Life Sciences Commons^™

Capturing Hammerhead Ribozyme Structures In Action By Modulating General Base Catalysis, Young-In Chi, Monika Martick, Monica Lares, Rosalind Kim, William G. Scott, Sung-Hou Kim

Center for Structural Biology Faculty Publications

We have obtained precatalytic (enzyme-substrate complex) and postcatalytic (enzyme-product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation …

Co-Up-Regulation Of Three P450 Genes In Response To Permethrin Exposure In Permethrin Resistant House Flies, Musca Domestica, Fang Zhu, Ting Li, Lee Zhang, Nannan Liu

Entomology Faculty Publications

BACKGROUND: Insects may use various biochemical pathways to enable them to tolerate the lethal action of insecticides. For example, increased cytochrome P450 detoxification is known to play an important role in many insect species. Both constitutively increased expression (overexpression) and induction of P450s are thought to be responsible for increased levels of detoxification of insecticides. However, unlike constitutively overexpressed P450 genes, whose expression association with insecticide resistance has been extensively studied, the induction of P450s is less well characterized in insecticide resistance. The current study focuses on the characterization of individual P450 genes that are induced in response to permethrin …

Inhibitors Of Plant Peptide Deformylase For Use As Broad-Spectrum Herbicides And Methods For Identifying The Same, Robert L. Houtz, Lynnette M. A. Dirk, Mark Alan Wiliams

Horticulture Faculty Patents

The invention relates to a method of identifying herbicides and to the use of inhibitors of plant peptide deformylase as broad spectrum herbicides.

Forage News [2008-09], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• Forage Spokesman Nomination
• KFGC Awards Nomination
• 29th Kentucky Alfalfa Conference - February 19
• How Good Is Your Hay?
• Brassicas and Cereals: High Quality Options for Fall Grazing
• Fall Fertilizer Applications to Hay Fields and Pastures
• USDA Forecasts 2% Less Alfalfa
• Switchgrass for Energy Will Take Time
• Upcoming Events

Accelerated High Fidelity Prion Amplification Within And Across Prion Species Barriers, Kristi M. Green, Joaquín Castilla, Tanya S. Seward, Dana L. Napier, Jean E. Jewell, Claudio Soto, Glenn C. Telling

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Experimental obstacles have impeded our ability to study prion transmission within and, more particularly, between species. Here, we used cervid prion protein expressed in brain extracts of transgenic mice, referred to as Tg(CerPrP), as a substrate for in vitro generation of chronic wasting disease (CWD) prions by protein misfolding cyclic amplification (PMCA). Characterization of this infectivity in Tg(CerPrP) mice demonstrated that serial PMCA resulted in the high fidelity amplification of CWD prions with apparently unaltered properties. Using similar methods to amplify mouse RML prions and characterize the resulting novel cervid prions, we show that serial PMCA abrogated a transmission barrier …

Alternation Of Tobacco Alkaloid Content Through Modification Of Specific Cytochrome P450 Genes, Ralph E. Dewey, Steven W. Bowen, Balazs Siminszky, Lily Gavilano

Plant and Soil Sciences Faculty Patents

Compositions and methods for reducing the level of nornicotine and N′-nitrosonornicotine (NNN) inNicotiana plants and plant parts thereof are provided. The compositions comprise isolated polynucleotides and polypeptides for cytochrome P450s that are involved in the metabolic conversion of nicotine to nornicotine in these plants. Expression cassettes, vectors, plants, and plant parts thereof comprising inhibitory sequences that target expression or function of the disclosed cytochrome P450 polypeptides are also provided. Methods for the use of these novel sequences to inhibit expression or function of cytochrome P450 polypeptides involved in this metabolic conversion are also provided. The methods find use in …

Cd5 Plays An Inhibitory Role In The Suppressive Function Of Murine Cd4(+) Cd25(+) T(Reg) Cells., Trivikram Dasu, Joseph E Qualls, Halide Tuna, Chander Raman, Donald A Cohen, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

A subset of CD4(+) T cells, the CD4(+) CD25(+) regulatory T (T(reg)) cells in the lymphoid organs and peripheral blood are known to possess suppressive function. Previous in vitro and in vivo studies have indicated that T cell receptor (TCR) signal is required for development of such 'natural regulatory (T(reg)) cells' and for activation of the effector function of CD4(+) CD25(+) regulatory T cells. CD5 is a cell surface molecule present on all T cells and a subtype of B lymphocytes, the B-1 cells, primarily localized to coelomic cavities, Peyer's patches, tonsils and spleen. CD5 acts as a negative regulator …

Cd5 Plays An Inhibitory Role In The Suppressive Function Of Murine Cd4+ Cd25+ TReg Cells, Trivikram Dasu, Joseph E. Qualls, Halide Tuna, Chander Raman, Donald A. Cohen, Subbarao Bondada

Microbiology, Immunology, and Molecular Genetics Faculty Publications

A subset of CD4⁺ T cells, the CD4⁺ CD25⁺ regulatory T (T_reg) cells in the lymphoid organs and peripheral blood are known to possess suppressive function. Previous in vitro and in vivo studies have indicated that T cell receptor (TCR) signal is required for development of such ‘natural regulatory (T_reg) cells’ and for activation of the effector function of CD4⁺ CD25⁺ regulatory T cells. CD5 is a cell surface molecule present on all T cells and a subtype of B lymphocytes, the B-1 cells, primarily localized to coelomic cavities, Peyer's patches, …

Relative Crystallinity Of Plant Biomass: Studies On Assembly, Adaptation And Acclimation, Darby Harris, Seth Debolt

Horticulture Faculty Publications

Plant biomechanical design is central to cell shape, morphogenesis, reproductive performance and protection against environmental and mechanical stress. The cell wall forms the central load bearing support structure for plant design, yet a mechanistic understanding of its synthesis is incomplete. A key tool for studying the structure of cellulose polymorphs has been x-ray diffraction and fourier transform infrared spectroscopy (FTIR). Relative crystallinity index (RCI) is based on the x-ray diffraction characteristics of two signature peaks and we used this technique to probe plant assembly, adaptation and acclimation. Confocal microscopy was used to visualize the dynamics of cellulose synthase in transgenic …

Forage News [2008-08], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• History Making Grassland Meeting
• KFGC Field Day
• Stockpiling
• 9th Kentucky Grazing Conference - Lexington, October 23
• Horse Pastures in The Fall: A Perfect Time to Renovate
• Bale at the Proper Moisture
• “One Man’s Pie Is Another Man’s Poison”
• Hauling Challenges Abound
• U.S. Hay Acreage Down Slightly
• KFGC Awards Nomination
• KFGC Forage Spokesman Nominations
• Upcoming Events

Genomic Analysis Of Gene Regulation Complexity, Brandon Barker, Jim Lund

Biology Presentations

With multiple metazoan genomes in each family being sequenced promoter analysis is becoming a useful tool in genomic analysis. Aligning the promoter regions in the DNA of C. elegans and C. briggsae identifies conserved promoter elements. While not all promoter elements are conserved and not all conserved regions are promoter elements, we find that conservation is a useful method for determining promoter complexity. Promoter complexity identifies which genes have particularly interesting regulation, identifying gene groups with a strong promoter complexity signal and cases where a gene's promoter complexity differs from the group's promoter complexity.

We identify potential promoter sequence by …

Identifying Regulatory Elements And Gene Boundaries With Comparative Genomic Sequence Analysis, Jim Lund

Biology Presentations

For several groups of organisms multiple genomes have been sequenced either completely or to the unfinished shotgun sequencing stage. Comparative sequence analysis can identify functional sequence elements for pairs of organisms that diverged far enough in the past to allow mutational drift of non-conserved sequences. While analysis of a pair of genomes identifies many of these functional elements adding additional genomes allows additional information to be elicited.

Additional conserved sequence elements are identified as additional genomes are analyzed. These conserved sequence elements are often regulatory elements although they are difficult to classify with in silico analysis. For an individual gene, …

Sumoylation Regulates Lamin A Function And Is Lost In Lamin A Mutants Associated With Familial Cardiomyopathies, Yu-Qian Zhang, Kevin D. Sarge

Molecular and Cellular Biochemistry Faculty Publications

Lamin A mutations cause many diseases, including cardiomyopathies and Progeria Syndrome. The covalent attachment of small ubiquitin-like modifier (SUMO) polypeptides regulates the function of many proteins. Until now, no examples of human disease-causing mutations that occur within a sumoylation consensus sequence and alter sumoylation were known. We show that lamin A is sumoylated at lysine 201 and that two lamin A mutants associated with familial dilated cardiomyopathy, E203G and E203K, exhibit decreased sumoylation. E203 occupies the conserved +2 position in the sumoylation consensus Psi KXE. Lamin A mutants E203G, E203K, and K201R all exhibit a similar aberrant subcellular localization and …

Forage News [2008-07], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• KFGC Field Day In Christian County
• KFGC Forage Spokesman Nominations
• KFGC Awards Nomination
• The UK Beef Bash 2008: A Different Kind of Field Day
• Certified Noxious Weed Seed Free Hay and Straw Program
• Nitrogen for Stockpiling Fescue
• Forage Seeding Rate Calculator
• Alfalfa Yield and Dollar Return From Wisconsin Green-Gold Program
• Relative Toxicity to Horses of Three Species of Blister Beetles
• Changes in U.S. Dairy Industry Since 1935
• Line Up For varieties Early for Fall Planting
• Roundup Ready Alfalfa on Track for 2009 Return
• Upcoming Events

Nitrite Reduction By Siderite, Sudipta Rakshit, Christopher J. Matocha, Mark S. Coyne

Plant and Soil Sciences Faculty Publications

Nitrate-dependent Fe(II) oxidation is an important process in the inhibition of soil Fe(III) reduction, yet the mechanisms are poorly understood. One proposed pathway includes chemical reoxidation of mineral forms of Fe(II) such as siderite [FeCO3(s)] by NO2 −. Accordingly, the objective of this study was to investigate the reactivity of FeCO3(s) with NO2 −. Stirred-batch reactions were performed in an anoxic chamber across a range of pH values (5.5, 6, 6.5, and 7.9), initial FeCO3(s) concentrations (5, 10, and 15 g L−1) and initial NO2 − concentrations (0.83–9.3 mmol L−1) for kinetic and stoichiometric determinations. Solid-phase products were characterized using …

Some Thoughts On Health Department Accreditation, F. Douglas Scutchfield Md

Preventive Medicine and Environmental Health Presentations

No abstract provided.

A Polyadenylation Factor Subunit Implicated In Regulating Oxidative Signaling In Arabidopsis Thaliana, Jingxian Zhang, Bala Subrahmanyam Addepalli, Kil-Young Yun, Arthur G. Hunt, Ruqiang Xu, Suryadevara Rao, Qingshun Q. Li, Deane L. Falcone

Kentucky Tobacco Research and Development Center Faculty Publications

BACKGROUND: Plants respond to many unfavorable environmental conditions via signaling mediated by altered levels of various reactive oxygen species (ROS). To gain additional insight into oxidative signaling responses, Arabidopsis mutants that exhibited tolerance to oxidative stress were isolated. We describe herein the isolation and characterization of one such mutant, oxt6.

METHODOLOGY/PRINCIPAL FINDINGS: The oxt6 mutation is due to the disruption of a complex gene (At1g30460) that encodes the Arabidopsis ortholog of the 30-kD subunit of the cleavage and polyadenylation specificity factor (CPSF30) as well as a larger, related 65-kD protein. Expression of mRNAs encoding Arabidopsis CPSF30 alone was able to …

Membrane-Permeable Peptide Capable Of Calpain Inhibition, Rodney Guttmann

Physiology Faculty Patents

5-mer peptides that can inhibit calpain I and calpain II are disclosed. The peptide sequence is as follows: Leu or Ala)-(Xaa)-(Asp or Glu)-(Xaa)-(Leu or Met), where Xaa can be any amino acid.

Issues And Challenges Facing The Field Of Phssr, F. Douglas Scutchfield Md

Preventive Medicine and Environmental Health Presentations

No abstract provided.

Public Health Professional Organizational Data, F. Douglas Scutchfield Md

Preventive Medicine and Environmental Health Presentations

No abstract provided.

Adaptation And Mal-Adaptation To Ambient Hypoxia; Andean, Ethiopian And Himalayan Patterns, Guoqiang Xing, Clifford Qualls, Luis Huicho, Maria Rivera-Ch, Tsering Stobdan, Marat Slessarev, Eitan Prisman, Shoji Ito, Hong Wu, Angchuk Norboo, Diskit Dolma, Moses Kunzang, Tsering Norboo, Jorge L Gamboa, Victoria E. Claydon, Joseph Fisher, Guta Zenebe, Amha Gebremedhin, Roger Hainsworth, Ajay Verma, Otto Appenzeller

Physiology Faculty Publications

The study of the biology of evolution has been confined to laboratories and model organisms. However, controlled laboratory conditions are unlikely to model variations in environments that influence selection in wild populations. Thus, the study of "fitness" for survival and the genetics that influence this are best carried out in the field and in matching environments.

Therefore, we studied highland populations in their native environments, to learn how they cope with ambient hypoxia. The Andeans, African highlanders and Himalayans have adapted differently to their hostile environment.

Chronic mountain sickness (CMS), a loss of adaptation to altitude, is common in the …

Forage News [2008-06], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• University of Kentucky Field Day - June 12, 2008
• Kfgc Forage Spokesman
• Kfgc Awards Nomination
• Reducing Forage Losses Can Save Big Bucks
• Weed-Seed-Free Straw Market Beats Hay
• Nutrient Value of Baled Hay
• Seeded Bermudagrass: Make Sure to Use a
• Winter Hardy Variety
• Upcoming Events

Arabidopsis Mrna Polyadenylation Machinery: Comprehensive Analysis Of Protein-Protein Interactions And Gene Expression Profiling, Arthur G. Hunt, Ruqiang Xu, Balasubrahmanyam Addepalli, Suryadevara Rao, Kevin P. Forbes, Lisa R. Meeks, Denghui Xing, Min Mo, Hongwei Zhao, Amrita Bandyopadhyay, Lavanya Dampanaboina, Amanda Marion, Carol Von Lanken, Qingshun Quinn Li

Plant and Soil Sciences Faculty Publications

BACKGROUND: The polyadenylation of mRNA is one of the critical processing steps during expression of almost all eukaryotic genes. It is tightly integrated with transcription, particularly its termination, as well as other RNA processing events, i.e. capping and splicing. The poly(A) tail protects the mRNA from unregulated degradation, and it is required for nuclear export and translation initiation. In recent years, it has been demonstrated that the polyadenylation process is also involved in the regulation of gene expression. The polyadenylation process requires two components, the cis-elements on the mRNA and a group of protein factors that recognize the cis-elements and …

Forage News [2008-05], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• KFGC Awards Nomination
• KFGC Forage Symposium
• Small Grain Silage or Balage
• Hay Making Reminders and Tips
• Hay Acreage Will Drop 2% Says USDA
• Armyworm Alert
• New Video Feature on KFGC Website
• UK Forage Team Wins Outstanding Extension Project Award
• Forage Analyses Are Estimates, Note Absolutes
• Should I Plant Switchgrass for Biomass?
• Upcoming Events

A Bbp-Mud2p Heterodimer Mediates Branchpoint Recognition And Influences Splicing Substrate Abundance In Budding Yeast, Qiang Wang, Li Zhang, Bert C. Lynn, Brian C. Rymond

Biology Faculty Publications

The 3′ end of mammalian introns is marked by the branchpoint binding protein, SF1, and the U2AF65-U2AF35 heterodimer bound at an adjacent sequence. Baker's yeast has equivalent proteins, branchpoint binding protein (BBP) (SF1) and Mud2p (U2AF65), but lacks an obvious U2AF35 homolog, leaving open the question of whether another protein substitutes during spliceosome assembly. Gel filtration, affinity selection and mass spectrometry were used to show that rather than a U2AF65/U2AF35-like heterodimer, Mud2p forms a complex with BBP without a third (U2AF35-like) factor. Using mutants of MUD2 and BBP, we show that the BBP–Mud2p complex bridges partner-specific Prp39p, Mer1p, Clf1p …

Recombinant Stokesia Epoxygenase Gene, David Hildebrand, Tomoko Hatanaka

Plant and Soil Sciences Faculty Patents

A chimeric gene comprising an isolated nucleic acid molecule encoding a delta 12-fatty acid epoxygenase enzyme and transgenic plants containing the chimeric gene are described. Expression of the chimeric delta 12-epoxygenase gene leads to altered levels of fatty acids in transformed cells.

Assessment Of A Non-Invasive High-Throughput Classifier For Behaviours Associated With Sleep And Wake In Mice, Kevin D. Donohue, Dharshan C. Medonza, Eli R. Crane, Bruce F. O'Hara

Biology Faculty Publications

This work presents a non-invasive high-throughput system for automatically detecting characteristic behaviours in mice over extended periods of time, useful for phenotyping experiments. The system classifies time intervals on the order of 2 to 4 seconds as corresponding to motions consistent with either active wake or inactivity associated with sleep. A single Polyvinylidine Difluoride (PVDF) sensor on the cage floor generates signals from motion resulting in pressure. This paper develops a linear classifier based on robust features extracted from normalized power spectra and autocorrelation functions, as well as novel features from the collapsed average (autocorrelation of complex spectrum), which characterize …

High Status Men (But Not Women) Capture The Eye Of The Beholder, C. Nathan Dewall, Jon K. Maner

Psychology Faculty Publications

Two studies tested the hypothesis that people attend preferentially to high status men (but not women). Participants overestimated the frequency of high status men in rapidly presented arrays (Experiment 1) and fixated their visual attention on high status men in an eye-tracking study (Experiment 2). Neither study showed any evidence of preferential attention to high status women, but there was evidence that physically attractive women captured attention. The results from both studies support evolutionary theories regarding differential prioritization of social status and physical attractiveness in men versus women. These findings illustrate how examination of early-in-the-stream social cognition can provide useful …

Forage News [2008-04], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• 28th Kentucky Alfalfa Conference
• Breeding Better Alfalfa
• Hay Preservatives: Propionic Acid and Microbial Inoculants
• Alternative Energy: Does It Make Sense?
• High Priced Nitrogen: Can I Still Afford to Fertilize Grass Hay
• Forages May Fuel Pellet Stoves
• Weed Management Options in the Spring Following a Dry Summer
• Upcoming Events

The Influence Of Citrate, Maltolate And Fluoride On The Gastrointestinal Absorption Of Aluminum At A Drinking Water-Relevant Concentration: A 26Al And 14C Study, Yuzhao Zhou, Wesley R. Harris, Robert A. Yokel

Pharmaceutical Sciences Faculty Publications

The objectives were to test the null hypotheses that (1) citrate, maltolate, and fluoride do not significantly influence oral Al bioavailability, C_max or T_max at an Al dose relevant to drinking water exposure; and (2) Al citrate and maltolate are absorbed intact from the gastrointestinal tract. Male Fisher rats were given 1 ml of solution intra-gastrically containing 1 nCi ²⁶Al (65 nmol total Al) as the Al³⁺ ion, or as complexes with ¹⁴C-citrate, ¹⁴C-maltolate or fluoride, during concurrent ²⁷Al iv infusion. Blood was repeatedly collected for serum ²⁶Al, total Al and ^{14 …}