A5060113553- Nanopore and Nanochannel Transport Studies
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Microfluidic and Bio-sensing Technologies
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- Insect symbiosis and bacterial influences
- Genomics and Phylogenetic Studies
- Microfluidic and Capillary Electrophoresis Applications
- Antibiotic Resistance in Bacteria
- Plant Virus Research Studies
- DNA and Nucleic Acid Chemistry
- Bacterial Identification and Susceptibility Testing
- Electrostatics and Colloid Interactions
- Autism Spectrum Disorder Research
- Monoclonal and Polyclonal Antibodies Research
- Gene Regulatory Network Analysis
- Mental Health Research Topics
- Biosensors and Analytical Detection
- Advanced biosensing and bioanalysis techniques
- Gene expression and cancer classification
- Neurological disorders and treatments
- Circadian rhythm and melatonin
- Sleep and Wakefulness Research
- Opinion Dynamics and Social Influence
Collaborative Group (United States)
2021
Harvard University
2016-2019
Inspire
2016-2018
Lund University
2013-2016
Chalmers University of Technology
2014
Northwestern University
2013
Diurnal fluctuations of motor and nonmotor symptoms a high prevalence sleep-wake disturbances in Parkinson disease (PD) suggest role the circadian system modulation these symptoms. However, surprisingly little is known regarding function PD whether dysfunction involved development PD.To determine relationship between timing amplitude 24-hour melatonin rhythm, marker endogenous rhythmicity, with self-reported sleep quality, severity daytime sleepiness, metrics.A cross-sectional study from...
The alteration of wild populations has been discussed as a solution to number humanity's most pressing ecological and public health concerns. Enabled by the recent revolution in genome editing, clustered regularly interspaced short palindromic repeats (CRISPR) gene drives-selfish genetic elements that can spread through even if they confer no advantage their host organism-are rapidly emerging promising approach. However, before real-world applications are considered, it is imperative develop...
If they are able to spread in wild populations, CRISPR-based gene-drive elements would provide new ways address ecological problems by altering the traits of organisms, but potential for uncontrolled tremendously complicates ethical development and use. Here, we detail a self-exhausting form drive system comprising genetic arranged daisy chain such that each drives next. “Daisy-drive” systems can locally duplicate any effect achievable using an equivalent self-propagating system, their...
Recent reports have suggested that self-propagating CRISPR-based gene drive systems are unlikely to efficiently invade wild populations due drive-resistant alleles prevent cutting. Here we develop mathematical models based on existing empirical data explicitly test this assumption for population alteration drives. Our show although resistance prevents spread fixation in large populations, even the least effective reported date likely be highly invasive. Releasing a small number of organisms...
Abstract We demonstrate a single DNA molecule optical mapping assay able to resolve specific Escherichia coli strain from other strains. The is based on competitive binding of the fluorescent dye YOYO-1 and AT-specific antibiotic netropsin. map visualized by stretching molecules in nanofluidic channels. optimize experimental conditions obtain reproducible barcodes containing as much information possible. implement multi-ligand transfer matrix method for calculating theoretical known...
Abstract RNA-guided gene drive elements could address many ecological problems by altering the traits of wild organisms, but likelihood global spread tremendously complicates ethical development and use. Here we detail a localized form CRISPR-based composed genetic arranged in daisy-chain such that each element drives next. “Daisy drive” systems can duplicate any effect achievable using an equivalent system, their capacity to is limited successive loss non-driving from base chain. Releasing...
The rapid spread of antibiotic resistance - currently one the greatest threats to human health according WHO is a large extent enabled by plasmid-mediated horizontal transfer genes. Rapid identification and characterization plasmids thus important both for individual clinical outcomes epidemiological monitoring resistance. Toward this aim, we have developed an optical DNA mapping procedure where intact are elongated within nanofluidic channels visualized through fluorescence microscopy,...
Abstract An ideal gene drive system to alter wild populations would 1) exclusively affect organisms within the political boundaries of consenting communities, and 2) be capable restoring any engineered population its original genetic state. Here we describe ‘daisy quorum’ systems that meet these criteria by combining daisy with underdominance. A quorum is predicted spread through a until all elements have been lost, at which point fitness becomes frequency-dependent: mostly altered become...
Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due the importance molecules in vivo. We here observe unfolding linear configuration as light-induced double-strand break occurs, characterize dynamics, compare equilibrium conformational statistics configurations. This is important because it allows us determine what extent existing statistical theories describe extension DNA. find that ratio extensions...
Abstract Methods of altering wild populations are most useful when inherently limited to local geographic areas. Here we describe a novel form gene drive based on the introduction multiple copies an engineered ‘daisy’ sequence into repeated elements genome. Each introduced copy encodes guide RNAs that target one or more loci carrying CRISPR nuclease and desired traits. When organisms encoding system released environment, each generation mating with wild-type will reduce average number RNA...
The contiguity and phase of sequence information are intrinsic to obtain complete understanding the genome its relationship phenotype. We report fabrication application a novel nanochannel design that folds megabase lengths genomic DNA into systematic back-and-forth meandering path. Such nanochannels enabled us visualize 5.7 Mbp (1 mm) stained length Schizosaccharomyces pombe chromosome in single frame CCD. were able hold situ while implementing partial denaturation barcode pattern we could...
We demonstrate how circular bacterial plasmids can be automatically sized and discriminated from linear DNA fragments<italic>via</italic>stretching in nanochannels.
Abstract Recent reports have suggested that CRISPR-based gene drives are unlikely to invade wild populations due drive-resistant alleles prevent cutting. Here we develop mathematical models based on existing empirical data explicitly test this assumption. We show although resistance prevents drive systems from spreading fixation in large populations, even the least effective reported date highly invasive. Releasing a small number of organisms often causes invasion local population, followed...
Abstract The alteration of wild populations has been discussed as a solution to number humanity’s most pressing ecological and public health concerns. Enabled by the recent revolution in genome editing, CRISPR gene drives, selfish genetic elements which can spread through even if they confer no advantage their host organism, are rapidly emerging promising approach. But before real-world applications considered, it is imperative develop clear understanding outcomes drive release nature....
Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge this technique is thermal motion the as it undergoes imaging; blurs patterns along results information loss. Correcting effect (a process referred to kymograph alignment) common preprocessing step nanochannel-based optical workflows, we present here highly efficient...
Optical mapping by direct visualization of individual DNA molecules, stretched in nanochannels with sequence-specific fluorescent labeling, represents a promising tool for disease diagnostics and genomics. An important challenge this technique is thermal motion the as it undergoes imaging; blurs patterns along results information loss. Correcting effect (a process referred to kymograph alignment) common preprocessing step nanochannel-based optical workflows, we present here highly efficient...