Nucleic Acid‐Based Microarrays and Nanostructures

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143726/1/cpnc1200.pd

DNA Nanotechnology

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143775/1/cpnc1200.pd

Purification and Analysis of Synthetic Nucleic Acids and Components

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143681/1/cpnc1000.pd

Nucleic Acid‐Based Microarrays and Nanostructures

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143608/1/cpnc1200.pd

Reversible Biotinylation of the 5′‐Terminus of Oligodeoxyribonucleotides and its Application in Affinity Purification

The preparation of two reversible biotinylation phosphoramidites and their application in labeling and affinity purification of synthetic oligodeoxyribonucleotides will be described. In both cases, the biotin is linked to the 5′‐terminus of DNA through a diisopropyl silyl acetal functionality. This linkage is completely stable under certain postsynthetic cleavage/deprotection conditions, but can be readily broken by fluoride ions, releasing unmodified 5′‐OH and 5′‐phosphate DNA, respectively. To demonstrate the use of these reversible biotinylation methods, crude DNA was incubated with NeutrAvidin‐coated microspheres, full‐length biotinylated DNA was efficiently attached to the solid phase, and nonbiotinylated failure sequences and other impurities were readily removed by washing with buffer. Cleavage of the silyl acetal linkage afforded high‐quality, full‐length, unmodified 5′‐OH and 5′‐phosphate DNA, respectively, depending on which of the two phosphoramidites was used. It is anticipated that this method will find applications in areas that require efficient isolation of DNA from a complex mixture.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143794/1/cpnc0420.pd

Palladium‐Mediated C5 Substitution of Pyrimidine Nucleosides

One of the most efficient ways to link a reporter group to oligonucleotides is through the incorporation of a modified nucleoside during automated oligonucleotide synthesis. To be useful, it is important that the reporter group not interfere in hybridization reactions. This unit describes two linkers that can be used for the incorporation of a reporter group at the C5 position of deoxyuridine: a flexible aminoethylthioether linker, and a rigid amidopropynyl linker. The latter is suffciently long and positioned so that the reporter group lies outside the major groove of the DNA duplex.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143730/1/cpnc0101.pd

Principal Component Analysis of Crop Yield Response to Climate Change

The objective of this study is to compare the effects of climate change on crop yields across different regions. A Principal Component Regression (PCR) model is developed to estimate the historical relationships between weather and crop yields for corn, soybeans, cotton, and peanuts for several northern and southern U.S. states. Climate change projection data from three climate models are applied to the estimated PCR model to forecast crop yield response. Instead of directly using weather variables as predictor variables, the PCR model uses weather indices transformed from original weather variables by the Principal Component Analysis (PCA) approach. A climate change impact index (CCII) is developed to compare climate change effects across different regions. The key contribution of our study is in identifying a different climate change effects in crop yields in different U.S. states. Specifically, our results indicate that future warmer weather will have a negative impact for southern U.S. counties, while it has insignificant impact for northern U.S. counties in the next four decades.Principal component regression, Crop yield response, Climate change., Crop Production/Industries,

Reversible linkage of two distinct small molecule inhibitors of myc generates a dimeric inhibitor with improved potency that is active in myc over-expressing cancer cell lines

We describe the successful application of a novel approach for generating dimeric Myc inhibitors by modifying and reversibly linking two previously described small molecules.We synthesized two directed libraries of monomers, each comprised of a ligand, a connector, and a bioorthogonal linker element, to identify the optimal dimer configuration required to inhibit Myc. We identified combinations of monomers, termed self-assembling dimeric inhibitors, which displayed synergistic inhibition of Myc-dependent cell growth. We confirmed that these dimeric inhibitors directly bind to Myc blocking its interaction with Max and affect transcription of MYC dependent genes. Control combinations that are unable to form a dimer do not show any synergistic effects in these assays. Collectively, these data validate our new approach to generate more potent and selective inhibitors of Myc by self-assembly from smaller, lower affinity components. This approach provides an opportunity for developing novel therapeutics against Myc and other challenging protein:protein interaction (PPI) target classes. © 2015 Wanner et al

Tobacco Upregulates P. gingivalis Fimbrial Proteins Which Induce TLR2 Hyposensitivity

Tobacco smokers are more susceptible to periodontitis than non-smokers but exhibit reduced signs of clinical inflammation. The underlying mechanisms are unknown. We have previously shown that cigarette smoke extract (CSE) represents an environmental stress to which P. gingivalis adapts by altering the expression of several virulence factors - including major and minor fimbrial antigens (FimA and Mfa1, respectively) and capsule - concomitant with a reduced pro-inflammatory potential of intact P. gingivalis.We hypothesized that CSE-regulation of capsule and fimbrial genes is reflected at the ultrastructural and functional levels, alters the nature of host-pathogen interactions, and contributes to the reduced pro- inflammatory potential of smoke exposed P. gingivalis. CSE induced ultrastructural alterations were determined by electron microscopy, confirmed by Western blot and physiological consequences studied in open-flow biofilms. Inflammatory profiling of specific CSE-dysregulated proteins, rFimA and rMfa1, was determined by quantifying cytokine induction in primary human innate and OBA-9 cells. CSE up-regulates P. gingivalis FimA at the protein level, suppresses the production of capsular polysaccharides at the ultrastructural level, and creates conditions that promote biofilm formation. We further show that while FimA is recognized by TLR2/6, it has only minimal inflammatory activity in several cell types. Furthermore, FimA stimulation chronically abrogates the pro-inflammatory response to subsequent TLR2 stimulation by other TLR-2-specific agonists (Pam3CSK4, FSL, Mfa1) in an IkappaBalpha- and IRAK-1-dependent manner.These studies provide some of the first information to explain, mechanistically, how tobacco smoke changes the P. gingivalis phenotype in a manner likely to promote P. gingivalis colonization and infection while simultaneously reducing the host response to this major mucosal pathogen

The evolution of language: a comparative review

For many years the evolution of language has been seen as a disreputable topic, mired in fanciful "just so stories" about language origins. However, in the last decade a new synthesis of modern linguistics, cognitive neuroscience and neo-Darwinian evolutionary theory has begun to make important contributions to our understanding of the biology and evolution of language. I review some of this recent progress, focusing on the value of the comparative method, which uses data from animal species to draw inferences about language evolution. Discussing speech first, I show how data concerning a wide variety of species, from monkeys to birds, can increase our understanding of the anatomical and neural mechanisms underlying human spoken language, and how bird and whale song provide insights into the ultimate evolutionary function of language. I discuss the ‘‘descended larynx’ ’ of humans, a peculiar adaptation for speech that has received much attention in the past, which despite earlier claims is not uniquely human. Then I will turn to the neural mechanisms underlying spoken language, pointing out the difficulties animals apparently experience in perceiving hierarchical structure in sounds, and stressing the importance of vocal imitation in the evolution of a spoken language. Turning to ultimate function, I suggest that communication among kin (especially between parents and offspring) played a crucial but neglected role in driving language evolution. Finally, I briefly discuss phylogeny, discussing hypotheses that offer plausible routes to human language from a non-linguistic chimp-like ancestor. I conclude that comparative data from living animals will be key to developing a richer, more interdisciplinary understanding of our most distinctively human trait: language