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Learning-Based Fusion For Data Deduplication, Sabra Dinerstein, Parris K. Egbert, Stephen W. Clyde, Jared Dinerstein Dec 2008

Learning-Based Fusion For Data Deduplication, Sabra Dinerstein, Parris K. Egbert, Stephen W. Clyde, Jared Dinerstein

Faculty Publications

Rule-based deduplication utilizes expert domain knowledge to identify and remove duplicate data records. Achieving high accuracy in a rule-based system requires the creation of rules containing a good combination of discriminatory clues. Unfortunately, accurate rule-based deduplication often requires significant manual tuning of both the rules and the corresponding thresholds. This need for manual tuning reduces the efficacy of rule-based deduplication and its applicability to real-world data sets. No adequate solution exists for this problem. We propose a novel technique for rule-based deduplication. We apply individual deduplication rules, and combine the resultant match scores via learning-based information fusion. We show empirically …


Two Evolutionarily Conserved Sequence Elements For Peg3/Usp29 Transcription, Jeong Do Kim, Sungryul Yu, Jung Ha Choo, Joomyeong Kim Dec 2008

Two Evolutionarily Conserved Sequence Elements For Peg3/Usp29 Transcription, Jeong Do Kim, Sungryul Yu, Jung Ha Choo, Joomyeong Kim

Faculty Publications

Background: Two evolutionarily Conserved Sequence Elements, CSE1 and CSE2 (YY1 binding sites), are found within the 3.8-kb CpG island surrounding the bidirectional promoter of two imprinted genes, Peg3 (Paternally expressed gene 3) and Usp29 (Ubiquitin-specific protease 29). This CpG island is a likely ICR (Imprinting Control Region) that controls transcription of the 500-kb genomic region of the Peg3 imprinted domain. Results: The current study investigated the functional roles of CSE1 and CSE2 in the transcriptional control of the two genes, Peg3 and Usp29, using cell line-based promoter assays. The mutation of 6 YY1 binding sites (CSE2) reduced the transcriptional activity …


L1 Recombination-Associated Deletions Generate Human Genomic Variation, Kyudong Han, Jungnam Lee, Thomas J. Meyer, Paul Remedios, Lindsey Goodwin, Mark A. Batzer Dec 2008

L1 Recombination-Associated Deletions Generate Human Genomic Variation, Kyudong Han, Jungnam Lee, Thomas J. Meyer, Paul Remedios, Lindsey Goodwin, Mark A. Batzer

Faculty Publications

Mobile elements have created structural variation in the human genome through their de novo insertions and post-insertional genomic rearrangements. L1 elements are a type of long interspersed element (LINE) that is dispersed at high copy numbers within most mammalian genomes. To determine the magnitude of L1 recombination-associated deletions (L1RADs), we computationally extracted L1RAD candidates by comparing the human and chimpanzee genomes and verified each of the L1RAD events by using wet-bench analyses. Through these analyses, we identified 73 human-specific L1RAD events that occurred subsequent to the divergence of the human and chimpanzee lineages. Despite their low frequency, the L1RAD events …


Identification Of Adropin As A Secreted Factor Linking Dietary Macronutrient Intake With Energy Homeostasis And Lipid Metabolism, K. Ganesh Kumar, James L. Trevaskis, Daniel D. Lam, Gregory M. Sutton, Robert A. Koza, Vladimir N. Chouljenko, Konstantin G. Kousoulas, Pamela M. Rogers, Robert A. Kesterson, Marie Thearle, Anthony W. Ferrante, Randall L. Mynatt, Thomas P. Burris, Jesse Z. Dong, Heather A. Halem, Michael D. Culler, Lora K. Heisler, Jacqueline M. Stephens, Andrew A. Butler Dec 2008

Identification Of Adropin As A Secreted Factor Linking Dietary Macronutrient Intake With Energy Homeostasis And Lipid Metabolism, K. Ganesh Kumar, James L. Trevaskis, Daniel D. Lam, Gregory M. Sutton, Robert A. Koza, Vladimir N. Chouljenko, Konstantin G. Kousoulas, Pamela M. Rogers, Robert A. Kesterson, Marie Thearle, Anthony W. Ferrante, Randall L. Mynatt, Thomas P. Burris, Jesse Z. Dong, Heather A. Halem, Michael D. Culler, Lora K. Heisler, Jacqueline M. Stephens, Andrew A. Butler

Faculty Publications

Obesity and nutrient homeostasis are linked by mechanisms that are not fully elucidated. Here we describe a secreted protein, adropin, encoded by a gene, Energy Homeostasis Associated (Enho), expressed in liver and brain. Liver Enho expression is regulated by nutrition: lean C57BL/6J mice fed high-fat diet (HFD) exhibited a rapid increase, while fasting reduced expression compared to controls. However, liver Enho expression declines with diet-induced obesity (DIO) associated with 3 months of HFD or with genetically induced obesity, suggesting an association with metabolic disorders in the obese state. In DIO mice, transgenic overexpression or systemic adropin treatment attenuated hepatosteatosis and …


Identification Of Adropin As A Secreted Factor Linking Dietary Macronutrient Intake With Energy Homeostasis And Lipid Metabolism, K. Ganesh Kumar, James L. Trevaskis, Daniel D. Lam, Gregory M. Sutton, Robert A. Koza, Vladimir N. Chouljenko, Konstantin G. Kousoulas, Pamela M. Rogers, Robert A. Kesterson, Marie Thearle, Anthony W. Ferrante, Randall L. Mynatt, Thomas P. Burris, Jesse Z. Dong, Heather A. Halem, Michael D. Culler, Lora K. Heisler, Jacqueline M. Stephens, Andrew A. Butler Dec 2008

Identification Of Adropin As A Secreted Factor Linking Dietary Macronutrient Intake With Energy Homeostasis And Lipid Metabolism, K. Ganesh Kumar, James L. Trevaskis, Daniel D. Lam, Gregory M. Sutton, Robert A. Koza, Vladimir N. Chouljenko, Konstantin G. Kousoulas, Pamela M. Rogers, Robert A. Kesterson, Marie Thearle, Anthony W. Ferrante, Randall L. Mynatt, Thomas P. Burris, Jesse Z. Dong, Heather A. Halem, Michael D. Culler, Lora K. Heisler, Jacqueline M. Stephens, Andrew A. Butler

Faculty Publications

Obesity and nutrient homeostasis are linked by mechanisms that are not fully elucidated. Here we describe a secreted protein, adropin, encoded by a gene, Energy Homeostasis Associated (Enho), expressed in liver and brain. Liver Enho expression is regulated by nutrition: lean C57BL/6J mice fed high-fat diet (HFD) exhibited a rapid increase, while fasting reduced expression compared to controls. However, liver Enho expression declines with diet-induced obesity (DIO) associated with 3 months of HFD or with genetically induced obesity, suggesting an association with metabolic disorders in the obese state. In DIO mice, transgenic overexpression or systemic adropin treatment attenuated hepatosteatosis and …


Geographic, Seasonal, And Precipitation Chemistry Influence On The Abundance And Activity Of Biological Ice Nucleators In Rain And Snow, Brent C. Christner, Rongman Cai, Cindy E. Morris, Kevin S. Mccarter, Christine M. Foreman, Mark L. Skidmore, Scott N. Montross, David C. Sands Dec 2008

Geographic, Seasonal, And Precipitation Chemistry Influence On The Abundance And Activity Of Biological Ice Nucleators In Rain And Snow, Brent C. Christner, Rongman Cai, Cindy E. Morris, Kevin S. Mccarter, Christine M. Foreman, Mark L. Skidmore, Scott N. Montross, David C. Sands

Faculty Publications

Biological ice nucleators (IN) function as catalysts for freezing at relatively warm temperatures (warmer than -10°C). We examined the concentration (per volume of liquid) and nature of IN in precipitation collected from Montana and Louisiana, the Alps and Pyrenees (France), Ross Island (Antarctica), and Yukon (Canada). The temperature of detectable ice-nucleating activity for more than half of the samples was ≥ -5°C based on immersion freezing testing. Digestion of the samples with lysozyme (i.e., to hydrolyze bacterial cell walls) led to reductions in the frequency of freezing (0-100%); heat treatment greatly reduced (95% average) or completely eliminated ice nucleation at …


Escherichia Coli Ftna Acts As An Iron Buffer For Re-Assembly Of Iron-Sulfur Clusters In Response To Hydrogen Peroxide Stress, Jacob P. Bitoun, Genfu Wu, Huangen Ding Dec 2008

Escherichia Coli Ftna Acts As An Iron Buffer For Re-Assembly Of Iron-Sulfur Clusters In Response To Hydrogen Peroxide Stress, Jacob P. Bitoun, Genfu Wu, Huangen Ding

Faculty Publications

Iron-sulfur clusters are one of the most ubiquitous redox centers in biology. Ironically, iron-sulfur clusters are highly sensitive to reactive oxygen species. Disruption of iron-sulfur clusters will not only change the activity of proteins that host iron-sulfur clusters, the iron released from the disrupted iron-sulfur clusters will further promote the production of deleterious hydroxyl free radicals via the Fenton reaction. Here, we report that ferritin A (FtnA), a major iron-storage protein in Escherichia coli, is able to scavenge the iron released from the disrupted iron-sulfur clusters and alleviates the production of hydroxyl free radicals. Furthermore, we find that the iron …


Identification Of Two Genes, Sll0804 And Slr1306, As Putative Components Of The Co2-Concentrating Mechanism In The Cyanobacterium Synechocystis Sp. Strain Pcc 6803, Shulu Zhang, Kevin W. Spann, Laurie K. Frankel, James V. Moroney, Terry M. Bricker Dec 2008

Identification Of Two Genes, Sll0804 And Slr1306, As Putative Components Of The Co2-Concentrating Mechanism In The Cyanobacterium Synechocystis Sp. Strain Pcc 6803, Shulu Zhang, Kevin W. Spann, Laurie K. Frankel, James V. Moroney, Terry M. Bricker

Faculty Publications

Insertional transposon mutations in the sll0804 and slr1306 genes were found to lead to a loss of optimal photoautotrophy in the cyanobacterium Synechocystis sp. strain PCC 6803 grown under ambient CO2 concentrations (350 ppm). Mutants containing these insertions (4BA2 and 3ZA12, respectively) could grow photoheterotrophically on glucose or photoautotrophically at elevated CO2 concentrations (50,000 ppm). Both of these mutants exhibited an impaired affinity for inorganic carbon. Consequently, the Sll0804 and Slr1306 proteins appear to be putative components of the carbon-concentrating mechanism in Synechocystis sp. strain PCC 6803. Copyright © 2008, American Society for Microbiology. All Rights Reserved.


Latent Common Genetic Components Of Obesity Traits, B. O. Tayo, R. Harders, A. Luke, X. Zhu, R. S. Cooper Dec 2008

Latent Common Genetic Components Of Obesity Traits, B. O. Tayo, R. Harders, A. Luke, X. Zhu, R. S. Cooper

Faculty Publications

Background: Obesity is rapidly becoming a global epidemic. Unlike many complex human diseases, obesity is defined not just by a single trait or phenotype, but jointly by measures of anthropometry and metabolic status. Methods: We applied maximum likelihood factor analysis to identify common latent factors underlying observed covariance in multiple obesity-related measures. Both the genetic components and the mode of inheritance of the common factors were evaluated. A total of 1775 participants from 590 families for whom measures on obesity-related traits were available were included in this study. Results: The average age of participants was 37 years, 39% of the …


Selection And Life History Traits Of Tebufenozide-Resistant Sugarcane Borer (Lepidoptera: Crambidae), W. Akbar, J. A. Ottea, J. M. Beuzelin, T. E. Reagan, F. Huang Dec 2008

Selection And Life History Traits Of Tebufenozide-Resistant Sugarcane Borer (Lepidoptera: Crambidae), W. Akbar, J. A. Ottea, J. M. Beuzelin, T. E. Reagan, F. Huang

Faculty Publications

Varying susceptibility to tebufenozide was recorded in the sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), collected from Louisiana sugarcane locations with different selection pressures. Results from diet incorporation bioassays with tebufenozide indicated significant increases in LC50 (3.78-fold) and LC90 (7-fold) values for a colony from Duson (DU), an area with higher selection pressure, compared with a colony from Alexandria (ALFX), an area with no selection pressure. Differences were not detected in LC50 values among colonies from areas where use of tebufenozide was discontinued or rotated with other chemistries. Selections with tebufenozide of DU larvae over 12 generations resulted in a …


Tfiiic Binding Sites Function As Both Heterochromatin Barriers And Chromatin Insulators In Saccharomyces Cerevisiae, Tiffany A. Simms, Sandra L. Dugas, Jason C. Gremillion, Megan E. Ibos, M. Nicole Dandurand, Tasha T. Toliver, Daniel J. Edwards, David Donze Dec 2008

Tfiiic Binding Sites Function As Both Heterochromatin Barriers And Chromatin Insulators In Saccharomyces Cerevisiae, Tiffany A. Simms, Sandra L. Dugas, Jason C. Gremillion, Megan E. Ibos, M. Nicole Dandurand, Tasha T. Toliver, Daniel J. Edwards, David Donze

Faculty Publications

Chromosomal sites of RNA polymerase III (Pol III) transcription have been demonstrated to have "extratranscriptional" functions, as the assembled Pol III complex can act as chromatin boundaries or pause sites for replication forks, can alter nucleosome positioning or affect transcription of neighboring genes, and can play a role in sister chromatid cohesion. Several studies have demonstrated that assembled Pol III complexes block the propagation of heterochromatin-mediated gene repression. Here we show that in Saccharomyces cerevisiae tRNA genes (tDNAs) and even partially assembled Pol III complexes containing only the transcription factor TFIIIC can exhibit chromatin boundary functions both as heterochromatin barriers …


Host-Pathogen Interactions, Insect Outbreaks, And Natural Selection For Disease Resistance, Bret D. Elderd, Jonathan Dushoff, Greg Dwyer Dec 2008

Host-Pathogen Interactions, Insect Outbreaks, And Natural Selection For Disease Resistance, Bret D. Elderd, Jonathan Dushoff, Greg Dwyer

Faculty Publications

The theory of insect population dynamics has shown that heterogeneity in natural-enemy attack rates is strongly stabilizing. We tested the usefulness of this theory for outbreaking insects, many of which are attacked by infectious pathogens. We measured heterogeneity among gypsy moth larvae in their risk of infection with a nucleopolyhedrovirus, which is effectively heterogeneity in the pathogen's attack rate. Our data show that heterogeneity in infection risk in this insect is so high that it leads to a stable equilibrium in the models, which is inconsistent with the outbreaks seen in North American gypsy moth populations. Our data further suggest …


Forcing And Dynamics Of Seafloor-Water Column Exchange On A Broad Continental Shelf, William B. Savidge, Ann Gargett, Richard A. Jahnke, James R. Nelson, Dana K. Savidge, R Timothy Short, George Voulgaris Dec 2008

Forcing And Dynamics Of Seafloor-Water Column Exchange On A Broad Continental Shelf, William B. Savidge, Ann Gargett, Richard A. Jahnke, James R. Nelson, Dana K. Savidge, R Timothy Short, George Voulgaris

Faculty Publications

Relict sediments of elevated permeability characterize the majority of continental shelves globally (Emery, 1968). In these settings, interactions between benthic boundary layer (BBL) flows and seabed topography generate pressure fluctuations that drive advective and dispersive porewater transport, dramatically increasing the magnitude and variability of porewater solute and particulate exchange across the sediment-water interface (Huettel et al., 1996; Huettel and Rusch, 2000). On broad shallow shelves with a relatively large area-to-volume ratio, the seafloor’s role is magnified. Energetic events may reorganize bedforms across a significant fraction of the shelf, leading to altered exchange dynamics that may persist long after the organizing …


Leucon (Crymoleucon) Rossi, A New Species (Crustacea: Cumacea: Leuconidae) From The Shelf Waters Of The Ross Sea (Antarctica), With A Key To The Genus Leucon South Of 60°S, Peter Rehm, Richard W. Heard Dec 2008

Leucon (Crymoleucon) Rossi, A New Species (Crustacea: Cumacea: Leuconidae) From The Shelf Waters Of The Ross Sea (Antarctica), With A Key To The Genus Leucon South Of 60°S, Peter Rehm, Richard W. Heard

Faculty Publications

A new leuconid cumacean, Leucon (Crymoleucon) rossi n. sp., is described from depths of 84 to 458 m in the Ross Sea off the Victoria Land coast. Leucon rossi n. sp. is distinguished from other members of the genus by a combination of characters including 1) a blunt, horizontally directed pseudorostrum) Without a distinctly protruding siphon; 2) strongly developed antennal notch; 3) entire dorsomedian margin of carapace appearing serrate, armed with 14 to 19 anteriorly Curved spines in female (up to 21 in subadult males); 4) a small, but distinct, spine behind the frontal lobe; and 5) the uropodal peduncle …


Continuous Microwave Processing Of Peanut Beverages, Cristina M. Sabliov, Dorin Boldor, Pablo Coronel, Timothy H. Sanders Dec 2008

Continuous Microwave Processing Of Peanut Beverages, Cristina M. Sabliov, Dorin Boldor, Pablo Coronel, Timothy H. Sanders

Faculty Publications

The feasibility of peanut beverage sterilization by continuous microwave heating as an alternative to conventional ultrahigh temperature (UHT) system processing was studied. Dielectric properties of two products, Peanut Punch (Nestle Trinidad and Tobago Ltd., Port of Spain, Trinidad and Tobago) and Jamaican Irish Moss Peanut Drink (distributed by Eve Sales Co., Bronx, NY) were measured. The products had similar dielectric properties. Values for the dielectric constant (average of 60) and dielectric loss (average of 23) indicated that the two products were good candidates for rapid microwave heating. The products were processed in a 5 kW focused microwave unit, at two …


Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman Dec 2008

Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman

Faculty Publications

Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings
Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based …


A Special-Purpose Architecture For Solving The Breakpoint Median Problem, Jason D. Bakos, Panormitis E. Elenis Dec 2008

A Special-Purpose Architecture For Solving The Breakpoint Median Problem, Jason D. Bakos, Panormitis E. Elenis

Faculty Publications

In this paper, we describe the design for a co-processor for whole-genome phylogenetic reconstruction. Our current design performs a parallelized breakpoint median computation, which is an expensive component of the overall application. When implemented on a field-programmable gate array (FPGA), our hardware breakpoint median achieves a maximum speedup of 1005times over software. When the coprocessor is used to accelerate the entire reconstruction procedure, we achieve a maximum application speedup of 417times. The results in this paper suggest that FPGA-based acceleration is a promising approach for computationally expensive phylogenetic problems, in spite of the fact that the involved algorithms are based …


Biological Invasions And Biocultural Diversity: Linking Ecological And Cultural Systems, Jeanine Pfeiffer, Robert Voeks Dec 2008

Biological Invasions And Biocultural Diversity: Linking Ecological And Cultural Systems, Jeanine Pfeiffer, Robert Voeks

Faculty Publications

Study of the ecological and economic effects of invasive species has paralleled their progressively pervasive influence worldwide, yet their cultural impacts remain largely unexamined and therefore unrecognized. Unlike biological systems, where the ecological consequences of biological invasions are primarily negative, from an ethnoscientific standpoint, invasive species' impacts on cultural systems span a range of effects. Biological invasions affect cultural groups in myriad, often unpredictable and at times contradictory ways. This review groups case studies into a conceptual matrix suggesting three categorically different cultural impacts of invasive species. Culturally impoverishing invasive species precipitate the loss or replacement of culturally important native …


Sequence Alignment With Traceback On Reconfigurable Hardware, Scott Lloyd, Quinn O. Snell Dec 2008

Sequence Alignment With Traceback On Reconfigurable Hardware, Scott Lloyd, Quinn O. Snell

Faculty Publications

Biological sequence alignment is an essential tool used in molecular biology and biomedical applications. The growing volume of genetic data and the complexity of sequence alignment present a challenge in obtaining alignment results in a timely manner. Known methods to accelerate alignment on reconfigurable hardware only address sequence comparison, limit the sequence length, or exhibit memory and I/O bottlenecks. A space-efficient, global sequence alignment algorithm and architecture is presented that accelerates the forward scan and traceback in hardware without memory and I/O limitations. With 256 processing elements in FPGA technology, a performance gain over 300 times that of a desktop …


Centers For Oceans And Human Health: Contributions To An Emerging Discipline, Edward A. Laws, Lora E. Fleming, John J. Stegeman Nov 2008

Centers For Oceans And Human Health: Contributions To An Emerging Discipline, Edward A. Laws, Lora E. Fleming, John J. Stegeman

Faculty Publications

No abstract provided.


Impacts Of Climate Variability And Future Climate Change On Harmful Algal Blooms And Human Health, Stephanie K. Moore, Vera L. Trainer, Nathan J. Mantua, Micaela S. Parker, Edward A. Laws, Lorraine C. Backer, Lora E. Fleming Nov 2008

Impacts Of Climate Variability And Future Climate Change On Harmful Algal Blooms And Human Health, Stephanie K. Moore, Vera L. Trainer, Nathan J. Mantua, Micaela S. Parker, Edward A. Laws, Lorraine C. Backer, Lora E. Fleming

Faculty Publications

Anthropogenically-derived increases in atmospheric greenhouse gas concentrations have been implicated in recent climate change, and are projected to substantially impact the climate on a global scale in the future. For marine and freshwater systems, increasing concentrations of greenhouse gases are expected to increase surface temperatures, lower pH, and cause changes to vertical mixing, upwelling, precipitation, and evaporation patterns. The potential consequences of these changes for harmful algal blooms (HABs) have received relatively little attention and are not well understood. Given the apparent increase in HABs around the world and the potential for greater problems as a result of climate change …


Timing Of Supplementation Of Selenium And Isoflavones Determines Prostate Cancer Risk Factor Reduction In Rats, Merrill J. Christensen, Jessica R. Tolman, Edwin D. Lephart, Dennis L. Eggett, Kenneth Setchell Nov 2008

Timing Of Supplementation Of Selenium And Isoflavones Determines Prostate Cancer Risk Factor Reduction In Rats, Merrill J. Christensen, Jessica R. Tolman, Edwin D. Lephart, Dennis L. Eggett, Kenneth Setchell

Faculty Publications

High dietary intake of selenium or isoflavones reduces risk factors for prostate cancer. We tested whether combined supplementation of these two dietary components would reduce prostate cancer risk factors in rats more than supplementation of each component individually. Methods Male Noble rat pups were exposed from conception to diets containing an adequate (0.33-0.45 mg/kg diet) or high (3.33-3.45 mg/kg) concentration of selenium as Se-methylselenocysteine and a low (10 mg/kg) or high (600 mg/kg) level of isoflavones in a 2 x 2 factorial design. Pups consumed their respective diets until sacrifice at 35, 100, or 200 days. Male Noble rat breeders, …


Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev Nov 2008

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …


Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang Nov 2008

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …


Redox-Triggered Contents Release From Liposomes, Winston Ong, Yuming Yang, Angela C. Cruciano, Robin L. Mccarley Nov 2008

Redox-Triggered Contents Release From Liposomes, Winston Ong, Yuming Yang, Angela C. Cruciano, Robin L. Mccarley

Faculty Publications

An exciting new direction in responsive liposome research is endogenous triggering of liposomal payload release by overexpressed enzyme activity in affected tissues and offers the unique possibility of active and site-specific release. Bringing to fruition the fully expected capabilities of this new class of triggered liposomal delivery system requires a collection of liposome systems that respond to different upregulated enzymes; however, a relatively small number currently exist. Here we show that stable, ∼100 nm diameter liposomes can be made from previously unreported quinone-dioleoyl phosphatidylethanolamine (Q-DOPE) lipids, and complete payload release (quenched fluorescent dye) from Q-DOPE liposomes occurs upon their redox …


Nitric Oxide-Induced Bacteriostasis And Modification Of Iron-Sulphur Proteins In Escherichia Coli, Binbin Ren, Nianhui Zhang, Juanjuan Yang, Huangen Ding Nov 2008

Nitric Oxide-Induced Bacteriostasis And Modification Of Iron-Sulphur Proteins In Escherichia Coli, Binbin Ren, Nianhui Zhang, Juanjuan Yang, Huangen Ding

Faculty Publications

The nitric oxide (NO) cytotoxicity has been well documented in bacteria and mammalian cells. However, the underlying mechanism is still not fully understood. Here we report that transient NO exposure effectively inhibits cell growth of Escherichia coli in minimal medium under anaerobic growth conditions and that cell growth is restored when the NO-exposed cells are either supplemented with the branched-chain amino acids (BCAA) anaerobically or returned to aerobic growth conditions. The enzyme activity measurements show that dihydroxyacid dehydratase (IlvD), an iron-sulphur enzyme essential for the BCAA biosynthesis, is completely inactivated in cells by NO with the concomitant formation of the …


Identification Of A Functionally Essential Amino Acid For Arabidopsis Cyclic Nucleotide Gated Ion Channels Using The Chimeric Atcngc11/12 Gene, Joyce Baxter, Wolfgang Moeder, William Urquhart, Dea Shahinas, Kimberley Chin, Dinesh Christendat, Hong Gu Kang, Magdalena Angelova, Naohiro Kato, Keiko Yoshioka Nov 2008

Identification Of A Functionally Essential Amino Acid For Arabidopsis Cyclic Nucleotide Gated Ion Channels Using The Chimeric Atcngc11/12 Gene, Joyce Baxter, Wolfgang Moeder, William Urquhart, Dea Shahinas, Kimberley Chin, Dinesh Christendat, Hong Gu Kang, Magdalena Angelova, Naohiro Kato, Keiko Yoshioka

Faculty Publications

We used the chimeric Arabidopsis cyclic nucleotide-gated ion channel AtCNGC11/12 to conduct a structure-function study of plant cyclic nucleotide-gated ion channels (CNGCs). AtCNGC11/12 induces multiple pathogen resistance responses in the Arabidopsis mutant constitutive expresser of PR genes 22 (cpr22). A genetic screen for mutants that suppress cpr22-conferred phenotypes identified an intragenic mutant, #73, which has a glutamate to lysine substitution (E519K) at the beginning of the eighth β-sheet of the cyclic nucleotide-binding domain in AtCNGC11/12. The #73 mutant is morphologically identical to wild-type plants and has lost cpr22-related phenotypes including spontaneous cell death and enhanced pathogen resistance. Heterologous expression analysis …


Transcriptional Profiling Of Mature Arabidopsis Trichomes Reveals That Noeck Encodes The Mixta-Like Transcriptional Regulator Myb106, Marc J. Jakoby, Doris Falkenhan, Michael T. Mader, Ginger Brininstool, Elisabeth Wischnitzki, Nicole Platz, Andrew Hudson, Martin Hülskamp, John Larkin, Arp Schnittger Nov 2008

Transcriptional Profiling Of Mature Arabidopsis Trichomes Reveals That Noeck Encodes The Mixta-Like Transcriptional Regulator Myb106, Marc J. Jakoby, Doris Falkenhan, Michael T. Mader, Ginger Brininstool, Elisabeth Wischnitzki, Nicole Platz, Andrew Hudson, Martin Hülskamp, John Larkin, Arp Schnittger

Faculty Publications

Leaf hairs (trichomes) of Arabidopsis (Arabidopsis thaliana) have been extensively used as a model to address general questions in cell and developmental biology. Here, we lay the foundation for a systems-level understanding of the biology of this model cell type by performing genome-wide gene expression analyses. We have identified 3,231 genes that are up-regulated in mature trichomes relative to leaves without trichomes, and we compared wild-type trichomes with two mutants, glabra3 and triptychon, that affect trichome morphology and physiology in contrasting ways. We found that cell wall-related transcripts were particularly overrepresented in trichomes, consistent with their highly elaborated structure. In …


Central Blockade Of Oxytocin Receptors During Mid-Late Gestation Reduces Amplitude Of Slow Afterhyperpolarization In Supraoptic Oxytocin Neurons, R. Teruyama, D. L. Lipschitz, L. Wang, G. R. Ramoz, W. R. Crowley, S. L. Bealer, W. E. Armstrong Nov 2008

Central Blockade Of Oxytocin Receptors During Mid-Late Gestation Reduces Amplitude Of Slow Afterhyperpolarization In Supraoptic Oxytocin Neurons, R. Teruyama, D. L. Lipschitz, L. Wang, G. R. Ramoz, W. R. Crowley, S. L. Bealer, W. E. Armstrong

Faculty Publications

The neurohypophysial hormone oxytocin (OT), synthesized in magnocellular paraventricular (PVN) and supraoptic (SON) nuclei, is well known for its effects in lactation. Our previous studies showed that central OT receptor (OTR) binding is increased during gestation and that blockade of central OTRs, specifically during mid-late gestation, causes a delay in OT release during suckling and reduces weight gain in pups, suggesting decreased milk delivery. In the present study, we tested whether central OTR blockade during late gestation disrupts the gestation-related plasticity in intrinsic membrane properties. Whole cell current-clamp recordings were performed in OT neurons from pregnant rats (19-22 days in …


Synthesis And Spectroelectrochemistry Of N-Cobaltacarborane Porphyrin Conjugates, Erhong Hao, Min Zhang, E. Wenbo, Karl M. Kadish, Frank R. Fronczek, Brandy H. Courtney, M. Graça H. Vicente Nov 2008

Synthesis And Spectroelectrochemistry Of N-Cobaltacarborane Porphyrin Conjugates, Erhong Hao, Min Zhang, E. Wenbo, Karl M. Kadish, Frank R. Fronczek, Brandy H. Courtney, M. Graça H. Vicente

Faculty Publications

N-Substituted porphyrins are well-known for the distortion they exhibit of the porphyrin plane through the sp3 hybridization of one of the pyrrolenic units. They have served as model compounds in investigations of many biochemical processes. In this paper, we developed an efficient route to N-substituted porphyrins, and report the synthesis of a series of new N-substituted cobaltacarborane - porphyrins containing one or two cobaltabisdicarbollide anions linked by (CH2CH2O) 2 chains to either the core porphyrin nitrogens or to a meso-aminophenyl group. These conjugates show different degrees of distortion of the porphyrin macrocycle, which affect their spectroscopic and electrochemical properties. In …