Illinois birds: tyrannidae

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Illinois Birds: Turdidae

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Illinois Birds: Sylviidae

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Illinois Birds: Laniidae

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Enumerative geometry of Calabi-Yau 4-folds

Gromov-Witten theory is used to define an enumerative geometry of curves in Calabi-Yau 4-folds. The main technique is to find exact solutions to moving multiple cover integrals. The resulting invariants are analogous to the BPS counts of Gopakumar and Vafa for Calabi-Yau 3-folds. We conjecture the 4-fold invariants to be integers and expect a sheaf theoretic explanation. Several local Calabi-Yau 4-folds are solved exactly. Compact cases, including the sextic Calabi-Yau in CP5, are also studied. A complete solution of the Gromov-Witten theory of the sextic is conjecturally obtained by the holomorphic anomaly equation.Comment: 44 page

PU(2) monopoles. II: Top-level Seiberg-Witten moduli spaces and Witten's conjecture in low degrees

In this article we complete the proof---for a broad class of four-manifolds---of Witten's conjecture that the Donaldson and Seiberg-Witten series coincide, at least through terms of degree less than or equal to c-2, where c is a linear combination of the Euler characteristic and signature of the four-manifold. This article is a revision of sections 4--7 of an earlier version, while a revision of sections 1--3 of that earlier version now appear in a separate companion article (math.DG/0007190). Here, we use our computations of Chern classes for the virtual normal bundles for the Seiberg-Witten strata from the companion article (math.DG/0007190), a comparison of all the orientations, and the PU(2) monopole cobordism to compute pairings with the links of level-zero Seiberg-Witten moduli subspaces of the moduli space of PU(2) monopoles. These calculations then allow us to compute low-degree Donaldson invariants in terms of Seiberg-Witten invariants and provide a partial verification of Witten's conjecture.Comment: Journal fur die Reine und Angewandte Mathematik, to appear; 65 pages. Revision of sections 4-7 of version v1 (December 1997

Long 3′-UTRs target wild-type mRNAs for nonsense-mediated mRNA decay in Saccharomyces cerevisiae

The nonsense-mediated mRNA decay (NMD) pathway, present in most eukaryotic cells, is a specialized pathway that leads to the recognition and rapid degradation of mRNAs with premature termination codons and, importantly, some wild-type mRNAs. Earlier studies demonstrated that aberrant mRNAs with artificially extended 3′-untranslated regions (3′-UTRs) are degraded by NMD. However, the extent to which wild-type mRNAs with long 3′-UTRs are degraded by NMD is not known. We used a global approach to identify wild-type mRNAs in Saccharomyces cerevisiae that have longer than expected 3′-UTRs, and of these mRNAs tested, 91% were degraded by NMD. We demonstrate for the first time that replacement of the natural, long 3′-UTR from wild-type PGA1 mRNA, which encodes a protein that is important for cell wall biosynthesis, with a short 3′-UTR renders it immune to NMD. The natural PGA1 3′-UTR is sufficient to target a NMD insensitive mRNA for decay by the NMD pathway. Finally, we show that nmd mutants are sensitive to Calcofluor White, which suggests that the regulation of PGA1 and other cell wall biosynthesis proteins by NMD is physiologically significant

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes