Digital Commons Network^™

Genome-Wide Association Scan Shows Genetic Variants In The Fto Gene Are Associated With Obesity-Related Traits, Angelo Scuteri, Serena Sanna, Wei Min Chen, Manuela Uda, Giuseppe Albai, James Strait, Samer Najjar, Ramaiah Nagaraja, Marco Orrú, Gianluca Usala, Mariano Dei, Sandra Lai, Andrea Maschio, Fabio Busonero, Antonella Mulas, Georg B. Ehret, Ashley A. Fink, Alan B. Weder, Richard S. Cooper, Pilar Galan, Aravinda Chakravarti, David Schlessinger, Antonio Cao, Edward Lakatta, Gonçalo R. Abecasis

Faculty Publications

The obesity epidemic is responsible for a substantial economic burden in developed countries and is a major risk factor for type 2 diabetes and cardiovascular disease. The disease is the result not only of several environmental risk factors, but also of genetic predisposition. To take advantage of recent advances in gene-mapping technology, we executed a genome-wide association scan to identify genetic variants associated with obesity-related quantitative traits in the genetically isolated population of Sardinia. Initial analysis suggested that several SNPs in the FTO and PFKP genes were associated with increased BMI, hip circumference, and weight. Within the FTO gene, rs9930506 …

Suppression Of Growth Of A Brown Rot Fungus, Gloeophyllum Trabeum, By Formosan Subterranean Termites (Isoptera: Rhinotermitidae), Poornima Jayasimha, Gregg Henderson

Faculty Publications

Although a brown rot fungus, Gloeophyllum trabeum (Pers.) Murrill, has been shown to be attractive and beneficial to subterranean termites, including Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae), no research has been conducted to determine whether the association is mutualistic. We first investigated whether the fungus could be spread by C. formosanus, because this would represent an obvious benefit to the fungus. We found that Formosan subterranean termites did not spread G. trabeum, rather they suppressed its growth. To further investigate this phenomenon, wood chips were inoculated with G. trabeum, and fungal growth was measured in treatments with termites or without termites …

Evolutionary Dynamics Of Transposable Elements In The Short-Tailed Opossum Monodelphis Domestica, Andrew J. Gentles, Matthew J. Wakefield, Oleksiy Kohany, Wanjun Gu, Mark A. Batzer, David D. Pollock, Jerzy Jurka

Faculty Publications

The genome of the gray short-tailed opossum Monodelphis domestica is notable for its large size (∼3.6 Gb). We characterized nearly 500 families of interspersed repeats from the Monodelphis. They cover ∼52% of the genome, higher than in any other amniotic lineage studied to date, and may account for the unusually large genome size. In comparison to other mammals, Monodelphis is significantly rich in non-LTR retrotransposons from the LINE-1, CR1, and RTE families, with <29% of the genome sequence comprised of copies of these elements. Monodelphis has at least four families of RTE, and we report support for horizontal transfer of this non-LTR retrotransposon. In addition to short interspersed elements (SINEs) mobilized by L1, we found several families of SINEs that appear to use RTE elements for mobilization. In contrast to L1-mobilized SINEs, the RTE-mobilized SINEs in Monodelphis appear to shift from G+C-rich to G+C-low regions with time. Endogenous retroviruses have colonized ∼10% of the opossum genome. We found that their density is enhanced in centromeric and/or telomeric regions of most Monodelphis chromosomes. We identified 83 new families of ancient repeats that are highly conserved across amniotic lineages, including 14 LINE-derived repeats; and a novel SINE element, MER131, that may have been exapted as a highly conserved functional noncoding RNA, and whose emergence dates back to ∼300 million years ago. Many of these conserved repeats are also present in human, and are highly over-represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals. ©2007 by Cold Spring Harbor Laboratory Press.

A Direct Substrate-Substrate Interaction Found In The Kinase Domain Of The Bifunctional Enzyme, 6-Phosphofructo-2-Kinase/Fructose-2,6-Bisphosphatase, Song Gun Kim, Michael Cavalier, M. Raafat El-Maghrabi, Yong Hwan Lee

Faculty Publications

To understand the molecular basis of a phosphoryl transfer reaction catalyzed by the 6-phosphofructo-2-kinase domain of the hypoxia-inducible bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB3), the crystal structures of PFKFB3{radical dot}AMPPCP{radical dot}fructose-6-phosphate and PFKFB3{radical dot}ADP{radical dot}phosphoenolpyruvate complexes were determined to 2.7 Å and 2.25 Å resolution, respectively. Kinetic studies on the wild-type and site-directed mutant proteins were carried out to confirm the structural observations. The experimentally varied liganding states in the active pocket cause no significant conformational changes. In the pseudo-substrate complex, a strong direct interaction between AMPPCP and fructose-6-phosphate (Fru-6-P) is found. By virtue of this direct substrate-substrate interaction, Fru-6-P is aligned …

The Stat5a-Mediated Induction Of Pyruvate Dehydrogenase Kinase 4 Expression By Prolactin Or Growth Hormone In Adipocytes, Ursula A. White, Ann A. Coulter, Tiffany K. Miles, Jacqueline M. Stephens

Faculty Publications

The purpose of this study was to determine whether pyruvate dehydrogenase kinase (PDK)4 was expressed in adipocytes and whether PDK4 expression was hormonally regulated in fat cells. Both Northern blot and Western blot analyses were conducted on samples isolated from 3T3-L1 adipocytes after various treatments with prolactin (PRL), growth hormone (GH), and/or insulin. Transfection of PDK4 promoter reporter constructs was performed. In addition, glucose uptake measurements were conducted. Our studies demonstrate that PRL and porcine GH can induce the expression of PDK4 in 3T3-L1 adipocytes. Our studies also show that insulin pretreatment can attenuate the ability of these hormones to …

Characterization Of Beaf Mutations Isolated By Homologous Recombination In Drosophila, Swarnava Roy, Matthew K. Gilbert, Craig M. Hart

Faculty Publications

The Drosophila BEAF-32A and BEAF-32B proteins bind to the scs′ insulator and to hundreds of other sites on Drosophila chromosomes. These two proteins are encoded by the same gene. We used ends-in homologous recombination to generate the null BEAFAB-KO allele and also isolated the BEAF A-KO allele that eliminates production of only the BEAF-32A protein. We find that the BEAF proteins together are essential, but BEAF-32B alone is sufficient to obtain viable flies. Our results show that BEAF is important for both oogenesis and development. Maternal or zygotic BEAF is sufficient to obtain adults, although having only maternal BEAF impairs …

Biology Intensive Orientation For Students (Bios): A Biology "Boot Camp", Sheri Maples Wischusen, E. William Wischusen

Faculty Publications

The Biology Intensive Orientation for Students (BIOS) Program was designed to assess the impact of a 5-d intensive prefreshman program on success and retention of biological science majors at Louisiana State University. The 2005 pilot program combined content lectures and examinations for BIOL 1201, Introductory Biology for Science Majors, as well as learning styles assessments and informational sessions to provide the students with a preview of the requirements of biology and the pace of college. Students were tracked after their BIOS participation, and their progress was compared with a control group composed of students on the BIOS waiting list and …

William Lowndes Yancey And The Coming Of The Civil War, Ben H. Severance

Civil War Book Review

Alabama's Leading Fire-Eater

Molecular Phylogeny Of The Scincid Lizards Of New Caledonia And Adjacent Areas: Evidence For A Single Origin Of The Endemic Skinks Of Tasmantis, Sarah A. Smith, Ross A. Sadlier, Aaron M. Bauer, Christopher C. Austin, Todd Jackman

Faculty Publications

We use ∼1900 bp of mitochondrial (ND2) and nuclear (c-mos and Rag-1) DNA sequence data to recover phylogenetic relationships among 58 species and 26 genera of Eugongylus group scincid lizards from New Caledonia, Lord Howe Island, New Zealand, Australia and New Guinea. Taxon sampling for New Caledonian forms was nearly complete. We find that the endemic skink genera occurring on New Caledonia, New Zealand and Lord Howe Island, which make up the Gondwanan continental block Tasmantis, form a monophyletic group. Within this group New Zealand and New Zealand + Lord Howe Island form monophyletic clades. These clades are nested within …

Endonuclease-Independent Insertion Provides An Alternative Pathway For L1 Retrotransposition In The Human Genome, Shurjo K. Sen, Charles T. Huang, Kyudong Han, Mark A. Batzer

Faculty Publications

LINE-1 elements (L1s) are a family of highly successful retrotransposons comprising ∼ 17% of the human genome, the majority of which have inserted through an endonuclease-dependent mechanism termed target-primed reverse transcription. Recent in vitro analyses suggest that in the absence of non-homologous end joining proteins, L1 elements may utilize an alternative, endonuclease-independent pathway for insertion. However, it remains unknown whether this pathway operates in vivo or in cell lines where all DNA repair mechanisms are functional. Here, we have analyzed the human genome to demonstrate that this alternative pathway for L1 insertion has been active in recent human evolution and …

Gonadotropin-Releasing Hormone And Receptor Distributions In The Visual Processing Regions Of Four Coral Reef Fishes, Karen P. Maruska, Timothy C. Tricas

Faculty Publications

Gonadotropin-releasing hormone (GnRH) is widely distributed in the brain of fishes where it may function as a neuromodulator of sensory processing and behavior. Immunocytochemical and neuronal label experiments were conducted on species from four families of coral reef fishes (Chaetodontidae, butterflyfish; Pomacentridae, damselfish; Gobiidae, goby; and Labridae, wrasse) to assess conservation of GnRH targets in the visual processing retina and brain. In all species, GnRH-immunoreactive (-ir) axons from the terminal nerve project principally to the boundary between the inner plexiform (IPL) and inner nuclear (INL) layers of the retina, and are less prominent in the optic nerve, ganglion cell, IPL …

The Extrinsic Proteins Of Photosystem Ii, Johnna L. Roose, Kimberly M. Wegener, Himadri B. Pakrasi

Faculty Publications

Years of genetic, biochemical, and structural work have provided a number of insights into the oxygen evolving complex (OEC) of Photosystem II (PSII) for a variety of photosynthetic organisms. However, questions still remain about the functions and interactions among the various subunits that make up the OEC. After a brief introduction to the individual subunits Psb27, PsbP, PsbQ, PsbR, PsbU, and PsbV, a current picture of the OEC as a whole in cyanobacteria, red algae, green algae, and higher plants will be presented. Additionally, the role that these proteins play in the dynamic life cycle of PSII will be discussed. …

Low Incidence Of Candidatus Liberibacter Asiaticus In Diaphorina Citri (Hemiptera: Psyllidae) Populations Between Nov 2005 And Jan 2006: Relevance To Management Of Citrus Greening Disease In Florida, Jason M. Meyer, Marjorie A. Hoy, Raghuwinder Singh

Faculty Publications

Populations of D. citri in Florida citrus were surveyed between Sep 2005 and Jan 2006 for Ca. L. asiaticus, the causal agent of HLB. No field-collected adults or immatures of the 1,972 D. citri tested were positive for the HLB pathogen in these samples, indicating that the proportion of D. citri populations hosting Ca. L. asiaticus in the regions sampled was very low (<0.05%) during this survey. More extensive surveys for Ca. L. asiaticus in D. citri are recommended to learn more about the epidemiology of disease transmission in Florida.

Citrus Leafminer, Phyllocnistis Citrella (Lepidoptera: Gracillariidae), And Natural Enemy Dynamics In Central Florida During 2005, Marjorie A. Hoy, Raghuwinder Singh, Michael E. Rogers

Faculty Publications

After the citrus leafminer (CLM), Phyllocnistis citrella Stainton (Lepidoptera: Gracillariidae), invaded Florida in 1993, the endoparasitoid Ageniaspis citricola Logvinovskaya (Hymenoptera: Encyrtidae) was introduced in 1994 in a classical biological control program. Subsequent to its establishment, only limited information has been obtained regarding the seasonal abundance of A. citricola and its host in central Florida citrus groves. During 2005, we monitored replicated plots treated with oil or imidacloprid once on 23 Jun 2005, along with untreated control trees, in a Polk County commercial Valencia orange grove on a weekly basis when tender new growth (= flush) was available. As expected, CLM …

Applications Of Chitosan For Improvement Of Quality And Shelf Life Of Foods: A Review, H. K. No, S. P. Meyers, W. Prinyawiwatkul, Z. Xu

Faculty Publications

Chitosan is a modified, natural biopolymer derived by deacetylation of chitin, a major component of the shells of crustacean. Recently, chitosan has received increased attention for its commercial applications in the biomedical, food, and chemical industries. Use of chitosan in food industry is readily seen due to its several distinctive biological activities and functional properties. The antimicrobial activity and film-forming property of chitosan make it a potential source of food preservative or coating material of natural origin. This review focuses on the applications of chitosan for improvement of quality and shelf life of various foods from agriculture, poultry, and seafood …

Modeling And Prediction Of Marine Microbial Populations In The Genomic Era, Raleigh R. Hood, Edward A. Laws, Michael J. Follows, David A. Siegel

Faculty Publications

No abstract provided.

Rnai Knockdown Of Nopp140 Induces Minute-Like Phenotypes In Drosophila, Zhengfang Cui, Patrick J. Dimario

Faculty Publications

Nopp140 associates with small nucleolar RNPs to chaperone pre-rRNA processing and ribosome assembly. Alternative splicing yields two isoforms in Drosophila: Nopp140-True is homologous to vertebrate Nopp140 particularly in its carboxy terminus, whereas Nopp140-RGG contains a glycine and arginine-rich (RGG) carboxy terminus typically found in vertebrate nucleolin. Loss of ribosome function or production at critical points in development leads to Minute phenotypes in Drosophila or the Treacher Collins syndrome (TCS) in humans. To ascertain the functional significance of Nopp140 in Drosophila development, we expressed interfering RNA using the GAL4/UAS system. Reverse transcription-PCR showed variable losses of Nopp140 mRNA in larvae from …

Impacts Of Hurricanes Katrina And Rita On The Microbial Landscape Of The New Orleans Area, C. D. Sinigalliano, M. L. Gidley, T. Shibata, D. Whitman, T. H. Dixon, E. Laws, A. Hou, D. Bachoon, L. Brand, L. Amaral-Zettler, R. J. Gast, G. F. Steward, O. D. Nigro, R. Fujioka, W. Q. Betancourf, G. Vithanage, J. Mathews, L. E. Fleming, H. M. Solo-Gabriele

Faculty Publications

Floodwaters in New Orleans from Hurricanes Katrina and Rita were observed to contain high levels of fecal indicator bacteria and microbial pathogens, generating concern about long-term impacts of these floodwaters on the sediment and water quality of the New Orleans area and Lake Pontchartrain. We show here that fecal indicator microbe concentrations in offshore waters from Lake Pontchartrain returned to prehurricane concentrations within 2 months of the flooding induced by these hurricanes. Vibrio and Legionella species within the lake were more abundant in samples collected shortly after the floodwaters had receded compared with samples taken within the subsequent 3 months; …

Genome Of The Marsupial Monodelphis Domestica Reveals Innovation In Non-Coding Sequences, Tarjei S. Mikkelsen, Matthew J. Wakefield, Bronwen Aken, Chris T. Amemiya, Jean L. Chang, Shannon Duke, Manuel Garber, Andrew J. Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen M.J. Searle, Ted Sharpe, Michelle L. Baker, Mark A. Batzer, Panayiotis V. Benos, Katherine Belov, Michele Clamp, April Cook, James Cuff, Radhika Das, Lance Davidow, Janine E. Deakin, Melissa J. Fazzari, Jacob L. Glass, Manfred Grabherr, John M. Greally, Wanjun Gu, Timothy A. Hore, Gavin A. Huttley, Michael Kleber, Randy L. Jirtle

Faculty Publications

We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in …

Analysis Of The Tfc6 Promoter In Saccharomyces Cerevisiae: Transcriptional Regulation Through Tf Iiic Binding At Etc6, Daniel Edwards

Honors Capstones

No abstract provided.

Retroposition And Evolution Of The Dna-Binding Motifs Of Yy1, Yy2 And Rex1, Jeong Do Kim, Christopher Faulk, Joomyeong Kim

Faculty Publications

YY1 is a DNA-binding transcription factor found in both vertebrates and invertebrates. Database searches identified 62 YY1 related sequences from all the available genome sequences ranging from flying insects to human. These sequences are characterized by high levels of sequence conservation, ranging from 66% to 100% similarity, in the zinc finger DNA-binding domain of the predicted proteins. Phylogenetic analyses uncovered duplication events of YY1 in several different lineages, including flies, fish and mammals. Retroposition is responsible for generating one duplicate in flies, PHOL from PHO, and two duplicates in placental mammals, YY2 and Reduced Expression 1 (REX1) from YY1. DNA-binding …

Caspase Activity During Cell Stasis: Avoidance Of Apoptosis In An Invertebrate Extremophile, Artemia Franciscana, Michael A. Menze, Steven C. Hand

Faculty Publications

Evaluation of apoptotic processes downstream of the mitochondrion reveals caspase-9- and low levels of caspase-3-like activities in partly purified extracts of Artemia franciscana embryos. However, in contrast to experiments with extracts of human hepatoma cells, cytochrome c fails to activate caspase-3 or -9 in extracts from A. franciscana. Furthermore, caspase-9 activity is sensitive to exogenous calcium. The addition of 5 mM calcium leads to a 4.86 ± 0.19 fold (SD) (n = 3) increase in activity, which is fully prevented with 150 mM KCl. As with mammalian systems, high ATP (>1.25 mM) suppresses caspase activity in A. franciscana extracts. …

Relationships Among Ecologically Important Dimensions Of Plant Trait Variation In Seven Neotropical Forests, Ian J. Wright, David D. Ackerly, Frans Bongers, Kyle E. Harms, Guillermo Ibarra-Manriquez, Miguel Martinez-Ramos, Susan J. Mazer, Helene C. Muller-Landau, Horacio Paz, Nigel C.A. Pitman, Lourens Poorter, Miles R. Silman, Corine F. Vriesendorp, Cam O. Webb, Mark Westoby, S. Joseph Wright

Faculty Publications

• Background and Aims: When ecologically important plant traits are correlated they may be said to constitute an ecological 'strategy' dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait combinations are favoured over others and into the implications of trait differences among species. Here we investigated relationships among several traits, and thus the strategy dimensions they represented, across 2134 woody species from seven Neotropical forests. • Methods: Six traits were studied: specific leaf area (SLA), the average size of leaves, seed and fruit, typical maximum plant height, and wood density (WD). Trait relationships …

Prediction Of Functional Sites Based On The Fuzzy Oil Drop Model, Michał Bryliński, Katarzyna Prymula, Wiktor Jurkowski, Marek Kochańczyk, Ewa Stawowczyk, Leszek Konieczny, Irena Roterman

Faculty Publications

A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, …

A Checklist Of The Amphibians And Reptiles Of México, Ernest A. Liner

Occasional Papers of the Museum of Natural Science, Louisiana State University

No abstract provided.

A Genome-Wide Scan Of Loci Linked To Serum Adiponectin In Two Populations Of African Descent, Chindo Hicks, Xiaofeng Zhu, Amy Luke, Donghui Kan, Adebowale Adeyemo, Xiaodong Wu, Richard S. Cooper

Faculty Publications

Objective: The objectives were to identify quantitative trait loci linked to serum adiponectin concentration and to estimate heritability in two populations of African descent. Research Methods and Procedures: We conducted a genome scan for serum adiponectin concentration in two populations of African descent. Genome-wide microsatelitte markers were typed in an African-American population consisting of 203 families from the Chicago area and in a Nigerian Yoruba population consisting of 146 families. Linkage analysis was performed to identify loci. Variance component model was used to estimate heritability. Results: Estimates of heritability adjusted for age, gender, and BMI were 0.45 and 0.70 for …

Association Studies Of Bmi And Type 2 Diabetes In The Neuropeptide Y Pathway: A Possible Role For Npy2r As A Candidate Gene For Type 2 Diabetes In Men, Catarina D. Campbell, Helen N. Lyon, James Nemesh, Jared A. Drake, Tiinamaija Tuomi, Daniel Gaudet, Xiaofeng Zhu, Richard S. Cooper, Kristin G. Ardlie, Leif C. Groop, Joel N. Hirschhorn

Faculty Publications

The neuropeptide Y (NPY) family of peptides and receptors regulate food intake. Inherited variation in this pathway could influence susceptibility to obesity and its complications, including type 2 diabetes. We genotyped a set of 71 single nucleotide polymorphisms (SNPs) that capture the most common variation in NPY, PPY, PYY, NPY1R, NPY2R, and NPY5R in 2,800 individuals of recent European ancestry drawn from the near extremes of BMI distribution. Five SNPs located upstream of NPY2R were nominally associated with BMI in men (P values = 0.001-0.009, odds ratios [ORs] 1.27-1.34). No association with BMI was observed in women, and no consistent …

Genetic Similarities Within And Between Human Populations, D. J. Witherspoon, S. Wooding, A. R. Rogers, E. E. Marchani, W. S. Watkins, M. A. Batzer, L. B. Jorde

Faculty Publications

The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of individuals into populations. Both findings can be obtained from the same data set, using the same number of polymorphic loci. This article explains why. Our analysis focuses on the frequency, ω, with which a pair of random individuals from two different populations is genetically more similar than a pair of individuals randomly selected from any single population. We compare ω to the …

Viscosity And Gravity Effects On The Kinetics Of E. Coli Alkaline Phosphatase, Sujatha Muralidharan

Honors Capstones

No abstract provided.

Feminism Divided: Feminists For Life Of America And The National Organization For Women, Monique Daley

Honors Capstones

No abstract provided.