Identification of functional cis-regulatory elements by sequential enrichment from a randomized synthetic DNA library

BACKGROUND: The identification of endogenous cis-regulatory DNA elements (CREs) responsive to endogenous and environmental cues is important for studying gene regulation and for biotechnological applications but is labor and time intensive. Alternatively, by taking a synthetic biology approach small specific DNA binding sites tailored to the needs of the scientist can be generated and rapidly identified. RESULTS: Here we report a novel approach to identify stimulus-responsive synthetic CREs (SynCREs) from an unbiased random synthetic element (SynE) library. Functional SynCREs were isolated by screening the SynE libray for elements mediating transcriptional activity in plant protoplasts. Responsive elements were chromatin immunoprecipitated by targeting the active Ser-5 phosphorylated RNA polymerase II CTD (Pol II ChIP). Using sequential enrichment, deep sequencing and a bioinformatics pipeline, candidate responsive SynCREs were identified within a pool of constitutively active DNA elements and further validated. These included bonafide biotic/abiotic stress-responsive motifs along with novel SynCREs. We tested several SynCREs in Arabidopsis and confirmed their response to biotic stimuli. CONCLUSIONS: Successful isolation of synthetic stress-responsive elements from our screen illustrates the power of the described methodology. This approach can be applied to any transfectable eukaryotic system since it exploits a universal feature of the eukaryotic Pol II

Sports Analytics With Computer Vision

Computer vision in sports analytics is a relatively new development. With multi-million dollar systems like STATS’s SportVu, professional basketball teams are able to collect extremely fine-detailed data better than ever before. This concept can be scaled down to provide similar statistics collection to college and high school basketball teams. Here we investigate the creation of such a system using open-source technologies and less expensive hardware. In addition, using a similar technology, we examine basketball free throws to see whether a shooter’s form has a specific relationship to a shot’s outcome. A system that learns this relationship could be used to provide feedback on a player’s shooting form

Students\u27 Epistemological Beliefs of Mathematics When Taught Using Traditional Versus Reform Curricula in Rural Maine High Schools

This study compared students’ epistemological beliefs of mathematics after completing 3 years of a reform-oriented curriculum developed by the Core-Plus Mathematics Project (CPMP) versus a more traditional curriculum developed by Glencoe Mathematics. The Conceptions of Mathematics Inventory (CMI; Grouws, Howald, & Colangelo, 1996) was administered to 11th-grade students in four rural Maine high schools (n=102) to measure student beliefs of mathematics. CPMP was used as the primary textbook series in 2 of the schools, while the other 2 schools used Glencoe Mathematics. A variation of the Reformed Teaching Observation Protocol (RTOP; Piburn & Sawada, 2000) and teacher questionnaires were used to characterize the level of reform-oriented instruction occurring in each of the schools. The results indicated that the students who were taught using the traditional curriculum combined with reform-oriented teaching practices expressed the most positive beliefs of mathematics, while the students who were taught using the reform-oriented curriculum expressed less healthy beliefs of mathematics, especially when taught using reform-oriented teaching practices. Some of the differences in beliefs appeared to be gender-related. This study extends the previous research of Grouws et al. (1996), Walker (1999), and Star and Hoffmann (2005) by demonstrating the feasibility of using instruments such as the CMI to assess students’ epistemological beliefs of mathematics in order to expand the notion of impact of reform-oriented curricula beyond students’ performance on achievement tests. This study also illustrates the importance of determining what is actually happening in the classrooms when performing such research

Predation and Parasitism of the Kamehameha Butterfly (Vanessa tameamea) on Oahu Island.

M.S. Thesis. University of Hawaiʻi at Mānoa 2017

MONEY ILLUSION, GORMAN AND LAU

Any demand equation satisfying Lau’s (1982) Fundamental Theorem of Exact Aggregation and 0° homogeneity in prices and income will have a Gorman (1981) functional form for each income term. This property does not depend on symmetry or adding up. The implications of this result are illustrated by an extensive example.Demand, exact aggregation, functional form, homogeneity

Unknotted Curves on Seifert Surfaces

We consider homologically essential simple closed curves on Seifert surfaces of genus one knots in $S^3$, and in particular those that are unknotted or slice in $S^3$. We completely characterize all such curves for most twist knots: they are either positive or negative braid closures; moreover, we determine exactly which of those are unknotted. A surprising consequence of our work is that the figure eight knot admits infinitely many unknotted essential curves up to isotopy on its genus one Seifert surface, and those curves are enumerated by Fibonacci numbers. On the other hand, we prove that many twist knots admit homologically essential curves that cannot be positive or negative braid closures. Indeed, among those curves, we exhibit an example of a slice but not unknotted homologically essential simple closed curve. We further investigate our study of unknotted essential curves for arbitrary Whitehead doubles of non-trivial knots, and obtain that there is a precisely one unknotted essential simple closed curve in the interior of the doubles' standard genus one Seifert surface. As a consequence of all these we obtain many new examples of 3-manifolds that bound contractible 4-manifolds.Comment: 26 page

The Comparative Toxicogenomics Database (CTD).

The Mount Desert Island Biological Laboratory in Salsbury Cove, Maine, USA, is developing the Comparative Toxicogenomics Database (CTD), a community-supported genomic resource devoted to genes and proteins of human toxicologic significance. CTD will be the first publicly available database to a) provide annotated associations among genes, proteins, references, and toxic agents, with a focus on annotating data from aquatic and mammalian organisms; b) include nucleotide and protein sequences from diverse species; c) offer a range of analysis tools for customized comparative studies; and d) provide information to investigators on available molecular reagents. This combination of features will facilitate cross-species comparisons of toxicologically significant genes and proteins. These comparisons will promote understanding of molecular evolution, the significance of conserved sequences, the genetic basis of variable sensitivity to environmental agents, and the complex interactions between the environment and human health. CTD is currently under development, and the planned scope and functions of the database are described herein. The intent of this report is to invite community participation in the development of CTD to ensure that it will be a valuable resource for environmental health, molecular biology, and toxicology research