Schwarz EM

References (3)

Title : The genome and transcriptome of the zoonotic hookworm Ancylostoma ceylanicum identify infection-specific gene families - Schwarz_2015_Nat.Genet_47_416
Author(s) : Schwarz EM , Hu Y , Antoshechkin I , Miller MM , Sternberg PW , Aroian RV
Ref : Nat Genet , 47 :416 , 2015
Abstract : Hookworms infect over 400 million people, stunting and impoverishing them. Sequencing hookworm genomes and finding which genes they express during infection should help in devising new drugs or vaccines against hookworms. Unlike other hookworms, Ancylostoma ceylanicum infects both humans and other mammals, providing a laboratory model for hookworm disease. We determined an A. ceylanicum genome sequence of 313 Mb, with transcriptomic data throughout infection showing expression of 30,738 genes. Approximately 900 genes were upregulated during early infection in vivo, including ASPRs, a cryptic subfamily of activation-associated secreted proteins (ASPs). Genes downregulated during early infection included ion channels and G protein-coupled receptors; this downregulation was observed in both parasitic and free-living nematodes. Later, at the onset of heavy blood feeding, C-lectin genes were upregulated along with genes for secreted clade V proteins (SCVPs), encoding a previously undescribed protein family. These findings provide new drug and vaccine targets and should help elucidate hookworm pathogenesis.
ESTHER : Schwarz_2015_Nat.Genet_47_416
PubMedSearch : Schwarz_2015_Nat.Genet_47_416
PubMedID: 25730766
Gene_locus related to this paper: 9bila-a0a016wyk0 , 9bila-a0a016u0c0 , 9bila-a0a016u0y8

Title : Genome and transcriptome of the porcine whipworm Trichuris suis - Jex_2014_Nat.Genet_46_701
Author(s) : Jex AR , Nejsum P , Schwarz EM , Hu L , Young ND , Hall RS , Korhonen PK , Liao S , Thamsborg S , Xia J , Xu P , Wang S , Scheerlinck JP , Hofmann A , Sternberg PW , Wang J , Gasser RB
Ref : Nat Genet , 46 :701 , 2014
Abstract : Trichuris (whipworm) infects 1 billion people worldwide and causes a disease (trichuriasis) that results in major socioeconomic losses in both humans and pigs. Trichuriasis relates to an inflammation of the large intestine manifested in bloody diarrhea, and chronic disease can cause malnourishment and stunting in children. Paradoxically, Trichuris of pigs has shown substantial promise as a treatment for human autoimmune disorders, including inflammatory bowel disease (IBD) and multiple sclerosis. Here we report whole-genome sequencing at approximately 140-fold coverage of adult male and female T. suis and approximately 80-Mb draft assemblies. We explore stage-, sex- and tissue-specific transcription of mRNAs and small noncoding RNAs.
ESTHER : Jex_2014_Nat.Genet_46_701
PubMedSearch : Jex_2014_Nat.Genet_46_701
PubMedID: 24929829
Gene_locus related to this paper: 9bila-a0a085nui3 , 9bila-a0a085mx66 , 9bila-a0a085lsb8 , 9bila-a0a085mja7 , 9bila-a0a085ly55 , 9bila-a0a085nlc5 , 9bila-a0a085nb82 , 9bila-a0a085n057 , 9bila-a0a085mjs6

Title : Multigenome DNA sequence conservation identifies Hox cis-regulatory elements - Kuntz_2008_Genome.Res_18_1955
Author(s) : Kuntz SG , Schwarz EM , DeModena JA , De Buysscher T , Trout D , Shizuya H , Sternberg PW , Wold BJ
Ref : Genome Res , 18 :1955 , 2008
Abstract : To learn how well ungapped sequence comparisons of multiple species can predict cis-regulatory elements in Caenorhabditis elegans, we made such predictions across the large, complex ceh-13/lin-39 locus and tested them transgenically. We also examined how prediction quality varied with different genomes and parameters in our comparisons. Specifically, we sequenced approximately 0.5% of the C. brenneri and C. sp. 3 PS1010 genomes, and compared five Caenorhabditis genomes (C. elegans, C. briggsae, C. brenneri, C. remanei, and C. sp. 3 PS1010) to find regulatory elements in 22.8 kb of noncoding sequence from the ceh-13/lin-39 Hox subcluster. We developed the MUSSA program to find ungapped DNA sequences with N-way transitive conservation, applied it to the ceh-13/lin-39 locus, and transgenically assayed 21 regions with both high and low degrees of conservation. This identified 10 functional regulatory elements whose activities matched known ceh-13/lin-39 expression, with 100% specificity and a 77% recovery rate. One element was so well conserved that a similar mouse Hox cluster sequence recapitulated the native nematode expression pattern when tested in worms. Our findings suggest that ungapped sequence comparisons can predict regulatory elements genome-wide.
ESTHER : Kuntz_2008_Genome.Res_18_1955
PubMedSearch : Kuntz_2008_Genome.Res_18_1955
PubMedID: 18981268
Gene_locus related to this paper: 9pelo-b6vbi9 , 9pelo-b6vbj0 , 9pelo-b6vbj1 , 9pelo-b6vbj2