Further characterization of complex chromosomal rearrangements in myeloid malignancies: spectral karyotyping adds precision in defining abnormalities associated with poor prognosis

The mixed lineage leukemia gene (MLL, also known as HRX, ALL-1 and Htrx) located at 11q23 is involved in translocations with over 40 different chromosomal bands in a variety of leukemia subtypes. Here we report our analysis of a rare but recurring translocation, t(11;15)(q23;q14). This translocation has been described in a small subset of cases with both acute myeloblastic leukemia and ALL. Recent studies have shown that MLL is fused to AF15q14 in the t(11;15). Here we analyse a sample from another patient with this translocation and confirm the presence of an MLL-AF15q14 fusion. However, we have also identified and cloned another fusion transcript from the same patient sample. In this fusion transcript, MLL is fused to a novel gene, MLL partner containing FYVE domain (MPFYVE). Both MLL-AF15q14 and MLL-MPFYVE are in-frame fusion transcripts with the potential to code for novel fusion proteins. MPFYVE is also located on chromosome 15, approximately 170 kb telomeric to AF15q14. MPFYVE contains a highly conserved motif, the FYVE domain which, in other proteins, has been shown to bind to phosphotidyl-inositol-3 phosphate (PtdIns(3)P). The MLL-MPFYVE fusion may be functionally important in the leukemia process in at least some patients containing this translocation

Parity violation in nuclear systems

Parity violation in nuclear systems is reviewed. A few ingredients relevant to the description of the parity-violating nucleon-nucleon force in terms of meson exchanges are reminded. Effects in nuclear systems are then considered. They involve pp scattering, some complex nuclei and the deuteron system.Comment: 4 pages, to be published in the proceedings of the worksho

Derivation of the effective action of a dilute Fermi gas in the unitary limit of the BCS-BEC crossover

The effective action describing the gapless Nambu-Goldstone, or Anderson-Bogoliubov, mode of a zero-temperature dilute Fermi gas at unitarity is derived up to next-to-leading order in derivatives from the microscopic theory. Apart from a next-to-leading order term that is suppressed in the BCS limit, the effective action obtained in the strong-coupling unitary limit is proportional to that in the weak-coupling BCS limit.Comment: 13 pages, no figures; v2: discussion of one-dimensional system and references adde

Molecular cytogenetic characterization of breakpoints in 19 patients with hematologic malignancies and 12p unbalanced translocations

Structural rearrangements of the short arm of chromosome 12 are frequent cytogenetic findings in various hematologic malignancies. The ETV6 gene is the most common target for rearrangements in 12p13. Fluorescence in situ hybridization (FISH) investigations have shown that translocations of 12p other than t(12;21) are frequently accompanied by small interstitial deletions that include ETV6. Unbalanced translocations involving ETV6 have rarely been described, and breakpoints outside ETV6 appear to be strongly associated with complex karyotypes. We studied bone marrow samples from 19 patients known to have 12p unbalanced translocations and complex karyotypes, using FISH and spectral karyotyping. FISH analysis confirmed the hemizygous deletion of the ETV6 and CDKN1B genes in 74% of cases. We found four cases with interstitial deletions. In these four cases and in two others (6/19, 31.5%), the fusion with the partner chromosome was in the subtelomeric region of 12p13.3, confirming that there is a recurrent breakpoint in this region

Spring-block model for a single-lane highway traffic

A simple one-dimensional spring-block chain with asymmetric interactions is considered to model an idealized single-lane highway traffic. The main elements of the system are blocks (modeling cars), springs with unidirectional interactions (modeling distance keeping interactions between neighbors), static and kinetic friction (modeling inertia of drivers and cars) and spatiotemporal disorder in the values of these friction forces (modeling differences in the driving attitudes). The traveling chain of cars correspond to the dragged spring-block system. Our statistical analysis for the spring-block chain predicts a non-trivial and rich complex behavior. As a function of the disorder level in the system a dynamic phase-transition is observed. For low disorder levels uncorrelated slidings of blocks are revealed while for high disorder levels correlated avalanches dominates.Comment: 6 pages, 7 figure

ZZ--Z′Z' mixing and oblique corrections in an SU(3)×U(1){\rm SU(3) \times U(1)} model

A global fit for experiments is included in this revised version.Comment: IFP-460-UNC, TRI-PP-93-11, 20 pages, 2 figures are appende

Identification of new translocations involving ETV6 in hematologic malignancies by fluorescence in situ hybridization and spectral karyotyping

TEL/ETV6 is the first transcription factor identified that is specifically required for hematopoiesis within the bone marrow. This gene has been found to have multiple fusion partners; 35 different chromosome bands have been involved in ETV6 translocations, of which 13 have been cloned. To identify additional ETV6 partner genes and to characterize the chromosomal abnormalities more fully, we studied bone marrow samples from patients known to have rearrangements of 12p, using fluorescence in situ hybridization (FISH) and spectral karyotyping (SKY). FISH analysis was done with 14 probes located on 12p12.1 to 12p13.3. Nine ETV6 rearrangements were identified using FISH. The aberrations include t(1;12)(p36;p13), t(4;12)(q12;p13) (two patients), t(4;12)(q22;p13), t(6;12)(p21;p13), der(6)t(6;21)(q15;q?)t(12;21)(p13;q22), t(6;12)(q25;p13), inv(12)(p13q24), and t(2;2;5;12;17)(p25;q23;q31;p13;q12). Six new ETV6 partner bands were identified: 1p36, 4q22, 6p21, 6q25, 12q24, and 17q12. Our present data as well previous data from us and from other researchers suggest that ETV6 is involved in 41 translocations. The breakpoints in ETV6 were upstream from the exons coding for the HLH (helix-loop-helix) domain in six cases. Although cytogenetic analysis identified 12p abnormalities in all cases, FISH and SKY detected new and unexpected chromosomal rearrangements in many of them. Thus, complete characterization of the samples was achieved by using all three techniques in combination

Pairing of fermions in atomic traps and nuclei

Pairing gaps for fermionic atoms in harmonic oscillator traps are calculated for a wide range of interaction strengths and particle number, and compared to pairing in nuclei. Especially systems, where the pairing gap exceeds the level spacing but is smaller than the shell splitting $\hbar\omega$, are studied which applies to most trapped Fermi atomic systems as well as to finite nuclei. When solving the gap equation for a large trap with such multi-level pairing, one finds that the matrix elements between nearby harmonic oscillator levels and the quasi-particle energies lead to a double logarithm of the gap, and a pronounced shell structure at magic numbers. It is argued that neutron and proton pairing in nuclei belongs to the class of multi-level pairing, that their shell structure follows naturally and that the gaps scale as $\sim A^{-1/3}$ - all in qualitative agreement with odd-even staggering of nuclear binding energies. Pairing in large systems are related to that in the bulk limit. For large nuclei the neutron and proton superfluid gaps approach the asymptotic value in infinite nuclear matter: $\Delta\simeq 1.1$ MeV.Comment: 11 pages, 5 figure

Resonance effects on the crossover of bosonic to fermionic superfluidity

Feshbach scattering resonances are being utilized in atomic gases to explore the entire crossover region from a Bose-Einstein Condensation (BEC) of composite bosons to a Bardeen-Cooper-Schrieffer (BCS) of Cooper pairs. Several theoretical descriptions of the crossover have been developed based on an assumption that the fermionic interactions are dependent only on the value of a single microscopic parameter, the scattering length for the interaction of fermion particles. Such a picture is not universal, however, and is only applicable to describe a system with an energetically broad Feshbach resonance. In the more general case in which narrow Feshbach resonances are included in the discussion, one must consider how the energy dependence of the scattering phase shift affects the physical properties of the system. We develop a theoretical framework which allows for a tuning of the scattering phase shift and its energy dependence, whose parameters can be fixed from realistic scattering solutions of the atomic physics. We show that BCS-like nonlocal solutions may build up in conditions of resonance scattering, depending on the effective range of the interactions.Comment: 8 pages,7 figure

Genome And Secretome Analysis Of The Hemibiotrophic Fungal Pathogen, Moniliophthora Roreri, Which Causes Frosty Pod Rot Disease Of Cacao: Mechanisms Of The Biotrophic And Necrotrophic Phases

Background: The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.Results: We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.Conclusions: Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. 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