'associe à un pronostic particulièrement bon. Le premier but du travail a été de développer uneméthode d'analyse automatique par hybridation in situ fluorescente interphasique (I-­FISH) à 4couleurs et de tester sa capacité à identifier la présence simultanée d'aneuploïdies 4, 6, 10 et 17 dans10 cas de LLA. Différentes combinaisons d'aneuploïdies ont été identifiées. Tous les clones détectéspar cytogénétique conventionnelle l'ont été par I-­FISH. Or, chez tous les patients, l'I-­FISH a révélé denombreux clones anormaux additionnels générant un degré élevé d'hétérogénéité clonale. Notredeuxième but a été d'investiguer la nature et l'origine de cette hétérogénéité et de tester la présenced'instabilité chromosomique (CIN) chez les patients avec une LLA HeH en presentation initiale. DixLLA HeH et 10 LLA non-­HeH ont été analysées par I-­FISH et les valeurs de CIN numérique ont étédéterminées pour les 4 chromosomes ensemble et pour chaque chromosome et groupe de patients,approche originale dans la LLA. Ces valeurs étant beaucoup plus élevées dans la LLA HeH que dansla LLA non-­HeH, elles favorisent l'hypothèse selon laquelle la CIN serait à l'origine de l'hétérogénéitéclonale révélée par I-­FISH. Le troisième but de notre travail a été d'étudier l'évolution de cescaractéristiques cytogénétiques au cours de la maladie dans 10 cas de LLA HeH. L'hétérogénéitéclonale a été retrouvée lors de la progression de la maladie, en particulier en rechute, où les clonesanormaux détectés en présentation initiale réapparaissent, généralement accompagnés de clonesnouveaux. La corrélation existant entre nombre de clones anormaux et valeurs de CIN suggère queplus l'instabilité est élevée, plus le nombre de clones anormaux est grand. Bien que l'hétérogénéitéclonale et son évolution résultent très probablement de l'instabilité chromosomique, les processus àl'oeuvre ne sont pas entièrement élucidés

Time-dependent quantum transport: an exact formulation based on TDDFT

An exact theoretical framework based on Time Dependent Density Functional Theory (TDDFT) is proposed in order to deal with the time-dependent quantum transport in fully interacting systems. We use a \textit{partition-free} approach by Cini in which the whole system is in equilibrium before an external electric field is switched on. Our theory includes the interactions between the leads and between the leads and the device. It is well suited for calculating measurable transient phenomena as well as a.c. and other time-dependent responses. We show that the steady-state current results from a \textit{dephasing mechanism} provided the leads are macroscopic and the device is finite. In the d.c. case, we obtain a Landauer-like formula when the effective potential of TDDFT is uniform deep inside the electrodes.Comment: final version, 7 pages, 1 figur

Bacterial α(2)-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?

BACKGROUND: Invasive bacteria are known to have captured and adapted eukaryotic host genes. They also readily acquire colonizing genes from other bacteria by horizontal gene transfer. Closely related species such as Helicobacter pylori and Helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. The protease inhibitor α(2)-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion. RESULTS: Database searches with metazoan α(2)-macroglobulin sequences revealed homologous sequences in bacterial proteomes. The bacterial α(2)-macroglobulin phylogenetic distribution is patchy and violates the vertical descent model. Bacterial α(2)-macroglobulin genes are found in diverse clades, including purple bacteria (proteobacteria), fusobacteria, spirochetes, bacteroidetes, deinococcids, cyanobacteria, planctomycetes and thermotogae. Most bacterial species with bacterial α(2)-macroglobulin genes exploit higher eukaryotes (multicellular plants and animals) as hosts. Both pathogenically invasive and saprophytically colonizing species possess bacterial α(2)-macroglobulins, indicating that bacterial α(2)-macroglobulin is a colonization rather than a virulence factor. CONCLUSIONS: Metazoan α(2)-macroglobulins inhibit proteases of pathogens. The bacterial homologs may function in reverse to block host antimicrobial defenses. α(2)-macroglobulin was probably acquired one or more times from metazoan hosts and has then spread widely through other colonizing bacterial species by more than 10 independent horizontal gene transfers. yfhM-like bacterial α(2)-macroglobulin genes are often found tightly linked with pbpC, encoding an atypical peptidoglycan transglycosylase, PBP1C, that does not function in vegetative peptidoglycan synthesis. We suggest that YfhM and PBP1C are coupled together as a periplasmic defense and repair system. Bacterial α(2)-macroglobulins might provide useful targets for enhancing vaccine efficacy in combating infections

Conductance of nano-systems with interactions coupled via conduction electrons: Effect of indirect exchange interactions

A nano-system in which electrons interact and in contact with Fermi leads gives rise to an effective one-body scattering which depends on the presence of other scatterers in the attached leads. This non local effect is a pure many-body effect that one neglects when one takes non interacting models for describing quantum transport. This enhances the non-local character of the quantum conductance by exchange interactions of a type similar to the RKKY-interaction between local magnetic moments. A theoretical study of this effect is given assuming the Hartree-Fock approximation for spinless fermions in an infinite chain embedding two scatterers separated by a segment of length L\_c. The fermions interact only inside the two scatterers. The dependence of one scatterer onto the other exhibits oscillations which decay as 1/L\_c and which are suppressed when L\_c exceeds the thermal length L\_T. The Hartree-Fock results are compared with exact numerical results obtained with the embedding method and the DMRG algorithm

Mass-Transport Models with Multiple-Chipping Processes

We study mass-transport models with multiple-chipping processes. The rates of these processes are dependent on the chip size and mass of the fragmenting site. In this context, we consider k-chip moves (where k = 1, 2, 3, ....); and combinations of 1-chip, 2-chip and 3-chip moves. The corresponding mean-field (MF) equations are solved to obtain the steady-state probability distributions, P (m) vs. m. We also undertake Monte Carlo (MC) simulations of these models. The MC results are in excellent agreement with the corresponding MF results, demonstrating that MF theory is exact for these models.Comment: 18 pages, 4 figures, To appear in European Physical Journal

A simplified protocol for the detection of blood, saliva, and semen from a single biological trace using immunochromatographic tests.

The detection of body fluids (e.g., blood, saliva or semen) provides information that is important both for the investigation and for the choice of the analytical protocols. Because of their sensitivity, specificity, as well as their simplicity of use, immunochromatographic tests are widely applied. These tests target different body fluids and generally require specific buffer solutions. If one needs to investigate whether the material is of a specific nature (e.g., blood), this is fine. However, if the material can also contain other material (e.g., saliva or semen) then the use of different tests can be problematic. Indeed, if the different tests require different buffers, it will not be possible to perform all tests on the exact same specimen.In this study, we assess the use of the RSID™-universal buffer to perform three immunochromatographic tests (HEXAGON OBTI, RSID-saliva, and PSA Semiquant) as well as spermatozoa detection. We use the same eluate for the detection of all three body fluids. The proposed protocol provides similar results to those obtained when each test is conducted independently. Furthermore, it does not affect the quality of the DNA profiles. The main advantage of this protocol is that the results of the presumptive test(s) and of the DNA analyses are representative of the exact same specimen

Monitoring the lucky strike vent field in real time

Peer Reviewe

Scaling of Heteroepitaxial Island Sizes

Monte Carlo simulations of an atomistic solid-on-solid model are used to study the effect of lattice misfit on the distribution of two-dimensional islands sizes as a function of coverage $\Theta$ in the submonolayer aggregation regime of epitaxial growth. Misfit promotes the detachment of atoms from the perimeter of large pseudomorphic islands and thus favors their dissolution into smaller islands that relieve strain more efficiently. The number density of islands composed of $s$ atoms exhibits scaling in the form \mbox{$N_s(\Theta) \sim \Theta / \langle s \rangle^2 \, g(s/\langle s \rangle$)} where $\langle s \rangle$ is the average island size. Unlike the case of homoepitaxy, a rate equation theory based on this observation leads to qualitatively different behavior than observed in the simulations.Comment: 10 pages, LaTeX 2.09, IC-DDV-94-00

Practical considerations for operability of an 8″ spiral wound forward osmosis module: Hydrodynamics, fouling behaviour and cleaning strategy

© 2016 Elsevier B.V. A better understanding of large spiral wound forward osmosis (SW FO) module operation is needed to provide practical insight for a full-scale FO practical implementation desalination plant. Therefore, this study investigated two different 8″ SW FO modules (i.e. cellulose tri acetate, CTA and thin film composite, TFC) in terms of hydrodynamics, operating pressure, water and solute fluxes, fouling behaviour and cleaning strategy. For both modules, a significantly lower flow rate was required in the draw channel than in the feed channel due to important pressure-drop in the draw channel and was a particularly critical operating challenge in the CTA module when permeate spacers are used. Under FO and pressure assisted osmosis (PAO, up to 2.5 bar) operations, the TFC module featured higher water flux and lower reverse salt flux than the CTA module. For both modules, fouling tests demonstrated that feed inlet pressure was more sensitive to foulant deposition than the flux, thus confirming that FO fouling deposition occurs in the feed channel rather than on the membrane surface. Osmotic backwash combined with physical cleaning used in this study confirmed to be effective and adapted to large-scale FO module operation