Nonsense-mediated mRNA decay (NMD) is a conserved mechanism that targets aberrant mRNAs for destruction. NMD has also been found to regulate the expression of large numbers of genes in diverse organisms, although the biological role for this is unclear and few evolutionarily conserved targets have been identified. Expression analyses of three Arabidopsis thaliana lines deficient in NMD reveal t...

Continuing discoveries of new and surprising mechanisms of gene regulation suggest that our understanding of this complex and ubiquitous biological process remains incomplete. Emerging examples illustrate that many and perhaps all genes are regulated at multiple steps including transcription, posttranscriptional processing, nuclear export and localization, stability, and translation of mature m...

Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger gen...

Open reading frames (6116) of the budding yeast Saccharomyces cerevisiae were PCR-amplified from genomic DNA using 12,232 primers specific to the ends of the coding sequences; the success rate of amplification was 97%. PCR-products were made accessible to hybridization by being arrayed at very high density on solid support media using various robotic devices. Probes made from total RNA preparat...

The rice disease resistance gene Xa21, encoding a receptor-like kinase, is a member of a multigene family. Sequence analysis of seven family members revealed two distinct classes of genes. One member from each class encodes a receptor kinase-like open reading frame. The other five members encode truncated open reading frames of the predicted receptor kinase. A highly conserved 233-bp sequence (...

We have reported previously that a recombinant DNA vaccine consisting of four Ehrlichia ruminantium (Welgevonden) open reading frames (ORFs) known as the 1H12 cocktail provided protection against a virulent E. ruminantium (Welgevonden) needle challenge in sheep. In this study, we have investigated the vaccine effectiveness of two other cocktails of E. ruminantium (Welgevonden) ORFs, as well as ...

This study reports a de novo-assembled draft genome sequence of Xylella fastidiosa subsp. multiplex strain BB01 causing blueberry bacterial leaf scorch in Georgia, USA. The BB01 genome is 2,517,579 bp, with a G+C content of 51.8%, 2,943 open reading frames (ORFs), and 48 RNA genes.

The 393bp nucleotide sequence of a HindIII genomic fragment mapping within the major long interspersed repeated sequence family (MIF-1, Bam, L1) of mouse is reported and compared to clone sequences of the same region of this repeated sequence. The consensus of the clone sequences significantly differs from the genomic fragment sequence by additions and deletions that are inconsistent with the p...

Mycobacterium smegmatis inactivates rifampin by ribosylating this antibiotic. The gene responsible for this ability was cloned and was shown to confer low-level resistance to this antibiotic (MIC increase, about 12-fold) in related organisms. A 600-bp subclone responsible for ribosylating activity and resistance carried an open reading frame of 429 bp. Targeted disruption of the gene in M. smeg...

Oleiagrimonas gudaosoli 3.5X(T) was isolated from an oil field and identified as a new member of a novel genus. The draft genome sequence of this strain, which comprises 3,379,958 bp encoding 3,010 open reading frames (ORFs), can provide insight into the life style of this newly identified genus in petroleum-contaminated soil.