Background: Short RNAs, and in particular microRNAs, are important regulators of gene
expression both within defined regulatory pathways and at the epigenetic scale. We investigated
the short RNA (sRNA) population (18-24 nt) of the transcriptome of green leaves from the
sequenced Populus trichocarpa using a concatenation strategy in combination with...
The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop,
maintain and use a set of structured, controlled
vocabularies for the annotation of genes, gene
products and sequences. The GO ontologies
are expanding both in content and in structure.
Several new relationship types have been introduced
and used, along with...
Small RNAs, including microRNAs (miRNAs), small interfering RNAs
(siRNAs), and trans-acting siRNAs (tasiRNAs), control gene expression
and epigenetic regulation. Although the roles of miRNAs and
siRNAs have been extensively studied, their expression diversity
and evolution in closely related species and interspecific hybrids
are poorly understood. Here, we show comprehensive analyses...
Soluble butane monooxygenase (sBMO), a three-component di-iron monooxygenase complex
expressed by the C2–C9 alkane-utilizing bacterium Thauera butanivorans, was kinetically
characterized by measuring substrate specificities for C1–C5 alkanes and product inhibition
profiles. sBMO has high sequence homology with soluble methane monooxygenase (sMMO) and
shares a similar substrate range, including gaseous and...
Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article,
we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate
both the forward and reverse genetics research. The QTL database contains the...
The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA
populations. However, these methods have been limited by several factors, including representational artifacts and lack of
established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing
and...
Primula sect. Parryi comprises five species endemic to western North America: P. parryi, P. angustifolia, P. rusbyi, P. capillaris, and P. cusickiana with four varieties. This section, derived from a clade with representatives in Asia and Europe, exemplifies a phytogeographic pattern in which a widespread species is accompanied by multiple...
The placement of ‘Pseudomonas butanovora’ in the genus Thauera was proposed previously, based on 16S rRNA gene sequence analysis, upon further studies of taxonomical characteristics. In this study, physiological characteristics and DNA–DNA reassociation data are presented and the transfer of ‘P. butanovora’ to the genus Thauera is proposed. The original...
Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to simultaneously sequence...
Nitrobacter hamburgensis X14 is a facultative lithoautotroph that conserves energy from the
oxidation of nitrite (NO
2 ) and fixes carbon dioxide (CO2) as its sole source of carbon. The
availability of the N. hamburgensis X14 genome sequence initiated a re-examination of its
mixotrophic and organotrophic potential, as genes encoding...