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Results for “second generation sequencing”

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PubMed2004

A single-LTR HIV-1 vector optimized for functional genomics applications.

The development of high-throughput methods of converting simple expression cassettes into lentiviral vectors and expediting the process of retrieving vector genomes that carry candidate genes from host DNA will facilitate the use of lentiviral vectors as an efficient means of screening novel gene function. To optimize lentiviral vectors for functional genomic applications we have developed a shuttle HIV-1 vector containing a single LTR. Incorporation of a LoxP site and the Sbfl restriction enzyme site into the vector LTR allowed for the rescue of integrated vector genomes into individual bacterial clones. Vector DNA isolated from bacteria was used for a second round of functional screening. Furthermore, we identified a continuous DNA sequence containing all the cis elements required for vector production. Incorporating the isolated sequence into expression cassettes resulted in the generation of HIV-1 vectors in a single cloning step, which imparts a simplified procedure for converting cDNA expression cassettes into single-LTR lentiviral vectors.

Base Sequence↗

PubMed2005

Transcriptional co-operativity between distant retinoic acid response elements in regulation of Cyp26A1 inducibility.

Cyp26A1 encodes an RA (retinoic acid)-catabolizing CYP (cytochrome P450) protein that plays a critical role in regulating RA distribution in vivo. Cyp26A1 expression is inducible by RA, and the locus has previously been shown to contain a RARE (RA response element), R1, within the minimal promoter [Loudig, Babichuk, White, Abu-Abed, Mueller and Petkovich (2000) Mol. Endocrinol. 14, 1483-1497]. In the present study, we report the identification of a second functional RARE (R2) located 2.0 kb upstream of the Cyp26A1 transcriptional start site. Constructs containing murine sequences encompassing both R1 and R2 showed that these elements work together to generate higher transcriptional activity upon treatment with RA than those containing R1 alone. Inclusion of R2 also dramatically enhanced the sensitivity of reporter constructs to RA, as even treatment with 10(-8) M RA resulted in a 5-fold induction of reporter activity. Mutational analysis identified R2 as the functional element responsible for the increased RA inducibility of promoter constructs. The element was shown to bind RARgamma (RA receptor gamma)/RXRalpha (retinoid X receptor alpha) heterodimers in vitro, and inclusion of nuclear receptors in transfections boosted the transcriptional response. A construct containing both R1 and R2 was used to generate a stable luciferase reporter cell line that can be used as a tool to identify factors regulating Cyp26A1 expression. The analysis of R1 and R2 has led to the proposal that the two elements work synergistically to provide a maximal response to RA and that R2 is an upstream enhancer.

Animals↗

PubMed2001

In vivo suppression of Bcl-XL expression facilitates chemotherapy-induced leukaemia cell death in a SCID/NOD-Hu model.

Bcl-XL, a member of the Bcl-2-related anti-apoptosis protein family, antagonizes a diverse range of apoptosis-inducing stimuli by preventing mitochondrial permeability transition, release of apoptogenic factors including cytochrome C, and caspase activation. We have tested the hypothesis that the susceptibility of Bcl-XL-expressing leukaemic cells to apoptosis induced by VP16 (etoposide) can be enhanced by pharmacological downregulation of Bcl-XL in vivo. Two subcutaneous xenograft models of B-cell leukaemia-employing SEMK-2 and BV173 cell lines were established in severe combined immunodeficient/non-obese diabetic mice followed by 14 d of continuous subcutaneous administration of Bcl-XL-specific second generation oligonucleotides ISIS 16009 or ISIS 15999. Tumours were disaggregated, enabling investigation of Bcl-XL expression and apoptosis susceptibility at single-cell resolution using cytofluorimetry. Marked sequence-specific reduction of Bcl-XL was associated with sequence-specific enhancement of VP16-induced mitochondrial permeability transition, caspase-3 activation and loss of membrane asymmetry. A negative correlation between Bcl-XL expression and apoptosis susceptibility was observed, together with a positive correlation with respect to a reduced redox state. Bcl-XL downregulation reduces the threshold for VP16-induced apoptosis by potentiating mitochondrial dysfunction and its sequelae, and therefore presents a novel therapeutic strategy for reversing chemoresistance.

Animals↗

PubMed1996

Fluorescence detection of symmetric GroEL14(GroES7)2 heterooligomers involved in protein release during the chaperonin cycle.

The GroEL14 chaperonin from Escherichia coli was labeled with 5-((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid (I-AEDANS), a hydrophobic probe whose fluorescent emission is sensitive to structural changes within the protein. Increasing concentrations of ATP or adenylyl imidodiphosphate but not ADP caused two successive GroES7-dependent changes in the fluorescence intensity of AEDANS-GroEL14, corresponding to the sequential binding of two GroES7 heptamers and the formation of two types of chaperonin heterooligomers, GroEL14GroES7 and GroEL14(GroES7)2. The binding of thermally denatured malate dehydrogenase (MDH) caused a specific increase in fluorescence intensity of AEDANS-GroEL14 that allowed the direct measurement in solution at equilibrium of ATP- and GroES7-dependent protein release from the chaperonin. Structure/function analysis during the generation of ATP from ADP indicated the following sequence of events: 1) ADP-stabilized MDH-GroEL14GroES7 particles bind newly formed ATP. 2) MDH-GroEL14GroES7 particles bind a second GroES7. 3) MDH-GroEL14(GroES7)2 particles productively release MDH. 4) Released MDH completes folding. Therefore, the symmetrical GroEL14(GroES7)2 heterooligomer is an intermediate after the formation of which the protein substrate is productively released during the chaperonin-mediated protein folding cycle.

Adenosine Diphosphate↗

PubMed1994

Reagents for the preparation of two oligonucleotides per synthesis (TOPS).

In order to increase the efficiency of use of automated DNA synthesizers (i.e. the number of oligomers prepared per day), we have devised and prepared novel phosphoramidite reagents that contain a linking group which, while stable under the normal synthesis conditions, is cleaved under basic conditions. When one of these linkers is introduced at the desired position in the synthesis of an oligonucleotide, subsequent detritylation enables the synthesis of a second oligonucleotides sequence upon the first. During deprotection of the oligonucleotide with ammonium hydroxide, the chain is cleaved at either side of the points of introduction of the novel reagent, generating two oligonucleotides free in solution. These reagents are of particular use in applications where oligomers are used in pairs (such as PCR, chemical synthesis of genes etc.) and means that an automated synthesis facility can be used more efficiently, without the need for operator intervention, after the working day is over.

Amides↗

PubMed2006

Towards second-generation proteome analysis of murine enamel-forming cells.

Proteome analysis of rat enamel-forming cells, initiated over a decade ago, has provided valuable insights to enamel biology. In preparation for a more comprehensive, second-generation proteomic exploration, we evaluated an updated microsample-profiling strategy that comprises sequential extraction of enamel epithelium, parallel one- and two-dimensional gel electrophoresis, and mass spectrometric sequence analysis. The results indicated that several hundred proteins, representing various cellular compartments (including membranes), are amenable to identification with a starting tissue volume of <10 microl. With its increased proteomic depth and breadth, this straightforward approach constitutes a major advance from the first-generation work (10-fold increased proteome coverage), although care was needed to ensure a comparably high stringency of protein identification. Expression proteomics has an exciting potential to elucidate the inner workings of murine enamel epithelial cells, leading to an improved understanding of enamel in health and disease.

Ameloblasts↗

PubMed1999

H-K-ATPase in the RCCT-28A rabbit cortical collecting duct cell line.

In the present study, we demonstrate that the rabbit cortical collecting duct cell line RCCT-28A possesses three distinct H-K-ATPase catalytic subunits (HKalpha). Intracellular measurements of RCCT-28A cells using the pH-sensitive dye 2', 7'-bis(2-carboxyethyl)-5(6)-carboxyfluorescein (BCECF) indicated that the mechanism accounting for recovery from an acid load exhibited both K+ dependence and sensitivity to Sch-28080 characteristic of H-K-ATPases. Recovery rates were 0.022 +/- 0.005 pH units/min in the presence of K+, 0.004 +/- 0.002 in the absence of K+, and 0.002 +/- 0.002 in the presence of Sch-28080. The mRNAs encoding the HKalpha1 subunit and the H-K-ATPase beta-subunit (HKbeta) were detected by RT-PCR. In addition, two HKalpha2 species were found by RT-PCR and 5' rapid amplification of cDNA ends (5'-RACE) in the rabbit renal cortex. One was homologous to HKalpha2 cDNAs generated from other species, and the second was novel. The latter, referred to as HKalpha2c, encoded an apparent 61-residue amino-terminal extension that bore no homology to reported sequences. Antipeptide antibodies were designed on the basis of this extension, and these antibodies recognized a protein of the appropriate mass in both rabbit renal tissue samples and RCCT-28A cells. Such findings constitute very strong evidence for expression of the HKalpha2c subunit in vivo. The results suggest that the rabbit kidney and RCCT-28A cells express at least three distinct H-K-ATPases.

Animals↗

PubMed2003

Chicken genome sequence: a centennial gift to poultry genetics.

A draft sequence of the chicken genome will be available by early 2004. This event conveniently marks the start of the second century of poultry genetics, coming 100 years after the use of the chicken to demonstrate Mendelian inheritance in animals by William Bateson. How will the second, post-genomic century of poultry genetics differ from the first? A whole genome shotgun (WGS) approach is being used to obtain the chicken sequence, with the goal of generating approximately six-fold coverage of the genome. Bacterial artificial chromosome (BAC) and fosmid clone end sequences, along with a BAC contig map integrated with genetic linkage and radiation hybrid maps, will form the platform for assembly of the WGS data. Rapid progress in global analysis of chicken gene expression patterns is also being made. Comparative genomics will link these new discoveries to the knowledge base for all other animal species. It's hoped that the genome sequence will also provide common ground on which to unite studies of the chicken as a model species with those aimed at agriculturally-relevant applications. The current status of chicken genomics will be assessed with projections for its near and long term future.

Animals↗

PubMed2001

A novel CBFA2 single-nucleotide mutation in familial platelet disorder with propensity to develop myeloid malignancies.

Hereditary mutations associated with hematologic malignancies are rare. Heterozygous mutations affecting the hematopoietic transcription factor CBFA2 (also AML1/RUNX1) were recently reported to be associated with familial platelet disorder with predisposition to acute myeloid leukemia (FPD/AML, MIM 601399). A new 3-generation family with FPD/AML with a novel CBFA2 mutation is described. In this family, AML was diagnosed in a second-generation male. After allogeneic stem cell transplantation from his human leukocyte antigen-identical sister, a donor-derived, genetically identical leukemia developed in the recipient and the donor. Sequencing analysis identified a G-to-T transition within the CBFA2 gene, which involves codon 198, encoding a conserved aspartic acid within the DNA- binding Runt domain. Three of 5 siblings affected with the FPD/AML trait harbored the mutation in a heterozygous form. This experience underscores the necessity of performing mutation analysis of the CBFA2 gene before sibling allogeneic transplantation in families with FPD/AML.

Acute Disease↗

PubMed1999

The effect of age on odor-stimulated functional MR imaging.

BACKGROUND AND PURPOSE: The effects of age, sex, and handedness on olfaction have not been adequately addressed with odor-stimulated functional MR imaging studies. We sought to determine the effect of age on functional MR imaging experiments performed with odor stimulation. METHODS: Five right-handed subjects with a mean age of 73 years and five right-handed subjects with a mean age of 24 years underwent gradient-echo echo-planar functional MR imaging using binasal olfactory stimulation. Imaging parameters included 3000/30 (TR/TE) and a 5-mm section thickness in a 6-minute sequence with 30 seconds of pulsed odorants alternating with 30 seconds of room air. The data were normalized to a standard atlas, and individual and group statistical parametric maps (SPMs) were generated for each task. The SPMs were thresholded for a P < .01, and the volumes of activation and distribution of cluster maxima were compared for the two groups. RESULTS: Analysis of the group SPMs revealed activated voxels in the frontal lobes, perisylvian regions, and cingulate gyri, with greater volume in the younger group than in the older group. The right inferior frontal, right perisylvian, and right and left cingulum had the largest number of voxels activated. The most common sites of activation on individual maps in both groups were the right inferior frontal regions and the right and left superior frontal and perisylvian zones. CONCLUSION: Given similar olfactory task paradigms, younger subjects showed a greater number of activated voxels than did older subjects. One must be cognizant of this effect when designing studies of odor-stimulated functional MR imaging.

Adolescent↗

PubMed1987

Alternative splicing of human p53 transcripts.

The human p53 gene is expressed in both normal and transformed human cells as a family of polypeptides. One type of heterogeneity, which results in variation in electrophoretic mobility, is found at amino acid residue 72 (Matlashewski et al, 1987). A second type of heterogeneity is described here which involves an alteration in the sequence of the open reading frame at the 5' end of the p53 mRNA. This heterogeneity is generated by alternative splicing at the acceptor site in intron 2 resulting in an altered 5' end coding region. This study represents the first description of an altered human p53 transcript arising by differential splicing.

Amino Acid Sequence↗

PubMed1988

Molecular cloning of the cDNA which encodes beta-N-acetylhexosaminidase A from Dictyostelium discoideum. Complete amino acid sequence and homology with the human enzyme.

beta-N-Acetylhexosaminidase A (EC 3.2.1.52), the product of the nag A gene, is a lysosomal enzyme which is developmentally regulated in Dictyostelium discoideum. The enzyme plays a role during the slug stage of development in the maintenance of pseudoplasmodia of normal size. We used a homogeneous preparation of deglycosylated enzyme subunits to generate antibody. The antibody was suitable for screening a lambda gt11 cDNA expression library derived from the mRNA of late log stage axenic cells. We isolated seven positive clones. One of these contains the complete coding sequence of the protein. We also isolated a genomic clone which contains 800 base pairs of 5'-flanking sequence and 728 base pairs of coding sequence. Analysis of the sequences and of primer extension studies indicates an inferred transcript size of 1665 bases which closely matches the 1.8-kilobase mRNA size estimated by Northern blot analysis of poly(A+) mRNA from the organism. The sequence contains an open reading frame which encodes a protein of 59,787 kDa. This equals the apparent molecular weight in sodium dodecyl sulfate-polyacrylamide gels of in vitro translated enzyme. The amino terminus of the purified enzyme appeared to be blocked, but internal peptide sequences were obtained by automated Edman degradation of gel-purified peptides generated by treatment of protein subunits with staphylococcal V-8 protease. These sequences are included in the inferred sequence. In addition to a typical signal sequence, the open reading frame encodes a second candidate transmembrane region, a serine-rich region, and four potential N-glycosylation sites. These are discussed with regard to the localization and processing of the enzyme during its biogenesis. Beginning at amino acid 100 of the Dictyostelium enzyme sequence, 36% of its amino acids are identical to the corresponding sequence of the beta chain, and 33% are identical with those of the alpha chain of human beta-N-acetylhexosaminidase. This is strong evidence that the Dictyostelium enzyme is homologous to the alpha and beta chains of the human enzyme.

Amino Acid Sequence↗

PubMed1988

The invariant tryptophan in an H chain V region is not essential to antibody binding.

The first amino acid residue of the second framework region in all antibody H and L chain V regions sequenced to date is invariably tryptophan. To test whether this invariance is essential to proper domain folding and generation of a functional antibody, the tryptophan residue in the heavy chain V region of a mouse anti-p-azophenylarsonate antibody was converted to an alanine residue by oligonucleotide-directed mutagenesis of the H chain gene. The mutant gene was transfected into mouse hybridoma cells that produce the homologous L chain, and the resulting mutant antibody was purified from the cell supernatant. It was shown to have essentially the same reactivity as wild type toward a series of anti-idiotypic antibodies and to bind Ag with a Ka similar to that of wild type.

Amino Acid Sequence↗

PubMed2005

Construction of engineered bifunctional enzymes and their overproduction in Aspergillus niger for improved enzymatic tools to degrade agricultural by-products.

Two chimeric enzymes, FLX and FLXLC, were designed and successfully overproduced in Aspergillus niger. FLX construct is composed of the sequences encoding the feruloyl esterase A (FAEA) fused to the endoxylanase B (XYNB) of A. niger. A C-terminal carbohydrate-binding module (CBM family 1) was grafted to FLX, generating the second hybrid enzyme, FLXLC. Between each partner, a hyperglycosylated linker was included to stabilize the constructs. Hybrid proteins were purified to homogeneity, and molecular masses were estimated to be 72 and 97 kDa for FLX and FLXLC, respectively. Integrity of hybrid enzymes was checked by immunodetection that showed a single form by using antibodies raised against FAEA and polyhistidine tag. Physicochemical properties of each catalytic module of the bifunctional enzymes corresponded to those of the free enzymes. In addition, we verified that FLXLC exhibited an affinity for microcrystalline cellulose (Avicel) with binding parameters corresponding to a Kd of 9.9 x 10(-8) M for the dissociation constant and 0.98 micromol/g Avicel for the binding capacity. Both bifunctional enzymes were investigated for their capacity to release ferulic acid from natural substrates: corn and wheat brans. Compared to free enzymes FAEA and XYNB, a higher synergistic effect was obtained by using FLX and FLXLC for both substrates. Moreover, the release of ferulic acid from corn bran was increased by using FLXLC rather than FLX. This result confirms a positive role of the CBM. In conclusion, these results demonstrated that the fusion of naturally free cell wall hydrolases and an A. niger-derived CBM onto bifunctional enzymes enables the increase of the synergistic effect on the degradation of complex substrates.

Agriculture↗

PubMed1998

Reconstitution of the N-terminal transcription activation function of human mineralocorticoid receptor in a defective human glucocorticoid receptor.

N-terminal sequences involved in transcription activation by the human mineralocorticoid receptor (hMR) have yet to be defined. We have addressed this issue and generated overlapping internal deletion mutants hMRDelta59-162, hMRDelta59-247, hMRDelta59-328, hMRDelta162-247, hMRDelta247-328, hMRDelta247-382, and hMRDelta328-382 with intact DNA-binding and hormone-binding domains. A second set of mutant receptors with unique BglII sites was generated to facilitate the isolations of fragments. Immunodetection with anti-hMR peptide antibodies and hormone-binding assays showed that the mutations did not affect the expression of the receptors or ability to bind aldosterone. Distribution of aldosterone binding activity of wild type and deletion mutants expressed in HeLa cells was predominantly nuclear. Furthermore, deletion of sequences between 59 and 390 did not affect DNA binding activity. Transfection studies with HeLa cells revealed a region around residue 247 that was crucial for normal receptor function. Deletion of amino acids 59-162 did not affect the transcriptional activity of the hMR. However, deletion of sequences 247-382 and 328-382 markedly decreased the transcription activation function. The induction of the reporter gene by the chimera hGRDelta71-262/hMR328-382 was 2-fold higher than with the wild type hGR, but 200-fold when compared with hGRDelta71-262, indicating that the AF-1 domain is located between positions 328 and 382 in the hMR.

Aldosterone↗

PubMed1996

Second messenger signaling in olfactory transduction.

Olfactory receptor neurons respond to odorants with G-protein mediated increases in the concentration of cyclic adenosine 3',5'-monophosphate (cAMP) and/or inositol 1,4,5-trisphospahte (InsP3). These two second messengers directly regulate opening of cAMP- and InsP3-regulated conductances localized to the apical transduction compartments of the cell (cilia and olfactory knob). In the presence of physiological concentrations of extracellular Ca2+, these second messenger regulated conductances mediate influx of Ca2+ into the olfactory neuron resulting in large, localized increases in intracellular Ca2+ ([Ca2+]i). A significant advance in our understanding of the molecular mechanisms of olfaction is the recent realization that this increase in [Ca2+]i plays an important role as a "third messenger" in olfactory transduction. Second messenger dependent increases in [Ca2+]i cause opening of ciliary Ca(2+)-activated Cl-, cation and/ or K+ channels that can carry a large percentage of the generator current, thus amplifying the signal substantially. As a result of this sequence of events, the generator potential in olfactory neurons can be depolarizing, leading to excitation of the neuron, or hyperpolarizing, leading to suppression of basal action potential firing rate. This dual effect of odorants on olfactory neurons may play an important role in quality coding and in the ability to detect low concentrations of odorants, particularly in complex mixtures.

Animals↗

PubMed1995

Interactions between residues in staphylococcal alpha-hemolysin revealed by reversion mutagenesis.

alpha-Hemolysin (alpha HL), a pore-forming polypeptide of 293 amino acids, is secreted by Staphylococcus aureus as a water-soluble monomer. Residues that play key roles in the formation of functional heptameric pores on rabbit red blood cells (rRBC) have been identified previously by site-directed mutagenesis. alpha HL-H35N, in which the histidine at position 35 of the wild-type sequence is replaced with asparagine, is nonlytic and is arrested in assembly as a heptameric prepore. In this study, second-site revertants of H35N that have the ability to lyse rRBC were generated by error-prone PCR under conditions designed to produce single base changes. The analysis of 22 revertants revealed new codons clustered predominantly in three distinct regions of the H35N gene. One cluster includes amino acids 107-111 (four revertants) and another residues 144-155 (five revertants). These two clusters flank the central glycine-rich loop of alpha HL, which previously has been implicated in formation of the transmembrane channel, and encompass residues Lys-110 and Asp-152 that, like His-35, are crucial for lytic activity. The third cluster lies in the region spanning amino acids 217-228 (eight revertants), a region previously unexplored by mutagenesis. Single revertants were found at amino acid positions 84 and 169. When compared with H35N, the heptameric prepores formed by the revertants underwent more rapid conversion to fully assembled pores, as determined by conformational analysis by limited proteolysis. The rate of conversion to the fully assembled pore was strongly correlated with hemolytic activity. Previous work has suggested that the N terminus of alpha HL and the central loop cooperate in the final step of assembly. The present study suggests that the key N-terminal residue His-35 operates in conjunction with residues flanking the loop and C-terminal residues in the region 217-228. Hence, reversion mutagenesis extends the linear analysis that has been provided by direct point mutagenesis.

Amino Acid Sequence↗

PubMed2000

HLA-DR51 expression failure caused by a two-base deletion at exon 2 of a DRB5 null allele (DRB5*0110N) in a Spanish gypsy family.

Here we describe a new HLA class II null allele at the DRB5 gene. Serologic HLA typing of a Spanish gypsy family rendered the following paternal haplotype: A2-Cblk-B52-Bw4-DR15-DQ5. However, DNA typing demonstrated the presence of a DRB5 gene in the haplotype DRB1*1502-DRB5*0102-DQB1*05031. Complete DRB5 cDNA sequencing revealed a DRB5*0102 allele with a deletion of two nucleotides at exon 2 (239-240) in codon 80. This change generates a frame shift leading to a stop codon at position 86, and could explain the lack of DR51 protein at the cell surface. This is the second DRB5 null allele described together with DRB5*0108N, raising the number of HLA alleles with an expression disorder.

Amino Acid Sequence↗