Molecular sampling at logarithmic rates for next-generation sequencing.

Next-generation sequencing is a cutting edge technology, but to quantify a dynamic range of abundances for different RNA or DNA species requires increasing sampling depth to levels that can be prohibitively expensive due to physical limits on molecular throughput of sequencers. To overcome this problem, we introduce a new general sampling theory which uses biophysical principles to functionally encode the abundance of a species before sampling, SeQUential depletIon and enriCHment (SQUICH). In theory and simulation, SQUICH enables sampling at a logarithmic rate to achieve the same precision as attained with conventional sequencing.

Hepatitis C virus direct-acting antiviral nonadherence: Relationship to sustained virologic response and identification of at-risk patients.

Objectives: There is a dearth of literature on effects of nonadherence to hepatitis C virus (HCV) direct-acting antiviral (DAA) regimens; thus, the objective of our study was to assess the impact of adherence on sustained virologic response (SVR) and evaluate factors associated with nonadherence, such as race, psychiatric comorbidities, and therapy length.

Methods: We conducted a retrospective cohort study of patients completing DAA treatment between January 2014 and May 2016 within an interdisciplinary hepatology clinic. Adherence was defined a priori as 95% or greater of DAA doses taken within the prescribed treatment period.

ciRS-7 exonic sequence is embedded in a long non-coding RNA locus.

ciRS-7 is an intensely studied, highly expressed and conserved circRNA. Essentially nothing is known about its biogenesis, including the location of its promoter. A prevailing assumption has been that ciRS-7 is an exceptional circRNA because it is transcribed from a locus lacking any mature linear RNA transcripts of the same sense.

Broad 4-hydroxyphenylpyruvate dioxygenase inhibitor herbicide tolerance in soybean with an optimized enzyme and expression cassette.

With an optimized expression cassette consisting of the soybean (Glycine max) native promoter modified for enhanced expression driving a chimeric gene coding for the soybean native amino-terminal 86 amino acids fused to an insensitive shuffled variant of maize (Zea mays) 4-hydroxyphenylpyruvate dioxygenase (HPPD), we achieved field tolerance in transgenic soybean plants to the HPPD-inhibiting herbicides mesotrione, isoxaflutole, and tembotrione. Directed evolution of maize HPPD was accomplished by progressively incorporating amino acids from naturally occurring diversity and novel substitutions identified by saturation mutagenesis, combined at random through shuffling. Localization of heterologously expressed HPPD mimicked that of the native enzyme, which was shown to be dually targeted to chloroplasts and the cytosol.