Engineering ligand-responsive RNA controllers in yeast through the assembly of RNase III tuning modules

The programming of cellular networks to achieve new biological functions depends on the development of genetic tools that link the presence of a molecular signal to gene-regulatory activity. Recently, a set of engineered RNA controllers was described that enabled predictable tuning of gene expression in the yeast Saccharomyces cerevisiae through directed cleavage of transcripts by an RNase III enzyme, Rnt1p. Here, we describe a strategy for building a new class of RNA sensing-actuation devices based on direct integration of RNA aptamers into a region of the Rnt1p hairpin that modulates Rnt1p cleavage rates. We demonstrate that ligand binding to the integrated aptamer domain is associated with a structural change sufficient to inhibit Rnt1p processing. Three tuning strategies based on the incorporation of different functional modules into the Rnt1p switch platform were demonstrated to optimize switch dynamics and ligand responsiveness. We further demonstrated that these tuning modules can be implemented combinatorially in a predictable manner to further improve the regulatory response properties of the switch. The modularity and tunability of the Rnt1p switch platform will allow for rapid optimization and tailoring of this gene control device, thus providing a useful tool for the design of complex genetic networks in yeast

Timing molecular motion and production with a synthetic transcriptional clock

The realization of artificial biochemical reaction networks with unique functionality is one of the main challenges for the development of synthetic biology. Due to the reduced number of components, biochemical circuits constructed in vitro promise to be more amenable to systematic design and quantitative assessment than circuits embedded within living organisms. To make good on that promise, effective methods for composing subsystems into larger systems are needed. Here we used an artificial biochemical oscillator based on in vitro transcription and RNA degradation reactions to drive a variety of “load” processes such as the operation of a DNA-based nanomechanical device (“DNA tweezers”) or the production of a functional RNA molecule (an aptamer for malachite green). We implemented several mechanisms for coupling the load processes to the oscillator circuit and compared them based on how much the load affected the frequency and amplitude of the core oscillator, and how much of the load was effectively driven. Based on heuristic insights and computational modeling, an “insulator circuit” was developed, which strongly reduced the detrimental influence of the load on the oscillator circuit. Understanding how to design effective insulation between biochemical subsystems will be critical for the synthesis of larger and more complex systems

Love at First Sight? Jane Austen and the Transformative Male Gaze

In this thesis, I claim that the gaze is central to the courtship process in Austen’s novels. I also propose that an analysis of the gaze is crucial to understanding the gendered power dynamics that are central to these relationships. We tend to think of male gazers as having all the power, but one of Austen’s subversive arguments is that women can also be subjects of the gaze and transform through it. However, limits exist to their power. As I will argue, while men are able to simply project their transformative gaze, women must first use their gaze to perceive their societal position before successfully having a transformative effect

The Academy for Student Ministry: a study in youth ministry

https://place.asburyseminary.edu/ecommonsatsdissertations/1330/thumbnail.jp

Many accurate small-discriminatory feature subsets exist in microarray transcript data: biomarker discovery

BACKGROUND: Molecular profiling generates abundance measurements for thousands of gene transcripts in biological samples such as normal and tumor tissues (data points). Given such two-class high-dimensional data, many methods have been proposed for classifying data points into one of the two classes. However, finding very small sets of features able to correctly classify the data is problematic as the fundamental mathematical proposition is hard. Existing methods can find "small" feature sets, but give no hint how close this is to the true minimum size. Without fundamental mathematical advances, finding true minimum-size sets will remain elusive, and more importantly for the microarray community there will be no methods for finding them. RESULTS: We use the brute force approach of exhaustive search through all genes, gene pairs (and for some data sets gene triples). Each unique gene combination is analyzed with a few-parameter linear-hyperplane classification method looking for those combinations that form training error-free classifiers. All 10 published data sets studied are found to contain predictive small feature sets. Four contain thousands of gene pairs and 6 have single genes that perfectly discriminate. CONCLUSION: This technique discovered small sets of genes (3 or less) in published data that form accurate classifiers, yet were not reported in the prior publications. This could be a common characteristic of microarray data, thus making looking for them worth the computational cost. Such small gene sets could indicate biomarkers and portend simple medical diagnostic tests. We recommend checking for small gene sets routinely. We find 4 gene pairs and many gene triples in the large hepatocellular carcinoma (HCC, Liver cancer) data set of Chen et al. The key component of these is the "placental gene of unknown function", PLAC8. Our HMM modeling indicates PLAC8 might have a domain like part of lP59's crystal structure (a Non-Covalent Endonuclease lii-Dna Complex). The previously identified HCC biomarker gene, glypican 3 (GPC3), is part of an accurate gene triple involving MT1E and ARHE. We also find small gene sets that distinguish leukemia subtypes in the large pediatric acute lymphoblastic leukemia cancer set of Yeoh et al

Evaluating Factors That Influence MVP Voting in the NBA

We develop and test an empirical model to study the factors that affect variation in the proportion of MVP votes received by NBA players over the years 2007 to 2017. Our explanatory variables fall into two categories: player performance and team performance. The empirical results suggest that player performance variables, such as points per game, steals per game, offensive rebounds per game, and fouls per game, help to explain the proportion of MVP votes received by players. We found that team characteristics did not have a statistically significant influence on the proportion of MVP votes received by players

Photoantimicrobial Biohybrids by Supramolecular Immobilization of Cationic Phthalocyanines onto Cellulose Nanocrystals

This is the peer-reviewed version of the following article: Anaya‐Plaza, E., van de Winckel, E., Mikkilä, J., Malho, J. M., Ikkala, O., Gulías, O., ... & Kostiainen, M. A. (2017). Photoantimicrobial biohybrids by supramolecular immobilization of cationic phthalocyanines onto cellulose nanocrystals. Chemistry–A European Journal, 23(18), 4320-4326., which has been published in final form at https://doi.org/10.1002/chem.201605285. This article may be used for non-commercial purposes in accordance with Wiley-VCH Terms and Conditions for Self-ArchivingThe development of photoactive and biocompatible nanostructures is a highly desirable goal to address the current threat of antibiotic resistance. Here, we describe a novel supramolecular biohybrid nanostructure based on the non-covalent immobilization of cationic zinc phthalocyanine (ZnPc) derivatives onto unmodified cellulose nanocrystals (CNC), following an easy and straightforward protocol, in which binding is driven by electrostatic interactions. These non-covalent biohybrids show strong photodynamic activity against S. aureus and E. coli, representative examples of Gram-positive and Gram-negative bacteria, respectively, and C. albicans, a representative opportunistic fungal pathogen, outperforming the free ZnPc counterparts and related nanosystems in which the photosensitizer is covalently linked to the CNC surfaceA.d.l.E. acknowledges a Ramón y Cajal contract from the Spanish Ministry of Economy (MINECO). The work at Madrid was supported by the EU [SO2S (FP7‐PEOPLE‐2012‐ITN, 316975); and CosmoPHOS‐nano (FP7‐NMP‐2012‐6, 310337‐2)], the Spanish MINECO [CTQ‐2014‐52869‐P (T.T.) and CTQ‐2014‐53673‐P (A.d.l.E.)] and Comunidad de Madrid [FOTOCARBON (S2013/MIT‐2841)]. J.M., V.L., and M.A.K. acknowledge support through the Emil Aaltonen Foundation and the Academy of Finland (grants 267497, 273645 and 263504). This work was supported by the Academy of Finland through its Centers of Excellence Programme (2014–2019) and made use of the Aalto University Nanomicroscopy Centre (Aalto NMC). The work in Barcelona was supported by the Spanish MINECO (grant CTQ2013‐48767‐C3‐1‐R). R.B.‐O. thanks the European Social Funds and the SUR del DEC de la Generalitat de Catalunya for his predoctoral fellowship (2016 FI B1 00021)

Betti tables forcing failure of the Weak Lefschetz Property

We study the Artinian reduction $A$ of a configuration of points $X \subset {\mathbb P}^n$, and the relation of the geometry of $X$ to Lefschetz properties of $A$. Migliore initiated the study of this connection, with a particular focus on the Hilbert function of $A$, and further results appear in work of Migliore--Mir\'o-Roig--Nagel. Our specific focus is on Betti tables rather than Hilbert functions, and we prove that a certain type of Betti table forces the failure of the Weak Lefschetz Property (WLP). The corresponding Artinian algebras are typically not level, and the failure of WLP in these cases is not detected in terms of the Hilbert function

Fundamental studies of the adhesion of explosives to textile and non-textile surfaces

This paper describes the use of atomic force microscopy (AFM) to investigate the interactions between explosives crystals and different surfaces. Crystals of TNT, PETN and RDX were mounted onto tipless AFM cantilevers and repeatedly brought into contact with a range of surfaces (n = 15), including textile and non-textile surfaces. The adhesion force during each contact was measured, and the results are presented in this work. The results suggest that explosives crystals display a higher adhesion to smoother, non-textile surfaces, particularly glass. This finding may be of use for forensic explosives investigators when deciding the best types of debris to target for explosives recovery

Early care and education in tribal communities: Research to policy resources

There are approximately 390,000 children age nine and under who are identified by their parents as being of American Indian or Alaska Native (AIAN) heritage alone, while more than 400,000 other children in the same age range share this heritage with that of other race and ethnic groups. The large majority--about 80 percent--of AIAN individuals live outside of tribal lands and reservations and, regardless of where they live, many have incomes below the federal poverty level. While about one-quarter of all individuals who report having some AIAN heritage have incomes below the federal poverty level, the poverty rate among children five and under is 33 percent. Following her visit to two Native American communities in August 2015, Sylvia Mathews Burwell, Secretary of the U. S. Department of Health and Human Services (HHS), wrote, "At HHS, we're committed to ensuring healthy, productive lives for families in all communities, and that is true in Indian Country as well." This commitment is exemplified in the federal government's continuing partnership with tribal governments through several programs within HHS, including the Tribal Early Learning Initiative (TELI), the National Center on Tribal Child Care Implementation and Innovation (NCTCCII), and the Tribal Maternal Infant Early Childhood Home Visiting Program (Tribal MIECHV)