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At least 847 records · Page 47Linked to original sources
PubMed2002

Optimisation of electron cone design in high energy radiotherapy using the Monte Carlo method.

Cylindrical solid-walled steel electron collimators are used at the Royal Adelaide Hospital with a Siemens KD2 Mevatron accelerator to produce circular fields 2-8 cm in diameter. The cones are used in contact with the patient's skin. A flat treatment field is required at the treatment depth and the beam should also satisfy the uniformity standards as specified by the International Electrotechnical Commission (IEC). However, the seven and eight centimetre diameter cones provided by the manufacturer did not meet these specifications. In particular, the maximum dose relative to the depth-dose maximum on the central axis exceeded 126% as compared with the IEC recommended value of 109%, when used with a 21 MeV electron beam. Cone modifications were previously investigated by others with the results demonstrating some improvement in the 'horn' (as it appears on surface dose profiles) but still not satisfying IEC requirements. In the present paper the EGS4 code was used to model the existing treatment head geometry and cones, as well as new suggested modifications to the cone. The results of the simulation for the existing cone geometry corresponded closely to previously obtained measurements. The suggested collimator modifications involved a plastic insert along the internal wall of the collimator. Variations of the insert width and height were simulated for a 21 MeV electron beam and the results plotted to indicate the optimal insert dimensions. A plastic insert with the dimensions taken from one of the best models was produced and tested. The measurements showed close agreement with the simulation results (for the 'horn' height, dose within 1% and radial position within 2 mm) and improvement of the "maximum ratio of absorbed dose" from 126% before modification to 108% with the plastic insert. The tested insert was also simulated for a 12 MeV electron beam, to see whether permanent fitting of such an insert would have a deleterious effect at lower energies. Neither penetration nor flatness was significantly compromised, with a small penalty being a slight increase in the central axis dose near the surface.

Computer Simulation↗
PubMed2001

Organisation and expression of the plastid genome of the dinoflagellate Amphidinium operculatum.

We show using PCR that psbC, atpA and petB genes are present in the plastid DNA minicircles from the dinoflagellate Amphidinium operculatum, extending the set of plastid genes identified from this organism. Unusually, the petBand atpA genes are located on the same minicircle. PCR using primers based on the "core" region found on all coding minicircles revealed the existence of a number of DNA minicircles with no apparent coding function. Northern analysis of total RNA from A. operculatum showed that the petB and atpA genes are represented on separate transcripts, despite being encoded in close proximity on the same minicircle. The possibility of transcript editing was investigated by RT-PCR, but psaA, psbA, psbB and atpB transcripts showed no evidence of editing, indicating that GUA can be used as an initiation codon in A. operculatum.

Amino Acid Sequence↗
PubMed2004

Cloning, expression, and structural analysis of recombinant BJcuL, a c-type lectin from the Bothrops jararacussu snake venom.

The lactose-binding lectin from Bothrops jararacussu venom (BJcuL) is a homodimer belonging to group VII of the c-type animal lectins. BJcuL has also been shown to serve as an interesting tool for combating tumor progression by inhibiting cancer and endothelial cell growth. However, detailed structural studies of BJcuL and its biological mechanisms of cytotoxicity are yet to be reported, perhaps because of the non-availability of recombinant proteins in necessary quantities. Intending to increase the present information about structural and consequently the understating of biological studies, the cDNA coding for BJcuL from a venom gland has been cloned and sequenced. The mature protein-coding region was amplified by PCR with specific oligonucleotides, and subcloned into the pET-15b vector to express the recombinant BJcuL in Escherichia coli BL21 (DE3). The deduced amino acid sequence exhibits a high degree of sequence identity with c-type lectins (CTLs) and c-type lectin-like domains (CTLDs). An insoluble and inactive 18.5-kDa protein was overexpressed after 1.0mM IPTG induction. The recombinant BJcuL was recovered and denatured in a buffer with 6M urea and purified on a nickel-affinity column. Protein refolding was carried out on this column, during procedure purification, followed by dialysis against CTBS and then by gel filtration for separation of the active dimmer. The refolding process of rBJcuL and the analysis of its structure were confirmed by biological assay, circular dichroism, and MALDI-TOF.

Amino Acid Sequence↗
PubMed1981

Identification of gene products programmed by restriction endonuclease DNA fragments using an E. coli in vitro system.

DNA restriction enzyme fragments have been used to programme the synthesis of polypeptides in an in vitro system without apparent loss in fidelity compared with supercoiled templates. The system is extremely sensitive, less than 1 microgram of DNA can be used to direct the synthesis of 35S-labelled polypeptides of sufficiently high specific activity such that products can be identified by SDS-PAGE after a few hours autoradiography. The ability to analyse fragments can be used to readily assign specific proteins to small regions of the coding template, to identify cloned gene products distinct from those of the vector, and to identify cloned genes expressed from their own promoters. The in vitro system can be used successfully with bacterial DNA from other species and efficient extracts can be prepared from any E. coli K-12 strain, which should greatly facilitate the purification of factors controlling the expression of specific genes by complementation assay.

Cloning, Molecular↗
PubMed1994

Cloning, expression, and spectroscopic studies of the Jun leucine zipper domain.

Association of the human c-Jun and c-Fos proteins depends upon interactions involving their leucine zipper domains. We are interested in elucidating the tertiary structure of the Jun and Fos leucine zipper domains with a view to understanding the precise intermolecular interactions which govern the affinity and specificity of interaction in these proteins, which have the unusual capacity to form either homodimeric or heterodimeric zipper pairs. With this goal in mind, we have developed a bacterial expression system for the efficient production of both unlabelled and isotopically labelled c-Jun leucine zipper domain. A synthetic junLZ gene was created by annealing, ligation, and polymerase-chain-reaction amplification of overlapping synthetic oligonucleotides which comprised 132 bp of coding sequence encompassing residues Arg276-Asn314 of c-Jun plus a total of five engineered non-native residues at the N- and C-termini. The junLZ gene was cloned into the pGEX-2T vector from which recombinant c-Jun leucine zipper domain (rJunLZ; 46 residues, 5.1 kDa) was overexpressed (approximately 15% total cell protein) in Escherichia coli as a fusion protein of 31.4 kDa, consisting of rJunLZ fused to the carboxy-terminal portion of Schistosoma japonicum glutathione S-transferase. Two markedly different expression strategies have been devised which allow purification of rJunLZ from the soluble or inclusion-body fraction of induced cells. We have used these strategies to produce unlabelled and uniformly 15N-labelled rJunLZ for NMR studies which, in combination with circular dichroic measurements, reveal that rJunLZ most likely forms a symmetric coiled-coil of parallel alpha-helices. We also present 15N-NMR chemical shift assignments for the backbone and sidechain amide nitrogens of rJunLZ, which should assist in determination of a high-resolution structure of the homodimeric Jun leucine zipper using heteronuclear three-dimensional NMR spectroscopy.

Amino Acid Sequence↗
PubMed1999

Hippocampal neuronal position selectivity remains fixed to room cues only in rats alternating between place navigation and beacon approach tasks.

To study the relationship between brain representations and behaviour, we recorded hippocampal neuronal activity in rats repeatedly alternating between two different tasks on a circular platform with four reward boxes along the edge. In the beacon approach task, rewards were provided only at the pair of diametrically opposite boxes that was illuminated. In the place navigation task, rewards were available only at the boxes positioned near the north-east and south-west corners of the room. Performance levels were high and rats rapidly reoriented to changes in lamp cues in the beacon approach task. Neuropsychological studies show that rats with hippocampal lesions readily employ beacon approach strategies, while place navigation is severely impaired. Previous studies suggested that the neurons might change their behavioural correlates as the rat performed the respective tasks. However, of 34 hippocampal 'place cells' recorded, all showed position selectivity fixed with respect to room cues, even in the beacon approach task where coding the position of the rat in the room was of no use for locating rewards. Whether or not hippocampal signals are actually employed for ongoing behaviour would then be decided by structures downstream from the hippocampus. If this is the case, then the 'counterproductive' room referred place-related discharges in the beacon approach task would be a background representation. This would provide support for proposals of multiple memory systems underlying different types of information processing and contrasts with the popular notion that local neuronal activity levels are selectively increased to the degree that the brain region is required for the ongoing function.

Acoustic Stimulation↗
PubMed2002

A 50-kb plasmid rich in mobile gene sequences isolated from a marine micrococcus.

A 50,709-bp cryptic plasmid isolated from a marine Micrococcus has been sequenced and found to contain a number of putative mobile genetic elements. The coding regions for 11 putative transposases comprise approximately 17% of the total plasmid sequence. The majority of these transposases are located within a 13-kb cluster which includes a 1553-bp direct repeat consisting of a duplicated pair of transposase genes. The remaining putative ORFs showed similarity to a variety of proteins, the most notable being spider silk.

Base Composition↗
PubMed1997

Characterization of two Escherichia coli isolates associated with poult enteritis and mortality syndrome.

Two colonial types (1 and 2) of Escherichia coli are represented predominantly in cultures isolated from turkey poults with poult enteritis and mortality syndrome (PEMS). Biotype codes determined using two systems (BBL: 36570 and 34560 for colony types 1 and 2, respectively; API-20E: 5144572 and 5144512 for colony types 1 and 2, respectively) clearly establish these organisms as E. coli. These isolates were not clearly divergent from the general profile for E. coli, but colony type 2 differs from colony type 1 with regard to its negative reactions for ornithine decarboxylase and the fermentation of dulcitol, rhamnose, sucrose, and melibiose, suggesting that it is atypical. Colony type 1 is nonserotypable and nonmotile, whereas colony type 2 is serotyped as O136: motile because it has H antigens associated with flagella. Capsular antigens were not found, but thin capsules were seen on cells from both colony types in stained preparations. Cultural morphology was different with colony type 1 having a circular, mucoid, raised morphology and colony type 2 having an irregular, flat, rough morphology. Colony type 1 has a doubling time at 37 C of about 20 min, whereas colony type 2 doubles in 30 min. Furthermore, colony type 1 is a potent colicin producer, but colony type 2 is not a colicin producer. Both E. coli isolates have resistance profiles for multiple antibiotics. Each strain responds to third generation fluoroquinolone antibiotics by changing their biotypes and become resistant after culturing once in their presence. These E. coli are proposed as possible etiological links in the complex series of events that take place in poults susceptible to PEMS.

Animals↗
PubMed1998

Mitochondrial DNA of the coral Sarcophyton glaucum contains a gene for a homologue of bacterial MutS: a possible case of gene transfer from the nucleus to the mitochondrion.

The nucleotide sequences of two segments of 6,737 ntp and 258 nto of the 18.4-kb circular mitochondrial (mt) DNA molecule of the soft coral Sarcophyton glaucum (phylum Cnidaria, class Anthozoa, subclass Octocorallia, order Alcyonacea) have been determined. The larger segment contains the 3' 191 ntp of the gene for subunit 1 of the respiratory chain NADH dehydrogenase (ND1), complete genes for cytochrome b (Cyt b), ND6, ND3, ND4L, and a bacterial MutS homologue (MSH), and the 5' terminal 1,124 ntp of the gene for the large subunit rRNA (1-rRNA). These genes are arranged in the order given and all are transcribed from the same strand of the molecule. The smaller segment contains the 3' terminal 134 ntp of the ND4 gene and a complete tRNA(f-Met) gene, and these genes are transcribed in opposite directions. As in the hexacorallian anthozoan, Metridium senile, the mt-genetic code of S. glaucum is near standard: that is, in contrast to the situation in mt-genetic codes of other invertebrate phyla, AGA and AGG specify arginine, and ATA specifies isoleucine. However, as appears to be universal for metazoan mt-genetic codes, TGA specifies tryptophan rather than termination. Also, as in M. senile the mt-tRNA(f-Met) gene has primary and secondary structural features resembling those of Escherichia coli initiator tRNA, including standard dihydrouridine and T psi C loop sequences, and a mismatched nucleotide pair at the top of the amino-acyl stem. The presence of a mutS gene homologue, which has not been reported to occur in any other known mtDNA, suggests that there is mismatch repair activity in S. glaucum mitochondria. In support of this, phylogenetic analysis of MutS family protein sequences indicates that the S. glaucum mtMSH protein is more closely related to the nuclear DNA-encoded mitochondrial mismatch repair protein (MSH1) of the yeast Saccharomyces cerevisiae than to eukaryotic homologues involved in nuclear function, or to bacterial homologues. Regarding the possible origin of the S. glaucum mtMSH gene, the phylogenetic analysis results, together with comparative base composition considerations, and the absence of an MSH gene in any other known mtDNA best support the hypothesis that S. glaucum mtDNA acquired the mtMSH gene from nuclear DNA early in the evolution of octocorals. The presence of mismatch repair activity in S. glaucum mitochondria might be expected to influence the rate of evolution of this organism's mtDNA.

Adenosine Triphosphatases↗
PubMed1998

Recombinant locust apolipophorin III: characterization and NMR spectroscopy.

Apolipophorin III (apoLp-III) from the locust Locusta migratoria is an exchangeable apolipoprotein that reversibly binds to lipoproteins. During lipid binding the protein has been proposed to undergo a major conformational change. To study the mechanism of lipid binding we have cloned and expressed recombinant protein in bacteria, permitting stable isotope enrichment for heteronuclear NMR spectroscopy and site-directed mutagenesis. The cDNA coding for apoLp-III was subcloned into the pET expression vector and transformed into Escherichia coli cells. Induction of expression resulted in the specific appearance of apoLp-III in the cell culture medium, indicating it escaped the bacteria without lysis. The protein was purified from the cell-free supernatant by reversed-phase HPLC, characterized and compared to the natural protein isolated from locust hemolymph. SDS-PAGE revealed the recombinant protein has a molecular mass of approximately 17 kDa, similar to that of deglycosylated natural apoLp-III. Monoclonal antibodies were used to detect recombinant apoLp-III in the cells as well as in cell-free medium of induced bacterial cultures. Amino acid sequencing and analysis confirmed the identity of the recombinant protein as L. migratoria apoLp-III. Circular dichroism spectroscopy of recombinant and natural apoLp-III showed similar spectra, both displaying high contents of alpha-helical secondary structure. Denaturation studies of lipid-free apoLp-III with guanidine hydrochloride showed that both proteins have similar denaturation midpoints and DeltaG values indicating similar protein stability. The natural and recombinant protein were functional in lipoprotein binding assays. Using recombinant protein, uniformly and specifically labeled with 15N-amino acids, two dimensional 1H-15N heteronuclear single quantum correlation spectra were obtained. The spectra revealed excellent chemical shift dispersion in both the 1H and 15N dimensions with a well defined resonance pattern. Studies with 15N-leucine specifically labeled apoLp-III in the presence and absence of the micelle forming lipid, dodecylphosphocholine, provided evidence for a significant conformational change upon lipid association.

Animals↗
PubMed2004

Inversion within the haloalkaliphilic virus phi Ch1 DNA results in differential expression of structural proteins.

The sequence of phi Ch1 contains an open reading frame (int1) in the central part of its genome that belongs to the lambda integrase family of site-specific recombinases. Sequence similarities to known integrases include the highly conserved tetrad R-H-R-Y. The flanking sequences of int1 contain several direct repeats of 30 bp in length (IR-L and IR-R), which are orientated in an inverted direction. Here, we show that a recombination active region exists in the genome of phi Ch1: the number of those repeats, non-homologous regions within the repeat clusters IR-L and IR-R and the orientation of the int1 gene vary in a given virus population. Within this study, we identified circular intermediates, composed of the int1 gene and the inwards orientated repeat regions IR-L and IR-R, which could be involved in the recombination process itself. IR-L and IR-R are embedded within ORF34 and ORF36 respectively. As a consequence of the inversion within this region of phi Ch1, the C-terminal parts of the proteins encoded by ORF34 and 36 are exchanged. Both proteins, expressed in Escherichia coli, interact with specific antisera against whole virus particles, indicating that they could be parts of phi Ch1 virions. Expression of the protein(s) in Natrialba magadii could be detected 98 h after inoculation, which is similar to other structural proteins of phi Ch1. Taken together, the data show that the genome of phi Ch1 contains an invertible region that codes for a recombinase and structural proteins. Inversion of this segment results in a variation of these structural proteins.

Amino Acid Sequence↗
PubMed2005

Cloning, biochemical properties, and distribution of mycobacterial haloalkane dehalogenases.

Haloalkane dehalogenases are enzymes that catalyze the cleavage of the carbon-halogen bond by a hydrolytic mechanism. Genomes of Mycobacterium tuberculosis and M. bovis contain at least two open reading frames coding for the polypeptides showing a high sequence similarity with biochemically characterized haloalkane dehalogenases. We describe here the cloning of the haloalkane dehalogenase genes dmbA and dmbB from M. bovis 5033/66 and demonstrate the dehalogenase activity of their translation products. Both of these genes are widely distributed among species of the M. tuberculosis complex, including M. bovis, M. bovis BCG, M. africanum, M. caprae, M. microti, and M. pinnipedii, as shown by the PCR screening of 48 isolates from various hosts. DmbA and DmbB proteins were heterologously expressed in Escherichia coli and purified to homogeneity. The DmbB protein had to be expressed in a fusion with thioredoxin to obtain a soluble protein sample. The temperature optimum of DmbA and DmbB proteins determined with 1,2-dibromoethane is 45 degrees C. The melting temperature assessed by circular dichroism spectroscopy of DmbA is 47 degrees C and DmbB is 57 degrees C. The pH optimum of DmbA depends on composition of a buffer with maximal activity at 9.0. DmbB had a single pH optimum at pH 6.5. Mycobacteria are currently the only genus known to carry more than one haloalkane dehalogenase gene, although putative haloalkane dehalogenases can be inferred in more then 20 different bacterial species by comparative genomics. The evolution and distribution of haloalkane dehalogenases among mycobacteria is discussed.

Animals↗
PubMed1970

A study on the transcription of the polyoma viral genome.

The transcription of polyoma (Py) viral RNA was studied in primary mouse kidney cell cultures (a) during normal, asynchronous infection, (b) under conditions where Py-induced DNA synthesis was inhibited with 5-fluorodeoxyuridine, and (c) after the synchronized onset of Py-induced DNA synthesis. The results obtained suggest that the bulk of Py RNA transcribed after the (asynchronous or synchronized) onset of Py-induced DNA synthesis, designated as "late" Py RNA, corresponds to the polycistronic transcript of most or all of the genetic information contained in a strand of circular Py DNA. The rate at which late Py RNA is transcribed is related to the amount of free Py DNA present in the cultures. Py-infected cultures contain a second, minor component of Py RNA (of one or possibly more species), designated as "early" Py RNA. At least some of this RNA continues to be transcribed if Py-induced DNA synthesis is inhibited with 5-fluorodeoxyuridine and, possibly, also late during normal infection.

Centrifugation, Density Gradient↗
PubMed1983

Sequence analysis of zein cDNAs obtained by an efficient mRNA cloning method.

A cDNA library was generated from mRNA isolated from the developing endosperm of W22 maize inbred. cDNA clones for zein, the maize storage protein family, were isolated and analyzed by DNA sequencing. The DNA sequences of four clones containing cDNA copies of mRNAs belonging to one zein subfamily were determined. The data support the following conclusions: a) genes encoding the larger of the two zein species contain eleven instead of nine repeat units within the coding sequence of the gene; b) transcription can be terminated at either of the two polyadenlation signals and c) transcription starts 31 basepairs downstream from the first T in the TATA box. To facilitate this analysis a new method for the construction of cDNA libraries was developed. The mRNA was annealed to linearized and oligo-dT tailed pUC9 plasmid DNA, which then primed synthesis of the first strand of the cDNA. Oligo-dG tails were added to the cDNA-plasmid molecules, which were then centrifuged through an alkaline sucrose gradient. The gradient step removed small molecules and separated the two cDNAs which were formerly attached to the same double stranded plasmid molecule. An excess of oligo-dC tailed denatured pUC9 DNA was added and the DNA was renatured under conditions that favor the circularization of monomers by the oligo-dC and oligo-dG tails. The oligo-dC tail served as primer for the synthesis of the second strand of the cDNA. The library was screened by colony hybridization using 32P-labelled cDNA and DNA from genomic zein clones as probes. We obtained 20,000 clones hybridizing total cDNA starting with 1 microgram of plasmid DNA and 1 microgram of mRNA.

Amino Acid Sequence↗
PubMed2002

Characterization and multiple molecular forms of TorD from Shewanella massilia, the putative chaperone of the molybdoenzyme TorA.

Several bacteria use trimethylamine N-oxyde (TMAO) as an exogenous electron acceptor for anaerobic respiration. This metabolic pathway involves expression of the tor operon that codes for a periplasmic molybdopterin-containing reductase of the DMSO/TMAO family, a pentahemic c-type cytochrome, and the TorD cytoplasmic chaperone, possibly required for acquisition of the molybdenum cofactor and translocation of the reductase by the twin-arginine translocation system. In this report, we show that the TorD chaperone from Shewanella massilia forms multiple and stable oligomeric species. The monomeric, dimeric, and trimeric forms were purified to homogeneity and characterized by analytical ultracentrifugation. Small-angle X-ray scattering (SAXS) and preliminary diffraction data indicated that the TorD dimer is made of identical protein modules of similar size to the monomeric species. Interconversion of the native oligomeric forms occurred at acidic pH value. In this condition, ANS fluorescence indicates a non-native conformation of the polypeptide chain in which, according to the circular dichroism spectra, the alpha-helical content is similar to that of the native species. Surface plasmon resonance showed that both the monomeric and dimeric species bind the mature TorA enzyme, but that the dimer binds its target protein more efficiently. The possible biologic significance of these oligomers is discussed in relation to the chaperone activity of TorD, and to the ability of another member of the TorD family to bind the Twin Arginine leader sequences of the precursor of DMSO/TMAO reductases.

Animals↗
PubMed1998

Int-B13, an unusual site-specific recombinase of the bacteriophage P4 integrase family, is responsible for chromosomal insertion of the 105-kilobase clc element of Pseudomonas sp. Strain B13.

Pseudomonas sp. strain B13 carries the clcRABDE genes encoding chlorocatechol-degradative enzymes on the self-transmissible 105-kb clc element. The element integrates site and orientation specifically into the chromosomes of various bacterial recipients, with a glycine tRNA structural gene (glyV) as the integration site. We report here the localization and nucleotide sequence of the integrase gene and the activity of the integrase gene product in mediating site-specific integration. The integrase gene (int-B13) was located near the right end of the clc element. It consisted of an open reading frame (ORF) of maximally 1,971 bp with a coding capacity for 657 amino acids (aa). The full-length protein (74 kDa) was observed upon overexpression and sodium dodecyl sulfate-polyacrylamide gel electrophoresis separation. The N-terminal 430 aa of the predicted Int-B13 protein had substantial similarity to integrases from bacteriophages of the P4 family, but Int-B13 was much larger than P4-type integrases. The C-terminal 220 aa of Int-B13 were homologous to an ORF flanking a gene cluster for naphthalene degradation in Pseudomonas aeruginosa PaK1. Similar to the bacteriophages phiR73 and P4, the clc element integrates into the 3' end of the target tRNA gene. This target site was characterized from four different recipient strains into which the clc element integrated, showing sequence specificity of the integration. In Pseudomonas sp. strain B13, a circular form of the clc element, which carries an 18-bp DNA sequence identical to the 3'-end portion of glyV as part of its attachment site (attP), could be detected. Upon chromosomal integration of the clc element into a bacterial attachment site (attB), a functional glyV was reconstructed at the right end of the element. The integration process could be demonstrated in RecA-deficient Escherichia coli with two recombinant plasmids, one carrying the int-B13 gene and the attP site and the other carrying the attB site of Pseudomonas putida F1.

Amino Acid Sequence↗
PubMed1985

Origin and initiation sites of lambda dv DNA replication in vitro.

The sequence of lambda DNA essential for the unique initiation of replication was analyzed in an in vitro replication system. Fragments of lambda DNA were inserted into pBR322 and used as templates or were circularized in vitro in the absence of pBR322 and employed in the same tests. A 165-bp region left of the EcoRI site in the O gene of the lambda genome was defined as the functional origin. This region, which we defined as the ori region, carries, in order, the 4 19-bp repeat sequences where the O protein binds (ori-repeats), an A+T-rich stretch, and a region that constitutes part of a large palindromic structure. Regions that have long been suspected to participate in lambda DNA replication initiation, ice and oop were not required for the O, P-dependent lambda-specific replication initiation. The lambda dv and the "ori region plus" recombinant plasmids initiated DNA synthesis at or around this region, and the reaction depended on the presence of lambda-coded initiators, O and P proteins. Early replicative intermediates of lambda dv were prepared in an in vitro replication system in the presence of ddCTP, an inhibitor of DNA chain elongation. This system allows only that DNA synthesis that is a result of replication initiation. Using this system, the initiation site(s) of the DNA synthesis was finely analyzed by mapping the transition sites from primer RNA to DNA synthesis. Short-chain DNAs produced from regions near the ori region were purified from the intermediates. A fraction of the short-chain DNAs was covalently linked to primer RNA. The 5'-ends that had been linked to RNA (transition sites) were exposed by alkaline hydrolysis, labeled with 32P, and the transition sites were mapped along the nucleotide sequence of the genome. Two striking features emerged from this analysis: (i) The transition sites are located on both sides of the ori region, and no transition arose within the 165-bp ori region; (ii) The transition sites on both sides are not unique, but multiple, and are clustered in one of the 2 strands. Furthermore, their orientation demonstrates that the DNA synthesis in initiation of replication from the 2 sides of the ori region converge. The frequency of the "leftward" DNA synthesis is several times higher than that of "rightward" synthesis. These results reflect asymmetric bidirectional replication of lambda dv DNA, and may also reflect replication of lambda phage DNA.

Bacteriophage lambda↗
PubMed2004

Cloning, expression, purification and crystallization of NHR3 domain from acute myelogenous leukemia-related protein AML1-ETO.

The t(8;21) translocation is one of the most frequent chromosome abnormalities in acute myeloid leukemia. This translocation creates a fusion between the acute myelogenous leukemia 1 (AML1, a transcription factor) gene on chromosome 21 and the eight-twenty-one (ETO, a zinc finger nuclear protein) gene on chromosome 8, leading to the repression of certain AML1 target genes. We cloned NHR3 domain coding fragment into vector pGEX-6p-1 using PCR and obtained recombinant plasmid pGEX-6p-1-NHR3, which can be induced to stably overexpress fusion protein in E. coli. Through the purification on GST affinity chromatography column and PreScission protease cleavage, a large amount of NHR3 protein with high purity was obtained. In order to avoid possible interference of some strong negative charged molecules, NHR3 protein was further purified by Mono Q anion exchange chromatography. The NHR3 crystals were grown with hanging drop/vapor diffusion method and the first crystals appeared after four weeks at 18 degrees in 0.2 M Tris-sodium citrate dihydrate, 0.1 M sodium cacodylate, pH 6.5, and 30% iso-propanol (V/V). ESI mass spectrum showed that the molecular weight of this domain was in agreement with its primary structure sequence prediction, and circular dichroism spectral data (190-250 nm) showed that NHR3 had a well-defined secondary structure of 25.9% alpha-helix, 23.2% random coil and 50.9% turn, which was consistent with GOV4 software prediction.

Base Sequence↗