Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least attention. Sequence validation is equally important for other kinds of...
The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the
application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity
is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary
conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids.
Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in...
Full Text:
siRNAs using bioinformatics tools. Furthermore, we prove
that this ‘siRNA omics’ approach can be used for
Since the discovery of penicillin in 1928, the fungal kingdom has remained a fertile source for the discovery of new, biologically active, natural products. Further, as natural products continue to be discovered from fungi, a deeper understanding of the critical role of specialized metabolism in fungal ecology is afforded. The...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
Full Text:
transcriptome sequencing and bioinformatics, we systematically investigated myosin genes in two
model plants
The soil bacterium Pseudomonas protegens Pf-5 (previously called P. fluorescens Pf-5) produces two siderophores, enantio-pyochelin and a compound in the large and diverse pyoverdine family. Using high-resolution mass spectroscopy, we determined the structure of the pyoverdine produced by Pf-5. In addition to producing its own siderophores, Pf-5 also utilizes ferric...
Drosophila suzukii (Spotted Wing Drosophila) has recently become a serious invasive pest of fruit crops in the USA, Canada, and Europe, leading to substantial economic losses. D. suzukii is a direct pest, ovipositing directly into ripe or ripening fruits; in contrast, other Drosophilids utilize decaying or blemished fruits and are...
Full Text:
this pest in fruit exports. Here we
used a combined phylogenetic and bioinformatic approach to discover
BACKGROUND: Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can
be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA
methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune modulations
in virtually any blood sample including...
Full Text:
and
neutrophils. We employ a bioinformatics-based approach to quantify these cell types in complex
Pantoea vagans C9-1 (C9-1) is a biological control agent sprayed onto apple and pear trees during bloom for suppression of fire blight, a devastating bacterial disease caused by Erwinia amylovora. Prior bioinformatics studies of C9-1 focused on predicted phenotypes associated with the three native megaplasmids, pPag1, pPag2, and pPag3, and...
Learning novel concepts from relational databases is an important problem with applications in several disciplines, such as data management, natural language processing, and bioinformatics. For a learning algorithm to be effective, the input data should be clean and in some desired representation. However, real-world data is usually heterogeneous – the...