Birds have played a central role in many biological disciplines, particularly ecology, evolution, and behavior. The chicken, as a model vertebrate, also represents an important experimental system for developmental biologists, immunologists, cell biologists, and geneticists. However, genomic resources for the chicken have lagged behind those for other model organisms, with only 1845 nonredundant full-length chicken cDNA sequences currently deposited in the EMBL databank. We describe a large-scale expressed-sequence-tag (EST) project aimed at gene discovery in chickens (http://www.chick.umist.ac.uk). In total, 339,314 ESTs have been sequenced from 64 cDNA libraries generated from 21 different embryonic and adult tissues. These were clustered and assembled into 85,486 contiguous sequences (contigs). We find that a minimum of 38% of the contigs have orthologs in other organisms and define an upper limit of 13,000 new chicken genes. The remaining contigs may include novel avian specific or rapidly evolving genes. Comparison of the contigs with known chicken genes and orthologs indicates that 30% include cDNAs that contain the start codon and 20% of the contigs represent full-length cDNA sequences. Using this dataset, we estimate that chickens have approximately 35,000 genes in total, suggesting that this number may be a characteristic feature of vertebrates.

Summary We describe a genetic variation map for the chicken genome containing 2.8 million single nucleotide polymorphisms (SNPs), based on a comparison of the sequences of 3 domestic chickens (broiler, layer, Silkie) to their wild ancestor Red Jungle Fowl (RJF). Subsequent experiments indicate that at least 90% are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about 5 SNP/kb for almost every possible comparison between RJF and domestic lines, between two different domestic lines, and within domestic lines - contrary to the idea that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated prior to domestication, and there is little to no evidence of selective sweeps for adaptive alleles on length scales of greater than 100 kb.

We present an analysis of the chicken (Gallus gallus) transcriptome based on the full insert sequences for 19,626 cDNAs, combined with 485,337 EST sequences. The cDNA data set has been functionally annotated and describes a minimum of 11,929 chicken coding genes, including the sequence for 2260 full-length cDNAs together with a collection of noncoding (nc) cDNAs that have been stringently filtered to remove untranslated regions of coding mRNAs. The combined collection of cDNAs and ESTs describe 62,546 clustered transcripts and provide transcriptional evidence for a total of 18,989 chicken genes, including 88% of the annotated Ensembl gene set. Analysis of the ncRNAs reveals a set that is highly conserved in chickens and mammals, including sequences for 14 pri-miRNAs encoding 23 different miRNAs. The data sets described here provide a transcriptome toolkit linked to physical clones for bioinformaticians and experimental biologists who wish to use chicken systems as a low-cost, accessible alternative to mammals for the analysis of vertebrate development, immunology, and cell biology.

Inhibitors of human transglutaminase 2 (TG2) are anticipated to be useful in the therapy of a variety of diseases including celiac sprue as well as certain CNS disorders and cancers. A class of 3-acylidene-2-oxoindoles was identified as potent reversible inhibitors of human TG2. Structureactivity relationship analysis of a lead compound led to the generation of several potent, competitive inhibitors. Analogues with significant non-competitive character were also identified, suggesting that the compounds bind at one or more allosteric regulatory sites on this multidomain enzyme. The most active compounds had Ki values below 1.0 µM in two different kinetic assays for human TG2, and may therefore be suitable for investigations into the role of TG2 in physiology and disease in animals.Keywords transglutaminase 2; oxoindole; celiac sprue; structure-activity relationships; allostery Transglutaminase 2 (TG2), a ubiquitous member of the mammalian transglutaminase enzyme family, is found in intracellular as well as extracellular environments of many organs. In the presence of Ca 2+ and the absence of guanine nucleotides, TG2 adopts an open, catalytically competent conformation, which activates γ-glutaminyl residues on proteins as acyl donors and cross-links these to ε-amino groups of lysyl residues. As a result, proteolytically resistant isopeptide bonds are formed between proteins. Hydrolysis of the γ-glutamyl acyl-enzyme intermediate results in deamidation of the substrate.1 , 2 TG2 is implicated in the pathogenesis of disorders including neurological diseases such as Huntington's, Alzheimer's and Parkinson's diseases, certain types of cancers and renal diseases, cystic fibrosis and celiac sprue,3 -8 and may therefore be a suitable therapeutic © 2010 Elsevier Ltd. All rights reserved. * Corresponding authors: khosla@stanford.edu (C.K.); john@numerate.com (J.H.G.).Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. Here, we present a structure-activity relationship (SAR) analysis for a new class of reversible inhibitors of human TG2, the acylidene oxoindoles. NIH Public AccessIsatin (indoline-2,3-dione) is an endogenous indole in mammals with a range of biological activities.19 , 20 Our motivation to screen this natural product as a candidate TG2 inhibitor was guided by the hypothesis that the cyclic α-keto amide structure of isatin may mimic the γ-carboxamide group of TG2 substrates. α-Keto amides, including isatin analogues, are widely utilized as reversible inhibitors of cysteine-dependent proteases.21 This led us to propose that isatin analogues may also be reversible inh...

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