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Results for “second generation sequencing”

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PubMed1991

Structural characterization of a cross-reactive idiotype shared by monoclonal antibodies specific for the human CD4 molecule.

A panel of mouse monoclonal anti-CD4 antibodies was characterized in terms of idiotypic expression by using specific anti-idiotypic antibody (anti-Id) reagents generated in rabbits immunized with anti-Leu3a, a monoclonal anti-CD4 which inhibits the human immunodeficiency virus (HIV) gp120 binding to CD4. Direct binding and competitive inhibition assays demonstrate that the majority of monoclonal anti-CD4 antibodies able to recognize CD4 epitopes overlapping the epitope recognized by anti-Leu3a expressed an antigen-combining site-related cross-reactive idiotype (IdX). Western blot analysis was used to demonstrate that this IdX is associated primarily with the light (L) chain of the monoclonal anti-CD4 antibodies. To further characterize the structural basis of the IdX, the nucleotide sequence of the variable region of the L kappa chain of anti-Leu3a was determined. Peptides corresponding to the first, second, and third complementarity determining regions (CDRs) of the L chain of anti-Leu3a were synthesized and used to immunize rabbits. All anti-peptide antisera recognized the immunizing peptide, the cognate anti-Leu3a molecule, and several other monoclonal anti-CD4 antibodies by direct binding assays. Western blot analysis utilizing the anti-CDR peptide reagents demonstrates that the reactivity to the monoclonal anti-CD4 antibodies was L chain-specific. The anti-Id generated by immunizing with the intact anti-Leu3a molecule failed to recognize the three L chain-derived CDR synthetic peptides, suggesting that the IdX requires the presence of the three-dimensional configuration of the L chain for its expression. The broad range of reactivity exhibited by the antipeptide antisera indicates that the majority of mouse monoclonal anti-CD4 antibodies characterized in this study utilize L chains encoded by a single germ line variable (V) region kappa (V kappa) chain gene or by V kappa genes that belong to the same gene family.

Amino Acid Sequence↗

PubMed2004

Alterations in subtelomeric tandem repeats during early stages of allopolyploidy in wheat.

The genomic content of the subtelomeric repeated sequences Spelt1 and Spelt52 was studied by dot, Southern, and in situ hybridization in 11 newly synthesized amphiploids of Aegilops and Triticum, and data were compared with the parental plants. Spelt1 had reduced copy numbers in the first generation of three synthetic amphiploids, but two others did not change; Spelt52 was amplified in nine amphiploids and did not change in two. In the second allopolyploid generation, Spelt1 copy number did not change, whereas there was amplification of Spelt52 in some allopolyploids and decreases in others. Neither allopolyploidy level nor the direction of the cross affected the patterns of change in the newly synthesized amphiploids. Changes did not result from intergenomic recombination because similar alterations were noticed in allopolyploids with and without Ph1, a gene that suppresses homoeologous pairing. No differences in Spelt1 and Spelt52 tandem organization were found by Southern hybridization. The significance of these data are discussed in relation to the establishment of newly formed allopolyploids.

Edible Grain↗

PubMed2005

Roles for nutrients in epigenetic events.

The field of epigenetics is the study of modifications of DNA and DNA-binding proteins that alter the structure of chromatin without altering the nucleotide sequence of DNA; some of these modifications may be associated with heritable changes in gene function. Nutrients play essential roles in the following epigenetic events. First, folate participates in the generation of S-adenosylmethionine, which acts as a methyl donor in the methylation of cytosines in DNA; methylation of cytosines is associated with gene silencing. Second, covalent attachment of biotin to histones (DNA-binding proteins) plays a role in gene silencing and in the cellular response to DNA damage. Third, tryptophan and niacin are converted to nicotinamide adenine dinucleotide, which is a substrate for poly(ADP-ribosylation) of histones and other DNA-binding proteins; poly(ADP-ribosylation) of these proteins participates in DNA repair and apoptosis. Here we present a novel procedure to map nutrient-dependent epigenetic marks in the entire genomes of any given species: the combined use of chromatin immunoprecipitation assays and DNA microarrays. This procedure is also an excellent tool to map the enzymes that mediate modifications of DNA and DNA-binding proteins in chromatin. Given the tremendous opportunities offered by the combined use of chromatin immunoprecipitation assays and DNA microarrays, the nutrition community can expect seeing a surge of information related to roles for nutrients in epigenetic events.

Base Sequence↗

PubMed2000

Histamine H2 receptor mediated dual signaling: mapping of structural requirements using beta2 adrenergic chimeric receptors.

Previously we demonstrated that the histamine H2 receptor can activate both the adenylate cyclase and phosphoinositide/protein kinase (PKC) signaling pathways. Although dual coupling occurs via separate GTP-dependent mechanisms the structural components of the H2 receptor directing differential signaling have not been established. We explored this question by attempting to confer to the beta2-adrenergic receptor (betaAR), which is known to stimulate cAMP formation, the ability to activate PKC through the construction of beta2/H2 chimeric receptors. Intracytoplasmic domains of the human beta2 adrenergic receptor were substituted with the corresponding sequences of the human H2 receptor and stably expressed in HEK-293 cells. Binding of [(3)H]-CGP to chimeric wild type beta2 receptors was comparable. Substitution of the second intracellular loop (2i) of the betaAR led to a significant decrease in coupling to adenylate cyclase while leading to a 139.5 +/- 9.4% control increase in epinephrine mediated PKC activation. Introduction of the H2 receptor 3i also led to a decrease in betaAR mediated cAMP generation but provided the latter with the ability to stimulate PKC (182.2 +/- 8% of control). Concomitant expression of both 2i and 3i led to a substantial increase in epinephrine mediated PKC activation (201.8 +/- 10.5% of control). Addition of the carboxyl terminal tail did not facilitate stimulation of PKC. In summary, the third intracellular loop of the H2 receptor plays an essential role in activating PKC with maximal efficiency conferred by the second intracellular domain.

Adenylyl Cyclases↗

PubMed1996

A discontinuous headful packaging model for packaging less than headful length DNA molecules by bacteriophage T4.

Bacteriophage T4 and other double-stranded DNA-containing bacteriophages package DNA by the classical headful packaging mechanism. In this mechanism, the packaging machinery cuts a DNA concatemer and packages a single unit length genome within the viral capsid. The length of the packaged DNA molecule is determined by the size of the viral capsid. Surprisingly, during large DNA cloning experiments, we observed that the in vitro phage T4 packaging system can package and transduce DNA molecules that are much smaller than the T4 headful size. We analyzed this phenomenon by using defined plasmid DNAs as substrates for in vitro packaging. The data showed that phage T4 can successfully package and transduce 4 to 29 kb plasmid DNA molecules. When two plasmid DNAs with different antibiotic markers were added to the packaging reaction mixture, transductants that are resistant to both the antibiotics were obtained, suggesting that both the plasmid DNAs are packaged within the same head. Analysis of the transducing particles by equilibrium CsCl density-gradient centrifugation showed that the particles have the same density as the wild-type phage. That the less than headful length molecules were not converted to T4 headful length prior to packaging was established by a number of independent approaches. Finally, unit length plasmid DNA molecules of appropriate size were isolated from the in vitro packaged particles. Based on these data, we propose a discontinuous headful packaging model for packaging less than headful length molecules. In this model, the packaging machinery packages the first available less than headful length DNA molecule and generates a partially full head. The partially full head then reinitiates packaging on a second DNA molecule. This process continues until the head is filled with DNA.

Bacteriophage T4↗

PubMed2006

A deletion and point mutation study of the human papillomavirus type 16 major capsid gene.

Recombinant human papillomavirus (HPV) virus-like particles (VLPs) made from the major capsid protein L1 are promising vaccine candidates for use as vaccines against genital and other HPV infections, and particularly against HPV-16. However, HPV-16 genotype variants have different binding affinities for neutralising mouse Mabs raised against HPV-16 L1 VLPs. This paper analyses, using a panel of well-characterised Mabs, the effects on the antigenicity of various C- and N-terminal deletants of HPV-16 L1 made in insect cells via recombinant baculovirus, of an A-->T mutation at residue 266 (A266T), and of a C-->G mutation at conserved position 428 (C428G). The effects of these changes on assembly of the variant L1s were studied by electron microscopy. Binding of Mab H16:E70 to A266T was reduced by almost half in comparison to wild type L1. Retention of the C-terminal region 428-483 was critical for the binding of conformation-specific Mabs (H16:V5, H16:E70, H16:U4 and H16:9A) whereas deletion of the nuclear localisation signal (NLS) or the C428G mutation or an N-terminal deletion (residues 2-9) did not affect the antigenicity. The N-terminal deletion resulted in a mixed population of 30 and 55nm VLPs, which differs from the same construct expressed in Escherichia coli, whereas pentamer aggregates resulted from deletion of the 428-465 region or the C428G mutation. The results have implications both for considering use of single-genotype HPV vaccines, and for design of novel second-generation vaccines.

Animals↗

PubMed1994

Glutamic acid-332 residue of the type C natriuretic peptide receptor guanylate cyclase is important for signaling.

The type C natriuretic peptide (CNP)-activated guanylate cyclase (CNP-RGC) is a single-chain transmembrane-spanning protein, predicted to contain both ligand binding and catalytic activities. Upon binding CNP, CNP-RGC catalyzes the formation of cyclic GMP. We now show that the Glu-332 residue residing in the extracellular region of CNP-RGC plays an important role in signal transduction. Deletion of the CNP-RGC intracellular region resulted in the CNP receptor which lacked cyclase activity; deletion or substitution of Glu-332 with His or Lys resulted in almost total loss of both CNP binding and the CNP-dependent cyclase activity without affecting the basal cyclase activity of the mutant proteins. These observations support the general signal transduction model of the subfamily of natriuretic factor receptor cyclases where it is predicted that ligand binding to the extracellular receptor domain of the protein activates the cytosolic catalytic domain, generating the second-messenger cyclic GMP, and identify an amino acid residue of CNP-RGC that plays an important role in CNP signaling.

Animals↗

PubMed2006

Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation.

DNA methylation has important functions in stable, transcriptional gene silencing, immobilization of transposable elements and genome organization. In Arabidopsis, DNA methylation can be induced by double-stranded RNA through the RNA interference (RNAi) pathway, a response known as RNA-directed DNA methylation. This requires a specialized set of RNAi components, including ARGONAUTE4 (AGO4). Here we show that AGO4 binds to small RNAs including small interfering RNAs (siRNAs) originating from transposable and repetitive elements, and cleaves target RNA transcripts. Single mutations in the Asp-Asp-His catalytic motif of AGO4 do not affect siRNA-binding activity but abolish its catalytic potential. siRNA accumulation and non-CpG DNA methylation at some loci require the catalytic activity of AGO4, whereas others are less dependent on this activity. Our results are consistent with a model in which AGO4 can function at target loci through two distinct and separable mechanisms. First, AGO4 can recruit components that signal DNA methylation in a manner independent of its catalytic activity. Second, AGO4 catalytic activity can be crucial for the generation of secondary siRNAs that reinforce its repressive effects.

Amino Acid Sequence↗

PubMed1988

Cloning and analysis of the dec-1 female-sterile locus, a gene required for proper assembly of the Drosophila eggshell.

Female-sterile mutations at the dec-1 (defective chorion-1) locus of Drosophila severely disrupt the organization of the eggshell late in oogenesis. Previous characterization of dec-1 mutations has correlated the defects with failure to accumulate an early eggshell protein that undergoes proteolytic cleavage during choriogenesis. To enable further study of the regulation and processing of dec-1 products, we have molecularly cloned the locus and characterized its transcripts. Chromosome jumping was used to isolate a deficiency breakpoint within the locus. Overlapping genomic clones from a wild-type library were then obtained, and a region including the dec-1 locus was identified by hybridization to cDNA probes complementary to RNA from stage 9-10 egg chambers. Analysis of genomic rearrangements associated with the locus verified its identity. Two transcripts from the locus have been identified and characterized using cDNA clones, RNase protection, and primer extension analyses. A 4.0-kb transcript accumulates maximally in stages 9-10, when the primary follicle cell protein associated with dec-1 mutations is synthesized. A second transcript of 5.8 kb, generated by alternative splicing, accumulates during stages 11-12. These results are discussed in light of previous analysis of dec-1 mutations.

Animals↗

PubMed1994

Use of double-replacement gene targeting to replace the murine alpha-lactalbumin gene with its human counterpart in embryonic stem cells and mice.

The mouse alpha-lactalbumin gene has been replaced with the human gene by two consecutive rounds of gene targeting in hypoxanthine phosphoribosyltransferase (HPRT)-deficient feeder-independent murine embryonic stem (ES) cells. One mouse alpha-lactalbumin allele was first replaced by an HPRT minigene which was in turn replaced by human alpha-lactalbumin. The end result is a clean exchange of defined DNA fragments with no other DNA remaining at the target locus. Targeted ES cells at each stage remained capable of contributing efficiently to the germ line of chimeric animals. Double replacement using HPRT-deficient ES cells and the HPRT selection system is therefore a powerful and flexible method of targeting specific alterations to animal genes. A typical strategy for future use would be to generate a null mutation which could then be used to produce multiple second-step alterations at the same locus.

Animals↗

PubMedDate not supplied

[Genetic variation at STR-TH01 locus in the South Polish population].

We report on a rare allelic variant of the TH01 STR locus. Within this commonly used tetranucleotide repeat system, we identified and characterized by denaturating gel electrophoresis an allele of the size corresponding to 10.3 repeats, analogous to the most common 9.3 allele. The novel allele segregated from a putative father to the child in a paternity case. We discuss the advantage of high resolution second generation multiplex systems (SGM) using internal size standards during electrophoresis.

Alleles↗

PubMed1994

Oxidative DNA damage induced by Cu(II)-oligopeptide complexes and hydrogen peroxide.

At physiological pH values, Cu(II)-tetraglycine and Cu(II) complexes with peptides containing a histidyl residue at the N-terminal caused DNA strand breakage in the presence of H2O2, whereas Cu(II) complexes with peptides containing histidyl residue in the second or third position did not. Because of the correlation between the generation of hydroxyl radical and DNA strand scission, a mechanism for the reaction is proposed.

Amino Acid Sequence↗

PubMed1991

Diversity of a ribonucleoprotein family in tobacco chloroplasts: two new chloroplast ribonucleoproteins and a phylogenetic tree of ten chloroplast RNA-binding domains.

Two new ribonucleoproteins (RNPs) have been identified from a tobacco chloroplast lysate. These two proteins (cp29A and cp29B) are nuclear-encoded and have a less affinity to single-stranded DNA as compared with three other chloroplast RNPs (cp28, cp31 and cp33) previously isolated. DNA sequencing revealed that both contain two consensus sequence-type homologous RNA-binding domains (CS-RBDs) and a very acidic amino-terminal domain but shorter than that of cp28, cp31 and cp33. Comparison of cp29A and cp29B showed a 19 amino acid insertion in the region separating the two CS-RBDs in cp29B. This insertion results in three tandem repeats of a glycine-rich sequence of 10 amino acids, which is a novel feature in RNPs. The two proteins are encoded by different single nuclear genes and no alternatively spliced transcripts could be identified. We constructed a phylogenetic tree for the ten chloroplast CS-RBDs. These results suggest that there is a sizable RNP family in chloroplasts and the diversity was mainly generated through a series of gene duplications rather than through alternative pre-mRNA splicing. The gene for cp29B contains three introns. The first and second introns interrupt the first CS-RBD and the third intron does the second CS-RBD. The position of the first intron site is the same as that in the human hnRNP A1 protein gene.

Amino Acid Sequence↗

PubMed1991

The adult alpha-globin locus of Old World monkeys: an abrupt breakdown of sequence similarity to human is defined by an Alu family repeat insertion site.

The haploid genomes of all known primates have two or more adult alpha-globin genes contained within tandemly arranged duplication units. Although the tandem duplication event generating these alpha-globin loci is believed to occur prior to the divergence of primates, a number of length polymorphisms exist within the loci among different primate species. In order to understand the molecular basis of these length polymorphisms, we have cloned and determined the nucleotide sequence of a major portion of the rhesus monkey adult alpha-globin locus. Sequence comparison to human suggests that the length difference between the adult alpha-globin loci of human and Old World monkey is the result of one or more DNA recombination processes, all of which appeared to be related to the transposition of Alu family repeats. First, the finding of a monomeric Alu family repeat at the junction between nonhomology block I and homology block Y of the alpha 2 gene-containing unit in rhesus macaque suggests that the dimeric Alu family repeat, Alu 3, at the orthologous position in human was generated by insertion of a monomeric Alu family repeat into the 3' end of another preexisting Alu family repeat. Second, two Alu family repeats, Alu 1 and Alu 2, exist in human at the 3' end of each of the two X homology blocks, respectively. However, this pair of paralogous Alu family repeats is absent at the corresponding positions in rhesus macaques. This raises interesting questions regarding the evolutionary origin of Alu 1 and Alu 2. Finally, DNA sequences immediately downstream from the insertion site of Alu 2 are completely different between human and rhesus macaque.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2006

Renal parenchymal tumors and lymphoma in the same patient: case series and review of the literature.

We reviewed the incidence of diagnosis of renal cell carcinoma and lymphoma in the same patient and analyzed the characteristics of this association. Nine patients in 4 years had the diagnosis of renal cell carcinoma (RCC) and lymphoma, including 2 with Hodgkin disease, 1 with chronic lymphocytic leukemia (CLL), and 3 each with low-grade follicular and intermediate-grade non-Hodgkin lymphoma (NHL). In SEER data, the observed/expected (O/E) ratio of NHL and RCC is 1.86 to 2.07. In our series, 2 patients were diagnosed with NHL after the diagnosis of RCC, 1 was diagnosed concurrently, and in the other 6, lymphoma preceded diagnosis of RCC. In reviews of second malignancies following treatment of Hodgkin disease, RCC is less common (O/E 1.5, with 1/3 being transitional cell carcinoma and 2/3 being adenocarcinoma). We report 2 cases with Hodgkin disease preceding RCC, and in both, Hodgkin disease occurred as an adult. There is a male predominance for patients with both diagnoses, which is greater than the male predominance for either RCC or NHL alone (2.2 vs. 2.0 vs. 1.2). There is an increased likelihood of the lymphoma being extranodal. There is an increased association of RCC and NHL more often among male patients, and often with extranodal lymphoma. Potential common etiological factors include prior treatment for malignancy, genetic predisposition, environmental factors, including a search for viral sequences, and possible immune dysregulation generating the lymphoma and subsequently leading to solid tumors such as RCC or melanoma.

Adult↗

PubMed2006

Dynamic causal modeling: a generative model of slice timing in fMRI.

Dynamic causal modeling (DCM) of functional magnetic resonance imaging (fMRI) data allows one to make inferences about the architecture of distributed networks in the brain, in terms of effective connectivity. fMRI data are usually acquired using echo planar imaging (EPI). EPI sequences typically acquire slices at different times over a few seconds. DCM, in its original inception, was not informed about these slice timings and assumed that all slices were acquired simultaneously. It has been shown that DCM can cope with slice timing differences of up to 1 s. However, many fMRI studies employ a repetition time (TR) of 3 to 5 s, which precludes a straightforward DCM of these data. We show that this limitation can be overcome easily by including slice timing in the DCM. Using synthetic data we show that the extended DCM furnishes veridical posterior means, even if there are large slice-timing differences. Model comparisons show that, in general, the extended DCM out-performs the original model. We contrast the modeling of slice timing, in the context of DCM, with the less effective approach of 'slice-timing correction', prior to modeling. We apply our procedure to real data and show that slice timings are important parameters. We conclude that, generally, one should use DCM with slice timing.

Humans↗

PubMed1981

Sequences of the joining region genes for immunoglobulin heavy chains and their role in generation of antibody diversity.

To assess the contribution to immunoglobulin heavy chain diversity made by recombination between variable region (VH) genes and joining region (JH) genes, we have determined the sequence of about 2000 nucleotides spanning the rearranged JH gene cluster associated with the VH gene expressed in plasmacytoma HPC76. The active VH76 gene has recombined with the second germ-line JH gene. The region we have studied contains two other JH genes, designated JH3 and JH4. No other JH gene was found within the region 1000 nucleotides downstream from JH4. Between JH3 and JH4 there is a pseudo-JH sequence with substantial homology to the authentic JH genes. The four JH genes whose sequences now are known can account for all known JH amino acid sequences. The JH genes are more divergent than the Jk genes and vary in length, encoding either 15 or 17 amino acid residues. Because JH regions comprise part of the third hypervariable region (HV3), combinatorial VH--JH joining substantially augments VH diversity. Moreover, a VH gene can recombine with each JH gene at several positions, and either one or two germ-line JH codons can be excised. This JH truncation markedly reduces the length of HV3 and hence must alter antigen-binding specificity. We have also determined the sequence of the JH4 region in two different gamma 2a mRNAs and have found that each has suffered a point mutation (aspartate to asparagine) which would alter the charge of the antigen-binding site.

Amino Acid Sequence↗

PubMed2003

Identification by site-directed mutagenesis of amino acids contributing to ligand-binding specificity or signal transduction properties of the human FP prostanoid receptor.

Prostanoid receptors belong to the class of heptahelical plasma membrane receptors. For the five prostanoids, eight receptor subtypes have been identified. They display an overall sequence similarity of roughly 30%. Based on sequence comparison, single amino acids in different subtypes of different species have previously been identified by site-directed mutagenesis or in hybrid receptors that appear to be essential for ligand binding or G-protein coupling. Based on this information, a series of mutants of the human FP receptor was generated and characterized in ligand-binding and second-messenger-formation studies. It was found that mutation of His-81 to Ala in transmembrane domain 2 and of Arg-291 to Leu in transmembrane domain 7, which are putative interaction partners for the prostanoid's carboxyl group, abolished ligand binding. Mutants in which Ser-263 in transmembrane domain 6 or Asp-300 in transmembrane domain 7 had been replaced by Ala or Gln, respectively, no longer discriminated between prostaglandins PGF(2alpha) and PGD(2). Thus distortion of the topology of transmembrane domains 6 and 7 appears to interfere with the cyclopentane ring selectivity of the receptor. PGF(2alpha)-induced inositol formation was strongly reduced in the mutant Asp-300Gln, inferring a role for this residue in agonist-induced G-protein activation.

Amino Acid Substitution↗