Engineering DNA-Based Self-Assembly Systems to Produce Nanostructures and Chemical Patterns

While commonly known as a material that stores biological information essential for life, few realize that deoxyribonucleic acid (DNA) is also a wonderful building (i.e., physical structures) and computing material. The field of DNA nanotechnology aims to use DNA primarily to build and control matter on the nanoscale. In 2006, a technique known as DNA origami was developed, which allows for the formation of about any shape on the nanoscale. Such DNA origami have been used in many applications: nanodevices, nanotubes, nanoreactors. However, the small surface area of the origami often limits its usefulness. One promising method for building large (micron-sized) DNA origami structures is to self-assemble multiple origami components into well-defined structures. To date, however, such structures suffer low yields, long reaction times and require experimental optimization with no guiding principles. One primary reason is that a governing theory and experimental measurements behind such a self-assembly process are lacking. In this work, we develop coarse-grained computational simulations to describe and understand the self-assembly of finite-sized, multicomponent complexes (e.g., nine different DNA-origami components that form a square grid complex). To help inform the model, we experimentally investigate how various interface architectures between two self-assembling DNA origami components affect the reaction kinetics and thermodynamics. We further develop the accuracy of our simulations by incorporating these measurements and other thermodynamic measurements from our group and implement a computational algorithm that optimizes the interaction strengths between self-assembling components for reaction efficiency (i.e., speed and yield of the complex). With these experimentally-informed simulations, we suggest design improvements and provide yield predictions to an experimentally demonstrated tetrameric complex. Finally, with the overarching idea of using DNA-based components to self-assemble to produce ordered structures and patterns, we build a reaction-diffusion system whose reactions are programmed using DNA strand displacement and diffusion which occurs in a hydrogel, wherein patterns develop, and liquid reservoirs, which are used to supply the high energy components. With this reaction-diffusion system we create stable (i.e., unchanging in space and time) one and two-dimensional patterns of DNA molecules with millimeter-scale features

Clustering Instabilities in Gas-Solid Systems: Role of Dissipative Collisions vs. Viscous Losses

https://digitalrepository.unm.edu/abq_mj_news/4755/thumbnail.jp

The SCOR Working Group 21 intercomparison of recording current meters on R/V "AKADEMIK KURCHATOV" – 50 years later

This paper describes the activities of SCOR WG21 that carried out intercomparisons of moored, recording current meters in the late 1960s and early 1970s. The paper focusses particularly on the WG’s involvement in the 7th voyage of the R/V “Akademik Kurchatov” and its participation in the ground-breaking Polygon–70 programme

A whey-protein supplement increases fat loss and spares lean muscle in obese subjects: a randomized human clinical study

<p>Abstract</p> <p>Background</p> <p>This study evaluated a specialized whey fraction (Prolibra™, high in leucine, bioactive peptides and milk calcium) for use as a dietary supplement to enhance weight loss.</p> <p>Methods</p> <p>This was a randomized, double-blind, parallel-arm, 12-week study. Caloric intake was reduced 500 calories per day. Subjects consumed Prolibra or an isocaloric ready-to-mix beverage 20 minutes before breakfast and 20 minutes before dinner. Body fat and lean muscle tissue were measured by dual-energy x-ray absorptiometry (DEXA). Body weight and anthropometric measurements were recorded every 4 weeks. Blood samples were taken at the beginning and end of the study. Statistical analyses were performed on all subjects that completed (completer analysis) and all subjects that lost at least 2.25 kg of body weight (responder analysis). Within group significance was determined at <it>P </it>< 0.05 using a two-tailed paired t-test and between group significance was determined using one way analysis of covariance with baseline data as a covariate.</p> <p>Results</p> <p>Both groups lost a significant amount of weight and the Prolibra group tended to lose more weight than the control group; however the amount of weight loss was not significantly different between groups after 12 weeks. Prolibra subjects lost significantly more body fat compared to control subjects for both the completer (2.81 vs. 1.62 kg <it>P </it>= 0.03) and responder (3.63 vs. 2.11 kg, <it>P </it>= 0.01) groups. Prolibra subjects lost significantly less lean muscle mass in the responder group (1.07 vs. 2.41 kg, <it>P </it>= 0.02). The ratio of fat to lean loss (kg fat lost/kg lean lost) was much larger for Prolibra subjects for both completer (3.75 vs. 1.05) and responder (3.39 vs. 0.88) groups.</p> <p>Conclusion</p> <p>Subjects in both the control and treatment group lost a significant amount of weight with a 500 calorie reduced diet. Subjects taking Prolibra lost significantly more body fat and showed a greater preservation of lean muscle compared to subjects consuming the control beverage. Because subjects taking Prolibra lost 6.1% of their body fat mass, and because a 5% reduction of body fat mass has been shown to reduce the risk of obesity related disease, the results have practical significance.</p

The anatomy of the Antarctic polar front in the Drake Passage

An intensive three-dimensional survey of the Antarctic Polar Front was made in the Drake Passage in March 1976. The front, which was imbedded within one of the high-velocity cores of the circumpolar current, is viewed as a water mass boundary demarking the northern extent of near-surface antarctic waters. Within the front, water masses are observed to intrude, one above the other, with characteristic vertical scales of 50–100 m. The intrusions are horizontally anisotropic, being elongated in the alongstream direction and constrained primarily to the upper 800 m of the front. The spatial and temporal persistence of the variability is examined through the analysis of continuous vertical profiles of horizontal velocity, temperature, salinity, and oxygen with discrete sampling of nutrients. Analysis of the velocity data showed the mean current flowing to the NNE with speeds of the order of 30–40 cm s−1 in the upper 600 m, with temporal variability over a 28-hour ‘yo-yo’ due primarily to internal gravity waves. The thermohaline variability was not internal wave induced but rather was associated with nearly isentropic advection of different water masses across the front. Cold fresh and warm salty intrusions did not conserve potential density, however, and double-diffusive transfers are strongly suggested as being crucial to an understanding of the dynamics of the intrusions. Applying a model (Joyce, 1977) for lateral mixing we estimate poleward temperature and salinity fluxes due to interleaving of 0.086°C cm s−1 and 0.069‰ cm s−1, respectively. If these values are typical, interleaving could play a significant role in large-scale balance of salt and, to a lesser extent, heat for the Southern Ocean

Recent changes in the surface salinity of the North Atlantic subpolar gyre

Sea surface salinity (SSS) was measured since 1896 along 60°N between Greenland and the North Sea and since 1993 between Iceland and Newfoundland. Along 60°N away from the shelves, and north of 53°N, the amplitude of the seasonal cycle is comparable to or less than interannual variability. In these parts of the North Atlantic subpolar gyre, large-scale deviations from the seasonal cycle correlate from one season to the next. This suggests that in these regions, summer and autumn surface data are useful for monitoring changes in upper ocean salinity best diagnosed from less common winter surface data. Further south near the subarctic front, the Labrador Current or near shelves where seasonal variability is strong, this is not the case. Along 60°N, the multiannual low-frequency variability is well correlated across the basin and exhibits fresher surface water since the mid 1970s than in the late 1920s to 1960s. SSS in the Irminger Sea along 60°N lags by 1-year SSS farther east in the Iceland Basin. Variability between Iceland and Newfoundland within the Irminger Sea north of 54°N presents similar characteristics to what is observed along 60°N. Variability near the northwest corner of the North Atlantic Current (52°N/45°W) is larger and is not correlated to what is found further north. Maps of SSS were constructed for a few recent seasons between July 1996 and June 2000, which illustrate the fresh conditions found usually during that period across the whole North Atlantic subpolar gyre, although this includes an episode of higher salinity. The SSS anomaly maps have large uncertainties but suggest that the highest SSS occurred before the spring of 1998 in the Iceland Basin, and after that, in the Irminger Sea. This is followed by fresher conditions, first in the Labrador and Iceland Basin, reaching recently the Irminger Sea

A natural mineral supplement provides relief from knee osteoarthritis symptoms: a randomized controlled pilot trial

<p>Abstract</p> <p>Background</p> <p>This small, pilot study evaluated the impact of treatment with a natural multi-mineral supplement from seaweed (Aquamin) on walking distance, pain and joint mobility in subjects with moderate to severe osteoarthritis of the knee.</p> <p>Methods</p> <p>Subjects (n = 70) with moderate to severe osteoarthritis of the knee were randomized to four double-blinded treatments for 12 weeks: (a) Glucosamine sulfate (1500 mg/d); (b) Aquamin (2400 mg/d); (c) Combined treatment composed of Glucosamine sulfate (1500 mg/d) plus Aquamin (2400 mg/d) and (d) Placebo. Primary outcome measures were WOMAC scores and 6 Minute Walking Distances (6 MWD). Laboratory based blood tests were used as safety measures.</p> <p>Results</p> <p>Fifty subjects completed the study and analysis of the data showed significant differences between the groups for changes in WOMAC pain scores over time (p = 0.009 ANCOVA); however, these data must be reviewed with caution since significant differences were found between the groups at baseline for WOMAC pain and stiffness scores (p = 0.0039 and p = 0.013, respectively, ANOVA). Only the Aquamin and Glucosamine groups demonstrated significant improvements in symptoms over the course of the study. The combination group (like the placebo group) did not show any significant improvements in OA symptoms in this trial. Within group analysis demonstrated significant improvements over time on treatment for the WOMAC pain, activity, composite and stiffness (Aquamin only) scores as well as the 6 minute walking distances for subjects in the Aquamin and Glucosamine treatment groups. The Aquamin and Glucosamine groups walked 101 feet (+7%) and 56 feet (+3.5%) extra respectively. All treatments were well tolerated and the adverse events profiles were not significantly different between the groups.</p> <p>Conclusion</p> <p>This small preliminary study suggested that a multi mineral supplement (Aquamin) may reduce the pain and stiffness of osteoarthritis of the knee over 12 weeks of treatment and warrants further study.</p> <p>Trial registration</p> <p>ClinicalTrials.gov number: NCT00452101.</p

A natural mineral supplement provides relief from knee osteoarthritis symptoms: a randomized controlled pilot trial

<p>Abstract</p> <p>Background</p> <p>This small, pilot study evaluated the impact of treatment with a natural multi-mineral supplement from seaweed (Aquamin) on walking distance, pain and joint mobility in subjects with moderate to severe osteoarthritis of the knee.</p> <p>Methods</p> <p>Subjects (n = 70) with moderate to severe osteoarthritis of the knee were randomized to four double-blinded treatments for 12 weeks: (a) Glucosamine sulfate (1500 mg/d); (b) Aquamin (2400 mg/d); (c) Combined treatment composed of Glucosamine sulfate (1500 mg/d) plus Aquamin (2400 mg/d) and (d) Placebo. Primary outcome measures were WOMAC scores and 6 Minute Walking Distances (6 MWD). Laboratory based blood tests were used as safety measures.</p> <p>Results</p> <p>Fifty subjects completed the study and analysis of the data showed significant differences between the groups for changes in WOMAC pain scores over time (p = 0.009 ANCOVA); however, these data must be reviewed with caution since significant differences were found between the groups at baseline for WOMAC pain and stiffness scores (p = 0.0039 and p = 0.013, respectively, ANOVA). Only the Aquamin and Glucosamine groups demonstrated significant improvements in symptoms over the course of the study. The combination group (like the placebo group) did not show any significant improvements in OA symptoms in this trial. Within group analysis demonstrated significant improvements over time on treatment for the WOMAC pain, activity, composite and stiffness (Aquamin only) scores as well as the 6 minute walking distances for subjects in the Aquamin and Glucosamine treatment groups. The Aquamin and Glucosamine groups walked 101 feet (+7%) and 56 feet (+3.5%) extra respectively. All treatments were well tolerated and the adverse events profiles were not significantly different between the groups.</p> <p>Conclusion</p> <p>This small preliminary study suggested that a multi mineral supplement (Aquamin) may reduce the pain and stiffness of osteoarthritis of the knee over 12 weeks of treatment and warrants further study.</p> <p>Trial registration</p> <p>ClinicalTrials.gov number: NCT00452101.</p

Observations of the Antarctic polar front during FDRAKE 76 : a cruise report

Figures 37 and 38 have been reduced from their original size for the purpose of scanning.During March/April 1976 the small-scale structure of the Antarctic Polar Front was observed in the Drake Passage. The observations were part of the International Southern Ocean Studies (ISOS) program called FDRAke 76. The purpose of the program was to obtain densely sampled measurements of temperature, salinity, dissolved oxygen, and chemical nutrients in the Polar Front Zone (PFZ) and pilot measurements of horizontal and vertical velocities in order to explain the above scalar variability. The PFZ is a region where Antarctic and sub-Antarctic waters intermingle and presumably mix to affect the properties of Antarctic Intermediate Water. A report on the third leg of Cruise 107 of the R. V. THOMPSON is presented as well as a description of the measurements and a preliminary report of the data. A feature of interest is the pinching off of a northward meander of the circumpolar current system into a cyclonic ring of Antarctic Waters.Prepared for the National Science Foundation, Office for the International Decade of Ocean Exploration, under Grant OCE75-14056 and the International Southern Ocean Studies (ISOS) Program