Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Published: August 2013
AI Article Synopsis
Article Abstract
Background: Primer design for highly variable DNA sequences is difficult, and experimental success requires attention to many interacting constraints. The advent of next-generation sequencing methods allows the investigation of rare variants otherwise hidden deep in large populations, but requires attention to population diversity and primer localization in relatively conserved regions, in addition to recognized constraints typically considered in primer design.
Results: Design constraints include degenerate sites to maximize population coverage, matching of melting temperatures, optimizing de novo sequence length, finding optimal bio-barcodes to allow efficient downstream analyses, and minimizing risk of dimerization. To facilitate primer design addressing these and other constraints, we created a novel computer program (PrimerDesign) that automates this complex procedure. We show its powers and limitations and give examples of successful designs for the analysis of HIV-1 populations.
Conclusions: PrimerDesign is useful for researchers who want to design DNA primers and probes for analyzing highly variable DNA populations. It can be used to design primers for PCR, RT-PCR, Sanger sequencing, next-generation sequencing, and other experimental protocols targeting highly variable DNA samples.
Interactions between magma oceans and overlying atmospheres on young rocky planets leads to an evolving feedback of outgassing, greenhouse forcing, and mantle melt fraction. Previous studies have predominantly focused on the solidification of oxidized Earth-similar planets, but the diversity in mean density and irradiation observed in the low-mass exoplanet census motivate exploration of strongly varying geochemical scenarios. We aim to explore how variable redox properties alter the duration of magma ocean solidification, the equilibrium thermodynamic state, melt fraction of the mantle, and atmospheric composition.
Study Design: Retrospective analysis of prospectively-collected data.
Objective: This study aims to define clinically relevant blood loss in adult spinal deformity (ASD) surgery.
Background: Current definitions of excessive blood loss following spine surgery are highly variable and may be suboptimal in predicting adverse events (AE).
Plant Molecular Biology and Biotechnology Laboratory, School of Agriculture, Food, and Ecosystem Sciences, The University of Melbourne, Parkville, Australia.
Climate change is leading to more frequent and severe extreme temperature events, negatively impacting agricultural productivity and threatening global food security. Plant reproduction, the process fundamental to crop yield, is highly susceptible to heatwaves, which disrupt pollen development and ultimately affect seed-set and crop yields. Recent research has increasingly focused on understanding how pollen grains from various crops react to heat stress at the molecular and cellular levels.
The thalamus is a collection of gray matter nuclei that play a crucial role in sensorimotor processing and modulation of cortical activity. Characterizing thalamic nuclei non-invasively with structural MRI is particularly relevant for patient populations with Parkinson's disease, epilepsy, dementia, and schizophrenia. However, severe head motion in these populations poses a significant challenge for in vivo mapping of thalamic nuclei.
Background And Objectives: The pharmacokinetics (PK) of piperacillin/tazobactam (PIP/TAZ) is highly variable across different patient populations and there are controversies regarding non-linear elimination as well as the fraction unbound of PIP (f). This has led to a plethora of subgroup-specific models, increasing the risk of misusing published models when optimising dosing regimens. In this study, we aimed to develop a single model to simultaneously describe the PK of PIP/TAZ in diverse patient populations and evaluate the current dosing recommendations by predicting the PK/pharmacodynamics (PD) target attainment throughout life.
