Context dependent splicing functions of Bud31/Ycr063w define its role in budding and cell cycle progression

The yeast Bud31 protein, a Prp19 complex (NTC) member, aids spliceosome assembly and thus promotes efficient pre-mRNA splicing. The bud31 null cells show mild budding abnormalities at optimal growth temperatures and, at higher temperatures, have growth defects with aberrant budding. Here we have assessed cell cycle transitions which require Bud31. We find Bud31 facilitates passage through G1-S regulatory point (Start) but is not needed for G2-M transition or for exit from mitosis. To co-relate Bud31 functions in cell division with splicing, we studied the splicing status of transcripts that encode proteins involved in budding. We find Bud31 promotes efficient splicing of only some of these pre-mRNAs, for example, ARP2 and SRC1. Wild type cells have a long and a short isoform of SRC1 mRNA and protein, out of which the shorter mRNA splice variant is predominant. bud31 Delta cells show inefficient SRC1 splicing and entirely lack the shorter SRC1 spliced mRNA isoform. Yeast PRP17, another NTC sub-complex member, is also required for G1-S and G2-M cell cycle transitions. We examined genetic interactions between BUD31 and PRP17. While both factors were needed for efficient cell cycle dependent gene expression, our data indicate that distinct pre-mRNAs depend on each of these non-essential splicing factors.

Plasmodium falciparum Prp16 homologue and its role in splicing

Large numbers of Plasmodium genes have been predicted to have introns. However, little information exists on the splicing mechanisms in this organism. Here, we describe the DExD/DExH-box containing Pre-mRNA processing proteins (Prps), PfPrp2p, PfPrp5p, PfPrp16p, PfPrp22p, PfPrp28p, PfPrp43p and PfBrr2p, present in the Plasmodium falciparum genome and characterized the role of one of these factors, PfPrp16p. It is a member of DEAH-box protein family with nine collinear sequence motifs, a characteristic of helicase proteins. Experiments with the recombinantly expressed and purified PfPrp16 helicase domain revealed binding to RNA, hydrolysis of ATP as well as catalytic helicase activities. Expression of helicase domain with the C-terminal helicase-associated domain (HA2) reduced these activities considerably, indicating that the helicase-associated domain may regulate the PfPrp16 function. Localization studies with the PfPrp16 GFP transgenic lines suggested a role of its N-terminal domain (1-80 amino acids) in nuclear targeting. Immunodepletion of PfPrp16p, from nuclear extracts of parasite cultures, blocked the second catalytic step of an in vitro constituted splicing reaction suggesting a role for PfPrp16p in splicing catalysis. Further we show by complementation assay in yeast that a chimeric yeast-Plasmodium Prp16 protein, not the full length PfPrp16, can rescue the yeast prp16 temperature-sensitive mutant. These results suggest that although the role of Prp16p in catalytic step II is highly conserved among Plasmodium, human and yeast, subtle differences exist with regards to its associated factors or its assembly with spliceosomes. (C) 2012 Elsevier B.V. All rights reserved.

Homology and enzymatic requirements of microhomology-dependent alternative end joining

Nonhomologous DNA end joining (NHEJ) is one of the major double-strand break (DSB) repair pathways in higher eukaryotes. Recently, it has been shown that alternative NHEJ (A-NHEJ) occurs in the absence of classical NHEJ and is implicated in chromosomal translocations leading to cancer. In the present study, we have developed a novel biochemical assay system utilizing DSBs flanked by varying lengths of microhomology to study microhomology-mediated alternative end joining (MMEJ). We show that MMEJ can operate in normal cells, when microhomology is present, irrespective of occurrence of robust classical NHEJ. Length of the microhomology determines the efficiency of MMEJ, 5 nt being obligatory. Using this biochemical approach, we show that products obtained are due to MMEJ, which is dependent on MRE11, NBS1, LIGASE III, XRCC1, FEN1 and PARP1. Thus, we define the enzymatic machinery and microhomology requirements of alternative NHEJ using a well-defined biochemical system.

Atomization Characteristics of Camelina-Based Alternative Aviation Fuels Discharging From Dual-Orifice Injector

The atomization characteristics of blends of bioderived camelina hydrogenated renewable jet (HRJ) alternative fuel with conventional aviation kerosene (Jet A-1) discharging into ambient atmospheric air from a dual-orifice atomizer used in aircraft engines are described. The spray tests are conducted in a spray test facility at six different test flow conditions to compare the atomization of alternative fuels with that of Jet A-1. The fuel sprays are characterized in terms of fuel discharge, spray cone angle, drop size distribution, and spray patternation. The measurements of spray drop size distribution are obtained using laser diffraction based Spraytec equipment. The characteristics of fuel discharge and cone angle of alternative fuel sprays do not show any changes from that of Jet A-1 sprays. The characteristics of spray drop size, evaluated in terms of the variation of mean drop size along the spray axis, for the alternative fuel sprays remain unaffected by the variation in fuel properties between the alternative fuels and Jet A-1. The measurements on spray patternation, obtained using a mechanical patternator at a distance 5.1 cm from the atomizer exit, show an enhanced fuel concentration in the vicinity of spray axis region for the alternative fuel sprays discharging from the dual-orifice atomizer.

Alternative Formulation of the Discrete Linear Quadratic Regulator (DLQR)

In this paper, an alternative apriori and aposteriori formulation has been derived for the discrete linear quadratic regulator (DLQR) in a manner analogous to that used in the discrete Kalman filter. It has been shown that the formulation seamlessly fits into the available formulation of the DLQR and the equivalent terms in the existing formulation and the proposed formulation have been identified. Thereafter, the significance of this alternative formulation has been interpreted in terms of the sensitivity of the controller performances to any changes in the states or to changes in the control inputs. The implications of this alternative formulation to adaptive controller tuning have also been discussed.

Novel Alternative Splice Variants of Mouse Cdk5rap2

Autosomal recessive primary microcephaly (MCPH) is a rare neurodevelopmental disorder characterized by a pronounced reduction of brain volume and intellectual disability. A current model for the microcephaly phenotype invokes a stem cell proliferation and differentiation defect, which has moved the disease into the spotlight of stem cell biology and neurodevelopmental science. Homozygous mutations of the Cyclin-dependent kinase-5 regulatory subunit-associated protein 2 gene CDK5RAP2 are one genetic cause of MCPH. To further characterize the pathomechanism underlying MCPH, we generated a conditional Cdk5rap2 LoxP/hCMV Cre mutant mouse. Further analysis, initiated on account of a lack of a microcephaly phenotype in these mutant mice, revealed the presence of previously unknown splice variants of the Cdk5rap2 gene that are at least in part accountable for the lack of microcephaly in the mice.

An alternative approach to study nonlinear inviscid flow over arbitrary bottom topography

This paper deals with a new approach to study the nonlinear inviscid flow over arbitrary bottom topography. The problem is formulated as a nonlinear boundary value problem which is reduced to a Dirichlet problem using certain transformations. The Dirichlet problem is solved by applying Plemelj-Sokhotski formulae and it is noticed that the solution of the Dirichlet problem depends on the solution of a coupled Fredholm integral equation of the second kind. These integral equations are solved numerically by using a modified method. The free-surface profile which is unknown at the outset is determined. Different kinds of bottom topographies are considered here to study the influence of bottom topography on the free-surface profile. The effects of the Froude number and the arbitrary bottom topography on the free-surface profile are demonstrated in graphical forms for the subcritical flow. Further, the nonlinear results are validated with the results available in the literature and compared with the results obtained by using linear theory. (C) 2015 Elsevier Inc. All rights reserved.

Alternative search strategies for a BSM resonance fitting the ATLAS diboson excess

We study an s-channel resonance R as a viable candidate to fit the diboson excess reported by ATLAS. We compute the contribution of the similar to 2 TeV resonance R to semileptonic and leptonic final states at the 13 TeV LHC. To explain the absence of an excess in the semileptonic channel, we explore the possibility where the particle R decays to additional light scalars X, X or X, Y. A modified analysis strategy has been proposed to study the three-particle final state of the resonance decay and to identify decay channels of X. Associated production of R with gauge bosons has been studied in detail to identify the production mechanism of R. We construct comprehensive categories for vector and scalar beyond-standard-model particles which may play the role of particles R, X, Y and find alternate channels to fix the new couplings and search for these particles.

COST AND PERFORMANCE TRADEOFFS OF ALTERNATIVE SOLAR-DRIVEN S-CO2 BRAYTON CYCLE CONFIGURATIONS

This paper evaluates cost and performance tradeoffs of alternative supercritical carbon dioxide (s-CO2) closed-loop Brayton cycle configurations with a concentrated solar heat source. Alternative s-CO2 power cycle configurations include simple, recompression, cascaded, and partial cooling cycles. Results show that the simple closed-loop Brayton cycle yielded the lowest power-block component costs while allowing variable temperature differentials across the s-CO2 heating source, depending on the level of recuperation. Lower temperature differentials led to higher sensible storage costs, but cycle configurations with lower temperature differentials (higher recuperation) yielded higher cycle efficiencies and lower solar collector and receiver costs. The cycles with higher efficiencies (simple recuperated, recompression, and partial cooling) yielded the lowest overall solar and power-block component costs for a prescribed power output.