Vesna Todorovic

Genetics. Predicting the impact of genomic variation.

An unsupervised approach with high predictive power provides a single measure of functional importance for each variant in the human genome.

A tissue-to-organelle view of cellular proteins

By coupling multiplex iterative indirect immunofluorescence imaging with computer vision methods, researchers can detect at least 40 different proteins with subcellular resolution.

Gene expression: Single-cell RNA-seq—now with protein

Ultralow concentrations of DNA can be optically sequenced with SMRT DNA sequencing. In principle, optical DNA-sequencing protocols have the advantage of reading long strands of DNA in real time and at high speeds. In practice, however, reading long DNA strands is a challenge with current methods, which require high concentrations and suffer from shortchain loading bias. To overcome these limitations, a research team led by Meni Wanunu at Northeastern University in Boston has now developed an efficient voltage-controlled DNAloading technology that enables single molecule, real time (SMRT) sequencing of long DNA strands at ultralow concentrations. In SMRT sequencing, the replication of DNA by a single DNA polymerase is optically recorded using fluorescently labeled dNTP analogues. The DNA replication occurs in a zeromode waveguide (ZMW), the base of a small cavity in an opaque film which allows molecules to freely flow in and out; but, unlike a standard waveguide, which guides light, the ZMW’s diameter is too small for light to enter. Since the film and ZMWs are both opaque, the background fluorescence from the dNTP analogues in the surrounding medium is blocked from reaching the detectors. However, since dNTP analogues are integrated into the DNA at the bottom of the waveguide, the fluorescence emission can still exit the waveguide at that location and be recorded. Until now, it has been a challenge to pack long strands of DNA into the zeptoliter-sized (a trillion times smaller than a nanoliter) waveguide cavity. For example, a 10 kilobase-pair (kb) DNA strand has an effective diameter, as it flows and bends in liquid, of over five times that of the ZMW. In previous work, the team introduced the nanopore ZMW (NZMW), in which the nanopore enabled the application of a voltage along the length of the waveguide cavity. The strong electric field pulls electrically charged DNA molecules into the NZMW, “allowing the DNA to cross over a huge entropic barrier,” as described by the paper’s first author, Joseph Larkin. This field “is actually compressing the DNA,” he notes. The early NZMW technology,

Sensors and probes: Making sense of NAD + subcellular localization

A fluorescent NAD+ biosensor targeted to specific cellular compartments detects local fluctuation in NAD+ concentration.

Genetics: Flies give wings to human disease studies

Chemically induced mutations on the fruit fly X chromosome reveal the genetic basis of certain human neurologic disorders.