4,611 research outputs found

    Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation

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    BACKGROUND: Overlapping transcripts in antisense orientation have the potential to form double-stranded RNA (dsRNA), a substrate for a number of different RNA-modification pathways. One prominent route for dsRNA is its breakdown by Dicer enzyme complexes into small RNAs, a pathway that is widely exploited by RNA interference technology to inactivate defined genes in transgenic lines. The significance of this pathway for endogenous gene regulation remains unclear. RESULTS: We have examined transcription data for overlapping gene pairs in Arabidopsis thaliana. On the basis of an analysis of transcripts with coding regions, we find the majority of overlapping gene pairs to be convergently overlapping pairs (COPs), with the potential for dsRNA formation. In all tissues, COP transcripts are present at a higher frequency compared to the overall gene pool. The probability that both the sense and antisense copy of a COP are co-transcribed matches the theoretical value for coexpression under the assumption that the expression of one partner does not affect the expression of the other. Among COPs, we observe an over-representation of spliced (intron-containing) genes (90%) and of genes with alternatively spliced transcripts. For loci where antisense transcripts overlap with sense transcript introns, we also find a significant bias in favor of alternative splicing and variation of polyadenylation. CONCLUSION: The results argue against a predominant RNA degradation effect induced by dsRNA formation. Instead, our data support alternative roles for dsRNAs. They suggest that at least for a subgroup of COPs, antisense expression may induce alternative splicing or polyadenylation

    Phylogenetic Studies of the United States Bluetongue Viruses and Characterization of the Viral VP4 Protein

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    Bluetongue virus (BTV) is transmitted by arthropod vectors and causes bluetongue disease with serious economic loss in many regions of the world. The replication mechanism of bluetongue virus is still not clear. To have a better understanding regarding the viral replication, the function of each individual protein has to be identified. This study used molecular biology techniques to investigate the function of the inner core protein VP4. The M1 genes of United States bluetongue virus serotypes-2, -10, -11, -13, and -17 were cloned and sequenced. The length of each of the five M1 genes is 1981 nucleotides. The coding region of the M1 gene, which encodes the VP4 protein, possesses an open reading frame with an initiation codon (ATG) at nucleotides #9-11 and a stop codon (TAA) at nucleotides #1941-1943. This open reading frame encodes a protein of 644 amino acid residues with a predicted molecular weight of about 75 kDa. A potential leucine zipper motif was detected near the carboxyl terminus of the deduced VP4 amino acid sequence. The phylogenetic analysis of bluetongue viruses using the sequences of these five cognate M1 genes is consistent with the results of previous phylogenetic studies. Serotypes-10, -11, -13, and -17 are closely related and serotype-2 is the most distantly related among the five US BTV serotypes. Heterologously expressed bluetongue virus VP4 protein was purified to near homogeneity. Six linear epitopes of VP4 were mapped at both termini and in the middle of the protein. By using enzyme-linked immunosorbent assay and peptide competition assay, six linear epitopes were found to be surface accessible. The VP4 protein was shown to be an oligomer by chemical cross-linking. VP4 protein was identified as a ssRNA-binding protein. The VP4 protein has binding activity towards both capped and non-capped ssRNA. RNA-binding activity was not specific to BTV ssRNA. A leucine-zipper motif of VP4 is not required for RNA-binding activity. One RNA-binding domain was mapped between amino acid residues #112-158 by a Northwestern assay and by deletion mutant analysis. Using sequence-specific synthetic peptides corresponding to VP4 in the arginine-and lysine-rich regions, four potential ssRNA-binding domains of VP4 protein were mapped

    Pawns of Policy and Problematized Perception: The Sustainability of Inequality Through the Space of African-American Childhood

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    African American children are simultaneously entrapped by the construct of race and while excluded from the construct of childhood. Race has bifurcated the timeline(s) and bastion of childhood in which one has clear milestones and expectations and the other is nonlinear, fickle, and subject to a suspicious gaze. Recent research describes this phenomenon as “dehumanization”, “age overestimation”, and “adultification.” However, the aforementioned classifications of African American children’s’ experience presents the assumption in which this particular group would first have to be viewed both as human and also as a child, which is arguable. Policy, both children centric and otherwise, along with the problematized perception of African American children interact in a way that has nearly automated the converging space of race and childhood as one of sustainable inequality. Within the trajectory of political economic transitions in the United States African American children, in terms of age categorization and grouping, have gone from being property to problematized; an ephemeral childhood without the assistance of the pre-established demarcations and safeguards. The violence perpetrated against African American children and youth, structurally and physically, demands further examination. While not unprecedented, contemporary technology and social media make the brutal incidents almost instantly accessible and widespread. Social media casts a larger net for the public to bear witness to the frequency and magnitude and in turn illuminates the sentiment of the viewers and how they perceive African American children. The recorded violence, more often than not, is deemed justified and goes unpunished which lays the foundation for larger questions regarding the confinement, exclusion, and assumptions of African American childhood. Who is considered a child when biological age is disregarded based on race? How does the perpetuation of “racialized innocence” and “privilege of protection” racialize potential, limit agency, and construct a future as a luxury? Is it possible to be both African American and a child or are these spaces mutually exclusive

    Rational Approximate Symmetries of KdV Equation

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    We construct one-parameter deformation of the Dorfman Hamiltonian operator for the Riemann hierarchy using the quasi-Miura transformation from topological field theory. In this way, one can get the approximately rational symmetries of KdV equation and then investigate its bi-Hamiltonian structure.Comment: 14 pages, no figure
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