Engineering a multi-functional DNA origami nanorod for the control of nanoscale processes

Processes that occur at the nanoscale are the foundational building blocks of our world. As such, there is considerable interest in ways to study and manipulate matter at this scale, with applications in biomedicine and other fields. DNA origami has emerged over the past decade as a promising technology for nanofabrication, offering the capacity for precise and tunable nanoscale synthesis while maintaining the ease and scale of bottom-up self-assembly. The goal of this work is to develop novel ways in which DNA origami can be used to manipulate nanoscale processes. To this end, I developed a single DNA origami nanorod which is used in two distinct studies, highlighting the multifunctionality of this structure. I first investigated the effect of iron oxide nanoparticle clustering on MRI contrast generation by organizing particles in precise patterns on the nanorod. I found that small changes in the number of attached iron oxide nanoparticles lead to significant enhancement in T2 relaxivity, while inter-particle spacing has a minimal effect. In the second part of thesis, I developed the first DNA origami molecular motor, which converts chemical energy into mechanical activity and demonstrates autonomous directed motion over micron distances. By leveraging the unique addressability of DNA origami, I found that these motors predominately exhibit a rolling motion and that this behavior can be tuned via small alterations to the nanorod. Combined, this work demonstrates two novel applications for DNA origami nanostructures. We expect this work will serve as an initial platform for further studies and open up a range of new possibilities for the use of DNA origami as MRI contrast agents and molecular motors.Ph.D

The Thin Blue Line Or Thick Blue Wall?

A routine traffic stop turns into a “sticky wicket” when charges are made that customary professional courtesies were not-extended between two officers from neighboring jurisdictions. Police professionalism issues, coupled with preferential treatment expectations and “thin-blue line” implications are embedded in the case study.  As this routine occurrence takes on a momentum of its own, complaints are filed, investigations are conducted, public “whistle-blowing” is revealed, and the chief of police is presented with conflicting opinions that were printed in the Courier—a regional newspaper. In the final analysis the issue of discretionary use of authority comes into the dynamics of the case study

Population response magnitude variation in inferotemporal cortex predicts image memorability

Most accounts of image and object encoding in inferotemporal cortex (IT) focus on the distinct patterns of spikes that different images evoke across the IT population. By analyzing data collected from IT as monkeys performed a visual memory task, we demonstrate that variation in a complementary coding scheme, the magnitude of the population response, can largely account for how well images will be remembered. To investigate the origin of IT image memorability modulation, we probed convolutional neural network models trained to categorize objects. We found that, like the brain, different natural images evoked different magnitude responses from these networks, and in higher layers, larger magnitude responses were correlated with the images that humans and monkeys find most memorable. Together, these results suggest that variation in IT population response magnitude is a natural consequence of the optimizations required for visual processing, and that this variation has consequences for visual memory

Hyperspectral unmixing with material variability using social sparsity

International audienceWe apply social-norms for the first time to the problem of hyperspectral unmixing while modeling spectral variability. These norms are built with inter-group penalties which are combined in a global intra-group penalization that can enforce selection of entire endmember bundles; this results in the selection of a few representative materials even in the presence of large endmembers bundles capturing each material's variability. We demonstrate improvements quantitatively on synthetic data and qualitatively on real data for three cases of social norms: group, elitist, and a fractional social norm, respectively. We find that the greatest improvements arise from using either the group or fractional flavor

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess sequencing quality (alternatively referred to as “noise” or “error”) within and/or between sequencing samples. DRISEE provides positional error estimates that can be used to inform read trimming within a sample. It also provides global (whole sample) error estimates that can be used to identify samples with high or varying levels of sequencing error that may confound downstream analyses, particularly in the case of studies that utilize data from multiple sequencing samples. For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference genomes or the use of scores (e.g. Phred). Here, DRISEE is applied to (non amplicon) data sets from both the 454 and Illumina platforms. The DRISEE error estimate is obtained by analyzing sets of artifactual duplicate reads (ADRs), a known by-product of both sequencing platforms. We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms.</p

Comparison of Neural Activity Related to Working Memory in Primate Dorsolateral Prefrontal and Posterior Parietal Cortex

Neurons in a distributed network of cortical and subcortical areas continue to discharge after the presentation and disappearance of stimuli, providing a neural correlate for working memory. While it is thought that the prefrontal cortex plays a central role in this network, the relative contributions of other brain areas are not as well understood. In order to compare the contributions of the dorsolateral prefrontal and posterior parietal cortex, we recorded neurophysiological activity in monkeys trained to perform two different visuo-spatial working memory tasks: a Match/Nonmatch task, and a Spatial Delayed-Match-to-Sample Task. Neurons in both areas exhibited discharges in the delay periods of the tasks that could be classified in two forms. Sustained discharges persisted after the presentation of a stimulus in the receptive field with a constant or declining rate. Anticipatory responses increased in rate during the delay period, often appearing after presentation of a stimulus out of the receptive field. Despite similarities, we uncovered distinct differences between patterns of delay period in each brain area. Only in the prefrontal cortex sustained responses related to the original stimulus survived presentation of a second stimulus, in the context of the Match/Nonmatch task. Our results provide insights on the nature of processing in two areas active during working memory, and on the unique role of the prefrontal cortex in memory maintenance

Growth and Performance of Terminal Sired Calves Grazing Range or Meadow Pasture

Multiparous dams were assigned to be bred by artificial insemination or natural service to bulls with terminal traits. Additionally, the cow- calf pairs grazed upland range or sub- irrigated meadow from June 1 to weaning in November. Two weeks aft er weaning, calves entered the feedlot as calffeds. Natural service range calves had the lightest weaning weights, final live weights, and hot carcass weights. Additional days on feed may be required for natural service range calves to reach similar body weights and carcass characteristics as other treatments. Average daily gain and feed conversion was improved in calves that grazed range pastures prior to feedlot entry. Estrus synchronization and artificial insemination may be an effective way to increase body weights and carcass characteristics of calves that graze range pastures prior to feedlot entry

The impact of cow size on cow-calf and postweaning progeny performance in the Nebraska Sandhills

Optimizing beef production system efficiency requires an understanding of genetic potential suitable for a given production environment. Therefore, the objective of this retrospective analysis was to determine the influence of cow body weight (BW) adjusted to a common body condition score (BCS) of 5 at weaning-influenced cow-calf performance and postweaning steer and heifer progeny performance. Data were collected at the Gudmundsen Sandhills Laboratory, Whitman, NE, on crossbred, mature cows (n = 1,607) from 2005 to 2017. Cow BCS at calving, prebreeding, and weaning were positively associated (P \u3c 0.01) with greater cow BW. Increasing cow BW was positively associated (P \u3c 0.01) with the percentage of cows that conceived during a 45-d breeding season. For every additional 100-kg increase in cow BW, calf BW increased (P \u3c 0.01) at birth by 2.70 kg and adjusted 205-d weaning BW by 14.76 kg. Calf preweaning average daily gain (ADG) increased (P \u3c 0.01) 0.06 kg/d for every additional 100-kg increase in cow BW. Heifer progeny BW increased (P \u3c 0.01) postweaning with every additional 100-kg increase in dam BW. Dam BW did not influence (P ≥ 0.11) heifer puberty status prior to breeding, overall pregnancy rates, or the percentage of heifers calving in the first 21 d of the calving season. Steer initial feedlot BW increased by 7.20 kg, reimplant BW increased by 10.47 kg, and final BW increased by 10.29 kg (P ≤ 0.01) for every additional 100-kg increase in dam BW. However, steer feedlot ADG was not influenced (P \u3e 0.67) by dam BW. Hot carcass weights of steers were increased (P = 0.01) by 6.48 kg with every additional 100-kg increase in cow BW. In a hypothetical model using the regression coefficients from this study, regardless of pricing method, cow-calf producers maximize the highest amount of profit by selecting smaller cows. Overall, larger-sized cows within this herd and production system of the current study had increased reproductive performance and offspring BW; however, total production output and economic returns would be potentially greater when utilizing smaller-sized cows

Prototype Catalytic Membrane Reactor for Dimethyl Ether Synthesis Via Co2hydrogenation

Dimethyl ether (DME) has become attractive as a potential environmentally friendly substitute for diesel and liquefied petroleum gas (LPG) due to its similar properties to those of LPG, high cetane number, but less carbon emissions. In this work, we developed a novel prototype-scale catalytic membrane reactor to synthesize DME directly from CO2and renewable H2, which could address the environmental and fuel security issues in a cost-effective way. This membrane reactor was equipped with superior hydrophilic NaA zeolite membranes and bifunctional Cu-ZnO-ZrO2-Al2O3/HZSM-5 catalysts. The effects of the reaction temperature and gas hourly space velocity (GHSV) on the DME synthesis were investigated. Compared with the fixed bed catalytic reactor, the catalytic membrane reactor with a unique NaA membrane significantly enhanced the DME yield and CO2conversion from 8.71 and 21.4 to 22.8 and 33.7%, respectively. The highest DME production rate of 1.31 kg/day was achieved at 300 °C and a GHSV of 8400 mL/(g·h). This work demonstrates the feasibility of the catalytic membrane reactor for DME production via CO2 hydrogenation as an approach to market readiness