Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Towards the electron EDM search. Theoretical study of PbF

We report ab initio relativistic correlation calculations of potential curves and spectroscopic constants for four lowest-lying electronic states of the lead monofluoride. We also calculated parameters of the spin-rotational Hamiltonian for the ground and the first excited states including P,T-odd and P-odd terms. In particular, we have obtained hyperfine constants of the $^{207}$Pb nucleus. For the $^2\Pi_{1/2}$ state $A_\perp=-6859.6$ MHz, $A_\|=9726.9$ MHz and for the A$^2\Sigma^+_{1/2}$ $A_\perp=1720.8$ MHz, $A_\|=3073.3$ MHz. Our values of the ground state hyperfine constants are in good agreement with the previous theoretical studies. We discuss and explain seeming disagreement in the sign of the constant $A_\perp$ with the recent experimental data. The effective electric field on the electron $E_{eff}$, which is important for the planned experiment to search for the electric dipole moment of the electron, is found to be 3.3 * 10^{10} V/cm

Towards the electron EDM search: Theoretical study of HfF+

We report first ab initio relativistic correlation calculations of potential curves for ten low-lying electronic states, effective electric field on the electron and hyperfine constants for the ^3\Delta_1 state of cation of a heavy transition metal fluoride, HfF^+, that is suggested to be used as the working state in experiments to search for the electric dipole moment of the electron. It is shown that HfF^+ has deeply bound ^1\Sigma^+ ground state, its dissociation energy is D_e=6.4 eV. The ^3\Delta_1 state is obtained to be the relatively long-lived first excited state lying about 0.2 eV higher. The calculated effective electric field E_eff=W_d|\Omega| acting on an electron in this state is 5.84*10^{24}Hz/(e*cm)Comment: 4 page

On Nonperturbative Calculations in Quantum Electrodynamics

A new approach to nonperturbative calculations in quantum electrodynamics is proposed. The approach is based on a regular iteration scheme for solution of Schwinger-Dyson equations for generating functional of Green functions. The approach allows one to take into account the gauge invariance conditions (Ward identities) and to perform the renormalization program. The iteration scheme can be realized in two versions. The first one ("perturbative vacuum") corresponds to chain summation in the diagram language. In this version in four-dimensional theory the non-physical singularity (Landau pole) arises which leads to the triviality of the renormalized theory. The second version ("nonperturbative vacuum") corresponds to ladder summation and permits one to make non-perturbative calculations of physical quantities in spite of the triviality problem. For chiral-symmetrical leading approximation two terms of the expansion of the first-step vertex function over photon momentum are calculated. A formula for anomalous magnetic moment is obtained. A problem of dynamical chiral symmetry breaking (DCSB) is considered, the calculations are performed for renormalized theory in Minkowsky space. In the strong coupling region DCSB-solutions arise. For the renormalized theory a DCSB-solution is also possible in the weak coupling region but with a subsidiary condition on the value of $\alpha$.Comment: 31 pages, Plain LaTex, no figures. Journal version: some discussion and refs. are adde

A Unifying Model of Genome Evolution Under Parsimony

We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph $G$, a finite set of AVGs describe all parsimonious interpretations of $G$, and this set can be explored with a few sampling moves.Comment: 52 pages, 24 figure

ИССЛЕДОВАНИЕ СОСТОЯНИЯ МЕТАЛЛА В ПРОЦЕССЕ РАДИАЛЬНО-СДВИГОВОЙ ПРОКАТКИ НА СТАНЕ СРВП-130

Radial-shear rolling is prominent in production of titanium alloys at «VSMPO-AVISMA» Open Society (V. Salda city) and has a number of advantages over other plastic metal working processes. In the present investigation on the basis of engineering design procedures, a complex of software has been developed for forming simulation and heat transfer in the metal volume,and with its help the rolling of VT-6 alloy bar of 155 mm in diameter has been studied. «ThermoRSR» program has been developed that allows us to visualize design data in «Mathcad» medium; rolling process simulation has been carried out by means of DEFORM-3D package; and the conditions of its application are shown. Prospective ways of rolled stock temperature and rolling torque measurement are considered.Радиально-сдвиговая прокатка (РСП) играет большую роль в производстве титановых сплавов в ОАО «ВСМПО-АВИСМА» (г. В. Салда), имея ряд преимуществ перед другими процессами обработки металлов давлением. В настоящем исследовании на базе инженерных методик расчета разработан комплекс программных средств для моделирования формоизменения и теплопередачи в объеме металла и с его помощью изучена прокатка прутка диаметром 155 мм из сплава ВТ-6. Разработана программа «ThermoRSR», позволяющая визуализировать расчетные данные в среде «Mathcad», проведено моделирование процесса прокатки с помощью пакета DEFORM-3D и показаны условия его применимости. Рассмотрены перспективные способы измерения температуры проката и крутящего момента на шпинделе прокатного стана

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Background: Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences. One model proposed to explain this mosaic patterns is a model of repeated aggregation and subsequent duplication of genomic sequences. Results: We describe a polynomial-time exact algorithm to compute duplication distance, a genomic distance defined as the most parsimonious way to build a target string by repeatedly copying substrings of a fixed source string. This distance models the process of repeated aggregation and duplication. We also describe extensions of this distance to include certain types of substring deletions and inversions. Finally, we provide an description of a sequence of duplication events as a context-free grammar (CFG). Conclusion: These new genomic distances will permit more biologically realistic analyses of segmental duplications in genomes.

Sampling and counting genome rearrangement scenarios

Even for moderate size inputs, there are a tremendous number of optimal rearrangement scenarios, regardless what the model is and which specific question is to be answered. Therefore giving one optimal solution might be misleading and cannot be used for statistical inferring. Statistically well funded methods are necessary to sample uniformly from the solution space and then a small number of samples are sufficient for statistical inferring

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction

Background Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs. Here we provide a cross-site study that evaluates the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. Results We find that all of the kits are capable of performing significant ribosomal depletion, though there are differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~ 14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes between kits suggests that transcript length may be a key factor in library production efficiency. Conclusions These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them. Keywords: RNAseqr; RNA depletion; Illumina; NGS; ABRF; TranscriptomicsNational Cancer Institute (U.S.) (Grant P30-CA14051)National Institute of Environmental Health Sciences (Grant P30-ES002109