Rapid and accurate detection of multidrug resistance (MDR) in Mycobacterium tuberculosis is essential to improve treatment outcomes and reduce global transmission but remains a challenge. Rifampin (RIF) resistance is a reliable marker of MDR tuberculosis (TB) since by far the majority of RIF-resistant strains are also isoniazid (INH) resistant. We have developed a rapid, sensitive, and specific...

Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiat...

We describe a PCR-based approach for the synthesis of circularizable ligation probes (CLiPs). CLiPs are single-stranded probes that consist of target-specific ends separated by a noncomplementary "linker" sequence. When hybridized to a target, the CLiP forms a nicked circle that may be sealed by DNA ligase only if the 5' and 3' ends show perfect Watson-Crick base pairing, thus enabling the disc...

Most ancient Chinese padlocks are key-operated locks with splitting springs, and partially keyless letter-combination locks. They can be characterized based on the types of locks, the shapes of locks, the engravings of locks, the materials of locks, and the mechanisms of locks. Some locks and keys are not only very beautiful and artistic colorful, but also with various designs. As a result, a s...

Studies of epigenetic modifications would benefit from improved methods for high-throughput methylation profiling. We introduce two complementary approaches that use next-generation sequencing technology to detect cytosine methylation. In the first method, we designed B10,000 bisulfite padlock probes to profile B7,000 CpG locations distributed over the ENCODE pilot project regions and applied t...

Specific single-molecule detection opens new possibilities in genomics and proteomics, and automated image analysis is needed for accurate quantification. This work presents image analysis methods for the detection and classification of single molecules and single-molecule interactions detected using padlock probes or proximity ligation. We use simple, widespread, and cost-efficient wide-field ...

Accurate identification of mycetoma causative agent is a priority for treatment. However, current identification tools are far from being satisfactory for both reliable diagnosis and epidemiological investigations. A rapid, simple, and highly efficient molecular based method for identification of agents of black grain eumycetoma is introduced, aiming to improve diagnostic in endemic areas. Roll...