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Mendelian Microsatellite Loci For The Caribbean Coral Acropora Palmata, Iliana B. Baums, Colin R. Hughes, Michael E. Hellberg Mar 2005

Mendelian Microsatellite Loci For The Caribbean Coral Acropora Palmata, Iliana B. Baums, Colin R. Hughes, Michael E. Hellberg

Faculty Publications

The genus Acropora constitutes the most species-rich clade of hermatypic corals, and its members are important reef builders throughout their broad tropical range. In the Caribbean, acroporid populations have declined over the last 2 decades due to disease, hurricanes, predation, and bleaching episodes, and some are now subjects of conservation efforts. Genetic estimates of population connectivity and clonal structure should be part of these efforts, but such studies have been hampered by low levels of mitochondrial DNA variation in corals, and an apparent dearth of variable single-copy nuclear markers. Developing microsatellite markers in Acropora has proven especially difficult. We used …

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Disrupting Integrin Transmembrane Domain Heterodimerization Increases Ligand Binding Affinity, Not Valency Or Clustering, Bing Hao Luo, Christopher V. Carman, Junichi Takagi, Timothy A. Springer Mar 2005

Disrupting Integrin Transmembrane Domain Heterodimerization Increases Ligand Binding Affinity, Not Valency Or Clustering, Bing Hao Luo, Christopher V. Carman, Junichi Takagi, Timothy A. Springer

Faculty Publications

Residues important in the interaction between the 23-residue transmembrane (TM) domains of the integrin αIIb- and β3- subunits were identified by mutating each non-Leu residue to Leu. Leu substitutions of αIIb at G972, G976, and T981, and of β3 at 1693 and G708, increased ligand binding. Substitutions with other amino acids at αIIbG972 and β3G708 could also increase ligand binding. The results are consistent with and extend the helical interface between the integrin α- and β-subunit TM domains previously defined by cysteine scanning and disulfide bond formation. We differentiated between affinity- and valency-based modes of activation by TM domain mutations. …

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Haplotypes Produced From Rare Variants In The Promoter And Coding Regions Of Angiotensinogen Contribute To Variation In Angiotensinogen Levels, Xiaofeng Zhu, Laura Fejerman, Amy Luke, Adebowale Adeyemo, Richard S. Cooper Mar 2005

Haplotypes Produced From Rare Variants In The Promoter And Coding Regions Of Angiotensinogen Contribute To Variation In Angiotensinogen Levels, Xiaofeng Zhu, Laura Fejerman, Amy Luke, Adebowale Adeyemo, Richard S. Cooper

Faculty Publications

The most efficient study design to map genes underlying complex traits will be determined by assumptions about whether the genetic effects are likely to be due to relatively few common variants or multiple rare variants. To examine the possibility that rare variants may influence blood pressure, we sequenced a 6.8 kb region of the angiotensinogen (AGT) gene in 29 male Nigerians with high plasma AGT levels and 28 with low levels. The frequency of haplotypes produced from rare variants in the promoter and coding regions was significantly different between the two groups, and it is unlikely that this difference was …

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Analysis Of The Human Alu Ye Lineage, Abdel Halim Salem, David A. Ray, Dale J. Hedges, Jerzy Jurka, Mark A. Batzer Feb 2005

Analysis Of The Human Alu Ye Lineage, Abdel Halim Salem, David A. Ray, Dale J. Hedges, Jerzy Jurka, Mark A. Batzer

Faculty Publications

Background: Alu elements are short (∼300 bp) interspersed elements that amplify in primate genomes through a process termed retroposition. The expansion of these elements has had a significant impact on the structure and function of primate genomes. Approximately 10 % of the mass of the human genome is comprised of Alu elements, making them the most abundant short interspersed element (SINE) in our genome. The majority of Alu amplification occurred early in primate evolution, and the current rate of Alu retroposition is at least 100 fold slower than the peak of amplification that occurred 30-50 million years ago. Alu elements …

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Multiplex Polymerase Chain Reaction For Simultaneous Quantitation Of Human Nuclear, Mitochondrial, And Male Y-Chromosome Dna: Application In Human Identification, Jerilyn A. Walker, Dale J. Hedges, Benjamin P. Perodeau, Kate E. Landry, Nadica Stoilova, Meredith E. Laborde, Jaiprakash Shewale, Sudhir K. Sinha, Mark A. Batzer Feb 2005

Multiplex Polymerase Chain Reaction For Simultaneous Quantitation Of Human Nuclear, Mitochondrial, And Male Y-Chromosome Dna: Application In Human Identification, Jerilyn A. Walker, Dale J. Hedges, Benjamin P. Perodeau, Kate E. Landry, Nadica Stoilova, Meredith E. Laborde, Jaiprakash Shewale, Sudhir K. Sinha, Mark A. Batzer

Faculty Publications

Human forensic casework requires sensitive quantitation of human nuclear (nDNA), mitochondrial (mtDNA), and male Y-chromosome DNA from complex biomaterials. Although many such systems are commercially available, no system is capable of simultaneously quantifying all three targets in a single reaction. Most available methods either are not multiplex compatible or lack human specificity. Here, we report the development of a comprehensive set of human-specific, target-specific multiplex polymerase chain reaction (PCR) assays for DNA quantitation. Using TaqMan-MGB probes, our duplex qPCR for nDNA/mtDNA had a linear quantitation range of 100 ng to 1 pg, and our triplex qPCR assay for nDNA/mtDNA/male Y …

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Meiotic Recombination In Drosophila Females Depends On Chromosome Continuity Between Genetically Defined Boundaries, Dalia Sherizen, Janet K. Jang, Rajal Bhagat, Naohiro Kato, Kim S. Mckim Feb 2005

Meiotic Recombination In Drosophila Females Depends On Chromosome Continuity Between Genetically Defined Boundaries, Dalia Sherizen, Janet K. Jang, Rajal Bhagat, Naohiro Kato, Kim S. Mckim

Faculty Publications

In the pairing-site model, specialized regions on each chromosome function to establish meiotic homolog pairing. Analysis of these sites could provide insights into the mechanism used by Drosophila females to form a synaptonemal complex (SC) in the absence of meiotic recombination. These specialized sites were first established on the X chromosome by noting that there were barriers to crossover suppression caused by translocation heterozygotes. These sites were genetically mapped and proposed to be pairing sites. By comparing the cytological breakpoints of third chromosome translocations to their patterns of crossover suppression, we have mapped two sites on chromosome 3R. We have …

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Standardization Of Photometric Measurement Of Sperm Concentration From Diploid And Tetraploid Pacific Oysters, Crassostrea Gigas (Thunberg), Qiaoxiang Dong, Benoit Eudeline, Changjiang Huang, Terrence R. Tiersch Jan 2005

Standardization Of Photometric Measurement Of Sperm Concentration From Diploid And Tetraploid Pacific Oysters, Crassostrea Gigas (Thunberg), Qiaoxiang Dong, Benoit Eudeline, Changjiang Huang, Terrence R. Tiersch

Faculty Publications

To provide necessary standardization of procedures for cryopreservation of sperm, a spectrophotomeric method was developed to determine the sperm concentration of diploid and tetraploid Pacific oysters, Crassostrea gigas. Wavelengths of 380, 550, 581 and 780 nm were compared, and 550 and 581 nm were found to be the most sensitive and reliable. A linear relationship between sperm concentration and photometric absorbance was observed for sperm concentrations between 2 × 107 and 2 × 109 cells mL -1. The regression equation for the standard curve at 550 nm for sperm of diploid oysters was Y = - 8.528+1.165 log X. The …

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The Structure Of Coral Allene Oxide Synthase Reveals A Catalase Adapted For Metabolism Of A Fatty Acid Hydroperoxide, Michael L. Oldham, Alan R. Brash, Marcia E. Newcomer Jan 2005

The Structure Of Coral Allene Oxide Synthase Reveals A Catalase Adapted For Metabolism Of A Fatty Acid Hydroperoxide, Michael L. Oldham, Alan R. Brash, Marcia E. Newcomer

Faculty Publications

8R-Lipoxygenase and allene oxide synthase (AOS) are parts of a naturally occurring fusion protein from the coral Plexaura homomalla. AOS catalyses the production of an unstable epoxide (an allene oxide) from the fatty acid hydroperoxide generated by the lipoxygenase activity. Here, we report the structure of the AOS domain and its striking structural homology to catalase. Whereas nominal sequence identity between the enzymes had been previously described, the extent of structural homology observed was not anticipated, given that this enzyme activity had been exclusively associated with the P450 superfamily, and conservation of a catalase fold without catalase activity is unprecedented. …

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Studying Multiprotein Complexes By Multisignal Sedimentation Velocity Analytical Ultracentrifugation, Andrea Balbo, Kenneth H. Minor, Carlos A. Velikovsky, Roy A. Mariuzza, Cynthia B. Peterson, Peter Schuck Jan 2005

Studying Multiprotein Complexes By Multisignal Sedimentation Velocity Analytical Ultracentrifugation, Andrea Balbo, Kenneth H. Minor, Carlos A. Velikovsky, Roy A. Mariuzza, Cynthia B. Peterson, Peter Schuck

Faculty Publications

Protein interactions can promote the reversible assembly of multiprotein complexes, which have been identified as critical elements in many regulatory processes in cells. The biophysical characterization of assembly products, their number and stoichiometry, and the dynamics of their interactions in solution can be very difficult. A classical first-principle approach for the study of purified proteins and their interactions is sedimentation velocity analytical ultracentrifugation. This approach allows one to distinguish different protein complexes based on their migration in the centrifugal field without isolating reversibly formed complexes from the individual components. An important existing limitation for systems with multiple components and assembly …

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Electrodeposition Of Auco Alloys And Multilayers, Maoshi Guan Jan 2005

Electrodeposition Of Auco Alloys And Multilayers, Maoshi Guan

LSU Master's Theses

Electrodeposited AuCo and Au/Co multilayers are of interest as potential materials for MEMS components. AuCo alloys have been fabricated by the electrodeposition technique, but from cyanide-containing electrolyte. In this study, we explored the electrodeposition of AuCo and Au/Co multilayer thin films, and nanowires, from a non-cyanide electrolyte. Two variables were considered: the concentration of citric acid and pH. The changes in composition were described by the differences in the partial current densities. The effect of pH and citric acid concentration on the deposit composition and current efficiency was investigated. Results showed that a lower citric acid concentration was favored for …

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Ernst Mayr And The Complexity Of Life, Dominique G. Homberger Jan 2005

Ernst Mayr And The Complexity Of Life, Dominique G. Homberger

Faculty Publications

No abstract provided.

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A Response To Reimportation, Marcia Newcomer Jan 2005

A Response To Reimportation, Marcia Newcomer

Faculty Publications

In this issue of Structure, Holmes et al. (2005) describe elements of an innate defense mechanism that provides mammals a means to restrict bacterial growth. The host protein siderocalin scavenges struc turally dissimilar bacterial siderophores and prevents the uptake of Fe 3+ already earmarked for bacterial import.

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Membrane On A Chip: A Functional Tethered Lipid Bilayer Membrane On Silicon Oxide Surfaces, Vladimir Atanasov, Nikolaus Knorr, Randolph S. Duran, Sven Ingebrandt, Andreas Offenhäusser, Wolfgang Knoll, Ingo Köper Jan 2005

Membrane On A Chip: A Functional Tethered Lipid Bilayer Membrane On Silicon Oxide Surfaces, Vladimir Atanasov, Nikolaus Knorr, Randolph S. Duran, Sven Ingebrandt, Andreas Offenhäusser, Wolfgang Knoll, Ingo Köper

Faculty Publications

Tethered membranes have been proven during recent years to be a powerful and flexible biomimetic platform. We reported in a previous article on the design of a new architecture based on the self-assembly of a thiolipid on ultrasmooth gold substrates, which shows extremely good electrical sealing properties as well as functionality of a bilayer membrane. Here, we describe the synthesis of lipids for a more modular design and the adaptation of the linker part to silane chemistry. We were able to form a functional tethered bilayer lipid membrane with good electrical sealing properties covering a silicon oxide surface. We demonstrate …

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Blaut's Early Natural/Social Theorization, Cultural Ecology, And Political Ecology, Andrew Sluyter Jan 2005

Blaut's Early Natural/Social Theorization, Cultural Ecology, And Political Ecology, Andrew Sluyter

Faculty Publications

No abstract provided.

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Testing Conjectures About Morphological Diversity In Cichlids Of Lakes Malawi And Tanganyika, Prosanta Chakrabarty Jan 2005

Testing Conjectures About Morphological Diversity In Cichlids Of Lakes Malawi And Tanganyika, Prosanta Chakrabarty

Faculty Publications

The morphological diversity of Malawi and Tanganyika cichlids has often been qualitatively described, but rarely have hypotheses based on these descriptions been tested empirically. Using landmark based geometric morphometrics, shapes are analyzed independent of other aspects of the body form (e.g., size). The estimation of shape disparity, the quantitative measure of the variance of these raw shapes, can then be applied in order to objectively test hypotheses about morphological diversity. The shape disparity within and between different groups is explored as well as how it is partitioned within the cichlid body. Tanganyika cichlids are found to have significantly greater shape …

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Increased Rates Of Molecular Evolution In An Equatorial Plant Clade: An Effect Of Environment Or Phylogenetic Nonindependence?, Jeremy M. Brown, Gregory B. Pauly Jan 2005

Increased Rates Of Molecular Evolution In An Equatorial Plant Clade: An Effect Of Environment Or Phylogenetic Nonindependence?, Jeremy M. Brown, Gregory B. Pauly

Faculty Publications

A recent study of environmental effects on rates of molecular evolution in the plant subgenus Mearnsia shows that species occurring in more equatorial latitudes have higher rates of substitution in rDNA sequences as compared to their more southerly congeners (Wright et al. 2003). However, we believe that the statistical approach employed by Wright et al. (2003) insufficiently accounts for the phylogenetic nonindependence of the species examined, given that all six equatorial species of Mearnsia form a clade. To distinguish between the effect of latitude and that of phylogenetic nonindependence, we have employed a variety of comparative approaches that use independent …

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Future Of Avian Genetic Resources Collections: Archives Of Evolutionary And Environmental History, Scott V. Edwards, Sharon Birks, Robb T. Brumfield, Robert Hanner Jan 2005

Future Of Avian Genetic Resources Collections: Archives Of Evolutionary And Environmental History, Scott V. Edwards, Sharon Birks, Robb T. Brumfield, Robert Hanner

Faculty Publications

No abstract provided.

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Mitochondrial Variation In Bolivian Populations Of The Variable Antshrike (Thamnophilus Caerulescens), Robb T. Brumfield Jan 2005

Mitochondrial Variation In Bolivian Populations Of The Variable Antshrike (Thamnophilus Caerulescens), Robb T. Brumfield

Faculty Publications

The Variable Antshrike (Thamnophilus caerulescens) is arguably the most polytypic thamnophilid, with males ranging from almost entirely jet black to nearly white. The four subspecies that occur in Bolivia are strikingly divergent in male plumage: T. c. aspersiventer (black with white-barred belly), T. c. connectens (black back and bib with white belly), T. c. dinellii (gray throat and back with rufous belly), and T. c. paraguayensis (light gray with white belly). To assess the genetic structure of those taxa in Bolivia, sequence variation at the mitochondrial cytochrome-b gene was screened in 126 individuals collected across transects spanning the plumage and …

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Louisiana Agriculture Winter, 2005, Lsu Agcenter Jan 2005

Louisiana Agriculture Winter, 2005, Lsu Agcenter

Louisiana Agriculture

No abstract provided.

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Norleucine, A Natural Occurrence In A Novel Ergot Alkaloid Γ-Ergokryptinine, L. Cvak, A. Jegorov, P. Sedmera, I. Císařová, J. Čejka, B. Kratochvíl, S. Pakhomova Jan 2005

Norleucine, A Natural Occurrence In A Novel Ergot Alkaloid Γ-Ergokryptinine, L. Cvak, A. Jegorov, P. Sedmera, I. Císařová, J. Čejka, B. Kratochvíl, S. Pakhomova

Faculty Publications

A novel natural peptide ergot alkaloid γ-ergokryptinine containing norleucine has been isolated from ergot sclerotia of the field-growing parasitic fungus Claviceps purpurea CCM 8059. Its structure was deduced from the NMR and mass spectral data. The final structural proof was provided by the crystal structure determination, which is the first X-ray structure of a natural Nle-containing secondary metabolite. The conformations of three ergopeptinines: γ-ergokryptinine, ergoladinine, and α-ergokryptinine were compared. © Springer-Verlag 2005.

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Marine Radiations At Small Geographic Scales: Speciation In Neotropical Reef Gobies (Elacatinus), Michael S. Taylor, Michael E. Hellberg Jan 2005

Marine Radiations At Small Geographic Scales: Speciation In Neotropical Reef Gobies (Elacatinus), Michael S. Taylor, Michael E. Hellberg

Faculty Publications

Studies of speciation in the marine environment have historically compared broad-scale distributions and estimated larval dispersal potential to infer the geographic barriers responsible for allopatric speciation. However, many marine clades show high species diversity in geographically restricted areas where barriers are not obvious and estimated dispersal potential should bring many sister taxa into contact. Genetic differentiation at small (separation <1000 >km) spatial scales could facilitate speciation by mechanisms other than the gradual accumulation of reproductive isolation during extended allopatry, such as ecological adaptation to local environmental conditions or the rapid evolution of genes tied to mate recognition, but the role of …

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The Structures Of The Unique Sulfotransferase Retinol Dehydratase With Product And Inhibitors Provide Insight Into Enzyme Mechanism And Inhibition, Svetlana Pakhomova, Jochen Buck, Marcia E. Newcomer Jan 2005

The Structures Of The Unique Sulfotransferase Retinol Dehydratase With Product And Inhibitors Provide Insight Into Enzyme Mechanism And Inhibition, Svetlana Pakhomova, Jochen Buck, Marcia E. Newcomer

Faculty Publications

The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotransferase superfamily, in complexes with the inactive form of the cofactor PAP 3′-phosphoadenosine 5′-phosphate (PAP) and (1) the product of the reaction with retinol anhydroretinol (AR), (2) the retinoid inhibitor all-frans-4-oxoretinol (OR), and (3) the potent steroid inhibitor androsterone (AND) have been determined and compared to the enzyme complex with PAP and retinol. The structures show that the geometry of the active-site amino acids is largely preserved in the various complexes. However, the β-ionone rings of the retinoids are oriented differently with respect to side chains that …

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Formosan Subterranean Termite (Isoptera: Rhinotermitidae) Soldiers Regulate Juvenile Hormone Levels And Caste Differentiation In Workers, Lixin Mao, Gregg Henderson, Yuxiu Liu, Roger A. Laine Jan 2005

Formosan Subterranean Termite (Isoptera: Rhinotermitidae) Soldiers Regulate Juvenile Hormone Levels And Caste Differentiation In Workers, Lixin Mao, Gregg Henderson, Yuxiu Liu, Roger A. Laine

Faculty Publications

A caste structure is maintained in termite societies and juvenile hormone (JH) is generally regarded as the most important regulator in these termite colonies. Here, we demonstrate that the soldier caste regulates JH in workers of Coptotermes formosanus Shiraki. Worker termites (80-100 individuals) were placed in petri dishes with 0, 5, 10, or 20% soldiers. JH III titers of groups of these workers were monitored at 14, 28, 42, and 56 d. Any changes in soldier caste proportions also were noted at each sample date. On the first sample date, the JH levels in workers were similar among treatments with …

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Snp Haplotypes In The Angiotensin I-Converting Enzyme (Ace) Gene: Analysis Of Nigerian Family Data Using Gamete Competition Models, Colin A. Mckenzie, J. S. Sinsheimer, A. A. Adeyemo, R. D. Cox, L. Southam, A. Hugill, N. Bouzekri, M. Lathrop, T. E. Forrester, R. S. Cooper, R. Ward Jan 2005

Snp Haplotypes In The Angiotensin I-Converting Enzyme (Ace) Gene: Analysis Of Nigerian Family Data Using Gamete Competition Models, Colin A. Mckenzie, J. S. Sinsheimer, A. A. Adeyemo, R. D. Cox, L. Southam, A. Hugill, N. Bouzekri, M. Lathrop, T. E. Forrester, R. S. Cooper, R. Ward

Faculty Publications

Gamete competition models were used to explore the relationships between 13 ACE gene polymorphisms and plasma ACE concentration in a set of Nigerian families. Several markers in the 5′ and 3′ regions of the gene were significantly associated with ACE concentration (P < 10-4). Multi-locus genotypes comprising different combinations of markers from the 5′ UTR and the 3′ region of the gene were also analysed; in addition to G2350A, in the 3′ region, two markers from the 5′ UTR (A-5466C and A-240T) were found to be associated with ACE concentration. These results are consistent with reports that have suggested the presence of at least two ACE-linked QTLs, and demonstrate the utility of gamete competition models in the exploratory investigation of the relationship between a quantitative trait and multiple variants in a small genomic region. © University College London 2005.

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Ethnicity And Human Genetic Linkage Maps, Eric Jorgenson, Hua Tang, Maya Gadde, Mike Province, Mark Leppert, Sharon Kardia, Nicholas Schork, Richard Cooper, D. C. Rao, Eric Boerwinkle, Neil Risch Jan 2005

Ethnicity And Human Genetic Linkage Maps, Eric Jorgenson, Hua Tang, Maya Gadde, Mike Province, Mark Leppert, Sharon Kardia, Nicholas Schork, Richard Cooper, D. C. Rao, Eric Boerwinkle, Neil Risch

Faculty Publications

Human genetic linkage maps are based on rates of recombination across the genome. These rates in humans vary by the sex of the parent from whom alleles are inherited, by chromosomal position, and by genomic features, such as GC content and repeat density. We have examined-for the first time, to our knowledge-racial/ethnic differences in genetic maps of humans. We constructed genetic maps based on 353 microsatellite markers in four racial/ethnic groups: whites, African Americans, Mexican Americans, and East Asians (Chinese and Japanese). These maps were generated using 9,291 subjects from 2,900 nuclear families who participated in the National Heart, Lung, …

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Colony Social Organization And Population Genetic Structure Of An Introduced Population Of Formosan Subterranean Termite From New Orleans, Louisiana, Claudia Husseneder, Matthew T. Messenger, Nan Yao Su, J. Kenneth Grace, Edward L. Vargo Jan 2005

Colony Social Organization And Population Genetic Structure Of An Introduced Population Of Formosan Subterranean Termite From New Orleans, Louisiana, Claudia Husseneder, Matthew T. Messenger, Nan Yao Su, J. Kenneth Grace, Edward L. Vargo

Faculty Publications

The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an invasive species in many parts of the world, including the U.S. mainland. The reasons for its invasive success may have to do with the flexible social and spatial organization of colonies. We investigated the population and breeding structure of 14 C. formosanus colonies in Louis Armstrong Park, New Orleans, LA. This population has been the focus of extensive study for many years, providing the opportunity to relate aspects of colony breeding structure to previous findings on colony characteristics such as body weight and number of workers, wood consumption, and intercolony aggression. …

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Components, Volume 1 (2005), Lsu Center For Computation & Technology Jan 2005

Components, Volume 1 (2005), Lsu Center For Computation & Technology

Components

No abstract provided.

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Reduced Susceptibility To Tebufenozide In Populations Of The Sugarcane Borer (Lepidoptera: Crambidae) In Louisiana, F. P.F. Reay-Jones, W. Akbar, C. D. Mcallister, T. E. Reagan, J. A. Ottea Jan 2005

Reduced Susceptibility To Tebufenozide In Populations Of The Sugarcane Borer (Lepidoptera: Crambidae) In Louisiana, F. P.F. Reay-Jones, W. Akbar, C. D. Mcallister, T. E. Reagan, J. A. Ottea

Faculty Publications

Susceptibility of the sugarcane borer, Diatraea saccharalis (F.), to tebufenozide was measured using a feeding bioassay, and values obtained were compared with baselines generated before the use of this insecticide in Louisiana sugarcane, Saccharum spp. Results from our study suggest that susceptibility to tebufenozide is decreasing in field-collected sugarcane borers. Inflections in the log dosage-probit lines were detected for many of the field collections, indicating increased heterogeneity within these populations in response to tebufenozide. Where appropriate, probit transformation was used to estimate susceptibility, and significant differences (1.6-2.7-fold) were measured in LC50 values between some field-collected cohorts and the previously measured …

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Alu Insertion Loci And Platyrrhine Primate Phylogeny, David A. Ray, Jinchuan Xing, Dale J. Hedges, Michael A. Hall, Meredith E. Laborde, Bridget A. Anders, Brittany R. White, Nadica Stoilova, Justin D. Fowlkes, Kate E. Landry, Leona G. Chemnick, Oliver A. Ryder, Mark A. Batzer Jan 2005

Alu Insertion Loci And Platyrrhine Primate Phylogeny, David A. Ray, Jinchuan Xing, Dale J. Hedges, Michael A. Hall, Meredith E. Laborde, Bridget A. Anders, Brittany R. White, Nadica Stoilova, Justin D. Fowlkes, Kate E. Landry, Leona G. Chemnick, Oliver A. Ryder, Mark A. Batzer

Faculty Publications

Short INterspersed Elements (SINEs) make very useful phylogenetic markers because the integration of a particular element at a location in the genome is irreversible and of known polarity. These attributes make analysis of SINEs as phylogenetic characters an essentially homoplasy-free affair. Alu elements are primate-specific SINEs that make up a large portion of the human genome and are also widespread in other primates. Using a combination wet-bench and computational approach we recovered 190 Alu insertions, 183 of which are specific to the genomes of nine New World primates. We used these loci to investigate branching order and have produced a …

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Modeling The Amplification Dynamics Of Human Alu Retrotransposons, Dale J. Hedges, Richard Cordaux, Jinchuan Xing, David J. Witherspoon, Alan R. Rogers, Lynn B. Jorde, Mark A. Batzer Jan 2005

Modeling The Amplification Dynamics Of Human Alu Retrotransposons, Dale J. Hedges, Richard Cordaux, Jinchuan Xing, David J. Witherspoon, Alan R. Rogers, Lynn B. Jorde, Mark A. Batzer

Faculty Publications

Retrotransposons have had a considerable impact on the overall architecture of the human genome. Currently, there are three lineages of retrotransposons (Alu, L1, and SVA) that are believed to be actively replicating in humans. While estimates of their copy number, sequence diversity, and levels of insertion polymorphism can readily be obtained from existing genomic sequence data and population sampling, a detailed understanding of the temporal pattern of retrotransposon amplification remains elusive. Here we pose the question of whether, using genomic sequence and population frequency data from extant taxa, one can adequately reconstruct historical amplification patterns. To this end, we developed …

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