Stuart M. Brown, Ph.D.

A Molecular Epidemiological Study of var Gene Diversity to Characterize the Reservoir of Plasmodium falciparum in Humans in Africa
Chen, Donald S; Barry, Alyssa E; Leliwa-Sytek, Aleksandra; Smith, Terry-Ann; Peterson, Ingrid; Brown, Stuart M; Migot-Nabias, Florence; Deloron, Philippe; Kortok, Moses M; Marsh, Kevin; Daily, Johanna P; Ndiaye, Daouda; Sarr, Ousmane; Mboup, Souleymane; Day, Karen P
2011 ;6(2):e16629-e16629, PLoS ONE
BACKGROUND: The reservoir of Plasmodium infection in humans has traditionally been defined by blood slide positivity. This study was designed to characterize the local reservoir of infection in relation to the diverse var genes that encode the major surface antigen of Plasmodium falciparum blood stages and underlie the parasite's ability to establish chronic infection and transmit from human to mosquito. METHODOLOGY/PRINCIPAL FINDINGS: We investigated the molecular epidemiology of the var multigene family at local sites in Gabon, Senegal and Kenya which differ in parasite prevalence and transmission intensity. 1839 distinct var gene types were defined by sequencing DBLalpha domains in the three sites. Only 76 (4.1%) var types were found in more than one population indicating spatial heterogeneity in var types across the African continent. The majority of var types appeared only once in the population sample. Non-parametric statistical estimators predict in each population at minimum five to seven thousand distinct var types. Similar diversity of var types was seen in sites with different parasite prevalences. CONCLUSIONS/SIGNIFICANCE: Var population genomics provides new insights into the epidemiology of P. falciparum in Africa where malaria has never been conquered. In particular, we have described the extensive reservoir of infection in local African sites and discovered a unique var population structure that can facilitate superinfection through minimal overlap in var repertoires among parasite genomes. Our findings show that var typing as a molecular surveillance system defines the extent of genetic complexity in the reservoir of infection to complement measures of malaria prevalence. The observed small scale spatial diversity of var genes suggests that var genetics could greatly inform current malaria mapping approaches and predict complex malaria population dynamics due to the import of var types to areas where no widespread pre-existing immunity in the population exists
— id: 124110, year: 2011, vol: 6, page: e16629, stat: Journal Article,

Effects of Nickel Treatment on H3K4 Trimethylation and Gene Expression
Tchou-Wong, Kam-Meng; Kiok, Kathrin; Tang, Zuojian; Kluz, Thomas; Arita, Adriana; Smith, Phillip R; Brown, Stuart; Costa, Max
2011 ;6(3):e17728-e17728, PLoS ONE
Occupational exposure to nickel compounds has been associated with lung and nasal cancers. We have previously shown that exposure of the human lung adenocarcinoma A549 cells to NiCl(2) for 24 hr significantly increased global levels of trimethylated H3K4 (H3K4me3), a transcriptional activating mark that maps to the promoters of transcribed genes. To further understand the potential epigenetic mechanism(s) underlying nickel carcinogenesis, we performed genome-wide mapping of H3K4me3 by chromatin immunoprecipitation and direct genome sequencing (ChIP-seq) and correlated with transcriptome genome-wide mapping of RNA transcripts by massive parallel sequencing of cDNA (RNA-seq). The effect of NiCl(2) treatment on H3K4me3 peaks within 5,000 bp of transcription start sites (TSSs) on a set of genes highly induced by nickel in both A549 cells and human peripheral blood mononuclear cells were analyzed. Nickel exposure increased the level of H3K4 trimethylation in both the promoters and coding regions of several genes including CA9 and NDRG1 that were increased in expression in A549 cells. We have also compared the extent of the H3K4 trimethylation in the absence and presence of formaldehyde crosslinking and observed that crosslinking of chromatin was required to observe H3K4 trimethylation in the coding regions immediately downstream of TSSs of some nickel-induced genes including ADM and IGFBP3. This is the first genome-wide mapping of trimethylated H3K4 in the promoter and coding regions of genes induced after exposure to NiCl(2). This study may provide insights into the epigenetic mechanism(s) underlying the carcinogenicity of nickel compounds
— id: 130306, year: 2011, vol: 6, page: e17728, stat: Journal Article,

Constitutive mTORC1 activation by a herpesvirus Akt surrogate stimulates mRNA translation and viral replication
Chuluunbaatar, Uyanga; Roller, Richard; Feldman, Morris E; Brown, Stuart; Shokat, Kevan M; Mohr, Ian
2010 Dec 1;24(23):2627-2639, Genes & development
All viruses require cellular ribosomes to translate their mRNAs. Viruses producing methyl-7 (m(7)) GTP-capped mRNAs, like Herpes Simplex Virus-1 (HSV-1), stimulate cap-dependent translation by activating mTORC1 to inhibit the translational repressor 4E-binding protein 1 (4E-BP1). Here, we establish that the HSV-1 kinase Us3 masquerades as Akt to activate mTORC1. Remarkably, Us3 displays no sequence homology with the cellular kinase Akt, yet directly phosphorylates tuberous sclerosis complex 2 (TSC2) on the same sites as Akt. TSC2 depletion rescued Us3-deficient virus replication, establishing that Us3 enhances replication by phosphorylating TSC2 to constitutively activate mTORC1, effectively bypassing S6K-mediated feedback inhibition. Moreover, Us3 stimulated Akt substrate phosphorylation in infected cells, including FOXO1 and GSK3. Thus, HSV-1 encodes an Akt surrogate with overlapping substrate specificity to activate mTORC1, stimulating translation and virus replication. This establishes Us3 as a unique viral kinase with promising drug development potential
— id: 114863, year: 2010, vol: 24, page: 2627, stat: Journal Article,

Diversity of 16S rRNA genes within individual prokaryotic genomes
Pei, Anna Y; Oberdorf, William E; Nossa, Carlos W; Agarwal, Ankush; Chokshi, Pooja; Gerz, Erika A; Jin, Zhida; Lee, Peng; Yang, Liying; Poles, Michael; Brown, Stuart M; Sotero, Steven; Desantis, Todd; Brodie, Eoin; Nelson, Karen; Pei, Zhiheng
2010 Jun;76(12):3886-3897, Applied & environmental microbiology
Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 +/- 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% +/- 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2 degrees structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in 'Candidatus Protochlamydia amoebophila.' Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases
— id: 133520, year: 2010, vol: 76, page: 3886, stat: Journal Article,

Targeted deletion of the genes encoding NTH1 and NEIL1 DNA N-glycosylases reveals the existence of novel carcinogenic oxidative damage to DNA
Chan, Michael K; Ocampo-Hafalla, Maria T; Vartanian, Vladimir; Jaruga, Pawel; Kirkali, Guldal; Koenig, Karen L; Brown, Stuart; Lloyd, R Stephen; Dizdaroglu, Miral; Teebor, George W
2009 Jul 4;8(7):786-794, DNA repair (Amsterdam)
We have generated a strain of mice lacking two DNA N-glycosylases of base excision repair (BER), NTH1 and NEIL1, homologs of bacterial Nth (endonuclease three) and Nei (endonuclease eight). Although these enzymes remove several oxidized bases from DNA, they do not remove the well-known carcinogenic oxidation product of guanine: 7,8-dihydro-8-oxoguanine (8-OH-Gua), which is removed by another DNA N-glycosylase, OGG1. The Nth1(-/-)Neil1(-/-) mice developed pulmonary and hepatocellular tumors in much higher incidence than either of the single knockouts, Nth1(-/-) and Neil1(-/-). The pulmonary tumors contained, exclusively, activating GGT-->GAT transitions in codon 12 of K-ras of their DNA. Such transitions contrast sharply with the activating GGT-->GTT transversions in codon 12 of K-ras of the pathologically similar pulmonary tumors, which arose in mice lacking OGG1 and a second DNA N-glycosylase, MUTY. To characterize the biochemical phenotype of the knockout mice, the content of oxidative DNA base damage was analyzed from three tissues isolated from control, single and double knockout mice. The content of 8-OH-Gua was indistinguishable among all genotypes. In contrast, the content of 4,6-diamino-5-formamidopyrimidine (FapyAde) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyGua) derived from adenine and guanine, respectively, were increased in some but not all tissues of Neil1(-/-) and Neil1(-/-)Nth1(-/-) mice. The high incidence of tumors in our Nth1(-/-)Neil1(-/-) mice together with the nature of the activating mutation in the K-ras gene of their pulmonary tumors, reveal for the first time, the existence of mutagenic and carcinogenic oxidative damage to DNA which is not 8-OH-Gua
— id: 100475, year: 2009, vol: 8, page: 786, stat: Journal Article,

Geographic population structure of the immune evasion (var) genes of Plasmodium falciparum
Barry, AE; Smith, TA; Chen, D; Sytek, AL; Imrie, H; Tavul, L; Migot-Nabias, F; Brown, SM; Deloron, P; Daily, J; Marsh, K; McVean, G; Day, KP
2008 JAN ;38(1):S38-S39, International journal for parasitology
— id: 76166, year: 2008, vol: 38, page: S38, stat: Journal Article,

Gene expression profiles of bronchoalveolar cells in pulmonary TB
Raju, Bindu; Hoshino, Yoshihiko; Belitskaya-Levy, Ilana; Dawson, Rod; Ress, Stanley; Gold, Jeffrey A; Condos, Rany; Pine, Richard; Brown, Stuart; Nolan, Anna; Rom, William N; Weiden, Michael D
2008 Jan;88(1):39-51, Tuberculosis (Edinburgh, Scotland)
The host response to Mycobacterium tuberculosis includes macrophage activation, inflammation with increased immune effector cells, tissue necrosis, and cavity formation, and fibrosis, distortion, and bronchiectasis. To evaluate the molecular basis of the immune response in the lungs of patients with active pulmonary tuberculosis (TB), we used bronchoalveolar lavage to obtain cells at the site of infection. Affymetrix GeneChip microarrays and cDNA nylon filter microarrays interrogated gene expression in bronchoalveolar lavage (BAL) cells from 11 healthy controls and 17 patients with active pulmonary TB. We found altered gene expression for 69 genes in TB versus normal controls that included cell surface markers, cytokines, chemokines, receptors, transcription factors, and complement components. In addition, TB BAL cell gene expression patterns segregated into 2 groups: one suggestive of a T helper type 1 (Th1) cellular immune response with increased signal transducer and activator of transcription-4 (STAT-4), interferon-gamma (IFN-gamma receptor), and monokine induced by IFN-gamma (MIG) expression with increased IFN-gamma protein levels in BAL fluid; the other group displayed characteristics of Th2 immunity with increased STAT-6, CD81, and IL-10 receptor expression. We were able to demonstrate that a Th2 presentation could change to a Th1 pattern after anti-tuberculous treatment in 1 TB patient studied serially. These gene expression data support the conclusion that pulmonary TB produces a global change in the BAL cell transcriptome with manifestations of either Th1 or Th2 immunity
— id: 74211, year: 2008, vol: 88, page: 39, stat: Journal Article,

Genetic classification of severe early childhood caries by use of subtracted DNA fragments from Streptococcus mutans
Saxena, Deepak; Caufield, Page W; Li, Yihong; Brown, Stuart; Song, Jinmei; Norman, Robert
2008 Sep;46(9):2868-2873, Journal of clinical microbiology
Streptococcus mutans is one of several members of the oral indigenous biota linked with severe early childhood caries (S-ECC). Because most humans harbor S. mutans, but not all manifest disease, it has been proposed that the strains of S. mutans associated with S-ECC are genetically distinct from those found in caries-free (CF) children. The objective of this study was to identify common DNA fragments from S. mutans present in S-ECC but not in CF children. Using suppressive subtractive hybridization, we found a number of DNA fragments (biomarkers) present in 88 to 95% of the S-ECC S. mutans strains but not in CF S. mutans strains. We then applied machine learning techniques including support vector machines and neural networks to identify the biomarkers with the most predictive power for disease status, achieving a 92% accurate classification of the strains as either S-ECC or CF associated. The presence of these gene fragments in 90 to 100% of the 26 S-ECC isolates tested suggested their possible functional role in the pathogenesis of S. mutans associated with dental caries
— id: 91090, year: 2008, vol: 46, page: 2868, stat: Journal Article,

Population genomics of the immune evasion (var) genes of Plasmodium falciparum
Barry, Alyssa E; Leliwa-Sytek, Aleksandra; Tavul, Livingston; Imrie, Heather; Migot-Nabias, Florence; Brown, Stuart M; McVean, Gilean A V; Day, Karen P
2007 Mar;3(3):e34-e34, PLoS pathogens
Var genes encode the major surface antigen (PfEMP1) of the blood stages of the human malaria parasite Plasmodium falciparum. Differential expression of up to 60 diverse var genes in each parasite genome underlies immune evasion. We compared the diversity of the DBLalpha domain of var genes sampled from 30 parasite isolates from a malaria endemic area of Papua New Guinea (PNG) and 59 from widespread geographic origins (global). Overall, we obtained over 8,000 quality-controlled DBLalpha sequences. Within our sampling frame, the global population had a total of 895 distinct DBLalpha 'types' and negligible overlap among repertoires. This indicated that var gene diversity on a global scale is so immense that many genomes would need to be sequenced to capture its true extent. In contrast, we found a much lower diversity in PNG of 185 DBLalpha types, with an average of approximately 7% overlap among repertoires. While we identify marked geographic structuring, nearly 40% of types identified in PNG were also found in samples from different countries showing a cosmopolitan distribution for much of the diversity. We also present evidence to suggest that recombination plays a key role in maintaining the unprecedented levels of polymorphism found in these immune evasion genes. This population genomic framework provides a cost effective molecular epidemiological tool to rapidly explore the geographic diversity of var genes
— id: 96299, year: 2007, vol: 3, page: e34, stat: Journal Article,

TBLR1 regulates the expression of nuclear hormone receptor co-repressors
Zhang, Xin-Min; Chang, Qing; Zeng, Lin; Gu, Judy; Brown, Stuart; Basch, Ross S
2006 ;7:31-31, BMC Cell Biology
BACKGROUND: Transcription is regulated by a complex interaction of activators and repressors. The effectors of repression are large multimeric complexes which contain both the repressor proteins that bind to transcription factors and a number of co-repressors that actually mediate transcriptional silencing either by inhibiting the basal transcription machinery or by recruiting chromatin-modifying enzymes. RESULTS: TBLR1 [GenBank: NM024665] is a co-repressor of nuclear hormone transcription factors. A single highly conserved gene encodes a small family of protein molecules. Different isoforms are produced by differential exon utilization. Although the ORF of the predominant form contains only 1545 bp, the human gene occupies approximately 200 kb of genomic DNA on chromosome 3q and contains 16 exons. The genomic sequence overlaps with the putative DC42 [GenBank: NM030921] locus. The murine homologue is structurally similar and is also located on Chromosome 3. TBLR1 is closely related (79% homology at the mRNA level) to TBL1X and TBL1Y, which are located on Chromosomes X and Y. The expression of TBLR1 overlaps but is distinct from that of TBL1. An alternatively spliced form of TBLR1 has been demonstrated in human material and it too has an unique pattern of expression. TBLR1 and the homologous genes interact with proteins that regulate the nuclear hormone receptor family of transcription factors. In resting cells TBLR1 is primarily cytoplasmic but after perturbation the protein translocates to the nucleus. TBLR1 co-precipitates with SMRT, a co-repressor of nuclear hormone receptors, and co-precipitates in complexes immunoprecipitated by antiserum to HDAC3. Cells engineered to over express either TBLR1 or N- and C-terminal deletion variants, have elevated levels of endogenous N-CoR. Co-transfection of TBLR1 and SMRT results in increased expression of SMRT. This co-repressor undergoes ubiquitin-mediated degradation and we suggest that the stabilization of the co-repressors by TBLR1 occurs because of a novel mechanism that protects them from degradation. Transient over expression of TBLR1 produces growth arrest. CONCLUSION: TBLR1 is a multifunctional co-repressor of transcription. The structure of this family of molecules is highly conserved and closely related co-repressors have been found in all eukaryotic organisms. Regulation of co-repressor expression and the consequent alterations in transcriptional silencing play an important role in the regulation of differentiation
— id: 68630, year: 2006, vol: 7, page: 31, stat: Journal Article,

Selection and validation of differentially expressed genes in head and neck cancer
Kuriakose, M A; Chen, W T; He, Z M; Sikora, A G; Zhang, P; Zhang, Z Y; Qiu, W L; Hsu, D F; McMunn-Coffran, C; Brown, S M; Elango, E M; Delacure, M D; Chen, F A
2004 Jun;61(11):1372-1383, Cellular & molecular life sciences: CMLS
We applied a robust combinatorial (multi-test) approach to microarray data to identify genes consistently up- or down-regulated in head and neck squamous cell carcinoma (HNSCC). RNA was extracted from 22 paired samples of HNSCC and normal tissue from the same donors and hybridized to the Affymetrix U95A chip. Forty-two differentially expressed probe sets (representing 38 genes and one expressed sequence tag) satisfied all statistical tests of significance and were selected for further validation. Selected probe sets were validated by hierarchical clustering, multiple probe set concordance, and target-subunit agreement. In addition, real-time PCR analysis of 8 representative (randomly selected from 38) genes performed on both microarray-tested and independently obtained samples correlated well with the microarray data. The genes identified and validated by this method were in comparatively good agreement with other rigorous HNSCC microarray studies. From this study, we conclude that combinatorial analysis of microarray data is a promising technique for identifying differentially expressed genes with few false positives
— id: 44893, year: 2004, vol: 61, page: 1372, stat: Journal Article,

Aerosolized gamma interferon (IFN-gamma) induces expression of the genes encoding the IFN-gamma-inducible 10-kilodalton protein but not inducible nitric oxide synthase in the lung during tuberculosis
Raju, Bindu; Hoshino, Yoshihiko; Kuwabara, Kenichi; Belitskaya, Ilana; Prabhakar, Savita; Canova, Antony; Gold, Jeffrey A; Condos, Rany; Pine, Richard I; Brown, Stuart; Rom, William N; Weiden, Michael D
2004 Mar;72(3):1275-1283, Infection & immunity
Gamma interferon (IFN-gamma) is critical in the immune response against Mycobacterium tuberculosis. In an ongoing trial of aerosol IFN-gamma in conjunction with standard drug therapy, we have observed activation of IFN signaling in bronchoalveolar lavage (BAL) cells from tuberculosis (TB) patients. We hypothesized that aerosol IFN-gamma treatment of pulmonary TB would increase expression of genes important for the control of TB. We investigated the expression of downstream genes by measuring inducible nitric oxide synthase (iNOS) and the chemokine IFN-inducible 10-kDa protein (IP-10) by real-time quantitative reverse transcription-PCR. In vitro, M. tuberculosis induced IP-10, and IFN-gamma stimulated this further, with no effect on iNOS expression. We studied 21 patients with pulmonary TB and 7 healthy subjects. Similar to the in vitro model, IP-10 mRNA was increased in BAL cells from TB patients and was augmented after treatment with aerosolized IFN-gamma. TB was also associated with elevated iNOS mRNA, but aerosolized IFN-gamma did not further enhance expression. Genomic analysis identified 1,300 of 4,058 genes expressed in BAL cells from six TB patients before and after 1 month of therapy, including aerosolized IFN-gamma. However, only 15 genes were differentially regulated by IFN-gamma. We conclude that iNOS and IP-10 mRNA expression is increased in TB but that aerosol IFN-gamma treatment increases expression of few genes in the human lung
— id: 42241, year: 2004, vol: 72, page: 1275, stat: Journal Article,

Transcriptome of axenic liver stages of Plasmodium yoelii
Wang, Qian; Brown, Stuart; Roos, David S; Nussenzweig, Victor; Bhanot, Purnima
2004 Sep;137(1):161-168, Molecular & biochemical parasitology
Plasmodium liver stages or early exo-eythrocytic forms (EEFs) contain antigens that are essential for achieving sterile, protective immunity against malaria. Yet, attempts at identifying these antigens have been hampered by the challenge of obtaining large numbers of purified EEFs, uncontaminated with hepatocyte material. Using a recently described system for producing axenically cultured EEFs from Plasmodium yoelii, we have constructed a cDNA library and generated 1453 expressed sequence tags (ESTs) resulting in 652 unique transcripts. Analysis of the library provides insight into processes required for the initiation and development of Plasmodium liver stages, such as protein degradation, cell cycle progression and nutrient transport. Analysis of the gene expression profile of liver stages, as revealed by this library, suggests that liver stages represent a shift from 'sporozoite-like' to 'blood-stage-like'. This is the first study of the transcriptional repertoire of Plasmodium liver stages
— id: 48869, year: 2004, vol: 137, page: 161, stat: Journal Article,

Bioinformatics becomes respectable
Brown, Stuart M
2003 Jun;34(6):1124-1127, Biotechniques
— id: 39192, year: 2003, vol: 34, page: 1124, stat: Journal Article,

Essentials of medical genomics
Brown, Stuart M; Hay, John G; Ostrer, Harry
Hoboken NJ : Wiley-Liss, 2003,
— id: 899, year: 2003, vol: , page: , stat: ,

Infectivity-associated changes in the transcriptional repertoire of the malaria parasite sporozoite stage
Matuschewski, Kai; Ross, Jessica; Brown, Stuart M; Kaiser, Karine; Nussenzweig, Victor; Kappe, Stefan H I
2002 Nov 1;277(44):41948-41953, Journal of biological chemistry
Injection of Plasmodium salivary gland sporozoites into the vertebrate host by Anopheles mosquitoes initiates malaria infection. Sporozoites develop within oocysts in the mosquito midgut and then enter and mature in the salivary glands. Although morphologically similar, oocyst sporozoites and salivary gland sporozoites differ strikingly in their infectivity to the mammalian host, ability to elicit protective immune responses, and cell motility. Here, we show that differential gene expression coincides with these dramatic phenotypic differences. Using suppression subtractive cDNA hybridization we identified highly up-regulated mRNAs transcribed from 30 distinct genes in salivary gland sporozoites. Of those genes, 29 are not significantly expressed in the parasite's blood stages. The most frequently recovered transcript encodes a protein kinase. Developmental up-regulation of specific mRNAs in the infectious transmission stage of Plasmodium indicates that their translation products may have unique roles in hepatocyte infection and/or development of liver stages
— id: 39415, year: 2002, vol: 277, page: 41948, stat: Journal Article,

Genomics-based identification of self-ligands with T cell receptor-specific biological activity
Santori, Fabio R; Brown, Stuart M; Vukmanovic, Stanislav
2002 Dec;190(4):146-160, Immunological reviews
Self-peptide/major histocompatibility complex (MHC) complexes profoundly influence the biology of T lymphocytes. They promote the selection of the T cell receptor (TCR) repertoire in the thymus, maintain the homeostasis of peripheral T cells prior to encounter with antigen, and modify the responsiveness of T cells to foreign antigens. In addition, they can serve as antigens for autoaggressive T cells that induce autoimmune diseases. The complete sequencing of the genomes of human, mouse, and many pathogenic organisms now provides us with a comprehensive list of all possible proteins that may be the source of foreign antigenic and self-peptides. A computational approach using profile-based similarity searches on potential self-MHC-binding peptides can be used to efficiently predict self-peptides with biological activities. The common feature of the identified peptides is similarity to antigen. Thus, self-peptides may form 'hazy' images of the universe of antigens that are used as templates to create and maintain the TCR repertoire
— id: 34692, year: 2002, vol: 190, page: 146, stat: Journal Article,

Rare, structurally homologous self-peptides promote thymocyte positive selection
Santori, Fabio R; Kieper, William C; Brown, Stuart M; Lu, Yun; Neubert, Thomas A; Johnson, Kenneth L; Naylor, Stephen; Vukmanovic, Stanislav; Hogquist, Kristin A; Jameson, Stephen C
2002 Aug;17(2):131-142, Immunity
Although it is clear that positive selection of T cells involves recognition of specific self-peptide/MHC complexes, the nature of these self-ligands and their relationship to the cognate antigen are controversial. Here we used two complementary strategies to identify naturally occurring self-peptides able to induce positive selection of T cells bearing a specific T cell receptor, OT-I. Both the bioassay- and bioinformatics-based strategies identified the same self-peptides, derived from F-actin capping protein and beta-catenin. These peptides displayed charge conservation at two key TCR contact residues. The biological activity of 43 other self-peptides and of complex peptide libraries directly correlated to the extent of conservation at TCR contact residues. These results demonstrate that selecting self-peptides are rare and can be identified by homology-based search strategies
— id: 32496, year: 2002, vol: 17, page: 131, stat: Journal Article,

Definitive Identification of Mammalian 5-Hydroxymethyluracil DNA N-Glycosylase Activity as SMUG1
Boorstein RJ; Cummings A Jr; Marenstein DR; Chan MK; Ma Y; Neubert TA; Brown SM; Teebor GW
2001 Nov 9;276(45):41991-41997, Journal of biological chemistry
Purification from calf thymus of a DNA N-glycosylase activity (HMUDG) that released 5-hydroxymethyluracil (5hmUra) from the DNA of Bacillus subtilis phage SPO1 was undertaken. Analysis of the most purified fraction by SDS-polyacrylamide gel electrophoresis revealed a multiplicity of protein species making it impossible to identify HMUDG by inspection. Therefore, we renatured the enzyme after SDS-polyacrylamide gel electrophoresis and assayed slices of the gel for DNA N-glycosylase activity directed against 5hmUra. Maximum enzymatic activity was identified between molecular mass markers 30 and 34 kDa. Protein was extracted from gel slices and subjected to tryptic digestion and analysis by mass spectrometry. Analysis revealed the presence of 11 peptides that were homologous or identical to the sequence of the recently characterized human single-stranded monofunctional uracil DNA N-glycosylase (hSMUG1). The cDNA of hSMUG1 was isolated and expressed as a recombinant glutathione S-transferase fusion protein that was shown to release 5hmUra with 20x the specific activity of the most purified bovine fraction. We conclude that hSMUG1 and HMUDG are the same protein
— id: 23928, year: 2001, vol: 276, page: 41991, stat: Journal Article,

Exploring the transcriptome of the malaria sporozoite stage
Kappe SH; Gardner MJ; Brown SM; Ross J; Matuschewski K; Ribeiro JM; Adams JH; Quackenbush J; Cho J; Carucci DJ; Hoffman SL; Nussenzweig V
2001 Aug 14;98(17):9895-9900, Proceedings of the National Academy of Sciences of the United States of America
Most studies of gene expression in Plasmodium have been concerned with asexual and/or sexual erythrocytic stages. Identification and cloning of genes expressed in the preerythrocytic stages lag far behind. We have constructed a high quality cDNA library of the Plasmodium sporozoite stage by using the rodent malaria parasite P. yoelii, an important model for malaria vaccine development. The technical obstacles associated with limited amounts of RNA material were overcome by PCR-amplifying the transcriptome before cloning. Contamination with mosquito RNA was negligible. Generation of 1,972 expressed sequence tags (EST) resulted in a total of 1,547 unique sequences, allowing insight into sporozoite gene expression. The circumsporozoite protein (CS) and the sporozoite surface protein 2 (SSP2) are well represented in the data set. A BLASTX search with all tags of the nonredundant protein database gave only 161 unique significant matches (P(N) < or = 10(-4)), whereas 1,386 of the unique sequences represented novel sporozoite-expressed genes. We identified ESTs for three proteins that may be involved in host cell invasion and documented their expression in sporozoites. These data should facilitate our understanding of the preerythrocytic Plasmodium life cycle stages and the development of preerythrocytic vaccines
— id: 25508, year: 2001, vol: 98, page: 9895, stat: Journal Article,

Cutting Edge: Positive Selection Induced by a Self-Peptide with TCR Antagonist Activity
Santori FR; Brown SM; Lu Y; Neubert TA; Vukmanovic S
2001 Dec 1;167(11):6092-6095, Journal of immunology
Antagonist-like engagement of the TCR has been proposed to induce T cell selection in the thymus. However, no natural TCR ligand with TCR antagonist activity is presently known. Using a combination of bioinformatics and functional testing we identified the first self-peptide that can both deliver antagonist-like signals and promote T cell selection in the thymus. The peptide is presented by appropriate MHC class I molecules in vivo. Thus, endogenous antagonist peptides exist and may be involved in TCR repertoire selection
— id: 23925, year: 2001, vol: 167, page: 6092, stat: Journal Article,

Squamous cell carcinoma of the nail bed: is finger predominance another clue to etiology? A report of 5 cases
Zabawski, E J Jr; Washak, R V; Cohen, J B; Cockerell, C J; Brown, S M
2001 Jan;67(1):59-64, Cutis
Although squamous cell carcinoma (SCC) is commonly found on sun-exposed skin, the occurrence of this malignancy in the nail bed is rare. We report 5 cases of SCC of the nail bed and suggest that the disproportionate number of neoplasms of this type on the second, third, and fourth fingers, combined with the known relationship of SCC and human papillomavirus (HPV), is evidence that most SCC of the nail bed result from contact with HPV. Moreover, we suggest that patients who present with new, verrucous lesions of the nail bed and have a history of cervical dysplasia, cervical carcinoma, or condyloma acuminata undergo diagnostic biopsy as opposed to traditional destructive therapy for a lesion presumed benign
— id: 123719, year: 2001, vol: 67, page: 59, stat: Journal Article,

Get your bioinformatics on the Web!
Brown SM
2000 Feb;28(2):244-246, Biotechniques
— id: 11829, year: 2000, vol: 28, page: 244, stat: Journal Article,

Be alert: free sequence alerting services
Brown, S M
2000 Dec;29(6):1210-1212, Biotechniques
— id: 111700, year: 2000, vol: 29, page: 1210, stat: Journal Article,

Dealing with Genome Project data
Brown SM
1999 ;26(2):266-26?, Biotechniques
— id: 8125, year: 1999, vol: 26, page: 266, stat: Journal Article,

Phylogenetics on the Web
Brown SM
1999 Dec;27(6):1146-1148, Biotechniques
— id: 11869, year: 1999, vol: 27, page: 1146, stat: Journal Article,

Snapping up SNPs
Brown SM
1999 Jun;26(6):1090-1093, Biotechniques
— id: 6141, year: 1999, vol: 26, page: 1090, stat: Journal Article,

Analyzing protein families and domains on the Web
Brown SM
1998 Oct;25(4):596-598, Biotechniques
— id: 7307, year: 1998, vol: 25, page: 596, stat: Journal Article,

Sequence similarity searches on the World Wide Web
Brown SM
1998 Feb;24(2):248-250, Biotechniques
— id: 7514, year: 1998, vol: 24, page: 248, stat: Journal Article,

Advanced similarity searches on the Web: Gapped BLAST, PSI-BLAST, FASTA 3.0 and INCA
Brown, SM
1998 AUG ;25(2):214-+, Biotechniques
— id: 53395, year: 1998, vol: 25, page: 214, stat: Journal Article,

Sequence alignment on the Web
Brown, SM
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Biologists and mathematicians: bridging the chasm
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