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  • 1
    Publication Date: 2015-08-07
    Description: We report the current status of the FlyBase annotated gene set for Drosophila melanogaster and highlight improvements based on high-throughput data. The FlyBase annotated gene set consists entirely of manually annotated gene models, with the exception of some classes of small non-coding RNAs. All gene models have been reviewed using evidence from high-throughput datasets, primarily from the modENCODE project. These datasets include RNA-Seq coverage data, RNA-Seq junction data, transcription start site profiles, and translation stop-codon read-through predictions. New annotation guidelines were developed to take into account the use of the high-throughput data. We describe how this flood of new data was incorporated into thousands of new and revised annotations. FlyBase has adopted a philosophy of excluding low-confidence and low-frequency data from gene model annotations; we also do not attempt to represent all possible permutations for complex and modularly organized genes. This has allowed us to produce a high-confidence, manageable gene annotation dataset that is available at FlyBase ( http://flybase.org ). Interesting aspects of new annotations include new genes (coding, non-coding, and antisense), many genes with alternative transcripts with very long 3' UTRs (up to 15–18 kb), and a stunning mismatch in the number of male-specific genes (approximately 13% of all annotated gene models) vs. female-specific genes (less than 1%). The number of identified pseudogenes and mutations in the sequenced strain also increased significantly. We discuss remaining challenges, for instance, identification of functional small polypeptides and detection of alternative translation starts.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 2
    Publication Date: 2015-08-07
    Description: In the context of the FlyBase annotated gene models in Drosophila melanogaster , we describe the many exceptional cases we have curated from the literature or identified in the course of FlyBase analysis. These range from atypical but common examples such as dicistronic and polycistronic transcripts, noncanonical splices, trans -spliced transcripts, noncanonical translation starts, and stop-codon readthroughs, to single exceptional cases such as ribosomal frameshifting and HAC1-type intron processing. In FlyBase, exceptional genes and transcripts are flagged with Sequence Ontology terms and/or standardized comments. Because some of the rule-benders create problems for handlers of high-throughput data, we discuss plans for flagging these cases in bulk data downloads.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 3
    Publication Date: 2019
    Description: 〈p〉Complex genetic mechanisms are thought to underlie many human diseases, yet experimental proof of this model has been elusive. Here, we show that a human cardiac anomaly can be caused by a combination of rare, inherited heterozygous mutations. Whole-exome sequencing of a nuclear family revealed that three offspring with childhood-onset cardiomyopathy had inherited three missense single-nucleotide variants in the 〈i〉MKL2〈/i〉, 〈i〉MYH7〈/i〉, and 〈i〉NKX2-5〈/i〉 genes. The 〈i〉MYH7〈/i〉 and 〈i〉MKL2〈/i〉 variants were inherited from the affected, asymptomatic father and the rare 〈i〉NKX2-5〈/i〉 variant (minor allele frequency, 0.0012) from the unaffected mother. We used CRISPR-Cas9 to generate mice encoding the orthologous variants and found that compound heterozygosity for all three variants recapitulated the human disease phenotype. Analysis of murine hearts and human induced pluripotent stem cell–derived cardiomyocytes provided histologic and molecular evidence for the 〈i〉NKX2-5〈/i〉 variant’s contribution as a genetic modifier.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2017-02-19
    Description: Replacement of precious noble metal catalysts with low-cost, non-noble heterogeneous catalysts for chemoselective reduction and reductive coupling of nitro compounds holds tremendous promise for the clean synthesis of nitrogen-containing chemicals. We report a robust cobalt–nitrogen/carbon (Co–N x /C-800-AT) catalyst for the reduction and reductive coupling of nitro compounds into amines and their derivates. The Co–N x /C-800-AT catalyst was prepared by the pyrolysis of cobalt phthalocyanine–silica colloid composites and the subsequent removal of silica template and cobalt nanoparticles. The Co–N x /C-800-AT catalyst showed extremely high activity, chemoselectivity, and stability toward the reduction of nitro compounds with H 2 , affording full conversion and 〉97% selectivity in water after 1.5 hours at 110°C and under a H 2 pressure of 3.5 bar for all cases. The hydrogenation of nitrobenzene over the Co–N x /C-800-AT catalyst can even be smoothly performed under very mild conditions (40°C and a H 2 pressure of 1 bar) with an aniline yield of 98.7%. Moreover, the Co–N x /C-800-AT catalyst has high activity toward the transfer hydrogenation of nitrobenzene into aniline and the reductive coupling of nitrobenzene into other derivates with high yields. These processes were carried out in an environmentally friendly manner without base and ligands.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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