Concordance of results of blood and tissue cultures from patients with pyogenic spondylitis: a retrospective cohort study

OBJECTIVES

To investigate the concordance of results of blood and tissue cultures in patients with pyogenic spondylitis.

METHODS

We searched for patients with pyogenic spondylitis in whom microorganisms were isolated from both blood and tissue cultures by retrospective review of medical records in three tertiary university-affiliated hospitals between January 2005 and December 2015. The species and antimicrobial susceptibility patterns of isolates from blood and tissue cultures were compared.

RESULTS

Among 141 patients with pyogenic spondylitis in whom microorganisms were isolated from both blood and tissue cultures, the species of blood and tissue isolates were identical in 135 patients (95.7%, 135/141). Excluding the four anaerobic isolates, we investigated antimicrobial susceptibility patterns of 131 isolates of the same species from blood and tissue cultures. Antibiotic susceptibility patterns were identical in 128 patients (97.7%, 128/131). The most common isolates were Staphylococcus aureus (86 patients; 85 concordant and one discordant), followed by streptococcus (24 patients; 22 concordant and two discordant), and Escherichia coli (eight patients; all concordant).

CONCLUSIONS

We suggest that a positive blood culture from patients with pyogenic spondylitis could preclude the need for additional tissue cultures, especially when S. aureus and streptococcus grew in blood cultures.

Effect of the Tube Diameter Distribution on the High-Temperature Structural Modification of Bundled Single-Walled Carbon Nanotubes

We present results of a systematic high-resolution transmission electron microscopy study of the thermal evolution of bundled single-walled carbon nanotubes (SWNTs) subjected to approximately 4-h high-temperature heat treatment (HTT) in a vacuum at successively higher temperatures up to 2200 degrees C. We have examined purified SWNT material derived from the HiPCO and ARC processes. These samples were found to thermally evolve along very different pathways that we propose depend on three factors: (1) initial diameter distribution, (2) concomitant tightness of the packing of the tubes in a bundle, and (3) the bundle size. Graphitic nanoribbons (GNR) were found to be the dominant high-temperature filament in ARC material after HTT = 2000 degrees C; they were not observed in any heat-treated HiPCO material. The first two major steps in the thermal evolution of HiPCO and ARC material agree with the literature, i.e., coalescence followed by the formation of multiwall carbon nanotubes (MWNTs). However, ARC material evolves to bundled MWNTs, while HiPCO evolves to isolated MWNTs. In ARC material, we find that the MWNTs collapse into multishell GNRs. The thermal evolution of these carbon systems is discussed in terms of the diameter distribution, nanotube coalescence pathways, C-C bond rearrangement, diffusion of carbon and subsequent island formation, as well as the nanotube collapse driven by van der Waals forces.

Thermal conversion of bundled carbon nanotubes into graphitic ribbons

High temperature heat treatment (HTT) of bundled single-walled carbon nanotubes (SWNTs) in vacuum ( approximately 10(-5) Torr) has been found to lead to the formation of two types of graphitic nanoribbons (GNRs), as observed by high-resolution transmission electron microscopy. Purified SWNT bundles were first found to follow two evolutionary steps, as reported previously, that is, tube coalescence (HTT approximately 1400 degrees C) and then massive bond rearrangement (HTT approximately 1600 degrees C), leading to the formation of bundled multiwall nanotubes (MWNTs) with 3-12 shells. At HTT > 1800 degrees C, we find that these MWNTs collapse into multishell GNRs. The first type of GNR we observed is driven by the collapse of diameter-doubled single-wall nanotubes, and their production is terminated at HTT approximately 1600 degrees C when the MWNTs also start to form. We propose that the collapse is driven by van der Waals forces between adjacent tubes in the same bundle. For HTT > 2000 degrees C, the heat-treated material is found to be almost completely in the multishell GNR form.

Infrared-active vibrational modes of single-walled carbon nanotubes

The IR-active vibrational modes of single-walled carbon nanotubes have been observed by optical transmission through thin films of bundled nanotubes. Because IR-active chemical functional groups, e.g., -COOH, -OH, might be attached to the tube walls and contribute additional spectral features, we have also studied the effects of chemical purification and long-term high-temperature vacuum annealing on the IR spectrum. Through comparison with theory, we are able to assign much of the sharp structure observed in our IR spectra.

Confined phonons in Si nanowires

Raman microprobe studies of long crystalline Si nanowires reveal for the first time the evolution of phonon confinement with wire diameter. The Raman band at approximately 520 cm-1 in bulk Si is found to downshift and asymmetrically broaden to lower frequency with decreasing wire diameter D, in good agreement with a phenomenological model first proposed by Richter et al. An adjustable parameter (alpha) is added to the theory that defines the width of the Gaussian phonon confinement function. We find that this parameter is not sensitive to diameter over the range 4-25 nm.

Debundling and dissolution of single-walled carbon nanotubes in amide solvents

Wet chemical methods involving ultrasound and amide solvents were used to purify and separate large bundles of single-walled carbon nanotubes (SWNTs) into individual nanotubes that could then be transported to silicon or mica substrates. The SWNTs studied were produced by the arc-discharge process. Dry oxidation was used in an initial step to remove amorphous carbon. Subsequently, two acid purification schemes were investigated (HCl- and HNO(3)-reflux) to remove the metal growth catalyst (Ni-Y). Finally, ultrasonic dispersion of isolated tubes into either N,N-dimethylformamide (DMF) or N-methyl-2-pyrrolidone (NMP) was carried out. Raman scattering, atomic force microscopy (AFM), and electron microscopy were used to study the evolution of the products. Raman scattering was used to probe possible wall damage during the chemical processing. We found that both HCl and HNO(3) could be used to successfully remove the Ni-Y below approximately 1 wt %. However, the HNO(3)-reflux produced significant wall damage (that could be reversed by vacuum annealing at 1000 degrees C). In the dispersion step, both amide solvents (DMF and NMP) produced a high degree of isolated tubes in the final product, and no damage during this dispersion step was observed. HNO(3)-refluxed tubes were found to disperse the best into the amide solvents, perhaps because of significant wall functionalization. AFM was used to study the filament diameter and length distributions in the final product, and interesting differences in these distributions were observed, depending on the chemical processing route.

Periodate oxidation of crystalline cellulose

Conversion of 1,2-dihydroxyl groups to dialdehyde by periodate oxidation is a useful method of derivatizing polysaccharides but has not been extensively utilized in derivatization of cellulose because of complicacy due to the crystalline nature of cellulose. To understand the influence of cellulose crystallinity on this reaction, we investigated how the periodate oxidation proceeds with a highly crystalline cellulose of the marine alga Cladophora sp. The crystallinity of the oxidized cellulose, determined by X-ray diffraction, decreased according to the oxidation level. The half-height widths of equatorial diffraction peaks were nearly unchanged. The solid-state 13C NMR spectra did not show peaks corresponding to aldehyde groups, but solution 13C NMR spectra showed the presence of dicarboxylic groups after subsequent oxidation by sodium chlorite. Transmission electron microscopy showed that microfibrils of Cladophora tended to be bent and more flexible than the original sample. Gold labeling of the aldehyde groups, mediated by thiosemicarbazide derivatization, revealed a highly uneven distribution of dialdehyde groups. When treated by 50% (w/v) sulfuric acid, partially oxidized Cladophora cellulose gave many short fragments of microfibril. These features indicate that the periodate oxidation proceeds by forming dialdehyde groups in longitudinally spaced, bandlike domains.

Mouse histamine N-methyltransferase: cDNA cloning, expression, gene cloning and chromosomal localization

OBJECTIVE

Histamine N-methyltransferase (HNMT) catalyzes the Ntau-methylation of histamine. We set out to clone a mouse liver HNMT cDNA and the mouse HNMT gene as steps toward characterizing molecular genetic mechanisms involved in the regulation of this important histamine-metabolizing enzyme.

DESIGN

A PCR-based strategy was used to clone both the mouse HNMT cDNA and the gene encoding that cDNA, Hnmt. The cDNA was used both to express recombinant mouse HNMT and to determine the chromosomal localization of Hnmt.

RESULTS

The mouse liver HNMT cDNA was 1657 bp in length with an 888 bp open reading frame (ORF) that encoded a 296 amino acid protein with a predicted Mr value of approximately 32.5 kDa. The amino acid sequence of the encoded protein was 84% identical to that of human kidney HNMT. Mouse HNMT was expressed in COS-1 cells, and its apparent Km values for histamine and S-adenosyl-L-methionine (Ado-Met), the two cosubstrates for the reaction, were 5.3 and 5.8 microM, respectively. The mouse HNMT gene, Hnmt, spanned approximately 25 kb and had 7 exons. Its structure differed from that of the human gene primarily by the presence of an additional exon at the 5'-terminus. Hnmt mapped to mouse chromosome 2 in an area of conserved synteny to human chromosome 2q, the location of the human gene (2q22) on the basis of fluorescence in situ hybridization.

CONCLUSIONS

Cloning and functional characterization of the mouse HNMT cDNA and gene will now make it possible to study in the mouse molecular genetic mechanisms involved the regulation of this important histamine-metabolizing enzyme.

Ion-exchange chromatography by dicarboxyl cellulose gel

A new column packing material for ion-exchange chromatography was prepared from cellulose gel by periodate oxidation followed by chlorite oxidation to form spatially paired carboxyl groups (dicarboxyl cellulose, DCC). The carboxyl group was quantitatively introduced to spherical cellulose gel by controlling the extent of oxidation. The DCC gels were examined for their ion-exchange activity for various amines at pH of 2.5-5.5. In this pH range, aromatic amines with acid dissociation constant (pKa) below 2.7 showed no interaction with DCC gels as expected from their lack of protonation. The amines with pKa greater than 3.3, both aromatic and aliphatic, showed strong interaction corresponding to the amount of carboxyl introduced to the gel. However, these amines showed anomalous dependence on pH of the mobile phase, showing a maximum in retention factor at around pH 4. This is in contrast with the nearly constant retention factor of these amines on conventional carboxylated cellulose packing at pH greater than 4.0. The maximum retention factor at pH 4 of DCC gel was 4-5-times greater than that of conventional gel having a similar amount of carboxyls. Since pKa of dicarboxyl groups ranges 3-5 as determined by acid-base titration, the pH giving maximum retention corresponds to the pH at which one of paired carboxyls is dissociated. Possible cause of this anomaly is presented in terms of dissociation state of dicarboxyl groups and its interaction with amines.

Construction of a BAC contig map of chromosome 16q by two-dimensional overgo hybridization

We have used sequence-based markers from an integrated YAC STS-content/somatic cell hybrid breakpoint physical map and radiation hybrid maps of human chromosome 16 to construct a new sequence-ready BAC map of the long arm of this chromosome. The integrated physical map was generated previously in our laboratory and contains 1150 STSs, providing a marker on average every 78 kb on the euchromatic arms of chromosome 16. The other two maps used for this effort were the radiation hybrid maps of chromosome 16 from Whitehead Institute and Stanford University. To create large sequenceable targets of this chromosome, we used a systematic approach to screen high-density BAC filters with probes generated from overlapping oligonucleotides (overgos). We first identified all available sequences in the three maps. These include sequences from genes, ESTs, STSs, and cosmid end sequences. We then used BLASTto identify 36-bp unique fragments of DNA for overgo probes. A total of 906 overgos were selected from the long arm of chromosome 16. Hybridizations occurred in three stages: (1) superpool hybridizations against the 12x coverage human BAC library (RPCI-11); (2) two-dimensional hybridizations against rearrayed positive BACs identified in the superpool hybridizations; and (3) pooled tertiary hybridizations for those overgos that had ambiguous positives remaining after the two-dimensional hybridization. For the superpool hybridizations, up to 236 overgos have been pooled in a single hybridization against the 12x BAC library. A total of 5187 positive BACs from chromosome 16q were identified as a result of five superpool hybridizations. These positive clones were rearrayed on membranes and hybridized with 161 two-dimensional subpools of overgos to determine which BAC clones were positive for individual overgos. An additional 46 tertiary hybridizations were required to resolve ambiguous overgo-BAC relationships. Thus, after a total of 212 hybridizations, we have constructed an initial probe-content BAC map of chromosome 16q consisting of 828 overgo markers and 3363 BACs providing >85% coverage of the long arm of this chromosome. The map has been confirmed by the fingerprinting data and BAC end PCR screening.

Rational design of landmark probes for quantitative DNA fiber mapping (QDFM)

Rapid construction of high-resolution physical maps requires accurate information about overlap between DNA clones and the size of gaps between clones or clone contigs. We recently developed a procedure termed 'quantitative DNA fiber mapping' (QDFM) to help construct physical maps by measuring the overlap between clones or the physical distance between non-overlapping contigs. QDFM is based on hybridization of non-isotopically labeled probes onto DNA molecules that were bound to a solid support and stretched homogeneously to approximately 2.3 kb/microm. In this paper, we describe the design of probes that bind specifically to the cloning vector of DNA recombinants to facilitate physical mapping. Probes described here delineate the most frequently used cloning vectors such as BACs, P1s, PACs and YACs. As demonstrated in representative hybridizations, vector-specific probes provide valuable information about molecule integrity, insert size and orientation as well as localization of hybridization domains relative to specifically-marked vector sequences.

Human sulfotransferases SULT1C1 and SULT1C2: cDNA characterization, gene cloning, and chromosomal localization

Sulfate conjugation catalyzed by sulfotransferase (SULT) enzymes is an important pathway in the biotransformation of many drugs, other xenobiotics, neurotransmitters, and hormones. We previously described a human cDNA, SULT1C1, that encoded a protein similar in sequence to that of rat ST1C1. Subsequently, a related human cDNA, SULT1C2, was reported. In the present study, we set out to characterize further the human SULT1C1 cDNA and then to clone, structurally characterize, and map its gene. As an initial step, we performed 5'- and 3'-RACE with SULT1C1 cDNA. Those experiments demonstrated that a small number of SULT1C1 transcripts contained an "insert," which we later showed resulted from alternative splicing that involved an Alu sequence in intron 3 of SULT1C1. We then cloned and structurally characterized the SULT1C1 gene from a human genomic BAC library. Because the sequence of SULT1C2 was closely related to that of SULT1C1 and because the genes for other human SULT paralogues occur in clusters, we screened the BAC clones that had been positive for SULT1C1 to search for SULT1C2 and discovered a clone that contained both genes. That BAC was used to sequence and structurally characterize SULT1C2. SULT1C1 and SULT1C2 were approximately 21 and 10 kb in length, respectively. Both genes contained seven exons that encoded protein, and both had structures that were similar to those of other genes that encode members of the SULT1 family. Finally, human SULT1C1 and SULT1C2 mapped to 2q11.2 by fluorescence in situ hybridization. The cloning and structural characterization of SULT1C1 and SULT1C2 will now make it possible to perform molecular genetic and pharmacogenomic studies of these sulfate-conjugating enzymes in humans.

Molecular cloning of translocation breakpoints in a case of constitutional translocation t(11;22)(q23;q11) and preparation of probes for preimplantation genetic diagnosis

In vitro fertilization (IVF) centres with preimplantation genetic diagnosis (PGD) programmes are often confronted with the problem of identifying chromosomal abnormalities in interphase cells biopsied from preimplantation embryos of carriers of a reciprocal translocation. The present authors have developed a DNA testing based approach to analyse embryos from translocation carriers, and this report describes breakpoint-spanning probes to detect abnormalities in cases of the most common human translocation (i.e. the t(11;22)(q23;q11)). Screening a yeast artificial chromosome (YAC) library for probes covering the respective breakpoint regions in the patient lead to probes for the breakpoint on chromosome 11q23. The physically mapped YAC and bacterial artificial chromosome (BAC) clones from chromosome 22 were then integrated with the cytogenetic map, which allowed localization of the breakpoint on chromosome 22q11 to an interval of less than 84 kb between markers D22S184 and KI457 and to prepare probes suitable for interphase cell analysis. In summary, breakpoint localization could be accomplished in about 4 weeks with additional time needed to optimize probes for use in PGD.

Human 3'-phosphoadenosine 5'-phosphosulfate synthetase 1 (PAPSS1) and PAPSS2: gene cloning, characterization and chromosomal localization

Sulfae conjugation is an important pathway in the metabolism of a large number of exogenous and endogenous compounds. These reactions are catalyzed by sulfotransferase (SULT) enzymes that utilize 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfate donor. PAPS is synthesized from ATP and inorganic sulfate by PAPS synthetase (PAPSS). Two separate PAPSS cDNAs, PAPSS1 and PAPSS2, have been identified in human tissues. We have cloned and characterized the genes for human PAPSS1 and PAPSS2 to make it possible to study the pharmacogenomics of these enzymes. Both genes consisted of 12 exons with virtually identical exon-intron splice junction locations. All splice junctions conformed to the "GT-AG" rule. The total length of PAPSS1 was approximately 108 kb, while that of PAPSS2 was greater than 37 kb. The 5'-flanking region of PAPSS1 did not include a TATA box sequence near the site of transcription initiation, but PAPSS2 had a TATA motif located 21 bp upstream from the site of transcription initiation. Northern blot analysis showed that the major PAPSS1 and PAPSS2 transcripts were approximately 2.7 and 4.2 kb in length, respectively. PAPSS1 mapped to human chromosome band 4q24 while PAPSS2 mapped to 10q22-23 by fluorescence in situ hybridization analysis. Cloning and structural characterization of PAPSS1 and PAPSS2 will make it possible to perform molecular genetic and pharmacogenomic studies of these important enzymes in humans.

Human indolethylamine N-methyltransferase: cDNA cloning and expression, gene cloning, and chromosomal localization

Indolethylamine N-methyltransferase (INMT) catalyzes the N-methylation of tryptamine and structurally related compounds. We recently cloned and characterized the rabbit INMT cDNA and gene as a step toward cloning the cDNA and gene for this enzyme in humans. We have now used a PCR-based approach to clone a human INMT cDNA that had a 792-bp open reading frame that encoded a 263-amino-acid protein 88% identical in sequence to rabbit INMT. Northern blot analysis of 35 tissues showed that a 2.7-kb INMT mRNA species was expressed in most tissues. When the cDNA was expressed in COS-1 cells, the recombinant enzyme catalyzed the methylation of tryptamine with an apparent K(m) value of 2.9 mM. The human cDNA was then used to clone the human INMT gene from a human genomic BAC library. The gene was 5471 bp in length, consisted of three exons, and was structurally similar to the rabbit INMT gene as well as genes for nicotinamide N-methyltransferase and phenylethanolamine N-methyltransferase in several species. All INMT exon-intron splice junctions conformed to the "GT-AG" rule, and no canonical TATA or CAAT sequences were present within the 5'-flanking region of the gene. Human INMT mapped to chromosome 7p15.2-p15.3 on the basis of both PCR analysis and fluorescence in situ hybridization. Finally, two possible single nucleotide polymorphisms were identified within exon 3, both of which altered the encoded amino acid. The cloning and expression of a human INMT cDNA, as well as the cloning, structural characterization, and mapping of its gene represent steps toward future studies of the function and regulation of this methyltransferase enzyme in humans.

In vivo and in vitro analyses of Myc for differential promoter activities of the human telomerase (hTERT) gene in normal and tumor cells

Induction of the catalytic subunit of human telomerase, hTERT, plays a critical role in the activation of telomerase during tumorigenesis. Here, we isolate the hTERT gene promoter and define the functional promoter region, which is inactive in normal cells but active in tumor cells. Myc directly interacts with the hTERT promoter and activates its transcription both in vivo and in vitro. Activation or repression of Myc can alter hTERT promoter activities in normal or tumor cells. Furthermore, we detect high levels of Myc protein in tumor cells compared with normal cells. The ability of Myc to modulate the activity of the hTERT promoter and, hence, the telomerase enzyme may contribute to its ability to promote tumor formation.

Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q

Several publicly funded large-scale sequencing efforts have been initiated with the goal of completing the first reference human genome sequence by the year 2005. Here we present the results of analysis of 11.8 Mb of genomic sequence from chromosome 16. The apparent gene density varies throughout the region, but the number of genes predicted (84) suggests that this is a gene-poor region. This result may also suggest that the total number of human genes is likely to be at the lower end of published estimates. One of the most interesting aspects of this region of the genome is the presence of highly homologous, recently duplicated tracts of sequence distributed throughout the p-arm. Such duplications have implications for mapping and gene analysis as well as the predisposition to recurrent chromosomal structural rearrangements associated with genetic disease.

Chromosomal localization of ESTs obtained from human fetal liver via BAC-mediated FISH mapping

A total of 55 expressed sequence tags (ESTs) randomly chosen from our collection of fetal liver ESTs were mapped to chromosomes by fluorescence in situ hybridization (FISH) mapping techniques. To generate FISH mapping probes, the genomic DNAs for each EST were selected by screening an arrayed human bacterial artificial chromosome (BAC) library. In total, 73 BACs were used for mapping of the 55 ESTs. Among them, 70 BACs representing 52 ESTs unequivocally mapped to single chromosomal regions. The remaining 3 BACs representing 3 ESTs were localized to multiple regions, suggesting that BACs may have very low chimerism. Our mapping results were compared with EST mapping databases deposited in NCBI. Thirty-six of 55 ESTs corresponded to previously mapped positions of ESTs, 2 ESTs mapped to different positions from previously determined ones, and it was found that 17 ESTs have been mapped on new locations from this study. These mapping data may be used for completing the framework of the human physical map, and also for providing a good starting point for searching disease-related genes.

A 12-Mb complete coverage BAC contig map in human chromosome 16p13.1-p11.2

We have constructed a complete coverage BAC contig map that spans a 12-Mb genomic segment in the human chromosome 16p13.1-p11.2 region. The map consists of 68 previously mapped STSs and 289 BAC clones, 51 of which-corresponding to a total of 7.721 Mb of genomic DNA-have been sequenced, and provides a high resolution physical map of the region. Contigs were initially built based mainly on the analysis of STS contents and restriction fingerprint patterns of the clones. To close the gaps, probes derived from BAC clone ends were used to screen deeper BAC libraries. Clone end sequence data obtained from chromosome 16-specific BACs, as well as from public databases, were used for the identification of BACs that overlap with fully sequenced BACs by means of sequence match. This approach allowed precise alignment of clone overlaps in addition to restriction fingerprint comparison. A freehand contig drawing software tool was developed and used to manage the map data graphically and generate a real scale physical map. The map we present here is approximately 3.5 x deep and provides a minimal tiling path that covers the region in an array of contigous, overlapping BACs.

High throughput direct end sequencing of BAC clones

Libraries constructed in bacterial artificial chromosome (BAC) vectors have become the choice for clone sets in high throughput genomic sequencing projects primarily because of their high stability. BAC libraries have been proposed as a source for minimally over-lapping clones for sequencing large genomic regions, and the use of BAC end sequences (i.e. sequences adjoining the insert sites) has been proposed as a primary means for selecting minimally overlapping clones for sequencing large genomic regions. For this strategy to be effective, high throughput methods for BAC end sequencing of all the clones in deep coverage BAC libraries needed to be developed. Here we describe a low cost, efficient, 96 well procedure for BAC end sequencing. These methods allow us to generate BAC end sequences from human and Arabidoposis libraries with an average read length of >450 bases and with a single pass sequencing average accuracy of >98%. Application of BAC end sequences in genomic sequen-cing is discussed.

Cloning and comparative mapping of the DiGeorge syndrome critical region in the mouse

Chromosome deletions leading to the hemizygous loss of groups of contiguous genes are a major cause of human congenital defects. In some syndromes haploinsufficiency of a single gene causes the majority of the syndromal features, whereas other diseases are thought to be the consequences of a combined haploinsufficiency. In the case of the DiGeorge and velocardiofacial syndromes, caused by deletions within 22q11, the genetic analyses have so far failed to implicate a single gene. By virtue of FISH analysis and the creation of a BAC/P1 genomic clone contig we have mapped 19 murine homologues of genes and nine EST groups from the region deleted in DiGeorge syndrome and found them to be linked on mouse chromosome 16. Rearrangements during the divergence of mouse and human have led to differing gene orders in the two species, with implications for the most appropriate means of mimicking particular human deletions. The map confirms and extends previous analyses and the contig resources toward the generation of targeted deletions in the mouse.

High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping

Large insert clone libraries have been the primary resource used for the physical mapping of the human genome. Research directions in the genome community now are shifting direction from purely mapping to large-scale sequencing, which in turn, require new standards to be met by physical maps and large insert libraries. Bacterial artificial chromosome libraries offer enormous potential as the chosen substrate for both mapping and sequencing studies. Physical mapping, however, has come under some scrutiny as being "redundant" in the age of large-scale automated sequencing. We report the development and applications of nonelectrophoretic, optical approaches for high-resolution mapping of bacterial artificial chromosome that offer the potential to complement and thereby advance large-scale sequencing projects.

A human gene similar to Drosophila melanogaster peanut maps to the DiGeorge syndrome region of 22q11

A Drosophila-related expressed sequence tag (DRES) with sequence similarity to the peanut gene has previously been localized to human chromosome 22q11. We have isolated the cDNA corresponding to this DRES and show that it is a novel member of the family of septin genes, which encode proteins with GTPase activity thought to interact during cytokinesis. The predicted protein has P-loop nucleotide binding and GTPase motifs. The gene, which we call PNUTL1, maps to the region of 22q11.2 frequently deleted in DiGeorge and velo-cardio-facial syndromes and is particularly highly expressed in the brain. The mouse homologue, Pnutl1, maps to MMU16 adding to the growing number of genes from the DiGeorge syndrome region that map to this chromosome.

High-resolution physical map of the immunoglobulin lambda variant gene cluster assembled by quantitative DNA fiber mapping

Quantitative DNA fiber mapping (QDFM) allows rapid construction of near-kilobase-resolution physical maps by hybridizing specific probes to individual stretched DNA molecules. We evaluated the utility of QDFM for the large-scale physical mapping of a rather unstable, repeat-rich 850-kb region encompassing the immunoglobulin lambda variant (IGLV) gene segments. We mapped a minimal tiling path composed of 32 cosmid clones to three partially overlapping yeast artificial chromosome (YAC) clones and determined the physical size of each clone, the extent of overlap between clones, and contig orientation, as well as the sizes of gaps between adjacent contigs. Regions of germline DNA for which we had no YAC coverage were characterized by cosmid to cosmid hybridizations. Compared to other methods commonly used for physical map assembly, QDFM is a rapid, versatile technique delivering unambiguous data necessary for map closure and preparation of sequence-ready minimal tiling paths.

BAC and PAC contigs covering 3.5 Mb of the Down syndrome congenital heart disease region between D21S55 and MX1 on chromosome 21

Chromosome 21 is a model for the study of human chromosomal aneuploidy, and the construction of its physical and transcriptional maps is a necessary step in understanding the molecular basis of aneuploidy-dependent phenotypes. To identify the gene(s) responsible for Down syndrome congenital heart disease (DS-CHD), we constructed a physical map of the D21S55 to MX1 region. A bacterial artificial chromosome (BAC) library was screened using several YACs spanning the interval, and a P1-derived artificial chromosome (PAC) library was screened using radiolabeled STS PCR products and whole BACs in gap-filling initiatives. FISH confirmed the location of all BAC and PAC clones to 21q22.2-q22.3. Overlaps were established using clone-to-clone Southerns and 24 new STSs, generated from the direct sequencing of BAC and PAC ends, along with 35 preexisting STSs. Approximately 3.5 Mb of the 4- to 5-Mb D21S55 to MX1 interval is covered in 85 BACs and 24 PACs, representing fourfold coverage within the contigs. These BAC and PAC contigs are valuable reagents for isolating the genes for DS-CHD.

A fosmid-based genomic map and identification of 474 genes of the hyperthermophilic archaeon Pyrobaculum aerophilum

We have constructed a physical map of the approximately 1.7-Mb genome of the hyperthermophilic archaeon Pyrobaculum aerophilum. Derived from a 12x coverage genomic fosmid library with an average insert size of 36 Kb, the map consists of a single circular contig of 96 overlapping fosmid clones with 211 markers ordered along them. One hundred of the sequence markers have strong similarities to known genes. Many overlaps were also checked using restriction fingerprint analysis. This map is an important step in the elucidation of the sequence of the entire genome of Pyrobaculum aerophilum. To this end we have determined more than 95% of the genome with 15,000 random sequences. Each sequence has been screened against the public sequence databases to identify similarities to known genes. We report here a list of the 474 putative genes we have identified.

Identification of a novel transcript disrupted by a balanced translocation associated with DiGeorge syndrome

Most cases of DiGeorge syndrome (DGS) and related abnormalities are associated with deletions within 22q11. Shortest region of deletion overlap (SRO) mapping previously identified a critical region (the DGCR) of 500 kb, which was presumed to contain a gene or genes of major effect in the haploinsufficiency syndromes. The DGCR also contains sequences disrupted by a balanced translocation that is associated with DGS--the ADU breakpoint. We have cloned sequences at the breakpoint and screened for novel genes in its vicinity. A series of alternatively spliced transcripts expressed during human and murine embryogenesis, but with no obvious protein encoding potential, were identified. The gene encoding these RNAs has been named DGCR5 and it is disrupted by the patient ADU breakpoint. DGCR5 is distinct from the DGCR3 open reading frame (ORF) previously shown to be interrupted by the ADU translocation, although DGCR3 is embedded within a DGCR5 intron and in the same (predicted) transcriptional orientation. No mutations of DGCR5 have yet been detected. By analogy to other loci encoding conserved, nontranslated RNAs, it is possible that DGCR5 originates from a cis-acting transcriptional control element in the vicinity of the ADU/VDU breakpoint. Disruption of such an element would result in altered transcription of neighboring genes secondary to a position effect, a hypothesis in keeping with recent refinement of the SRO placing the ADU breakpoint outside the DGCR.

Bacterial artificial chromosome cloning and mapping of a 630-kb human extrachromosomal structure

We have cloned and mapped a circular 630-kb human extrachromosomal structure (termed amplisome) using the bacterial artificial chromosome (BAC) cloning system. Twenty-one BACs were isolated from an amplisome-enriched library by colony hybridization. The insert sizes range from 25 to 143 kb, with an average size of 82 kb. The coverage of the amplisome in clones is approximately 2.7-fold. To construct a physical map of the amplisome, we used three different but complementary methods: hybridization, STS content mapping, and fingerprinting. In addition, we compared the advantages and the drawbacks of these techniques in mapping the amplisomal BACs. The 21 BACs were grouped into two contigs and the two small gaps (3.5 and 26.5 kb) were filled by screening of a human genomic BAC library. The organization of the amplisome revealed by the BAC-based physical map is consistent with the long-range restriction map reported previously. Our results demonstrate that a 630-kb region can be rapidly cloned and mapped into contigs by use of the BAC system. Because of the low frequency (<0.1%) of chimerism and rearrangement, these BAC clones are ready for DNA sequencing and functional analysis.

A bacterial artificial chromosome-based framework contig map of human chromosome 22q

We have constructed a physical map of human chromosome 22q using bacterial artificial chromosome (BAC) clones. The map consists of 613 chromosome 22-specific BAC clones that have been localized and assembled into contigs using 452 landmarks, 346 of which were previously ordered and mapped to specific regions of the q arm of the chromosome by means of chromosome 22-specific yeast artificial chromosome clones. The BAC-based map provides immediate access to clones that are stable and convenient for direct genome analysis. The approach to rapidly developing marker-specific BAC contigs is relatively straightforward and can be extended to generate scaffold BAC contig maps of the rest of the chromosomes. These contigs will provide substrates for sequencing the entire human genome. We discuss how to efficiently close contig gaps using the end sequences of BAC clone inserts.

Construction and characterization of a human bacterial artificial chromosome library

We have constructed an arrayed human genomic BAC library with approximately 4x coverage that is represented by 96,000 BAC clones with average insert size of nearly 140 kb. A new BAC vector that allows color-based positive screening to identify transformants with inserts has increased BAC cloning efficiency. The library was gridded onto hybridization filters at high density for efficient identification of BAC clones by colony hybridization. The library was also formulated into characteristic DNA pools to allow for PCR screening of the library for STS content. We have characterized the library mainly by screening with more than 300 different landmarks that include cDNA, STSs, and cosmid clones. We describe methods for using BAC clones and discuss the implications for genome characterization, mapping, and sequencing.

A human chromosome 22 fosmid resource: mapping and analysis of 96 clones

We have created a resource for chromosome 22 consisting of 96 unique, well-characterized Fosmids. The Fosmid vector permits efficient cloning of DNA fragments averaging 40 kb in a single-copy vector based on the F factor of Escherichia coli. We have found that Fosmid clones from human chromosome 22 show remarkable stability and are useful for a wide variety of applications in genome analysis. These 96 clones have been localized by FISH, using high-resolution fluorescent banding and multicolor mapping techniques, and their position on the chromosome was correlated with their content of a number of common repeated sequence elements. We identified a subset of clones likely to contain genes by restriction analysis using the enzymes NotI, MluI, SacII, and BssHII. This collection of cytogenetically anchored clones, representing nearly 7% of the chromosome, is of immediate value for detecting chromosomal rearrangements, for use in gene isolation, and as a framework for physical mapping.

Mutations in a C. elegans Gqalpha gene disrupt movement, egg laying, and viability

We find that C. elegans egl-30 encodes a heterotrimeric G protein a subunit more than 80% identical to mammalian Gqalpha family proteins, and which can function as a Gqalpha subunit in COS-7 cells. We have identified new egl-30 alleles in a selection for genes involved in the C. elegans acetylcholine response. Two egl-30 alleles specify premature termination of Gqalpha and are essentially lethal in homozygotes. Animals homozygous for six other egl-30 alleles are viable and fertile, but exhibit delayed egg laying and leave flattened tracks. Overexpression of the wild-type egl-30 gene produces the opposite behavior. Analysis of these mutants suggest that their phenotypes reflect defects in the muscle or neuromuscular junction.

Framework for a physical map of the human 22q13 region using bacterial artificial chromosomes (BACs)

Detailed physical maps of entire chromosomes based on combined genetic, cytogenetic, and structural information are essential components for positional cloning and genomic sequencing. Despite the wealth of genetic information of the known diseases in the chromosome 22q13, the construction of a detailed physical map of the terminal region is difficult due to the sparsity of the genetic markers. We present here a map of bacterial artificial chromosome (BAC) contigs that cover a number of genetic loci in the 22q13 region. One hundred thirty-six BACs with an average insert size of 140 kb are assembled into 35 contigs defined by 64 markers in 22q13-qter. Twenty-three anonymous markers are now linked to the previously mapped genetic anchor points.

A transcription map in the CATCH22 critical region: identification, mapping, and ordering of four novel transcripts expressed in heart

The acronym CATCH22 is used to indicate collectively a group of related phenotypes, namely velocardiofacial syndrome (VCFS), DiGeorge anomaly (DGA), and conotruncal anomaly face, which are associated with deletions within 22q11.2 in the great majority of patients. A deletion map has allowed us to delimit a smallest region of deletion overlap, considerably smaller than the commonly deleted region. We have mapped within this region the chromosomal breakpoint of a balanced translocation patient presenting with a DGA/VCFS phenotype, making this region the strongest candidate for the location of the gene(s) responsible for the disease phenotype. We report a systematic gene search in this region and show the presence of at least six distinct transcripts, two of which have been previously described. The region searched was approximately 270 kb; therefore, an average of one transcript every 45 kb was found. We generated eight new ESTs and mapped two ESTs present in public databases. All six transcripts are expressed in heart, an organ involved in 70%-80% of CATCH22 patients. We show that the multimethod approach to search for expressed sequences is effective and indeed necessary for a comprehensive search and provides molecular tools for further characterization of the potential genes identified.

Characterization of a human chromosome 22 enriched bacterial artificial chromosome sublibrary

Selection of chromosomal sublibraries from total human genomic libraries is critical for chromosome-based physical mapping approaches. We have previously reported a method of screening total human genomic library using flow sorted chromosomal DNA as a hybridization probe and selection of a human chromosome 22-enriched sublibrary from a total human bacterial artificial chromosome (BAC) library (Nucleic Acids Res 1995; 23: 1838-39). We describe here further details of the method of construction as well as characterization of the chromosome 22-enriched sublibrary thus constructed. Nearly 40% of the BAC clones that have been mapped by fluorescence in situ hybridization (FISH) analysis were localized to chromosome 22. By screening the sublibrary using chromosome 22-specific hybridization probes, we estimated that the sublibrary represents at least 2.5 x coverage of chromosome 22. This is in good agreement with the results from FISH mapping experiments. FISH map data also indicate that chromosome 22-specific BACs in the sublibrary represent all the subregions of chromosome 22.

Construction and utility of a human chromosome 22-specific Fosmid library

We have previously demonstrated the capability of the Fosmid vector based on Escherichia coli F-factor replicon to stably propagate cosmid-sized human genomic DNA fragments. Using the Fosmid vector, we have constructed and arrayed a 10 x human chromosome 22-specific library, partly by picking human positive clones from a total Fosmid library constructed using DNA from human-hamster hybrid cell line containing human chromosome 22, and partly by using flow-sorted chromosomal DNA. The clones and physical contig maps of the clones in the library will serve as a valuable resource for detailed analysis of the chromosome by providing reliable materials for high resolution mapping and sequencing. In order to efficiently build physical maps for the chromosomal regions of interest spanning several hundred kilobases to a megabase, it is necessary to rapidly identify subsets of the Fosmid clones from the library that cover such regions. In this report, we describe a method of using random amplification products derived from YAC clones to rapidly identify a subset of Fosmid clones that cover a specific genomic subregion.

Selection of a sublibrary enriched for a chromosome from total human bacterial artificial chromosome library using DNA from flow sorted chromosomes as hybridization probes

Images

Isolation and characterization of a candidate gene for progressive myoclonus epilepsy on 21q22.3

The Unverricht-Lundborg type of progressive myoclonus epilepsy (EPM1) and autoimmune polyglandular disease type I (APECED) have been mapped to human chromosome 21q22.3 by genetic linkage analysis and/or linkage disequilibrium studies. In order to isolate the genes for these disorders, we have constructed BAC contigs in this region and a 14 week trisomy 21 fetal brain cDNA library. A direct cDNA selection technique, modified to permit the recovery 5' and 3' ends of cDNA, was applied to gene identification using the BAC contigs. We have isolated and characterized a novel gene defined by three overlapping but distinct cDNAs of 5, 3, and 3 kb in size all named EHOC-1 (Epilepsy, HOloprosencephaly Candidate-1). This gene maps less than 45 kb centromeric of D21S25, and spans at least 56 kb of genomic DNA. Northern analysis of the 5 kb cDNA revealed that 8, 7.5 and 5.3 kb transcripts are ubiquitously expressed in adult tissues. DNA sequence analysis of the 5 kb cDNA showed a complete coding sequence of 3570 bp that has multiple putative transmembrane domains and has partial homologies to transmembrane proteins including sodium channel proteins. This gene (EHOC-1) is a good candidate for APECED, and particularly for EPM1 because of the location, size, structure and homologies.

Identification of thyrotropin-releasing hormone receptor in the rat testis

We have recently documented the expression of preprothyrotropin-releasing hormone (TRH) gene in murine, human and rat testis. Moreover, we have localized TRH to rat Leydig cells immunohistochemically, and found that both prepro TRH mRNA and TRH levels are developmentally regulated in the rat testis. To investigate the potential roles of TRH in testicular function, characterization of TRH receptors (TRH-R) in this tissue was undertaken. Recently, a cDNA encoding murine TRH-R has been isolated, making possible cloning of a rat TRH-R cDNA from the anterior pituitary gland. This cDNA was used for detection of TRH-R gene expression in the rat testis by Northern blot analysis and reverse transcription-polymerase chain reaction (RT-PCR). TRH receptor assays were also performed with (3H)MeHisTRH as the radioactive ligand. In Northern blot analysis, a single and specific hybridization band, approximately 3.8 kb in size, was identified in whole testis RNA, identical in size with that found in the anterior pituitary gland. The concentration of TRH-R mRNA in the testis was approximately 10% of that in the pituitary. TRH-R mRNA was also detected by RT-PCR in Metrizamide gradient-purified Leydig cells. TRH receptor binding assays revealed the presence of specific, high affinity binding sites with a Kd of 1.6 x 10(-8) M in the testis. Such TRH binding was inhibited by chlordiazepoxide, a specific antagonist of TRH receptor binding. We conclude that TRH may exert local, probably autocrine, actions in the testis via a transmembrane receptor very similar or identical to that in pituitary.

Selection of chromosome 22-specific clones from human genomic BAC library using a chromosome-specific cosmid library pool

A new approach to rapidly identify chromosome-specific subsets of clones from a total human genomic library is described. We report here the results of screening a human bacterial artificial chromosome (BAC) library using the total pool of clones from a chromosome 22-specific cosmid library as a composite probe. The human BAC library was gridded on filters at high density and hybridized with DNA from the pooled chromosome 22-specific Lawrist library under suppressive conditions. In a single hybridization, we picked 280 candidates from the BAC library representing over 30,000 clones (or 1.2x coverage of human genome). This subset contained more than 60% of the chromosome 22-specific BAC clones that were previously found to be present in the original BAC library. In principle, this approach can be applied to select a subset of clones from other global libraries with relatively large inserts using a pool from a regional library as a composite probe. It is important to note that the target and probe libraries must be based on vectors that share no homology with each other.

Identification of thyrotropin-releasing hormone receptor messenger RNA in the rat central nervous system and eye

TRH exerts a wide variety of neuropharmacological actions by interacting with specific receptors in the central nervous system (CNS). Specific binding sites for TRH have been identified also in the mammalian retina. However, whether TRH receptors (TRH-R) in the brain and retina are identical in structure with those in the anterior pituitary gland is presently unknown. In this study, TRH-R gene expression was examined by Northern blot analysis in the CNS and eye using a cloned rat pituitary TRH-R cDNA. Northern analysis demonstrated a specific hybridization band of approximately 3.8 kb in hypothalamus, cerebrum, cerebellum, brain stem, spinal cord, and eye, indistinguishable from that characterized in pituitary gland. These data strongly support the hypothesis that a TRH receptor similar or identical to that cloned from the pituitary occurs in the retina and throughout the CNS.

Identification, localization and developmental studies of rat prepro thyrotropin-releasing hormone mRNA in the testis

Thyrotropin-releasing hormone (TRH) plays the central regulatory role in the hypothalamic-pituitary-thyroid axis, but is also present in many extra-hypothalamic loci. The adult rat testis has been identified previously as a source of hypothalamic neuropeptides including TRH. To investigate whether the TRH gene is transcribed in testis, the identification and localization of prepro(pp) TRH mRNA and TRH were studied. Northern blot analyses of ppTRH mRNA in the adult rat testis showed a 2.0 kb band, hybridized with a ppTRH cRNA probe. This band was 0.4 kb greater than the 1.6 kb hypothalamic band. The concentration of ppTRH mRNA in the adult testis was approximately 13% of that found in the hypothalamus. Developmental studies of testicular ppTRH mRNA revealed that no ppTRH mRNA could be detected at the earliest stage (day 8). However, hybridization signals were detected on day 20 and increased progressively on days 35, 45 and 70 by 5.8, 6.4, and 9.8-fold, respectively. In addition, ppTRH mRNA was determined in Leydig cells by Northern analyses of elutriated testicular cell fractions. TRH was also measured in the rat testes at different developmental stages by RIA. TRH concentrations paralleled ppTRH mRNA during development. TRH was localized to Leydig cells by immunohistochemistry. These results indicate that ppTRH mRNA and TRH are present in the rat testis, especially in the Leydig cells. The changes of ppTRH gene expression and the concentration of TRH in the rat testis are developmentally dependent. TRH may function as a new paracrine or autocrine regulator of testicular function.

Identification of a new set of cell cycle-regulatory genes that regulate S-phase transcription of histone genes in Saccharomyces cerevisiae

Histone mRNA synthesis is tightly regulated to S phase of the yeast Saccharomyces cerevisiae cell cycle as a result of transcriptional and posttranscriptional controls. Moreover, histone gene transcription decreases rapidly if DNA replication is inhibited by hydroxyurea or if cells are arrested in G1 by the mating pheromone alpha-factor. To identify the transcriptional controls responsible for cycle-specific histone mRNA synthesis, we have developed a selection for mutations which disrupt this process. Using this approach, we have isolated five mutants (hpc1, hpc2, hpc3, hpc4, and hpc5) in which cell cycle regulation of histone gene transcription is altered. All of these mutations are recessive and belong to separate complementation groups. Of these, only one (hpc1) falls in one of the three complementation groups identified previously by other means (M. A. Osley and D. Lycan, Mol. Cell. Biol. 7:4204-4210, 1987), indicating that at least seven different genes are involved in the cell cycle-specific regulation of histone gene transcription. hpc4 is unique in that derepression occurs only in the presence of hydroxyurea but not alpha-factor, suggesting that at least one of the regulatory factors is specific to histone gene transcription after DNA replication is blocked. One of the hpc mutations (hpc2) suppresses delta insertion mutations in the HIS4 and LYS2 loci. This effect allowed the cloning and sequence analysis of HPC2, which encodes a 67.5-kDa, highly charged basic protein.

Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector

A bacterial cloning system for mapping and analysis of complex genomes has been developed. The BAC system (for bacterial artificial chromosome) is based on Escherichia coli and its single-copy plasmid F factor. It is capable of maintaining human genomic DNA fragments of greater than 300 kilobase pairs. Individual clones of human DNA appear to be maintained with a high degree of structural stability in the host, even after 100 generations of serial growth. Because of high cloning efficiency, easy manipulation of the cloned DNA, and stable maintenance of inserted DNA, the BAC system may facilitate construction of DNA libraries of complex genomes with fuller representation and subsequent rapid analysis of complex genomic structure.

Preprothyrotropin-releasing hormone mRNA and TRH are present in the rat heart

PreproTRH mRNA has been identified in rat cardiac tissues by Northern analyses and RNase protection assays with a specific rat 32P-TRH cRNA probe. Densitometric analyses revealed that atrial ppTRH mRNA concentrations were approximately five-fold greater than those of the ventricles. TRH concentrations (RIA), by contrast, were two-fold higher in ventricles. These data suggest that TRH and TRH mRNA are present in the rat heart, but their concentrations are dissociated, possibly because of differential post-transcriptional or post-translational processing. TRH is postulated to play an autocrine or paracrine role in cardiac physiology.

Stable propagation of cosmid sized human DNA inserts in an F factor based vector

Instability of complex mammalian genomic DNA inserts is commonplace in cosmid libraries constructed in conventional multicopy vectors. To develop a means to construct stable libraries, we have developed a low copy number cosmid vector based on the E. coli F factor replicon (Fosmid). We have tested relative stability of human DNA inserts in Fosmids and in two conventional multicopy vectors (Lawrist 16 and Supercos) by comparing the frequency of changes in restriction patterns of the inserts after propagating randomly picked human genomic clones based on these vectors. We found that the clones based on Fosmid vector undergo detectable changes at a greatly reduced frequency. We also observed that sequences that undergo drastic rearrangements and deletions during propagation in a conventional vector were stably propagated when recloned as Fosmids. The results indicate that Fosmid system may be useful for constructing stable libraries from complex genomes.