Patents and royalties

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/62916/1/387546a0.pd

Ultraviolet light-induced recombination

Stimulation of transduction in by ultraviolet irradiation of the transducing phage P1 requires the nuclease but not the product or DNA polymerase I. It is hypothesized that the first step in "normal" recombination can be bypassed by any procedure generating single-stranded ends of DNA (as, for example, by nuclease activity).Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/33755/1/0000007.pd

The glutamate dehydrogenase structural gene of Escherichin coli

The glutamate dehydrogenase structural gene, gdhA , was mapped at 38.6 min on the genetic map and at 1860 kb on the physical map. A detailed map of this region is presented.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47574/1/438_2004_Article_BF00264460.pd

Sequence and evolution of the regions between the rrn operons in the chloroplast genome of Euglena gracilis bacillaris

The rRNA genes are arranged in three sequential operons preceded by a fourth partial operon. Part or all of a 1462 nucleotide sequence extending from within the 3′-end of the 23S rRNA gene, across the 5S rRNA gene and a presumptive transcription terminator, to within the first structural gene (for 16S rRNA) of the rrn operon was determined for each region between operons. Homologies of the 3′-end of the 23S rRNA gene with the 4.5S rRNA genes of higher plant chloroplasts, and of the 5S rRNA gene with other 5S rRNA genes were examined. The region preceding the 16S rRNA gene, which is expected to contain sites for initiation and regulation of rrn transcription, includes a 305 base-pair sequence with substantial homology with structural genes elsewhere in the chloroplast genome. The homologies suggest that this portion of the leader evolved from copies of parts of the structural genes which had been inserted before the 16S rRNA genes. Thus the chloroplast rrn leader may provide a unique opportunity to study how a regulatory sequence evolved from well-defined structural genes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47554/1/438_2004_Article_BF00425555.pd

Location of a phenylalanine tRNA gene on the physical map of the Euglena gracilis chloroplast genome

A tRNAphe from Euglena gracilis bacillaris chloroplasts was purified and hybridized with restriction fragments of chloroplast DNA. From the hybridization pattern, the location of the corresponding gene on the physical map of the chloroplast genome was determined.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/24051/1/0000301.pd

Structure and rearrangements of rRNA genes in chloroplast DNA in two strains of Euglena gracilis

The organisation of the rRNA genes in the chloroplast genomes of two strains of Euglena gracilis were analyzed and compared. It was previously shown that the bacillaris strain contains three complete rrn (rRNA) operons (7) and that the Z-S strain contains one operon (21). Using heteroduplex analysis it was found that the bacillaris strain contains, apart from the three complete rrn operons, an extra 16S rRNA gene, an extra partial 23S rRNA gene sequence and an inverted duplication of a stretch within the 5S–16S spacer. In addition a short (<100 bp) inverted repeat sequence (13) which forms a stem/loop structure in single-stranded cpDNA was located between the 3′-end of the extra 16S rRNA gene and the partial 23 S rRNA sequence.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43440/1/11103_2004_Article_BF00016060.pd

Organization of the chloroplast ribosomal RNA genes of Euglena gracilis bacillaris

The order of eight of the 29 endonuclease EcoRI-generated fragments of chloroplast DNA was determined. Three sets of rRNA genes aligned sequentially in the same orientation form part of this region. The repeated sets differ in the length and sequence of the spacers among themselves and with the rRNA genes of E. gracilis strain Z .Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47546/1/438_2004_Article_BF00433298.pd

Perturbative Instabilities on the Non-Commutative Torus, Morita Duality and Twisted Boundary Conditions

We study one-loop corrections in scalar and gauge field theories on the non-commutative torus. For rational theta, Morita equivalence allows these theories to be reformulated in terms of ordinary theories on a commutative torus with twisted boundary conditions. UV/IR mixing does not lead to singularities, however there can be large corrections. In particular, gauge theories show tachyonic instabilities for some of the modes. We discuss their relevance to spontaneous Z_N x Z_N symmetry breaking in the Morita dual SU(N) theory due to electric flux condensation.Comment: 30 page

African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans

BACKGROUND: Asthma is the most common chronic disease in children, occurring at higher frequencies and with more severe disease in children with African ancestry. METHODS: We tested for association with haplotypes at the most replicated and significant childhood-onset asthma locus at 17q12-q21 and asthma in European American and African American children. Following this, we used whole-genome sequencing data from 1060 African American and 100 European American individuals to identify novel variants on a high-risk African American-specific haplotype. We characterized these variants in silico using gene expression and ATAC-seq data from airway epithelial cells, functional annotations from ENCODE, and promoter capture (pc)Hi-C maps in airway epithelial cells. Candidate causal variants were then assessed for correlation with asthma-associated phenotypes in African American children and adults. RESULTS: Our studies revealed nine novel African-specific common variants, enriched on a high-risk asthma haplotype, which regulated the expression of GSDMA in airway epithelial cells and were associated with features of severe asthma. Using ENCODE annotations, ATAC-seq, and pcHi-C, we narrowed the associations to two candidate causal variants that are associated with features of T2 low severe asthma. CONCLUSIONS: Previously unknown genetic variation at the 17q12-21 childhood-onset asthma locus contributes to asthma severity in individuals with African ancestries. We suggest that many other population-specific variants that have not been discovered in GWAS contribute to the genetic risk for asthma and other common diseases

Complete Genome Sequence of the N2-Fixing Broad Host Range Endophyte Klebsiella pneumoniae 342 and Virulence Predictions Verified in Mice

We report here the sequencing and analysis of the genome of the nitrogen-fixing endophyte, Klebsiella pneumoniae 342. Although K. pneumoniae 342 is a member of the enteric bacteria, it serves as a model for studies of endophytic, plant-bacterial associations due to its efficient colonization of plant tissues (including maize and wheat, two of the most important crops in the world), while maintaining a mutualistic relationship that encompasses supplying organic nitrogen to the host plant. Genomic analysis examined K. pneumoniae 342 for the presence of previously identified genes from other bacteria involved in colonization of, or growth in, plants. From this set, approximately one-third were identified in K. pneumoniae 342, suggesting additional factors most likely contribute to its endophytic lifestyle. Comparative genome analyses were used to provide new insights into this question. Results included the identification of metabolic pathways and other features devoted to processing plant-derived cellulosic and aromatic compounds, and a robust complement of transport genes (15.4%), one of the highest percentages in bacterial genomes sequenced. Although virulence and antibiotic resistance genes were predicted, experiments conducted using mouse models showed pathogenicity to be attenuated in this strain. Comparative genomic analyses with the presumed human pathogen K. pneumoniae MGH78578 revealed that MGH78578 apparently cannot fix nitrogen, and the distribution of genes essential to surface attachment, secretion, transport, and regulation and signaling varied between each genome, which may indicate critical divergences between the strains that influence their preferred host ranges and lifestyles (endophytic plant associations for K. pneumoniae 342 and presumably human pathogenesis for MGH78578). Little genome information is available concerning endophytic bacteria. The K. pneumoniae 342 genome will drive new research into this less-understood, but important category of bacterial-plant host relationships, which could ultimately enhance growth and nutrition of important agricultural crops and development of plant-derived products and biofuels