Digital Commons Network^™

Estimating The Degree Of Saturation In Mutant Screens, David D. Pollock, John C. Larkin

Faculty Publications

Large-scale screens for loss-of-function mutants have played a significant role in recent advances in developmental biology and other fields. In such mutant screens, it is desirable to estimate the degree of "saturation" of the screen (i.e., what fraction of the possible target genes has been identified). We applied Bayesian and maximum-likelihood methods for estimating the number of loci remaining undetected in large-scale screens and produced credibility intervals to assess the uncertainty of these estimates. Since different loci may mutate to alleles with detectable phenotypes at different rates, we also incorporated variation in the degree of mutability among genes, using either …

The Woman In Battle: The Civil War Narrative Of Loreta Velazquez, Cuban Woman & Confederate Soldier, L.M. Berkowitz

Civil War Book Review

Daring disguise

Loreta Janet Velasquez's service to the slave states

Macrocycle-Derived Functional Xanthenes And Progress Towards Concurrent Detection Of Glucose And Fructose, Oleksandr Rusin, Onur Alpturk, Ming He, Jorge O. Escobedo, Shan Jiang, Fareed Dawan, Kun Lian, Matthew E. Mccarroll, Isiah M. Warner, Robert M. Strongin

Faculty Publications

The detection of saccharides in biological media is of great current importance for the monitoring of disease states. We have previously reported that solutions of boronic acid-functionalized macrocycles form acyclic oligomeric materials in situ. The oligomers contain fluorescent xanthene moieties. Current efforts are aimed at modulating the spectroscopic responses of these materials for the analysis of specific sugars. We describe conditions whereby the xanthene boronic acids exhibit high colorimetric fructose selectivity. In contrast, at physiological levels selective glucose monitoring can be achieved via fluorescence. Additionally, we describe a method which exhibits promise for detecting both glucose and fructose at dual …

Test Of The Mechanotactile Hypothesis: Neuromast Morphology And Response Dynamics Of Mechanosensory Lateral Line Primary Afferents In The Stingray, Karen P. Maruska, Timothy C. Tricas

Faculty Publications

The mechanotactile hypothesis proposes that ventral non-pored lateral line canals in the stingray function to facilitate localization of prey that contact the skin during benthic feeding. This study used comparative neurophysiological and morphological techniques to test whether ventral non-pored canals encode the velocity of skin movements, and show other adaptations that may enhance detection of tactile stimuli from their prey. Resting discharge rate of lateral line primary afferent neurons was lower among units from ventral than dorsal canal groups. The ventral non-pored canals had a higher proportion of silent units (31%) than either ventral (3%) or dorsal (13%) pored canals, …

The Chlamydomonas Reinhardtii Proteins Ccp1 And Ccp2 Are Required For Long-Term Growth, But Are Not Necessary For Efficient Photosynthesis, In A Low-Co2 Environment, Steve V. Pollock, Davey L. Prout, Ashley C. Godfrey, Stephane D. Lemaire, James V. Moroney

Faculty Publications

The unicellular green alga Chlamydomonas reinhardtii acclimates to a low-CO2 environment by modifying the expression of a number of messages. Many of the genes that increase in abundance during acclimation to low-CO2 are under the control of the putative transcription factor Cia5. C. reinhardtii mutants null for cia5 do not express several of the known low-CO2 inducible genes and do not grow in a low-CO2 environment. Two of the genes under the control of Cia5, Ccp1 and Ccp2, encode polypeptides that are localized to the chloroplast envelope and have a high degree of similarity to members of the mitochondrial carrier …

Assignment Of The Four Disulfides In The N-Terminal Somatomedin B Domain Of Native Vitronectin Isolated From Human Plasma, Nancy A. Horn, Gregory B. Hurst, Anand Mayasundari, Neil A. Whittemore, Engin H. Serpersu, Cynthia B. Peterson

Faculty Publications

The primary sequence of the N-terminal somatomedin B (SMB) domain of native vitronectin contains 44 amino acids, including a framework of four disulfide bonds formed by 8 closely spaced cysteines in sequence patterns similar to those found in the cystine knot family of proteins. The SMB domain of vitronectin was isolated by digesting the protein with endoproteinase Glu-C and purifying the N-terminal 1-55 peptide by reverse-phase high performance liquid chromatography. Through a combination of techniques, including stepwise reduction and alkylation at acidic pH, peptide mapping with matrix-assisted laser desorption ionization mass spectrometry and NMR, the disulfide bonds contained in the …

Membrane Lipid Biosynthesis In Chlamydomonas Reinhardtii: Expression And Characterization Of Ctp:Phosphoethanolamine Cytidylyltransferase, Wenyu Yang, Catherine B. Mason, Steve V. Pollock, Tracey Lavezzi, James V. Moroney, Thomas S. Moore

Faculty Publications

CTP:phosphoethanolamine cytidylyltransferase (ECT) is considered to be the regulatory enzyme in the CDP-ethanolamine pathway of phosphatidylethanolamine (PE) biosynthesis. The ECT cDNA of Chlamydomonas reinhardtii encodes a protein of 443 amino acid residues, which is longer than the same protein in yeast, rat or human. The translated product of cloned cDNA was expressed as a fusion protein in Escherichia coli, and was shown to have ECT activity. The deduced amino acid sequence has 41% identity with that of human or rat, and 30% with yeast. The ECT protein has a repetitive internal sequence in its N-and C-terminal halves and a signature …

Crystal Structure Of A High-Affinity Variant Of Rat Α-Parvalbumin, Yong Hwan Lee, John J. Tanner, John D. Larson, Michael T. Henzl

Faculty Publications

In model peptide systems, Ca2+ affinity is maximized in EF-hand motifs containing four carboxylates positioned on the +x and -x and +z and -z axes; introduction of a fifth carboxylate ligand reduces the affinity. However, in rat β-parvalbumin, replacement of Ser-55 with aspartate heightens divalent ion affinity [Henzl, M. T., et al. (1996) Biochemistry 35, 5856-5869]. The corresponding α-parvalbumin variant (S55D/E59D) likewise exhibits elevated affinity [Henzl, M. T., et al. (2003) Anal. Biochem. 319, 216-233]. To determine whether these mutations produce a variation on the archetypal EF-hand coordination scheme, we have obtained high-resolution X-ray crystallographic data for α S55D/E59D. As …

Low Levels Of Nucleotide Diversity In Crocodylus Moreletii And Evidence Of Hybridization With C. Acutus, David A. Ray, Jennifer A. Dever, Steven G. Platt, Thomas R. Rainwater, Adam G. Finger, Scott T. Mcmurry, Mark A. Batzer, Brady Barr, Peter J. Stafford, Jenna Mcknight, Llewellyn D. Densmore

Faculty Publications

Examinations of both population genetic structure and the processes that lead to such structure in crocodilians have been initiated in several species in response to a call by the IUCN Crocodile Specialist Group. A recent study used microsatellite markers to characterize Morelet's crocodile (Crocodylus moreletii) populations in north-central Belize and presented evidence for isolation by distance. To further investigate this hypothesis, we sequenced a portion of the mitochondrial control region for representative animals after including samples from additional locales in Belize, Guatemala and Mexico. While there is limited evidence of subdivision involving other locales, we found that most of the …

Herbicide Retention And Runoff Losses As Affected By Sugarcane Mulch Residue (Bulletin #883), H. Magdi Selim, Brian J. Naquin, Richard L. Bengtson, Hongxia Zhu, James L. Griffin, Liuzong Zhou

LSU AgCenter Bulletins

The purpose of this study was to evaluate the effectiveness of sugarcane residue (mulch cover) in reducing non-point source contamination of applied chemicals from sugarcane fields.

Homologs Of Plant Psbp And Psbq Proteins Are Necessary For Regulation Of Photosystem Ii Activity In The Cyanobacterium Synechocystis 6803 W Inside Box Sign, Leeann E. Thomton, Hiroshi Ohkawa, Johnna L. Roose, Yasuhiro Kashino, Nir Keren, Himadri B. Pakrasi

Faculty Publications

The mechanism of oxygen evolution by photosystem II (PSII) has remained highly conserved during the course of evolution from ancestral cyanobacteria to green plants. A cluster of manganese, calcium, and chloride ions, whose binding environment is optimized by PSII extrinsic proteins, catalyzes this water-splitting reaction. The accepted view is that in plants and green algae, the three extrinsic proteins are PsbO, PsbP, and PsbQ, whereas in cyanobacteria, they are PsbO, PsbV, and PsbU. Our previous proteomic analysis established the presence of a PsbQ homolog in the cyanobacterium Synechocystis 6803. The current study additionally demonstrates the presence of a PsbP homolog …

Hydrothermal Venting In Magma Deserts: The Ultraslow-Spreading Gakkel And Southwest Indian Ridges, Edward T. Baker, Henrietta N. Edmonds, Peter J. Michael, Wolfgang Bach, Henry J.B. Dick, Jonathan E. Snow, Sharon L. Walker, Neil R. Banerjee, Charles H. Langmuir

Faculty Publications

Detailed hydrothermal surveys over ridges with spreading rates of 50-150 mm/yr have found a linear relation between spreading rate and the spatial frequency of hydrothermal venting, but the validity of this relation at slow and ultraslow ridges is unproved. Here we compare hydrothermal plume surveys along three sections of the Gakkel Ridge (Arctic Ocean) and the Southwest Indian Ridge (SWIR) to determine if hydrothermal activity is similarly distributed among these ultraslow ridge sections and if these distributions follow the hypothesized linear trend derived from surveys along fast ridges. Along the Gakkel Ridge, most apparent vent sites occur on volcanic highs, …

Weight History, Perception Of Body Size, And Self-Rated Physical And Mental Health In Black Female Food Stamp Recipients Living In Southeast Louisiana, Catharine Grace Wolfe

Honors Capstones

No abstract provided.

Visualizing Chromosome Structure/Organization, Eric Lam, Naohiro Kato, Koichi Watanabe

Faculty Publications

With the rapid development of sequencing technologies in the past decade, many eukaryotic genomes have been resolved at the primary sequence level. However, organization of the genome within nuclei and the principles that govern such properties remain largely unclear. Optimization of fluorescence probe-based hybridization technologies combined with new advances in the instrumentation for microscopy has steadily yielded more structural information on chromosome organization in eukaryote model systems. These studies provide static snapshots of the detailed organization of chromatin. More recently, the successful application of a chromatin tagging strategy utilizing auto fluorescent fusion proteins opened a new era of chromatin studies …

Polymorphisms Within A Polymorphism: Snps In And Around A Polymorphic Alu Insertion In Intron 44 Of The Human Dystrophin Gene, Alan D. Lovell, Vania Yotova, Fengxia Xiao, Mark A. Batzer, Damian Labuda

Faculty Publications

A polymorphic Yb-type Alu insertion on Xp21.3 shows a genotypic gradient across worldwide populations. We used single strand conformational polymorphism (SSCP), denaturing high-pressure liquid chromatography (DHPLC), and sequencing to characterize the level of polymorphism within this region. Two novel polymorphic sites were found within the Alu insertion itself, and a further seven novel polymorphic sites in the 2-kb flanking region. Our results showed that while DHPLC was more sensitive than SSCP, the limitations of DHPLC included the lack of ability to distinguish between multiple alleles or safely identify mutations on a polymorphic background. We believe that this is the first …

The Solution Structure Of The N-Terminal Domain Of Human Vitronectin: Proximal Sites That Regulate Fibrinolysis And Cell Migration, Anand Mayasundari, Neil A. Whittemore, Engin H. Serpersu, Cynthia B. Peterson

Faculty Publications

The three-dimensional structure of an N-terminal fragment comprising the first 51 amino acids from human plasma vitronectin, the somatomedin B (SMB) domain, has been determined by two-dimensional NMR approaches. An average structure was calculated, representing the overall fold from a set of 20 minimized structures. The core residues (18-41) overlay with a root mean square deviation of 2.29 ± 0.62 Å. The N- and C-terminal segments exhibit higher root mean square deviations, reflecting more flexibility in solution and/or fewer long-range NOEs for these regions. Residues 26-30 form a unique single-turn α-helix, the locus where plasminogen activator inhibitor type-1 (PAI-1) is …

Molecular Analysis Of Carbon Monoxide-Oxidizing Bacteria Associated With Recent Hawaiian Volcanic Deposits, Kari E. Dunfield, Gary M. King

Faculty Publications

Genomic DNA extracts from four sites at Kilauea Volcano were used as templates for PCR amplification of the large subunit (coxL) of aerobic carbon monoxide dehydrogenase. The sites included a 42-year-old tephra deposit, a 108-year-old lava flow, a 212-year-old partially vegetated ash-and-tephra deposit, and an approximately 300-year-old forest. PCR primers amplified coxL sequences from the OMP clade of CO oxidizers, which includes isolates such as Oligotropha carboxidovorans, Mycobacterium tuberculosis, and Pseudomonas thermocarboxydovorans. PCR products were used to create clone libraries that provide the first insights into the diversity and phylogenetic affiliations of CO oxidizers in situ. On the basis of …

Louisiana Agriculture Summer, 2004, Lsu Agcenter

Louisiana Agriculture

No abstract provided.

Initial Studies On Sperm Cryopreservation Of A Live-Bearing Fish, The Green Swordtail Xiphophorus Helleri, Changjiang Huang, Qiaoxiang Dong, Ronald B. Walter, Terrence R. Tiersch

Faculty Publications

Swordtails and platyfish of the genus Xiphophorus are valuable models for biomedical research and are also commercially raised as ornamental fish valued by aquarists. While research use and commercial interest increases yearly in these fish, cryopreservation of sperm is unexplored in this genus. Xiphophorus are live-bearing fishes characterized by small body sizes, limited sperm volumes, and internal fertilization, an atypical reproductive mode for fish. These attributes make research involving cryopreservation of Xiphophorus germplasm challenging. To explore methods for sperm cryopreservation, this study evaluated the effect of different loading volumes of sperm suspension in 0.25-ml French straws, different dilution ratios of …

Allosteric Β1 Integrin Antibodies That Stabilize The Low Affinity State By Preventing The Swing-Out Of The Hybrid Domain, Bing Hao Luo, Konstantin Strokovich, Thomas Walz, Timothy A. Springer, Junichi Takagi

Faculty Publications

The ligand binding function of integrins can be modulated by various monoclonal antibodies by both direct and indirect mechanisms. We have characterized an anti-β1 antibody, SG/19, that had been reported to inhibit the function of the β1 integrin on the cell surface. SG/19 recognized the wild type β1 subunit that exists in a conformational equilibrium between the high and low affinity states but bound poorly to a mutant β1 integrin that had been locked in a high affinity state. Epitope mapping of SG/19 revealed that Thr82 in the β1 subunit, located at the outer face of the boundary between the …

Proteomic Analysis Of Arabidopsis Glutathione S-Transferases From Benoxacor- And Copper-Treated Seedlings, Aaron P. Smith, Ben P. Deridder, Woei Jiun Guo, Erin H. Seeley, Fred E. Regnier, Peter B. Goldsbrough

Faculty Publications

Glutathione S-transferases (GSTs) are involved in many stress responses in plants, for example, participating in the detoxification of xenobiotics and limiting oxidative damage. Studies examining the regulation of this gene family in diverse plant species have focused primarily on RNA expression. A proteomics method was developed to identify GSTs expressed in Arabidopsis seedlings and to determine how the abundance of these proteins changed in response to copper, a promoter of oxidative stress, and benoxacor, a herbicide safener. Eight GSTs were identified in seedlings grown under control conditions, and only one, AtGSTU19, was induced by benoxacor. In contrast, four GSTs, AtGSTF2, …

Universal Primers For The Amplification Of Chloroplast Microsatellites In Grasses (Poaceae), Jim Provan, Pamela M. Biss, Darragh Mcmeel, Sarah Mathews

Faculty Publications

Attempts to design truly universal primers to amplify chloroplast microsatellites have met with limited success due to nonconservation of repeat loci across widely divergent taxa. We have used the complete chloroplast genome sequences of rice, maize and wheat to design five pairs of primers that amplify homologous mononucleotide repeats across the Poaceae (grasses). Sequencing confirmed conservation of repeat motifs across subfamilies and a preliminary study in Anthoxanthum odoratum revealed polymorphism at two loci with a haplotype diversity value of 0.495. These primers provide a valuable tool to study cytoplasmic diversity in this extensively studied and economically important range of taxa.

Kaposi's Sarcoma-Associated Herpesvirus Glycoprotein K8.1 Is Dispensable For Virus Entry, Rafael E. Luna, Fuchun Zhou, Abolgashem Baghian, Vladimir Chouljenko, Bagher Forghani, Shou Jiang Gao, Konstantin G. Kousoulas

Faculty Publications

Kaposi's sarcoma-associated herpesvirus (KSHV) is considered the etiologic agent of Kaposi's sarcoma and several lymphoproliferative disorders. Recently, the KSHV genome was cloned into a bacterial artificial chromosome and used to construct a recombinant KSHV carrying a deletion of the viral interferon regulatory factor gene (F. C. Zhou, Y. J. Zhang, J. H. Deng, X. P. Wang, H. Y. Pan, E. Hettler, and S. J. Gao, J. Virol. 76:6185-6196, 2002). The K8.1 glycoprotein is a structural component of the KSHV particle and is thought to facilitate virus entry by binding to heparan sulfate moieties on cell surfaces. To further address the …

Differential Alu Mobilization And Polymorphism Among The Human And Chimpanzee Lineages, Dale J. Hedges, Pauline A. Callinan, Richard Cordaux, Jinchuan Xing, Erin Barnes, Mark A. Batzer

Faculty Publications

Alu elements are primate-specific members of the SINE (short interspersed element) retroposon family, which comprise ∼10% of the human genome. Here we report the first chromosomal-level comparison examining the Alu retroposition dynamics following the divergence of humans and chimpanzees. We find a twofold increase in Alu insertions in humans in comparison to the common chimpanzee (Pan troglodytes). The genomic diversity (polymorphism for presence or absence of the Alu insertion) associated with these inserts indicates that, analogous to recent nucleotide diversity studies, the level of chimpanzee Alu diversity is ∼1.7 times higher than that of humans. Evolutionarily recent Alu subfamily structure …

Angiotensin I-Converting Enzyme Polymorphisms, Ace Level And Blood Pressure Among Nigerians, Jamaicans And African-Americans, Nourdine Bouzekri, Xiaofeng Zhu, Yanming Jiang, Colin A. Mckenzie, Amy Luke, Terrence Forrester, Adebowale Adeyemo, Donghui Kan, Martin Farrall, Simon Anderson, Richard S. Cooper, Ryk Ward

Faculty Publications

The genes in the renin-angiotensin system are important physiologic candidates in studies of the genetic susceptibility to hypertension. Limited information has been available in most studies on the extent of variation in the candidate loci or the modifying effects of different environmental settings. We consequently genotyped 13 polymorphisms at the angiotensin I-converting enzyme (ACE) locus at an average distance of 2 kb in 2776 family members from Nigeria, Jamaica and an African-American community in the US. Allele and haplotype frequencies were similar in the three populations, with modest evidence of European admixture in the US. Two markers were consistently associated …

Identification Of A New Chloroplast Carbonic Anhydrase In Chlamydomonas Reinhardtii, Mautusi Mitra, Scott M. Lato, Ruby A. Ynalvez, Ying Xiao, James V. Moroney

Faculty Publications

Carbonic anhydrases (CA) are zinc-containing metalloenzymes that catalyze the reversible hydration of CO2. The three evolutionarily unrelated families of CAs are designated α-, β-, and γ-CA. Aquatic photosynthetic organisms have evolved different forms of CO2 concentrating mechanisms (CCMs) to aid Rubisco in capturing CO2 from the surrounding environment. One aspect of all CCMs is the critical roles played by various specially localized extracellular and intracellular CAs. Five CAs have previously been identified in Chlamydomonas reinhardtii, a green alga with a well-studied CCM. Here we identify a sixth gene encoding a β-type CA. This new β-CA, designated Cah6, is distinct from …

Structure Of Fosfomycin Resistance Protein Fosa From Transposon Tn2921, Svetlana Pakhomova, Chris L. Rife, Richard N. Armstrong, Marcia E. Newcomer

Faculty Publications

The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been established at a resolution of 2.5 Å. The protein crystallized without bound Mn(II) and K+, ions crucial for efficient catalysis, providing a structure of the apo enzyme. The protein maintains the three-dimensional domain-swapped arrangement of the paired βαβββ-motifs observed in the genomically encoded homologous enzyme from Pseudomonas aeruginosa (PA1129). The basic architecture of the active site is also maintained, despite the absence of the catalytically essential Mn(II). However, the absence of K+, which has been shown to enhance enzymatic activity, appears to contribute to conformational heterogeneity in …

Properties And Performance Of The Prototype Instrument For The Pierre Auger Observatory, J. Abraham, M. Aglietta, I. C. Aguirre, M. Albrow, D. Allard, I. Allekotte, P. Allison, J. Alvarez Muñiz, M. G. Do Amaral, M. Ambrosio, L. Anchordoqui, R. Andrews, M. Anguiano, J. C. Dos Anjos, C. Aramo, S. Argiro, K. Arisaka, J. C. Arteaga, S. Atulugama, M. Ave, G. Avila, R. Baggio, X. Bai, A. F. Barbosa, H. M.J. Barbosa, D. Barnhill, S. L.C. Barroso, P. Bauleo, J. Beatty, T. Beau, K. H. Becker, J. A. Bellido, P. Bello

Faculty Publications

Construction of the first stage of the Pierre Auger Observatory has begun. The aim of the Observatory is to collect unprecedented information about cosmic rays above 1018 eV. The first phase of the project, the construction and operation of a prototype system, known as the engineering array, has now been completed. It has allowed all of the sub-systems that will be used in the full instrument to be tested under field conditions. In this paper, the properties and performance of these sub-systems are described and their success illustrated with descriptions of some of the events recorded thus far. © 2003 …

Isolation And Characterization Of T-Dna Insertional Mutations In Arabidopsis Thaliana And Its Use In Determining Siamese, Taylor S. Gwin

Honors Capstones

No abstract provided.

The Effects Of Resistant Starch And Fructooligosaccharides On Mineral Absorption In Rats, Katherine Ann Nolen

Honors Capstones

No abstract provided.