Digital Commons Network^™

Mobile Dna In Old World Monkeys: A Glimpse Through The Rhesus Macaque Genome, Kyudong Han, Miriam K. Konkel, Jinchuan Xing, Hui Wang, Jungnam Lee, Thomas J. Meyer, Charles T. Huang, Erin Sandifer, Kristi Hebert, Erin W. Barnes, Robert Hubley, Webb Miller, Arian F.A. Smit, Brygg Ullmer, Mark A. Batzer

Faculty Publications

The completion of the draft sequence of the rhesus macaque genome allowed us to study the genomic composition and evolution of transposable elements in this representative of the Old World monkey lineage, a group of diverse primates closely related to humans. The L1 family of long interspersed elements appears to have evolved as a single lineage, and Alu elements have evolved into four currently active lineages. We also found evidence of elevated horizontal transmissions of retroviruses and the absence of DNA transposon activity in the Old World monkey lineage. In addition, ∼100 precursors of composite SVA (short interspersed element, variable …

Evolutionary And Biomedical Insights From The Rhesus Macaque Genome, Richard A. Gibbs, Jeffrey Rogers, Michael G. Katze, Roger Bumgarner, George M. Weinstock, Elaine R. Mardis, Karin A. Remington, Robert L. Strausberg, J. Craig Venter, Richard K. Wilson, Mark A. Batzer, Carlos D. Bustamante, Evan E. Eichler, Matthew W. Hahn, Ross C. Hardison, Kateryna D. Makova, Webb Miller, Aleksandar Milosavljevic, Robert E. Palermo, Adam Siepel, James M. Sikela, Tony Attaway, Stephanie Bell, Kelly E. Bernard, Christian J. Buhay, Mimi N. Chandrabose, Marvin Dao, Clay Davis, Kimberly D. Delehaunty, Yan Ding, Huyen H. Dinh, Shannon Dugan-Rocha, Lucinda A. Fulton, Ramatu Ayiesha Gabisi

Faculty Publications

The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedical research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate …

Haplotype Association Between Haptoglobin (Hp2) And Hp Promoter Snp (A-61c) May Explain Previous Controversy Of Haptoglobin And Malaria Protection, Sharon E. Cox, Conor Doherty, Sarah H. Atkinson, Chidi V. Nweneka, Anthony J.C. Fulford, Hala Ghattas Ph.D., Kirk A. Rockett, Dominic P. Kwiatkowski, Andrew M. Prentice

Faculty Publications

Background.

Malaria is one of the strongest recent selective pressures on the human genome, as evidenced by the high levels of varying haemoglobinopathies in human populations-despite the increased risk of mortality in the homozygous states. Previously, functional polymorphisms of Hp, coded by the co-dominant alleles Hp1 and Hp2, have been variously associated with several infectious diseases, including malaria susceptibility.

Methodology/Principal Findings.

Risk of a clinical malarial episode over the course of a malarial transmission season was assessed using active surveillance in a cohort of Gambian children aged 10-72 months. We report for the first time that the major haplotype for …

Haplotype Association Between Haptoglobin (Hp2) And Hp Promoter Snp (A-61c) May Explain Previous Controversy Of Haptoglobin And Malaria Protection, Sharon E. Cox, Conor Doherty, Sarah H. Atkinson, Chidi V. Nweneka, Anthony J.C. Fulford, Hala Ghattas Ph.D., Kirk A. Rockett, Dominic P. Kwiatkowski, Andrew M. Prentice

Faculty Publications

Background

Malaria is one of the strongest recent selective pressures on the human genome, as evidenced by the high levels of varying haemoglobinopathies in human populations–despite the increased risk of mortality in the homozygous states. Previously, functional polymorphisms of Hp, coded by the co-dominant alleles Hp1 and Hp2, have been variously associated with several infectious diseases, including malaria susceptibility.

Methodology/Principal Findings

Risk of a clinical malarial episode over the course of a malarial transmission season was assessed using active surveillance in a cohort of Gambian children aged 10–72 months. We report for the first time that the major haplotype for …

Palmitoylation Of The Cysteine-Rich Endodomain Of The Sars-Coronavirus Spike Glycoprotein Is Important For Spike-Mediated Cell Fusion, Chad M. Petit, Vladimir N. Chouljenko, Arun Iyer, Robin Colgrove, Michael Farzan, David M. Knipe, K. G. Kousoulas

Faculty Publications

The SARS-coronavirus (SARS-CoV) is the etiological agent of the severe acute respiratory syndrome (SARS). The SARS-CoV spike (S) glycoprotein mediates membrane fusion events during virus entry and virus-induced cell-to-cell fusion. The cytoplasmic portion of the S glycoprotein contains four cysteine-rich amino acid clusters. Individual cysteine clusters were altered via cysteine-to-alanine amino acid replacement and the modified S glycoproteins were tested for their transport to cell-surfaces and ability to cause cell fusion in transient transfection assays. Mutagenesis of the cysteine cluster I, located immediately proximal to the predicted transmembrane, domain did not appreciably reduce cell-surface expression, although S-mediated cell fusion was …

Inhibitory Effects Of Estrogen Receptor Beta On Specific Hormone-Responsive Gene Expression And Association With Disease Outcome In Primary Breast Cancer, Chin-Yo Lin, Anders Strom, Li Say Kong, Silke Kietz, Jane S. Thomsen, Jason B. S. Tee, Vinsensius B. Vega, Lance D. Miller, Johanna Smeds, Jonas Bergh, Jan-Ake Gustafsson, Edison T. Liu

Faculty Publications

The impact of interactions between the two estrogen receptor (ER) subtypes, ER(alpha) and ER(beta), on gene expression in breast cancer biology is not clear. The goal of this study was to examine transcriptomic alterations in cancer cells co-expressing both receptors and the association of gene expression signatures with disease outcome. Methods: Transcriptional effects of ER(beta) overexpression were determined in a stably transfected cell line derived from ER(alpha) -positive T-47D cells. Microarray analysis was carried out to identify differential gene expression in the cell line, and expression of key genes was validated by quantitative polymerase chain reaction. Microarray and clinical data …

Investigation Of The Summer Kara Sea Circulation Employing A Variational Data Assimilation Technique, G. Panteleev, A. Proshutinsky, M. Kulakov, Dmitri A. Nechaev, W. Maslowski

Faculty Publications

[ 1] The summer circulations and hydrographic fields of the Kara Sea are reconstructed for mean, positive and negative Arctic Oscillation regimes employing a variational data assimilation technique which provides the best fit of reconstructed fields to climatological data and satisfies dynamical and kinematic constraints of a quasi-stationary primitive equation ocean circulation model. The reconstructed circulations agree well with the measurements and are characterized by inflow of 0.63, 0.8, 0.51 Sv through Kara Gate and 1.18, 1.1, 1.12 Sv between Novaya Zemlya and Franz Josef Land, for mean climatologic conditions, positive and negative AO indexes, respectively. The major regions of …

Hikorocodium Endo Is Not An Alga But An Inozoid Sponge, J. Keith Rigby, Baba Senowbari-Daryan

Faculty Publications

The genus Hikorocodium, with the type species Hikorocodium elegantae from the Permian of Japan, was described originally as a codiacean alga by Endo. It is not a codiacean alga but an inozoid sponge of the family Preperonidellidae. Several fossils described later by Endo and other authors as H. elegantae should be assigned to different inozoid sponge taxa. Specimens of H. fertiliz, described by Endo from the Jurassic of Japan, are also sponge fragments. The taxonomic positions of H. transversum Endo and H. kuramotoi Nakamura, as sponges or

Disparate Distributions Of Chemolithotrophs Containing Form Ia Or Ic Large Subunit Genes For Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase In Intertidal Marine And Littoral Lake Sediments, Lisa M. Nigro, Gary M. King

Faculty Publications

The distributions of bacterial form IA and form IC ribulose-1,5- bisphosphate carboxylase/oxygenase (RuBisCO) were investigated using Lowes Cove intertidal mudflat and Damariscotta Lake littoral sediments by PCR amplification of 492-495 bp fragments of the large subunit RuBisCO gene, cbbL. Genomic extracts for amplification were obtained from lake surface (upper 2 mm), mudflat surface (upper 2 mm), subsurface (5-7 cm), and soft-shell clam (Mya arenaria) burrow-wall sediments, as well as from a sulfide-oxidizing mat. Phylogenetic analyses of cbbL clone libraries revealed that Lowes Cove sediments were dominated by form IA cbbL-containing sequences most closely related to cbbL genes of sulfur-oxidizing bacteria …

Bayesian Change-Point Analyses In Ecology, Brian Beckage, Lawrence Joseph, Patrick Belisle, David B. Wolfson, William J. Platt

Faculty Publications

• Ecological and biological processes can change from one state to another once a threshold has been crossed in space or time. Threshold responses to incremental changes in underlying variables can characterize diverse processes from climate change to the desertification of arid lands from overgrazing. • Simultaneously estimating the location of thresholds and associated ecological parameters can be difficult: ecological data are often 'noisy', which can make the identification of the locations of ecological thresholds challenging. • We illustrate this problem using two ecological examples and apply a class of statistical models well-suited to addressing this problem. We first consider …

Ancestral Alleles And Population Origins: Inferences Depend On Mutation Rate, Alan R. Rogers, Stephen Wooding, Chad D. Huff, Mark A. Batzer, Lynn B. Jorde

Faculty Publications

Previous studies have found that at most human loci, ancestral alleles are "African," in the sense that they reach their highest frequency there. Conventional wisdom holds that this reflects a recent African origin of modern humans. This paper challenges that view by showing that the empirical pattern (of elevated allele frequencies within Africa) is not as pervasive as has been thought. We confirm this African bias in a set of mainly protein-coding loci, but find a smaller bias in Alu insertion polymorphisms, and an even smaller bias in noncoding loci. Thus, the strong bias that was originally observed must reflect …

Introduction For The Gene Special Issue Dedicated To The Meeting "Genomic Impact Of Eukaryotic Transposable Elements" At Asilomar, Mark A. Batzer, Prescott L. Deininger, Jerzy Jurka, John V. Moran

Faculty Publications

The issues related to 'Genomic Impact of Eukaryotic Transposable Elements', which took place in Pacific Grove, California between March 31st and April 4th 2006, are discussed. The meeting celebrated the extraordinary contributions of Dr. Carl W. Schmid to the study of repeated DNA sequences and mobile elements. With the advent of recombinant DNA technology, he led the discovery of human Alu elements, and the discovery of their amplification. The idea of the conference was to gather and disseminate information in transposable elements (TEs) on the state-of-the-art tools and approaches. The core sessions from the conference covered research on transposable elements …

Identification And Characterization Of Novel Polymorphic Line-1 Insertions Through Comparison Of Two Human Genome Sequence Assemblies, Miriam K. Konkel, Jianxin Wang, Ping Liang, Mark A. Batzer

Faculty Publications

Mobile elements represent a relatively new class of markers for the study of human evolution. Long interspersed elements (LINEs) belong to a group of retrotransposons comprising approximately 21% of the human genome. Young LINE-1 (L1) elements that have integrated recently into the human genome can be polymorphic for insertion presence/absence in different human populations at particular chromosomal locations. To identify putative novel L1 insertion polymorphisms, we computationally compared two draft assemblies of the whole human genome (Public and Celera Human Genome assemblies). We identified a total of 148 potential polymorphic L1 insertion loci, among which 73 were candidates for novel …

Formation Of Tellurium Nanocrystals During Anaerobic Growth Of Bacteria That Use Te Oxyanions As Respiratory Electron Acceptors, Shaun M. Baesman, Thomas D. Bullen, James Dewald, Donghui Zhang, Seamus Curran, Farhana S. Islam, Terry J. Beveridge, Ronald S. Oremland

Faculty Publications

Certain toxic elements support the metabolism of diverse prokaryotes by serving as respiratory electron acceptors for growth. Here, we demonstrate that two anaerobes previously shown to be capable of respiring oxyanions of selenium also achieve growth by reduction of either tellurate [Te(VI)] or tellurite [Te(IV)] to elemental tellurium [Te(0)]. This reduction achieves a sizeable stable-Te-isotopic fractionation (isotopic enrichment factor [ε] = -0.4 to -1.0 per ml per atomic mass unit) and results in the formation of unique crystalline Te(0) nanoarchitectures as end products. The Te(0) crystals occur internally within but mainly externally from the cells, and each microorganism forms a …

Interspecific Spawning Between A Recent Immigrant And An Endemic Damselfish (Pisces: Pomacentridae) In The Hawaiian Islands, Karen P. Maruska, Kimberly A. Peyton

Faculty Publications

The Indo-Pacific damselfish Abudefduf vaigiensis (Quoy & Gaimard, 1825) was first observed in the Hawaiian Islands in the early 1990s and is now clearly established as a breeding population in the Islands. Sightings of fish with color patterns intermediate between those of A. vaigiensis and the very similar endemic Hawaiian sergeant, Abudefduf abdominalis (Quoy & Gaimard, 1825), suggest that hybridization of the two has occurred naturally. This study provides direct evidence of crossbreeding from observations and video footage of two separate spawnings in nearshore waters of O'ahu and a third spawning in a public aquarium display tank. Reproductive behaviors were …

Induction Of Host Chemotactic Response By Encephalitozoon Spp., Jeffrey Fischer, Jeffrey West, Nnenaya Agochukwu, Colby Suire, Hollie Hale-Donze

Faculty Publications

Microsporidians are a group of emerging pathogens typically associated with chronic diarrhea in immunocompromised individuals. The number of reports of infections with these organisms and the disseminated pathology is growing as diagnostic tools become more readily available. However, little is known about the innate immune response induced by and generated against these parasites. Using a coculture chemotaxis system, primary human macrophages were infected with Encephalitozoon cuniculi or Encephalitozoon intestinalis, and the recruitment of naïve monocytes was monitored. Encephalitozoon spp. induced an average threefold increase in migration of naïve cells 48 h postinfection, which corresponded to optimal infection of monocyte-derived- macrophages. …

Comparative Bacterial Diversity In Recent Hawaiian Volcanic Deposits Of Different Ages, Vicente Gomez-Alvarez, Gary M. King, Klaus Nüsslein

Faculty Publications

Volcanic activity creates new landforms that can change dramatically over time as a consequence of biotic succession. Nonetheless, volcanic deposits present severe constraints for microbial colonization and activity. We have characterized bacterial diversity on four recent deposits at Kilauea volcano, Hawaii (KVD). Much of the diversity was either closely related to uncultured organisms or distinct from any reported 16S rRNA gene sequences. Diversity indices suggested that diversity was highest in a moderately vegetated 210-year-old ash deposit (1790-KVD), and lowest for a 79-year-old lava flow (1921-KVD). Diversity for a 41-year-old tephra deposit (1959-KVD) and a 300-year-old rainforest (1700-KVD) reached intermediate values. …

Corin I555(P568) Allele Is Associated With Enhanced Cardiac Hypertrophic Response To Increased Systemic Afterload, J. Eduardo Rame, Mark H. Drazner, Wendy Post, Ronald Peshock, Joao Lima, Richard S. Cooper, Daniel L. Dries

Faculty Publications

Corin activates pro-A-type naturetic peptide and pro-B-type naturetic peptide into biologically active molecules. We recently identified a minor allele in the corin gene defined by 2 highly linked single nucleotide polymorphisms (T555I and Q568P), which was associated with hypertension in blacks. Because of the direct antihypertrophic effects of the natriuretic peptide system, we hypothesized that the minor corin I555(P568) allele would be associated with an enhanced hypertrophic response to pressure overload. The relationship between systolic blood pressure and indexed left ventricular mass, derived from cardiac MRI, was analyzed in the Dallas Heart Study as a function of corin allele status. …

Paired Ig-Like Receptors Bind To Bacteria And Shape Tlr-Mediated Cytokine Production, Masafumi Nakayama, David M. Underhill, Timothy W. Petersen, Bin Li, Toshio Kitamura, Toshiyuki Takai, Alan Aderem

Faculty Publications

The innate immune system uses a wide variety of pattern recognition receptors including TLRs, scavenger receptors, and lectins to identify potential pathogens. A carefully regulated balance between activation and inhibition must be kept to avoid detrimental and inappropriate inflammatory responses. In this study, we identify murine-paired Ig-like receptor (PIR)-B, and its human orthologs Ig-like transcript 2 and Ig-like transcript 5 as novel receptors for Staphylococcus aureus. PIR-B contains four ITIM motifs and is thought to be an inhibitory receptor. Expression of these receptors enables NIH3T3 cells to bind S. aureus. In mouse bone marrow-derived macrophages, masking of PIR-B by anti-PIR …

A Sine-Based Dichotomous Key For Primate Identification, Scott W. Herke, Jinchuan Xing, David A. Ray, Jacquelyn W. Zimmerman, Richard Cordaux, Mark A. Batzer

Faculty Publications

For DNA samples or 'divorced' tissues, identifying the organism from which they were taken generally requires some type of analytical method. The ideal approach would be robust even in the hands of a novice, requiring minimal equipment, time, and effort. Genotyping SINEs (Short INterspersed Elements) is such an approach as it requires only PCR-related equipment, and the analysis consists solely of interpreting fragment sizes in agarose gels. Modern primate genomes are known to contain lineage-specific insertions of Alu elements (a primate-specific SINE); thus, to demonstrate the utility of this approach, we used members of the Alu family to identify DNA …

Different Evolutionary Fates Of Recently Integrated Human And Chimpanzee Line-1 Retrotransposons, Jungnam Lee, Richard Cordaux, Kyudong Han, Jianxin Wang, Dale J. Hedges, Ping Liang, Mark A. Batzer

Faculty Publications

The long interspersed element-1 (LINE-1 or L1) is a highly successful retrotransposon in mammals. L1 elements have continued to actively propagate subsequent to the human-chimpanzee divergence, ∼ 6 million years ago, resulting in species-specific inserts. Here, we report a detailed characterization of chimpanzee-specific L1 subfamily diversity and a comparison with their human-specific counterparts. Our results indicate that L1 elements have experienced different evolutionary fates in humans and chimpanzees within the past ∼ 6 million years. Although the species-specific L1 copy numbers are on the same order in both species (1200-2000 copies), the number of retrotransposition-competent elements appears to be much …

Gstm1, Gstt1, Gstp1, And Gsta1 Polymorphisms And Urinary Isothiocyanate Metabolites Following Broccoli Consumption In Humans, Susan E. Steck, Marilie D. Gammon, James R. Hébert, Denise E. Wall, Steven H. Zeisel

Faculty Publications

Isothiocyanates (ITC) are potentially anticarcinogenic phytochemicals formed from the metabolism of glucosinolates and are found in cruciferous vegetables as well as a select number of other foods. ITC are both substrates for and inducers of glutathione S-transferase (GST) phase II metabolizing enzymes involved in carcinogen detoxification as well as effectors of phase I pathways. Previous studies report mixed results on the interaction between cruciferous vegetable intake, GST polymorphisms, and risk of cancer. We conducted a study of 114 healthy human subjects between 18 and 50 y of age to examine the biologic mechanism underlying the associations, specifically, to assess …

Fpga Acceleration Of Gene Rearrangement Analysis, Jason D. Bakos

Faculty Publications

In this paper we present our work toward FPGA acceleration of phylogenetic reconstruction, a type of analysis that is commonly performed in the fields of systematic biology and comparative genomics. In our initial study, we have targeted a specific application that reconstructs maximum-parsimony (MP) phylogenies for gene-rearrangement data. Like other prevalent applications in computational biology, this application relies on a control-dependent, memory-intensive, and non-arithmetic combinatorial optimization algorithm. To achieve hardware acceleration, we developed an FPGA core design that implements the application's primary bottleneck computation. Because our core is lightweight, we are able to synthesize multiple cores on a single FPGA. …

Federated Searching: Do Undergraduates Prefer It And Does It Add Value?, C. Jeffrey Belliston, Jared L. Howland, Brian C. Roberts

Faculty Publications

Randomly selected undergraduates at Brigham Young University, Brigham Young University Idaho and Brigham Young University Hawaii, all private universities sponsored by The Church of Jesus Christ of Latter-day Saints, participated in a study of federated searching. This paper reports the study results including differences in time spent between searching databases in federated and non-federated fashion, satisfaction with citations gathered using each method, preference between methods, and quality of citations retrieved by each method judged by two different rubrics. Undergraduates rated their satisfaction with the citations gathered by federated searching 6.5% higher than their satisfaction using non-federated search methods. Additionally, 70% …

Family Structure, Children, And Law, Vivian E. Hamilton

Faculty Publications

No abstract provided.

Response Of A Native Bamboo [Arundinaria Gigantea (Walt.) Muhl.] In A Wind-Disturbed Forest, Paul R. Gagnon, William J. Platt, E. Barry Moser

Faculty Publications

Numerous bamboos are known to form extensive single-species stands, including species in the United States. Formerly prominent in the southeastern US, canebrakes are dense stands of the bamboos collectively called "cane" [Arundinaria (Michx)]. Canebrakes are now a critically endangered component of the bottomland hardwood forest ecosystem. Cane still occurs in its historic range, primarily in small remnant patches. A poor understanding of the ecological processes that generated large canebrakes limits their restoration and management. We hypothesize that cane's spreading clonal structure enables these bamboos to persist beneath a forest canopy and then respond rapidly to large-scale wind disturbances. We quantified …

Tandem Repeat Regions Within The Burkholderia Pseudomallei Genome And Their Application For High Resolution Genotyping, Richard A. Robison, Jana M. U'Ren, James M. Schupp, Talima Pearson, Heidie Hornstra, Christine L. Friedman Clark, Kimothy L. Smith, Rebecca R. Leadem Daugherty, Shane D. Rhoton, Ben Leadem, Shalamar Georgia, Michelle Cardon, Lynn Y. Huynh, David Deshazer, Steven P. Harvey, Daniel Gal, Mark J. Mayo, David Wagner, Bart J. Currie, Paul Keim

Faculty Publications

The facultative, intracellular bacterium Burkholderia pseudomalle is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine …

Biogeochemical Stoichiometry Of Antarctic Dry Valley Ecosystems, J. E. Barrett, R. A. Virginia, W. B. Lyons, D. M. Mcknight, J. C. Priscu, P. T. Doran, A. G. Fountain, D. H. Wall, D. L. Moorhead

Faculty Publications

Among aquatic and terrestrial landscapes of the McMurdo Dry Valleys, Antarctica, ecosystem stoichiometry ranges from values near the Redfield ratios for C:N:P to nutrient concentrations in proportions far above or below ratios necessary to support balanced microbial growth. This polar desert provides an opportunity to evaluate stoichiometric approaches to understand nutrient cycling in an ecosystem where biological diversity and activity are low, and controls over the movement and mass balances of nutrients operate over 10-106 years. The simple organisms (microbial and metazoan) comprising dry valley foodwebs adhere to strict biochemical requirements in the composition of their biomass, and when activated …

Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua Udall, Lex E. Flagel, Foo Chung, Andrew W. Woodward, Ran Hovav, Ryan A. Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel

Faculty Publications

Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Results: Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from <50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results. Conclusion: The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.

The Niemann-Pick Type C2 Protein Loads Isoglobotrihexosylceramide Onto Cd1d Molecules And Contributes To The Thymic Selection Of Nkt Cells, Paul B. Savage, Nicolas Schrantz, Yuval Sagiv, Yang Liu, Albert Bendelac, Luc Teyton

Faculty Publications

The Niemann-Pick type C2 (NPC2) protein is a small, soluble, lysosomal protein important for cholesterol and sphingolipid transport in the lysosome. The immunological phenotype of NPC2-deficient mice was limited to an impaired thymic selection of Valpha 14 natural killer T cells (NKT cells) and a subsequent reduction of NKT cells in the periphery. The remaining NKT cells failed to produce measurable quantities of interferon-gamma in vivo and in vitro after activation with alpha-galactosylceramide. In addition, thymocytes and splenocytes from NPC2-deficient mice were poor presenters of endogenous and exogenous lipids to CD1d-restricted Valpha 14 hybridoma cells. Importantly, we determined that similar …