Madison, WI, United States

University of Wisconsin - Madison
Madison, WI, United States

The University of Wisconsin–Madison is a selective public research university located in Madison, Wisconsin, United States. Founded when Wisconsin achieved statehood in 1848, UW–Madison is the official state university of Wisconsin, and the flagship campus of the University of Wisconsin System. It was the first public university established in Wisconsin and remains the oldest and largest public university in the state. It became a land-grant institution in 1866. The 933-acre main campus includes four National Historic Landmarks.UW–Madison is organized into 20 schools and colleges, which enrolled 29,504 undergraduate, 9,430 graduate, and 2,526 professional students and granted 6,494 bachelor's, 3,560 graduate and professional degrees in 2012-2013. The University employs over 21,727 faculty and staff. Its comprehensive academic program offers 132 undergraduate majors, along with 149 master's degree programs and 120 doctoral programs.The UW is categorized as an RU/VH Research University in the Carnegie Classification of Institutions of Higher Education. In 2012, it had research expenditures of more than $1.1 billion, the third highest among universities in the country. Wisconsin is a founding member of the Association of American Universities.The Wisconsin Badgers compete in 25 intercollegiate sports in the NCAA's Division I Big Ten Conference and have won 28 national championships. Wikipedia.

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Hein P.P.,University of Wisconsin - Madison
Nature Structural and Molecular Biology | Year: 2014

The rates of RNA synthesis and the folding of nascent RNA into biologically active structures are linked via pausing by RNA polymerase (RNAP). Structures that form within the RNA-exit channel can either increase pausing by interacting with RNAP or decrease pausing by preventing backtracking. Conversely, pausing is required for proper folding of some RNAs. Opening of the RNAP clamp domain has been proposed to mediate some effects of nascent-RNA structures. However, the connections among RNA structure formation and RNAP clamp movement and catalytic activity remain uncertain. Here, we assayed exit-channel structure formation in Escherichia coli RNAP with disulfide cross-links that favor closed- or open-clamp conformations and found that clamp position directly influences RNA structure formation and RNAP catalytic activity. We report that exit-channel RNA structures slow pause escape by favoring clamp opening through interactions with the flap that slow translocation.

Hoover J.M.,University of Wisconsin - Madison
Nature protocols | Year: 2012

This protocol describes a practical laboratory-scale method for aerobic oxidation of primary alcohols to aldehydes, using a chemoselective Cu(I)/TEMPO (TEMPO = 2,2,6,6-tetramethyl-1-piperidinyloxyl) catalyst system. The catalyst is prepared in situ from commercially available reagents, and the reactions are performed in a common organic solvent (acetonitrile) with ambient air as the oxidant. Three different reaction conditions and three procedures for the isolation and purification of the aldehyde product are presented. The oxidations of eight different alcohols, described here, include representative examples of each reaction condition and purification method. Reaction times vary from 20 min to 24 h, depending on the alcohol, whereas the purification methods each take about 2 h. The total time necessary for the complete protocol ranges from 3 to 26 h.

Schultz D.M.,University of Wisconsin - Madison | Yoon T.P.,University of Wisconsin - Madison
Science | Year: 2014

Chemists have long aspired to synthesize molecules the way that plants do - using sunlight to facilitate the construction of complex molecular architectures. Nevertheless, the use of visible light in photochemical synthesis is fundamentally challenging because organic molecules tend not to interact with the wavelengths of visible light that are most strongly emitted in the solar spectrum. Recent research has begun to leverage the ability of visible light-absorbing transition metal complexes to catalyze a broad range of synthetically valuable reactions. In this review, we highlight how an understanding of the mechanisms of photocatalytic activation available to these transition metal complexes, and of the general reactivity patterns of the intermediates accessible via visible light photocatalysis, has accelerated the development of this diverse suite of reactions.

Frey P.A.,University of Wisconsin - Madison
Accounts of Chemical Research | Year: 2014

As a graduate student under Professor R. H. Abeles, I began my journey with 5′-deoxyadenosine, studying the coenzyme B12 (adenosylcobalamin)-dependent dioldehydrase (DDH). I proved that suicide inactivation of dioldehydrase by glycolaldehyde proceeded with irreversible cleavage of adenosylcobalamin to 5′-deoxyadenosine. I further showed that suicide inactivation by [2-3H]glycolaldehyde produced 5′-deoxy[3H]adenosine, the first demonstration of hydrogen transfer to adenosyl-C5′ of adenosylcobalamin. The tritium kinetic isotope effect Tk was 15, which correlated well with the measurement Dk = 12 for transformation of [1-2H]propane-1,2-diol to [2-2H]propionaldehyde by DDH. After establishing my own research program, I returned to the glycolaldehyde inactivation of DDH, showing by EPR that suicide inactivation produced glycolaldehyde-2-yl. In retrospect, suicide inactivation involved scission of adenosylcobalamin to 5′-deoxyadenosine- 5′-yl, which abstracted a hydrogen from glycolaldehyde. Captodative-stabilized glycolaldehyde-2-yl could not react further, leading to suicide inactivation.In 1986, my colleagues and I took up the problem of the mechanism by which lysine 2,3-aminomutase (LAM) catalyzes S-adenosylmethionine (SAM) and pyridoxal-5′-phosphate (PLP)-dependent interconversion of l-lysine and l-β-lysine. Because the reaction followed the pattern of adenosylcobalamin-dependent rearrangements, I postulated that SAM might be an evolutionary predecessor to adenosylcobalamin. Testing this hypothesis, we traced hydrogen transfer from lysine through the adenosyl-C5′ of SAM to β-lysine. Thus, the 5′-deoxyadenosyl of SAM mediated hydrogen transfer by LAM exactly as in adenosylcobalamin mediated hydrogen transfer in B12-dependent isomerizations. The mechanism postulated that SAM cleaves to form 5′-deoxyadenosine-5′-yl followed by abstraction of C3(H) from PLP-α-lysine aldimine to form PLP-α-lysine-3-yl. PLP-α-lysine-3-yl isomerizes to pyridoxal-β-lysine-2-yl, and a hydrogen abstraction from 5′-deoxyadenosine regenerates 5′-deoxyadenosine-5′-yl and releases β-lysine. Of four radicals in the postulated mechanism, three have been characterized by EPR spectroscopy as kinetically competent intermediates.The analysis of the role of iron allowed researchers to elucidate the mechanism by which SAM is cleaved to 5′-deoxyadenosine-5′-yl. LAM contains one [4Fe-4S] cluster ligated by three cysteine residues. As shown by ENDOR spectroscopy and X-ray crystallography, the fourth ligand to the cluster is SAM, through the methionyl carboxylate and amino groups. Inner sphere electron transfer within the [4Fe-4S]1+-SAM complex leads to [4Fe-4S]2+-Met and 5′-deoxyadenosine-5′-yl.The iron-binding motif in LAM, CxxxCxxC, found by other groups in four other SAM-dependent enzymes, is the founding motif for the radical SAM superfamily. These enzymes number in the tens of thousands and are responsible for highly diverse and chemically difficult transformations in the biosphere. Available information supports the hypothesis that this superfamily provides the chemical context from which the much more structurally complex adenosylcobalamin evolved. © 2013 American Chemical Society.

Kent K.C.,University of Wisconsin - Madison
New England Journal of Medicine | Year: 2014

A 76-year-old woman presents with a 2-day history of left-lower-quadrant pain. A computed tomographic (CT) scan reveals diverticulitis and an incidental 5.6-cm infrarenal abdominal aortic aneurysm. Her medical history is notable for hypertension, hypercholesterolemia, and obesity. She is a current smoker, with an 80 pack-year history. How should her case be managed? Copyright © 2014 Massachusetts Medical Society.

Hittinger C.T.,University of Wisconsin - Madison
Trends in Genetics | Year: 2013

Saccharomyces cerevisiae is one of the best-understood and most powerful genetic model systems. Several disciplines are now converging to turn Saccharomyces into an exciting model genus for evolutionary genetics and genomics. Yeast taxonomists and ecologists have dramatically expanded and clarified Saccharomyces diversity, more than doubling the number of bona fide species since 2000. High-quality genome sequences are available (or soon will be) for all seven known species. Haploid laboratory strains are enabling a deep integration of classic genetic approaches with modern genomic tools. Population genomic surveys and quantitative trait mapping of variation within species are underway across the genus. Finally, several case studies have illuminated general and novel genetic mechanisms of evolution. Expanding strain collections, low-cost genome sequencing, and tools for precise genetic manipulation promise to usher in a golden era for this surprisingly diverse genus as an evolutionary model. © 2013 Elsevier Ltd.

McFall-Ngai M.J.,University of Wisconsin Madison
Annual Review of Microbiology | Year: 2014

Developmental biology is among the many subdisciplines of the life sciences being transformed by our increasing awareness of the role of coevolved microbial symbionts in health and disease. Most symbioses are horizontally acquired, i.e., they begin anew each generation. In such associations, the embryonic period prepares the animal to engage with the coevolved partner(s) with fidelity following birth or hatching. Once interactions are underway, the microbial partners drive maturation of tissues that are either directly associated with or distant from the symbiont populations. Animal alliances often involve complex microbial communities, such as those in the vertebrate gastrointestinal tract. A series of simpler-model systems is providing insight into the basic rules and principles that govern the establishment and maintenance of stable animal-microbe partnerships. This review focuses on what biologists have learned about the developmental trajectory of horizontally acquired symbioses through the study of the binary squid-vibrio model. Copyright © 2014 by Annual Reviews. All rights reserved.

Chubukov A.,University of Wisconsin - Madison
Annual Review of Condensed Matter Physics | Year: 2012

I review recent works on the symmetry and the structure of the superconducting gap in Fe-based superconductors (FeSCs) and on the underlying pairing mechanism in these systems. The experimental data on superconductivity show very rich behavior, with potentially different symmetry of a superconducting state for different compositions of the same material. The variety of different pairing states raises the issue of whether the physics of FeSCs is model dependent or is universal, governed by a single underlying pairing mechanism. I argue that the physics is universal and that all pairing states obtained so far can be understood within the same universal pairing scenario and are well described by the effective low-energy model with small numbers of input parameters. Copyright © 2012 by Annual Reviews. All rights reserved.

Reich H.J.,University of Wisconsin - Madison
Chemical Reviews | Year: 2013

Organolithium reagents show an astonishingly wide range of aggregated structures in the solid state, with numerous arrangements of the lithium cations, the basic sites in the carbanion and the associated solvent and cosolvent molecules. The generally higher reactivity of lower aggregates has stood up well to close scrutiny, although the reactivity difference between different aggregates varies enormously, from 1 to <8 orders of magnitude. Mixed aggregates are routinely formed during organolithium reactions, and they can be close in reactivity to the reactant aggregates, much less reactive, causing autoinhibition, or more reactive, causing autocatalysis. The crucial role solvents play in the structure and reactivity of lithium reagents continues to be probed. Organolithium compounds are rich in diverse structures, often closely balanced energetically, and the transition states for reactions are similarly diverse, often with closely competing pathways.

Yu L.,University of Wisconsin - Madison
Accounts of Chemical Research | Year: 2010

Diamond and graphite are polymorphs of each other: they have the same composition but different structures and properties. Many other substances exhibit polymorphism: inorganic and organic, natural and manmade. Polymorphs are encountered in studies of crystallization, phase transition, materials synthesis, and biomineralization and in the manufacture of specialty chemicals. Polymorphs can provide valuable insights into crystal packing and structure-property relationships. 5-Methyl-2-[(2-nitrophenyl)amino]-3- thiophenecarbonitrile, known as ROY for its red, orange, and yellow crystals, has seven polymorphs with solved structures, the largest number in the Cambridge Structural Database. First synthesized by medicinal chemists, ROY has attracted attention from solid-state chemists because it demonstrates the remarkable diversity possible in organic solids. Many structures of ROY polymorphs and their thermodynamic properties are known, making ROY an important model system for testing computational models. Though not the most polymorphic substance on record, ROY is extraordinary in that many of its polymorphs can crystallize simultaneously from the same liquid and are kinetically stable under the same conditions. Studies of ROY polymorphs have revealed a new crystallization mechanism that invalidates the common view that nucleation defines the polymorph of crystallization. A slow-nucleating polymorph can still dominate the product if it grows rapidly and nucleates on another polymorph. Studies of ROY have also helped understand a new, surprisingly fast mode of crystal growth in organic liquids cooled to the glass transition temperature. This growth mode exists only for those polymorphs that have more isotropic, and perhaps more liquid-like, packing. The rich polymorphism of ROY results from a combination of favorable thermodynamics and kinetics. Not only must there be many polymorphs of comparable energies or free energies, many polymorphs must be kinetically stable and crystallize at comparable rates to be observed. This system demonstrates the unique insights that polymorphism provides into solid-state structures and properties, as well as the inadequacy of our current understanding of the phenomenon. Despite many studies of ROY, it is still impossible to predict the next molecule that is equally or more polymorphic. ROY is a lucky gift from medicinal chemists. © 2010 American Chemical Society.

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