2,009 research outputs found

    The PSEA promoter element of the Drosophila U1 snRNA gene is sufficient to bring DmSNAPc into contact with 20 base pairs of downstream DNA

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    Most of the major spliceosomal small nuclear RNAs (snRNAs) (i.e. U1, U2, U4 and U5) are synthesized by RNA polymerase II (pol II). In Drosophila melanogaster, the 5′-flanking DNA of these genes contains two conserved elements: the proximal sequence element A (PSEA) and the proximal sequence element B (PSEB). The PSEA is essential for transcription and is recognized by DmSNAPc, a multi-subunit protein complex. Previous site-specific protein–DNA photo-cross-linking assays demonstrated that one of the subunits of DmSNAPc, DmSNAP43, remains in close contact with the DNA for 20 bp beyond the 3′ end of the PSEA, a region that contains the PSEB. The current work demonstrates that mutation of the PSEB does not abolish the cross-linking of DmSNAP43 to the PSEB. Thus the U1 PSEA alone is capable of bringing DmSNAP43 into close contact with this downstream DNA. However, mutation of the PSEB perturbs the cross-linking pattern. In concordance with these findings, PSEB mutations result in a 2- to 4-fold reduction in U1 promoter activity when assayed by transient transfection

    Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity

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    In animals, most small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II (Pol II), but U6 snRNA is synthesized by RNA polymerase III (Pol III). In Drosophila melanogaster, the promoters for the Pol II-transcribed snRNA genes consist of ∼21 bp PSEA and ∼8 bp PSEB. U6 genes utilize a PSEA but have a TATA box instead of the PSEB. The PSEAs of the two classes of genes bind the same protein complex, DmSNAPc. However, the PSEAs that recruit Pol II and Pol III differ in sequence at a few nucleotide positions that play an important role in determining RNA polymerase specificity. We have now performed a bioinformatic analysis to examine the conservation and divergence of the snRNA gene promoter elements in other species of insects. The 5′ half of the PSEA is well-conserved, but the 3′ half is divergent. Moreover, within each species positions exist where the PSEAs of the Pol III-transcribed genes differ from those of the Pol II-transcribed genes. Interestingly, the specific positions vary among species. Nevertheless, we speculate that these nucleotide differences within the 3′ half of the PSEA act similarly to induce conformational alterations in DNA-bound SNAPc that result in RNA polymerase specificity

    MEASURING PROTECTION IN AGRICULTURE: THE PRODUCER SUBSIDY EQUIVALENT REVISITED

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    In the 1980s, the Producer Subsidy Equivalent (PSE) became the dominant measure of protection in applied studies of international agricultural trade. This paper analyzes potential biases in the ratio form of the PSE introduced by using actual domestic prices rather than social opportunity costs in the denominator. It is shown that doing so introduces a consistent under-estimation of the effects of trade restrictions and other price-support policies, relative to deficiency payments and other income-support policies. It is found that under plausible conditions this bias leads the PSE to rank protection levels across countries or crops incorrectly. In a sample of 250 activities across 33 countries, such errors were found to occur in 5% of crop comparisons and 8% of country comparisons, including a number of politically sensitive cases. An improved formula would therefore provide significantly more accurate results than the conventional PSE, with no additional data or more restrictive assumptions.Agricultural and Food Policy, International Relations/Trade,

    Finite-Size Effect of Hadron Masses with Kogut-Susskind Quarks

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    We present numerical results and their analyses of finite-size effects of hadron masses for both quenched and full QCD calculations. We show that they are much larger for full QCD due to dynamical sea quarks and the associated breaking of Z(3)Z(3) symmetry. We also argue that finite-size effects are non-negligible even for the largest lattice size simulation currently being made for a very small quark mass. (talk at lattice93)Comment: 4 pages, compressed, uuencoded PostScript file(name:lat93.ps.Z

    On the possibility of stable renegotiation. A note

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    Van Damme (Oct 87) claims that renegotiation and stability may be mutually inconsistent concepts. This note shows that this claim may be incorrect and proposes a way to restore the compatibility of these two concepts that, in general, do not apply in the same context

    FARM LABOR TRENDS AND MANAGEMENT IN WASHINGTON STATE

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    The Washington State farm labor market is a pivotal point in the western migrant stream. Farm employers argue that the seasonal labor market has tightened as a result of changes in immigration policy and economic conditions, even as they increase acreage of labor-intensive crops and the demand for labor. Yet, one could argue that a sufficient labor supply is available if workers are offered competitive wages and sufficient hours. To address some of these questions and issues, this study explores whether employer-specific factors (commodity, region, size, and management practices) influence worker turnover and the ability of employers to attract return workers.farm labor, Washington agriculture, worker turnover, Labor and Human Capital,

    Measurement Report: Long-Range Transport Patterns into the Tropical Northwest Pacific during the CAMP²Ex Aircraft Campaign: Chemical Composition, Size Distributions, and the Impact of Convection

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    The tropical Northwest Pacific (TNWP) is a receptor for pollution sources throughout Asia and is highly susceptible to climate change, making it imperative to understand long-range transport in this complex aerosol-meteorological environment. Measurements from the NASA Cloud, Aerosol, and Monsoon Processes Philippines Experiment (CAMP2Ex; 24 August to 5 October 2019) and back trajectories from the National Oceanic and Atmospheric Administration Hybrid Single Particle Lagrangian Integrated Trajectory Model (HYSPLIT) were used to examine transport into the TNWP from the Maritime Continent (MC), peninsular Southeast Asia (PSEA), East Asia (EA), and the West Pacific (WP). A mid-campaign monsoon shift on 20 September 2019 led to distinct transport patterns between the southwest monsoon (SWM; before 20 September) and monsoon transition (MT; after 20 September). During the SWM, long-range transport was a function of southwesterly winds and cyclones over the South China Sea. Low- (high-) altitude air generally came from MC (PSEA), implying distinct aerosol processing related to convection and perhaps wind shear. The MT saw transport from EA and WP, driven by Pacific northeasterly winds, continental anticyclones, and cyclones over the East China Sea. Composition of transported air differed by emission source and accumulated precipitation along trajectories (APT). MC air was characterized by biomass burning tracers while major components of EA air pointed to Asian outflow and secondary formation. Convective scavenging of PSEA air was evidenced by considerable vertical differences between aerosol species but not trace gases, as well as notably higher APT and smaller particles than other regions. Finally, we observed a possible wet scavenging mechanism acting on MC air aloft that was not strictly linked to precipitation. These results are important for understanding the transport and processing of air masses with further implications for modeling aerosol lifecycles and guiding international policymaking to public health and climate, particularly during the SWM and MT

    Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats

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    Friedreich ataxia is caused by an expanded (GAA·TTC)(n) sequence in intron 1 of the FXN gene. Small pool PCR analysis showed that pure (GAA·TTC)(44+) sequences at the FXN locus are unstable in somatic cells in vivo, displaying both expansions and contractions. On searching the entire human and mouse genomes we identified three other genomic loci with pure (GAA·TTC)(44+) sequences. Alleles at these loci showed mutation loads of <1% compared with 6.3–30% for FXN alleles of similar length, indicating that somatic instability in vivo is regulated by locus-specific factors. Since distance between the origin of replication and the (CTG·CAG)(n) sequence modulates repeat instability in mammalian cells, we tested if this could also recapitulate the locus-specific differences for genomic (GAA·TTC)(n) sequences. Repeat instability was evaluated following replication of a (GAA·TTC)(115) sequence in transfected COS1 cells under the control of the SV40 origin of replication located at one of five different distances from the repeat. Indeed, depending on the location of the SV40 origin relative to the (GAA·TTC)(n) sequence, we noted either no instability, predominant expansion or both expansion and contraction. These data suggest that mammalian DNA replication is a possible mechanism underlying locus-specific differences in instability of GAA triplet-repeat sequences
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